[med-svn] [khmer] 01/10: New upstream version 2.0~pre2.1-20170216-b2ab51575c2fa4c6bff078387ed8b67c4299df12
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sun Jun 25 16:46:30 UTC 2017
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository khmer.
commit cb1975f6981e846dd50dad7350efcf8abddf060d
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Mon Feb 20 01:44:51 2017 -0800
New upstream version 2.0~pre2.1-20170216-b2ab51575c2fa4c6bff078387ed8b67c4299df12
---
.dictionary | 155 +
CONTRIBUTING.md => .github/CONTRIBUTING.md | 18 +-
.github/PULL_REQUEST_TEMPLATE.md | 16 +
.gitignore | 4 +-
.mailmap | 3 +-
.travis.yml | 88 +
.ycm_extra_conf.py | 105 +
CHANGELOG.md | 65 +
CITATION | 12 +-
IDEAS | 18 -
Makefile | 182 +-
README.rst | 68 +-
TODO | 80 -
ci_scripts/install.sh | 31 +
doc/conf.py | 13 +-
doc/contributors.rst | 14 +-
doc/dev/a-quick-guide-to-testing.rst | 14 +-
doc/dev/codebase-guide.rst | 16 +-
doc/dev/coding-guidelines-and-review.rst | 64 +-
doc/dev/development.rst | 62 +-
doc/dev/getting-started.rst | 52 +-
doc/dev/python-api.rst | 152 +
doc/dev/release.rst | 40 +-
doc/dev/scripts-and-sandbox.rst | 47 +-
doc/index.rst | 22 +-
doc/introduction.rst | 92 +-
doc/requirements.txt | 4 +-
doc/roadmap.rst | 16 +-
doc/user/api-examples.rst | 94 +
doc/user/blog-posts.rst | 22 +-
doc/user/guide.rst | 16 +-
doc/user/index.rst | 16 +-
doc/user/install.rst | 14 -
doc/whats-new-2.0.rst | 12 +-
examples/README.txt | 5 -
examples/c++-api/.gitignore | 1 +
examples/c++-api/Makefile | 10 +
examples/c++-api/count-demo.cc | 41 +
ez_setup.py | 332 +
khmer/__init__.py | 159 +-
khmer/_cpy_counttable.hh | 128 +
khmer/_cpy_hashgraph.hh | 1587 +
khmer/_cpy_nodetable.hh | 131 +
khmer/_cpy_smallcountgraph.hh | 181 +
khmer/_cpy_smallcounttable.hh | 127 +
khmer/_khmer.cc | 6098 +-
khmer/_version.py | 430 +-
khmer/kfile.py | 38 +-
khmer/khmer_args.py | 340 +-
khmer/khmer_logger.py | 13 +-
khmer/thread_utils.py | 68 +-
khmer/{khmer_logger.py => trimming.py} | 66 +-
khmer/utils.py | 115 +-
ChangeLog => legacy/ChangeLog | 662 +-
jenkins-build.sh => legacy/jenkins-build.sh | 12 +-
lib/.gitignore | 1 +
lib/Makefile | 18 +-
lib/{test-compile.cc => alphabets.cc} | 21 +-
lib/{test-compile.cc => alphabets.hh} | 22 +-
lib/assembler.cc | 523 +
lib/assembler.hh | 177 +
lib/counting.cc | 1041 -
lib/counting.hh | 348 -
lib/get_version.py | 52 -
lib/hashbits.cc | 215 -
lib/hashbits.hh | 215 -
lib/{hashtable.cc => hashgraph.cc} | 760 +-
lib/hashgraph.hh | 298 +
lib/hashtable.cc | 1200 +-
lib/hashtable.hh | 432 +-
lib/hllcounter.cc | 39 +-
lib/hllcounter.hh | 33 +-
lib/khmer.hh | 23 +-
lib/kmer_filters.cc | 159 +
lib/{test-Colors.cc => kmer_filters.hh} | 42 +-
lib/kmer_hash.cc | 47 +-
lib/kmer_hash.hh | 98 +-
lib/labelhash.cc | 198 +-
lib/labelhash.hh | 110 +-
lib/magic | 62 +-
lib/oxli.pc.in | 4 +-
lib/read_aligner.cc | 24 +-
lib/read_aligner.hh | 8 +-
lib/read_parsers.cc | 406 +-
lib/read_parsers.hh | 185 +-
lib/storage.cc | 916 +
lib/storage.hh | 651 +
lib/subset.cc | 339 +-
lib/subset.hh | 31 +-
lib/test-Colors.cc | 2 +-
lib/test-compile.cc | 4 +-
lib/traversal.cc | 302 +-
lib/traversal.hh | 259 +-
oxli/__init__.py | 15 +-
oxli/build_graph.py | 14 +-
oxli/functions.py | 21 +-
oxli/partition.py | 49 +
pylintrc | 384 +
pytest.ini | 4 +
sandbox/Makefile.read_aligner_training | 26 +-
sandbox/README.rst | 16 +-
sandbox/abundance-hist-by-position.py | 70 -
sandbox/assemble-and-track.py | 139 +
sandbox/assemble-on-the-go.py | 118 +
sandbox/assembly-diff.py | 4 +-
sandbox/assemstats3.py | 3 +-
sandbox/bloom-count.py | 3 +
sandbox/collect-reads.py | 3 +-
sandbox/collect-variants.py | 3 +-
sandbox/count-kmers-single.py | 5 +-
sandbox/count-kmers.py | 3 +-
sandbox/extract-compact-dbg.py | 230 +
sandbox/extract-unassembled-reads-2.py | 72 +
sandbox/extract-unassembled-reads.py | 86 +
sandbox/find-high-abund-kmers.py | 107 -
sandbox/graph-size.py | 2 +-
sandbox/link-compact-dbg.py | 198 +
sandbox/memusg | 46 +
sandbox/optimal_args_hashbits.py | 5 +-
sandbox/readaligner_pairhmm_train.py | 14 +-
sandbox/reassemble-contigs.py | 51 +
sandbox/saturate-by-median.py | 3 +-
sandbox/stoptag-abundance-hist.py | 2 +
sandbox/streaming-assembly-simple.py | 145 +
sandbox/sweep-out-reads-with-contigs.py | 2 +-
sandbox/sweep-reads2.py | 63 +-
sandbox/sweep-reads3.py | 5 +-
scripts/abundance-dist-single.py | 69 +-
scripts/abundance-dist.py | 60 +-
scripts/annotate-partitions.py | 11 +-
scripts/count-median.py | 16 +-
scripts/do-partition.py | 46 +-
scripts/extract-long-sequences.py | 11 +-
scripts/extract-paired-reads.py | 28 +-
scripts/extract-partitions.py | 300 +-
scripts/fastq-to-fasta.py | 20 +-
scripts/filter-abund-single.py | 103 +-
scripts/filter-abund.py | 94 +-
scripts/filter-stoptags.py | 15 +-
scripts/find-knots.py | 13 +-
scripts/interleave-reads.py | 46 +-
scripts/load-graph.py | 6 +-
scripts/load-into-counting.py | 61 +-
scripts/make-initial-stoptags.py | 10 +-
scripts/merge-partitions.py | 13 +-
scripts/normalize-by-median.py | 50 +-
scripts/partition-graph.py | 48 +-
scripts/readstats.py | 25 +-
scripts/sample-reads-randomly.py | 38 +-
scripts/split-paired-reads.py | 36 +-
scripts/trim-low-abund.py | 477 +-
scripts/unique-kmers.py | 27 +-
setup.cfg | 24 +-
setup.py | 46 +-
tests/__init__.py | 1 +
tests/khmer_tst_utils.py | 108 +-
tests/test-data/README.rst | 10 +
tests/test-data/paired-mixed-witherror.fa.pe | 12 +
tests/test-data/paired.malformat.fq | 24 +
tests/test-data/paired.malformat.fq.2 | 12 +
tests/test-data/simple-genome-reads.fa | 2000 +
tests/test-data/simple-genome.fa | 2 +
tests/test-data/single-read.fa | 2 +
tests/test-data/unclean-reads.fastq | 8 +
tests/test_assembly.py | 886 +
tests/test_countgraph.py | 357 +-
tests/test_counting_single.py | 60 +-
.../test_counttable.py | 50 +-
.../test_cpython_hierarchy.py | 59 +-
tests/test_filter.py | 91 -
tests/test_filter_abund.py | 432 +
tests/test_functions.py | 280 +-
tests/test_graph.py | 32 +-
tests/test_hashset.py | 169 +
tests/test_hll.py | 73 +-
tests/test_labelhash.py | 78 +-
tests/test_lump.py | 31 +-
tests/test_nibblestorage.py | 129 +
tests/test_nodegraph.py | 462 +-
tests/test_normalize_by_median.py | 254 +-
tests/test_oxli_functions.py | 9 +-
tests/test_read_aligner.py | 127 +-
tests/test_read_handling.py | 789 +
tests/test_read_parsers.py | 136 +-
tests/test_sandbox_scripts.py | 100 +-
tests/test_script_arguments.py | 235 +-
tests/test_script_output.py | 184 +
tests/test_scripts.py | 1581 +-
tests/test_streaming_io.py | 92 +-
tests/test_subset_graph.py | 143 +-
tests/test_tabletype.py | 446 +
tests/test_threaded_sequence_processor.py | 47 +-
tests/test_version.py | 11 +-
third-party/bzip2/.gitignore | 2 +
third-party/bzip2/CHANGES | 327 +
third-party/bzip2/LICENSE | 42 +
third-party/bzip2/Makefile | 217 +
third-party/bzip2/Makefile-libbz2_so | 59 +
third-party/bzip2/README | 215 +
third-party/bzip2/README.COMPILATION.PROBLEMS | 58 +
third-party/bzip2/README.XML.STUFF | 45 +
third-party/bzip2/blocksort.c | 1094 +
third-party/bzip2/bz-common.xsl | 39 +
third-party/bzip2/bz-fo.xsl | 276 +
third-party/bzip2/bz-html.xsl | 20 +
third-party/bzip2/bzdiff | 76 +
third-party/bzip2/bzdiff.1 | 47 +
third-party/bzip2/bzgrep | 75 +
third-party/bzip2/bzgrep.1 | 56 +
third-party/bzip2/bzip.css | 74 +
third-party/bzip2/bzip2.1 | 454 +
third-party/bzip2/bzip2.1.preformatted | 399 +
third-party/bzip2/bzip2.c | 2034 +
third-party/bzip2/bzip2.txt | 391 +
third-party/bzip2/bzip2recover.c | 514 +
third-party/bzip2/bzlib.c | 1572 +
third-party/bzip2/bzlib.h | 282 +
third-party/bzip2/bzlib_private.h | 509 +
third-party/bzip2/bzmore | 61 +
third-party/bzip2/bzmore.1 | 152 +
third-party/bzip2/compress.c | 672 +
third-party/bzip2/crctable.c | 104 +
third-party/bzip2/decompress.c | 646 +
third-party/bzip2/dlltest.c | 175 +
third-party/bzip2/dlltest.dsp | 93 +
third-party/bzip2/entities.xml | 9 +
third-party/bzip2/format.pl | 68 +
third-party/bzip2/huffman.c | 205 +
third-party/bzip2/libbz2.def | 27 +
third-party/bzip2/libbz2.dsp | 130 +
third-party/bzip2/makefile.msc | 63 +
third-party/bzip2/manual.html | 2540 +
third-party/bzip2/manual.pdf | Bin 0 -> 256905 bytes
third-party/bzip2/manual.ps | 72843 +++++++++++++++++++
third-party/bzip2/manual.xml | 2964 +
third-party/bzip2/mk251.c | 31 +
third-party/bzip2/randtable.c | 84 +
third-party/bzip2/sample1.bz2 | Bin 0 -> 32348 bytes
third-party/bzip2/sample1.ref | Bin 0 -> 98696 bytes
third-party/bzip2/sample2.bz2 | Bin 0 -> 73732 bytes
third-party/bzip2/sample2.ref | Bin 0 -> 212340 bytes
third-party/bzip2/sample3.bz2 | Bin 0 -> 235 bytes
third-party/bzip2/sample3.ref | 30007 ++++++++
third-party/bzip2/spewG.c | 54 +
third-party/bzip2/unzcrash.c | 141 +
third-party/bzip2/words0 | 9 +
third-party/bzip2/words1 | 4 +
third-party/bzip2/words2 | 5 +
third-party/bzip2/words3 | 30 +
third-party/bzip2/xmlproc.sh | 114 +
third-party/seqan/ChangeLog | 5 +
.../core/include/seqan/basic/debug_test_system.h | 2 +-
third-party/zlib/.gitignore | 5 +
third-party/zlib/CMakeLists.txt | 249 +
third-party/zlib/ChangeLog | 1472 +
third-party/zlib/FAQ | 368 +
third-party/zlib/INDEX | 68 +
third-party/zlib/Makefile.in | 288 +
third-party/zlib/Makefile.pic | 3 +
third-party/zlib/README | 115 +
third-party/zlib/adler32.c | 179 +
third-party/zlib/compress.c | 80 +
third-party/zlib/configure | 831 +
third-party/zlib/crc32.c | 425 +
third-party/zlib/crc32.h | 441 +
third-party/zlib/deflate.c | 1967 +
third-party/zlib/deflate.h | 346 +
third-party/zlib/doc/algorithm.txt | 209 +
third-party/zlib/doc/rfc1950.txt | 619 +
third-party/zlib/doc/rfc1951.txt | 955 +
third-party/zlib/doc/rfc1952.txt | 675 +
third-party/zlib/doc/txtvsbin.txt | 107 +
third-party/zlib/gzclose.c | 25 +
third-party/zlib/gzguts.h | 209 +
third-party/zlib/gzlib.c | 634 +
third-party/zlib/gzread.c | 594 +
third-party/zlib/gzwrite.c | 577 +
third-party/zlib/infback.c | 640 +
third-party/zlib/inffast.c | 340 +
third-party/zlib/inffast.h | 11 +
third-party/zlib/inffixed.h | 94 +
third-party/zlib/inflate.c | 1512 +
third-party/zlib/inflate.h | 122 +
third-party/zlib/inftrees.c | 306 +
third-party/zlib/inftrees.h | 62 +
third-party/zlib/make_vms.com | 867 +
third-party/zlib/test/example.c | 601 +
third-party/zlib/test/infcover.c | 671 +
third-party/zlib/test/minigzip.c | 651 +
third-party/zlib/treebuild.xml | 116 +
third-party/zlib/trees.c | 1226 +
third-party/zlib/trees.h | 128 +
third-party/zlib/uncompr.c | 59 +
third-party/zlib/win32/DLL_FAQ.txt | 397 +
third-party/zlib/win32/Makefile.bor | 110 +
third-party/zlib/win32/Makefile.gcc | 182 +
third-party/zlib/win32/Makefile.msc | 163 +
third-party/zlib/win32/README-WIN32.txt | 103 +
third-party/zlib/win32/VisualC.txt | 3 +
third-party/zlib/win32/zlib.def | 86 +
third-party/zlib/win32/zlib1.rc | 40 +
third-party/zlib/zconf.h.cmakein | 513 +
third-party/zlib/zconf.h.in | 511 +
third-party/zlib/zlib.3 | 151 +
third-party/zlib/zlib.3.pdf | Bin 0 -> 8734 bytes
third-party/zlib/zlib.h | 1768 +
third-party/zlib/zlib.map | 83 +
third-party/zlib/zlib.pc.cmakein | 13 +
third-party/zlib/zlib.pc.in | 13 +
third-party/zlib/zlib2ansi | 152 +
third-party/zlib/zutil.c | 324 +
third-party/zlib/zutil.h | 253 +
versioneer.py | 1668 +-
313 files changed, 167591 insertions(+), 12466 deletions(-)
diff --git a/.dictionary b/.dictionary
new file mode 100644
index 0000000..f517d74
--- /dev/null
+++ b/.dictionary
@@ -0,0 +1,155 @@
+usr
+env
+fileencoding
+utf
+khmer
+https
+github
+dib
+bsd
+txt
+org
+http
+stackoverflow
+numpy
+distutils
+ccompiler
+py
+yt
+bitbucket
+src
+openmp
+zlib
+cfg
+mcrusoe
+msu
+edu
+setupscript
+html
+nosetests
+countgraph
+casava
+fastq
+abund
+nodegraph
+cpython
+readthedocs
+bigcount
+ksize
+mers
+dna
+hmm
+paramaters
+json
+unstrusted
+stdin
+fifo
+ok
+stderr
+stdlib
+sts
+multithreaded
+rst
+rhs
+sra
+fasta
+fileobj
+config
+args
+fp
+megabyteish
+loadgraph
+kmers
+kmer
+arg
+docstring
+pmap
+ptname
+histout
+prebuilt
+stoptags
+al
+arxiv
+infile
+abundtrim
+abundfilt
+coungraph
+readstats
+basepair
+num
+csv
+graphname
+genomic
+metagenomic
+seqs
+stddev
+diginormed
+ctb
+outputfile
+stdout
+stopfilt
+pe
+se
+diginorm
+ns
+noqa
+resample
+wikipedia
+wiki
+subsampled
+ged
+oxli
+scriptname
+ints
+hackery
+dev
+os
+argv
+attr
+www
+printprimes
+hashtable
+longify
+gzipped
+rc
+init
+builtin
+camillescott
+todo
+tagset
+fakelump
+camillescott
+todo
+tagset
+fakelump
+kb
+hashtables
+tagfile
+tmp
+hh
+multicopy
+snp
+prefetch
+threadsaftey
+fq
+dir
+obv
+gen'd
+nodegraphs
+gzip
+bzip
+roundtrip
+versioneer
+seqpath
+utils
+wp
+De
+filetype
+tabstop
+softtabstop
+shiftwidth
+expandtab
+textwidth
+read's
+argparse
+reflow
diff --git a/CONTRIBUTING.md b/.github/CONTRIBUTING.md
similarity index 87%
rename from CONTRIBUTING.md
rename to .github/CONTRIBUTING.md
index f701fde..94383ec 100644
--- a/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -1,27 +1,27 @@
<!--
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2014-2015 Michigan State University
- Copyright (C) 2015 The Regents of the University of California.
+ Copyright (C) 2015-2016 The Regents of the University of California.
It is licensed under the three-clause BSD license; see LICENSE.
Contact: khmer-project at idyll.org
-
+
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
-
+
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
-
+
* Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided
with the distribution.
-
+
* Neither the name of the Michigan State University nor the names
of its contributors may be used to endorse or promote products
derived from this software without specific prior written
permission.
-
+
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -33,10 +33,10 @@
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
+
Contact: khmer-project at idyll.org
-->
-See [our development docs](https://khmer.readthedocs.org/en/latest/dev/).
+See [our development docs](https://khmer.readthedocs.io/en/latest/dev/).
-Be sure to copy and paste the [checklist](https://khmer.readthedocs.org/en/latest/dev/coding-guidelines-and-review.html#checklist) in the Pull-Request comment
+Be sure to copy and paste the [checklist](https://khmer.readthedocs.io/en/latest/dev/coding-guidelines-and-review.html#checklist) in the Pull-Request comment
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
new file mode 100644
index 0000000..e3e74f2
--- /dev/null
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -0,0 +1,16 @@
+- [ ] Is it mergeable?
+- [ ] `make test` Did it pass the tests?
+- [ ] `make clean diff-cover` If it introduces new functionality in
+ `scripts/` is it tested?
+- [ ] `make format diff_pylint_report cppcheck doc pydocstyle` Is it well
+ formatted?
+- [ ] Did it change the command-line interface? Only backwards-compatible
+ additions are allowed without a major version increment. Changing file
+ formats also requires a major version number increment.
+- [ ] For substantial changes or changes to the command-line interface, is it
+ documented in `CHANGELOG.md`? See [keepachangelog](http://keepachangelog.com/)
+ for more details.
+- [ ] Was a spellchecker run on the source code and documentation after
+ changes were made?
+- [ ] Do the changes respect streaming IO? (Are they
+ tested for streaming IO?)
diff --git a/.gitignore b/.gitignore
index 7ac5abd..7df2e67 100644
--- a/.gitignore
+++ b/.gitignore
@@ -29,7 +29,7 @@ khmer-cov.tgz
cppcheck-result.xml
MANIFEST
TAGS
-nosetests.xml
+pytests.xml
pep8.out
pylint.out
.coverage
@@ -37,6 +37,7 @@ doxygen.out
Doxyfile
doc/doxygen
third-party/zlib/zconf.h
+third-party/zlib/zlib.3.pdf
sloccount.sc
cov-int/
*.orig
@@ -50,3 +51,4 @@ compile_commands.json
pylint_report.txt
pep8_report.txt
pep257_report.txt
+.cache/
diff --git a/.mailmap b/.mailmap
index c084c8c..c3bd441 100644
--- a/.mailmap
+++ b/.mailmap
@@ -9,7 +9,8 @@ Susan R Steinman <susan.steinman at gmail.com> <steinman.tutoring at gmail.com>
Adina Howe <adina at iastate.edu> <howead at msu.edu>
Elmar Bucher <buchere at ohsu.edu> <elmbeech at zoho.com>
Luiz Irber <luiz.irber at gmail.com> <luizirber at users.noreply.github.com>
-Luiz Irber <luiz.irber at gmail.com> <irberlui at msu.edu>
+Luiz Irber <luiz.irber at gmail.com> <irberlui at msu.edu>
+Luiz Irber <luiz.irber at gmail.com> <khmer at luizirber.org>
Qingpeng Zhang <qingpeng at gmail.com> <qingpeng at msu.edu>
Qingpeng Zhang <qingpeng at gmail.com>
Reed Cartwright <cartwright at asu.edu>
diff --git a/.travis.yml b/.travis.yml
new file mode 100644
index 0000000..23f8ee3
--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1,88 @@
+language: python
+
+# Tell travis we want Ubuntu 14.04
+sudo: required
+dist: trusty
+
+notifications:
+ email: false
+
+# with building pushes enabled on travis we would get
+# two builds for every new commit pushed to a branch
+# for a PR. So we disable build-on-push for all branches
+# except the ones whitelisted here.
+branches:
+ only:
+ - master
+
+matrix:
+ fast_finish: true
+ include:
+ - os: linux
+ python: "2.7"
+ # Tell travis we want debian trusty
+ sudo: required
+ dist: trusty
+ env:
+ - TESTATTR="'not huge and not known_failing'"
+ addons:
+ apt:
+ packages:
+ - astyle
+ - cppcheck
+ - enchant
+
+ - os: linux
+ python: "3.5"
+ # Tell travis we want debian trusty
+ sudo: required
+ dist: trusty
+ env:
+ - TESTATTR="'not huge and not known_failing'"
+ addons:
+ apt:
+ packages:
+ - astyle
+ - cppcheck
+ - enchant
+
+ - os: osx
+ language: generic
+ osx_image: xcode7.3
+ env:
+ - TESTATTR="'not linux and not known_failing and not huge'"
+ before_install:
+ - source ci_scripts/install.sh
+
+# command to install common dependencies
+install:
+ - python --version
+ - which python
+ - gcc --version
+ - which gcc
+ - make install-dependencies
+
+# command to run tests
+script:
+ - make test
+ - make pep8
+
+# generate all the diagnostic reports
+after_success:
+ - make clean
+ - PYTEST_ADDOPTS=-qqq make coverage-gcovr.xml coverage.xml
+ # Fix suggested by http://diff-cover.readthedocs.io/en/latest/#troubleshooting
+ - git fetch origin master:refs/remotes/origin/master
+ - PYTEST_ADDOPTS=-qqq make diff-cover
+ - make format
+ - make diff_pylint_report
+ - make cppcheck
+ - make pydocstyle
+ # do the docs build?
+ - make doc
+ # XXX Do not upload results from travis yet. Currently jenkins is considered
+ # XXX the source of truth about coverage
+ # only upload one coverage report to codecov as it merges all reports
+ # from all builds into one.
+ - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then pip install codecov; fi
+ - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then codecov -X pycov search gcov -f coverage.xml coverage-gcovr.xml; fi
diff --git a/.ycm_extra_conf.py b/.ycm_extra_conf.py
new file mode 100644
index 0000000..fcc7939
--- /dev/null
+++ b/.ycm_extra_conf.py
@@ -0,0 +1,105 @@
+# This file is NOT licensed under the GPLv3, which is the license for the rest
+# of YouCompleteMe.
+#
+# Here's the license text for this file:
+#
+# This is free and unencumbered software released into the public domain.
+#
+# Anyone is free to copy, modify, publish, use, compile, sell, or
+# distribute this software, either in source code form or as a compiled
+# binary, for any purpose, commercial or non-commercial, and by any
+# means.
+#
+# In jurisdictions that recognize copyright laws, the author or authors
+# of this software dedicate any and all copyright interest in the
+# software to the public domain. We make this dedication for the benefit
+# of the public at large and to the detriment of our heirs and
+# successors. We intend this dedication to be an overt act of
+# relinquishment in perpetuity of all present and future rights to this
+# software under copyright law.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+# IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR
+# OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+# ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+# OTHER DEALINGS IN THE SOFTWARE.
+#
+# For more information, please refer to <http://unlicense.org/>
+
+import os
+import ycm_core
+
+SOURCE_EXTENSIONS = ['.cpp', '.cxx', '.cc', '.c', '.m', '.mm']
+
+database = ycm_core.CompilationDatabase(
+ os.path.dirname(os.path.abspath(__file__)))
+
+def MakeRelativePathsInFlagsAbsolute(flags, working_directory):
+ if not working_directory:
+ return list(flags)
+ new_flags = []
+ make_next_absolute = False
+ path_flags = ['-isystem', '-I', '-iquote', '--sysroot=']
+ for flag in flags:
+ new_flag = flag
+
+ if make_next_absolute:
+ make_next_absolute = False
+ if not flag.startswith('/'):
+ new_flag = os.path.join(working_directory, flag)
+
+ for path_flag in path_flags:
+ if flag == path_flag:
+ make_next_absolute = True
+ break
+
+ if flag.startswith(path_flag):
+ path = flag[len(path_flag):]
+ new_flag = path_flag + os.path.join(working_directory, path)
+ break
+
+ if new_flag:
+ new_flags.append(new_flag)
+ return new_flags
+
+
+def IsHeaderFile(filename):
+ extension = os.path.splitext(filename)[1]
+ return extension in ['.h', '.hxx', '.hpp', '.hh']
+
+
+def GetCompilationInfoForFile(filename):
+ # The compilation_commands.json file generated by CMake does not have entries
+ # for header files. So we do our best by asking the db for flags for a
+ # corresponding source file, if any. If one exists, the flags for that file
+ # should be good enough.
+ if IsHeaderFile(filename):
+ basename = os.path.splitext(filename)[0]
+ for extension in SOURCE_EXTENSIONS:
+ replacement_file = basename + extension
+ if os.path.exists(replacement_file):
+ compilation_info = database.GetCompilationInfoForFile(
+ replacement_file)
+ if compilation_info.compiler_flags_:
+ return compilation_info
+ return None
+ return database.GetCompilationInfoForFile(filename)
+
+
+def FlagsForFile(filename, **kwargs):
+ # Bear in mind that compilation_info.compiler_flags_ does NOT return a
+ # python list, but a "list-like" StringVec object
+ compilation_info = GetCompilationInfoForFile(filename)
+ if not compilation_info:
+ return None
+
+ final_flags = MakeRelativePathsInFlagsAbsolute(
+ compilation_info.compiler_flags_,
+ compilation_info.compiler_working_dir_)
+
+ return {
+ 'flags': final_flags,
+ 'do_cache': True
+ }
diff --git a/CHANGELOG.md b/CHANGELOG.md
new file mode 100644
index 0000000..7b3d45c
--- /dev/null
+++ b/CHANGELOG.md
@@ -0,0 +1,65 @@
+# Change Log
+All notable changes to the khmer project will be documented in this file.
+See [keepachangelog](http://keepachangelog.com/) for more info.
+
+The khmer project's command line scripts adhere to
+[Semantic Versioning](http://semver.org/). The Python and C++ APIs are not yet
+under semantic versioning, but will be in future versions of khmer.
+
+## [Unreleased]
+### Added
+- New `--no-reformat` option for `interleave-reads.py` script disables default
+ read name correction behavior.
+- New `HashSet` data structure for managing collections of k-mer hashes and
+ tags.
+- khmer package version now included in `.info` files.
+- New `-o|--outfile` option for `filter-abund-single.py` script.
+- New sandbox script `extract-compact-dbg.py` for computing a compact de Bruijn
+ graph from sequence data.
+- New `--quiet` flag to several scripts, silencing diagnostic messages in
+ terminal output.
+- Support for human-friendly memory requests (2G instead of 2000000000 or 2e9).
+- Support for variable-coverage trimming in the `filter-abund-single.py` script.
+- A simple example of the C++ API in `examples/c++-api`.
+- New `assemble_linear_path` function for baiting unambiguous contigs with a
+ seed k-mer from a hashtable.
+- Support for assembling directly from k-mer graphs, and a new
+ JunctionCountAssembler class.
+- Add --info flag for obtaining citation information.
+- Added Counttable and Nodetable to support non-reversible hashing
+ functionality and k > 32.
+- Add a new storage class using half a byte per entry. Exposed as
+ SmallCounttable and SmallCountgraph.
+- Added `cleaned_seq` attribute to `khmer.Read` class which provides a cleaned
+ version of the sequence of each read.
+
+### Changed
+- Switch from nose to py.test as the testing framework.
+- Switch from internally managed Jenkins setup to Travis CI for continuous
+ integration testing.
+- Renamed core data structures: CountingHash --> Countgraph,
+ Hashbits --> Nodegraph.
+- Replaced the IParser and FastxParser classes with a single ReadParser class.
+ Different input formats are supported by templating ReadParser with a reader
+ class.
+- Renamed `consume_fasta` and related functions to `consume_seqfile`, with
+ support for reading sequences from additional formats pending.
+
+### Fixed
+- Bug in compressed(gzip) streaming output from scripts
+- The hashbits `update_from` function to correctly track occupied bins for
+ calculating FPR.
+- Bug in the `filter-abund.py` script when `--gzip` and `-o` flags are used
+ simultaneously.
+- Bug in the hashtable `get_kmers` function based on incorrect usage of the
+ `substr` function.
+- Bug in `broken_paired_reader` related to dropping short reads when
+ `require_paired` is set.
+- Bug related to handling lowercase [acgtn] characters in input data.
+- Bug in `load-graph.py` that calculated required graph space incorrectly.
+- Fix loading of empty partion map files
+
+## [2.0] - 2015-10-08
+
+Previous to the khmer 2.1 release, all changes were documented in a file named
+`ChangeLog`. This file is now at `legacy/ChangeLog` for posterity.
diff --git a/CITATION b/CITATION
index e830d26..d9e7869 100644
--- a/CITATION
+++ b/CITATION
@@ -4,24 +4,24 @@
Copyright (C) 2015 The Regents of the University of California.
It is licensed under the three-clause BSD license; see LICENSE.
Contact: khmer-project at idyll.org
-
+
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
-
+
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
-
+
* Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided
with the distribution.
-
+
* Neither the name of the Michigan State University nor the names
of its contributors may be used to endorse or promote products
derived from this software without specific prior written
permission.
-
+
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -33,7 +33,7 @@
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
+
Contact: khmer-project at idyll.org
.. If you update this file then you may need to update the citations in
diff --git a/IDEAS b/IDEAS
deleted file mode 100644
index a42026f..0000000
--- a/IDEAS
+++ /dev/null
@@ -1,18 +0,0 @@
-get callback from partitioning working again!
-
-also 1 bit/hash table entry, for basic partitioning? (REDUCE MEM USAGE/FP)
-
-replace memory structures for map, set to be cheaper; see Matt Austern's
- treatise.
-
-run velvet??
-
-probably want to randomize which group files different partitions go into...?
-
-TODO in the future
-----
-
-put locks around the I/O functions.
-
-Use SWIG for Python wrapper around C++.
- (Pure Cython - atomic ops? I/O performance tuning? probably bad idea...)
diff --git a/Makefile b/Makefile
index b3127b5..c12d902 100644
--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,6 @@
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2010-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -33,43 +33,59 @@
#
# Contact: khmer-project at idyll.org
-# make pep8 to check for basic Python code compliance
-# make autopep8 to fix most pep8 errors
-# make pylint to check Python code for enhanced compliance including naming
-# and documentation
-# make coverage-report to check coverage of the python scripts by the tests
+# `make help` for a summary of useful targets
# `SHELL=bash` Will break Titus's laptop, so don't use BASH-isms like
# `[[` conditional expressions.
-CPPSOURCES=$(wildcard lib/*.cc lib/*.hh khmer/_khmer.cc) setup.py
-PYSOURCES=$(wildcard khmer/*.py scripts/*.py)
+CPPSOURCES=$(wildcard lib/*.cc lib/*.hh khmer/_khmer.cc khmer/*.hh) setup.py
+PYSOURCES=$(filter-out khmer/_version.py, \
+ $(wildcard khmer/*.py scripts/*.py oxli/*.py) )
SOURCES=$(PYSOURCES) $(CPPSOURCES) setup.py
-DEVPKGS=pep8==1.5.7 diff_cover autopep8 pylint coverage gcovr nose pep257 \
- screed
+DEVPKGS=pep8==1.6.2 diff_cover autopep8 pylint coverage gcovr pytest \
+ pydocstyle screed pyenchant
GCOVRURL=git+https://github.com/nschum/gcovr.git@never-executed-branches
-VERSION=$(shell git describe --tags --dirty | sed s/v//)
+
+VERSION=$(shell ./setup.py version | grep Version | awk '{print $$4}' \
+ | sed 's/+/-/')
+
+# wrapping the command with `printf "%q" some-text` shell-escapes the string
+# http://stackoverflow.com/a/2856010
+# list of preprocessor defines works for GCC and clang
+# http://nadeausoftware.com/articles/2011/12/c_c_tip_how_list_compiler_predefined_macros
+DEFINES=$(shell printf "%q" "$$( c++ -dM -E -x c++ /dev/null | \
+ awk '{print "-D" $$2 "=" $$3}' | tr '\n' ' ')" | sed 's/\\ / /g' )
+DEFINES += -DNDEBUG -DVERSION=$(VERSION) -DSEQAN_HAS_BZIP2=1 \
+ -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC
+
+INCLUDESTRING=$(shell gcc -E -x c++ - -v < /dev/null 2>&1 >/dev/null \
+ | grep '^ /' | grep -v cc1plus)
+INCLUDEOPTS=$(shell gcc -E -x c++ - -v < /dev/null 2>&1 >/dev/null \
+ | grep '^ /' | grep -v cc1plus | awk '{print "-I" $$1 " "}')
+PYINCLUDE=$(shell python -c \
+ "import sysconfig;print(sysconfig.get_path('include'))")
+
CPPCHECK=ls lib/*.cc khmer/_khmer.cc | grep -v test | cppcheck -DNDEBUG \
-DVERSION=0.0.cppcheck -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 \
-UNO_UNIQUE_RC --enable=all --suppress='*:/usr/*' \
- --file-list=- --platform=unix64 --std=c++11 --inline-suppr \
- --quiet -Ilib -Ithird-party/bzip2 -Ithird-party/zlib \
- -Ithird-party/smhasher -I/usr/include/python3.4m -DHAVE_SSIZE_T \
- -D__linux__ -D__x86_64__ -D__LP64__ -I/usr/include \
- -I/usr/include/x86_64-linux-gnu/ -I/usr/include/linux \
- -I/usr/lib/gcc/x86_64-linux-gnu/4.9/include/
+ --suppress='*:$(PYINCLUDE)/*' --file-list=- --platform=unix64 \
+ --std=c++11 --inline-suppr --quiet -Ilib -Ithird-party/bzip2 \
+ -Ithird-party/zlib -Ithird-party/smhasher -I$(PYINCLUDE) \
+ $(DEFINES) $(INCLUDEOPTS)
UNAME := $(shell uname)
ifeq ($(UNAME),Linux)
- TESTATTR ?= '!known_failing,!jenkins,!huge'
+ TESTATTR ?= 'not known_failing and not jenkins and not huge'
else
- TESTATTR ?= '!known_failing,!jenkins,!huge,!linux'
+ TESTATTR ?= 'not known_failing and not jenkins and not huge and not linux'
endif
-
-MODEXT=$(shell python -c "import sysconfig;print(sysconfig.get_config_var('SO'))")
+MODEXT=$(shell python -c \
+ "import sysconfig;print(sysconfig.get_config_var('SO'))")
EXTENSION_MODULE = khmer/_khmer$(MODEXT)
+PYLINT_TEMPLATE="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}"
+
## all : default task; compile C++ code, build shared object library
all: sharedobj
@@ -81,7 +97,8 @@ help: Makefile
install-dep: install-dependencies
install-dependencies:
- pip install --upgrade $(DEVPKGS)
+ pip install git+https://github.com/dib-lab/screed.git
+ pip install --upgrade --ignore-installed $(DEVPKGS)
pip install --upgrade --requirement doc/requirements.txt
## sharedobj : build khmer shared object file
@@ -107,18 +124,23 @@ dist/khmer-$(VERSION).tar.gz: $(SOURCES)
## clean : clean up all temporary / machine-generated files
clean: FORCE
- cd lib && ${MAKE} clean || true
+ cd lib && $(MAKE) clean || true
cd tests && rm -rf khmertest_* || true
+ rm -f pytest_runner-*.egg pytests.xml
rm -f $(EXTENSION_MODULE)
- rm -f khmer/*.pyc lib/*.pyc scripts/*.pyc tests/*.pyc oxli/*.pyc
+ rm -f khmer/*.pyc lib/*.pyc scripts/*.pyc tests/*.pyc oxli/*.pyc \
+ sandbox/*.pyc khmer/__pycache__/* sandbox/__pycache__/*
./setup.py clean --all || true
rm -f coverage-debug
- rm -Rf .coverage
+ rm -Rf .coverage coverage-gcovr.xml coverage.xml
rm -f diff-cover.html
+ rm -Rf build dist
+ rm -rf __pycache__/ .eggs/ khmer.egg-info/
+ -rm -f *.gcov
debug: FORCE
export CFLAGS="-pg -fprofile-arcs -D_GLIBCXX_DEBUG_PEDANTIC \
- -D_GLIBCXX_DEBUG"; python setup.py build_ext --debug \
+ -D_GLIBCXX_DEBUG -DDEBUG_ASSEMBLY=1 -DDEBUG_FILTERS=1"; python setup.py build_ext --debug \
--inplace
## doc : render documentation in HTML
@@ -138,76 +160,76 @@ pdf: build/sphinx/latex/khmer.pdf
build/sphinx/latex/khmer.pdf: $(SOURCES) doc/conf.py $(wildcard doc/*.rst) \
$(wildcard doc/user/*.rst) $(wildcard doc/dev/*.rst) sharedobj
./setup.py build_sphinx --fresh-env --builder latex
- cd build/sphinx/latex && ${MAKE} all-pdf
+ cd build/sphinx/latex && $(MAKE) all-pdf
@echo ''
@echo '--> pdf in build/sphinx/latex/khmer.pdf'
cppcheck-result.xml: $(CPPSOURCES)
- ${CPPCHECK} --xml-version=2 2> cppcheck-result.xml
+ $(CPPCHECK) --xml-version=2 2> cppcheck-result.xml
## cppcheck : run static analysis on C++ code
-cppcheck: $(CPPSOURCES)
- ${CPPCHECK}
+cppcheck: FORCE
+ @$(CPPCHECK)
+
+cppcheck-long: FORCE
+ @$(CPPCHECK) -Ithird-party/seqan/core/include
## pep8 : check Python code style
pep8: $(PYSOURCES) $(wildcard tests/*.py)
- pep8 --exclude=_version.py --show-source --show-pep8 setup.py khmer/ \
- scripts/ tests/ oxli/ || true
+ pep8 setup.py khmer/*.py scripts/*.py tests/*.py oxli/*.py
pep8_report.txt: $(PYSOURCES) $(wildcard tests/*.py)
- pep8 --exclude=_version.py setup.py khmer/ scripts/ tests/ oxli/ \
+ pep8 setup.py khmer/ scripts/ tests/ oxli/ \
> pep8_report.txt || true
diff_pep8_report: pep8_report.txt
diff-quality --violations=pep8 pep8_report.txt
-## pep257 : check Python code style
-pep257: $(PYSOURCES) $(wildcard tests/*.py)
- pep257 --ignore=D100,D101,D102,D103 \
+## pydocstyle : check Python doc strings
+pydocstyle: $(PYSOURCES) $(wildcard tests/*.py)
+ pydocstyle --ignore=D100,D101,D102,D103,D203 \
setup.py khmer/ scripts/ tests/ oxli/ || true
-pep257_report.txt: $(PYSOURCES) $(wildcard tests/*.py)
- pep257 setup.py khmer/ scripts/ tests/ oxli/ \
- > pep257_report.txt 2>&1 || true
+pydocstyle_report.txt: $(PYSOURCES) $(wildcard tests/*.py)
+ pydocstyle setup.py khmer/ scripts/ tests/ oxli/ \
+ > pydocstyle_report.txt 2>&1 || true
-diff_pep257_report: pep257_report.txt
- diff-quality --violations=pep8 pep257_report.txt
+diff_pydocstyle_report: pydocstyle_report.txt
+ diff-quality --violations=pep8 pydocstyle_report.txt
## astyle : fix most C++ code indentation and formatting
astyle: $(CPPSOURCES)
- astyle -A10 --max-code-length=80 $(CPPSOURCES)
+ astyle -A10 --max-code-length=80 $(filter-out setup.py,$(CPPSOURCES))
## autopep8 : fix most Python code indentation and formatting
autopep8: $(PYSOURCES) $(wildcard tests/*.py)
autopep8 --recursive --in-place --exclude _version.py --ignore E309 \
setup.py khmer/*.py scripts/*.py tests/*.py oxli/*.py
-# A command to automatically run astyle and autopep8 on appropriate files
-## format : check/fix all code indentation and formatting (runs astyle and autopep8)
+## format : check/fix all code formatting (astyle and autopep8)
format: astyle autopep8
# Do nothing
## pylint : run static code analysis on Python code
pylint: $(PYSOURCES) $(wildcard tests/*.py)
- pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \
- --extension-pkg-whitelist=khmer \
- setup.py khmer/[!_]*.py khmer/__init__.py scripts/*.py tests \
- oxli/*.py || true
+ pylint --msg-template=$(PYLINT_TEMPLATE) \
+ setup.py $(PYSOURCES) tests/*.py || true
-pylint_report.txt: ${PYSOURCES} $(wildcard tests/*.py)
- pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \
- setup.py khmer/[!_]*.py khmer/__init__.py scripts/*.py tests \
- sandbox/*.py oxli/*.py > pylint_report.txt || true
+pylint_report.txt: $(PYSOURCES) $(wildcard tests/*.py) $(wildcard sandbox/*.py)
+ pylint --msg-template=$(PYLINT_TEMPLATE) \
+ $(PYSOURCES) tests sandbox > pylint_report.txt || true
diff_pylint_report: pylint_report.txt
diff-quality --violations=pylint pylint_report.txt
# We need to get coverage to look at our scripts. Since they aren't in a
-# python module we can't tell nosetests to look for them (via an import
-# statement). So we run nose inside of coverage.
+# python module we can't tell pytest to look for them (via an import
+# statement). So we run pytest inside of coverage.
.coverage: $(PYSOURCES) $(wildcard tests/*.py) $(EXTENSION_MODULE)
- coverage run --branch --source=scripts,khmer,oxli --omit=khmer/_version.py \
- -m nose --with-xunit --attr $(TESTATTR) --processes=0
+ ./setup.py develop
+ coverage run --branch --source=scripts,khmer,oxli \
+ --omit=khmer/_version.py -m pytest --junitxml=pytests.xml \
+ -m $(TESTATTR)
coverage.xml: .coverage
coverage xml
@@ -233,19 +255,18 @@ diff-cover.html: coverage-gcovr.xml coverage.xml
diff-cover coverage-gcovr.xml coverage.xml \
--html-report diff-cover.html
-nosetests.xml: FORCE
- ./setup.py nosetests --with-xunit --attr ${TESTATTR}
+pytests.xml: FORCE
+ py.test --junitxml=$@ -m ${TESTATTR}
## doxygen : generate documentation of the C++ and Python code
# helpful packages: doxygen graphviz
# ignore warning re: _formulas.aux
doxygen: doc/doxygen/html/index.html
-doc/doxygen/html/index.html: ${CPPSOURCES} ${PYSOURCES}
+doc/doxygen/html/index.html: $(CPPSOURCES) $(PYSOURCES)
mkdir -p doc/doxygen
- sed "s/\$${VERSION}/$$(python ./lib/get_version.py)/" Doxyfile.in | \
- sed "s@\$${INCLUDES}@$$($$(gcc -print-prog-name=cc1plus) -v /dev/null \
- 2>&1 >/dev/null | grep '^ '|tr '\n' ' ')@" > Doxyfile
+ sed "s=\$${VERSION}=$$(python ./lib/get_version.py)=" Doxyfile.in | \
+ sed "s=\$${INCLUDES}=$(INCLUDESTRING)=" > Doxyfile
doxygen
lib: FORCE
@@ -264,31 +285,35 @@ libtest: FORCE
test -f install_target/include/oxli/khmer.hh
test -d install_target/lib
test -f install_target/lib/liboxli.a
- $(CXX) -std=c++11 -o install_target/test-prog-static -I install_target/include \
- lib/test-compile.cc install_target/lib/liboxli.a
- $(CXX) -std=c++11 -o install_target/test-prog-dynamic -I install_target/include \
- -L install_target/lib lib/test-compile.cc -loxli
+ $(CXX) -std=c++11 -o install_target/test-prog-static \
+ -I install_target/include lib/test-compile.cc \
+ install_target/lib/liboxli.a
+ $(CXX) -std=c++11 -o install_target/test-prog-dynamic \
+ -I install_target/include -L install_target/lib \
+ lib/test-compile.cc -loxli
rm -rf install_target
## test : run the khmer test suite
test: FORCE
./setup.py develop
- ./setup.py nosetests --attr ${TESTATTR}
+ py.test -m ${TESTATTR}
-sloccount.sc: ${CPPSOURCES} ${PYSOURCES} $(wildcard tests/*.py) Makefile
+sloccount.sc: $(CPPSOURCES) $(PYSOURCES) $(wildcard tests/*.py) Makefile
sloccount --duplicates --wide --details lib khmer scripts tests \
setup.py Makefile > sloccount.sc
## sloccount : count lines of code
-sloccount:
+sloccount:
sloccount lib khmer scripts tests setup.py Makefile
coverity-build:
if [ -x "${cov_analysis_dir}/bin/cov-build" ]; \
then \
export PATH=${PATH}:${cov_analysis_dir}/bin; \
- cov-build --dir cov-int --c-coverage gcov --disable-gcov-arg-injection make coverage-debug; \
- cov-capture --dir cov-int --c-coverage gcov python -m nose --attr ${TESTATTR} ; \
+ cov-build --dir cov-int --c-coverage gcov \
+ --disable-gcov-arg-injection make coverage-debug; \
+ cov-capture --dir cov-int --c-coverage gcov python -m pytest \
+ -m $(TESTATTR) ; \
cov-import-scm --dir cov-int --scm git 2>/dev/null; \
else echo 'bin/cov-build does not exist in $$cov_analysis_dir: '\
'${cov_analysis_dir}. Skipping coverity scan.'; \
@@ -300,7 +325,7 @@ coverity-upload: cov-int
tar czf khmer-cov.tgz cov-int; \
curl --form token=${COVERITY_TOKEN} --form \
email=mcrusoe at msu.edu --form file=@khmer-cov.tgz \
- --form version=${VERSION} \
+ --form version=$(VERSION) \
https://scan.coverity.com/builds?project=ged-lab%2Fkhmer ; \
else echo 'Missing coverity credentials in $$COVERITY_TOKEN,'\
'skipping scan'; \
@@ -313,8 +338,10 @@ coverity-configure:
if [[ -x ${cov_analysis_dir}/bin/cov-configure ]]; \
then \
export PATH=${PATH}:${cov_analysis_dir}/bin; \
- for compiler in /usr/bin/gcc-4.8 /usr/bin/x86_64-linux-gnu-gcc; do \
- cov-configure --comptype gcc --compiler $${compiler}; \
+ for compiler in \
+ /usr/bin/gcc-4.8 /usr/bin/x86_64-linux-gnu-gcc; do \
+ cov-configure --comptype gcc \
+ --compiler $${compiler}; \
done; \
else echo 'bin/cov-configure does not exist in $$cov_analysis_dir: '\
'${cov_analysis_dir}. Skipping coverity configuration.'; \
@@ -323,7 +350,7 @@ coverity-configure:
# may need to `sudo apt-get install bear`
compile_commands.json: clean
export PATH=$(shell echo $$PATH | sed 's=/usr/lib/ccache:==g') ; \
- bear -- ./setup.py build_ext
+ bear ./setup.py build_ext
convert-release-notes:
for file in doc/release-notes/*.md; do \
@@ -356,3 +383,8 @@ list-citation:
python sort-authors-list.py
FORCE:
+
+# Use this to print the value of a Makefile variable
+# Example `make print-VERSION`
+# From https://www.cmcrossroads.com/article/printing-value-makefile-variable
+print-% : ; @echo $* = $($*)
diff --git a/README.rst b/README.rst
index 22ed675..06bd2b4 100644
--- a/README.rst
+++ b/README.rst
@@ -1,27 +1,27 @@
..
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2010-2015 Michigan State University
- Copyright (C) 2015 The Regents of the University of California.
+ Copyright (C) 2015-2016 The Regents of the University of California.
It is licensed under the three-clause BSD license; see LICENSE.
Contact: khmer-project at idyll.org
-
+
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
-
+
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
-
+
* Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided
with the distribution.
-
+
* Neither the name of the Michigan State University nor the names
of its contributors may be used to endorse or promote products
derived from this software without specific prior written
permission.
-
+
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -33,9 +33,14 @@
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
+
Contact: khmer-project at idyll.org
+|Research software impact|
+
+.. |Research software impact| image:: http://depsy.org/api/package/pypi/khmer/badge.svg
+ :target: http://depsy.org/package/python/khmer
+
khmer
=====
@@ -47,7 +52,7 @@ https://github.com/dib-lab/khmer
and you can read the docs online here:
-http://khmer.readthedocs.org/
+http://khmer.readthedocs.io/
There are two mailing lists dedicated to khmer, an announcements-only
list and a discussion list. To search their archives and sign-up for
@@ -57,38 +62,47 @@ them, please visit the following URLs:
- Announcements: http://lists.idyll.org/listinfo/khmer-announce
-We chat at https://gitter.im/dib-lab/khmer and the maintainers can be
-contacted at khmer-project at idyll.org.
+The maintainers can be contacted at khmer-project at idyll.org.
+
+For getting help please see this guide: http://khmer.readthedocs.io/en/stable/user/getting-help.html
+Your first port of call when looking for help should be: https://github.com/dib-lab/khmer/issues
-For getting help please see this guide: http://khmer.readthedocs.org/en/stable/user/getting-help.html
-IMPORTANT NOTE: CITE US!
+Important note: cite us!
------------------------
khmer is *research software*, so you should cite us when you use it
in scientific publications! Please see the `CITATION
-<http://khmer.readthedocs.org/en/stable/citations.html>`__ file for
+<http://khmer.readthedocs.io/en/stable/citations.html>`__ file for
citation information.
-INSTALL INSTRUCTIONS:
----------------------
-khmer requires a 64-bit operating system and Python version 2.7.x, 3.3.x, or
-3.4.x. Linux users will need the Python development libraries and gcc. OS X
-users may need XCode installed to build from source.
+Install
+-------
+
+khmer works with Python version 2.7 or 3.5. Create a
+`virtual environemnt <http://docs.python-guide.org/en/latest/dev/virtualenvs/>`_
+and install khmer with:
+
+```
+pip install khmer
+```
-In short:
+You are ready to go. For more details see `doc/install.rst
+<https://khmer.readthedocs.io/en/stable/user/install.html>`_
-``pip install khmer`` to download, build, and install the latest stable
-version.
-For more details see `doc/install.rst <https://khmer.readthedocs.org/en/stable/user/install.html>`_
+Contributing
+------------
-The use of a virtualenv is recommended, see
-https://virtualenv.readthedocs.org/en/latest/installation.html
+If you want to modify khmer or contribute to its development read the
+`developer instructions
+<https://khmer.readthedocs.io/en/stable/dev/getting-started.html>`_
-khmer is under the BSD license; see doc/LICENSE.txt. Distribution,
+
+License
+-------
+
+khmer is distributed under the BSD license; see doc/LICENSE.txt. Distribution,
modification and redistribution, incorporation into other software, and
pretty much everything else is allowed.
-
-MRC 2015-09-07
diff --git a/TODO b/TODO
deleted file mode 100644
index eeb5d77..0000000
--- a/TODO
+++ /dev/null
@@ -1,80 +0,0 @@
-find-knot speedup:
- - too many redundant rounds of partitioning?
-
-memory improvement for counting hash
-
-sequence loading into both counting & hashbits
-
-graphsize filtering with stop-big-traversal
-
-why does stop-big-traversal still connect???
-
-cython integrate!
-
-pull reads into partitions?
-
-look more assiduously for memory leaks
-
-----
-
-counting hash generalization to n < 8 bits => memory efficiency
-
-load-counting/bigcount loading is slooooow
-
-----
-
-screed slice
-screed fasta/fastq output
-
-
----
-
-fix tests cleanup
-pyrex/cython stuff
-docs!
-
----
-
-the N dilemma
-
----
-
-
-put in logging.
-
-fix tests and test cases to properly isolate/remove temp files.
-
-fix dir(ht)
-
-###
-
-Semi-obsolete comments, pre partitioning:
-
-also, can probably arrange parallelization split & hash table size so
-that modulus exactly fills split portion of table.
-
-mismatch hashing - compute min num - each base?
-
-copyright, C++ file comments at top; license; etc.
-
-tests for readmask updating, etc. in various circumstances!
-
-tests for khmer saturation vs valid reads
-
-profiling
-
-
-reading on hash functions:
-
- http://www.burtleburtle.net/bob/hash/doobs.html
- http://www.burtleburtle.net/bob/c/lookup3.c
- http://www.burtleburtle.net/bob/hash/doobs.html
- http://www.codinghorror.com/blog/2007/12/hashtables-pigeonholes-and-birthdays.html
- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1131890/
-
-things to reference or at least look at:
-
- http://sourceforge.net/apps/mediawiki/kmer/index.php?title=Getting_Started_with_Meryl
- http://www.hgsc.bcm.tmc.edu/cascade-tech-software_bang-ti.hgsc
- http://www.hgsc.bcm.tmc.edu/cascade-tech-software_cbt-ti.hgsc
- http://code.google.com/p/google-sparsehash/
diff --git a/ci_scripts/install.sh b/ci_scripts/install.sh
new file mode 100644
index 0000000..826eda5
--- /dev/null
+++ b/ci_scripts/install.sh
@@ -0,0 +1,31 @@
+# Used to prepare OSX builds
+
+if [ "${TRAVIS_OS_NAME}" != "osx" ]; then
+ echo "This is not a OSX build"
+ exit 1
+fi
+
+brew update;
+brew install astyle;
+brew install enchant;
+brew install cppcheck;
+
+pushd .
+cd
+mkdir -p download
+cd download
+wget http://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh \
+ -O miniconda.sh
+chmod +x miniconda.sh && ./miniconda.sh -b
+cd ..
+export PATH=/Users/travis/miniconda3/bin:$PATH
+conda update --yes conda
+popd
+
+# Create a fresh environment
+conda create -n testenv --yes python=2.7
+
+source activate testenv
+
+# Without this `make install-dependencies` fails
+pip install --ignore-installed setuptools
diff --git a/doc/conf.py b/doc/conf.py
index d7455d0..dc8e55d 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -57,16 +57,9 @@ Rajaram Srinivasan, Qingpeng Zhang, and C. Titus Brown'''
# The full version, including alpha/beta/rc tags.
-sys.path.insert(0, '../')
-import versioneer
-versioneer.VCS = 'git'
-versioneer.versionfile_source = '../khmer/_version.py'
-versioneer.versionfile_build = '../khmer/_version.py'
-versioneer.tag_prefix = 'v' # tags are like v1.2.0
-versioneer.parentdir_prefix = '..'
-release = versioneer.get_version()
-del versioneer
-sys.path.remove('../')
+from khmer._version import get_versions
+release = get_versions()['version']
+del get_versions
# The short X.Y version.
diff --git a/doc/contributors.rst b/doc/contributors.rst
index d176399..bac61f1 100644
--- a/doc/contributors.rst
+++ b/doc/contributors.rst
@@ -4,24 +4,24 @@
Copyright (C) 2015 The Regents of the University of California.
It is licensed under the three-clause BSD license; see LICENSE.
Contact: khmer-project at idyll.org
-
+
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
-
+
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
-
+
* Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided
with the distribution.
-
+
* Neither the name of the Michigan State University nor the names
of its contributors may be used to endorse or promote products
derived from this software without specific prior written
permission.
-
+
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -33,7 +33,7 @@
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
+
Contact: khmer-project at idyll.org
*********************************
@@ -58,7 +58,7 @@ Adina Howe, Rosangela Canino-Koning, and Arend Hintze contributed
significantly to discussions of approaches and algorithms; Adina wrote
a number of scripts.
-Jared T. Simpson (University of Cambridge, Sanger Institute) contributed
+Jared T. Simpson (University of Cambridge, Sanger Institute) contributed
paired-end support for digital normalization.
Eric McDonald thoroughly revised many aspects of the code base, made
diff --git a/doc/dev/a-quick-guide-to-testing.rst b/doc/dev/a-quick-guide-to-testing.rst
index 7ba696e..157cd5c 100644
--- a/doc/dev/a-quick-guide-to-testing.rst
+++ b/doc/dev/a-quick-guide-to-testing.rst
@@ -119,10 +119,10 @@ scratch, or copy an existing one. (We recommend the latter.)
To write a new one, you'll need to know how to write tests. For
getting an idea of the syntax, read this `introductory guide
-<http://ivory.idyll.org/articles/nose-intro.html>`__ and the `official
-documentation
-<https://nose.readthedocs.org/en/latest/writing_tests.html>`__. Then
-find the right file in ``tests/*.py`` and add your test!
+<http://ivory.idyll.org/articles/nose-intro.html>`__ and the `writing tests
+documentation from Astropy
+<http://docs.astropy.org/en/v1.1/development/testguide.html#writing-tests>`__.
+Then find the right file in ``tests/*.py`` and add your test!
A better approach is, frankly, to go into the existing test code, find
a test that does something similar to what you want to do, copy it,
@@ -139,7 +139,11 @@ review.
To run one specific test rather than all of them, you can do::
- ./setup.py nosetests --tests tests/test_scripts.py:test_load_into_counting
+ ./setup.py test --addopts "tests/test_scripts.py::test_load_into_counting"
Here, you're running just one test -- the test function named
``test_load_into_counting`` in the file ``test_scripts.py``.
+
+You can also use py.test directly, it is a bit less verbose::
+
+ py.test tests/test_scripts.py::test_load_into_counting
diff --git a/doc/dev/codebase-guide.rst b/doc/dev/codebase-guide.rst
index 0701220..20cb55e 100644
--- a/doc/dev/codebase-guide.rst
+++ b/doc/dev/codebase-guide.rst
@@ -1,27 +1,27 @@
..
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2014-2015 Michigan State University
- Copyright (C) 2015 The Regents of the University of California.
+ Copyright (C) 2015-2016 The Regents of the University of California.
It is licensed under the three-clause BSD license; see LICENSE.
Contact: khmer-project at idyll.org
-
+
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
-
+
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
-
+
* Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided
with the distribution.
-
+
* Neither the name of the Michigan State University nor the names
of its contributors may be used to endorse or promote products
derived from this software without specific prior written
permission.
-
+
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -33,7 +33,7 @@
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
+
Contact: khmer-project at idyll.org
A quick guide to the khmer codebase
@@ -48,7 +48,7 @@ The ChangeLog file lists changes to the codebase, most recent first.
The ``lib/`` directory contains all of the C++ code.
The ``khmer/`` directory contains the `khmer` package (``khmer/__init__.py``,
-etc) and the C++-to-Python bridge (``khmer/_khmermodule.cc``).
+etc) and the C++-to-Python bridge (``khmer/_khmer.cc``).
The ``scripts/`` and ``sandbox/`` directory contain Python command-line scripts.
diff --git a/doc/dev/coding-guidelines-and-review.rst b/doc/dev/coding-guidelines-and-review.rst
index 7c9a692..2d93a14 100644
--- a/doc/dev/coding-guidelines-and-review.rst
+++ b/doc/dev/coding-guidelines-and-review.rst
@@ -1,27 +1,27 @@
..
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2014-2015 Michigan State University
- Copyright (C) 2015 The Regents of the University of California.
+ Copyright (C) 2015-2016 The Regents of the University of California.
It is licensed under the three-clause BSD license; see LICENSE.
Contact: khmer-project at idyll.org
-
+
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
-
+
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
-
+
* Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided
with the distribution.
-
+
* Neither the name of the Michigan State University nor the names
of its contributors may be used to endorse or promote products
derived from this software without specific prior written
permission.
-
+
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -33,7 +33,7 @@
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
+
Contact: khmer-project at idyll.org
Coding guidelines and code review checklist
@@ -46,8 +46,9 @@ C++ standards
-------------
Any feature in C++11 is fine to use. Specifically we support features found in
-GCC 4.8.2. See https://github.com/dib-lab/khmer/issues/598 for an in-depth
-discussion.
+GCC 4.8.2. Our automated tests use gcc 4.8.4 on linux. See
+https://github.com/dib-lab/khmer/issues/598 for an in-depth discussion. Please
+do not use features from C++14 or newer.
Coding standards
----------------
@@ -70,11 +71,11 @@ indentation can be set with::
set softtabstop=4
For Python, `PEP 8 <http://www.python.org/dev/peps/pep-0008/>`__ is our
-standard. The ```pep8``` and ```autopep8``` Makefile targets are helpful.
+standard. The ```pep8``` and ```autopep8``` Makefile targets are helpful.
-Code, scripts, and documentation must have their spelling checked.
+Code, scripts, and documentation must have their spelling checked.
-Python-based `codespell` can be applied to multiple files easily. `codespell`
+Python-based `codespell` can be applied to multiple files easily. `codespell`
can be installed via the following::
mkdir ~/bin
@@ -98,12 +99,12 @@ To run codespell over a single file::
To make codespell fix the issues it finds automatically::
codespell -w path/to/file
-
+
Please note that as `codespell` works off of a listing of possible
misspellings it may not catch all errors. If you find a spelling error that
is not caught by `codespell` feel free to open a pull request at the `project
-page <https://github.com/lucasdemarchi/codespell>`_ to add it to the
-dictionary.
+page <https://github.com/lucasdemarchi/codespell>`_ to add it to the
+dictionary.
Vim users can run::
@@ -130,28 +131,27 @@ See also `Code reviews: the lab meeting for code
Checklist
---------
-Copy and paste the following into a pull request comment when it is
-ready for review::
-
+Each pull request should be automatically populated with the following
+checklist::
+
- [ ] Is it mergeable?
- - [ ] Did it pass the tests?
- - [ ] If it introduces new functionality in scripts/ is it tested?
- Check for code coverage with `make clean diff-cover`
- - [ ] Is it well formatted? Look at `make pep8`, `make diff_pylint_report`,
- `make cppcheck`, and `make doc` output. Use `make format` and manual
- fixing as needed.
- - [ ] Did it change the command-line interface? Only additions are allowed
- without a major version increment. Changing file formats also requires a
- major version number increment.
- - [ ] Is it documented in the ChangeLog?
- http://en.wikipedia.org/wiki/Changelog#Format
+ - [ ] `make test` Did it pass the tests?
+ - [ ] `make clean diff-cover` If it introduces new functionality in
+ `scripts/` is it tested?
+ - [ ] `make format diff_pylint_report cppcheck doc pydocstyle` Is it well
+ formatted?
+ - [ ] Did it change the command-line interface? Only backwards-compatible
+ additions are allowed without a major version increment. Changing file
+ formats also requires a major version number increment.
+ - [ ] For substantial changes or changes to the command-line interface, is it
+ documented in `CHANGELOG.md`? See [keepachangelog](http://keepachangelog.com/)
+ for more details.
- [ ] Was a spellchecker run on the source code and documentation after
changes were made?
- [ ] Do the changes respect streaming IO? (Are they
tested for streaming IO?)
- - [ ] Is the Copyright year up to date?
-**Note** that after you submit the comment you can check and uncheck
+**Note** that after you submit the pull request you can check and uncheck
the individual boxes on the formatted comment; no need to put x or y
in the middle.
@@ -184,6 +184,6 @@ Here's a checklist for new CPython types with future-proofing for Python 3::
(`Py_DECREF(self);`) before each error-path exit (`return NULL;`)
- [ ] No factory methods. Example: `khmer_new_readaligner`
- [ ] Type object is passed to `PyType_Ready` and its return code is checked
- in `init_khmer()`
+ in `MOD_INIT()`
- [ ] The reference count for the type object is incremented before adding
it to the module: `Py_INCREF(&khmer_${OBJECTNAME}_Type);`.
diff --git a/doc/dev/development.rst b/doc/dev/development.rst
index 655d718..8705d34 100644
--- a/doc/dev/development.rst
+++ b/doc/dev/development.rst
@@ -1,27 +1,27 @@
..
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2012-2015 Michigan State University
- Copyright (C) 2015 The Regents of the University of California.
+ Copyright (C) 2015-2016 The Regents of the University of California.
It is licensed under the three-clause BSD license; see LICENSE.
Contact: khmer-project at idyll.org
-
+
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
-
+
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
-
+
* Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided
with the distribution.
-
+
* Neither the name of the Michigan State University nor the names
of its contributors may be used to endorse or promote products
derived from this software without specific prior written
permission.
-
+
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -33,7 +33,7 @@
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
+
Contact: khmer-project at idyll.org
Development miscellany
@@ -144,12 +144,12 @@ Python / C integration
----------------------
The Python extension that wraps the C++ core of khmer lives in
-``khmer/_khmermodule.cc``
+``khmer/_khmer.cc``
This wrapper code is tedious and annoying so we use a static analysis tool to
check for correctness.
-https://gcc-python-plugin.readthedocs.org/en/latest/cpychecker.html
+https://gcc-python-plugin.readthedocs.io/en/latest/cpychecker.html
Developers using Ubuntu Precise will want to install the gcc-4.6-plugin-dev
package
@@ -168,13 +168,13 @@ Errors to ignore: "Unhandled Python exception raised calling 'execute' method",
Warnings to address: ::
- khmer/_khmermodule.cc:3109:1: note: this function is too complicated
+ khmer/_khmer.cc:3109:1: note: this function is too complicated
for the reference-count checker to fully analyze: not all paths were
analyzed
Adjust --maxtrans and re-run. ::
- khmer/_khmermodule.cc:2191:61: warning: Mismatching type in call to
+ khmer/_khmer.cc:2191:61: warning: Mismatching type in call to
Py_BuildValue with format code "i" [enabled by default]
argument 2 ("D.68937") had type
"long long unsigned int"
@@ -183,7 +183,45 @@ Adjust --maxtrans and re-run. ::
for format code "i"
See below for a format string cheat sheet One also benefits by matching C type
-with the function signature used later.
+with the function signature used later.
"I" for unsigned int
"K" for unsigned long long a.k.a khmer::HashIntoType.
+
+Read handling
+-------------
+
+Several bugs have gone unnoticed due to inconsistencies in read handling.
+On the C++ side, there are an abundance of ``consume`` functions for loading
+Fasta/Fastq sequences. On the Python side, read handling is sometimes delegated
+to the C++ library, and sometimes handled in Python using screed.
+
+In an attempt to normalize read handling in Python, the functions in
+``khmer/utils.py`` should be used whenever possible. Here,
+``broken_paired_reader`` in ``khmer/utils.py`` should be used to do all
+paired-end sequence handling, and sequence loading should
+go through ``khmer.utils.clean_input_reads(iter)``; this is a
+generator that wraps the iterator produced by ``screed.open``, and it
+adds a ``cleaned_seq`` attribute to screed ``Record`` objects. This
+attribute should be used for any k-mer or graph operations, while
+the normal ``sequence`` attribute is what should be written out.
+``write_record`` and ``write_record_pair`` should be used to output
+records. All of these functions are aware of FASTA and FASTQ records,
+too.
+
+For applying operations to collections of reads, the ``ReadBundle`` class is
+available. This is used to wrap a collection of reads for examination and
+processing in situations where (for example) something should be done to
+either both reads in a pair, or neither.
+
+Some basic rules of sequence handling in khmer are:
+
+* consume and produce "broken paired" format, such that pairs of sequences
+ always stay together; see ``khmer.utils.broken_paired_reader``.
+
+* when looking at the coverage of reads (for trimming or digital normalization)
+ always consider pairs; see ``khmer.utils.ReadBundle(...)``.
+
+* only apply graph or k-mer operations to sequences consisting only of ATCG;
+ typically this will be ``record.cleaned_seq``. See
+ ``khmer.utils.clean_input_read(...)``.
diff --git a/doc/dev/getting-started.rst b/doc/dev/getting-started.rst
index c10eb96..b56add3 100644
--- a/doc/dev/getting-started.rst
+++ b/doc/dev/getting-started.rst
@@ -1,27 +1,27 @@
..
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2014-2015 Michigan State University
- Copyright (C) 2015 The Regents of the University of California.
+ Copyright (C) 2015-2016 The Regents of the University of California.
It is licensed under the three-clause BSD license; see LICENSE.
Contact: khmer-project at idyll.org
-
+
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
-
+
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
-
+
* Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided
with the distribution.
-
+
* Neither the name of the Michigan State University nor the names
of its contributors may be used to endorse or promote products
derived from this software without specific prior written
permission.
-
+
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -33,7 +33,7 @@
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
+
Contact: khmer-project at idyll.org
Getting started with khmer development
@@ -80,17 +80,13 @@ One-time Preparation
On recent Debian and Ubuntu this can be done with::
sudo apt-get install python2.7-dev python-virtualenv python-pip gcc \
- g++ git astyle gcovr cppcheck
+ g++ git astyle gcovr cppcheck enchant
For RHEL6::
- sudo yum install -y python-devel python-pip git gcc gcc-c++ make
+ sudo yum install -y python-devel python-pip git gcc gcc-c++ make enchant
sudo pip install virtualenv
- For Arch Linux::
-
- sudo pacman -S python2 python2-pip python2-virtualenv gcc make
-
#. Get a `GitHub <http://github.com>`__ account.
(We use GitHub to manage khmer contributions.)
@@ -137,9 +133,9 @@ One-time Preparation
`Mac ports <https://www.macports.org/>`__ users on the OS X platform can
install pip by execution from the command line::
-
+
sudo port install py27-pip
-
+
`Homebrew <http://brew.sh/>`__ users on the OS X platform will have pip
already installed
@@ -155,8 +151,8 @@ One-time Preparation
cd khmer
make install-dependencies
- (This installs `Sphinx <http://sphinx-doc.org/>`__ and `nose
- <https://nose.readthedocs.org/en/latest/>`__, packages we use for
+ (This installs `Sphinx <http://sphinx-doc.org/>`__ and `pytest
+ <https://pytest.org/>`__, packages we use for
building the documentation and running the tests.)
In Conda to activate the previously created environment and install
@@ -165,23 +161,23 @@ One-time Preparation
source activate khmer
cd khmer
make install-dependencies
-
+
#. Cppcheck installation:
-
+
`Debian <https://www.debian.org/>`__ and
`Ubuntu <http://www.ubuntu.com/>`__ Linux distro users can
install cppcheck by executing from the command line::
-
+
sudo apt-get install cppcheck
`Mac ports <https://www.macports.org/>`__ users on the OS X platform can
install cppcheck by executing from the command line::
-
+
sudo port install cppcheck
`Homebrew <http://brew.sh/>`__ users on the OS X platform can
install cppcheck by executing from the command line::
-
+
sudo brew install cppcheck
@@ -227,9 +223,7 @@ Building khmer and running the tests
You should see lots of output, with something like::
- Ran 633 tests in 47.446s
-
- OK
+ ====== 658 passed, 22 deselected in 40.93 seconds =======
at the end.
@@ -324,7 +318,7 @@ Claiming an issue and starting to develop
message -- this is a short (typically 1-3 sentence) description of the
changes you've made. Please make your commit message informative but
concise -- these messages become part of the 'official' history of the
- project.
+ project.
Once your changes have been committed, push them up to the remote branch::
@@ -373,7 +367,7 @@ Claiming an issue and starting to develop
* add a descriptive title ("updated tests for XXX")
* put the issue number in the comment ("fixes issue #532")
-
+
then click "Create pull request."
(This creates a new issue where we can all discuss your proposed
@@ -390,12 +384,12 @@ Claiming an issue and starting to develop
git push origin
-#. When you are ready to have the pull request reviewed, please mention
+#. When you are ready to have the pull request reviewed, please mention
@luizirber, @camillescott, @mr-c, or @ctb with a comment 'Ready for review!'
#. The khmer team will now review your pull request and communicate
with you through the pull request page. Please feel free to add
- 'ping!' and an @ in the comments if you are looking for feedback
+ 'ping!' and an @ in the comments if you are looking for feedback
-- this will alert us that you are still on the line -- but we will
automatically get notified of your pull request and any new
comments, so use sparingly.
diff --git a/doc/dev/python-api.rst b/doc/dev/python-api.rst
new file mode 100644
index 0000000..a770596
--- /dev/null
+++ b/doc/dev/python-api.rst
@@ -0,0 +1,152 @@
+Some notes on the Python API
+============================
+
+Some programming guidelines
+---------------------------
+
+...
+
+Valid and invalid DNA
+~~~~~~~~~~~~~~~~~~~~~
+
+Generally speaking, the Python API for khmer and oxli assume that
+they are receiving valid DNA (ACGT). Low-level hash functions like
+``hash(kmer)`` and mid-level hash functions like ``hash_kmer_hashes(str)``
+will neither check for correct DNA nor is their output with respect to
+incorrect DNA characters specified.
+
+However, bulk loading functions provide a ``cleaned_seq`` attribute that
+will ... document me here.
+
+Table types
+-----------
+
+Type names consist of two parts. The first part indicates how far the type
+can count and the second part whether it is a table or a graph.
+
+Possible choices for the first part:
+* Node, uses 1bit counter
+* SmallCount, uses a 4bit counter
+* Count, uses a 8bit counter
+
+Possible choices for the second part:
+* Table, keep track of kmers
+* Graph, navigate, tag, etc the de Bruijn graph formed by the k-mers
+
+C++ class name:
+
+Python methods:
+
+* k = ksize() - return the k-mer size (a positive integer).
+
+* hashval = hash(dna_kmer) - return the result of hashing ``dna_kmer``, which will be a non-negative integer. ``len(dna_kmer)`` must be exactly the k-mer size. Which hash function is used is dependent on the table type (@document).
+
+* dna_kmer = reverse_hash(hashval) - return a DNA string that will hash to ``hashval``. If there are multiple such strings, return only one. May be unimplemented for particular table types in which case a ValueError will be returned.
+
+* sizelist = hashsizes() - return the list of table sizes used in construction.
+
+* n = n_unique_kmers() - retrieve an estimate for the number of unique k-mers inserted into the table. Note, this may be order dependent.
+
+* n = n_occupied() - retrieve the fraction of bins occupied in the table.
+
+* add(dna_kmer_or_hashval) - increment the count associated with either a DNA k-mer or a hashval. Depending on max count for the tabletype and bigcount settings, the count may top out at 1, 15, 255, or 65535. (@CTB add method for retrieving max_count)
+
+* count (synonym for add)
+
+* get(dna_kmer or hashval) - retrieve the count associated with a DNA k-mer or a hashval.
+
+* list_of_strings = get_kmers(seq) - return the list of k-mer strings in the given sequence.
+* list_of_hashes = get_kmer_hashes(seq) - return the list of the hashed k-mers in the given sequence.
+* hashset = get_kmer_hashes_as_hashset(seq) - return the hashset of hashed k-mers in the given sequence.
+
+* list_of_counts = get_kmer_counts(seq) - return the list of the counts of the k-mers in the given sequence.
+
+* save(filename) - save the data to a file on disk.
+* load(filename) - load the data from a file on disk.
+
+* min_count = get_min_count(seq) - return the minimum count for k-mers in seq
+* med_count, avg_count, stddev_count = get_median_count(seq) - return the median, average, and stddev of the counts for k-mers in the sequence.
+
+* max_count = get_max_count(seq) - return the maximum count for k-mers in the sequence.
+
+* num_kmers = consume(seq) - count all the k-mers in the given DNA string. @CTB should be consume string
+* consume_fasta(filename) - count all the k-mers in a (DNA) FASTA/FASTQ file.
+* consume_fasta_with_reads_parser(khmer.ReadParser object) - count all the k-mers in (DNA) sequences returned from a ReadParser object. This can be used to ensure various forms of pairing are present, etc.
+
+* (trim_seq, trim_pos) = trim_on_abundance(seq, abund) - trim the sequence at the first k-mer with an abundance strictly below (<) the provided abundance.
+* (trim_seq, trim_pos) = trim_below_abundance(seq, abund) - trim the sequence at the first k-mer with an abundance strictly above (>) the provided abundance.
+* list_of_posns = find_spectral_error_positions(seq, abund) - find potential locations of errors in input sequence, where k-mers are below given abundance.
+
+* set_use_bigcount(bool) - some table types (Counttable and Countgraph) support counting past their max value, using a (memory intensive) C++ stl::map. That turns on this "bigcount" behavior. This will raise a ValueError when called on a table type that does not support it.
+* get_use_bigcount - return the bigcount value (False by default).
+
+* dist = abundance_distribution(filename, tracking_obj) - generate an abundance distribution for the k-mers in the given file, using the tracking_obj to avoid double-counting identical k-mers.
+* dist = abundance_distribution_with_reads_parser(readparser_obj, tracking_obj) - generate an abundance distribution for the k-mers loaded from the given readparser, using the tracking_obj to avoid double-counting identical k-mers.
+
+Graph types
+-----------
+
+All the methods of table types, and in addition:
+
+* neighbors
+* calc_connected_graph_size
+* kmer_degree
+* count_kmers_within_radius
+* find_high_degree_nodes
+* traverse_linear_path
+* assemble_linear_path
+* consume_and_tag
+* get_tags_and_positions
+* find_all_tags_list
+* consume_fasta_and_tag
+* extract_unique_paths
+* print_tagset
+* add_tag
+* get_tagset
+* load_tagset
+* save_tagset
+* n_tags
+* divide_tags_into_subsets
+* _get_tag_density
+* _set_tag_density
+* do_subset_partition
+* find_all_tags
+* assign_partition_id
+* output_partitions
+* load_partitionmap
+* save_partitionmap
+* _validate_partitionmap
+* consume_fasta_and_tag_with_reads_parser
+* consume_partitioned_fasta
+* merge_subset
+* merge_subset_from_disk
+* count_partitions
+* subset_count_partitions
+* subset_partition_size_distribution
+* save_subset_partitionmap
+* load_subset_partitionmap
+* _validate_subset_partitionmap
+* set_partition_id
+* join_partitions
+* get_partition_id
+* repartition_latest_partition
+* load_stop_tags
+* save_stop_tags
+* print_stop_tags
+* trim_on_stoptags
+* add_stop_tags
+* get_stop_tags
+
+Smallcountgraph:
+
+* get_raw_tables
+
+Countgraph:
+
+* get_raw_tables
+* do_subset_partition_with_abundance
+
+Nodegraph:
+
+* update
+* get_raw_tables
diff --git a/doc/dev/release.rst b/doc/dev/release.rst
index 9f14505..57d3894 100644
--- a/doc/dev/release.rst
+++ b/doc/dev/release.rst
@@ -1,27 +1,27 @@
..
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2013-2015 Michigan State University
- Copyright (C) 2015 The Regents of the University of California.
+ Copyright (C) 2015-2016 The Regents of the University of California.
It is licensed under the three-clause BSD license; see LICENSE.
Contact: khmer-project at idyll.org
-
+
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
-
+
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
-
+
* Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided
with the distribution.
-
+
* Neither the name of the Michigan State University nor the names
of its contributors may be used to endorse or promote products
derived from this software without specific prior written
permission.
-
+
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -33,7 +33,7 @@
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
+
Contact: khmer-project at idyll.org
================================
@@ -61,9 +61,9 @@ release makers, following this checklist by MRC.
versioneer-installer
git diff
-
+
./setup.py versioneer
- git diff
+ git diff
git commit -m -a "new version of versioneer.py"
# or
git checkout -- versioneer.py khmer/_version.py khmer/__init__.py MANIFEST.in
@@ -76,8 +76,16 @@ release makers, following this checklist by MRC.
#. Review the issue list for any new bugs that will not be fixed in this
release. Add them to ``doc/known-issues.txt``
+#. Check for new authors. Update ``.mailmap`` to normalize their email address
+ and name spelling. If they want to opt out update the ``list-*`` Makefile
+ targets to exclude them. Run ``make list-citation`` and adapt the output to
+ the relevant parts of ``CITATION``, ``setup.py``, ``doc/index.rst``.
+
#. Verify that the build is clean: http://ci.oxli.org/job/khmer-master/
+#. Run through the `API examples <../user/api-examples.html>`__ to verify they
+ are still valid.
+
#. Submit a build to Coverity Scan if it hasn't been done
recently. You can get the token from
https://gitlab.msu.edu/ged-lab/ged-internal-docs/wikis/coverity-scan
@@ -111,7 +119,7 @@ release makers, following this checklist by MRC.
virtualenv testenv3
virtualenv testenv4
# First we test the tag
-
+
cd testenv1
source bin/activate
git clone --depth 1 --branch v${new_version}-${rc} https://github.com/dib-lab/khmer.git
@@ -127,7 +135,7 @@ release makers, following this checklist by MRC.
# Secondly we test via pip
-
+
cd ../../testenv2
source bin/activate
pip install -U setuptools==3.4.1
@@ -145,7 +153,7 @@ release makers, following this checklist by MRC.
# Is the distribution in testenv2 complete enough to build another
# functional distribution?
-
+
cd ../testenv3/
source bin/activate
pip install -U setuptools==3.4.1
@@ -219,11 +227,11 @@ so:
./setup.py bdist_wheel upload
#. Update Read the Docs to point to the new version. Visit
- https://readthedocs.org/builds/khmer/ and 'Build Version: master' to pick up
+ https://readthedocs.io/builds/khmer/ and 'Build Version: master' to pick up
the new tag. Once that build has finished check the "Activate" box next to
- the new version at https://readthedocs.org/dashboard/khmer/versions/ under
+ the new version at https://readthedocs.io/dashboard/khmer/versions/ under
"Choose Active Versions". Finally change the default version at
- https://readthedocs.org/dashboard/khmer/advanced/ to the new version.
+ https://readthedocs.io/dashboard/khmer/advanced/ to the new version.
#. Delete any RC tags created::
@@ -272,7 +280,7 @@ files ``versioneer.py``, the top of ``khmer/__init__.py``,
``khmer/_version.py``, ``setup.py``, and ``doc/conf.py`` for the
implementation.
-The version number is determined through several methods: see
+The version number is determined through several methods: see
https://github.com/warner/python-versioneer#version-identifiers
If the source tree is from a git checkout then the version number is derived by
diff --git a/doc/dev/scripts-and-sandbox.rst b/doc/dev/scripts-and-sandbox.rst
index ed311c6..65f7955 100644
--- a/doc/dev/scripts-and-sandbox.rst
+++ b/doc/dev/scripts-and-sandbox.rst
@@ -4,24 +4,24 @@
Copyright (C) 2015 The Regents of the University of California.
It is licensed under the three-clause BSD license; see LICENSE.
Contact: khmer-project at idyll.org
-
+
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
-
+
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
-
+
* Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided
with the distribution.
-
+
* Neither the name of the Michigan State University nor the names
of its contributors may be used to endorse or promote products
derived from this software without specific prior written
permission.
-
+
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -33,7 +33,7 @@
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
+
Contact: khmer-project at idyll.org
Command line scripts, ``scripts/``, and ``sandbox/``
@@ -88,15 +88,32 @@ All *new* scripts being added to ``sandbox/`` should:
* be used in a protocol (see khmer-protocols) or a recipe (see khmer-recipes)
* be pep8 clean and pylint clean-ish (see ``make pep8`` and ``make_diff_pylint``).
-Command line standard options for scripts/
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-All scripts in scripts/ should have the following options, if they could apply:
-
-* ``--version`` - should always apply
-* ``--help`` - should always apply
-* ``--force`` - override any sanity checks that may prevent the script from running
-* ``--loadgraph`` and ``--savegraph`` - where appropriate (see khmer_args.py)
+Standard and reserved command line options for ``scripts/``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The following options are reserved, and the short option flag cannot be
+redefined in any official script.
+
+* ``-h|--help`` - this must always print out a descriptive usage statement
+* ``-v|--version`` - this must always print out the khmer version number
+* ``-x|--max-tablesize`` - this must always specify the approximate table size
+ for storing sketches of k-mer hashes
+* ``-N|--n_tables`` - this must always specify the number of tables for storing
+ sketches of k-mer hashes
+* ``-M|--max-memory-usage`` - this must always specify the maximum amount of
+ memory to be consumed for storing sketches of k-mer hashes
+* ``-U|--unique-kmers`` - this must always specify the approximate number of
+ unique k-mers in the data set
+* ``-k|--ksize`` - this must always specify the k-mer size to use
+* ``-q|--quiet`` - this must always indicate that the script's diagnostic output
+ should be minimized or altogether eliminated
+
+Additionally, all scripts in ``scripts/`` should have the following options.
+
+* ``-h|--help``
+* ``-v|--version``
+* ``-f|--force`` - if applicable, override any sanity checks that may prevent
+ the script from running
If an option is of type ``type=argparse.FileType('w')`` then you need to also
specify a ``metavar`` for the documentation and help formatting. Example::
diff --git a/doc/index.rst b/doc/index.rst
index dfa9934..68b0f69 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -1,27 +1,27 @@
..
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2010-2015 Michigan State University
- Copyright (C) 2015 The Regents of the University of California.
+ Copyright (C) 2015-2016 The Regents of the University of California.
It is licensed under the three-clause BSD license; see LICENSE.
Contact: khmer-project at idyll.org
-
+
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
-
+
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
-
+
* Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided
with the distribution.
-
+
* Neither the name of the Michigan State University nor the names
of its contributors may be used to endorse or promote products
derived from this software without specific prior written
permission.
-
+
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -33,7 +33,7 @@
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
+
Contact: khmer-project at idyll.org
###################################################################
@@ -61,8 +61,8 @@ line. See :doc:`our command line documentation <user/scripts>`.
We have **additional documentation** in several places, including
`protocols for metagenome and mRNAseq assembly
-<https://khmer-protocols.readthedocs.org/>`__ and `recipes for several
-common research tasks <https://khmer-recipes.readthedocs.org/>`__.
+<https://khmer-protocols.readthedocs.io/>`__ and `recipes for several
+common research tasks <https://khmer-recipes.readthedocs.io/>`__.
You might also be interested in :doc:`papers using or citing khmer
<user/biblio>`.
@@ -113,12 +113,12 @@ Details
There are two mailing lists dedicated to khmer, an announcements-only list and
a discussion list. To search their archives and sign-up for them, please visit
the following URLs:
-
+
* Discussion: http://lists.idyll.org/listinfo/khmer
* Announcements: http://lists.idyll.org/listinfo/khmer-announce
-The archives for the khmer mailing list are available at:
+The archives for the khmer mailing list are available at:
http://lists.idyll.org/pipermail/khmer/
khmer development was initially supported by AFRI Competitive Grant
diff --git a/doc/introduction.rst b/doc/introduction.rst
index 8d395b1..8023c2c 100644
--- a/doc/introduction.rst
+++ b/doc/introduction.rst
@@ -1,27 +1,27 @@
..
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2011-2015 Michigan State University
- Copyright (C) 2015 The Regents of the University of California.
+ Copyright (C) 2015-2016 The Regents of the University of California.
It is licensed under the three-clause BSD license; see LICENSE.
Contact: khmer-project at idyll.org
-
+
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
-
+
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
-
+
* Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided
with the distribution.
-
+
* Neither the name of the Michigan State University nor the names
of its contributors may be used to endorse or promote products
derived from this software without specific prior written
permission.
-
+
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -33,7 +33,7 @@
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
+
Contact: khmer-project at idyll.org
*********************
@@ -43,46 +43,46 @@ Introduction to khmer
Introduction
============
-khmer is a library and toolkit for doing k-mer-based dataset analysis and
-transformations. Our focus in developing it has been on scaling assembly of
+khmer is a library and toolkit for doing k-mer-based dataset analysis and
+transformations. Our focus in developing it has been on scaling assembly of
metagenomes and mRNA.
-khmer can be used for a number of transformations, including inexact
-transformations (abundance filtering and error trimming) and exact
-transformations (graph-size filtering, to throw away disconnected reads; and
-partitioning, to split reads into disjoint sets). Of these, only partitioning
-is not constant memory. In all cases, the memory required for assembly with
-Velvet or another de Bruijn graph assembler will be more than the memory
-required to use our software. Our software will not increase the memory required
-for Velvet, either, although we may not be able to *decrease* the memory
+khmer can be used for a number of transformations, including inexact
+transformations (abundance filtering and error trimming) and exact
+transformations (graph-size filtering, to throw away disconnected reads; and
+partitioning, to split reads into disjoint sets). Of these, only partitioning
+is not constant memory. In all cases, the memory required for assembly with
+Velvet or another de Bruijn graph assembler will be more than the memory
+required to use our software. Our software will not increase the memory required
+for Velvet, either, although we may not be able to *decrease* the memory
required for assembly for every data set.
-Most of khmer relies on an underlying probabilistic data structure known as a
-`Bloom filter <http://en.wikipedia.org/wiki/Bloom_filter>`__ (also see
-`Count-Min Sketch <http://dimacs.rutgers.edu/~graham/pubs/papers/cm-full.pdf>`__
-and `These Are Not The k-mers You're Looking For
-<http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4111482/>`__), which is essentially
-a set of hash tables, each of different size, with no collision detection. These
-hash tables are used to store the presence of specific k-mers and/or their
-count. The lack of collision detection means that the Bloom filter may report a
-k-mer as being "present" when it is not, in fact, in the data set; however, it
-will never incorrectly report a k-mer as being absent when it *is* present.
-This one-sided error makes the Bloom filter very useful for certain kinds of
+Most of khmer relies on an underlying probabilistic data structure known as a
+`Bloom filter <http://en.wikipedia.org/wiki/Bloom_filter>`__ (also see
+`Count-Min Sketch <http://dimacs.rutgers.edu/~graham/pubs/papers/cm-full.pdf>`__
+and `These Are Not The k-mers You're Looking For
+<http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4111482/>`__), which is essentially
+a set of hash tables, each of different size, with no collision detection. These
+hash tables are used to store the presence of specific k-mers and/or their
+count. The lack of collision detection means that the Bloom filter may report a
+k-mer as being "present" when it is not, in fact, in the data set; however, it
+will never incorrectly report a k-mer as being absent when it *is* present.
+This one-sided error makes the Bloom filter very useful for certain kinds of
operations.
-khmer is also independent of a specific k-size (K), and currently works for
+khmer is also independent of a specific k-size (K), and currently works for
K <= 32. We will be integrating code for K<=64 soon.
-khmer is implemented in C++ with a Python wrapper, which is what all of the
+khmer is implemented in C++ with a Python wrapper, which is what all of the
scripts use.
-Documentation for khmer is provided on the Web sites for
-`khmer-protocols <http://khmer-protocols.readthedocs.org>`__ and `khmer-recipes
-<http://khmer-recipes.readthedocs.org>`__. khmer-protocols provides detailed
-protocols for using khmer to analyze either a transcriptome or a metagenome.
-khmer-recipes provides individual recipes for using khmer in a variety of
-sequence-oriented tasks such as extracting reads by coverage, estimating a
-genome or metagenome size from unassembled reads, and error-trimming reads via
+Documentation for khmer is provided on the Web sites for
+`khmer-protocols <http://khmer-protocols.readthedocs.io>`__ and `khmer-recipes
+<http://khmer-recipes.readthedocs.io>`__. khmer-protocols provides detailed
+protocols for using khmer to analyze either a transcriptome or a metagenome.
+khmer-recipes provides individual recipes for using khmer in a variety of
+sequence-oriented tasks such as extracting reads by coverage, estimating a
+genome or metagenome size from unassembled reads, and error-trimming reads via
streaming k-mer abundance.
Using khmer
@@ -114,16 +114,16 @@ and a few other random functions.
Practical considerations
========================
-The most important thing to think about when using khmer is whether or not the
-transformation or filter you're applying is appropriate for the data you're
-trying to assemble. Two of the most powerful operations available in khmer,
-graph-size filtering and graph partitioning, only make sense for assembly
-datasets with many theoretically unconnected components. This is typical of
+The most important thing to think about when using khmer is whether or not the
+transformation or filter you're applying is appropriate for the data you're
+trying to assemble. Two of the most powerful operations available in khmer,
+graph-size filtering and graph partitioning, only make sense for assembly
+datasets with many theoretically unconnected components. This is typical of
metagenomic data sets.
-The second most important consideration is memory usage. The effectiveness of
-all of the Bloom filter-based functions (which is everything interesting in
-khmer!) depends critically on having enough memory to do a good job. See
+The second most important consideration is memory usage. The effectiveness of
+all of the Bloom filter-based functions (which is everything interesting in
+khmer!) depends critically on having enough memory to do a good job. See
:doc:`user/choosing-table-sizes` for more information.
Copyright and license
@@ -132,5 +132,5 @@ Copyright and license
Portions of khmer are Copyright California Institute of Technology,
where the exact counting code was first developed. All other code developed
through 2014 is copyright Michigan State University. Portions are copyright
-Michigan State University and Regents of the University of California.
+Michigan State University and Regents of the University of California.
All the code is freely available for use and re-use under the BSD License.
diff --git a/doc/requirements.txt b/doc/requirements.txt
index 43af8b1..68e3152 100644
--- a/doc/requirements.txt
+++ b/doc/requirements.txt
@@ -1,2 +1,2 @@
-http://ci.oxli.org:8080/userContent/sphinxcontrib-autoprogram-0.1.1-khmerdev-20140331.tar.gz#egg=sphinxcontrib-autoprogram==0.1.1-khmerdev-20140331
-setuptools==3.4.1
+sphinxcontrib-autoprogram==0.1.2
+setuptools>=3.4.1
diff --git a/doc/roadmap.rst b/doc/roadmap.rst
index deb9842..866fb23 100644
--- a/doc/roadmap.rst
+++ b/doc/roadmap.rst
@@ -1,27 +1,27 @@
..
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2014-2015 Michigan State University
- Copyright (C) 2015 The Regents of the University of California.
+ Copyright (C) 2015-2016 The Regents of the University of California.
It is licensed under the three-clause BSD license; see LICENSE.
Contact: khmer-project at idyll.org
-
+
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
-
+
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
-
+
* Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided
with the distribution.
-
+
* Neither the name of the Michigan State University nor the names
of its contributors may be used to endorse or promote products
derived from this software without specific prior written
permission.
-
+
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -33,7 +33,7 @@
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
+
Contact: khmer-project at idyll.org
***************************
@@ -49,7 +49,7 @@ while minimizing the impact of these changes on our existing users. The
version numbers are approximate; there may be additional major number
releases to support needed changes to the API along the way. This document has
been updated for v2.0 onwards from the `original roadmap
-<http://khmer.readthedocs.org/en/v1.2/roadmap.html>`__.
+<http://khmer.readthedocs.io/en/v1.2/roadmap.html>`__.
The discussion that lead to this document can be read at
https://github.com/dib-lab/khmer/issues/389
diff --git a/doc/user/api-examples.rst b/doc/user/api-examples.rst
new file mode 100644
index 0000000..cf4ccf5
--- /dev/null
+++ b/doc/user/api-examples.rst
@@ -0,0 +1,94 @@
+..
+ This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+ Copyright (C) 2016 The Regents of the University of California.
+ It is licensed under the three-clause BSD license; see LICENSE.
+ Contact: khmer-project at idyll.org
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are
+ met:
+
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following
+ disclaimer in the documentation and/or other materials provided
+ with the distribution.
+
+ * Neither the name of the Michigan State University nor the names
+ of its contributors may be used to endorse or promote products
+ derived from this software without specific prior written
+ permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+ Contact: khmer-project at idyll.org
+
+Example API Usage
+=================
+
+Examples of how to run khmer command-line scripts are included in the main khmer documentation, as well as the `khmer protocols collection <http://khmer-protocols.readthedocs.io>`__.
+This document is intended for programmers and developers who want to use khmer's Python or C++ API.
+
+**Note**: The khmer command-line scripts are under `semantic versioning <http://semver.org/>`__, but (as of khmer v2) neither the Python API nor the C++ API are covered under semantic versioning.
+Consequently, updates to the khmer code base may require changes to the examples below at any time.
+We expect to have the Python API under semantic versioning by version 5.0.
+
+
+Python API
+----------
+
+The following example demonstrates the basics of counting k-mers with khmer.
+
+.. code:: python
+
+ >>> import khmer
+ >>>
+ >>> ksize = 11
+ >>>
+ >>> # exact counting with and odd k requires a single table with 4^k bytes
+ >>> # even k will collapse k-mers with their reverse complement, and requires 4^(k-1) + k bytes
+ >>> cg = khmer.Countgraph(ksize, 4**ksize, 1)
+ >>>
+ >>> # load all k-mers from the given string (returns the number of k-mers processed)
+ >>> cg.consume('ATGGCGATGGCAAGTAGGACCCAGATGGACCAAAG')
+ 25
+ >>>
+ >>> # what is the count of the k-mer "ATGGCGATGGC"?
+ >>> cg.get('ATGGCGATGGC')
+ 1
+ >>> # increase the count of the k-mer by 1
+ >>> cg.add('ATGGCGATGGC')
+ 1
+ >>> # what is the k-mer's count now?
+ >>> cg.get('ATGGCGATGGC')
+ 2
+ >>>
+ >>> # what is the count of this bogus k-mer?
+ >>> cg.get('GTGGCGATGGC')
+ 0
+ >>>
+
+C++ API
+-------
+
+The `count-stuff.cpp` file in the `examples/c++-api/` directory contains source code that calls khmer's C++ API directly.
+To run this example, issue the following commands from your terminal.
+The `Makefile` in `examples/c++-api/` shows how to compile and link against the khmer library.
+
+.. code:: bash
+
+ cd examples/c++-api/
+ make
+ ./count-stuff
diff --git a/doc/user/blog-posts.rst b/doc/user/blog-posts.rst
index 7ab78b3..5ce2cc6 100644
--- a/doc/user/blog-posts.rst
+++ b/doc/user/blog-posts.rst
@@ -1,27 +1,27 @@
..
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2010-2015 Michigan State University
- Copyright (C) 2015 The Regents of the University of California.
+ Copyright (C) 2015-2016 The Regents of the University of California.
It is licensed under the three-clause BSD license; see LICENSE.
Contact: khmer-project at idyll.org
-
+
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
-
+
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
-
+
* Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided
with the distribution.
-
+
* Neither the name of the Michigan State University nor the names
of its contributors may be used to endorse or promote products
derived from this software without specific prior written
permission.
-
+
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -33,7 +33,7 @@
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
+
Contact: khmer-project at idyll.org
=======================================
@@ -87,3 +87,11 @@ You can assess high/low abundance k-mer distributions with the
This will produce two output files, <filename>.pos.abund=1 and
<filename>.pos.abund=255.
+
+
+Finding valleys/minima in *k*-mer abundance profiles
+====================================================
+
+Using *k*-mer abundance profiles to dynamically calculate the abundance threshold separating erroneous *k*-mers from real *k*-mers is described in this blog post:
+
+ https://bitsandbugs.org/2016/07/29/mash-and-khmer-abundance/
diff --git a/doc/user/guide.rst b/doc/user/guide.rst
index d32e45d..677a40d 100644
--- a/doc/user/guide.rst
+++ b/doc/user/guide.rst
@@ -4,24 +4,24 @@
Copyright (C) 2015 The Regents of the University of California.
It is licensed under the three-clause BSD license; see LICENSE.
Contact: khmer-project at idyll.org
-
+
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
-
+
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
-
+
* Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided
with the distribution.
-
+
* Neither the name of the Michigan State University nor the names
of its contributors may be used to endorse or promote products
derived from this software without specific prior written
permission.
-
+
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -33,7 +33,7 @@
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
+
Contact: khmer-project at idyll.org
An assembly handbook for khmer - rough draft
@@ -94,7 +94,7 @@ Broadly, normalize each insert library separately, in the following way:
For high-coverage libraries (> ~50x), do three-pass digital
normalization: run :program:`normalize-by-median.py` with :option:`--cutoff=20
<normalize-by-median.py --cutoff>` and then run :program:`filter-abund.py` with
-:option:`--cutoff=1 <filter-abund.py --cutoff>`. Now split out the remaining
+:option:`--cutoff=2 <filter-abund.py --cutoff>`. Now split out the remaining
paired-end/interleaved and single-end reads using
:program:`extract-paired-reads.py`, and run :program:`normalize-by-median.py`
on the paired-end and single-end files (using :option:`--unpaired-reads
@@ -144,7 +144,7 @@ Metagenome assembly
<normalize-by-median.py --cutoff>`) or wiht ``--cutoff=100`` if you ran
:program:`normalize-by-median.py` with :option:`--cutoff=20
<normalize-by-median.py --cutoff>`)
-
+
3. Partition reads with :program:`load-graph.py`, etc. etc.
4. Assemble groups as normal, extracting paired-end reads and lumping
diff --git a/doc/user/index.rst b/doc/user/index.rst
index 77fd37d..76801f5 100644
--- a/doc/user/index.rst
+++ b/doc/user/index.rst
@@ -1,27 +1,27 @@
..
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2014-2015 Michigan State University
- Copyright (C) 2015 The Regents of the University of California.
+ Copyright (C) 2015-2016 The Regents of the University of California.
It is licensed under the three-clause BSD license; see LICENSE.
Contact: khmer-project at idyll.org
-
+
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
-
+
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
-
+
* Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided
with the distribution.
-
+
* Neither the name of the Michigan State University nor the names
of its contributors may be used to endorse or promote products
derived from this software without specific prior written
permission.
-
+
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -33,7 +33,7 @@
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
+
Contact: khmer-project at idyll.org
The khmer user documentation
@@ -51,8 +51,8 @@ Contents:
blog-posts
choosing-table-sizes
partitioning-big-data
+ api-examples
known-issues
galaxy
biblio
getting-help
-
diff --git a/doc/user/install.rst b/doc/user/install.rst
index 5cc1815..712d4fb 100644
--- a/doc/user/install.rst
+++ b/doc/user/install.rst
@@ -94,17 +94,3 @@ Installing khmer inside the virtualenv
reactivate the virtualenv first::
source khmerEnv/bin/activate
-
-Run the tests
-^^^^^^^^^^^^^
-
-After installing you can run the embedded test suite. If you are running an
-OSX system you should also add `!linux` to prevent linux-specific tests from
-failing.::
-
- nosetests khmer --attr '!known_failing,!huge'
-
-If the nosetests binary isn't installed then::
-
- pip2 install khmer[tests]
- nosetests khmer --attr '!known_failing,!huge'
diff --git a/doc/whats-new-2.0.rst b/doc/whats-new-2.0.rst
index 346fc1c..756c4bb 100644
--- a/doc/whats-new-2.0.rst
+++ b/doc/whats-new-2.0.rst
@@ -3,24 +3,24 @@
Copyright (C) 2015 The Regents of the University of California.
It is licensed under the three-clause BSD license; see LICENSE.
Contact: khmer-project at idyll.org
-
+
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
-
+
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
-
+
* Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided
with the distribution.
-
+
* Neither the name of the Michigan State University nor the names
of its contributors may be used to endorse or promote products
derived from this software without specific prior written
permission.
-
+
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -32,7 +32,7 @@
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
+
Contact: khmer-project at idyll.org
************************
diff --git a/examples/README.txt b/examples/README.txt
deleted file mode 100644
index a72e994..0000000
--- a/examples/README.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-Some example notebooks and data set manipulations.
-
- stamps/ -- some examples of diginorm and partitioning on fake data.
- stamps k-mer distributions.ipynb -- ipython notebook to show distributions.
-
diff --git a/examples/c++-api/.gitignore b/examples/c++-api/.gitignore
new file mode 100644
index 0000000..aec96b3
--- /dev/null
+++ b/examples/c++-api/.gitignore
@@ -0,0 +1 @@
+count-demo
diff --git a/examples/c++-api/Makefile b/examples/c++-api/Makefile
new file mode 100644
index 0000000..25af57e
--- /dev/null
+++ b/examples/c++-api/Makefile
@@ -0,0 +1,10 @@
+all: count-demo
+
+clean:
+ -rm -f count-demo
+
+count-demo: count-demo.cc ../../lib/liboxli.a
+ $(CXX) --std=c++11 -I ../../lib count-demo.cc -o count-demo ../../lib/liboxli.a
+
+../../lib/liboxli.a:
+ cd ../../lib && make
diff --git a/examples/c++-api/count-demo.cc b/examples/c++-api/count-demo.cc
new file mode 100644
index 0000000..be3a857
--- /dev/null
+++ b/examples/c++-api/count-demo.cc
@@ -0,0 +1,41 @@
+// A demonstration of using khmer to count k-mers; in this case, the request
+// was for exact counting.
+
+#include <vector>
+#include <cmath>
+#include "khmer.hh"
+#include "hashtable.hh"
+
+using namespace khmer;
+
+int main()
+{
+ unsigned int ksize = 11;
+
+ // For exact counting, you need to create one table that is >= 4**k. This
+ // will be that size in bytes, note, so you will need the appropriate amount
+ // of memory.
+
+ // If `ksize` is even, note that k-mers will collapse with their reverse
+ // complement. In that case, a table size of 4**(k-1) + k is required.
+
+ std::vector<HashIntoType> tablesize;
+ tablesize.push_back(pow(4, ksize));
+
+ Counttable ktable(ksize, tablesize);
+
+ ktable.consume_string("ATGGCGATGGCAAGTAGGACCCAGATGGACCAAAG");
+
+ std::cout << "count for: " << "ATGGCGATGGC" << " is " <<
+ ktable.get_count("ATGGCGATGGC") << "\n";
+
+ ktable.add("ATGGCGATGGC");
+
+ std::cout << "count for: " << "ATGGCGATGGC" << " is " <<
+ ktable.get_count("ATGGCGATGGC") << "\n";
+
+ std::cout << "count for: " << "GTGGCGATGGC" << " is " <<
+ ktable.get_count("GTGGCGATGGC") << "\n";
+
+ return 0;
+}
diff --git a/ez_setup.py b/ez_setup.py
new file mode 100644
index 0000000..f5fa741
--- /dev/null
+++ b/ez_setup.py
@@ -0,0 +1,332 @@
+#!/usr/bin/env python
+"""Bootstrap setuptools installation
+
+To use setuptools in your package's setup.py, include this
+file in the same directory and add this to the top of your setup.py::
+
+ from ez_setup import use_setuptools
+ use_setuptools()
+
+To require a specific version of setuptools, set a download
+mirror, or use an alternate download directory, simply supply
+the appropriate options to ``use_setuptools()``.
+
+This file can also be run as a script to install or upgrade setuptools.
+"""
+import os
+import shutil
+import sys
+import tempfile
+import zipfile
+import optparse
+import subprocess
+import platform
+import textwrap
+import contextlib
+
+from distutils import log
+
+try:
+ from site import USER_SITE
+except ImportError:
+ USER_SITE = None
+
+DEFAULT_VERSION = "3.4.1"
+DEFAULT_URL = "https://pypi.python.org/packages/source/s/setuptools/"
+
+def _python_cmd(*args):
+ """
+ Return True if the command succeeded.
+ """
+ args = (sys.executable,) + args
+ return subprocess.call(args) == 0
+
+
+def _install(archive_filename, install_args=()):
+ with archive_context(archive_filename):
+ # installing
+ log.warn('Installing Setuptools')
+ if not _python_cmd('setup.py', 'install', *install_args):
+ log.warn('Something went wrong during the installation.')
+ log.warn('See the error message above.')
+ # exitcode will be 2
+ return 2
+
+
+def _build_egg(egg, archive_filename, to_dir):
+ with archive_context(archive_filename):
+ # building an egg
+ log.warn('Building a Setuptools egg in %s', to_dir)
+ _python_cmd('setup.py', '-q', 'bdist_egg', '--dist-dir', to_dir)
+ # returning the result
+ log.warn(egg)
+ if not os.path.exists(egg):
+ raise IOError('Could not build the egg.')
+
+
+def get_zip_class():
+ """
+ Supplement ZipFile class to support context manager for Python 2.6
+ """
+ class ContextualZipFile(zipfile.ZipFile):
+ def __enter__(self):
+ return self
+ def __exit__(self, type, value, traceback):
+ self.close
+ return zipfile.ZipFile if hasattr(zipfile.ZipFile, '__exit__') else \
+ ContextualZipFile
+
+
+ at contextlib.contextmanager
+def archive_context(filename):
+ # extracting the archive
+ tmpdir = tempfile.mkdtemp()
+ log.warn('Extracting in %s', tmpdir)
+ old_wd = os.getcwd()
+ try:
+ os.chdir(tmpdir)
+ with get_zip_class()(filename) as archive:
+ archive.extractall()
+
+ # going in the directory
+ subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0])
+ os.chdir(subdir)
+ log.warn('Now working in %s', subdir)
+ yield
+
+ finally:
+ os.chdir(old_wd)
+ shutil.rmtree(tmpdir)
+
+
+def _do_download(version, download_base, to_dir, download_delay):
+ egg = os.path.join(to_dir, 'setuptools-%s-py%d.%d.egg'
+ % (version, sys.version_info[0], sys.version_info[1]))
+ if not os.path.exists(egg):
+ archive = download_setuptools(version, download_base,
+ to_dir, download_delay)
+ _build_egg(egg, archive, to_dir)
+ sys.path.insert(0, egg)
+
+ # Remove previously-imported pkg_resources if present (see
+ # https://bitbucket.org/pypa/setuptools/pull-request/7/ for details).
+ if 'pkg_resources' in sys.modules:
+ del sys.modules['pkg_resources']
+
+ import setuptools
+ setuptools.bootstrap_install_from = egg
+
+
+def use_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
+ to_dir=os.curdir, download_delay=15):
+ to_dir = os.path.abspath(to_dir)
+ rep_modules = 'pkg_resources', 'setuptools'
+ imported = set(sys.modules).intersection(rep_modules)
+ try:
+ import pkg_resources
+ except ImportError:
+ return _do_download(version, download_base, to_dir, download_delay)
+ try:
+ pkg_resources.require("setuptools>=" + version)
+ return
+ except pkg_resources.DistributionNotFound:
+ return _do_download(version, download_base, to_dir, download_delay)
+ except pkg_resources.VersionConflict as VC_err:
+ if imported:
+ msg = textwrap.dedent("""
+ The required version of setuptools (>={version}) is not available,
+ and can't be installed while this script is running. Please
+ install a more recent version first, using
+ 'easy_install -U setuptools'.
+
+ (Currently using {VC_err.args[0]!r})
+ """).format(VC_err=VC_err, version=version)
+ sys.stderr.write(msg)
+ sys.exit(2)
+
+ # otherwise, reload ok
+ del pkg_resources, sys.modules['pkg_resources']
+ return _do_download(version, download_base, to_dir, download_delay)
+
+def _clean_check(cmd, target):
+ """
+ Run the command to download target. If the command fails, clean up before
+ re-raising the error.
+ """
+ try:
+ subprocess.check_call(cmd)
+ except subprocess.CalledProcessError:
+ if os.access(target, os.F_OK):
+ os.unlink(target)
+ raise
+
+def download_file_powershell(url, target):
+ """
+ Download the file at url to target using Powershell (which will validate
+ trust). Raise an exception if the command cannot complete.
+ """
+ target = os.path.abspath(target)
+ cmd = [
+ 'powershell',
+ '-Command',
+ "(new-object System.Net.WebClient).DownloadFile(%(url)r, %(target)r)" % vars(),
+ ]
+ _clean_check(cmd, target)
+
+def has_powershell():
+ if platform.system() != 'Windows':
+ return False
+ cmd = ['powershell', '-Command', 'echo test']
+ devnull = open(os.path.devnull, 'wb')
+ try:
+ try:
+ subprocess.check_call(cmd, stdout=devnull, stderr=devnull)
+ except Exception:
+ return False
+ finally:
+ devnull.close()
+ return True
+
+download_file_powershell.viable = has_powershell
+
+def download_file_curl(url, target):
+ cmd = ['curl', url, '--silent', '--output', target]
+ _clean_check(cmd, target)
+
+def has_curl():
+ cmd = ['curl', '--version']
+ devnull = open(os.path.devnull, 'wb')
+ try:
+ try:
+ subprocess.check_call(cmd, stdout=devnull, stderr=devnull)
+ except Exception:
+ return False
+ finally:
+ devnull.close()
+ return True
+
+download_file_curl.viable = has_curl
+
+def download_file_wget(url, target):
+ cmd = ['wget', url, '--quiet', '--output-document', target]
+ _clean_check(cmd, target)
+
+def has_wget():
+ cmd = ['wget', '--version']
+ devnull = open(os.path.devnull, 'wb')
+ try:
+ try:
+ subprocess.check_call(cmd, stdout=devnull, stderr=devnull)
+ except Exception:
+ return False
+ finally:
+ devnull.close()
+ return True
+
+download_file_wget.viable = has_wget
+
+def download_file_insecure(url, target):
+ """
+ Use Python to download the file, even though it cannot authenticate the
+ connection.
+ """
+ try:
+ from urllib.request import urlopen
+ except ImportError:
+ from urllib2 import urlopen
+ src = dst = None
+ try:
+ src = urlopen(url)
+ # Read/write all in one block, so we don't create a corrupt file
+ # if the download is interrupted.
+ data = src.read()
+ dst = open(target, "wb")
+ dst.write(data)
+ finally:
+ if src:
+ src.close()
+ if dst:
+ dst.close()
+
+download_file_insecure.viable = lambda: True
+
+def get_best_downloader():
+ downloaders = [
+ download_file_powershell,
+ download_file_curl,
+ download_file_wget,
+ download_file_insecure,
+ ]
+
+ for dl in downloaders:
+ if dl.viable():
+ return dl
+
+def download_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
+ to_dir=os.curdir, delay=15, downloader_factory=get_best_downloader):
+ """
+ Download setuptools from a specified location and return its filename
+
+ `version` should be a valid setuptools version number that is available
+ as an egg for download under the `download_base` URL (which should end
+ with a '/'). `to_dir` is the directory where the egg will be downloaded.
+ `delay` is the number of seconds to pause before an actual download
+ attempt.
+
+ ``downloader_factory`` should be a function taking no arguments and
+ returning a function for downloading a URL to a target.
+ """
+ # making sure we use the absolute path
+ to_dir = os.path.abspath(to_dir)
+ zip_name = "setuptools-%s.zip" % version
+ url = download_base + zip_name
+ saveto = os.path.join(to_dir, zip_name)
+ if not os.path.exists(saveto): # Avoid repeated downloads
+ log.warn("Downloading %s", url)
+ downloader = downloader_factory()
+ downloader(url, saveto)
+ return os.path.realpath(saveto)
+
+def _build_install_args(options):
+ """
+ Build the arguments to 'python setup.py install' on the setuptools package
+ """
+ return ['--user'] if options.user_install else []
+
+def _parse_args():
+ """
+ Parse the command line for options
+ """
+ parser = optparse.OptionParser()
+ parser.add_option(
+ '--user', dest='user_install', action='store_true', default=False,
+ help='install in user site package (requires Python 2.6 or later)')
+ parser.add_option(
+ '--download-base', dest='download_base', metavar="URL",
+ default=DEFAULT_URL,
+ help='alternative URL from where to download the setuptools package')
+ parser.add_option(
+ '--insecure', dest='downloader_factory', action='store_const',
+ const=lambda: download_file_insecure, default=get_best_downloader,
+ help='Use internal, non-validating downloader'
+ )
+ parser.add_option(
+ '--version', help="Specify which version to download",
+ default=DEFAULT_VERSION,
+ )
+ options, args = parser.parse_args()
+ # positional arguments are ignored
+ return options
+
+def main():
+ """Install or upgrade setuptools and EasyInstall"""
+ options = _parse_args()
+ archive = download_setuptools(
+ version=options.version,
+ download_base=options.download_base,
+ downloader_factory=options.downloader_factory,
+ )
+ return _install(archive, _build_install_args(options))
+
+if __name__ == '__main__':
+ sys.exit(main())
diff --git a/khmer/__init__.py b/khmer/__init__.py
index 72b8580..cf8bfe0 100644
--- a/khmer/__init__.py
+++ b/khmer/__init__.py
@@ -1,6 +1,6 @@
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2010-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -32,19 +32,29 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
-"""This is khmer; please see http://khmer.readthedocs.org/."""
+# pylint: disable=too-few-public-methods,no-init,missing-docstring
+"""This is khmer; please see http://khmer.readthedocs.io/."""
from __future__ import print_function
+from collections import namedtuple
from math import log
import json
from khmer._khmer import Countgraph as _Countgraph
+from khmer._khmer import SmallCountgraph as _SmallCountgraph
+from khmer._khmer import Counttable as _Counttable
+from khmer._khmer import SmallCounttable as _SmallCounttable
from khmer._khmer import GraphLabels as _GraphLabels
from khmer._khmer import Nodegraph as _Nodegraph
+from khmer._khmer import Nodetable as _Nodetable
from khmer._khmer import HLLCounter as _HLLCounter
from khmer._khmer import ReadAligner as _ReadAligner
-
+from khmer._khmer import LinearAssembler
+from khmer._khmer import SimpleLabeledAssembler
+from khmer._khmer import JunctionCountAssembler
+from khmer._khmer import HashSet
+from khmer._khmer import Read
from khmer._khmer import forward_hash
# tests/test_{functions,countgraph,counting_single}.py
@@ -56,6 +66,8 @@ from khmer._khmer import reverse_hash # tests/test_functions.py
from khmer._khmer import hash_murmur3 # tests/test_functions.py
from khmer._khmer import hash_no_rc_murmur3 # tests/test_functions.py
+from khmer._khmer import reverse_complement
+
from khmer._khmer import get_version_cpp as __version_cpp__
# tests/test_version.py
@@ -63,6 +75,8 @@ from khmer._khmer import ReadParser # sandbox/to-casava-1.8-fastq.py
# tests/test_read_parsers.py,scripts/{filter-abund-single,load-graph}.py
# scripts/{abundance-dist-single,load-into-counting}.py
+from khmer._khmer import FILETYPES
+
import sys
from struct import pack, unpack
@@ -72,6 +86,13 @@ __version__ = get_versions()['version']
del get_versions
+_buckets_per_byte = {
+ 'countgraph': 1,
+ 'smallcountgraph': 2,
+ 'nodegraph': 8,
+}
+
+
def load_nodegraph(filename):
"""Load a nodegraph object from the given filename and return it.
@@ -84,18 +105,42 @@ def load_nodegraph(filename):
return nodegraph
-def load_countgraph(filename):
+def load_countgraph(filename, small=False):
"""Load a countgraph object from the given filename and return it.
Keyword argument:
filename -- the name of the countgraph file
+ small -- set this to load a SmallCountgraph instance
"""
- countgraph = _Countgraph(1, [1])
- countgraph.load(filename)
+ if small:
+ countgraph = _SmallCountgraph(1, [1])
+ countgraph.load(filename)
+
+ else:
+ countgraph = _Countgraph(1, [1])
+ countgraph.load(filename)
return countgraph
+def load_counttable(filename, small=False):
+ """Load a counttable object from the given filename and return it.
+
+ Keyword argument:
+ filename -- the name of the counttable file
+ small -- set this to load a SmallCounttable instance
+ """
+ if small:
+ counttable = _SmallCounttable(1, [1])
+ counttable.load(filename)
+
+ else:
+ counttable = _Counttable(1, [1])
+ counttable.load(filename)
+
+ return counttable
+
+
def extract_nodegraph_info(filename):
"""Open the given nodegraph file and return a tuple of information.
@@ -130,7 +175,7 @@ def extract_nodegraph_info(filename):
raise ValueError("Node graph '{}' is missing file type "
"signature".format(filename) + str(signature))
except:
- raise ValueError("Presence table '{}' is corrupt ".format(filename))
+ raise ValueError("Node graph '{}' is corrupt ".format(filename))
return ksize, round(table_size, -2), n_tables, version, ht_type, occupied
@@ -144,6 +189,9 @@ def extract_countgraph_info(filename):
Keyword argument:
filename -- the name of the countgraph file to inspect
"""
+ CgInfo = namedtuple("CgInfo", ['ksize', 'n_tables', 'table_size',
+ 'use_bigcount', 'version', 'ht_type',
+ 'n_occupied'])
ksize = None
n_tables = None
table_size = None
@@ -161,7 +209,10 @@ def extract_countgraph_info(filename):
signature, = unpack('4s', countgraph.read(4))
version, = unpack('B', countgraph.read(1))
ht_type, = unpack('B', countgraph.read(1))
- use_bigcount, = unpack('B', countgraph.read(1))
+ if ht_type != FILETYPES['SMALLCOUNT']:
+ use_bigcount, = unpack('B', countgraph.read(1))
+ else:
+ use_bigcount = None
ksize, = unpack('I', countgraph.read(uint_size))
n_tables, = unpack('B', countgraph.read(1))
occupied, = unpack('Q', countgraph.read(ulonglong_size))
@@ -172,12 +223,12 @@ def extract_countgraph_info(filename):
except:
raise ValueError("Count graph file '{}' is corrupt ".format(filename))
- return ksize, round(table_size, -2), n_tables, use_bigcount, version, \
- ht_type, occupied
+ return CgInfo(ksize, n_tables, round(table_size, -2), use_bigcount,
+ version, ht_type, occupied)
def calc_expected_collisions(graph, force=False, max_false_pos=.2):
- """Do a quick & dirty expected collision rate calculation on a graph
+ """Do a quick & dirty expected collision rate calculation on a graph.
Also check to see that collision rate is within threshold.
@@ -246,7 +297,7 @@ def get_n_primes_near_x(number, target):
i -= 1
while len(primes) != number and i > 0:
if is_prime(i):
- primes.append(i)
+ primes.append(int(i))
i -= 2
if len(primes) != number:
@@ -266,41 +317,75 @@ class Countgraph(_Countgraph):
def __new__(cls, k, starting_size, n_tables):
primes = get_n_primes_near_x(n_tables, starting_size)
- c = _Countgraph.__new__(cls, k, primes)
- c.primes = primes
- return c
+ countgraph = _Countgraph.__new__(cls, k, primes)
+ countgraph.primes = primes
+ return countgraph
+
+
+class SmallCountgraph(_SmallCountgraph):
+
+ def __new__(cls, k, starting_size, n_tables):
+ primes = get_n_primes_near_x(n_tables, starting_size)
+ countgraph = _SmallCountgraph.__new__(cls, k, primes)
+ countgraph.primes = primes
+ return countgraph
+
+
+class Counttable(_Counttable):
+
+ def __new__(cls, k, starting_size, n_tables):
+ primes = get_n_primes_near_x(n_tables, starting_size)
+ counttable = _Counttable.__new__(cls, k, primes)
+ counttable.primes = primes
+ return counttable
+
+
+class SmallCounttable(_SmallCounttable):
+ def __new__(cls, k, starting_size, n_tables):
+ primes = get_n_primes_near_x(n_tables, starting_size)
+ counttable = _SmallCounttable.__new__(cls, k, primes)
+ counttable.primes = primes
+ return counttable
class GraphLabels(_GraphLabels):
def __new__(cls, k, starting_size, n_tables):
- hb = Nodegraph(k, starting_size, n_tables)
- c = _GraphLabels.__new__(cls, hb)
- c.graph = hb
- return c
+ nodegraph = Nodegraph(k, starting_size, n_tables)
+ graphlabels = _GraphLabels.__new__(cls, nodegraph)
+ graphlabels.graph = nodegraph
+ return graphlabels
class CountingGraphLabels(_GraphLabels):
def __new__(cls, k, starting_size, n_tables):
primes = get_n_primes_near_x(n_tables, starting_size)
- hb = _Countgraph(k, primes)
- c = _GraphLabels.__new__(cls, hb)
- c.graph = hb
- return c
+ countgraph = _Countgraph(k, primes)
+ class_ = _GraphLabels.__new__(cls, countgraph)
+ class_.graph = countgraph
+ return class_
class Nodegraph(_Nodegraph):
def __new__(cls, k, starting_size, n_tables):
primes = get_n_primes_near_x(n_tables, starting_size)
- c = _Nodegraph.__new__(cls, k, primes)
- c.primes = primes
- return c
+ nodegraph = _Nodegraph.__new__(cls, k, primes)
+ nodegraph.primes = primes
+ return nodegraph
-class HLLCounter(_HLLCounter):
+class Nodetable(_Nodetable):
+
+ def __new__(cls, k, starting_size, n_tables):
+ primes = get_n_primes_near_x(n_tables, starting_size)
+ nodetable = _Nodetable.__new__(cls, k, primes)
+ nodetable.primes = primes
+ return nodetable
+
+class HLLCounter(_HLLCounter):
"""HyperLogLog counter.
A HyperLogLog counter is a probabilistic data structure specialized on
@@ -318,11 +403,11 @@ class HLLCounter(_HLLCounter):
"""
def __len__(self):
- return self.estimate_cardinality()
+ """Return the cardinality estimate."""
+ return _HLLCounter.estimate_cardinality(self)
class ReadAligner(_ReadAligner):
-
"""Sequence to graph aligner.
ReadAligner uses a Countgraph (the counts of k-mers in the target DNA
@@ -373,15 +458,15 @@ class ReadAligner(_ReadAligner):
else:
transition_probabilities = \
ReadAligner.defaultTransitionProbabilities
- r = _ReadAligner.__new__(cls, count_graph, trusted_cov_cutoff,
- bits_theta, scoring_matrix,
- transition_probabilities)
- r.graph = count_graph
- return r
+ readaligner = _ReadAligner.__new__(
+ cls, count_graph, trusted_cov_cutoff, bits_theta, scoring_matrix,
+ transition_probabilities)
+ readaligner.graph = count_graph
+ return readaligner
- def __init__(self, *args, **kwargs):
+ def __init__(self, *args, **kwargs): # pylint: disable=unused-argument
"""
- ReadAligner initialization.
+ Initialize ReadAligner.
HMM state notation abbreviations:
M_t - trusted match; M_u - untrusted match
@@ -391,7 +476,7 @@ class ReadAligner(_ReadAligner):
Keyword arguments:
filename - a path to a JSON encoded file providing the scoring matrix
for the HMM in an entry named 'scoring_matrix' and the transition
- probababilties for the HMM in an entry named
+ probabilities for the HMM in an entry named
'transition_probabilities'. If provided the remaining keyword
arguments are ignored. (default: None)
scoring_matrix - a list of floats: trusted match, trusted mismatch,
diff --git a/khmer/_cpy_counttable.hh b/khmer/_cpy_counttable.hh
new file mode 100644
index 0000000..429e95e
--- /dev/null
+++ b/khmer/_cpy_counttable.hh
@@ -0,0 +1,128 @@
+/*
+This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+Copyright (C) 2010-2015, Michigan State University.
+Copyright (C) 2015-2016, The Regents of the University of California.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following
+ disclaimer in the documentation and/or other materials provided
+ with the distribution.
+
+ * Neither the name of the Michigan State University nor the names
+ of its contributors may be used to endorse or promote products
+ derived from this software without specific prior written
+ permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+LICENSE (END)
+
+Contact: khmer-project at idyll.org
+*/
+
+typedef struct {
+ khmer_KHashtable_Object khashtable;
+ Counttable * counttable;
+} khmer_KCounttable_Object;
+
+static PyObject* khmer_counttable_new(PyTypeObject * type, PyObject * args,
+ PyObject * kwds);
+
+static PyTypeObject khmer_KCounttable_Type
+CPYCHECKER_TYPE_OBJECT_FOR_TYPEDEF("khmer_KCounttable_Object")
+= {
+ PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
+ "_khmer.Counttable", /* tp_name */
+ sizeof(khmer_KCounttable_Object), /* tp_basicsize */
+ 0, /* tp_itemsize */
+ 0, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ 0, /*tp_compare*/
+ 0, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ 0, /*tp_as_mapping*/
+ 0, /*tp_hash */
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ 0, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ "counttable object", /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+ 0, /* tp_iter */
+ 0, /* tp_iternext */
+ 0, /* tp_methods */
+ 0, /* tp_members */
+ 0, /* tp_getset */
+ 0, /* tp_base */
+ 0, /* tp_dict */
+ 0, /* tp_descr_get */
+ 0, /* tp_descr_set */
+ 0, /* tp_dictoffset */
+ 0, /* tp_init */
+ 0, /* tp_alloc */
+ khmer_counttable_new, /* tp_new */
+};
+
+
+//
+// khmer_counttable_new
+//
+
+static PyObject* khmer_counttable_new(PyTypeObject * type, PyObject * args,
+ PyObject * kwds)
+{
+ khmer_KCounttable_Object * self;
+
+ self = (khmer_KCounttable_Object *)type->tp_alloc(type, 0);
+
+ if (self != NULL) {
+ WordLength k = 0;
+ PyListObject * sizes_list_o = NULL;
+
+ if (!PyArg_ParseTuple(args, "bO!", &k, &PyList_Type, &sizes_list_o)) {
+ Py_DECREF(self);
+ return NULL;
+ }
+
+ std::vector<uint64_t> sizes;
+ if (!convert_Pytablesizes_to_vector(sizes_list_o, sizes)) {
+ Py_DECREF(self);
+ return NULL;
+ }
+
+ try {
+ self->counttable = new Counttable(k, sizes);
+ } catch (std::bad_alloc &e) {
+ Py_DECREF(self);
+ return PyErr_NoMemory();
+ }
+ self->khashtable.hashtable =
+ dynamic_cast<Hashtable*>(self->counttable);
+ }
+
+ return (PyObject *) self;
+}
diff --git a/khmer/_cpy_hashgraph.hh b/khmer/_cpy_hashgraph.hh
new file mode 100644
index 0000000..ea5ba1a
--- /dev/null
+++ b/khmer/_cpy_hashgraph.hh
@@ -0,0 +1,1587 @@
+/*
+This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+Copyright (C) 2010-2015, Michigan State University.
+Copyright (C) 2015-2016, The Regents of the University of California.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following
+ disclaimer in the documentation and/or other materials provided
+ with the distribution.
+
+ * Neither the name of the Michigan State University nor the names
+ of its contributors may be used to endorse or promote products
+ derived from this software without specific prior written
+ permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+LICENSE (END)
+
+Contact: khmer-project at idyll.org
+*/
+
+static PyTypeObject khmer_KHashgraph_Type
+CPYCHECKER_TYPE_OBJECT_FOR_TYPEDEF("khmer_KHashgraph_Object")
+= {
+ PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
+ "_khmer.Hashgraph", /* tp_name */
+ sizeof(khmer_KHashgraph_Object), /* tp_basicsize */
+ 0, /* tp_itemsize */
+ 0, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ 0, /*tp_compare*/
+ 0, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ 0, /*tp_as_mapping*/
+ 0, /*tp_hash */
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ 0, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ "hashgraph object" /* tp_doc */
+};
+
+//
+// Method definitions
+//
+
+static
+PyObject *
+hashgraph_find_high_degree_nodes(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * long_str;
+
+ if (!PyArg_ParseTuple(args, "s", &long_str)) {
+ return NULL;
+ }
+
+ if (strlen(long_str) < hashgraph->ksize()) {
+ PyErr_SetString(PyExc_ValueError,
+ "string length must >= the hashgraph k-mer size");
+ return NULL;
+ }
+
+ SeenSet * hashes = new SeenSet;
+ hashgraph->find_high_degree_nodes(long_str, *hashes);
+
+ khmer_HashSet_Object * o;
+ o = create_HashSet_Object(hashes, hashgraph->ksize());
+
+ return (PyObject *) o;
+}
+
+static
+PyObject *
+hashgraph_neighbors(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+ PyObject * val_obj;
+
+ if (!PyArg_ParseTuple(args, "O", &val_obj)) {
+ return NULL;
+ }
+
+ Kmer start_kmer;
+ if (!ht_convert_PyObject_to_Kmer(val_obj, start_kmer, hashgraph)) {
+ return NULL;
+ }
+
+ KmerQueue node_q;
+ Traverser traverser(hashgraph);
+
+ traverser.traverse(start_kmer, node_q);
+
+ PyObject * x = PyList_New(node_q.size());
+ if (x == NULL) {
+ return NULL;
+ }
+
+ unsigned int i;
+ PyObject * value = nullptr;
+ for (i = 0; node_q.size() > 0; i++) {
+ const HashIntoType h = node_q.front();
+ node_q.pop();
+ convert_HashIntoType_to_PyObject(h, &value);
+ PyList_SET_ITEM(x, i, value);
+ }
+
+ return x;
+}
+
+static
+PyObject *
+hashgraph_traverse_linear_path(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ PyObject * val_o;
+ khmer_KNodegraph_Object * nodegraph_o = NULL;
+ khmer_HashSet_Object * hdn_o = NULL;
+
+ if (!PyArg_ParseTuple(args, "OO!O!", &val_o,
+ &khmer_HashSet_Type, &hdn_o,
+ &khmer_KNodegraph_Type, &nodegraph_o)) {
+ return NULL;
+ }
+ Kmer start_kmer;
+ if (!ht_convert_PyObject_to_Kmer(val_o, start_kmer, hashgraph)) {
+ return NULL;
+ }
+
+ SeenSet * adj = new SeenSet;
+ SeenSet * visited = new SeenSet;
+ unsigned int size = hashgraph->traverse_linear_path(start_kmer,
+ *adj, *visited,
+ *nodegraph_o->nodegraph,
+ *hdn_o->hashes);
+
+ khmer_HashSet_Object * adj_o = create_HashSet_Object(adj,
+ hashgraph->ksize());
+ khmer_HashSet_Object * visited_o = create_HashSet_Object(visited,
+ hashgraph->ksize());
+
+ PyObject * ret = Py_BuildValue("kOO", (unsigned long) size,
+ (PyObject *) adj_o, (PyObject *) visited_o);
+ Py_DECREF(adj_o);
+ Py_DECREF(visited_o);
+
+ return ret;
+}
+
+static
+PyObject *
+hashgraph_assemble_linear_path(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ PyObject * val_o;
+ khmer_KNodegraph_Object * nodegraph_o = NULL;
+ Nodegraph * stop_bf = NULL;
+
+ if (!PyArg_ParseTuple(args, "O|O!", &val_o,
+ &khmer_KNodegraph_Type, &nodegraph_o)) {
+ return NULL;
+ }
+
+ Kmer start_kmer;
+ if (!ht_convert_PyObject_to_Kmer(val_o, start_kmer, hashgraph)) {
+ return NULL;
+ }
+
+ if (nodegraph_o) {
+ stop_bf = nodegraph_o->nodegraph;
+ }
+ LinearAssembler assembler(hashgraph);
+
+ std::string contig = assembler.assemble(start_kmer, stop_bf);
+
+ PyObject * ret = Py_BuildValue("s", contig.c_str());
+
+ return ret;
+}
+
+static
+PyObject *
+hashgraph_n_tags(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ if (!PyArg_ParseTuple(args, "")) {
+ return NULL;
+ }
+
+ return PyLong_FromSize_t(hashgraph->n_tags());
+}
+
+static
+PyObject *
+hashgraph_print_stop_tags(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * filename = NULL;
+
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
+ return NULL;
+ }
+
+ hashgraph->print_stop_tags(filename);
+
+ Py_RETURN_NONE;
+}
+
+static
+PyObject *
+hashgraph_print_tagset(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * filename = NULL;
+
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
+ return NULL;
+ }
+
+ hashgraph->print_tagset(filename);
+
+ Py_RETURN_NONE;
+}
+
+static
+PyObject *
+hashgraph_load_stop_tags(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * filename = NULL;
+ PyObject * clear_tags_o = NULL;
+
+ if (!PyArg_ParseTuple(args, "s|O", &filename, &clear_tags_o)) {
+ return NULL;
+ }
+
+ bool clear_tags = true;
+ if (clear_tags_o && !PyObject_IsTrue(clear_tags_o)) {
+ clear_tags = false;
+ }
+
+
+ try {
+ hashgraph->load_stop_tags(filename, clear_tags);
+ } catch (khmer_file_exception &e) {
+ PyErr_SetString(PyExc_OSError, e.what());
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
+}
+
+
+static
+PyObject *
+hashgraph_save_stop_tags(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * filename = NULL;
+
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
+ return NULL;
+ }
+
+ try {
+ hashgraph->save_stop_tags(filename);
+ } catch (khmer_file_exception &e) {
+ PyErr_SetString(PyExc_OSError, e.what());
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
+}
+
+static PyObject * hashgraph_repartition_largest_partition(
+ khmer_KHashgraph_Object * me,
+ PyObject * args);
+
+static
+PyObject *
+hashgraph_calc_connected_graph_size(khmer_KHashgraph_Object * me,
+ PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * _kmer;
+ unsigned int max_size = 0;
+ PyObject * break_on_circum_o = NULL;
+ if (!PyArg_ParseTuple(args, "s|IO", &_kmer, &max_size, &break_on_circum_o)) {
+ return NULL;
+ }
+
+ bool break_on_circum = false;
+ if (break_on_circum_o && PyObject_IsTrue(break_on_circum_o)) {
+ break_on_circum = true;
+ }
+
+ unsigned long long size = 0;
+ Kmer start_kmer = hashgraph->build_kmer(_kmer);
+
+ Py_BEGIN_ALLOW_THREADS
+ KmerSet keeper;
+ hashgraph->calc_connected_graph_size(start_kmer, size, keeper, max_size,
+ break_on_circum);
+ Py_END_ALLOW_THREADS
+
+ return PyLong_FromUnsignedLongLong(size);
+}
+
+static
+PyObject *
+hashgraph_kmer_degree(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * kmer_s = NULL;
+
+ if (!PyArg_ParseTuple(args, "s", &kmer_s)) {
+ return NULL;
+ }
+
+ return PyLong_FromLong(hashgraph->kmer_degree(kmer_s));
+}
+
+static
+PyObject *
+hashgraph_trim_on_stoptags(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * seq = NULL;
+
+ if (!PyArg_ParseTuple(args, "s", &seq)) {
+ return NULL;
+ }
+
+ size_t trim_at;
+ Py_BEGIN_ALLOW_THREADS
+
+ trim_at = hashgraph->trim_on_stoptags(seq);
+
+ Py_END_ALLOW_THREADS;
+
+ PyObject * trim_seq = PyUnicode_FromStringAndSize(seq, trim_at);
+ if (trim_seq == NULL) {
+ return NULL;
+ }
+ PyObject * ret = Py_BuildValue("Ok", trim_seq, (unsigned long) trim_at);
+ Py_DECREF(trim_seq);
+
+ return ret;
+}
+
+static
+PyObject *
+hashgraph_do_subset_partition(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ PyObject * start_kmer_obj;
+ PyObject * end_kmer_obj;
+ HashIntoType start_kmer, end_kmer;
+ PyObject * break_on_stop_tags_o = NULL;
+ PyObject * stop_big_traversals_o = NULL;
+
+ if (!PyArg_ParseTuple(args, "|OOOO", &start_kmer_obj, &end_kmer_obj,
+ &break_on_stop_tags_o,
+ &stop_big_traversals_o)) {
+ return NULL;
+ }
+ if (!ht_convert_PyObject_to_HashIntoType(start_kmer_obj, start_kmer,
+ hashgraph)) {
+ return NULL;
+ }
+ if (!ht_convert_PyObject_to_HashIntoType(end_kmer_obj, end_kmer,
+ hashgraph)) {
+ return NULL;
+ }
+
+ bool break_on_stop_tags = false;
+ if (break_on_stop_tags_o && PyObject_IsTrue(break_on_stop_tags_o)) {
+ break_on_stop_tags = true;
+ }
+ bool stop_big_traversals = false;
+ if (stop_big_traversals_o && PyObject_IsTrue(stop_big_traversals_o)) {
+ stop_big_traversals = true;
+ }
+
+ SubsetPartition * subset_p = NULL;
+ try {
+ Py_BEGIN_ALLOW_THREADS
+ subset_p = new SubsetPartition(hashgraph);
+ subset_p->do_partition(start_kmer, end_kmer, break_on_stop_tags,
+ stop_big_traversals);
+ Py_END_ALLOW_THREADS
+ } catch (std::bad_alloc &e) {
+ return PyErr_NoMemory();
+ }
+
+ khmer_KSubsetPartition_Object * subset_obj = (khmer_KSubsetPartition_Object *)\
+ PyObject_New(khmer_KSubsetPartition_Object, &khmer_KSubsetPartition_Type);
+
+ if (subset_obj == NULL) {
+ delete subset_p;
+ return NULL;
+ }
+
+ subset_obj->subset = subset_p;
+
+ return (PyObject *) subset_obj;
+}
+
+
+static
+PyObject *
+hashgraph_merge_subset(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ khmer_KSubsetPartition_Object * subset_obj = NULL;
+ if (!PyArg_ParseTuple(args, "O!", &khmer_KSubsetPartition_Type,
+ &subset_obj)) {
+ return NULL;
+ }
+
+ SubsetPartition * subset_p = subset_obj->subset;
+
+ hashgraph->partition->merge(subset_p);
+
+ Py_RETURN_NONE;
+}
+
+static
+PyObject *
+hashgraph_merge_from_disk(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * filename = NULL;
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
+ return NULL;
+ }
+
+ try {
+ hashgraph->partition->merge_from_disk(filename);
+ } catch (khmer_file_exception &e) {
+ PyErr_SetString(PyExc_OSError, e.what());
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
+}
+
+static
+PyObject *
+hashgraph_consume_seqfile_and_tag_with_reads_parser(khmer_KHashgraph_Object * me,
+ PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ python::khmer_ReadParser_Object * rparser_obj = NULL;
+
+ if (!PyArg_ParseTuple( args, "O!", &python::khmer_ReadParser_Type,
+ &rparser_obj)) {
+ return NULL;
+ }
+
+ FastxParserPtr& rparser = rparser_obj->parser;
+
+ // call the C++ function, and trap signals => Python
+ const char *value_exception = NULL;
+ const char *file_exception = NULL;
+ unsigned long long n_consumed = 0;
+ unsigned int total_reads = 0;
+ std::string exc_string;
+
+ Py_BEGIN_ALLOW_THREADS
+ try {
+ hashgraph->consume_seqfile_and_tag<FastxReader>(rparser, total_reads, n_consumed);
+ } catch (khmer_file_exception &exc) {
+ exc_string = exc.what();
+ file_exception = exc_string.c_str();
+ } catch (khmer_value_exception &exc) {
+ exc_string = exc.what();
+ value_exception = exc_string.c_str();
+ }
+ Py_END_ALLOW_THREADS
+
+ if (file_exception != NULL) {
+ PyErr_SetString(PyExc_OSError, file_exception);
+ return NULL;
+ }
+ if (value_exception != NULL) {
+ PyErr_SetString(PyExc_ValueError, value_exception);
+ }
+
+ return Py_BuildValue("IK", total_reads, n_consumed);
+}
+
+static
+PyObject *
+hashgraph_consume_partitioned_fasta(khmer_KHashgraph_Object * me,
+ PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * filename;
+
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
+ return NULL;
+ }
+
+ // call the C++ function, and trap signals => Python
+
+ unsigned long long n_consumed;
+ unsigned int total_reads;
+
+ try {
+ hashgraph->consume_partitioned_fasta<FastxReader>(filename, total_reads, n_consumed);
+ } catch (khmer_file_exception &exc) {
+ PyErr_SetString(PyExc_OSError, exc.what());
+ return NULL;
+ } catch (khmer_value_exception &exc) {
+ PyErr_SetString(PyExc_ValueError, exc.what());
+ return NULL;
+ }
+
+ return Py_BuildValue("IK", total_reads, n_consumed);
+}
+
+static
+PyObject *
+hashgraph_find_all_tags(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * kmer_s = NULL;
+
+ if (!PyArg_ParseTuple(args, "s", &kmer_s)) {
+ return NULL;
+ }
+
+ if (strlen(kmer_s) != hashgraph->ksize()) {
+ PyErr_SetString( PyExc_ValueError,
+ "k-mer size must equal the k-mer size of the presence table");
+ return NULL;
+ }
+
+ pre_partition_info * ppi = NULL;
+
+ Kmer kmer = hashgraph->build_kmer(kmer_s);
+
+ Py_BEGIN_ALLOW_THREADS
+
+ try {
+ ppi = new pre_partition_info(kmer);
+ } catch (std::bad_alloc &e) {
+ return PyErr_NoMemory();
+ }
+ hashgraph->partition->find_all_tags(kmer, ppi->tagged_kmers,
+ hashgraph->all_tags);
+ hashgraph->add_kmer_to_tags(kmer);
+
+ Py_END_ALLOW_THREADS
+
+ khmer_PrePartitionInfo_Object * ppi_obj = (khmer_PrePartitionInfo_Object *) \
+ PyObject_New(khmer_PrePartitionInfo_Object, &khmer_PrePartitionInfo_Type);
+
+ ppi_obj->PrePartitionInfo = ppi;
+
+ return (PyObject*)ppi_obj;
+}
+
+static
+PyObject *
+hashgraph_assign_partition_id(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ khmer_PrePartitionInfo_Object * ppi_obj;
+ if (!PyArg_ParseTuple(args, "O!", &khmer_PrePartitionInfo_Type, &ppi_obj)) {
+ return NULL;
+ }
+
+ pre_partition_info * ppi;
+ ppi = ppi_obj->PrePartitionInfo;
+
+ PartitionID p;
+ p = hashgraph->partition->assign_partition_id(ppi->kmer,
+ ppi->tagged_kmers);
+
+ return PyLong_FromLong(p);
+}
+
+static
+PyObject *
+hashgraph_add_tag(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * kmer_s = NULL;
+ if (!PyArg_ParseTuple(args, "s", &kmer_s)) {
+ return NULL;
+ }
+
+ HashIntoType kmer = hashgraph->hash_dna(kmer_s);
+ hashgraph->add_tag(kmer);
+
+ Py_RETURN_NONE;
+}
+
+static
+PyObject *
+hashgraph_add_stop_tag(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * kmer_s = NULL;
+ if (!PyArg_ParseTuple(args, "s", &kmer_s)) {
+ return NULL;
+ }
+
+ HashIntoType kmer = hashgraph->hash_dna(kmer_s);
+ hashgraph->add_stop_tag(kmer);
+
+ Py_RETURN_NONE;
+}
+
+static
+PyObject *
+hashgraph_get_stop_tags(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ if (!PyArg_ParseTuple(args, "")) {
+ return NULL;
+ }
+
+ SeenSet::const_iterator si;
+
+ PyObject * x = PyList_New(hashgraph->stop_tags.size());
+ unsigned long long i = 0;
+ for (si = hashgraph->stop_tags.begin(); si != hashgraph->stop_tags.end();
+ ++si) {
+ std::string s = hashgraph->unhash_dna(*si);
+ PyList_SET_ITEM(x, i, Py_BuildValue("s", s.c_str()));
+ i++;
+ }
+
+ return x;
+}
+
+static
+PyObject *
+hashgraph_get_tagset(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ if (!PyArg_ParseTuple(args, "")) {
+ return NULL;
+ }
+
+ SeenSet::const_iterator si;
+
+ PyObject * x = PyList_New(hashgraph->all_tags.size());
+ unsigned long long i = 0;
+ for (si = hashgraph->all_tags.begin(); si != hashgraph->all_tags.end();
+ ++si) {
+ std::string s = hashgraph->unhash_dna(*si);
+ PyList_SET_ITEM(x, i, Py_BuildValue("s", s.c_str()));
+ i++;
+ }
+
+ return x;
+}
+
+static
+PyObject *
+hashgraph_output_partitions(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * filename = NULL;
+ const char * output = NULL;
+ PyObject * output_unassigned_o = NULL;
+
+ if (!PyArg_ParseTuple(args, "ss|O", &filename, &output,
+ &output_unassigned_o)) {
+ return NULL;
+ }
+
+ bool output_unassigned = false;
+ if (output_unassigned_o != NULL && PyObject_IsTrue(output_unassigned_o)) {
+ output_unassigned = true;
+ }
+
+ size_t n_partitions = 0;
+
+ try {
+ SubsetPartition * subset_p = hashgraph->partition;
+ n_partitions = subset_p->output_partitioned_file(filename,
+ output,
+ output_unassigned);
+ } catch (khmer_file_exception &e) {
+ PyErr_SetString(PyExc_OSError, e.what());
+ return NULL;
+ } catch (khmer_value_exception &exc) {
+ PyErr_SetString(PyExc_ValueError, exc.what());
+ return NULL;
+ }
+
+ return PyLong_FromLong(n_partitions);
+}
+
+static
+PyObject *
+hashgraph_save_partitionmap(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * filename = NULL;
+
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
+ return NULL;
+ }
+
+ try {
+ hashgraph->partition->save_partitionmap(filename);
+ } catch (khmer_file_exception &e) {
+ PyErr_SetString(PyExc_OSError, e.what());
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
+}
+
+static
+PyObject *
+hashgraph_load_partitionmap(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * filename = NULL;
+
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
+ return NULL;
+ }
+
+ try {
+ hashgraph->partition->load_partitionmap(filename);
+ } catch (khmer_file_exception &e) {
+ PyErr_SetString(PyExc_OSError, e.what());
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
+}
+
+static
+PyObject *
+hashgraph__validate_partitionmap(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ if (!PyArg_ParseTuple(args, "")) {
+ return NULL;
+ }
+
+ hashgraph->partition->_validate_pmap();
+
+ Py_RETURN_NONE;
+}
+
+static
+PyObject *
+hashgraph_count_partitions(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ if (!PyArg_ParseTuple(args, "")) {
+ return NULL;
+ }
+
+ size_t n_partitions = 0, n_unassigned = 0;
+ hashgraph->partition->count_partitions(n_partitions, n_unassigned);
+
+ return Py_BuildValue("nn", (Py_ssize_t) n_partitions,
+ (Py_ssize_t) n_unassigned);
+}
+
+static
+PyObject *
+hashgraph_subset_count_partitions(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ khmer_KSubsetPartition_Object * subset_obj = NULL;
+
+ if (!PyArg_ParseTuple(args, "O!", &khmer_KSubsetPartition_Type,
+ &subset_obj)) {
+ return NULL;
+ }
+
+
+ size_t n_partitions = 0, n_unassigned = 0;
+ subset_obj->subset->count_partitions(n_partitions, n_unassigned);
+
+ return Py_BuildValue("nn", (Py_ssize_t) n_partitions,
+ (Py_ssize_t) n_unassigned);
+}
+
+static
+PyObject *
+hashgraph_subset_partition_size_distribution(khmer_KHashgraph_Object * me,
+ PyObject * args)
+{
+ khmer_KSubsetPartition_Object * subset_obj = NULL;
+ if (!PyArg_ParseTuple(args, "O!", &khmer_KSubsetPartition_Type,
+ &subset_obj)) {
+ return NULL;
+ }
+
+ SubsetPartition * subset_p = subset_obj->subset;
+
+ PartitionCountDistribution d;
+
+ unsigned int n_unassigned = 0;
+ subset_p->partition_size_distribution(d, n_unassigned);
+
+ PyObject * x = PyList_New(d.size());
+ if (x == NULL) {
+ return NULL;
+ }
+ PartitionCountDistribution::iterator di;
+
+ unsigned int i;
+ for (i = 0, di = d.begin(); di != d.end(); ++di, i++) {
+ PyObject * value = Py_BuildValue("KK", di->first, di->second);
+ if (value == NULL) {
+ Py_DECREF(x);
+ return NULL;
+ }
+ PyList_SET_ITEM(x, i, value);
+ }
+ if (!(i == d.size())) {
+ throw khmer_exception();
+ }
+
+ PyObject * returnValue = Py_BuildValue("NI", x, n_unassigned);
+ if (returnValue == NULL) {
+ Py_DECREF(x);
+ return NULL;
+ }
+ return returnValue;
+}
+
+static
+PyObject *
+hashgraph_load_tagset(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * filename = NULL;
+ PyObject * clear_tags_o = NULL;
+
+ if (!PyArg_ParseTuple(args, "s|O", &filename, &clear_tags_o)) {
+ return NULL;
+ }
+
+ bool clear_tags = true;
+ if (clear_tags_o && !PyObject_IsTrue(clear_tags_o)) {
+ clear_tags = false;
+ }
+
+ try {
+ hashgraph->load_tagset(filename, clear_tags);
+ } catch (khmer_file_exception &e) {
+ PyErr_SetString(PyExc_OSError, e.what());
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
+}
+
+static
+PyObject *
+hashgraph_save_tagset(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * filename = NULL;
+
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
+ return NULL;
+ }
+
+ try {
+ hashgraph->save_tagset(filename);
+ } catch (khmer_file_exception &e) {
+ PyErr_SetString(PyExc_OSError, e.what());
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
+}
+
+static
+PyObject *
+hashgraph_save_subset_partitionmap(khmer_KHashgraph_Object * me,
+ PyObject * args)
+{
+ const char * filename = NULL;
+ khmer_KSubsetPartition_Object * subset_obj = NULL;
+
+ if (!PyArg_ParseTuple(args, "O!s", &khmer_KSubsetPartition_Type,
+ &subset_obj, &filename)) {
+ return NULL;
+ }
+
+ SubsetPartition * subset_p = subset_obj->subset;
+
+ Py_BEGIN_ALLOW_THREADS
+
+ try {
+ subset_p->save_partitionmap(filename);
+ } catch (khmer_file_exception &e) {
+ PyErr_SetString(PyExc_OSError, e.what());
+ return NULL;
+ }
+
+ Py_END_ALLOW_THREADS
+
+ Py_RETURN_NONE;
+}
+
+static
+PyObject *
+hashgraph_load_subset_partitionmap(khmer_KHashgraph_Object * me,
+ PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * filename = NULL;
+
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
+ return NULL;
+ }
+
+ SubsetPartition * subset_p;
+ try {
+ subset_p = new SubsetPartition(hashgraph);
+ } catch (std::bad_alloc &e) {
+ return PyErr_NoMemory();
+ }
+
+ const char *file_exception = NULL;
+
+ std::string exc_string ;
+ Py_BEGIN_ALLOW_THREADS
+ try {
+ subset_p->load_partitionmap(filename);
+ } catch (khmer_file_exception &exc) {
+ exc_string = exc.what();
+ file_exception = exc_string.c_str();
+ }
+ Py_END_ALLOW_THREADS
+
+ if (file_exception != NULL) {
+ PyErr_SetString(PyExc_OSError, file_exception);
+ delete subset_p;
+ return NULL;
+ }
+
+ khmer_KSubsetPartition_Object * subset_obj = (khmer_KSubsetPartition_Object *)\
+ PyObject_New(khmer_KSubsetPartition_Object, &khmer_KSubsetPartition_Type);
+
+ if (subset_obj == NULL) {
+ delete subset_p;
+ return NULL;
+ }
+
+ subset_obj->subset = subset_p;
+
+ return (PyObject *) subset_obj;
+}
+
+static
+PyObject *
+hashgraph__set_tag_density(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ unsigned int d;
+ if (!PyArg_ParseTuple(args, "I", &d)) {
+ return NULL;
+ }
+
+ hashgraph->_set_tag_density(d);
+
+ Py_RETURN_NONE;
+}
+
+static
+PyObject *
+hashgraph__get_tag_density(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ if (!PyArg_ParseTuple(args, "")) {
+ return NULL;
+ }
+
+ unsigned int d = hashgraph->_get_tag_density();
+
+ return PyLong_FromLong(d);
+}
+
+static
+PyObject *
+hashgraph__validate_subset_partitionmap(khmer_KHashgraph_Object * me,
+ PyObject * args)
+{
+ khmer_KSubsetPartition_Object * subset_obj = NULL;
+
+ if (!PyArg_ParseTuple(args, "O!", &khmer_KSubsetPartition_Type,
+ &subset_obj)) {
+ return NULL;
+ }
+
+ SubsetPartition * subset_p = subset_obj->subset;
+
+ subset_p->_validate_pmap();
+
+ Py_RETURN_NONE;
+}
+
+static
+PyObject *
+hashgraph_set_partition_id(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * kmer = NULL;
+ PartitionID p = 0;
+
+ if (!PyArg_ParseTuple(args, "sI", &kmer, &p)) {
+ return NULL;
+ }
+
+ hashgraph->partition->set_partition_id(kmer, p);
+
+ Py_RETURN_NONE;
+}
+
+static
+PyObject *
+hashgraph_join_partitions(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ PartitionID p1 = 0, p2 = 0;
+
+ if (!PyArg_ParseTuple(args, "II", &p1, &p2)) {
+ return NULL;
+ }
+
+ p1 = hashgraph->partition->join_partitions(p1, p2);
+
+ return PyLong_FromLong(p1);
+}
+
+static
+PyObject *
+hashgraph_get_partition_id(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * kmer = NULL;
+
+ if (!PyArg_ParseTuple(args, "s", &kmer)) {
+ return NULL;
+ }
+
+ PartitionID partition_id;
+ partition_id = hashgraph->partition->get_partition_id(kmer);
+
+ return PyLong_FromLong(partition_id);
+}
+
+static
+PyObject *
+hashgraph_divide_tags_into_subsets(khmer_KHashgraph_Object * me,
+ PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ unsigned int subset_size = 0;
+
+ if (!PyArg_ParseTuple(args, "I", &subset_size)) {
+ return NULL;
+ }
+
+ SeenSet * divvy = new SeenSet;
+ hashgraph->divide_tags_into_subsets(subset_size, *divvy);
+
+ PyObject * x = (PyObject *) create_HashSet_Object(divvy,
+ hashgraph->ksize());
+ return x;
+}
+
+static
+PyObject *
+hashgraph_count_kmers_within_radius(khmer_KHashgraph_Object * me,
+ PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * kmer = NULL;
+ unsigned int radius = 0;
+ unsigned int max_count = 0;
+
+ if (!PyArg_ParseTuple(args, "sI|I", &kmer, &radius, &max_count)) {
+ return NULL;
+ }
+
+ unsigned int n;
+
+ Py_BEGIN_ALLOW_THREADS
+ Kmer start_kmer = hashgraph->build_kmer(kmer);
+ KmerSet seen;
+ n = hashgraph->traverse_from_kmer(start_kmer, radius,
+ seen, max_count);
+
+ Py_END_ALLOW_THREADS
+
+ return PyLong_FromUnsignedLong(n);
+}
+
+static
+PyObject *
+hashgraph_extract_unique_paths(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * sequence = NULL;
+ unsigned int min_length = 0;
+ float min_unique_f = 0;
+ if (!PyArg_ParseTuple(args, "sIf", &sequence, &min_length, &min_unique_f)) {
+ return NULL;
+ }
+
+ std::vector<std::string> results;
+ hashgraph->extract_unique_paths(sequence, min_length, min_unique_f, results);
+
+ PyObject * x = PyList_New(results.size());
+ if (x == NULL) {
+ return NULL;
+ }
+
+ for (unsigned int i = 0; i < results.size(); i++) {
+ PyList_SET_ITEM(x, i, PyUnicode_FromString(results[i].c_str()));
+ }
+
+ return x;
+}
+
+static
+PyObject *
+hashgraph_consume_and_tag(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * seq;
+
+ if (!PyArg_ParseTuple(args, "s", &seq)) {
+ return NULL;
+ }
+
+ // call the C++ function, and trap signals => Python
+
+ unsigned long long n_consumed = 0;
+
+ // @CTB needs to normalize
+ hashgraph->consume_sequence_and_tag(seq, n_consumed);
+
+ return Py_BuildValue("K", n_consumed);
+}
+
+static
+PyObject *
+hashgraph_get_tags_and_positions(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * seq;
+
+ if (!PyArg_ParseTuple(args, "s", &seq)) {
+ return NULL;
+ }
+
+ // call the C++ function, and trap signals => Python
+
+ std::vector<unsigned int> posns;
+ std::vector<HashIntoType> tags;
+
+ unsigned int pos = 1;
+ KmerIterator kmers(seq, hashgraph->ksize());
+
+ while (!kmers.done()) {
+ HashIntoType kmer = kmers.next();
+ if (set_contains(hashgraph->all_tags, kmer)) {
+ posns.push_back(pos);
+ tags.push_back(kmer);
+ }
+ pos++;
+ }
+
+ PyObject * tag = nullptr;
+ PyObject * posns_list = PyList_New(posns.size());
+ for (size_t i = 0; i < posns.size(); i++) {
+ convert_HashIntoType_to_PyObject(tags[i], &tag);
+ PyObject * tup = Py_BuildValue("IO", posns[i], tag);
+ PyList_SET_ITEM(posns_list, i, tup);
+ }
+
+ return posns_list;
+}
+
+static
+PyObject *
+hashgraph_find_all_tags_list(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * kmer_s = NULL;
+
+ if (!PyArg_ParseTuple(args, "s", &kmer_s)) {
+ return NULL;
+ }
+
+ if (strlen(kmer_s) != hashgraph->ksize()) {
+ PyErr_SetString(PyExc_ValueError,
+ "k-mer length must equal the counting table k-mer size");
+ return NULL;
+ }
+
+ SeenSet * tags = new SeenSet;
+
+ Kmer start_kmer = hashgraph->build_kmer(kmer_s);
+
+ Py_BEGIN_ALLOW_THREADS
+
+ hashgraph->partition->find_all_tags(start_kmer, *tags,
+ hashgraph->all_tags);
+
+ Py_END_ALLOW_THREADS
+
+ PyObject * x = (PyObject *) create_HashSet_Object(tags,
+ hashgraph->ksize());
+ return x;
+}
+
+static
+PyObject *
+hashgraph_consume_seqfile_and_tag(khmer_KHashgraph_Object * me, PyObject * args)
+{
+ Hashgraph * hashgraph = me->hashgraph;
+
+ const char * filename;
+
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
+ return NULL;
+ }
+
+ // call the C++ function, and trap signals => Python
+
+ unsigned long long n_consumed;
+ unsigned int total_reads;
+
+ try {
+ hashgraph->consume_seqfile_and_tag<FastxReader>(filename, total_reads, n_consumed);
+ } catch (khmer_file_exception &exc) {
+ PyErr_SetString(PyExc_OSError, exc.what());
+ return NULL;
+ } catch (khmer_value_exception &exc) {
+ PyErr_SetString(PyExc_ValueError, exc.what());
+ return NULL;
+ }
+
+ return Py_BuildValue("IK", total_reads, n_consumed);
+}
+
+static PyMethodDef khmer_hashgraph_methods[] = {
+ //
+ // graph/traversal functionality
+ //
+
+ {
+ "neighbors",
+ (PyCFunction)hashgraph_neighbors, METH_VARARGS,
+ "Get a list of neighbor nodes for this k-mer.",
+ },
+ {
+ "calc_connected_graph_size",
+ (PyCFunction)hashgraph_calc_connected_graph_size, METH_VARARGS, ""
+ },
+ {
+ "kmer_degree",
+ (PyCFunction)hashgraph_kmer_degree, METH_VARARGS,
+ "Calculate the number of immediate neighbors this k-mer has in "
+ "the graph."
+ },
+ {
+ "count_kmers_within_radius",
+ (PyCFunction)hashgraph_count_kmers_within_radius, METH_VARARGS,
+ "Calculate the number of neighbors with given radius in the graph."
+ },
+ {
+ "find_high_degree_nodes",
+ (PyCFunction)hashgraph_find_high_degree_nodes, METH_VARARGS,
+ "Examine the given sequence for degree > 2 nodes and add to "
+ "list; used in graph contraction.",
+ },
+ {
+ "traverse_linear_path",
+ (PyCFunction)hashgraph_traverse_linear_path, METH_VARARGS,
+ "Traverse the path through the graph starting with the given "
+ "k-mer and avoiding high-degree nodes, finding (and returning) "
+ "traversed k-mers and any encountered high-degree nodes.",
+ },
+ {
+ "assemble_linear_path",
+ (PyCFunction)hashgraph_assemble_linear_path, METH_VARARGS,
+ "Assemble a purely linear path starting with the given "
+ "k-mer, returning traversed k-mers and any encountered high-degree "
+ "nodes.",
+ },
+
+ //
+ // tagging / sparse graph functionality
+ //
+
+ {
+ "consume_and_tag",
+ (PyCFunction)hashgraph_consume_and_tag, METH_VARARGS,
+ "Consume a sequence and tag it."
+ },
+ {
+ "get_tags_and_positions",
+ (PyCFunction)hashgraph_get_tags_and_positions, METH_VARARGS,
+ "Retrieve tags and their positions in a sequence."
+ },
+ {
+ "find_all_tags_list",
+ (PyCFunction)hashgraph_find_all_tags_list, METH_VARARGS,
+ "Find all tags within range of the given k-mer, return as list"
+ },
+ {
+ "consume_seqfile_and_tag",
+ (PyCFunction)hashgraph_consume_seqfile_and_tag, METH_VARARGS,
+ "Consume all sequences in a FASTA/FASTQ file and tag the resulting "
+ "graph."
+ },
+ {
+ "extract_unique_paths",
+ (PyCFunction)hashgraph_extract_unique_paths, METH_VARARGS,
+ "@CTB remove."
+ },
+ {
+ "print_tagset",
+ (PyCFunction)hashgraph_print_tagset, METH_VARARGS,
+ "Print out all of the tags."
+ },
+ {
+ "add_tag",
+ (PyCFunction)hashgraph_add_tag, METH_VARARGS,
+ "Add a k-mer to the tagset."
+ },
+ {
+ "get_tagset",
+ (PyCFunction)hashgraph_get_tagset, METH_VARARGS,
+ "Get all tagged k-mers as DNA strings."
+ },
+ {
+ "load_tagset",
+ (PyCFunction)hashgraph_load_tagset, METH_VARARGS,
+ "Load tags from a file."
+ },
+ {
+ "save_tagset",
+ (PyCFunction)hashgraph_save_tagset, METH_VARARGS,
+ "Save tags to a file."
+ },
+ {
+ "n_tags",
+ (PyCFunction)hashgraph_n_tags, METH_VARARGS,
+ "Return the count of all tags."
+ },
+ {
+ "divide_tags_into_subsets",
+ (PyCFunction)hashgraph_divide_tags_into_subsets, METH_VARARGS,
+ "Divide tags equally up into subsets of given size."
+ },
+ {
+ "_get_tag_density",
+ (PyCFunction)hashgraph__get_tag_density, METH_VARARGS,
+ "Get the tagging density."
+ },
+ {
+ "_set_tag_density",
+ (PyCFunction)hashgraph__set_tag_density, METH_VARARGS,
+ "Set the tagging density."
+ },
+
+ //
+ // partitioning
+ //
+ {
+ "do_subset_partition",
+ (PyCFunction)hashgraph_do_subset_partition, METH_VARARGS,
+ "Partition the graph starting from a given subset of tags."
+ },
+ {
+ "find_all_tags",
+ (PyCFunction)hashgraph_find_all_tags, METH_VARARGS,
+ "Starting from the given k-mer, find all closely connected tags."
+ },
+ {
+ "assign_partition_id",
+ (PyCFunction)hashgraph_assign_partition_id, METH_VARARGS,
+ "Assign a partition ID to a given tag."
+ },
+ {
+ "output_partitions",
+ (PyCFunction)hashgraph_output_partitions, METH_VARARGS,
+ "Write out sequences in given filename to another file, annotating "
+ "with partition IDs."
+ },
+ {
+ "load_partitionmap",
+ (PyCFunction)hashgraph_load_partitionmap, METH_VARARGS,
+ "Load a partitionmap for a given subset."
+ },
+ {
+ "save_partitionmap",
+ (PyCFunction)hashgraph_save_partitionmap, METH_VARARGS,
+ "Save a partitionmap for the given subset."
+ },
+ {
+ "_validate_partitionmap",
+ (PyCFunction)hashgraph__validate_partitionmap, METH_VARARGS,
+ "Run internal validation checks."
+ },
+ {
+ "consume_seqfile_and_tag_with_reads_parser",
+ (PyCFunction)hashgraph_consume_seqfile_and_tag_with_reads_parser,
+ METH_VARARGS,
+ "Count all k-mers using the given reads parser"
+ },
+ {
+ "consume_partitioned_fasta",
+ (PyCFunction)hashgraph_consume_partitioned_fasta, METH_VARARGS,
+ "Count all k-mers in a given file"
+ },
+ {
+ "merge_subset",
+ (PyCFunction)hashgraph_merge_subset, METH_VARARGS,
+ "Merge the given subset into this one."
+ },
+ {
+ "merge_subset_from_disk",
+ (PyCFunction)hashgraph_merge_from_disk, METH_VARARGS,
+ "Merge the given subset (filename) into this one."
+ },
+ {
+ "count_partitions",
+ (PyCFunction)hashgraph_count_partitions, METH_VARARGS,
+ "Count the number of partitions in the master partitionmap."
+ },
+ {
+ "subset_count_partitions",
+ (PyCFunction)hashgraph_subset_count_partitions, METH_VARARGS,
+ "Count the number of partitions in this subset partitionmap."
+ },
+ {
+ "subset_partition_size_distribution",
+ (PyCFunction)hashgraph_subset_partition_size_distribution,
+ METH_VARARGS,
+ "Get the size distribution of partitions in this subset."
+ },
+ {
+ "save_subset_partitionmap",
+ (PyCFunction)hashgraph_save_subset_partitionmap, METH_VARARGS,
+ "Save the partition map for this subset."
+ },
+ {
+ "load_subset_partitionmap",
+ (PyCFunction)hashgraph_load_subset_partitionmap, METH_VARARGS,
+ "Save the partition map for this subset."
+ },
+ {
+ "_validate_subset_partitionmap",
+ (PyCFunction)hashgraph__validate_subset_partitionmap, METH_VARARGS,
+ "Run internal validation checks on this subset."
+ },
+ {
+ "set_partition_id",
+ (PyCFunction)hashgraph_set_partition_id, METH_VARARGS,
+ "Set the partition ID for this tag."
+ },
+ {
+ "join_partitions",
+ (PyCFunction)hashgraph_join_partitions, METH_VARARGS,
+ "Join the partitions of these two tags."
+ },
+ {
+ "get_partition_id",
+ (PyCFunction)hashgraph_get_partition_id, METH_VARARGS,
+ "Get the partition ID of this tag."
+ },
+ {
+ "repartition_largest_partition",
+ (PyCFunction)hashgraph_repartition_largest_partition, METH_VARARGS,
+ "Repartition the largest partition (in the face of stop tags)."
+ },
+
+ // stop tags
+ {
+ "load_stop_tags",
+ (PyCFunction)hashgraph_load_stop_tags, METH_VARARGS,
+ "Load the set of stop tags."
+ },
+ {
+ "save_stop_tags",
+ (PyCFunction)hashgraph_save_stop_tags, METH_VARARGS,
+ "Save the set of stop tags."
+ },
+ {
+ "print_stop_tags",
+ (PyCFunction)hashgraph_print_stop_tags, METH_VARARGS,
+ "Print out the set of stop tags."
+ },
+ {
+ "trim_on_stoptags",
+ (PyCFunction)hashgraph_trim_on_stoptags, METH_VARARGS,
+ "Trim the reads on the given stop tags."
+ },
+ {
+ "add_stop_tag",
+ (PyCFunction)hashgraph_add_stop_tag, METH_VARARGS,
+ "Add this k-mer as a stop tag."
+ },
+ {
+ "get_stop_tags",
+ (PyCFunction)hashgraph_get_stop_tags, METH_VARARGS,
+ "Return a DNA list of all of the stop tags."
+ },
+ {NULL, NULL, 0, NULL} /* sentinel */
+};
diff --git a/khmer/_cpy_nodetable.hh b/khmer/_cpy_nodetable.hh
new file mode 100644
index 0000000..64956d5
--- /dev/null
+++ b/khmer/_cpy_nodetable.hh
@@ -0,0 +1,131 @@
+/*
+This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+Copyright (C) 2010-2015, Michigan State University.
+Copyright (C) 2015-2016, The Regents of the University of California.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following
+ disclaimer in the documentation and/or other materials provided
+ with the distribution.
+
+ * Neither the name of the Michigan State University nor the names
+ of its contributors may be used to endorse or promote products
+ derived from this software without specific prior written
+ permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+LICENSE (END)
+
+Contact: khmer-project at idyll.org
+*/
+
+typedef struct {
+ khmer_KHashtable_Object khashtable;
+ Nodetable * nodetable;
+} khmer_KNodetable_Object;
+
+static PyMethodDef khmer_nodetable_methods[] = {
+ {NULL, NULL, 0, NULL} /* sentinel */
+};
+
+static PyObject* khmer_nodetable_new(PyTypeObject * type, PyObject * args,
+ PyObject * kwds);
+
+static PyTypeObject khmer_KNodetable_Type
+CPYCHECKER_TYPE_OBJECT_FOR_TYPEDEF("khmer_KNodetable_Object")
+= {
+ PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
+ "_khmer.Nodetable", /* tp_name */
+ sizeof(khmer_KNodetable_Object), /* tp_basicsize */
+ 0, /* tp_itemsize */
+ 0, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ 0, /*tp_compare*/
+ 0, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ 0, /*tp_as_mapping*/
+ 0, /*tp_hash */
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ 0, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ "nodetable object", /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+ 0, /* tp_iter */
+ 0, /* tp_iternext */
+ khmer_nodetable_methods, /* tp_methods */
+ 0, /* tp_members */
+ 0, /* tp_getset */
+ 0, /* tp_base */
+ 0, /* tp_dict */
+ 0, /* tp_descr_get */
+ 0, /* tp_descr_set */
+ 0, /* tp_dictoffset */
+ 0, /* tp_init */
+ 0, /* tp_alloc */
+ khmer_nodetable_new, /* tp_new */
+};
+
+//
+// khmer_nodetable_new
+//
+
+static PyObject* khmer_nodetable_new(PyTypeObject * type, PyObject * args,
+ PyObject * kwds)
+{
+ khmer_KNodetable_Object * self;
+
+ self = (khmer_KNodetable_Object *)type->tp_alloc(type, 0);
+
+ if (self != NULL) {
+ WordLength k = 0;
+ PyListObject * sizes_list_o = NULL;
+
+ if (!PyArg_ParseTuple(args, "bO!", &k, &PyList_Type, &sizes_list_o)) {
+ Py_DECREF(self);
+ return NULL;
+ }
+
+ std::vector<uint64_t> sizes;
+ if (!convert_Pytablesizes_to_vector(sizes_list_o, sizes)) {
+ Py_DECREF(self);
+ return NULL;
+ }
+
+ try {
+ self->nodetable = new Nodetable(k, sizes);
+ } catch (std::bad_alloc &e) {
+ Py_DECREF(self);
+ return PyErr_NoMemory();
+ }
+ self->khashtable.hashtable =
+ dynamic_cast<Hashtable*>(self->nodetable);
+ }
+
+ return (PyObject *) self;
+}
diff --git a/khmer/_cpy_smallcountgraph.hh b/khmer/_cpy_smallcountgraph.hh
new file mode 100644
index 0000000..40c18f3
--- /dev/null
+++ b/khmer/_cpy_smallcountgraph.hh
@@ -0,0 +1,181 @@
+/*
+This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+Copyright (C) 2016, The Regents of the University of California.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following
+ disclaimer in the documentation and/or other materials provided
+ with the distribution.
+
+ * Neither the name of the Michigan State University nor the names
+ of its contributors may be used to endorse or promote products
+ derived from this software without specific prior written
+ permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+LICENSE (END)
+
+Contact: khmer-project at idyll.org
+*/
+
+//
+// KSmallCountgraph object
+//
+
+typedef struct {
+ khmer_KHashgraph_Object khashgraph;
+ SmallCountgraph * countgraph;
+} khmer_KSmallCountgraph_Object;
+
+static void khmer_smallcountgraph_dealloc(khmer_KSmallCountgraph_Object * obj);
+
+static
+PyObject *
+smallcount_get_raw_tables(khmer_KSmallCountgraph_Object * self, PyObject * args)
+{
+ SmallCountgraph * countgraph = self->countgraph;
+
+ khmer::Byte ** table_ptrs = countgraph->get_raw_tables();
+ std::vector<uint64_t> sizes = countgraph->get_tablesizes();
+
+ PyObject * raw_tables = PyList_New(sizes.size());
+ for (unsigned int i=0; i<sizes.size(); ++i) {
+ Py_buffer buffer;
+ int res = PyBuffer_FillInfo(&buffer, NULL, table_ptrs[i],
+ sizes[i] / 2 +1, 0,
+ PyBUF_FULL_RO);
+ if (res == -1) {
+ return NULL;
+ }
+ PyObject * buf = PyMemoryView_FromBuffer(&buffer);
+ if(!PyMemoryView_Check(buf)) {
+ return NULL;
+ }
+ PyList_SET_ITEM(raw_tables, i, buf);
+ }
+
+ return raw_tables;
+}
+
+static PyMethodDef khmer_smallcountgraph_methods[] = {
+ {
+ "get_raw_tables",
+ (PyCFunction)smallcount_get_raw_tables, METH_VARARGS,
+ "Get a list of the raw storage tables as memoryview objects."
+ },
+ {NULL, NULL, 0, NULL} /* sentinel */
+};
+
+static PyObject* khmer_smallcountgraph_new(PyTypeObject * type, PyObject * args,
+ PyObject * kwds);
+
+static PyTypeObject khmer_KSmallCountgraph_Type
+CPYCHECKER_TYPE_OBJECT_FOR_TYPEDEF("khmer_KSmallCountgraph_Object")
+= {
+ PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
+ "_khmer.SmallCountgraph", /*tp_name*/
+ sizeof(khmer_KSmallCountgraph_Object), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ (destructor)khmer_smallcountgraph_dealloc, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ 0, /*tp_compare*/
+ 0, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ 0, /*tp_as_mapping*/
+ 0, /*tp_hash */
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ 0, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ "SmallCountgraph hash object", /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+ 0, /* tp_iter */
+ 0, /* tp_iternext */
+ khmer_smallcountgraph_methods, /* tp_methods */
+ 0, /* tp_members */
+ 0, /* tp_getset */
+ 0, /* tp_base */
+ 0, /* tp_dict */
+ 0, /* tp_descr_get */
+ 0, /* tp_descr_set */
+ 0, /* tp_dictoffset */
+ 0, /* tp_init */
+ 0, /* tp_alloc */
+ khmer_smallcountgraph_new, /* tp_new */
+};
+
+//
+// khmer_smallcountgraph_dealloc -- clean up a countgraph hash object.
+//
+
+static void khmer_smallcountgraph_dealloc(khmer_KSmallCountgraph_Object * obj)
+{
+ delete obj->countgraph;
+ obj->countgraph = NULL;
+ Py_TYPE(obj)->tp_free((PyObject*)obj);
+}
+
+//
+// khmer_smallcountgraph_new
+//
+
+static PyObject* khmer_smallcountgraph_new(PyTypeObject * type, PyObject * args,
+ PyObject * kwds)
+{
+ khmer_KSmallCountgraph_Object * self;
+
+ self = (khmer_KSmallCountgraph_Object *)type->tp_alloc(type, 0);
+
+ if (self != NULL) {
+ WordLength k = 0;
+ PyListObject * sizes_list_o = NULL;
+
+ if (!PyArg_ParseTuple(args, "bO!", &k, &PyList_Type, &sizes_list_o)) {
+ Py_DECREF(self);
+ return NULL;
+ }
+
+ std::vector<uint64_t> sizes;
+ if (!convert_Pytablesizes_to_vector(sizes_list_o, sizes)) {
+ Py_DECREF(self);
+ return NULL;
+ }
+
+ try {
+ self->countgraph = new SmallCountgraph(k, sizes);
+ } catch (std::bad_alloc &e) {
+ Py_DECREF(self);
+ return PyErr_NoMemory();
+ }
+ self->khashgraph.khashtable.hashtable =
+ dynamic_cast<Hashtable*>(self->countgraph);
+ self->khashgraph.hashgraph = dynamic_cast<Hashgraph*>(self->countgraph);
+ }
+
+ return (PyObject *) self;
+}
diff --git a/khmer/_cpy_smallcounttable.hh b/khmer/_cpy_smallcounttable.hh
new file mode 100644
index 0000000..decef6c
--- /dev/null
+++ b/khmer/_cpy_smallcounttable.hh
@@ -0,0 +1,127 @@
+/*
+This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+Copyright (C) 2016, The Regents of the University of California.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following
+ disclaimer in the documentation and/or other materials provided
+ with the distribution.
+
+ * Neither the name of the Michigan State University nor the names
+ of its contributors may be used to endorse or promote products
+ derived from this software without specific prior written
+ permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+LICENSE (END)
+
+Contact: khmer-project at idyll.org
+*/
+
+typedef struct {
+ khmer_KHashtable_Object khashtable;
+ SmallCounttable * counttable;
+} khmer_KSmallCounttable_Object;
+
+static PyObject* khmer_smallcounttable_new(PyTypeObject * type, PyObject * args,
+ PyObject * kwds);
+
+static PyTypeObject khmer_KSmallCounttable_Type
+CPYCHECKER_TYPE_OBJECT_FOR_TYPEDEF("khmer_KSmallCounttable_Object")
+= {
+ PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
+ "_khmer.SmallCounttable", /* tp_name */
+ sizeof(khmer_KSmallCounttable_Object), /* tp_basicsize */
+ 0, /* tp_itemsize */
+ 0, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ 0, /*tp_compare*/
+ 0, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ 0, /*tp_as_mapping*/
+ 0, /*tp_hash */
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ 0, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ "SmallCounttable object", /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+ 0, /* tp_iter */
+ 0, /* tp_iternext */
+ 0, /* tp_methods */
+ 0, /* tp_members */
+ 0, /* tp_getset */
+ 0, /* tp_base */
+ 0, /* tp_dict */
+ 0, /* tp_descr_get */
+ 0, /* tp_descr_set */
+ 0, /* tp_dictoffset */
+ 0, /* tp_init */
+ 0, /* tp_alloc */
+ khmer_smallcounttable_new, /* tp_new */
+};
+
+
+//
+// khmer_smallcounttable_new
+//
+
+static PyObject* khmer_smallcounttable_new(PyTypeObject * type, PyObject * args,
+ PyObject * kwds)
+{
+ khmer_KSmallCounttable_Object * self;
+
+ self = (khmer_KSmallCounttable_Object *)type->tp_alloc(type, 0);
+
+ if (self != NULL) {
+ WordLength k = 0;
+ PyListObject * sizes_list_o = NULL;
+
+ if (!PyArg_ParseTuple(args, "bO!", &k, &PyList_Type, &sizes_list_o)) {
+ Py_DECREF(self);
+ return NULL;
+ }
+
+ std::vector<uint64_t> sizes;
+ if (!convert_Pytablesizes_to_vector(sizes_list_o, sizes)) {
+ Py_DECREF(self);
+ return NULL;
+ }
+
+ try {
+ self->counttable = new SmallCounttable(k, sizes);
+ } catch (std::bad_alloc &e) {
+ Py_DECREF(self);
+ return PyErr_NoMemory();
+ }
+ self->khashtable.hashtable =
+ dynamic_cast<Hashtable*>(self->counttable);
+ }
+
+ return (PyObject *) self;
+}
diff --git a/khmer/_khmer.cc b/khmer/_khmer.cc
index 7f89ecd..80062b7 100644
--- a/khmer/_khmer.cc
+++ b/khmer/_khmer.cc
@@ -1,7 +1,7 @@
/*
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2010-2015, Michigan State University.
-Copyright (C) 2015, The Regents of the University of California.
+Copyright (C) 2015-2016, The Regents of the University of California.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
@@ -48,8 +48,8 @@ Contact: khmer-project at idyll.org
#include "khmer.hh"
#include "kmer_hash.hh"
#include "hashtable.hh"
-#include "hashbits.hh"
-#include "counting.hh"
+#include "hashgraph.hh"
+#include "assembler.hh"
#include "read_aligner.hh"
#include "labelhash.hh"
#include "khmer_exception.hh"
@@ -66,6 +66,7 @@ using namespace read_parsers;
#define PyInt_Check(arg) PyLong_Check(arg)
#define PyInt_AsLong(arg) PyLong_AsLong(arg)
#define PyInt_FromLong(arg) PyLong_FromLong(arg)
+#define Py_TPFLAGS_HAVE_ITER 0
#endif
//
@@ -108,6 +109,178 @@ extern "C" {
/***********************************************************************/
+// Convert a hash to a python long object.
+static bool convert_HashIntoType_to_PyObject(const HashIntoType &hashval,
+ PyObject **value)
+{
+ *value = PyLong_FromUnsignedLongLong(hashval);
+ return true;
+}
+
+
+// Convert a python long to a hash
+static bool convert_PyLong_to_HashIntoType(PyObject * value,
+ HashIntoType &hashval)
+{
+ if (PyLong_Check(value)) {
+ //(PyLongObject *)
+ hashval = PyLong_AsUnsignedLongLong(value);
+ return true;
+ } else if (PyInt_Check(value)) {
+ hashval = PyInt_AsLong(value);
+ return true;
+ } else {
+ PyErr_SetString(PyExc_ValueError, "could not convert to hash");
+ return false;
+ }
+}
+
+
+// Take a Python object and (try to) convert it to a HashIntoType.
+// Note: will set error condition and return false if cannot do.
+
+static bool convert_PyObject_to_HashIntoType(PyObject * value,
+ HashIntoType& hashval,
+ WordLength ksize)
+{
+ if (PyInt_Check(value) || PyLong_Check(value)) {
+ return convert_PyLong_to_HashIntoType(value, hashval);
+ } else {
+ PyErr_SetString(PyExc_ValueError,
+ "must use a hash");
+ return false;
+ }
+}
+
+// Take a Python object and (try to) convert it to a HashIntoType.
+// Note: will set error condition and return false if cannot do.
+// Further note: the main difference between this and
+// ht_convert_PyObject_to_Kmer is that this will not pass HashIntoType
+// numbers through the Kmer class, which means reverse complements
+// will not be calculated. There is a test in test_nodegraph.py
+// that checks this.
+
+static bool ht_convert_PyObject_to_HashIntoType(PyObject * value,
+ HashIntoType& hashval,
+ const Hashtable * ht)
+{
+ if (PyInt_Check(value) || PyLong_Check(value)) {
+ return convert_PyLong_to_HashIntoType(value, hashval);
+ } else if (PyUnicode_Check(value)) {
+ PyObject* val_as_str = PyUnicode_AsEncodedString(value,
+ "utf-8", "strict");
+ std::string s = PyBytes_AsString(val_as_str);
+ if (strlen(s.c_str()) != ht->ksize()) {
+ Py_DECREF(val_as_str);
+ PyErr_SetString(PyExc_ValueError,
+ "k-mer length must equal the k-mer size");
+ return false;
+ }
+
+ try {
+ hashval = ht->hash_dna(s.c_str());
+ } catch (khmer_exception &e) {
+ PyErr_SetString(PyExc_ValueError, e.what());
+ Py_DECREF(val_as_str);
+ return false;
+ }
+
+ Py_DECREF(val_as_str);
+ return true;
+
+ } else if (PyBytes_Check(value)) {
+ std::string s = PyBytes_AsString(value);
+ if (strlen(s.c_str()) != ht->ksize()) {
+ PyErr_SetString(PyExc_ValueError,
+ "k-mer length must equal the k-mer size");
+ return false;
+ }
+ try {
+ hashval = ht->hash_dna(s.c_str());
+ } catch (khmer_exception &e) {
+ PyErr_SetString(PyExc_ValueError, e.what());
+ return false;
+ }
+ return true;
+ } else {
+ PyErr_SetString(PyExc_ValueError,
+ "k-mers must be either a hash or a string");
+ return false;
+ }
+}
+
+// Take a Python object and (try to) convert it to a khmer::Kmer.
+// Note: will set error condition and return false if cannot do.
+
+static bool ht_convert_PyObject_to_Kmer(PyObject * value,
+ Kmer& kmer, const Hashtable * ht)
+{
+ if (PyInt_Check(value) || PyLong_Check(value)) {
+ HashIntoType h;
+ if (!convert_PyLong_to_HashIntoType(value, h)) {
+ return false;
+ }
+ kmer.set_from_unique_hash(h, ht->ksize());
+ return true;
+ } else if (PyUnicode_Check(value)) {
+ std::string s = PyBytes_AsString(PyUnicode_AsEncodedString(
+ value, "utf-8", "strict"));
+ if (strlen(s.c_str()) != ht->ksize()) {
+ PyErr_SetString(PyExc_ValueError,
+ "k-mer length must equal the k-mer size");
+ return false;
+ }
+ kmer = Kmer(s, ht->ksize());
+ return true;
+
+ } else if (PyBytes_Check(value)) {
+ std::string s = PyBytes_AsString(value);
+ if (strlen(s.c_str()) != ht->ksize()) {
+ PyErr_SetString(PyExc_ValueError,
+ "k-mer length must equal the k-mer size");
+ return false;
+ }
+ kmer = Kmer(s, ht->ksize());
+ return true;
+ } else {
+ PyErr_SetString(PyExc_ValueError,
+ "k-mers must be either a hash or a string");
+ return false;
+ }
+}
+
+
+static bool convert_Pytablesizes_to_vector(PyListObject * sizes_list_o,
+ std::vector<uint64_t>& sizes)
+{
+ Py_ssize_t sizes_list_o_length = PyList_GET_SIZE(sizes_list_o);
+ if (sizes_list_o_length < 1) {
+ PyErr_SetString(PyExc_ValueError,
+ "tablesizes needs to be one or more numbers");
+ return false;
+ }
+ for (Py_ssize_t i = 0; i < sizes_list_o_length; i++) {
+ PyObject * size_o = PyList_GET_ITEM(sizes_list_o, i);
+ if (PyLong_Check(size_o)) {
+ sizes.push_back(PyLong_AsUnsignedLongLong(size_o));
+ } else if (PyInt_Check(size_o)) {
+ sizes.push_back(PyInt_AsLong(size_o));
+ } else if (PyFloat_Check(size_o)) {
+ sizes.push_back(PyFloat_AS_DOUBLE(size_o));
+ } else {
+ PyErr_SetString(PyExc_TypeError,
+ "2nd argument must be a list of ints, longs, or floats");
+ return false;
+ }
+ }
+ return true;
+}
+
+
+static FastxParserPtr& _PyObject_to_khmer_ReadParser(PyObject * py_object);
+
+/***********************************************************************/
+
//
// Read object -- name, sequence, and FASTQ stuff
//
@@ -126,6 +299,57 @@ typedef struct {
static
+PyObject*
+khmer_Read_new(PyTypeObject * type, PyObject * args, PyObject * kwds)
+{
+ khmer_Read_Object * self;
+ self = (khmer_Read_Object *)type->tp_alloc(type, 0);
+ if (self != NULL) {
+ try {
+ self->read = new Read;
+ } catch (std::bad_alloc &exc) {
+ Py_DECREF(self);
+ return PyErr_NoMemory();
+ }
+ }
+ return (PyObject *)self;
+}
+
+static
+int
+khmer_Read_init(khmer_Read_Object *self, PyObject *args, PyObject *kwds)
+{
+ const char * name{};
+ const char * description{};
+ const char * sequence{};
+ const char * quality{};
+ char *kwlist[5] = {
+ const_cast<char *>("name"), const_cast<char *>("sequence"),
+ const_cast<char *>("quality"), const_cast<char *>("description"), NULL
+ };
+
+ if (!PyArg_ParseTupleAndKeywords(args, kwds, "ss|zz", kwlist,
+ &name, &sequence, &quality, &description)) {
+ return -1;
+ }
+
+ if (name != NULL) {
+ self->read->name = name;
+ }
+ if (sequence != NULL) {
+ self->read->sequence = sequence;
+ self->read->set_clean_seq();
+ }
+ if (quality != NULL) {
+ self->read->quality = quality;
+ }
+ if (description != NULL) {
+ self->read->description = description;
+ }
+ return 0;
+}
+
+static
void
khmer_Read_dealloc(khmer_Read_Object * obj)
{
@@ -135,11 +359,28 @@ khmer_Read_dealloc(khmer_Read_Object * obj)
}
+static Py_ssize_t
+khmer_Read_len(khmer_Read_Object* obj)
+{
+ return obj->read->sequence.size();
+}
+
+static PySequenceMethods khmer_Read_sequence_methods = {
+ (lenfunc)khmer_Read_len, /* sq_length */
+};
+
+
static
PyObject *
Read_get_name(khmer_Read_Object * obj, void * closure )
{
- return PyUnicode_FromString(obj->read->name.c_str()) ;
+ if (obj->read->name.size() > 0) {
+ return PyUnicode_FromString(obj->read->name.c_str());
+ } else {
+ PyErr_SetString(PyExc_AttributeError,
+ "'Read' object has no attribute 'name'.");
+ return NULL;
+ }
}
@@ -147,7 +388,13 @@ static
PyObject *
Read_get_sequence(khmer_Read_Object * obj, void * closure)
{
- return PyUnicode_FromString(obj->read->sequence.c_str()) ;
+ if (obj->read->sequence.size() > 0) {
+ return PyUnicode_FromString(obj->read->sequence.c_str());
+ } else {
+ PyErr_SetString(PyExc_AttributeError,
+ "'Read' object has no attribute 'sequence'.");
+ return NULL;
+ }
}
@@ -155,15 +402,44 @@ static
PyObject *
Read_get_quality(khmer_Read_Object * obj, void * closure)
{
- return PyUnicode_FromString(obj->read->quality.c_str()) ;
+ if (obj->read->quality.size() > 0) {
+ return PyUnicode_FromString(obj->read->quality.c_str());
+ } else {
+ PyErr_SetString(PyExc_AttributeError,
+ "'Read' object has no attribute 'quality'.");
+ return NULL;
+ }
+}
+
+
+static
+PyObject *
+Read_get_description(khmer_Read_Object * obj, void * closure)
+{
+ if (obj->read->description.size() > 0) {
+ return PyUnicode_FromString(obj->read->description.c_str());
+ } else {
+ PyErr_SetString(PyExc_AttributeError,
+ "'Read' object has no attribute 'description'.");
+ return NULL;
+ }
}
static
PyObject *
-Read_get_annotations(khmer_Read_Object * obj, void * closure)
+Read_get_cleaned_seq(khmer_Read_Object * obj, void * closure)
{
- return PyUnicode_FromString(obj->read->annotations.c_str()) ;
+ if (obj->read->cleaned_seq.size() > 0) {
+ return PyUnicode_FromString(obj->read->cleaned_seq.c_str());
+ } else if (obj->read->sequence.size() > 0) {
+ obj->read->set_clean_seq();
+ return PyUnicode_FromString(obj->read->cleaned_seq.c_str());
+ } else {
+ PyErr_SetString(PyExc_AttributeError,
+ "'Read' object has no attribute 'cleaned_seq'.");
+ return NULL;
+ }
}
@@ -187,9 +463,14 @@ static PyGetSetDef khmer_Read_accessors [ ] = {
(char *)"Quality scores.", NULL
},
{
- (char *)"annotations",
- (getter)Read_get_annotations, (setter)NULL,
- (char *)"Annotations.", NULL
+ (char *)"description",
+ (getter)Read_get_description, (setter)NULL,
+ (char *)"Description.", NULL
+ },
+ {
+ (char *)"cleaned_seq",
+ (getter)Read_get_cleaned_seq, (setter)NULL,
+ (char *)"Cleaned sequence.", NULL
},
{ NULL, NULL, NULL, NULL, NULL } // sentinel
@@ -198,7 +479,7 @@ static PyGetSetDef khmer_Read_accessors [ ] = {
static PyTypeObject khmer_Read_Type = {
PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
- "_khmer.Read", /* tp_name */
+ "khmer.Read", /* tp_name */
sizeof(khmer_Read_Object), /* tp_basicsize */
0, /* tp_itemsize */
(destructor)khmer_Read_dealloc, /* tp_dealloc */
@@ -208,7 +489,7 @@ static PyTypeObject khmer_Read_Type = {
0, /* tp_compare */
0, /* tp_repr */
0, /* tp_as_number */
- 0, /* tp_as_sequence */
+ &khmer_Read_sequence_methods, /* tp_as_sequence */
0, /* tp_as_mapping */
0, /* tp_hash */
0, /* tp_call */
@@ -227,8 +508,17 @@ static PyTypeObject khmer_Read_Type = {
0, /* tp_methods */
0, /* tp_members */
(PyGetSetDef *)khmer_Read_accessors, /* tp_getset */
+ 0, /* tp_base */
+ 0, /* tp_dict */
+ 0, /* tp_descr_get */
+ 0, /* tp_descr_set */
+ 0, /* tp_dictoffset */
+ (initproc)khmer_Read_init, /* tp_init */
+ 0, /* tp_alloc */
+ khmer_Read_new, /* tp_new */
};
+
/***********************************************************************/
//
@@ -239,15 +529,14 @@ static PyTypeObject khmer_Read_Type = {
typedef struct {
PyObject_HEAD
- //! Pointer to the low-level parser object.
- read_parsers:: IParser * parser;
+ FastxParserPtr parser;
} khmer_ReadParser_Object;
typedef struct {
PyObject_HEAD
//! Pointer to Python parser object for reference counting purposes.
- PyObject * parent;
+ PyObject * parent;
//! Persistent value of pair mode across invocations.
int pair_mode;
} khmer_ReadPairIterator_Object;
@@ -257,8 +546,6 @@ static
void
_ReadParser_dealloc(khmer_ReadParser_Object * obj)
{
- Py_DECREF(obj->parser);
- obj->parser = NULL;
Py_TYPE(obj)->tp_free((PyObject*)obj);
}
@@ -273,8 +560,7 @@ khmer_ReadPairIterator_dealloc(khmer_ReadPairIterator_Object * obj)
}
-static
-PyObject *
+static PyObject *
_ReadParser_new( PyTypeObject * subtype, PyObject * args, PyObject * kwds )
{
const char * ifile_name_CSTR;
@@ -292,8 +578,7 @@ _ReadParser_new( PyTypeObject * subtype, PyObject * args, PyObject * kwds )
// Wrap the low-level parser object.
try {
- myself->parser =
- IParser:: get_parser( ifile_name );
+ myself->parser = get_parser<FastxReader>(ifile_name);
} catch (khmer_file_exception &exc) {
PyErr_SetString( PyExc_OSError, exc.what() );
return NULL;
@@ -307,7 +592,8 @@ PyObject *
_ReadParser_iternext( PyObject * self )
{
khmer_ReadParser_Object * myself = (khmer_ReadParser_Object *)self;
- IParser * parser = myself->parser;
+ FastxParserPtr& parser = myself->parser;
+ std::string exc_string;
bool stop_iteration = false;
const char *value_exception = NULL;
@@ -323,13 +609,15 @@ _ReadParser_iternext( PyObject * self )
stop_iteration = parser->is_complete( );
if (!stop_iteration) {
try {
- parser->imprint_next_read( *the_read_PTR );
+ *the_read_PTR = parser->get_next_read();
} catch (NoMoreReadsAvailable &exc) {
stop_iteration = true;
} catch (khmer_file_exception &exc) {
- file_exception = exc.what();
+ exc_string = exc.what();
+ file_exception = exc_string.c_str();
} catch (khmer_value_exception &exc) {
- value_exception = exc.what();
+ exc_string = exc.what();
+ value_exception = exc_string.c_str();
}
}
Py_END_ALLOW_THREADS
@@ -363,25 +651,28 @@ PyObject *
_ReadPairIterator_iternext(khmer_ReadPairIterator_Object * myself)
{
khmer_ReadParser_Object * parent = (khmer_ReadParser_Object*)myself->parent;
- IParser *parser = parent->parser;
+ FastxParserPtr& parser = parent->parser;
uint8_t pair_mode = myself->pair_mode;
ReadPair the_read_pair;
bool stop_iteration = false;
const char *value_exception = NULL;
const char *file_exception = NULL;
+ std::string exc_string;
Py_BEGIN_ALLOW_THREADS
stop_iteration = parser->is_complete( );
if (!stop_iteration) {
try {
- parser->imprint_next_read_pair( the_read_pair, pair_mode );
+ the_read_pair = parser->get_next_read_pair(pair_mode);
} catch (NoMoreReadsAvailable &exc) {
stop_iteration = true;
} catch (khmer_file_exception &exc) {
- file_exception = exc.what();
+ exc_string = exc.what();
+ file_exception = exc_string.c_str();
} catch (khmer_value_exception &exc) {
- value_exception = exc.what();
+ exc_string = exc.what();
+ value_exception = exc_string.c_str();
}
}
Py_END_ALLOW_THREADS
@@ -470,7 +761,7 @@ static
PyObject *
ReadParser_iter_read_pairs(PyObject * self, PyObject * args )
{
- int pair_mode = IParser:: PAIR_MODE_ERROR_ON_UNPAIRED;
+ int pair_mode = ReadParser<FastxReader>::PAIR_MODE_ERROR_ON_UNPAIRED;
if (!PyArg_ParseTuple( args, "|i", &pair_mode )) {
return NULL;
@@ -495,6 +786,16 @@ ReadParser_iter_read_pairs(PyObject * self, PyObject * args )
}
+PyObject *
+ReadParser_close(PyObject * self, PyObject * args)
+{
+ FastxParserPtr& rparser = _PyObject_to_khmer_ReadParser(self);
+ rparser->close();
+
+ Py_INCREF(Py_None);
+ return Py_None;
+}
+
static PyMethodDef _ReadParser_methods [ ] = {
{
"iter_reads", (PyCFunction)ReadParser_iter_reads,
@@ -504,6 +805,10 @@ static PyMethodDef _ReadParser_methods [ ] = {
"iter_read_pairs", (PyCFunction)ReadParser_iter_read_pairs,
METH_VARARGS, "Iterates over paired reads as pairs."
},
+ {
+ "close", (PyCFunction)ReadParser_close,
+ METH_NOARGS, "Close associated files."
+ },
{ NULL, NULL, 0, NULL } // sentinel
};
@@ -570,21 +875,8 @@ void _init_ReadParser_Type_constants()
// Place pair mode constants into class dictionary.
int result;
-
- PyObject * value = PyLong_FromLong( IParser:: PAIR_MODE_ALLOW_UNPAIRED );
- if (value == NULL) {
- Py_DECREF(cls_attrs_DICT);
- return;
- }
- result = PyDict_SetItemString(cls_attrs_DICT,
- "PAIR_MODE_ALLOW_UNPAIRED", value);
- Py_XDECREF(value);
- if (!result) {
- Py_DECREF(cls_attrs_DICT);
- return;
- }
-
- value = PyLong_FromLong( IParser:: PAIR_MODE_IGNORE_UNPAIRED );
+ PyObject *value = PyLong_FromLong(
+ ReadParser<FastxReader>::PAIR_MODE_IGNORE_UNPAIRED);
if (value == NULL) {
Py_DECREF(cls_attrs_DICT);
return;
@@ -597,7 +889,7 @@ void _init_ReadParser_Type_constants()
return;
}
- value = PyLong_FromLong( IParser:: PAIR_MODE_ERROR_ON_UNPAIRED );
+ value = PyLong_FromLong(ReadParser<FastxReader>::PAIR_MODE_ERROR_ON_UNPAIRED);
if (value == NULL) {
Py_DECREF(cls_attrs_DICT);
return;
@@ -618,9 +910,7 @@ void _init_ReadParser_Type_constants()
} // namespace khmer
-static
-read_parsers:: IParser *
-_PyObject_to_khmer_ReadParser( PyObject * py_object )
+static FastxParserPtr& _PyObject_to_khmer_ReadParser(PyObject * py_object)
{
// TODO: Add type-checking.
@@ -667,1096 +957,1027 @@ static PyTypeObject khmer_PrePartitionInfo_Type = {
/***********************************************************************/
+/***********************************************************************/
typedef struct {
PyObject_HEAD
- Hashtable * hashtable;
-} khmer_KHashtable_Object;
-
-typedef struct {
- PyObject_HEAD
- SubsetPartition * subset;
-} khmer_KSubsetPartition_Object;
+ SeenSet * hashes;
+ WordLength ksize;
+} khmer_HashSet_Object;
-static void khmer_subset_dealloc(khmer_KSubsetPartition_Object * obj);
+static khmer_HashSet_Object * create_HashSet_Object(SeenSet * h, WordLength k);
-static PyTypeObject khmer_KSubsetPartition_Type = {
- PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
- "_khmer.KSubsetPartition", /* tp_name */
- sizeof(khmer_KSubsetPartition_Object), /* tp_basicsize */
- 0, /* tp_itemsize */
- (destructor)khmer_subset_dealloc, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- 0, /*tp_compare*/
- 0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
- 0, /*tp_hash */
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT, /*tp_flags*/
- "subset object", /* tp_doc */
-};
+static
+void
+khmer_HashSet_dealloc(khmer_HashSet_Object * obj)
+{
+ delete obj->hashes;
+ obj->hashes = NULL;
+ obj->ksize = 0;
+ Py_TYPE(obj)->tp_free((PyObject*)obj);
+}
-typedef struct {
- khmer_KHashtable_Object khashtable;
- Hashbits * hashbits;
-} khmer_KHashbits_Object;
+static PyObject* khmer_HashSet_new(PyTypeObject * type, PyObject * args,
+ PyObject * kwds)
+{
+ khmer_HashSet_Object * self;
-static void khmer_hashbits_dealloc(khmer_KHashbits_Object * obj);
-static PyObject* khmer_hashbits_new(PyTypeObject * type, PyObject * args,
- PyObject * kwds);
+ self = (khmer_HashSet_Object *)type->tp_alloc(type, 0);
-static PyTypeObject khmer_KNodegraph_Type
-CPYCHECKER_TYPE_OBJECT_FOR_TYPEDEF("khmer_KHashbits_Object")
-= {
- PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
- "_khmer.Nodegraph", /* tp_name */
- sizeof(khmer_KHashbits_Object), /* tp_basicsize */
- 0, /* tp_itemsize */
- (destructor)khmer_hashbits_dealloc, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- 0, /*tp_compare*/
- 0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
- 0, /*tp_hash */
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/
- "hashbits object", /* tp_doc */
- 0, /* tp_traverse */
- 0, /* tp_clear */
- 0, /* tp_richcompare */
- 0, /* tp_weaklistoffset */
- 0, /* tp_iter */
- 0, /* tp_iternext */
- 0, /* tp_methods */
- 0, /* tp_members */
- 0, /* tp_getset */
- 0, /* tp_base */
- 0, /* tp_dict */
- 0, /* tp_descr_get */
- 0, /* tp_descr_set */
- 0, /* tp_dictoffset */
- 0, /* tp_init */
- 0, /* tp_alloc */
- khmer_hashbits_new, /* tp_new */
-};
+ if (self != NULL) {
+ PyObject * list_o = NULL;
+ WordLength k;
+ if (!PyArg_ParseTuple(args, "b|O!", &k, &PyList_Type, &list_o)) {
+ Py_DECREF(self);
+ return NULL;
+ }
+ try {
+ self->hashes = new SeenSet;
+ self->ksize = k;
+ } catch (std::bad_alloc &e) {
+ Py_DECREF(self);
+ return PyErr_NoMemory();
+ }
-static
-PyObject *
-hashtable_get_ksize(khmer_KHashtable_Object * me, PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
+ if (list_o) {
+ Py_ssize_t size = PyList_Size(list_o);
+ for (Py_ssize_t i = 0; i < size; i++) {
+ PyObject * item = PyList_GET_ITEM(list_o, i);
+ HashIntoType h;
- if (!PyArg_ParseTuple(args, "")) {
- return NULL;
+ if (!convert_PyObject_to_HashIntoType(item, h, self->ksize)) {
+ return NULL;
+ }
+ self->hashes->insert(h);
+ }
+ }
}
+ return (PyObject *) self;
+}
- unsigned int k = hashtable->ksize();
+/***********************************************************************/
- return PyLong_FromLong(k);
-}
+typedef struct {
+ PyObject_HEAD
+ khmer_HashSet_Object * parent;
+ SeenSet::iterator * it;
+} _HashSet_iterobj;
static
-PyObject *
-hashtable_n_occupied(khmer_KHashtable_Object * me, PyObject * args)
+void
+_HashSet_iter_dealloc(_HashSet_iterobj * obj)
{
- Hashtable * hashtable = me->hashtable;
+ delete obj->it;
+ obj->it = NULL;
+ Py_DECREF(obj->parent);
+ Py_TYPE(obj)->tp_free((PyObject*)obj);
+}
- if (!PyArg_ParseTuple(args, "")) {
- return NULL;
- }
+static PyObject * _HashSet_iter(PyObject * self)
+{
+ Py_INCREF(self);
+ return self;
+}
- HashIntoType n = hashtable->n_occupied();
+static PyObject * _HashSet_iternext(PyObject * self)
+{
+ _HashSet_iterobj * iter_obj = (_HashSet_iterobj *) self;
+ SeenSet * hashes = iter_obj->parent->hashes;
+ if (*iter_obj->it != hashes->end()) {
+ PyObject * ret = nullptr;
+ convert_HashIntoType_to_PyObject((**iter_obj->it), &ret);
+ (*(iter_obj->it))++;
+ return ret;
+ }
- return PyLong_FromUnsignedLongLong(n);
+ PyErr_SetString(PyExc_StopIteration, "end of HashSet");
+ return NULL;
}
-static
-PyObject *
-hashtable_n_unique_kmers(khmer_KHashtable_Object * me, PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
-
- HashIntoType n = hashtable->n_unique_kmers();
-
- return PyLong_FromUnsignedLongLong(n);
-}
+static PyTypeObject _HashSet_iter_Type = {
+ PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
+ "_khmer.HashSet_iter", /* tp_name */
+ sizeof(_HashSet_iterobj), /* tp_basicsize */
+ 0, /* tp_itemsize */
+ (destructor)_HashSet_iter_dealloc, /* tp_dealloc */
+ 0, /* tp_print */
+ 0, /* tp_getattr */
+ 0, /* tp_setattr */
+ 0, /* tp_compare */
+ 0, /* tp_repr */
+ 0, /* tp_as_number */
+ 0, /* tp_as_sequence */
+ 0, /* tp_as_mapping */
+ 0, /* tp_hash */
+ 0, /* tp_call */
+ 0, /* tp_str */
+ 0, /* tp_getattro */
+ 0, /* tp_setattro */
+ 0, /* tp_as_buffer */
+ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_ITER, /* tp_flags */
+ "iterator object for HashSet objects.", /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+ _HashSet_iter, /* tp_iter */
+ _HashSet_iternext, /* tp_iternext */
+ 0, /* tp_methods */
+ 0, /* tp_members */
+ 0, /* tp_getset */
+ 0, /* tp_base */
+ 0, /* tp_dict */
+ 0, /* tp_descr_get */
+ 0, /* tp_descr_set */
+ 0, /* tp_dictoffset */
+ 0, /* tp_init */
+ 0, /* tp_alloc */
+ 0, /* tp_new */
+};
-static
-PyObject *
-hashtable_count(khmer_KHashtable_Object * me, PyObject * args)
+static PyObject * khmer_HashSet_iter(PyObject * self)
{
- Hashtable * hashtable = me->hashtable;
-
- const char * kmer;
-
- if (!PyArg_ParseTuple(args, "s", &kmer)) {
- return NULL;
- }
+ khmer_HashSet_Object * me = (khmer_HashSet_Object *) self;
+ _HashSet_iterobj * iter_obj = (_HashSet_iterobj *)
+ _HashSet_iter_Type.tp_alloc(&_HashSet_iter_Type, 0);
+ if (iter_obj != NULL) {
+ Py_INCREF(me);
+ iter_obj->parent = me;
- if (strlen(kmer) != hashtable->ksize()) {
- PyErr_SetString(PyExc_ValueError,
- "k-mer length must be the same as the hashtable k-size");
- return NULL;
+ iter_obj->it = new SeenSet::iterator;
+ *iter_obj->it = me->hashes->begin();
}
-
- hashtable->count(kmer);
-
- return PyLong_FromLong(1);
+ return (PyObject *) iter_obj;
}
-static
-PyObject *
-hashtable_consume_fasta(khmer_KHashtable_Object * me, PyObject * args)
+static int khmer_HashSet_len(khmer_HashSet_Object * o)
{
- Hashtable * hashtable = me->hashtable;
-
- const char * filename;
-
- if (!PyArg_ParseTuple(args, "s", &filename)) {
- return NULL;
- }
-
- // call the C++ function, and trap signals => Python
- unsigned long long n_consumed = 0;
- unsigned int total_reads = 0;
- try {
- hashtable->consume_fasta(filename, total_reads, n_consumed);
- } catch (khmer_file_exception &exc) {
- PyErr_SetString(PyExc_OSError, exc.what());
- return NULL;
- } catch (khmer_value_exception &exc) {
- PyErr_SetString(PyExc_ValueError, exc.what());
- return NULL;
- }
-
- return Py_BuildValue("IK", total_reads, n_consumed);
+ return (Py_ssize_t) o->hashes->size();
}
-static
-PyObject *
-hashtable_consume_fasta_with_reads_parser(khmer_KHashtable_Object * me,
- PyObject * args)
+static PyObject * khmer_HashSet_concat(khmer_HashSet_Object * o,
+ khmer_HashSet_Object * o2)
{
- Hashtable * hashtable = me->hashtable;
-
- PyObject * rparser_obj = NULL;
-
- if (!PyArg_ParseTuple(args, "O", &rparser_obj)) {
- return NULL;
- }
-
- read_parsers:: IParser * rparser =
- _PyObject_to_khmer_ReadParser( rparser_obj );
-
- // call the C++ function, and trap signals => Python
- unsigned long long n_consumed = 0;
- unsigned int total_reads = 0;
- const char *value_exception = NULL;
- const char *file_exception = NULL;
-
- Py_BEGIN_ALLOW_THREADS
- try {
- hashtable->consume_fasta(rparser, total_reads, n_consumed);
- } catch (khmer_file_exception &exc) {
- file_exception = exc.what();
- } catch (khmer_value_exception &exc) {
- value_exception = exc.what();
- }
- Py_END_ALLOW_THREADS
-
- if (file_exception != NULL) {
- PyErr_SetString(PyExc_OSError, file_exception);
- return NULL;
- }
- if (value_exception != NULL) {
- PyErr_SetString(PyExc_ValueError, value_exception);
+ if (o->ksize != o2->ksize) {
+ PyErr_SetString(PyExc_ValueError,
+ "cannot add HashSets with different ksizes");
return NULL;
}
+ khmer_HashSet_Object * no = create_HashSet_Object(new SeenSet,
+ o->ksize);
+ no->hashes->insert(o->hashes->begin(), o->hashes->end());
+ no->hashes->insert(o2->hashes->begin(), o2->hashes->end());
- return Py_BuildValue("IK", total_reads, n_consumed);
+ return (PyObject *) no;
}
-static
-PyObject *
-hashtable_consume(khmer_KHashtable_Object * me, PyObject * args)
+static PyObject * khmer_HashSet_concat_inplace(khmer_HashSet_Object * o,
+ khmer_HashSet_Object * o2)
{
- Hashtable * hashtable = me->hashtable;
-
- const char * long_str;
-
- if (!PyArg_ParseTuple(args, "s", &long_str)) {
- return NULL;
- }
-
- if (strlen(long_str) < hashtable->ksize()) {
+ if (o->ksize != o2->ksize) {
PyErr_SetString(PyExc_ValueError,
- "string length must >= the hashtable k-mer size");
+ "cannot add HashSets with different ksizes");
return NULL;
}
+ o->hashes->insert(o2->hashes->begin(), o2->hashes->end());
- unsigned int n_consumed;
- n_consumed = hashtable->consume_string(long_str);
-
- return PyLong_FromLong(n_consumed);
+ Py_INCREF(o);
+ return (PyObject *) o;
}
-static
-PyObject *
-hashtable_get(khmer_KHashtable_Object * me, PyObject * args)
+static int khmer_HashSet_contains(khmer_HashSet_Object * o, PyObject * val)
{
- Hashtable * hashtable = me->hashtable;
-
- PyObject * arg;
-
- if (!PyArg_ParseTuple(args, "O", &arg)) {
- return NULL;
- }
-
- unsigned long count = 0;
-
- if (PyInt_Check(arg) || PyLong_Check(arg)) {
- long pos = PyInt_AsLong(arg);
- count = hashtable->get_count((unsigned int) pos);
- } else if (PyUnicode_Check(arg)) {
- std::string s = PyBytes_AsString(PyUnicode_AsEncodedString(
- arg, "utf-8", "strict"));
- if (strlen(s.c_str()) != hashtable->ksize()) {
- PyErr_SetString(PyExc_ValueError,
- "k-mer size must equal the presence table k-mer size");
- return NULL;
- }
- count = hashtable->get_count(s.c_str());
- } else if (PyBytes_Check(arg)) {
- std::string s = PyBytes_AsString(arg);
+ HashIntoType v;
- if (strlen(s.c_str()) != hashtable->ksize()) {
- PyErr_SetString(PyExc_ValueError,
- "k-mer size must equal the counting table k-mer size");
- return NULL;
+ if (convert_PyObject_to_HashIntoType(val, v, 0)) {
+ if (set_contains(*o->hashes, v)) {
+ return 1;
}
-
- count = hashtable->get_count(s.c_str());
- } else {
- PyErr_SetString(PyExc_ValueError,
- "please pass either a hash value or a string");
- return NULL;
}
-
- return PyLong_FromLong(count);
+ return 0;
}
-static
-PyObject *
-hashtable_load(khmer_KHashtable_Object * me, PyObject * args)
+static PyObject *
+hashset_add(khmer_HashSet_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
-
- const char * filename = NULL;
-
- if (!PyArg_ParseTuple(args, "s", &filename)) {
+ PyObject * hash_obj;
+ HashIntoType h;
+ if (!PyArg_ParseTuple(args, "O", &hash_obj)) {
return NULL;
}
- try {
- hashtable->load(filename);
- } catch (khmer_file_exception &e) {
- PyErr_SetString(PyExc_OSError, e.what());
+ if (!convert_PyObject_to_HashIntoType(hash_obj, h, 0)) {
return NULL;
}
+ me->hashes->insert(h);
- Py_RETURN_NONE;
+ Py_INCREF(Py_None);
+ return Py_None;
}
-static
-PyObject *
-hashtable_save(khmer_KHashtable_Object * me, PyObject * args)
+static PyObject *
+hashset_remove(khmer_HashSet_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
-
- const char * filename = NULL;
-
- if (!PyArg_ParseTuple(args, "s", &filename)) {
+ PyObject * hash_obj;
+ HashIntoType h;
+ if (!PyArg_ParseTuple(args, "O", &hash_obj)) {
return NULL;
}
- try {
- hashtable->save(filename);
- } catch (khmer_file_exception &e) {
- PyErr_SetString(PyExc_OSError, e.what());
+ if (!convert_PyObject_to_HashIntoType(hash_obj, h, 0)) {
+ return NULL;
+ }
+ SeenSet::iterator it = me->hashes->find(h);
+ if (it == me->hashes->end()) {
+ PyErr_SetString(PyExc_ValueError, "h not in list");
return NULL;
}
+ me->hashes->erase(it);
- Py_RETURN_NONE;
+ Py_INCREF(Py_None);
+ return Py_None;
}
-static
-PyObject *
-hashtable_get_hashsizes(khmer_KHashtable_Object * me, PyObject * args)
+static PyObject *
+hashset_update(khmer_HashSet_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
-
-
- if (!PyArg_ParseTuple(args, "")) {
+ PyObject * obj;
+ if (!PyArg_ParseTuple(args, "O", &obj)) {
return NULL;
}
- std::vector<HashIntoType> ts = hashtable->get_tablesizes();
-
- PyObject * x = PyList_New(ts.size());
- for (size_t i = 0; i < ts.size(); i++) {
- PyList_SET_ITEM(x, i, PyLong_FromUnsignedLongLong(ts[i]));
+ PyObject * iterator = PyObject_GetIter(obj);
+ if (iterator == NULL) {
+ return NULL;
}
+ PyObject * item = PyIter_Next(iterator);
+ while(item) {
+ HashIntoType h;
- return x;
-}
-
-static
-PyObject *
-hashtable_consume_and_tag(khmer_KHashtable_Object * me, PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
-
- const char * seq;
+ if (!convert_PyObject_to_HashIntoType(item, h, 0)) {
+ PyErr_SetString(PyExc_ValueError, "unknown item type for update");
+ Py_DECREF(item);
+ return NULL;
+ }
+ me->hashes->insert(h);
- if (!PyArg_ParseTuple(args, "s", &seq)) {
+ Py_DECREF(item);
+ item = PyIter_Next(iterator);
+ }
+ Py_DECREF(iterator);
+ if (PyErr_Occurred()) {
return NULL;
}
- // call the C++ function, and trap signals => Python
+ Py_INCREF(Py_None);
+ return Py_None;
+}
- unsigned long long n_consumed = 0;
+static PyMethodDef khmer_HashSet_methods[] = {
+ {
+ "add",
+ (PyCFunction)hashset_add, METH_VARARGS,
+ "Add element to the HashSet."
+ },
+ {
+ "remove",
+ (PyCFunction)hashset_remove, METH_VARARGS,
+ "Remove an element from the HashSet."
+ },
+ {
+ "update",
+ (PyCFunction)hashset_update, METH_VARARGS,
+ "Add a list of elements to the HashSet."
+ },
+ {NULL, NULL, 0, NULL} /* sentinel */
+};
- // @CTB needs to normalize
- hashtable->consume_sequence_and_tag(seq, n_consumed);
+static PySequenceMethods khmer_HashSet_seqmethods[] = {
+ (lenfunc)khmer_HashSet_len, /* sq_length */
+ (binaryfunc)khmer_HashSet_concat, /* sq_concat */
+ 0, /* sq_repeat */
+ 0, /* sq_item */
+ 0, /* sq_slice */
+ 0, /* sq_ass_item */
+ 0, /* sq_ass_slice */
+ (objobjproc)khmer_HashSet_contains, /* sq_contains */
+ (binaryfunc)khmer_HashSet_concat_inplace, /* sq_inplace_concat */
+ 0 /* sq_inplace_repeat */
+};
- return Py_BuildValue("K", n_consumed);
-}
+static PyTypeObject khmer_HashSet_Type = {
+ PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
+ "_khmer.HashSet", /* tp_name */
+ sizeof(khmer_HashSet_Object), /* tp_basicsize */
+ 0, /* tp_itemsize */
+ (destructor)khmer_HashSet_dealloc, /* tp_dealloc */
+ 0, /* tp_print */
+ 0, /* tp_getattr */
+ 0, /* tp_setattr */
+ 0, /* tp_compare */
+ 0, /* tp_repr */
+ 0, /* tp_as_number */
+ khmer_HashSet_seqmethods, /* tp_as_sequence */
+ 0, /* tp_as_mapping */
+ 0, /* tp_hash */
+ 0, /* tp_call */
+ 0, /* tp_str */
+ 0, /* tp_getattro */
+ 0, /* tp_setattro */
+ 0, /* tp_as_buffer */
+ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_ITER, /* tp_flags */
+ "Stores a set of hashed k-mers.", /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+ khmer_HashSet_iter, /* tp_iter */
+ 0, /* tp_iternext */
+ khmer_HashSet_methods, /* tp_methods */
+ 0, /* tp_members */
+ 0, /* tp_getset */
+ 0, /* tp_base */
+ 0, /* tp_dict */
+ 0, /* tp_descr_get */
+ 0, /* tp_descr_set */
+ 0, /* tp_dictoffset */
+ 0, /* tp_init */
+ 0, /* tp_alloc */
+ khmer_HashSet_new, /* tp_new */
+};
-static
-PyObject *
-hashtable_get_tags_and_positions(khmer_KHashtable_Object * me, PyObject * args)
+static khmer_HashSet_Object * create_HashSet_Object(SeenSet * h, WordLength k)
{
- Hashtable * hashtable = me->hashtable;
-
- const char * seq;
+ khmer_HashSet_Object * self;
- if (!PyArg_ParseTuple(args, "s", &seq)) {
- return NULL;
+ self = (khmer_HashSet_Object *)
+ khmer_HashSet_Type.tp_alloc(&khmer_HashSet_Type, 0);
+ if (self != NULL) {
+ self->hashes = h;
+ self->ksize = k;
}
+ return self;
+}
- // call the C++ function, and trap signals => Python
+/***********************************************************************/
- std::vector<unsigned int> posns;
- std::vector<HashIntoType> tags;
+typedef struct {
+ PyObject_HEAD
+ Hashtable * hashtable;
+} khmer_KHashtable_Object;
- unsigned int pos = 1;
- KmerIterator kmers(seq, hashtable->ksize());
+typedef struct {
+ khmer_KHashtable_Object khashtable;
+ Hashgraph * hashgraph;
+} khmer_KHashgraph_Object;
- while (!kmers.done()) {
- HashIntoType kmer = kmers.next();
- if (set_contains(hashtable->all_tags, kmer)) {
- posns.push_back(pos);
- tags.push_back(kmer);
- }
- pos++;
- }
+typedef struct {
+ PyObject_HEAD
+ SubsetPartition * subset;
+} khmer_KSubsetPartition_Object;
- PyObject * posns_list = PyList_New(posns.size());
- for (size_t i = 0; i < posns.size(); i++) {
- PyObject * tup = Py_BuildValue("IK", posns[i], tags[i]);
- PyList_SET_ITEM(posns_list, i, tup);
- }
+static void khmer_subset_dealloc(khmer_KSubsetPartition_Object * obj);
+
+static PyTypeObject khmer_KSubsetPartition_Type = {
+ PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
+ "_khmer.KSubsetPartition", /* tp_name */
+ sizeof(khmer_KSubsetPartition_Object), /* tp_basicsize */
+ 0, /* tp_itemsize */
+ (destructor)khmer_subset_dealloc, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ 0, /*tp_compare*/
+ 0, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ 0, /*tp_as_mapping*/
+ 0, /*tp_hash */
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ 0, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT, /*tp_flags*/
+ "subset object", /* tp_doc */
+};
+
+typedef struct {
+ khmer_KHashgraph_Object khashgraph;
+ Nodegraph * nodegraph;
+} khmer_KNodegraph_Object;
+
+static void khmer_nodegraph_dealloc(khmer_KNodegraph_Object * obj);
+static PyObject* khmer_nodegraph_new(PyTypeObject * type, PyObject * args,
+ PyObject * kwds);
+
+static PyTypeObject khmer_KNodegraph_Type
+CPYCHECKER_TYPE_OBJECT_FOR_TYPEDEF("khmer_KNodegraph_Object")
+= {
+ PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
+ "_khmer.Nodegraph", /* tp_name */
+ sizeof(khmer_KNodegraph_Object), /* tp_basicsize */
+ 0, /* tp_itemsize */
+ (destructor)khmer_nodegraph_dealloc, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ 0, /*tp_compare*/
+ 0, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ 0, /*tp_as_mapping*/
+ 0, /*tp_hash */
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ 0, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ "nodegraph object", /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+ 0, /* tp_iter */
+ 0, /* tp_iternext */
+ 0, /* tp_methods */
+ 0, /* tp_members */
+ 0, /* tp_getset */
+ 0, /* tp_base */
+ 0, /* tp_dict */
+ 0, /* tp_descr_get */
+ 0, /* tp_descr_set */
+ 0, /* tp_dictoffset */
+ 0, /* tp_init */
+ 0, /* tp_alloc */
+ khmer_nodegraph_new, /* tp_new */
+};
- return posns_list;
-}
static
PyObject *
-hashtable_find_all_tags_list(khmer_KHashtable_Object * me, PyObject * args)
+hashtable_ksize(khmer_KHashtable_Object * me, PyObject * args)
{
Hashtable * hashtable = me->hashtable;
- const char * kmer_s = NULL;
-
- if (!PyArg_ParseTuple(args, "s", &kmer_s)) {
- return NULL;
- }
-
- if (strlen(kmer_s) != hashtable->ksize()) {
- PyErr_SetString(PyExc_ValueError,
- "k-mer length must equal the counting table k-mer size");
+ if (!PyArg_ParseTuple(args, "")) {
return NULL;
}
- SeenSet tags;
-
- Kmer start_kmer = hashtable->build_kmer(kmer_s);
-
- Py_BEGIN_ALLOW_THREADS
-
- hashtable->partition->find_all_tags(start_kmer, tags,
- hashtable->all_tags);
-
- Py_END_ALLOW_THREADS
-
- PyObject * x = PyList_New(tags.size());
- if (x == NULL) {
- return NULL;
- }
- SeenSet::iterator si;
- unsigned long long i = 0;
- for (si = tags.begin(); si != tags.end(); ++si) {
- // type K for python unsigned long long
- PyList_SET_ITEM(x, i, Py_BuildValue("K", *si));
- i++;
- }
+ unsigned int k = hashtable->ksize();
- return x;
+ return PyLong_FromLong(k);
}
static
PyObject *
-hashtable_consume_fasta_and_tag(khmer_KHashtable_Object * me, PyObject * args)
+hashtable_hash(khmer_KHashtable_Object * me, PyObject * args)
{
Hashtable * hashtable = me->hashtable;
- const char * filename;
-
- if (!PyArg_ParseTuple(args, "s", &filename)) {
+ char * kmer;
+ if (!PyArg_ParseTuple(args, "s", &kmer)) {
return NULL;
}
- // call the C++ function, and trap signals => Python
-
- unsigned long long n_consumed;
- unsigned int total_reads;
+ if (strlen(kmer) != hashtable->ksize()) {
+ PyErr_SetString(PyExc_ValueError,
+ "provided k-mer is wrong length");
+ return NULL;
+ }
try {
- hashtable->consume_fasta_and_tag(filename, total_reads, n_consumed);
- } catch (khmer_file_exception &exc) {
- PyErr_SetString(PyExc_OSError, exc.what());
- return NULL;
- } catch (khmer_value_exception &exc) {
- PyErr_SetString(PyExc_ValueError, exc.what());
+ PyObject * hash = nullptr;
+ const HashIntoType h(hashtable->hash_dna(kmer));
+ convert_HashIntoType_to_PyObject(h, &hash);
+ return hash;
+ } catch (khmer_exception &e) {
+ PyErr_SetString(PyExc_ValueError, e.what());
return NULL;
}
-
- return Py_BuildValue("IK", total_reads, n_consumed);
}
static
PyObject *
-hashtable_get_median_count(khmer_KHashtable_Object * me, PyObject * args)
+hashtable_reverse_hash(khmer_KHashtable_Object * me, PyObject * args)
{
Hashtable * hashtable = me->hashtable;
- const char * long_str;
-
- if (!PyArg_ParseTuple(args, "s", &long_str)) {
+ PyObject * val_o;
+ HashIntoType val;
+ if (!PyArg_ParseTuple(args, "O", &val_o)) {
return NULL;
}
- if (strlen(long_str) < hashtable->ksize()) {
- PyErr_SetString(PyExc_ValueError,
- "string length must >= the hashtable k-mer size");
+ if (!ht_convert_PyObject_to_HashIntoType(val_o, val, hashtable)) {
return NULL;
}
- BoundedCounterType med = 0;
- float average = 0, stddev = 0;
-
- hashtable->get_median_count(long_str, med, average, stddev);
-
- return Py_BuildValue("iff", med, average, stddev);
+ try {
+ return PyUnicode_FromString(hashtable->unhash_dna(val).c_str());
+ } catch (khmer_exception &e) {
+ PyErr_SetString(PyExc_ValueError, e.what());
+ return NULL;
+ }
}
static
PyObject *
-hashtable_median_at_least(khmer_KHashtable_Object * me, PyObject * args)
+hashtable_n_occupied(khmer_KHashtable_Object * me, PyObject * args)
{
Hashtable * hashtable = me->hashtable;
- const char * long_str;
- unsigned int cutoff;
-
- if (!PyArg_ParseTuple(args, "sI", &long_str, &cutoff)) {
- return NULL;
- }
-
- if (strlen(long_str) < hashtable->ksize()) {
- PyErr_SetString(PyExc_ValueError,
- "string length must >= the hashtable k-mer size");
+ if (!PyArg_ParseTuple(args, "")) {
return NULL;
}
- if (hashtable->median_at_least(long_str, cutoff)) {
- Py_RETURN_TRUE;
- }
- Py_RETURN_FALSE;
+ uint64_t n = hashtable->n_occupied();
+ return PyLong_FromUnsignedLongLong(n);
}
static
PyObject *
-hashtable_n_tags(khmer_KHashtable_Object * me, PyObject * args)
+hashtable_n_unique_kmers(khmer_KHashtable_Object * me, PyObject * args)
{
Hashtable * hashtable = me->hashtable;
- if (!PyArg_ParseTuple(args, "")) {
- return NULL;
- }
+ uint64_t n = hashtable->n_unique_kmers();
- return PyLong_FromSize_t(hashtable->n_tags());
+ return PyLong_FromUnsignedLongLong(n);
}
static
PyObject *
-hashtable_print_stop_tags(khmer_KHashtable_Object * me, PyObject * args)
+hashtable_count(khmer_KHashtable_Object * me, PyObject * args)
{
Hashtable * hashtable = me->hashtable;
- const char * filename = NULL;
+ PyObject * v;
+ if (!PyArg_ParseTuple(args, "O", &v)) {
+ return NULL;
+ }
- if (!PyArg_ParseTuple(args, "s", &filename)) {
+ HashIntoType hashval;
+
+ if (!ht_convert_PyObject_to_HashIntoType(v, hashval, hashtable)) {
return NULL;
}
- hashtable->print_stop_tags(filename);
+ hashtable->count(hashval);
- Py_RETURN_NONE;
+ return PyLong_FromLong(1);
}
static
PyObject *
-hashtable_print_tagset(khmer_KHashtable_Object * me, PyObject * args)
+hashtable_consume_seqfile(khmer_KHashtable_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ Hashtable * hashtable = me->hashtable;
- const char * filename = NULL;
+ const char * filename;
if (!PyArg_ParseTuple(args, "s", &filename)) {
return NULL;
}
- hashtable->print_tagset(filename);
+ // call the C++ function, and trap signals => Python
+ unsigned long long n_consumed = 0;
+ unsigned int total_reads = 0;
+ try {
+ hashtable->consume_seqfile<FastxReader>(filename, total_reads, n_consumed);
+ } catch (khmer_file_exception &exc) {
+ PyErr_SetString(PyExc_OSError, exc.what());
+ return NULL;
+ } catch (khmer_value_exception &exc) {
+ PyErr_SetString(PyExc_ValueError, exc.what());
+ return NULL;
+ }
- Py_RETURN_NONE;
+ return Py_BuildValue("IK", total_reads, n_consumed);
}
static
PyObject *
-hashtable_load_stop_tags(khmer_KHashtable_Object * me, PyObject * args)
+hashtable_consume_seqfile_with_reads_parser(khmer_KHashtable_Object * me,
+ PyObject * args)
{
Hashtable * hashtable = me->hashtable;
- const char * filename = NULL;
- PyObject * clear_tags_o = NULL;
+ PyObject * rparser_obj = NULL;
- if (!PyArg_ParseTuple(args, "s|O", &filename, &clear_tags_o)) {
+ if (!PyArg_ParseTuple(args, "O", &rparser_obj)) {
return NULL;
}
- bool clear_tags = true;
- if (clear_tags_o && !PyObject_IsTrue(clear_tags_o)) {
- clear_tags = false;
- }
+ FastxParserPtr& rparser = _PyObject_to_khmer_ReadParser( rparser_obj );
+ // call the C++ function, and trap signals => Python
+ unsigned long long n_consumed = 0;
+ unsigned int total_reads = 0;
+ const char *value_exception = NULL;
+ const char *file_exception = NULL;
+ std::string exc_string;
+ Py_BEGIN_ALLOW_THREADS
try {
- hashtable->load_stop_tags(filename, clear_tags);
- } catch (khmer_file_exception &e) {
- PyErr_SetString(PyExc_OSError, e.what());
+ hashtable->consume_seqfile<FastxReader>(rparser, total_reads, n_consumed);
+ } catch (khmer_file_exception &exc) {
+ exc_string = exc.what();
+ file_exception = exc_string.c_str();
+ } catch (khmer_value_exception &exc) {
+ exc_string = exc.what();
+ value_exception = exc_string.c_str();
+ }
+ Py_END_ALLOW_THREADS
+
+ if (file_exception != NULL) {
+ PyErr_SetString(PyExc_OSError, file_exception);
+ return NULL;
+ }
+ if (value_exception != NULL) {
+ PyErr_SetString(PyExc_ValueError, value_exception);
return NULL;
}
- Py_RETURN_NONE;
+ return Py_BuildValue("IK", total_reads, n_consumed);
}
-
static
PyObject *
-hashtable_save_stop_tags(khmer_KHashtable_Object * me, PyObject * args)
+hashtable_consume(khmer_KHashtable_Object * me, PyObject * args)
{
Hashtable * hashtable = me->hashtable;
- const char * filename = NULL;
+ const char * long_str;
- if (!PyArg_ParseTuple(args, "s", &filename)) {
+ if (!PyArg_ParseTuple(args, "s", &long_str)) {
return NULL;
}
- try {
- hashtable->save_stop_tags(filename);
- } catch (khmer_file_exception &e) {
- PyErr_SetString(PyExc_OSError, e.what());
+ if (strlen(long_str) < hashtable->ksize()) {
+ PyErr_SetString(PyExc_ValueError,
+ "string length must >= the hashtable k-mer size");
return NULL;
}
- Py_RETURN_NONE;
-}
-
-static PyObject * hashtable_traverse_from_tags(khmer_KHashtable_Object * me,
- PyObject * args);
+ unsigned int n_consumed;
+ n_consumed = hashtable->consume_string(long_str);
-static PyObject * hashtable_repartition_largest_partition(
- khmer_KHashtable_Object * me,
- PyObject * args);
+ return PyLong_FromLong(n_consumed);
+}
static
PyObject *
-hashtable_calc_connected_graph_size(khmer_KHashtable_Object * me,
- PyObject * args)
+hashtable_get(khmer_KHashtable_Object * me, PyObject * args)
{
Hashtable * hashtable = me->hashtable;
- const char * _kmer;
- unsigned int max_size = 0;
- PyObject * break_on_circum_o = NULL;
- if (!PyArg_ParseTuple(args, "s|IO", &_kmer, &max_size, &break_on_circum_o)) {
- return NULL;
- }
+ PyObject * arg;
- bool break_on_circum = false;
- if (break_on_circum_o && PyObject_IsTrue(break_on_circum_o)) {
- break_on_circum = true;
+ if (!PyArg_ParseTuple(args, "O", &arg)) {
+ return NULL;
}
- unsigned long long size = 0;
- Kmer start_kmer = hashtable->build_kmer(_kmer);
+ HashIntoType hashval;
- Py_BEGIN_ALLOW_THREADS
- KmerSet keeper;
- hashtable->calc_connected_graph_size(start_kmer, size, keeper, max_size,
- break_on_circum);
- Py_END_ALLOW_THREADS
+ if (!ht_convert_PyObject_to_HashIntoType(arg, hashval, hashtable)) {
+ return NULL;
+ }
- return PyLong_FromUnsignedLongLong(size);
+ unsigned int count = hashtable->get_count(hashval);
+ return PyLong_FromLong(count);
}
static
PyObject *
-hashtable_kmer_degree(khmer_KHashtable_Object * me, PyObject * args)
+hashtable_set_use_bigcount(khmer_KHashtable_Object * me, PyObject * args)
{
Hashtable * hashtable = me->hashtable;
- const char * kmer_s = NULL;
-
- if (!PyArg_ParseTuple(args, "s", &kmer_s)) {
+ PyObject * x;
+ if (!PyArg_ParseTuple(args, "O", &x)) {
+ return NULL;
+ }
+ int setme = PyObject_IsTrue(x);
+ if (setme < 0) {
+ return NULL;
+ }
+ try {
+ hashtable->set_use_bigcount((bool)setme);
+ } catch (khmer_exception &e) {
+ PyErr_SetString(PyExc_ValueError, e.what());
return NULL;
}
- return PyLong_FromLong(hashtable->kmer_degree(kmer_s));
+ Py_RETURN_NONE;
}
static
PyObject *
-hashtable_trim_on_stoptags(khmer_KHashtable_Object * me, PyObject * args)
+hashtable_get_use_bigcount(khmer_KHashtable_Object * me, PyObject * args)
{
Hashtable * hashtable = me->hashtable;
- const char * seq = NULL;
-
- if (!PyArg_ParseTuple(args, "s", &seq)) {
+ if (!PyArg_ParseTuple(args, "")) {
return NULL;
}
- size_t trim_at;
- Py_BEGIN_ALLOW_THREADS
-
- trim_at = hashtable->trim_on_stoptags(seq);
+ bool val = hashtable->get_use_bigcount();
- Py_END_ALLOW_THREADS;
-
- PyObject * trim_seq = PyUnicode_FromStringAndSize(seq, trim_at);
- if (trim_seq == NULL) {
- return NULL;
- }
- PyObject * ret = Py_BuildValue("Ok", trim_seq, (unsigned long) trim_at);
- Py_DECREF(trim_seq);
-
- return ret;
-}
+ return PyBool_FromLong((int)val);
+}
static
PyObject *
-hashtable_identify_stoptags_by_position(khmer_KHashtable_Object * me,
- PyObject * args)
+hashtable_get_min_count(khmer_KHashtable_Object * me, PyObject * args)
{
Hashtable * hashtable = me->hashtable;
- const char * seq = NULL;
+ const char * long_str;
- if (!PyArg_ParseTuple(args, "s", &seq)) {
+ if (!PyArg_ParseTuple(args, "s", &long_str)) {
return NULL;
}
- std::vector<unsigned int> posns;
- Py_BEGIN_ALLOW_THREADS
-
- hashtable->identify_stop_tags_by_position(seq, posns);
-
- Py_END_ALLOW_THREADS;
-
- PyObject * x = PyList_New(posns.size());
-
- for (unsigned int i = 0; i < posns.size(); i++) {
- PyList_SET_ITEM(x, i, Py_BuildValue("I", posns[i]));
+ if (strlen(long_str) < hashtable->ksize()) {
+ PyErr_SetString(PyExc_ValueError,
+ "string length must >= the hashtable k-mer size");
+ return NULL;
}
- return x;
+ BoundedCounterType c = hashtable->get_min_count(long_str);
+ unsigned int N = c;
+
+ return PyLong_FromLong(N);
}
static
PyObject *
-hashtable_do_subset_partition(khmer_KHashtable_Object * me, PyObject * args)
+hashtable_get_max_count(khmer_KHashtable_Object * me, PyObject * args)
{
Hashtable * hashtable = me->hashtable;
- HashIntoType start_kmer = 0, end_kmer = 0;
- PyObject * break_on_stop_tags_o = NULL;
- PyObject * stop_big_traversals_o = NULL;
+ const char * long_str;
- if (!PyArg_ParseTuple(args, "|KKOO", &start_kmer, &end_kmer,
- &break_on_stop_tags_o,
- &stop_big_traversals_o)) {
+ if (!PyArg_ParseTuple(args, "s", &long_str)) {
return NULL;
}
- bool break_on_stop_tags = false;
- if (break_on_stop_tags_o && PyObject_IsTrue(break_on_stop_tags_o)) {
- break_on_stop_tags = true;
- }
- bool stop_big_traversals = false;
- if (stop_big_traversals_o && PyObject_IsTrue(stop_big_traversals_o)) {
- stop_big_traversals = true;
- }
-
- SubsetPartition * subset_p = NULL;
- try {
- Py_BEGIN_ALLOW_THREADS
- subset_p = new SubsetPartition(hashtable);
- subset_p->do_partition(start_kmer, end_kmer, break_on_stop_tags,
- stop_big_traversals);
- Py_END_ALLOW_THREADS
- } catch (std::bad_alloc &e) {
- return PyErr_NoMemory();
- }
-
- khmer_KSubsetPartition_Object * subset_obj = (khmer_KSubsetPartition_Object *)\
- PyObject_New(khmer_KSubsetPartition_Object, &khmer_KSubsetPartition_Type);
-
- if (subset_obj == NULL) {
- delete subset_p;
+ if (strlen(long_str) < hashtable->ksize()) {
+ PyErr_SetString(PyExc_ValueError,
+ "string length must >= the hashtable k-mer size");
return NULL;
}
- subset_obj->subset = subset_p;
+ BoundedCounterType c = hashtable->get_max_count(long_str);
+ unsigned int N = c;
- return (PyObject *) subset_obj;
+ return PyLong_FromLong(N);
}
+// fwd decls to replace function definitions
+static PyObject * hashtable_abundance_distribution_with_reads_parser(khmer_KHashtable_Object * me, PyObject * args);
+static PyObject * hashtable_abundance_distribution(khmer_KHashtable_Object * me, PyObject * args);
static
PyObject *
-hashtable_join_partitions_by_path(khmer_KHashtable_Object * me, PyObject * args)
+hashtable_trim_on_abundance(khmer_KHashtable_Object * me, PyObject * args)
{
Hashtable * hashtable = me->hashtable;
- const char * sequence = NULL;
- if (!PyArg_ParseTuple(args, "s", &sequence)) {
+ const char * seq = NULL;
+ unsigned int min_count_i = 0;
+
+ if (!PyArg_ParseTuple(args, "sI", &seq, &min_count_i)) {
return NULL;
}
- hashtable->partition->join_partitions_by_path(sequence);
+ unsigned long trim_at;
+ Py_BEGIN_ALLOW_THREADS
- Py_RETURN_NONE;
-}
+ BoundedCounterType min_count = min_count_i;
-static
-PyObject *
-hashtable_merge_subset(khmer_KHashtable_Object * me, PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
+ trim_at = hashtable->trim_on_abundance(seq, min_count);
+
+ Py_END_ALLOW_THREADS;
- khmer_KSubsetPartition_Object * subset_obj = NULL;
- if (!PyArg_ParseTuple(args, "O!", &khmer_KSubsetPartition_Type,
- &subset_obj)) {
+ PyObject * trim_seq = PyUnicode_FromStringAndSize(seq, trim_at);
+ if (trim_seq == NULL) {
return NULL;
}
+ PyObject * ret = Py_BuildValue("Ok", trim_seq, trim_at);
+ Py_DECREF(trim_seq);
- SubsetPartition * subset_p = subset_obj->subset;
-
- hashtable->partition->merge(subset_p);
-
- Py_RETURN_NONE;
+ return ret;
}
static
PyObject *
-hashtable_merge_from_disk(khmer_KHashtable_Object * me, PyObject * args)
+hashtable_trim_below_abundance(khmer_KHashtable_Object * me, PyObject * args)
{
Hashtable * hashtable = me->hashtable;
- const char * filename = NULL;
- if (!PyArg_ParseTuple(args, "s", &filename)) {
+ const char * seq = NULL;
+ BoundedCounterType max_count_i = 0;
+
+ if (!PyArg_ParseTuple(args, "sH", &seq, &max_count_i)) {
return NULL;
}
- try {
- hashtable->partition->merge_from_disk(filename);
- } catch (khmer_file_exception &e) {
- PyErr_SetString(PyExc_OSError, e.what());
+ unsigned long trim_at;
+ Py_BEGIN_ALLOW_THREADS
+
+ BoundedCounterType max_count = max_count_i;
+
+ trim_at = hashtable->trim_below_abundance(seq, max_count);
+
+ Py_END_ALLOW_THREADS;
+
+ PyObject * trim_seq = PyUnicode_FromStringAndSize(seq, trim_at);
+ if (trim_seq == NULL) {
return NULL;
}
+ PyObject * ret = Py_BuildValue("Ok", trim_seq, trim_at);
+ Py_DECREF(trim_seq);
- Py_RETURN_NONE;
+ return ret;
}
static
PyObject *
-hashtable_consume_fasta_and_tag_with_reads_parser(khmer_KHashtable_Object * me,
- PyObject * args)
+hashtable_find_spectral_error_positions(khmer_KHashtable_Object * me,
+ PyObject * args)
{
Hashtable * hashtable = me->hashtable;
- python::khmer_ReadParser_Object * rparser_obj = NULL;
+ const char * seq = NULL;
+ BoundedCounterType max_count = 0; // unsigned short int
- if (!PyArg_ParseTuple( args, "O!", &python::khmer_ReadParser_Type,
- &rparser_obj)) {
+ if (!PyArg_ParseTuple(args, "sH", &seq, &max_count)) {
return NULL;
}
- read_parsers:: IParser * rparser = rparser_obj-> parser;
-
- // call the C++ function, and trap signals => Python
- const char *value_exception = NULL;
- const char *file_exception = NULL;
- unsigned long long n_consumed = 0;
- unsigned int total_reads = 0;
+ std::vector<unsigned int> posns;
- Py_BEGIN_ALLOW_THREADS
try {
- hashtable->consume_fasta_and_tag(rparser, total_reads, n_consumed);
- } catch (khmer_file_exception &exc) {
- file_exception = exc.what();
- } catch (khmer_value_exception &exc) {
- value_exception = exc.what();
+ posns = hashtable->find_spectral_error_positions(seq, max_count);
+ } catch (khmer_exception &e) {
+ PyErr_SetString(PyExc_ValueError, e.what());
+ return NULL;
}
- Py_END_ALLOW_THREADS
- if (file_exception != NULL) {
- PyErr_SetString(PyExc_OSError, file_exception);
+ Py_ssize_t posns_size = posns.size();
+
+ PyObject * x = PyList_New(posns_size);
+ if (x == NULL) {
return NULL;
}
- if (value_exception != NULL) {
- PyErr_SetString(PyExc_ValueError, value_exception);
+ for (Py_ssize_t i = 0; i < posns_size; i++) {
+ PyList_SET_ITEM(x, i, PyLong_FromLong(posns[i]));
}
- return Py_BuildValue("IK", total_reads, n_consumed);
+ return x;
}
-static PyObject * hashtable_consume_fasta_and_traverse(
- khmer_KHashtable_Object * me,
- PyObject * args);
-
-
static
PyObject *
-hashtable_consume_fasta_and_tag_with_stoptags(khmer_KHashtable_Object * me,
- PyObject * args)
+hashtable_load(khmer_KHashtable_Object * me, PyObject * args)
{
Hashtable * hashtable = me->hashtable;
- const char * filename;
+ const char * filename = NULL;
if (!PyArg_ParseTuple(args, "s", &filename)) {
return NULL;
}
- // call the C++ function, and trap signals => Python
-
- unsigned long long n_consumed;
- unsigned int total_reads;
try {
- hashtable->consume_fasta_and_tag_with_stoptags(filename,
- total_reads, n_consumed);
- } catch (khmer_file_exception &exc) {
- PyErr_SetString(PyExc_OSError, exc.what());
- return NULL;
- } catch (khmer_value_exception &exc) {
- PyErr_SetString(PyExc_ValueError, exc.what());
+ hashtable->load(filename);
+ } catch (khmer_file_exception &e) {
+ PyErr_SetString(PyExc_OSError, e.what());
return NULL;
}
- return Py_BuildValue("IK", total_reads, n_consumed);
+ Py_RETURN_NONE;
}
static
PyObject *
-hashtable_consume_partitioned_fasta(khmer_KHashtable_Object * me,
- PyObject * args)
+hashtable_save(khmer_KHashtable_Object * me, PyObject * args)
{
Hashtable * hashtable = me->hashtable;
- const char * filename;
+ const char * filename = NULL;
if (!PyArg_ParseTuple(args, "s", &filename)) {
return NULL;
}
- // call the C++ function, and trap signals => Python
-
- unsigned long long n_consumed;
- unsigned int total_reads;
-
try {
- hashtable->consume_partitioned_fasta(filename, total_reads, n_consumed);
- } catch (khmer_file_exception &exc) {
- PyErr_SetString(PyExc_OSError, exc.what());
- return NULL;
- } catch (khmer_value_exception &exc) {
- PyErr_SetString(PyExc_ValueError, exc.what());
+ hashtable->save(filename);
+ } catch (khmer_file_exception &e) {
+ PyErr_SetString(PyExc_OSError, e.what());
return NULL;
}
- return Py_BuildValue("IK", total_reads, n_consumed);
+ Py_RETURN_NONE;
}
static
PyObject *
-hashtable_find_all_tags(khmer_KHashtable_Object * me, PyObject * args)
+hashtable_get_hashsizes(khmer_KHashtable_Object * me, PyObject * args)
{
Hashtable * hashtable = me->hashtable;
- const char * kmer_s = NULL;
-
- if (!PyArg_ParseTuple(args, "s", &kmer_s)) {
- return NULL;
- }
- if (strlen(kmer_s) != hashtable->ksize()) {
- PyErr_SetString( PyExc_ValueError,
- "k-mer size must equal the k-mer size of the presence table");
+ if (!PyArg_ParseTuple(args, "")) {
return NULL;
}
- pre_partition_info * ppi = NULL;
-
- Kmer kmer = hashtable->build_kmer(kmer_s);
+ std::vector<uint64_t> ts = hashtable->get_tablesizes();
- Py_BEGIN_ALLOW_THREADS
-
- try {
- ppi = new pre_partition_info(kmer);
- } catch (std::bad_alloc &e) {
- return PyErr_NoMemory();
+ PyObject * x = PyList_New(ts.size());
+ for (size_t i = 0; i < ts.size(); i++) {
+ PyList_SET_ITEM(x, i, PyLong_FromUnsignedLongLong(ts[i]));
}
- hashtable->partition->find_all_tags(kmer, ppi->tagged_kmers,
- hashtable->all_tags);
- hashtable->add_kmer_to_tags(kmer);
- Py_END_ALLOW_THREADS
-
- khmer_PrePartitionInfo_Object * ppi_obj = (khmer_PrePartitionInfo_Object *) \
- PyObject_New(khmer_PrePartitionInfo_Object, &khmer_PrePartitionInfo_Type);
-
- ppi_obj->PrePartitionInfo = ppi;
-
- return (PyObject*)ppi_obj;
+ return x;
}
static
PyObject *
-hashtable_assign_partition_id(khmer_KHashtable_Object * me, PyObject * args)
+hashtable_get_median_count(khmer_KHashtable_Object * me, PyObject * args)
{
Hashtable * hashtable = me->hashtable;
- khmer_PrePartitionInfo_Object * ppi_obj;
- if (!PyArg_ParseTuple(args, "O!", &khmer_PrePartitionInfo_Type, &ppi_obj)) {
+ const char * long_str;
+
+ if (!PyArg_ParseTuple(args, "s", &long_str)) {
+ return NULL;
+ }
+
+ if (strlen(long_str) < hashtable->ksize()) {
+ PyErr_SetString(PyExc_ValueError,
+ "string length must >= the hashtable k-mer size");
return NULL;
}
- pre_partition_info * ppi;
- ppi = ppi_obj->PrePartitionInfo;
+ BoundedCounterType med = 0;
+ float average = 0, stddev = 0;
- PartitionID p;
- p = hashtable->partition->assign_partition_id(ppi->kmer,
- ppi->tagged_kmers);
+ hashtable->get_median_count(long_str, med, average, stddev);
- return PyLong_FromLong(p);
+ return Py_BuildValue("iff", med, average, stddev);
}
static
PyObject *
-hashtable_add_tag(khmer_KHashtable_Object * me, PyObject * args)
+hashtable_median_at_least(khmer_KHashtable_Object * me, PyObject * args)
{
Hashtable * hashtable = me->hashtable;
- const char * kmer_s = NULL;
- if (!PyArg_ParseTuple(args, "s", &kmer_s)) {
+ const char * long_str;
+ unsigned int cutoff;
+
+ if (!PyArg_ParseTuple(args, "sI", &long_str, &cutoff)) {
return NULL;
}
- HashIntoType kmer = _hash(kmer_s, hashtable->ksize());
- hashtable->add_tag(kmer);
-
- Py_RETURN_NONE;
-}
-
-static
-PyObject *
-hashtable_add_stop_tag(khmer_KHashtable_Object * me, PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
-
- const char * kmer_s = NULL;
- if (!PyArg_ParseTuple(args, "s", &kmer_s)) {
+ if (strlen(long_str) < hashtable->ksize()) {
+ PyErr_SetString(PyExc_ValueError,
+ "string length must >= the hashtable k-mer size");
return NULL;
}
- HashIntoType kmer = _hash(kmer_s, hashtable->ksize());
- hashtable->add_stop_tag(kmer);
+ if (hashtable->median_at_least(long_str, cutoff)) {
+ Py_RETURN_TRUE;
+ }
+ Py_RETURN_FALSE;
- Py_RETURN_NONE;
}
static
PyObject *
-hashtable_get_stop_tags(khmer_KHashtable_Object * me, PyObject * args)
+hashtable_get_kmers(khmer_KHashtable_Object * me, PyObject * args)
{
Hashtable * hashtable = me->hashtable;
+ const char * sequence;
- if (!PyArg_ParseTuple(args, "")) {
+ if (!PyArg_ParseTuple(args, "s", &sequence)) {
return NULL;
}
- WordLength k = hashtable->ksize();
- SeenSet::const_iterator si;
+ std::vector<std::string> kmers;
- PyObject * x = PyList_New(hashtable->stop_tags.size());
- unsigned long long i = 0;
- for (si = hashtable->stop_tags.begin(); si != hashtable->stop_tags.end();
- ++si) {
- std::string s = _revhash(*si, k);
- PyList_SET_ITEM(x, i, Py_BuildValue("s", s.c_str()));
- i++;
+ hashtable->get_kmers(sequence, kmers);
+
+ PyObject * x = PyList_New(kmers.size());
+ for (unsigned int i = 0; i < kmers.size(); i++) {
+ PyObject * obj = PyUnicode_FromString(kmers[i].c_str());
+ PyList_SET_ITEM(x, i, obj);
}
return x;
@@ -1764,289 +1985,509 @@ hashtable_get_stop_tags(khmer_KHashtable_Object * me, PyObject * args)
static
PyObject *
-hashtable_get_tagset(khmer_KHashtable_Object * me, PyObject * args)
+hashtable_get_kmer_counts(khmer_KHashtable_Object * me, PyObject * args)
{
Hashtable * hashtable = me->hashtable;
+ const char * sequence;
- if (!PyArg_ParseTuple(args, "")) {
+ if (!PyArg_ParseTuple(args, "s", &sequence)) {
return NULL;
}
- WordLength k = hashtable->ksize();
- SeenSet::const_iterator si;
+ std::vector<BoundedCounterType> counts;
+ try {
+ hashtable->get_kmer_counts(sequence, counts);
+ } catch (khmer_exception &e) {
+ PyErr_SetString(PyExc_ValueError, e.what());
+ return NULL;
+ }
- PyObject * x = PyList_New(hashtable->all_tags.size());
- unsigned long long i = 0;
- for (si = hashtable->all_tags.begin(); si != hashtable->all_tags.end();
- ++si) {
- std::string s = _revhash(*si, k);
- PyList_SET_ITEM(x, i, Py_BuildValue("s", s.c_str()));
- i++;
+ PyObject * x = PyList_New(counts.size());
+ for (unsigned int i = 0; i <counts.size(); i++) {
+ PyObject * obj = PyInt_FromLong(counts[i]);
+ PyList_SET_ITEM(x, i, obj);
}
return x;
}
+
static
PyObject *
-hashtable_output_partitions(khmer_KHashtable_Object * me, PyObject * args)
+hashtable_get_kmer_hashes(khmer_KHashtable_Object * me, PyObject * args)
{
Hashtable * hashtable = me->hashtable;
+ const char * sequence;
- const char * filename = NULL;
- const char * output = NULL;
- PyObject * output_unassigned_o = NULL;
-
- if (!PyArg_ParseTuple(args, "ss|O", &filename, &output,
- &output_unassigned_o)) {
+ if (!PyArg_ParseTuple(args, "s", &sequence)) {
return NULL;
}
- bool output_unassigned = false;
- if (output_unassigned_o != NULL && PyObject_IsTrue(output_unassigned_o)) {
- output_unassigned = true;
- }
-
- size_t n_partitions = 0;
-
+ std::vector<HashIntoType> hashes;
try {
- SubsetPartition * subset_p = hashtable->partition;
- n_partitions = subset_p->output_partitioned_file(filename,
- output,
- output_unassigned);
- } catch (khmer_file_exception &e) {
- PyErr_SetString(PyExc_OSError, e.what());
- return NULL;
- } catch (khmer_value_exception &exc) {
- PyErr_SetString(PyExc_ValueError, exc.what());
+ hashtable->get_kmer_hashes(sequence, hashes);
+ } catch (khmer_exception &e) {
+ PyErr_SetString(PyExc_ValueError, e.what());
return NULL;
}
- return PyLong_FromLong(n_partitions);
+ PyObject * x = PyList_New(hashes.size());
+ for (unsigned int i = 0; i < hashes.size(); i++) {
+ PyObject * obj = nullptr;
+ convert_HashIntoType_to_PyObject(hashes[i], &obj);
+ PyList_SET_ITEM(x, i, obj);
+ }
+
+ return x;
}
+
static
PyObject *
-hashtable_find_unpart(khmer_KHashtable_Object * me, PyObject * args)
+hashtable_get_kmer_hashes_as_hashset(khmer_KHashtable_Object * me,
+ PyObject * args)
{
Hashtable * hashtable = me->hashtable;
+ const char * sequence;
- const char * filename = NULL;
- PyObject * traverse_o = NULL;
- PyObject * stop_big_traversals_o = NULL;
-
- if (!PyArg_ParseTuple(args, "sOO", &filename, &traverse_o,
- &stop_big_traversals_o)) {
+ if (!PyArg_ParseTuple(args, "s", &sequence)) {
return NULL;
}
- bool traverse = PyObject_IsTrue(traverse_o);
- bool stop_big_traversals = PyObject_IsTrue(stop_big_traversals_o);
- unsigned int n_singletons = 0;
-
+ SeenSet * hashes = new SeenSet;
try {
- SubsetPartition * subset_p = hashtable->partition;
- n_singletons = subset_p->find_unpart(filename, traverse,
- stop_big_traversals);
- } catch (khmer_file_exception &exc) {
- PyErr_SetString(PyExc_OSError, exc.what());
- return NULL;
- } catch (khmer_value_exception &exc) {
- PyErr_SetString(PyExc_ValueError, exc.what());
+ hashtable->get_kmer_hashes_as_hashset(sequence, *hashes);
+ } catch (khmer_exception &e) {
+ PyErr_SetString(PyExc_ValueError, e.what());
return NULL;
}
- return PyLong_FromLong(n_singletons);
+ PyObject * x = (PyObject *) create_HashSet_Object(hashes,
+ hashtable->ksize());
+
+ return x;
}
-static
-PyObject *
-hashtable_filter_if_present(khmer_KHashtable_Object * me, PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
- const char * filename = NULL;
- const char * output = NULL;
+static PyMethodDef khmer_hashtable_methods[] = {
+ //
+ // Basic methods
+ //
- if (!PyArg_ParseTuple(args, "ss", &filename, &output)) {
- return NULL;
- }
+ {
+ "ksize",
+ (PyCFunction)hashtable_ksize, METH_VARARGS,
+ "Returns the k-mer size of this graph."
+ },
+ {
+ "hash",
+ (PyCFunction)hashtable_hash, METH_VARARGS,
+ "Returns the hash of this k-mer. For Nodetables and Counttables, this "
+ "function will fail if the supplied k-mer contains non-ACGT "
+ "characters."
+ },
+ {
+ "reverse_hash",
+ (PyCFunction)hashtable_reverse_hash, METH_VARARGS,
+ "Turns a k-mer hash back into a DNA k-mer, if possible."
+ },
+ {
+ "hashsizes",
+ (PyCFunction)hashtable_get_hashsizes, METH_VARARGS,
+ "" },
+ {
+ "n_unique_kmers",
+ (PyCFunction)hashtable_n_unique_kmers, METH_VARARGS,
+ "Count the number of unique kmers in this graph."
+ },
+ {
+ "n_occupied", (PyCFunction)hashtable_n_occupied, METH_VARARGS,
+ "Count the number of occupied bins."
+ },
+ {
+ "count",
+ (PyCFunction)hashtable_count, METH_VARARGS,
+ "Increment the count of this k-mer."
+ },
+ {
+ "add",
+ (PyCFunction)hashtable_count, METH_VARARGS,
+ "Increment the count of this k-mer. (Synonym for 'count'.)"
+ },
+ {
+ "consume",
+ (PyCFunction)hashtable_consume, METH_VARARGS,
+ "Increment the counts of all of the k-mers in the string."
+ },
+ {
+ "consume_seqfile",
+ (PyCFunction)hashtable_consume_seqfile, METH_VARARGS,
+ "Incrment the counts of all the k-mers in the sequences in the "
+ "given file"
+ },
+ {
+ "consume_seqfile_with_reads_parser",
+ (PyCFunction)hashtable_consume_seqfile_with_reads_parser, METH_VARARGS,
+ "Count all k-mers retrieved with this reads parser object."
+ },
+ {
+ "get",
+ (PyCFunction)hashtable_get, METH_VARARGS,
+ "Retrieve the count for the given k-mer. For Nodetables and "
+ "Counttables, this function will fail if the supplied k-mer contains "
+ "non-ACGT characters."
+ },
+ {
+ "load",
+ (PyCFunction)hashtable_load, METH_VARARGS,
+ "Load the graph from the specified file."
+ },
+ {
+ "save",
+ (PyCFunction)hashtable_save, METH_VARARGS,
+ "Save the graph to the specified file."
+ },
+ {
+ "get_kmers",
+ (PyCFunction)hashtable_get_kmers, METH_VARARGS,
+ "Generate an ordered list of all substrings of length k in the string."
+ },
+ {
+ "get_kmer_hashes",
+ (PyCFunction)hashtable_get_kmer_hashes, METH_VARARGS,
+ "Retrieve an ordered list of all hashes of all k-mers in the string."
+ },
+ {
+ "get_kmer_hashes_as_hashset",
+ (PyCFunction)hashtable_get_kmer_hashes_as_hashset, METH_VARARGS,
+ "Retrieve a HashSet containing all the k-mers in the string."
+ },
+ {
+ "get_kmer_counts",
+ (PyCFunction)hashtable_get_kmer_counts, METH_VARARGS,
+ "Retrieve an ordered list of the counts of all k-mers in the string."
+ },
- try {
- hashtable->filter_if_present(filename, output);
- } catch (khmer_file_exception &exc) {
- PyErr_SetString(PyExc_OSError, exc.what());
- return NULL;
- } catch (khmer_value_exception &exc) {
- PyErr_SetString(PyExc_ValueError, exc.what());
- return NULL;
- }
+ {
+ "set_use_bigcount",
+ (PyCFunction)hashtable_set_use_bigcount, METH_VARARGS,
+ "Count past maximum binsize of hashtable (set to T/F)"
+ },
+ {
+ "get_use_bigcount",
+ (PyCFunction)hashtable_get_use_bigcount, METH_VARARGS,
+ "Get value of bigcount flag (T/F)"
+ },
+ {
+ "get_min_count",
+ (PyCFunction)hashtable_get_min_count, METH_VARARGS,
+ "Get the smallest count of all the k-mers in the string"
+ },
+ {
+ "get_max_count",
+ (PyCFunction)hashtable_get_max_count, METH_VARARGS,
+ "Get the largest count of all the k-mers in the string"
+ },
+ {
+ "trim_on_abundance",
+ (PyCFunction)hashtable_trim_on_abundance, METH_VARARGS,
+ "Trim string at first k-mer below the given abundance"
+ },
+ {
+ "trim_below_abundance",
+ (PyCFunction)hashtable_trim_below_abundance, METH_VARARGS,
+ "Trim string at first k-mer above the given abundance"
+ },
+ {
+ "find_spectral_error_positions",
+ (PyCFunction)hashtable_find_spectral_error_positions, METH_VARARGS,
+ "Identify positions of low-abundance k-mers"
+ },
+ {
+ "abundance_distribution",
+ (PyCFunction)hashtable_abundance_distribution, METH_VARARGS,
+ "Calculate the k-mer abundance distribution of the given file"
+ },
+ {
+ "abundance_distribution_with_reads_parser",
+ (PyCFunction)hashtable_abundance_distribution_with_reads_parser,
+ METH_VARARGS,
+ "Calculate the k-mer abundance distribution for a reads parser handle"
+ },
+ {
+ "get_median_count",
+ (PyCFunction)hashtable_get_median_count, METH_VARARGS,
+ "Get the median, average, and stddev of the k-mer counts in the string"
+ },
+ {
+ "median_at_least",
+ (PyCFunction)hashtable_median_at_least, METH_VARARGS,
+ "Return true if the median is at least the given cutoff"
+ },
+ {NULL, NULL, 0, NULL} /* sentinel */
+};
- Py_RETURN_NONE;
-}
+static PyTypeObject khmer_KHashtable_Type
+CPYCHECKER_TYPE_OBJECT_FOR_TYPEDEF("khmer_KHashtable_Object")
+= {
+ PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
+ "_khmer.KHashtable ", /*tp_name*/
+ sizeof(khmer_KHashtable_Object), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ 0, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ 0, /*tp_compare*/
+ 0, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ 0, /*tp_as_mapping*/
+ 0, /*tp_hash */
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ 0, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT, /*tp_flags*/
+ "base hashtable object", /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+ 0, /* tp_iter */
+ 0, /* tp_iternext */
+ khmer_hashtable_methods, /* tp_methods */
+ 0, /* tp_members */
+ 0, /* tp_getset */
+ 0, /* tp_base */
+ 0, /* tp_dict */
+ 0, /* tp_descr_get */
+ 0, /* tp_descr_set */
+ 0, /* tp_dictoffset */
+ 0, /* tp_init */
+ 0, /* tp_alloc */
+ 0, /* tp_new */
+};
-static
-PyObject *
-hashtable_save_partitionmap(khmer_KHashtable_Object * me, PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
+#include "_cpy_nodetable.hh"
+#include "_cpy_counttable.hh"
+#include "_cpy_smallcounttable.hh"
+#include "_cpy_hashgraph.hh"
+#include "_cpy_smallcountgraph.hh"
- const char * filename = NULL;
+//
+// KCountgraph object
+//
- if (!PyArg_ParseTuple(args, "s", &filename)) {
- return NULL;
- }
+typedef struct {
+ khmer_KHashgraph_Object khashgraph;
+ Countgraph * countgraph;
+} khmer_KCountgraph_Object;
- try {
- hashtable->partition->save_partitionmap(filename);
- } catch (khmer_file_exception &e) {
- PyErr_SetString(PyExc_OSError, e.what());
- return NULL;
- }
+typedef struct {
+ PyObject_HEAD
+ ReadAligner * aligner;
+} khmer_ReadAligner_Object;
- Py_RETURN_NONE;
-}
+static void khmer_countgraph_dealloc(khmer_KCountgraph_Object * obj);
static
PyObject *
-hashtable_load_partitionmap(khmer_KHashtable_Object * me, PyObject * args)
+count_get_raw_tables(khmer_KCountgraph_Object * self, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ Countgraph * countgraph = self->countgraph;
- const char * filename = NULL;
-
- if (!PyArg_ParseTuple(args, "s", &filename)) {
- return NULL;
- }
+ khmer::Byte ** table_ptrs = countgraph->get_raw_tables();
+ std::vector<uint64_t> sizes = countgraph->get_tablesizes();
- try {
- hashtable->partition->load_partitionmap(filename);
- } catch (khmer_file_exception &e) {
- PyErr_SetString(PyExc_OSError, e.what());
- return NULL;
+ PyObject * raw_tables = PyList_New(sizes.size());
+ for (unsigned int i=0; i<sizes.size(); ++i) {
+ Py_buffer buffer;
+ int res = PyBuffer_FillInfo(&buffer, NULL, table_ptrs[i], sizes[i], 0,
+ PyBUF_FULL_RO);
+ if (res == -1) {
+ return NULL;
+ }
+ PyObject * buf = PyMemoryView_FromBuffer(&buffer);
+ if(!PyMemoryView_Check(buf)) {
+ return NULL;
+ }
+ PyList_SET_ITEM(raw_tables, i, buf);
}
- Py_RETURN_NONE;
+ return raw_tables;
}
static
PyObject *
-hashtable__validate_partitionmap(khmer_KHashtable_Object * me, PyObject * args)
+count_do_subset_partition_with_abundance(khmer_KCountgraph_Object * me,
+ PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ Countgraph * countgraph = me->countgraph;
- if (!PyArg_ParseTuple(args, "")) {
- return NULL;
+ HashIntoType start_kmer = 0, end_kmer = 0;
+ PyObject * break_on_stop_tags_o = NULL;
+ PyObject * stop_big_traversals_o = NULL;
+ BoundedCounterType min_count, max_count;
+
+ if (!PyArg_ParseTuple(args, "HH|KKOO",
+ &min_count, &max_count,
+ &start_kmer, &end_kmer,
+ &break_on_stop_tags_o,
+ &stop_big_traversals_o)) {
+ return NULL;
}
- hashtable->partition->_validate_pmap();
+ bool break_on_stop_tags = false;
+ if (break_on_stop_tags_o && PyObject_IsTrue(break_on_stop_tags_o)) {
+ break_on_stop_tags = true;
+ }
+ bool stop_big_traversals = false;
+ if (stop_big_traversals_o && PyObject_IsTrue(stop_big_traversals_o)) {
+ stop_big_traversals = true;
+ }
- Py_RETURN_NONE;
-}
+ SubsetPartition * subset_p = NULL;
+ try {
+ Py_BEGIN_ALLOW_THREADS
+ subset_p = new SubsetPartition(countgraph);
+ subset_p->do_partition_with_abundance(start_kmer, end_kmer,
+ min_count, max_count,
+ break_on_stop_tags,
+ stop_big_traversals);
+ Py_END_ALLOW_THREADS
+ } catch (std::bad_alloc &e) {
+ return PyErr_NoMemory();
+ }
-static
-PyObject *
-hashtable_count_partitions(khmer_KHashtable_Object * me, PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
+ khmer_KSubsetPartition_Object * subset_obj = (khmer_KSubsetPartition_Object *)\
+ PyObject_New(khmer_KSubsetPartition_Object, &khmer_KSubsetPartition_Type);
- if (!PyArg_ParseTuple(args, "")) {
+ if (subset_obj == NULL) {
+ delete subset_p;
return NULL;
}
- size_t n_partitions = 0, n_unassigned = 0;
- hashtable->partition->count_partitions(n_partitions, n_unassigned);
+ subset_obj->subset = subset_p;
- return Py_BuildValue("nn", (Py_ssize_t) n_partitions,
- (Py_ssize_t) n_unassigned);
+ return (PyObject *) subset_obj;
}
-static
-PyObject *
-hashtable_subset_count_partitions(khmer_KHashtable_Object * me, PyObject * args)
-{
- khmer_KSubsetPartition_Object * subset_obj = NULL;
-
- if (!PyArg_ParseTuple(args, "O!", &khmer_KSubsetPartition_Type,
- &subset_obj)) {
- return NULL;
- }
+static PyMethodDef khmer_countgraph_methods[] = {
+ {
+ "get_raw_tables",
+ (PyCFunction)count_get_raw_tables, METH_VARARGS,
+ "Get a list of the raw storage tables as memoryview objects."
+ },
+ { "do_subset_partition_with_abundance", (PyCFunction)count_do_subset_partition_with_abundance, METH_VARARGS, "" },
+ {NULL, NULL, 0, NULL} /* sentinel */
+};
+static PyObject* khmer_countgraph_new(PyTypeObject * type, PyObject * args,
+ PyObject * kwds);
- size_t n_partitions = 0, n_unassigned = 0;
- subset_obj->subset->count_partitions(n_partitions, n_unassigned);
+static PyTypeObject khmer_KCountgraph_Type
+CPYCHECKER_TYPE_OBJECT_FOR_TYPEDEF("khmer_KCountgraph_Object")
+= {
+ PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
+ "_khmer.Countgraph", /*tp_name*/
+ sizeof(khmer_KCountgraph_Object), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ (destructor)khmer_countgraph_dealloc, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ 0, /*tp_compare*/
+ 0, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ 0, /*tp_as_mapping*/
+ 0, /*tp_hash */
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ 0, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ "countgraph hash object", /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+ 0, /* tp_iter */
+ 0, /* tp_iternext */
+ khmer_countgraph_methods, /* tp_methods */
+ 0, /* tp_members */
+ 0, /* tp_getset */
+ 0, /* tp_base */
+ 0, /* tp_dict */
+ 0, /* tp_descr_get */
+ 0, /* tp_descr_set */
+ 0, /* tp_dictoffset */
+ 0, /* tp_init */
+ 0, /* tp_alloc */
+ khmer_countgraph_new, /* tp_new */
+};
- return Py_BuildValue("nn", (Py_ssize_t) n_partitions,
- (Py_ssize_t) n_unassigned);
-}
+//
+// khmer_countgraph_new
+//
-static
-PyObject *
-hashtable_subset_partition_size_distribution(khmer_KHashtable_Object * me,
- PyObject * args)
+static PyObject* khmer_countgraph_new(PyTypeObject * type, PyObject * args,
+ PyObject * kwds)
{
- khmer_KSubsetPartition_Object * subset_obj = NULL;
- if (!PyArg_ParseTuple(args, "O!", &khmer_KSubsetPartition_Type,
- &subset_obj)) {
- return NULL;
- }
-
- SubsetPartition * subset_p = subset_obj->subset;
+ khmer_KCountgraph_Object * self;
- PartitionCountDistribution d;
+ self = (khmer_KCountgraph_Object *)type->tp_alloc(type, 0);
- unsigned int n_unassigned = 0;
- subset_p->partition_size_distribution(d, n_unassigned);
+ if (self != NULL) {
+ WordLength k = 0;
+ PyListObject * sizes_list_o = NULL;
- PyObject * x = PyList_New(d.size());
- if (x == NULL) {
- return NULL;
- }
- PartitionCountDistribution::iterator di;
+ if (!PyArg_ParseTuple(args, "bO!", &k, &PyList_Type, &sizes_list_o)) {
+ Py_DECREF(self);
+ return NULL;
+ }
- unsigned int i;
- for (i = 0, di = d.begin(); di != d.end(); ++di, i++) {
- PyObject * value = Py_BuildValue("KK", di->first, di->second);
- if (value == NULL) {
- Py_DECREF(x);
+ std::vector<uint64_t> sizes;
+ if (!convert_Pytablesizes_to_vector(sizes_list_o, sizes)) {
+ Py_DECREF(self);
return NULL;
}
- PyList_SET_ITEM(x, i, value);
- }
- if (!(i == d.size())) {
- throw khmer_exception();
- }
- PyObject * returnValue = Py_BuildValue("NI", x, n_unassigned);
- if (returnValue == NULL) {
- Py_DECREF(x);
- return NULL;
+ try {
+ self->countgraph = new Countgraph(k, sizes);
+ } catch (std::bad_alloc &e) {
+ Py_DECREF(self);
+ return PyErr_NoMemory();
+ }
+ self->khashgraph.khashtable.hashtable =
+ dynamic_cast<Hashtable*>(self->countgraph);
+ self->khashgraph.hashgraph = dynamic_cast<Hashgraph*>(self->countgraph);
}
- return returnValue;
+
+ return (PyObject *) self;
}
static
PyObject *
-hashtable_load_tagset(khmer_KHashtable_Object * me, PyObject * args)
+nodegraph_update(khmer_KNodegraph_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
-
- const char * filename = NULL;
- PyObject * clear_tags_o = NULL;
+ Nodegraph * nodegraph = me->nodegraph;
+ Nodegraph * other;
+ khmer_KNodegraph_Object * other_o;
- if (!PyArg_ParseTuple(args, "s|O", &filename, &clear_tags_o)) {
+ if (!PyArg_ParseTuple(args, "O!", &khmer_KNodegraph_Type, &other_o)) {
return NULL;
}
- bool clear_tags = true;
- if (clear_tags_o && !PyObject_IsTrue(clear_tags_o)) {
- clear_tags = false;
- }
+ other = other_o->nodegraph;
try {
- hashtable->load_tagset(filename, clear_tags);
- } catch (khmer_file_exception &e) {
- PyErr_SetString(PyExc_OSError, e.what());
+ nodegraph->update_from(*other);
+ } catch (khmer_exception &e) {
+ PyErr_SetString(PyExc_ValueError, e.what());
return NULL;
}
@@ -2055,734 +2496,683 @@ hashtable_load_tagset(khmer_KHashtable_Object * me, PyObject * args)
static
PyObject *
-hashtable_save_tagset(khmer_KHashtable_Object * me, PyObject * args)
+nodegraph_get_raw_tables(khmer_KNodegraph_Object * self, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ Nodegraph * countgraph = self->nodegraph;
- const char * filename = NULL;
+ khmer::Byte ** table_ptrs = countgraph->get_raw_tables();
+ std::vector<uint64_t> sizes = countgraph->get_tablesizes();
- if (!PyArg_ParseTuple(args, "s", &filename)) {
- return NULL;
+ PyObject * raw_tables = PyList_New(sizes.size());
+ for (unsigned int i=0; i<sizes.size(); ++i) {
+ Py_buffer buffer;
+ int res = PyBuffer_FillInfo(&buffer, NULL, table_ptrs[i], sizes[i], 0,
+ PyBUF_FULL_RO);
+ if (res == -1) {
+ return NULL;
+ }
+ PyObject * buf = PyMemoryView_FromBuffer(&buffer);
+ if(!PyMemoryView_Check(buf)) {
+ return NULL;
+ }
+ PyList_SET_ITEM(raw_tables, i, buf);
}
- try {
- hashtable->save_tagset(filename);
- } catch (khmer_file_exception &e) {
- PyErr_SetString(PyExc_OSError, e.what());
- return NULL;
- }
+ return raw_tables;
+}
- Py_RETURN_NONE;
+static PyMethodDef khmer_nodegraph_methods[] = {
+ {
+ "update",
+ (PyCFunction) nodegraph_update, METH_VARARGS,
+ "a set update: update this nodegraph with all the entries from the other"
+ },
+ {
+ "get_raw_tables",
+ (PyCFunction) nodegraph_get_raw_tables, METH_VARARGS,
+ "Get a list of the raw tables as memoryview objects"
+ },
+ {NULL, NULL, 0, NULL} /* sentinel */
+};
+
+// __new__ for nodegraph; necessary for proper subclassing
+// This will essentially do what the old factory function did. Unlike many __new__
+// methods, we take our arguments here, because there's no "uninitialized" nodegraph
+// object; we have to have k and the table sizes before creating the new objects
+static PyObject* khmer_nodegraph_new(PyTypeObject * type, PyObject * args,
+ PyObject * kwds)
+{
+ khmer_KNodegraph_Object * self;
+ self = (khmer_KNodegraph_Object *)type->tp_alloc(type, 0);
+
+ if (self != NULL) {
+ WordLength k = 0;
+ PyListObject* sizes_list_o = NULL;
+
+ if (!PyArg_ParseTuple(args, "bO!", &k, &PyList_Type, &sizes_list_o)) {
+ Py_DECREF(self);
+ return NULL;
+ }
+
+ std::vector<uint64_t> sizes;
+ if (!convert_Pytablesizes_to_vector(sizes_list_o, sizes)) {
+ Py_DECREF(self);
+ return NULL;
+ }
+
+ try {
+ self->nodegraph = new Nodegraph(k, sizes);
+ } catch (std::bad_alloc &e) {
+ Py_DECREF(self);
+ return PyErr_NoMemory();
+ }
+ self->khashgraph.khashtable.hashtable =
+ dynamic_cast<Hashtable*>(self->nodegraph);
+ self->khashgraph.hashgraph = dynamic_cast<Hashgraph*>(self->nodegraph);
+ }
+ return (PyObject *) self;
}
+////////////////////////////////////////////////////////////////////////////
+
static
PyObject *
-hashtable_save_subset_partitionmap(khmer_KHashtable_Object * me,
- PyObject * args)
+subset_count_partitions(khmer_KSubsetPartition_Object * me, PyObject * args)
{
- const char * filename = NULL;
- khmer_KSubsetPartition_Object * subset_obj = NULL;
+ SubsetPartition * subset_p = me->subset;
- if (!PyArg_ParseTuple(args, "O!s", &khmer_KSubsetPartition_Type,
- &subset_obj, &filename)) {
+ if (!PyArg_ParseTuple(args, "")) {
return NULL;
}
- SubsetPartition * subset_p = subset_obj->subset;
+ size_t n_partitions = 0, n_unassigned = 0;
+ subset_p->count_partitions(n_partitions, n_unassigned);
- Py_BEGIN_ALLOW_THREADS
+ return Py_BuildValue("nn", (Py_ssize_t) n_partitions,
+ (Py_ssize_t) n_unassigned);
+}
- try {
- subset_p->save_partitionmap(filename);
- } catch (khmer_file_exception &e) {
- PyErr_SetString(PyExc_OSError, e.what());
+static
+PyObject *
+subset_report_on_partitions(khmer_KSubsetPartition_Object * me, PyObject * args)
+{
+ SubsetPartition * subset_p = me->subset;
+
+ if (!PyArg_ParseTuple(args, "")) {
return NULL;
}
- Py_END_ALLOW_THREADS
+ subset_p->report_on_partitions();
Py_RETURN_NONE;
}
static
PyObject *
-hashtable_load_subset_partitionmap(khmer_KHashtable_Object * me,
+subset_partition_size_distribution(khmer_KSubsetPartition_Object * me,
PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
-
- const char * filename = NULL;
+ SubsetPartition * subset_p = me->subset;
- if (!PyArg_ParseTuple(args, "s", &filename)) {
+ if (!PyArg_ParseTuple(args, "")) {
return NULL;
}
- SubsetPartition * subset_p;
- try {
- subset_p = new SubsetPartition(hashtable);
- } catch (std::bad_alloc &e) {
- return PyErr_NoMemory();
- }
-
- const char *file_exception = NULL;
+ PartitionCountDistribution d;
- Py_BEGIN_ALLOW_THREADS
- try {
- subset_p->load_partitionmap(filename);
- } catch (khmer_file_exception &exc) {
- file_exception = exc.what();
- }
- Py_END_ALLOW_THREADS
+ unsigned int n_unassigned = 0;
+ subset_p->partition_size_distribution(d, n_unassigned);
- if (file_exception != NULL) {
- PyErr_SetString(PyExc_OSError, file_exception);
- delete subset_p;
+ PyObject * x = PyList_New(d.size());
+ if (x == NULL) {
return NULL;
}
+ PartitionCountDistribution::iterator di;
- khmer_KSubsetPartition_Object * subset_obj = (khmer_KSubsetPartition_Object *)\
- PyObject_New(khmer_KSubsetPartition_Object, &khmer_KSubsetPartition_Type);
-
- if (subset_obj == NULL) {
- delete subset_p;
- return NULL;
+ unsigned int i;
+ for (i = 0, di = d.begin(); di != d.end(); ++di, i++) {
+ PyObject * tup = Py_BuildValue("KK", di->first, di->second);
+ if (tup != NULL) {
+ PyList_SET_ITEM(x, i, tup);
+ }
+ Py_XDECREF(tup);
}
-
- subset_obj->subset = subset_p;
-
- return (PyObject *) subset_obj;
-}
-
-static
-PyObject *
-hashtable__set_tag_density(khmer_KHashtable_Object * me, PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
-
- unsigned int d;
- if (!PyArg_ParseTuple(args, "I", &d)) {
- return NULL;
+ if (!(i == d.size())) {
+ throw khmer_exception();
}
- hashtable->_set_tag_density(d);
-
- Py_RETURN_NONE;
+ PyObject * ret = Py_BuildValue("OI", x, n_unassigned);
+ Py_DECREF(x);
+ return ret;
}
static
PyObject *
-hashtable__get_tag_density(khmer_KHashtable_Object * me, PyObject * args)
+subset_partition_sizes(khmer_KSubsetPartition_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ SubsetPartition * subset_p = me->subset;
- if (!PyArg_ParseTuple(args, "")) {
+ unsigned int min_size = 0;
+
+ if (!PyArg_ParseTuple(args, "|I", &min_size)) {
return NULL;
}
- unsigned int d = hashtable->_get_tag_density();
-
- return PyLong_FromLong(d);
-}
+ PartitionCountMap cm;
+ unsigned int n_unassigned = 0;
+ subset_p->partition_sizes(cm, n_unassigned);
-static
-PyObject *
-hashtable__validate_subset_partitionmap(khmer_KHashtable_Object * me,
- PyObject * args)
-{
- khmer_KSubsetPartition_Object * subset_obj = NULL;
+ unsigned int i = 0;
+ PartitionCountMap::const_iterator mi;
+ for (mi = cm.begin(); mi != cm.end(); ++mi) {
+ if (mi->second >= min_size) {
+ i++;
+ }
+ }
- if (!PyArg_ParseTuple(args, "O!", &khmer_KSubsetPartition_Type,
- &subset_obj)) {
+ PyObject * x = PyList_New(i);
+ if (x == NULL) {
return NULL;
}
- SubsetPartition * subset_p = subset_obj->subset;
+ // this should probably be a dict. @CTB
+ for (i = 0, mi = cm.begin(); mi != cm.end(); ++mi) {
+ if (mi->second >= min_size) {
+ PyObject * tup = Py_BuildValue("II", mi->first, mi->second);
+ if (tup != NULL) {
+ PyList_SET_ITEM(x, i, tup);
+ }
+ i++;
+ }
+ }
- subset_p->_validate_pmap();
+ PyObject * ret = Py_BuildValue("OI", x, n_unassigned);
+ Py_DECREF(x);
- Py_RETURN_NONE;
+ return ret;
}
static
PyObject *
-hashtable_set_partition_id(khmer_KHashtable_Object * me, PyObject * args)
+subset_partition_average_coverages(khmer_KSubsetPartition_Object * me,
+ PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ SubsetPartition * subset_p = me->subset;
- const char * kmer = NULL;
- PartitionID p = 0;
+ khmer_KCountgraph_Object * countgraph_o;
- if (!PyArg_ParseTuple(args, "sI", &kmer, &p)) {
+ if (!PyArg_ParseTuple(args, "O!", &khmer_KCountgraph_Type, &countgraph_o)) {
return NULL;
}
- hashtable->partition->set_partition_id(kmer, p);
-
- Py_RETURN_NONE;
-}
-
-static
-PyObject *
-hashtable_join_partitions(khmer_KHashtable_Object * me, PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
+ PartitionCountMap cm;
+ subset_p->partition_average_coverages(cm, countgraph_o -> countgraph);
- PartitionID p1 = 0, p2 = 0;
+ unsigned int i;
+ PartitionCountMap::iterator mi;
- if (!PyArg_ParseTuple(args, "II", &p1, &p2)) {
+ PyObject * x = PyList_New(cm.size());
+ if (x == NULL) {
return NULL;
}
- p1 = hashtable->partition->join_partitions(p1, p2);
+ // this should probably be a dict. @CTB
+ for (i = 0, mi = cm.begin(); mi != cm.end(); ++mi, i++) {
+ PyObject * tup = Py_BuildValue("II", mi->first, mi->second);
+ if (tup != NULL) {
+ PyList_SET_ITEM(x, i, tup);
+ }
+ }
- return PyLong_FromLong(p1);
+ return x;
}
-static
-PyObject *
-hashtable_get_partition_id(khmer_KHashtable_Object * me, PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
+static PyMethodDef khmer_subset_methods[] = {
+ {
+ "count_partitions",
+ (PyCFunction)subset_count_partitions,
+ METH_VARARGS,
+ ""
+ },
+ {
+ "report_on_partitions",
+ (PyCFunction)subset_report_on_partitions,
+ METH_VARARGS,
+ ""
+ },
+ {
+ "partition_size_distribution",
+ (PyCFunction)subset_partition_size_distribution,
+ METH_VARARGS,
+ ""
+ },
+ {
+ "partition_sizes",
+ (PyCFunction)subset_partition_sizes,
+ METH_VARARGS,
+ ""
+ },
+ {
+ "partition_average_coverages",
+ (PyCFunction)subset_partition_average_coverages,
+ METH_VARARGS,
+ ""
+ },
+ {NULL, NULL, 0, NULL} /* sentinel */
+};
- const char * kmer = NULL;
+typedef struct {
+ PyObject_HEAD
+ LabelHash * labelhash;
+} khmer_KGraphLabels_Object;
- if (!PyArg_ParseTuple(args, "s", &kmer)) {
- return NULL;
- }
+static PyObject * khmer_graphlabels_new(PyTypeObject * type, PyObject *args,
+ PyObject *kwds);
- PartitionID partition_id;
- partition_id = hashtable->partition->get_partition_id(kmer);
+static void khmer_graphlabels_dealloc(khmer_KGraphLabels_Object * obj)
+{
+ delete obj->labelhash;
+ obj->labelhash = NULL;
- return PyLong_FromLong(partition_id);
+ Py_TYPE(obj)->tp_free((PyObject*)obj);
}
-static
-PyObject *
-hashtable_is_single_partition(khmer_KHashtable_Object * me, PyObject * args)
+static PyObject * khmer_graphlabels_new(PyTypeObject *type, PyObject *args,
+ PyObject *kwds)
{
- Hashtable * hashtable = me->hashtable;
+ khmer_KGraphLabels_Object *self;
+ self = (khmer_KGraphLabels_Object*)type->tp_alloc(type, 0);
- const char * seq = NULL;
+ if (self != NULL) {
+ PyObject * hashgraph_o;
+ khmer::Hashgraph * hashgraph = NULL; // @CTB
- if (!PyArg_ParseTuple(args, "s", &seq)) {
- return NULL;
- }
+ if (!PyArg_ParseTuple(args, "O", &hashgraph_o)) {
+ Py_DECREF(self);
+ return NULL;
+ }
- bool v = hashtable->partition->is_single_partition(seq);
+ if (PyObject_TypeCheck(hashgraph_o, &khmer_KNodegraph_Type)) {
+ khmer_KNodegraph_Object * kho = (khmer_KNodegraph_Object *) hashgraph_o;
+ hashgraph = kho->nodegraph;
+ } else if (PyObject_TypeCheck(hashgraph_o, &khmer_KCountgraph_Type)) {
+ khmer_KCountgraph_Object * cho = (khmer_KCountgraph_Object *) hashgraph_o;
+ hashgraph = cho->countgraph;
+ } else {
+ PyErr_SetString(PyExc_ValueError,
+ "graph object must be a NodeGraph or CountGraph");
+ Py_DECREF(self);
+ return NULL;
+ }
- PyObject * val;
- if (v) {
- val = Py_True;
- } else {
- val = Py_False;
+ try {
+ self->labelhash = new LabelHash(hashgraph);
+ } catch (std::bad_alloc &e) {
+ Py_DECREF(self);
+ return PyErr_NoMemory();
+ }
}
- Py_INCREF(val);
- return val;
+ return (PyObject *) self;
}
static
PyObject *
-hashtable_divide_tags_into_subsets(khmer_KHashtable_Object * me,
- PyObject * args)
+labelhash_get_all_labels(khmer_KGraphLabels_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
-
- unsigned int subset_size = 0;
+ LabelHash * hb = me->labelhash;
- if (!PyArg_ParseTuple(args, "I", &subset_size)) {
+ PyObject * d = PyList_New(hb->all_labels.size());
+ if (d == NULL) {
return NULL;
}
+ LabelSet::iterator it;
- SeenSet divvy;
- hashtable->divide_tags_into_subsets(subset_size, divvy);
-
- PyObject * x = PyList_New(divvy.size());
- unsigned int i = 0;
- for (SeenSet::const_iterator si = divvy.begin(); si != divvy.end();
- ++si, i++) {
- PyList_SET_ITEM(x, i, PyLong_FromUnsignedLongLong(*si));
+ unsigned long long i = 0;
+ for (it = hb->all_labels.begin(); it != hb->all_labels.end(); ++it) {
+ PyObject * val = Py_BuildValue("K", *it);
+ if (val != NULL) {
+ PyList_SetItem(d, i, val);
+ }
+ i++;
}
- return x;
+ return d;
}
static
PyObject *
-hashtable_count_kmers_within_radius(khmer_KHashtable_Object * me,
- PyObject * args)
+labelhash_consume_seqfile_and_tag_with_labels(khmer_KGraphLabels_Object * me,
+ PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ LabelHash * hb = me->labelhash;
- const char * kmer = NULL;
- unsigned int radius = 0;
- unsigned int max_count = 0;
+ const char * filename;
- if (!PyArg_ParseTuple(args, "sI|I", &kmer, &radius, &max_count)) {
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
return NULL;
}
- unsigned int n;
+ const char *value_exception = NULL;
+ const char *file_exception = NULL;
+ unsigned long long n_consumed = 0;
+ unsigned int total_reads = 0;
+ std::string exc_string;
- Py_BEGIN_ALLOW_THREADS
- Kmer start_kmer = hashtable->build_kmer(kmer);
- KmerSet seen;
- n = hashtable->traverse_from_kmer(start_kmer, radius,
- seen, max_count);
+ //Py_BEGIN_ALLOW_THREADS
+ try {
+ hb->consume_seqfile_and_tag_with_labels<FastxReader>(filename, total_reads,
+ n_consumed);
+ } catch (khmer_file_exception &exc) {
+ exc_string = exc.what();
+ file_exception = exc_string.c_str();
+ } catch (khmer_value_exception &exc) {
+ exc_string = exc.what();
+ value_exception = exc_string.c_str();
+ }
+ //Py_END_ALLOW_THREADS
- Py_END_ALLOW_THREADS
+ if (file_exception != NULL) {
+ PyErr_SetString(PyExc_OSError, file_exception);
+ return NULL;
+ }
+ if (value_exception != NULL) {
+ PyErr_SetString(PyExc_ValueError, value_exception);
+ return NULL;
+ }
- return PyLong_FromUnsignedLong(n);
+ return Py_BuildValue("IK", total_reads, n_consumed);
}
static
PyObject *
-hashtable_extract_unique_paths(khmer_KHashtable_Object * me, PyObject * args)
+labelhash_consume_partitioned_fasta_and_tag_with_labels(
+ khmer_KGraphLabels_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ LabelHash * labelhash = me->labelhash;
+
+ const char * filename;
- const char * sequence = NULL;
- unsigned int min_length = 0;
- float min_unique_f = 0;
- if (!PyArg_ParseTuple(args, "sIf", &sequence, &min_length, &min_unique_f)) {
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
return NULL;
}
- std::vector<std::string> results;
- hashtable->extract_unique_paths(sequence, min_length, min_unique_f, results);
+ // call the C++ function, and trap signals => Python
- PyObject * x = PyList_New(results.size());
- if (x == NULL) {
- return NULL;
- }
+ unsigned long long n_consumed = 0;
+ unsigned int total_reads = 0;
- for (unsigned int i = 0; i < results.size(); i++) {
- PyList_SET_ITEM(x, i, PyUnicode_FromString(results[i].c_str()));
+ try {
+ labelhash->consume_partitioned_fasta_and_tag_with_labels<FastxReader>(filename,
+ total_reads, n_consumed);
+ } catch (khmer_file_exception &exc) {
+ PyErr_SetString(PyExc_OSError, exc.what());
+ return NULL;
+ } catch (khmer_value_exception &exc) {
+ PyErr_SetString(PyExc_ValueError, exc.what());
+ return NULL;
}
- return x;
+ return Py_BuildValue("IK", total_reads, n_consumed);
}
-
static
PyObject *
-hashtable_get_kmers(khmer_KHashtable_Object * me, PyObject * args)
+labelhash_consume_sequence_and_tag_with_labels(khmer_KGraphLabels_Object * me,
+ PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
- const char * sequence;
-
- if (!PyArg_ParseTuple(args, "s", &sequence)) {
+ LabelHash * hb = me->labelhash;
+ const char * seq = NULL;
+ unsigned long long c = 0;
+ if (!PyArg_ParseTuple(args, "sK", &seq, &c)) {
return NULL;
}
+ unsigned long long n_consumed = 0;
- std::vector<std::string> kmers;
-
- hashtable->get_kmers(sequence, kmers);
-
- PyObject * x = PyList_New(kmers.size());
- for (unsigned int i = 0; i < kmers.size(); i++) {
- PyObject * obj = PyUnicode_FromString(kmers[i].c_str());
- PyList_SET_ITEM(x, i, obj);
- }
-
- return x;
-}
+ hb->consume_sequence_and_tag_with_labels(seq, n_consumed, c);
+ return Py_BuildValue("K", n_consumed);
+}
static
PyObject *
-hashtable_get_kmer_counts(khmer_KHashtable_Object * me, PyObject * args)
+labelhash_sweep_label_neighborhood(khmer_KGraphLabels_Object * me,
+ PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
- const char * sequence;
+ LabelHash * hb = me->labelhash;
- if (!PyArg_ParseTuple(args, "s", &sequence)) {
+ const char * seq = NULL;
+ int r = 0;
+ PyObject * break_on_stop_tags_o = NULL;
+ PyObject * stop_big_traversals_o = NULL;
+
+ if (!PyArg_ParseTuple(args, "s|iOO", &seq, &r,
+ &break_on_stop_tags_o,
+ &stop_big_traversals_o)) {
return NULL;
}
- std::vector<BoundedCounterType> counts;
- hashtable->get_kmer_counts(sequence, counts);
-
- PyObject * x = PyList_New(counts.size());
- for (unsigned int i = 0; i <counts.size(); i++) {
- PyObject * obj = PyInt_FromLong(counts[i]);
- PyList_SET_ITEM(x, i, obj);
+ unsigned int range = (2 * hb->graph->_get_tag_density()) + 1;
+ if (r >= 0) {
+ range = r;
}
- return x;
-}
-
-
-static
-PyObject *
-hashtable_get_kmer_hashes(khmer_KHashtable_Object * me, PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
- const char * sequence;
+ bool break_on_stop_tags = false;
+ if (break_on_stop_tags_o && PyObject_IsTrue(break_on_stop_tags_o)) {
+ break_on_stop_tags = true;
+ }
+ bool stop_big_traversals = false;
+ if (stop_big_traversals_o && PyObject_IsTrue(stop_big_traversals_o)) {
+ stop_big_traversals = true;
+ }
- if (!PyArg_ParseTuple(args, "s", &sequence)) {
+ if (strlen(seq) < hb->graph->ksize()) {
+ PyErr_SetString(PyExc_ValueError,
+ "string length must >= the hashtable k-mer size");
return NULL;
}
- std::vector<HashIntoType> hashes;
- hashtable->get_kmer_hashes(sequence, hashes);
+ //std::pair<TagLabelPair::iterator, TagLabelPair::iterator> ret;
+ LabelSet found_labels;
- PyObject * x = PyList_New(hashes.size());
- for (unsigned int i = 0; i < hashes.size(); i++) {
- PyObject * obj = PyLong_FromUnsignedLongLong(hashes[i]);
- PyList_SET_ITEM(x, i, obj);
+ //unsigned int num_traversed = 0;
+ //Py_BEGIN_ALLOW_THREADS
+ hb->sweep_label_neighborhood(seq, found_labels, range, break_on_stop_tags,
+ stop_big_traversals);
+ //Py_END_ALLOW_THREADS
+
+ //printf("...%u kmers traversed\n", num_traversed);
+
+ PyObject * x = PyList_New(found_labels.size());
+ LabelSet::const_iterator si;
+ unsigned long long i = 0;
+ for (si = found_labels.begin(); si != found_labels.end(); ++si) {
+ PyList_SET_ITEM(x, i, Py_BuildValue("K", *si));
+ i++;
}
return x;
}
+// Similar to find_all_tags, but returns tags in a way actually usable by python
+// need a tags_in_sequence iterator or function in c++ land for reuse in all
+// these functions
-static PyMethodDef khmer_hashtable_methods[] = {
- //
- // Basic methods
- //
-
- {
- "ksize",
- (PyCFunction)hashtable_get_ksize, METH_VARARGS,
- "Returns the k-mer size of this graph."
- },
- { "hashsizes", (PyCFunction)hashtable_get_hashsizes, METH_VARARGS, "" },
- {
- "n_unique_kmers",
- (PyCFunction)hashtable_n_unique_kmers, METH_VARARGS,
- "Count the number of unique kmers in this graph."
- },
- {
- "n_occupied", (PyCFunction)hashtable_n_occupied, METH_VARARGS,
- "Count the number of occupied bins."
- },
- {
- "count",
- (PyCFunction)hashtable_count, METH_VARARGS,
- "Increment the count of this k-mer."
- },
- {
- "consume",
- (PyCFunction)hashtable_consume, METH_VARARGS,
- "Increment the counts of all of the k-mers in the string."
- },
- {
- "consume_fasta",
- (PyCFunction)hashtable_consume_fasta, METH_VARARGS,
- "Incrment the counts of all the k-mers in the sequences in the "
- "given file"
- },
- {
- "consume_fasta_with_reads_parser",
- (PyCFunction)hashtable_consume_fasta_with_reads_parser, METH_VARARGS,
- "Count all k-mers retrieved with this reads parser object."
- },
- {
- "get",
- (PyCFunction)hashtable_get, METH_VARARGS,
- "Retrieve the count for the given k-mer."
- },
- {
- "load",
- (PyCFunction)hashtable_load, METH_VARARGS,
- "Load the graph from the specified file."
- },
- {
- "save",
- (PyCFunction)hashtable_save, METH_VARARGS,
- "Save the graph to the specified file."
- },
- {
- "get_median_count",
- (PyCFunction)hashtable_get_median_count, METH_VARARGS,
- "Get the median, average, and stddev of the k-mer counts "
- " in the string"
- },
- {
- "get_kmers",
- (PyCFunction)hashtable_get_kmers, METH_VARARGS,
- "Generate an ordered list of all substrings of length k in the string."
- },
- {
- "get_kmer_hashes",
- (PyCFunction)hashtable_get_kmer_hashes, METH_VARARGS,
- "Retrieve an ordered list of all hashes of all k-mers in the string."
- },
- {
- "get_kmer_counts",
- (PyCFunction)hashtable_get_kmer_counts, METH_VARARGS,
- "Retrieve an ordered list of the counts of all k-mers in the string."
- },
-
- //
- // graph/traversal functionality
- //
+static
+PyObject *
+labelhash_sweep_tag_neighborhood(khmer_KGraphLabels_Object * me,
+ PyObject * args)
+{
+ LabelHash * labelhash = me->labelhash;
- {
- "calc_connected_graph_size",
- (PyCFunction)hashtable_calc_connected_graph_size, METH_VARARGS, ""
- },
- {
- "kmer_degree",
- (PyCFunction)hashtable_kmer_degree, METH_VARARGS,
- "Calculate the number of immediate neighbors this k-mer has in "
- "the graph."
- },
- {
- "count_kmers_within_radius",
- (PyCFunction)hashtable_count_kmers_within_radius, METH_VARARGS,
- "Calculate the number of neighbors with given radius in the graph."
- },
+ const char * seq = NULL;
+ int r = 0;
+ PyObject * break_on_stop_tags_o = NULL;
+ PyObject * stop_big_traversals_o = NULL;
- //
- // tagging / sparse graph functionality
- //
+ if (!PyArg_ParseTuple(args, "s|iOO", &seq, &r,
+ &break_on_stop_tags_o,
+ &stop_big_traversals_o)) {
+ return NULL;
+ }
- { "consume_and_tag", (PyCFunction)hashtable_consume_and_tag, METH_VARARGS, "Consume a sequence and tag it" },
- { "get_tags_and_positions", (PyCFunction)hashtable_get_tags_and_positions, METH_VARARGS, "Retrieve tags and their positions in a sequence." },
- { "find_all_tags_list", (PyCFunction)hashtable_find_all_tags_list, METH_VARARGS, "Find all tags within range of the given k-mer, return as list" },
- { "consume_fasta_and_tag", (PyCFunction)hashtable_consume_fasta_and_tag, METH_VARARGS, "Count all k-mers in a given file" },
- { "get_median_count", (PyCFunction)hashtable_get_median_count, METH_VARARGS, "Get the median, average, and stddev of the k-mer counts in the string" },
- { "median_at_least", (PyCFunction)hashtable_median_at_least, METH_VARARGS, "Return true if the median is at least the given cutoff" },
- { "extract_unique_paths", (PyCFunction)hashtable_extract_unique_paths, METH_VARARGS, "" },
- { "print_tagset", (PyCFunction)hashtable_print_tagset, METH_VARARGS, "" },
- { "add_tag", (PyCFunction)hashtable_add_tag, METH_VARARGS, "" },
- { "get_tagset", (PyCFunction)hashtable_get_tagset, METH_VARARGS, "" },
- { "load_tagset", (PyCFunction)hashtable_load_tagset, METH_VARARGS, "" },
- { "save_tagset", (PyCFunction)hashtable_save_tagset, METH_VARARGS, "" },
- { "n_tags", (PyCFunction)hashtable_n_tags, METH_VARARGS, "" },
- { "divide_tags_into_subsets", (PyCFunction)hashtable_divide_tags_into_subsets, METH_VARARGS, "" },
- { "_get_tag_density", (PyCFunction)hashtable__get_tag_density, METH_VARARGS, "" },
- { "_set_tag_density", (PyCFunction)hashtable__set_tag_density, METH_VARARGS, "" },
-
- // partitioning
- { "do_subset_partition", (PyCFunction)hashtable_do_subset_partition, METH_VARARGS, "" },
- { "find_all_tags", (PyCFunction)hashtable_find_all_tags, METH_VARARGS, "" },
- { "assign_partition_id", (PyCFunction)hashtable_assign_partition_id, METH_VARARGS, "" },
- { "output_partitions", (PyCFunction)hashtable_output_partitions, METH_VARARGS, "" },
- { "find_unpart", (PyCFunction)hashtable_find_unpart, METH_VARARGS, "" },
- { "load_partitionmap", (PyCFunction)hashtable_load_partitionmap, METH_VARARGS, "" },
- { "save_partitionmap", (PyCFunction)hashtable_save_partitionmap, METH_VARARGS, "" },
- { "_validate_partitionmap", (PyCFunction)hashtable__validate_partitionmap, METH_VARARGS, "" },
- { "consume_fasta_and_traverse", (PyCFunction)hashtable_consume_fasta_and_traverse, METH_VARARGS, "" },
- {
- "consume_fasta_and_tag_with_reads_parser", (PyCFunction)hashtable_consume_fasta_and_tag_with_reads_parser,
- METH_VARARGS, "Count all k-mers using a given reads parser"
- },
- { "consume_partitioned_fasta", (PyCFunction)hashtable_consume_partitioned_fasta, METH_VARARGS, "Count all k-mers in a given file" },
- { "join_partitions_by_path", (PyCFunction)hashtable_join_partitions_by_path, METH_VARARGS, "" },
- { "merge_subset", (PyCFunction)hashtable_merge_subset, METH_VARARGS, "" },
- { "merge_subset_from_disk", (PyCFunction)hashtable_merge_from_disk, METH_VARARGS, "" },
- { "count_partitions", (PyCFunction)hashtable_count_partitions, METH_VARARGS, "" },
- { "subset_count_partitions", (PyCFunction)hashtable_subset_count_partitions, METH_VARARGS, "" },
- { "subset_partition_size_distribution", (PyCFunction)hashtable_subset_partition_size_distribution, METH_VARARGS, "" },
- { "save_subset_partitionmap", (PyCFunction)hashtable_save_subset_partitionmap, METH_VARARGS },
- { "load_subset_partitionmap", (PyCFunction)hashtable_load_subset_partitionmap, METH_VARARGS },
- { "_validate_subset_partitionmap", (PyCFunction)hashtable__validate_subset_partitionmap, METH_VARARGS, "" },
- { "set_partition_id", (PyCFunction)hashtable_set_partition_id, METH_VARARGS, "" },
- { "join_partitions", (PyCFunction)hashtable_join_partitions, METH_VARARGS, "" },
- { "get_partition_id", (PyCFunction)hashtable_get_partition_id, METH_VARARGS, "" },
- { "is_single_partition", (PyCFunction)hashtable_is_single_partition, METH_VARARGS, "" },
- { "traverse_from_tags", (PyCFunction)hashtable_traverse_from_tags, METH_VARARGS, "" },
- { "repartition_largest_partition", (PyCFunction)hashtable_repartition_largest_partition, METH_VARARGS, "" },
-
- // stop tags
- { "load_stop_tags", (PyCFunction)hashtable_load_stop_tags, METH_VARARGS, "" },
- { "save_stop_tags", (PyCFunction)hashtable_save_stop_tags, METH_VARARGS, "" },
- { "print_stop_tags", (PyCFunction)hashtable_print_stop_tags, METH_VARARGS, "" },
- { "trim_on_stoptags", (PyCFunction)hashtable_trim_on_stoptags, METH_VARARGS, "" },
- { "identify_stoptags_by_position", (PyCFunction)hashtable_identify_stoptags_by_position, METH_VARARGS, "" },
- { "filter_if_present", (PyCFunction)hashtable_filter_if_present, METH_VARARGS, "" },
- { "add_stop_tag", (PyCFunction)hashtable_add_stop_tag, METH_VARARGS, "" },
- { "get_stop_tags", (PyCFunction)hashtable_get_stop_tags, METH_VARARGS, "" },
- { "consume_fasta_and_tag_with_stoptags", (PyCFunction)hashtable_consume_fasta_and_tag_with_stoptags, METH_VARARGS, "Count all k-mers in a given file" },
+ unsigned int range = (2 * labelhash->graph->_get_tag_density()) + 1;
+ if (r >= 0) {
+ range = r;
+ }
- {NULL, NULL, 0, NULL} /* sentinel */
-};
+ bool break_on_stop_tags = false;
+ if (break_on_stop_tags_o && PyObject_IsTrue(break_on_stop_tags_o)) {
+ break_on_stop_tags = true;
+ }
+ bool stop_big_traversals = false;
+ if (stop_big_traversals_o && PyObject_IsTrue(stop_big_traversals_o)) {
+ stop_big_traversals = true;
+ }
-static PyTypeObject khmer_KHashtable_Type
-CPYCHECKER_TYPE_OBJECT_FOR_TYPEDEF("khmer_KHashtable_Object")
-= {
- PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
- "_khmer.KHashtable ", /*tp_name*/
- sizeof(khmer_KHashtable_Object) , /*tp_basicsize*/
- 0, /*tp_itemsize*/
- 0, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- 0, /*tp_compare*/
- 0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
- 0, /*tp_hash */
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT, /*tp_flags*/
- "base hashtable object", /* tp_doc */
- 0, /* tp_traverse */
- 0, /* tp_clear */
- 0, /* tp_richcompare */
- 0, /* tp_weaklistoffset */
- 0, /* tp_iter */
- 0, /* tp_iternext */
- khmer_hashtable_methods, /* tp_methods */
- 0, /* tp_members */
- 0, /* tp_getset */
- 0, /* tp_base */
- 0, /* tp_dict */
- 0, /* tp_descr_get */
- 0, /* tp_descr_set */
- 0, /* tp_dictoffset */
- 0, /* tp_init */
- 0, /* tp_alloc */
- 0, /* tp_new */
-};
+ if (strlen(seq) < labelhash->graph->ksize()) {
+ PyErr_SetString(PyExc_ValueError,
+ "string length must >= the hashtable k-mer size");
+ return NULL;
+ }
-#define is_hashtable_obj(v) (Py_TYPE(v) == &khmer_KHashtable_Type)
+ SeenSet * tagged_kmers = new SeenSet;
-//
-// KCountingHash object
-//
+ //Py_BEGIN_ALLOW_THREADS
-typedef struct {
- khmer_KHashtable_Object khashtable;
- CountingHash * counting;
-} khmer_KCountingHash_Object;
+ labelhash->graph->partition->sweep_for_tags(seq, *tagged_kmers,
+ labelhash->graph->all_tags,
+ range, break_on_stop_tags,
+ stop_big_traversals);
-typedef struct {
- PyObject_HEAD
- ReadAligner * aligner;
-} khmer_ReadAligner_Object;
+ //Py_END_ALLOW_THREADS
-static void khmer_counting_dealloc(khmer_KCountingHash_Object * obj);
+ PyObject * x = (PyObject *) create_HashSet_Object(tagged_kmers,
+ labelhash->graph->ksize());
+ return x;
+}
static
PyObject *
-count_trim_on_abundance(khmer_KCountingHash_Object * me, PyObject * args)
+labelhash_get_tag_labels(khmer_KGraphLabels_Object * me, PyObject * args)
{
- CountingHash * counting = me->counting;
+ LabelHash * labelhash = me->labelhash;
- const char * seq = NULL;
- unsigned int min_count_i = 0;
+ PyObject * tag_o;
+ HashIntoType tag;
- if (!PyArg_ParseTuple(args, "sI", &seq, &min_count_i)) {
+ if (!PyArg_ParseTuple(args, "O", &tag_o)) {
+ return NULL;
+ }
+ if (!ht_convert_PyObject_to_HashIntoType(tag_o, tag,
+ labelhash->graph)) {
return NULL;
}
- unsigned long trim_at;
- Py_BEGIN_ALLOW_THREADS
+ LabelSet labels;
+ labelhash->get_tag_labels(tag, labels);
- BoundedCounterType min_count = min_count_i;
+ PyObject * x = PyList_New(labels.size());
+ LabelSet::const_iterator si;
+ unsigned long long i = 0;
+ for (si = labels.begin(); si != labels.end(); ++si) {
+ PyList_SET_ITEM(x, i, Py_BuildValue("K", *si));
+ i++;
+ }
- trim_at = counting->trim_on_abundance(seq, min_count);
+ return x;
+}
- Py_END_ALLOW_THREADS;
+static
+PyObject *
+labelhash_n_labels(khmer_KGraphLabels_Object * me, PyObject * args)
+{
+ LabelHash * labelhash = me->labelhash;
- PyObject * trim_seq = PyUnicode_FromStringAndSize(seq, trim_at);
- if (trim_seq == NULL) {
+ if (!PyArg_ParseTuple(args, "")) {
return NULL;
}
- PyObject * ret = Py_BuildValue("Ok", trim_seq, trim_at);
- Py_DECREF(trim_seq);
- return ret;
+ return PyLong_FromSize_t(labelhash->n_labels());
}
static
PyObject *
-count_trim_below_abundance(khmer_KCountingHash_Object * me, PyObject * args)
+labelhash_label_across_high_degree_nodes(khmer_KGraphLabels_Object * me,
+ PyObject * args)
{
- CountingHash * counting = me->counting;
+ LabelHash * labelhash = me->labelhash;
- const char * seq = NULL;
- BoundedCounterType max_count_i = 0;
+ const char * long_str;
+ khmer_HashSet_Object * hdn_o = NULL;
+ Label label;
- if (!PyArg_ParseTuple(args, "sH", &seq, &max_count_i)) {
+ if (!PyArg_ParseTuple(args, "sO!K", &long_str,
+ &khmer_HashSet_Type, &hdn_o, &label)) {
return NULL;
}
- unsigned long trim_at;
- Py_BEGIN_ALLOW_THREADS
-
- BoundedCounterType max_count = max_count_i;
-
- trim_at = counting->trim_below_abundance(seq, max_count);
-
- Py_END_ALLOW_THREADS;
-
- PyObject * trim_seq = PyUnicode_FromStringAndSize(seq, trim_at);
- if (trim_seq == NULL) {
- return NULL;
+ if (strlen(long_str) < labelhash->graph->ksize()) {
+ Py_INCREF(Py_None);
+ return Py_None;
}
- PyObject * ret = Py_BuildValue("Ok", trim_seq, trim_at);
- Py_DECREF(trim_seq);
- return ret;
+ labelhash->label_across_high_degree_nodes(long_str, *hdn_o->hashes, label);
+
+ Py_INCREF(Py_None);
+ return Py_None;
}
static
PyObject *
-count_find_spectral_error_positions(khmer_KCountingHash_Object * me,
- PyObject * args)
+labelhash_assemble_labeled_path(khmer_KGraphLabels_Object * me,
+ PyObject * args)
{
- khmer::CountingHash * counting = me->counting;
+ LabelHash* labelhash = me->labelhash;
- const char * seq = NULL;
- khmer::BoundedCounterType max_count = 0; // unsigned short int
+ PyObject * val_o;
+ khmer_KNodegraph_Object * nodegraph_o = NULL;
+ Nodegraph * stop_bf = NULL;
- if (!PyArg_ParseTuple(args, "sH", &seq, &max_count)) {
+ if (!PyArg_ParseTuple(args, "O|O!", &val_o,
+ &khmer_KNodegraph_Type, &nodegraph_o)) {
return NULL;
}
- std::vector<unsigned int> posns;
-
- try {
- posns = counting->find_spectral_error_positions(seq, max_count);
- } catch (khmer_exception &e) {
- PyErr_SetString(PyExc_ValueError, e.what());
+ Kmer start_kmer;
+ if (!ht_convert_PyObject_to_Kmer(val_o, start_kmer, labelhash->graph)) {
return NULL;
}
- Py_ssize_t posns_size = posns.size();
-
- PyObject * x = PyList_New(posns_size);
- if (x == NULL) {
- return NULL;
+ if (nodegraph_o) {
+ stop_bf = nodegraph_o->nodegraph;
}
- for (Py_ssize_t i = 0; i < posns_size; i++) {
- PyList_SET_ITEM(x, i, PyLong_FromLong(posns[i]));
+
+ SimpleLabeledAssembler assembler(labelhash);
+ std::vector<std::string> contigs = assembler.assemble(start_kmer, stop_bf);
+
+ PyObject * ret = PyList_New(contigs.size());
+ for (unsigned int i = 0; i < contigs.size(); i++) {
+ PyList_SET_ITEM(ret, i, PyUnicode_FromString(contigs[i].c_str()));
}
- return x;
+ return ret;
}
static
PyObject *
-count_fasta_dump_kmers_by_abundance(khmer_KCountingHash_Object * me,
- PyObject * args)
+labelhash_save_labels_and_tags(khmer_KGraphLabels_Object * me, PyObject * args)
{
- CountingHash * counting = me->counting;
-
- const char * inputfile;
- int limit_by = 0;
+ const char * filename = NULL;
+ LabelHash * labelhash = me->labelhash;
- if (!PyArg_ParseTuple(args, "si", &inputfile, &limit_by)) {
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
return NULL;
}
try {
- counting->fasta_dump_kmers_by_abundance(inputfile,
- limit_by);
- } catch (khmer_file_exception &exc) {
- PyErr_SetString(PyExc_OSError, exc.what());
- return NULL;
- } catch (khmer_value_exception &exc) {
- PyErr_SetString(PyExc_ValueError, exc.what());
+ labelhash->save_labels_and_tags(filename);
+ } catch (khmer_file_exception &e) {
+ PyErr_SetString(PyExc_OSError, e.what());
return NULL;
}
@@ -2791,1948 +3181,1371 @@ count_fasta_dump_kmers_by_abundance(khmer_KCountingHash_Object * me,
static
PyObject *
-count_get_raw_tables(khmer_KCountingHash_Object * self, PyObject * args)
+labelhash_load_labels_and_tags(khmer_KGraphLabels_Object * me, PyObject * args)
{
- CountingHash * counting = self->counting;
+ const char * filename = NULL;
+ LabelHash * labelhash = me->labelhash;
- khmer::Byte ** table_ptrs = counting->get_raw_tables();
- std::vector<HashIntoType> sizes = counting->get_tablesizes();
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
+ return NULL;
+ }
- PyObject * raw_tables = PyList_New(sizes.size());
- for (unsigned int i=0; i<sizes.size(); ++i) {
- Py_buffer buffer;
- int res = PyBuffer_FillInfo(&buffer, NULL, table_ptrs[i], sizes[i], 0,
- PyBUF_FULL_RO);
- if (res == -1) {
- return NULL;
- }
- PyObject * buf = PyMemoryView_FromBuffer(&buffer);
- if(!PyMemoryView_Check(buf)) {
- return NULL;
- }
- PyList_SET_ITEM(raw_tables, i, buf);
+ try {
+ labelhash->load_labels_and_tags(filename);
+ } catch (khmer_file_exception &e) {
+ PyErr_SetString(PyExc_OSError, e.what());
+ return NULL;
}
- return raw_tables;
+ Py_RETURN_NONE;
}
+static PyMethodDef khmer_graphlabels_methods[] = {
+ { "consume_seqfile_and_tag_with_labels", (PyCFunction)labelhash_consume_seqfile_and_tag_with_labels, METH_VARARGS, "" },
+ { "sweep_label_neighborhood", (PyCFunction)labelhash_sweep_label_neighborhood, METH_VARARGS, "" },
+ {"consume_partitioned_fasta_and_tag_with_labels", (PyCFunction)labelhash_consume_partitioned_fasta_and_tag_with_labels, METH_VARARGS, "" },
+ {"sweep_tag_neighborhood", (PyCFunction)labelhash_sweep_tag_neighborhood, METH_VARARGS, "" },
+ {"get_tag_labels", (PyCFunction)labelhash_get_tag_labels, METH_VARARGS, ""},
+ {"consume_sequence_and_tag_with_labels", (PyCFunction)labelhash_consume_sequence_and_tag_with_labels, METH_VARARGS, "" },
+ {"n_labels", (PyCFunction)labelhash_n_labels, METH_VARARGS, ""},
+ {"get_all_labels", (PyCFunction)labelhash_get_all_labels, METH_VARARGS, "" },
+ {
+ "label_across_high_degree_nodes",
+ (PyCFunction)labelhash_label_across_high_degree_nodes, METH_VARARGS,
+ "Connect graph across high degree nodes using labels.",
+ },
+ {
+ "assemble_labeled_path",
+ (PyCFunction)labelhash_assemble_labeled_path, METH_VARARGS,
+ "Assemble all paths, using labels to negotiate tricky bits."
+ },
+ { "save_labels_and_tags", (PyCFunction)labelhash_save_labels_and_tags, METH_VARARGS, "" },
+ { "load_labels_and_tags", (PyCFunction)labelhash_load_labels_and_tags, METH_VARARGS, "" }, {NULL, NULL, 0, NULL} /* sentinel */
+};
+
+static PyTypeObject khmer_KGraphLabels_Type = {
+ PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
+ "_khmer.LabelHash", /* tp_name */
+ sizeof(khmer_KGraphLabels_Object), /* tp_basicsize */
+ 0, /* tp_itemsize */
+ (destructor)khmer_graphlabels_dealloc, /* tp_dealloc */
+ 0, /* tp_print */
+ 0, /* tp_getattr */
+ 0, /* tp_setattr */
+ 0, /* tp_compare */
+ 0, /* tp_repr */
+ 0, /* tp_as_number */
+ 0, /* tp_as_sequence */
+ 0, /* tp_as_mapping */
+ 0, /* tp_hash */
+ 0, /* tp_call */
+ 0, /* tp_str */
+ 0, /* tp_getattro */
+ 0, /* tp_setattro */
+ 0, /* tp_as_buffer */
+ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */
+ 0, /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+ 0, /* tp_iter */
+ 0, /* tp_iternext */
+ khmer_graphlabels_methods, /* tp_methods */
+ 0, /* tp_members */
+ 0, /* tp_getset */
+ 0, /* tp_base */
+ 0, /* tp_dict */
+ 0, /* tp_descr_get */
+ 0, /* tp_descr_set */
+ 0, /* tp_dictoffset */
+ 0, /* tp_init */
+ 0, /* tp_alloc */
+ khmer_graphlabels_new, /* tp_new */
+};
+
static
PyObject *
-count_set_use_bigcount(khmer_KCountingHash_Object * me, PyObject * args)
+hashgraph_repartition_largest_partition(khmer_KHashgraph_Object * me,
+ PyObject * args)
{
- CountingHash * counting = me->counting;
+ Hashgraph * hashgraph = me->hashgraph;
+ khmer_KCountgraph_Object * countgraph_o = NULL;
+ PyObject * subset_o = NULL;
+ SubsetPartition * subset_p;
+ unsigned int distance, threshold, frequency;
- PyObject * x;
- if (!PyArg_ParseTuple(args, "O", &x)) {
- return NULL;
- }
- int setme = PyObject_IsTrue(x);
- if (setme < 0) {
+ if (!PyArg_ParseTuple(args, "OO!III",
+ &subset_o,
+ &khmer_KCountgraph_Type, &countgraph_o,
+ &distance, &threshold, &frequency)) {
return NULL;
}
- counting->set_use_bigcount((bool)setme);
- Py_RETURN_NONE;
-}
+ if (PyObject_TypeCheck(subset_o, &khmer_KSubsetPartition_Type)) {
+ subset_p = ((khmer_KSubsetPartition_Object *) subset_o)->subset;
+ } else {
+ subset_p = hashgraph->partition;
+ }
-static
-PyObject *
-count_get_use_bigcount(khmer_KCountingHash_Object * me, PyObject * args)
-{
- CountingHash * counting = me->counting;
+ Countgraph * countgraph = countgraph_o->countgraph;
- if (!PyArg_ParseTuple(args, "")) {
+ unsigned long next_largest;
+ try {
+ next_largest = subset_p->repartition_largest_partition(distance,
+ threshold, frequency, *countgraph);
+ } catch (khmer_exception &e) {
+ PyErr_SetString(PyExc_RuntimeError, e.what());
return NULL;
}
- bool val = counting->get_use_bigcount();
-
- return PyBool_FromLong((int)val);
+ return PyLong_FromLong(next_largest);
}
-static
-PyObject *
-count_get_min_count(khmer_KCountingHash_Object * me, PyObject * args)
+static PyObject * readaligner_align(khmer_ReadAligner_Object * me,
+ PyObject * args)
{
- CountingHash * counting = me->counting;
-
- const char * long_str;
+ const char * read;
- if (!PyArg_ParseTuple(args, "s", &long_str)) {
+ if (!PyArg_ParseTuple(args, "s", &read)) {
return NULL;
}
- if (strlen(long_str) < counting->ksize()) {
+ /*if (strlen(read) < (unsigned int)aligner->ksize()) {
PyErr_SetString(PyExc_ValueError,
"string length must >= the hashtable k-mer size");
return NULL;
- }
+ }*/
- BoundedCounterType c = counting->get_min_count(long_str);
- unsigned int N = c;
+ Alignment * aln = me->aligner->Align(read);
- return PyLong_FromLong(N);
+ const char* alignment = aln->graph_alignment.c_str();
+ const char* readAlignment = aln->read_alignment.c_str();
+ PyObject * ret = Py_BuildValue("dssO", aln->score, alignment,
+ readAlignment, (aln->truncated)? Py_True : Py_False);
+ delete aln;
+
+ return ret;
}
-static
-PyObject *
-count_get_max_count(khmer_KCountingHash_Object * me, PyObject * args)
+static PyObject * readaligner_align_forward(khmer_ReadAligner_Object * me,
+ PyObject * args)
{
- CountingHash * counting = me->counting;
+ ReadAligner * aligner = me->aligner;
- const char * long_str;
+ const char * read;
- if (!PyArg_ParseTuple(args, "s", &long_str)) {
+ if (!PyArg_ParseTuple(args, "s", &read)) {
return NULL;
}
- if (strlen(long_str) < counting->ksize()) {
+ /*if (strlen(read) < (unsigned int)aligner->ksize()) {
PyErr_SetString(PyExc_ValueError,
"string length must >= the hashtable k-mer size");
return NULL;
+ }*/
+
+ Alignment * aln;
+ aln = aligner->AlignForward(read);
+
+ const char* alignment = aln->graph_alignment.c_str();
+ const char* readAlignment = aln->read_alignment.c_str();
+ PyObject * x = PyList_New(aln->covs.size());
+ for (size_t i = 0; i < aln->covs.size(); i++ ) {
+ PyList_SET_ITEM(x, i, PyLong_FromLong(aln->covs[i]));
}
- BoundedCounterType c = counting->get_max_count(long_str);
- unsigned int N = c;
+ PyObject * ret = Py_BuildValue("dssOO", aln->score, alignment,
+ readAlignment,
+ (aln->truncated)? Py_True : Py_False,
+ x);
+ delete aln;
+ Py_DECREF(x);
- return PyLong_FromLong(N);
+ return ret;
}
-static
-PyObject *
-count_output_fasta_kmer_pos_freq(khmer_KCountingHash_Object * me,
- PyObject * args)
+static PyObject* khmer_ReadAligner_get_scoring_matrix(
+ khmer_ReadAligner_Object * me, PyObject * args)
{
- CountingHash * counting = me->counting;
- const char * infile;
- const char * outfile;
-
- if (!PyArg_ParseTuple(args, "ss", &infile, &outfile)) {
+ if (!PyArg_ParseTuple(args, "")) {
return NULL;
}
+ ScoringMatrix matrix = me->aligner->getScoringMatrix();
- counting->output_fasta_kmer_pos_freq(infile, outfile);
-
- return PyLong_FromLong(0);
+ return Py_BuildValue( "dddd", matrix.trusted_match, matrix.trusted_mismatch,
+ matrix.untrusted_match, matrix.untrusted_mismatch);
}
-static
-PyObject *
-count_fasta_count_kmers_by_position(khmer_KCountingHash_Object * me,
- PyObject * args)
+static PyObject* khmer_ReadAligner_get_transition_probabilities(
+ khmer_ReadAligner_Object * me, PyObject * args)
{
- CountingHash * counting = me->counting;
-
- const char * inputfile;
- unsigned int max_read_len = 0;
- long max_read_len_long;
- int limit_by_count_int;
-
- if (!PyArg_ParseTuple(args, "sli", &inputfile, &max_read_len_long,
- &limit_by_count_int)) {
- return NULL;
- }
- if (max_read_len_long < 0 || max_read_len_long >= pow(2, 32)) {
- PyErr_SetString(
- PyExc_ValueError,
- "The 2nd argument must be positive and less than 2^32");
- return NULL;
- }
- if (limit_by_count_int < 0 || limit_by_count_int >= pow(2, 16)) {
- PyErr_SetString(
- PyExc_ValueError,
- "The 3rd argument must be positive and less than 2^16");
- return NULL;
- }
- max_read_len = (unsigned int) max_read_len_long;
-
- unsigned long long * counts;
- try {
- counts = counting->fasta_count_kmers_by_position(inputfile,
- max_read_len,
- (unsigned short) limit_by_count_int);
- } catch (khmer_file_exception &exc) {
- PyErr_SetString(PyExc_OSError, exc.what());
- return NULL;
- } catch (khmer_value_exception &exc) {
- PyErr_SetString(PyExc_ValueError, exc.what());
- return NULL;
- }
-
- PyObject * x = PyList_New(max_read_len);
- if (x == NULL) {
- delete[] counts;
- return NULL;
- }
-
- for (unsigned int i = 0; i < max_read_len; i++) {
- int ret = PyList_SetItem(x, i, PyLong_FromUnsignedLongLong(counts[i]));
- if (ret < 0) {
- delete[] counts;
- return NULL;
- }
- }
-
- delete[] counts;
-
- return x;
-}
-
-static
-PyObject *
-count_abundance_distribution_with_reads_parser(khmer_KCountingHash_Object * me,
- PyObject * args)
-{
- CountingHash * counting = me->counting;
-
- khmer :: python :: khmer_ReadParser_Object * rparser_obj = NULL;
- khmer_KHashbits_Object *tracking_obj = NULL;
-
- if (!PyArg_ParseTuple(args, "O!O!", &python::khmer_ReadParser_Type,
- &rparser_obj, &khmer_KNodegraph_Type, &tracking_obj)) {
- return NULL;
- }
-
- read_parsers::IParser *rparser = rparser_obj->parser;
- Hashbits *hashbits = tracking_obj->hashbits;
- HashIntoType *dist = NULL;
- const char *value_exception = NULL;
- const char *file_exception = NULL;
-
- Py_BEGIN_ALLOW_THREADS
- try {
- dist = counting->abundance_distribution(rparser, hashbits);
- } catch (khmer_file_exception &exc) {
- file_exception = exc.what();
- } catch (khmer_value_exception &exc) {
- value_exception = exc.what();
- }
- Py_END_ALLOW_THREADS
-
- if (file_exception != NULL) {
- PyErr_SetString(PyExc_OSError, file_exception);
- return NULL;
- }
- if (value_exception != NULL) {
- PyErr_SetString(PyExc_ValueError, value_exception);
- return NULL;
- }
-
- PyObject * x = PyList_New(MAX_BIGCOUNT + 1);
- if (x == NULL) {
- delete[] dist;
- return NULL;
- }
- for (int i = 0; i < MAX_BIGCOUNT + 1; i++) {
- PyList_SET_ITEM(x, i, PyLong_FromUnsignedLongLong(dist[i]));
- }
-
- delete[] dist;
- return x;
-}
-
-static
-PyObject *
-count_abundance_distribution(khmer_KCountingHash_Object * me, PyObject * args)
-{
- CountingHash * counting = me->counting;
-
- const char * filename = NULL;
- khmer_KHashbits_Object * tracking_obj = NULL;
- if (!PyArg_ParseTuple(args, "sO!", &filename, &khmer_KNodegraph_Type,
- &tracking_obj)) {
- return NULL;
- }
-
- Hashbits *hashbits = tracking_obj->hashbits;
- HashIntoType *dist = NULL;
- const char *value_exception = NULL;
- const char *file_exception = NULL;
- Py_BEGIN_ALLOW_THREADS
- try {
- dist = counting->abundance_distribution(filename, hashbits);
- } catch (khmer_file_exception &exc) {
- file_exception = exc.what();
- } catch (khmer_value_exception &exc) {
- value_exception = exc.what();
- }
- Py_END_ALLOW_THREADS
-
- if (file_exception != NULL) {
- PyErr_SetString(PyExc_OSError, file_exception);
- if (dist != NULL) {
- delete []dist;
- }
- return NULL;
- }
- if (value_exception != NULL) {
- PyErr_SetString(PyExc_ValueError, value_exception);
- if (dist != NULL) {
- delete []dist;
- }
- return NULL;
- }
-
- PyObject * x = PyList_New(MAX_BIGCOUNT + 1);
- if (x == NULL) {
- if (dist != NULL) {
- delete []dist;
- }
- return NULL;
- }
- for (int i = 0; i < MAX_BIGCOUNT + 1; i++) {
- PyList_SET_ITEM(x, i, PyLong_FromUnsignedLongLong(dist[i]));
- }
-
- if (dist != NULL) {
- delete []dist;
- }
-
- return x;
-}
-
-static
-PyObject *
-count_do_subset_partition_with_abundance(khmer_KCountingHash_Object * me,
- PyObject * args)
-{
- CountingHash * counting = me->counting;
-
- HashIntoType start_kmer = 0, end_kmer = 0;
- PyObject * break_on_stop_tags_o = NULL;
- PyObject * stop_big_traversals_o = NULL;
- BoundedCounterType min_count, max_count;
-
- if (!PyArg_ParseTuple(args, "HH|KKOO",
- &min_count, &max_count,
- &start_kmer, &end_kmer,
- &break_on_stop_tags_o,
- &stop_big_traversals_o)) {
- return NULL;
- }
-
- bool break_on_stop_tags = false;
- if (break_on_stop_tags_o && PyObject_IsTrue(break_on_stop_tags_o)) {
- break_on_stop_tags = true;
- }
- bool stop_big_traversals = false;
- if (stop_big_traversals_o && PyObject_IsTrue(stop_big_traversals_o)) {
- stop_big_traversals = true;
- }
-
- SubsetPartition * subset_p = NULL;
- try {
- Py_BEGIN_ALLOW_THREADS
- subset_p = new SubsetPartition(counting);
- subset_p->do_partition_with_abundance(start_kmer, end_kmer,
- min_count, max_count,
- break_on_stop_tags,
- stop_big_traversals);
- Py_END_ALLOW_THREADS
- } catch (std::bad_alloc &e) {
- return PyErr_NoMemory();
- }
-
- khmer_KSubsetPartition_Object * subset_obj = (khmer_KSubsetPartition_Object *)\
- PyObject_New(khmer_KSubsetPartition_Object, &khmer_KSubsetPartition_Type);
-
- if (subset_obj == NULL) {
- delete subset_p;
- return NULL;
- }
-
- subset_obj->subset = subset_p;
-
- return (PyObject *) subset_obj;
-}
-
-static PyMethodDef khmer_counting_methods[] = {
- { "set_use_bigcount", (PyCFunction)count_set_use_bigcount, METH_VARARGS, "" },
- { "get_use_bigcount", (PyCFunction)count_get_use_bigcount, METH_VARARGS, "" },
- { "output_fasta_kmer_pos_freq", (PyCFunction)count_output_fasta_kmer_pos_freq, METH_VARARGS, "" },
- { "get_min_count", (PyCFunction)count_get_min_count, METH_VARARGS, "Get the smallest count of all the k-mers in the string" },
- { "get_max_count", (PyCFunction)count_get_max_count, METH_VARARGS, "Get the largest count of all the k-mers in the string" },
- { "trim_on_abundance", (PyCFunction)count_trim_on_abundance, METH_VARARGS, "Trim on >= abundance" },
- { "trim_below_abundance", (PyCFunction)count_trim_below_abundance, METH_VARARGS, "Trim on >= abundance" },
- { "find_spectral_error_positions", (PyCFunction)count_find_spectral_error_positions, METH_VARARGS, "Identify positions of low-abundance k-mers" },
- { "abundance_distribution", (PyCFunction)count_abundance_distribution, METH_VARARGS, "" },
- { "abundance_distribution_with_reads_parser", (PyCFunction)count_abundance_distribution_with_reads_parser, METH_VARARGS, "" },
- { "fasta_count_kmers_by_position", (PyCFunction)count_fasta_count_kmers_by_position, METH_VARARGS, "" },
- { "fasta_dump_kmers_by_abundance", (PyCFunction)count_fasta_dump_kmers_by_abundance, METH_VARARGS, "" },
- {
- "get_raw_tables", (PyCFunction)count_get_raw_tables,
- METH_VARARGS, "Get a list of the raw tables as memoryview objects"
- },
- { "do_subset_partition_with_abundance", (PyCFunction)count_do_subset_partition_with_abundance, METH_VARARGS, "" },
- {NULL, NULL, 0, NULL} /* sentinel */
-};
-
-static PyObject* _new_counting_hash(PyTypeObject * type, PyObject * args,
- PyObject * kwds);
-
-static PyTypeObject khmer_KCountgraph_Type
-CPYCHECKER_TYPE_OBJECT_FOR_TYPEDEF("khmer_KCountingHash_Object")
-= {
- PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
- "_khmer.Countgraph", /*tp_name*/
- sizeof(khmer_KCountingHash_Object), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- (destructor)khmer_counting_dealloc, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- 0, /*tp_compare*/
- 0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
- 0, /*tp_hash */
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/
- "counting hash object", /* tp_doc */
- 0, /* tp_traverse */
- 0, /* tp_clear */
- 0, /* tp_richcompare */
- 0, /* tp_weaklistoffset */
- 0, /* tp_iter */
- 0, /* tp_iternext */
- khmer_counting_methods, /* tp_methods */
- 0, /* tp_members */
- 0, /* tp_getset */
- 0, /* tp_base */
- 0, /* tp_dict */
- 0, /* tp_descr_get */
- 0, /* tp_descr_set */
- 0, /* tp_dictoffset */
- 0, /* tp_init */
- 0, /* tp_alloc */
- _new_counting_hash, /* tp_new */
-};
-
-#define is_counting_obj(v) (Py_TYPE(v) == &khmer_KCountgraph_Type)
-
-//
-// _new_counting_hash
-//
-
-static PyObject* _new_counting_hash(PyTypeObject * type, PyObject * args,
- PyObject * kwds)
-{
- khmer_KCountingHash_Object * self;
-
- self = (khmer_KCountingHash_Object *)type->tp_alloc(type, 0);
-
- if (self != NULL) {
- WordLength k = 0;
- PyListObject * sizes_list_o = NULL;
-
- if (!PyArg_ParseTuple(args, "bO!", &k, &PyList_Type, &sizes_list_o)) {
- Py_DECREF(self);
- return NULL;
- }
-
- std::vector<HashIntoType> sizes;
- Py_ssize_t sizes_list_o_length = PyList_GET_SIZE(sizes_list_o);
- if (sizes_list_o_length == -1) {
- Py_DECREF(self);
- PyErr_SetString(PyExc_ValueError, "error with hashtable primes!");
- return NULL;
- }
- for (Py_ssize_t i = 0; i < sizes_list_o_length; i++) {
- PyObject * size_o = PyList_GET_ITEM(sizes_list_o, i);
- if (PyLong_Check(size_o)) {
- sizes.push_back((HashIntoType) PyLong_AsUnsignedLongLong(size_o));
- } else if (PyInt_Check(size_o)) {
- sizes.push_back((HashIntoType) PyInt_AsLong(size_o));
- } else if (PyFloat_Check(size_o)) {
- sizes.push_back((HashIntoType) PyFloat_AS_DOUBLE(size_o));
- } else {
- Py_DECREF(self);
- PyErr_SetString(PyExc_TypeError,
- "2nd argument must be a list of ints, longs, or floats");
- return NULL;
- }
- }
-
- try {
- self->counting = new CountingHash(k, sizes);
- } catch (std::bad_alloc &e) {
- Py_DECREF(self);
- return PyErr_NoMemory();
- }
- self->khashtable.hashtable = dynamic_cast<Hashtable*>(self->counting);
- }
-
- return (PyObject *) self;
-}
-
-static
-PyObject *
-hashbits_update(khmer_KHashbits_Object * me, PyObject * args)
-{
- Hashbits * hashbits = me->hashbits;
- Hashbits * other;
- khmer_KHashbits_Object * other_o;
-
- if (!PyArg_ParseTuple(args, "O!", &khmer_KNodegraph_Type, &other_o)) {
- return NULL;
- }
-
- other = other_o->hashbits;
-
- try {
- hashbits->update_from(*other);
- } catch (khmer_exception &e) {
- PyErr_SetString(PyExc_ValueError, e.what());
- return NULL;
- }
-
- Py_RETURN_NONE;
-}
-
-static PyMethodDef khmer_hashbits_methods[] = {
- {
- "update",
- (PyCFunction) hashbits_update, METH_VARARGS,
- "a set update: update this nodegraph with all the entries from the other"
- },
- {NULL, NULL, 0, NULL} /* sentinel */
-};
-
-// __new__ for hashbits; necessary for proper subclassing
-// This will essentially do what the old factory function did. Unlike many __new__
-// methods, we take our arguments here, because there's no "uninitialized" hashbits
-// object; we have to have k and the table sizes before creating the new objects
-static PyObject* khmer_hashbits_new(PyTypeObject * type, PyObject * args,
- PyObject * kwds)
-{
- khmer_KHashbits_Object * self;
- self = (khmer_KHashbits_Object *)type->tp_alloc(type, 0);
-
- if (self != NULL) {
- WordLength k = 0;
- PyListObject* sizes_list_o = NULL;
-
- if (!PyArg_ParseTuple(args, "bO!", &k, &PyList_Type, &sizes_list_o)) {
- Py_DECREF(self);
- return NULL;
- }
-
- std::vector<HashIntoType> sizes;
- Py_ssize_t sizes_list_o_length = PyList_GET_SIZE(sizes_list_o);
- for (Py_ssize_t i = 0; i < sizes_list_o_length; i++) {
- PyObject * size_o = PyList_GET_ITEM(sizes_list_o, i);
- if (PyLong_Check(size_o)) {
- sizes.push_back((HashIntoType) PyLong_AsUnsignedLongLong(size_o));
- } else if (PyInt_Check(size_o)) {
- sizes.push_back((HashIntoType) PyInt_AsLong(size_o));
- } else if (PyFloat_Check(size_o)) {
- sizes.push_back((HashIntoType) PyFloat_AS_DOUBLE(size_o));
- } else {
- Py_DECREF(self);
- PyErr_SetString(PyExc_TypeError,
- "2nd argument must be a list of ints, longs, or floats");
- return NULL;
- }
- }
-
- try {
- self->hashbits = new Hashbits(k, sizes);
- } catch (std::bad_alloc &e) {
- Py_DECREF(self);
- return PyErr_NoMemory();
- }
- self->khashtable.hashtable = self->hashbits;
- }
- return (PyObject *) self;
-}
-
-#define is_hashbits_obj(v) (Py_TYPE(v) == &khmer_KNodegraph_Type)
-
-////////////////////////////////////////////////////////////////////////////
-
-static
-PyObject *
-subset_count_partitions(khmer_KSubsetPartition_Object * me, PyObject * args)
-{
- SubsetPartition * subset_p = me->subset;
-
- if (!PyArg_ParseTuple(args, "")) {
- return NULL;
- }
-
- size_t n_partitions = 0, n_unassigned = 0;
- subset_p->count_partitions(n_partitions, n_unassigned);
-
- return Py_BuildValue("nn", (Py_ssize_t) n_partitions,
- (Py_ssize_t) n_unassigned);
-}
-
-static
-PyObject *
-subset_report_on_partitions(khmer_KSubsetPartition_Object * me, PyObject * args)
-{
- SubsetPartition * subset_p = me->subset;
-
- if (!PyArg_ParseTuple(args, "")) {
- return NULL;
- }
-
- subset_p->report_on_partitions();
-
- Py_RETURN_NONE;
-}
-
-static
-PyObject *
-subset_compare_partitions(khmer_KSubsetPartition_Object * me, PyObject * args)
-{
- SubsetPartition * subset1_p = me->subset;
-
- PyObject * subset2_obj = NULL;
- PartitionID pid1, pid2; // @CTB ensure that these are unsigned?
-
- if (!PyArg_ParseTuple(args, "IOI",
- &pid1, &subset2_obj, &pid2)) {
- return NULL;
- }
-
- khmer_KSubsetPartition_Object *other = (khmer_KSubsetPartition_Object *)
- subset2_obj;
- SubsetPartition * subset2_p = other->subset;
-
- unsigned int n_only1 = 0, n_only2 = 0, n_shared = 0;
- subset1_p->compare_to_partition(pid1, subset2_p, pid2,
- n_only1, n_only2, n_shared);
-
- return Py_BuildValue("III", n_only1, n_only2, n_shared);
-}
-
-static
-PyObject *
-subset_partition_size_distribution(khmer_KSubsetPartition_Object * me,
- PyObject * args)
-{
- SubsetPartition * subset_p = me->subset;
if (!PyArg_ParseTuple(args, "")) {
return NULL;
}
+ ScoringMatrix matrix = me->aligner->getScoringMatrix();
- PartitionCountDistribution d;
-
- unsigned int n_unassigned = 0;
- subset_p->partition_size_distribution(d, n_unassigned);
-
- PyObject * x = PyList_New(d.size());
- if (x == NULL) {
- return NULL;
- }
- PartitionCountDistribution::iterator di;
-
- unsigned int i;
- for (i = 0, di = d.begin(); di != d.end(); ++di, i++) {
- PyObject * tup = Py_BuildValue("KK", di->first, di->second);
- if (tup != NULL) {
- PyList_SET_ITEM(x, i, tup);
- }
- Py_XDECREF(tup);
- }
- if (!(i == d.size())) {
- throw khmer_exception();
- }
-
- PyObject * ret = Py_BuildValue("OI", x, n_unassigned);
- Py_DECREF(x);
- return ret;
-}
-
-static
-PyObject *
-subset_partition_sizes(khmer_KSubsetPartition_Object * me, PyObject * args)
-{
- SubsetPartition * subset_p = me->subset;
-
- unsigned int min_size = 0;
-
- if (!PyArg_ParseTuple(args, "|I", &min_size)) {
- return NULL;
- }
-
- PartitionCountMap cm;
- unsigned int n_unassigned = 0;
- subset_p->partition_sizes(cm, n_unassigned);
-
- unsigned int i = 0;
- PartitionCountMap::const_iterator mi;
- for (mi = cm.begin(); mi != cm.end(); ++mi) {
- if (mi->second >= min_size) {
- i++;
- }
- }
-
- PyObject * x = PyList_New(i);
- if (x == NULL) {
- return NULL;
- }
-
- // this should probably be a dict. @CTB
- for (i = 0, mi = cm.begin(); mi != cm.end(); ++mi) {
- if (mi->second >= min_size) {
- PyObject * tup = Py_BuildValue("II", mi->first, mi->second);
- if (tup != NULL) {
- PyList_SET_ITEM(x, i, tup);
- }
- i++;
- }
- }
-
- PyObject * ret = Py_BuildValue("OI", x, n_unassigned);
- Py_DECREF(x);
-
- return ret;
-}
-
-static
-PyObject *
-subset_partition_average_coverages(khmer_KSubsetPartition_Object * me,
- PyObject * args)
-{
- SubsetPartition * subset_p = me->subset;
-
- khmer_KCountingHash_Object * counting_o;
-
- if (!PyArg_ParseTuple(args, "O!", &khmer_KCountgraph_Type, &counting_o)) {
- return NULL;
- }
-
- PartitionCountMap cm;
- subset_p->partition_average_coverages(cm, counting_o -> counting);
-
- unsigned int i;
- PartitionCountMap::iterator mi;
-
- PyObject * x = PyList_New(cm.size());
- if (x == NULL) {
- return NULL;
- }
-
- // this should probably be a dict. @CTB
- for (i = 0, mi = cm.begin(); mi != cm.end(); ++mi, i++) {
- PyObject * tup = Py_BuildValue("II", mi->first, mi->second);
- if (tup != NULL) {
- PyList_SET_ITEM(x, i, tup);
- }
- }
-
- return x;
+ return Py_BuildValue( "(dddddd)(dddd)(dddd)(dddddd)(dddd)(dddd)",
+ matrix.tsc[0], matrix.tsc[1], matrix.tsc[2],
+ matrix.tsc[3], matrix.tsc[4], matrix.tsc[5],
+ matrix.tsc[6], matrix.tsc[7], matrix.tsc[8],
+ matrix.tsc[9], matrix.tsc[10], matrix.tsc[11],
+ matrix.tsc[12], matrix.tsc[13], matrix.tsc[14],
+ matrix.tsc[15], matrix.tsc[16], matrix.tsc[17],
+ matrix.tsc[18], matrix.tsc[19], matrix.tsc[20],
+ matrix.tsc[21], matrix.tsc[22], matrix.tsc[23],
+ matrix.tsc[24], matrix.tsc[25], matrix.tsc[26],
+ matrix.tsc[27]);
}
-static PyMethodDef khmer_subset_methods[] = {
- {
- "count_partitions",
- (PyCFunction)subset_count_partitions,
- METH_VARARGS,
- ""
- },
- {
- "report_on_partitions",
- (PyCFunction)subset_report_on_partitions,
- METH_VARARGS,
- ""
- },
- {
- "compare_partitions",
- (PyCFunction)subset_compare_partitions,
- METH_VARARGS,
- ""
- },
- {
- "partition_size_distribution",
- (PyCFunction)subset_partition_size_distribution,
- METH_VARARGS,
- ""
- },
+static PyMethodDef khmer_ReadAligner_methods[] = {
+ {"align", (PyCFunction)readaligner_align, METH_VARARGS, ""},
+ {"align_forward", (PyCFunction)readaligner_align_forward, METH_VARARGS, ""},
{
- "partition_sizes",
- (PyCFunction)subset_partition_sizes,
+ "get_scoring_matrix", (PyCFunction)khmer_ReadAligner_get_scoring_matrix,
METH_VARARGS,
- ""
+ "Get the scoring matrix in use.\n\n\
+Returns a tuple of floats: (trusted_match, trusted_mismatch, untrusted_match, \
+untrusted_mismatch)"
},
{
- "partition_average_coverages",
- (PyCFunction)subset_partition_average_coverages,
+ "get_transition_probabilities",
+ (PyCFunction)khmer_ReadAligner_get_transition_probabilities,
METH_VARARGS,
- ""
+ "Get the transition probabilties in use.\n\n\
+HMM state notation abbreviations:\n\
+ M_t - trusted match; M_u - untrusted match\n\
+ Ir_t - trusted read insert; Ir_u - untrusted read insert\n\
+ Ig_t - trusted graph insert; Ig_u - untrusted graph insert\n\
+\
+Returns a sparse matrix as a tuple of six tuples.\n\
+The inner tuples contain 6, 4, 4, 6, 4, and 4 floats respectively.\n\
+Transition are notated as 'StartState-NextState':\n\
+(\n\
+ ( M_t-M_t, M_t-Ir_t, M_t-Ig_t, M_t-M_u, M_t-Ir_u, M_t-Ig_u),\n\
+ (Ir_t-M_t, Ir_t-Ir_t, Ir_t-M_u, Ir_t-Ir_u ),\n\
+ (Ig_t-M_t, , Ig_t-Ig_t, Ig_t-M_u, Ig_t-Ig_u),\n\
+ ( M_u-M_t, M_u-Ir_t, M_u-Ig_t, M_u-M_u, M_u-Ir_u, M_u-Ig_u),\n\
+ (Ir_u-M_t, Ir_u-Ir_t, Ir_u-M_u, Ir_u-Ir_u ),\n\
+ (Ig_u-M_t, , Ig_u-Ig_t, Ig_u-M_u, Ig_u-Ig_u)\n\
+)"
},
- {NULL, NULL, 0, NULL} /* sentinel */
+ {NULL} /* Sentinel */
};
-typedef struct {
- PyObject_HEAD
- LabelHash * labelhash;
-} khmer_KGraphLabels_Object;
-
-static PyObject * khmer_graphlabels_new(PyTypeObject * type, PyObject *args,
- PyObject *kwds);
-
-#define is_graphlabels_obj(v) (Py_TYPE(v) == &khmer_KGraphLabels_Type)
-
-static void khmer_graphlabels_dealloc(khmer_KGraphLabels_Object * obj)
+//
+// khmer_readaligner_dealloc -- clean up readaligner object
+// GRAPHALIGN addition
+//
+static void khmer_readaligner_dealloc(khmer_ReadAligner_Object* obj)
{
- delete obj->labelhash;
- obj->labelhash = NULL;
-
+ delete obj->aligner;
+ obj->aligner = NULL;
Py_TYPE(obj)->tp_free((PyObject*)obj);
}
-static PyObject * khmer_graphlabels_new(PyTypeObject *type, PyObject *args,
- PyObject *kwds)
+//
+// new_readaligner
+//
+static PyObject* khmer_ReadAligner_new(PyTypeObject *type, PyObject * args,
+ PyObject *kwds)
{
- khmer_KGraphLabels_Object *self;
- self = (khmer_KGraphLabels_Object*)type->tp_alloc(type, 0);
+ khmer_ReadAligner_Object * self;
- if (self != NULL) {
- PyObject * hashtable_o;
- khmer::Hashtable * hashtable = NULL;
+ self = (khmer_ReadAligner_Object *)type->tp_alloc(type, 0);
- if (!PyArg_ParseTuple(args, "O", &hashtable_o)) {
- Py_DECREF(self);
- return NULL;
- }
+ if (self != NULL) {
+ khmer_KCountgraph_Object * ch = NULL;
+ unsigned short int trusted_cov_cutoff = 2;
+ double bits_theta = 1;
+ double scoring_matrix[] = { 0, 0, 0, 0 };
+ double * transitions = new double[28];
- if (PyObject_TypeCheck(hashtable_o, &khmer_KNodegraph_Type)) {
- khmer_KHashbits_Object * kho = (khmer_KHashbits_Object *) hashtable_o;
- hashtable = kho->hashbits;
- } else if (PyObject_TypeCheck(hashtable_o, &khmer_KCountgraph_Type)) {
- khmer_KCountingHash_Object * cho = (khmer_KCountingHash_Object *) hashtable_o;
- hashtable = cho->counting;
- } else {
- PyErr_SetString(PyExc_ValueError,
- "graph object must be a NodeGraph or CountGraph");
+ if(!PyArg_ParseTuple(
+ args,
+ "O!Hd|(dddd)((dddddd)(dddd)(dddd)(dddddd)(dddd)(dddd))",
+ &khmer_KCountgraph_Type, &ch, &trusted_cov_cutoff,
+ &bits_theta, &scoring_matrix[0], &scoring_matrix[1],
+ &scoring_matrix[2], &scoring_matrix[3], &transitions[0],
+ &transitions[1], &transitions[2], &transitions[3],
+ &transitions[4], &transitions[5], &transitions[6],
+ &transitions[7], &transitions[8], &transitions[9],
+ &transitions[10], &transitions[11], &transitions[12],
+ &transitions[13], &transitions[14], &transitions[15],
+ &transitions[16], &transitions[17], &transitions[18],
+ &transitions[19], &transitions[20], &transitions[21],
+ &transitions[22], &transitions[23], &transitions[24],
+ &transitions[25], &transitions[26], &transitions[27])) {
Py_DECREF(self);
return NULL;
}
- try {
- self->labelhash = new LabelHash(hashtable);
- } catch (std::bad_alloc &e) {
- Py_DECREF(self);
- return PyErr_NoMemory();
- }
+ self->aligner = new ReadAligner(ch->countgraph, trusted_cov_cutoff,
+ bits_theta, scoring_matrix,
+ transitions);
}
return (PyObject *) self;
}
-static
-PyObject *
-labelhash_get_label_dict(khmer_KGraphLabels_Object * me, PyObject * args)
-{
- LabelHash * hb = me->labelhash;
-
- PyObject * d = PyDict_New();
- if (d == NULL) {
- return NULL;
- }
- LabelPtrMap::iterator it;
-
- for (it = hb->label_ptrs.begin(); it != hb->label_ptrs.end(); ++it) {
- PyObject * key = Py_BuildValue("K", it->first);
- PyObject * val = Py_BuildValue("K", it->second);
- if (key != NULL && val != NULL) {
- PyDict_SetItem(d, key, val);
- }
- Py_XDECREF(key);
- Py_XDECREF(val);
- }
-
- return d;
-}
-
-static
-PyObject *
-labelhash_consume_fasta_and_tag_with_labels(khmer_KGraphLabels_Object * me,
- PyObject * args)
-{
- LabelHash * hb = me->labelhash;
-
- const char * filename;
-
- if (!PyArg_ParseTuple(args, "s", &filename)) {
- return NULL;
- }
-
- const char *value_exception = NULL;
- const char *file_exception = NULL;
- unsigned long long n_consumed = 0;
- unsigned int total_reads = 0;
- //Py_BEGIN_ALLOW_THREADS
- try {
- hb->consume_fasta_and_tag_with_labels(filename, total_reads,
- n_consumed);
- } catch (khmer_file_exception &exc) {
- file_exception = exc.what();
- } catch (khmer_value_exception &exc) {
- value_exception = exc.what();
- }
- //Py_END_ALLOW_THREADS
-
- if (file_exception != NULL) {
- PyErr_SetString(PyExc_OSError, file_exception);
- return NULL;
- }
- if (value_exception != NULL) {
- PyErr_SetString(PyExc_ValueError, value_exception);
- return NULL;
- }
-
- return Py_BuildValue("IK", total_reads, n_consumed);
-}
-
-static
-PyObject *
-labelhash_consume_partitioned_fasta_and_tag_with_labels(
- khmer_KGraphLabels_Object * me, PyObject * args)
-{
- LabelHash * labelhash = me->labelhash;
-
- const char * filename;
-
- if (!PyArg_ParseTuple(args, "s", &filename)) {
- return NULL;
- }
-
- // call the C++ function, and trap signals => Python
-
- unsigned long long n_consumed = 0;
- unsigned int total_reads = 0;
-
- try {
- labelhash->consume_partitioned_fasta_and_tag_with_labels(filename,
- total_reads, n_consumed);
- } catch (khmer_file_exception &exc) {
- PyErr_SetString(PyExc_OSError, exc.what());
- return NULL;
- } catch (khmer_value_exception &exc) {
- PyErr_SetString(PyExc_ValueError, exc.what());
- return NULL;
- }
+static PyTypeObject khmer_ReadAlignerType = {
+ PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
+ "_khmer.ReadAligner", /*tp_name*/
+ sizeof(khmer_ReadAligner_Object), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ (destructor)khmer_readaligner_dealloc, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ 0, /*tp_compare*/
+ 0, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ 0, /*tp_as_mapping*/
+ 0, /*tp_hash */
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ 0, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ "ReadAligner object", /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+ 0, /* tp_iter */
+ 0, /* tp_iternext */
+ khmer_ReadAligner_methods, /* tp_methods */
+ 0, /* tp_members */
+ 0, /* tp_getset */
+ 0, /* tp_base */
+ 0, /* tp_dict */
+ 0, /* tp_descr_get */
+ 0, /* tp_descr_set */
+ 0, /* tp_dictoffset */
+ 0, /* tp_init */
+ 0, /* tp_alloc */
+ khmer_ReadAligner_new, /* tp_new */
+};
- return Py_BuildValue("IK", total_reads, n_consumed);
-}
+//
+// khmer_countgraph_dealloc -- clean up a countgraph hash object.
+//
-static
-PyObject *
-labelhash_consume_sequence_and_tag_with_labels(khmer_KGraphLabels_Object * me,
- PyObject * args)
+static void khmer_countgraph_dealloc(khmer_KCountgraph_Object * obj)
{
- LabelHash * hb = me->labelhash;
- const char * seq = NULL;
- unsigned long long c = 0;
- if (!PyArg_ParseTuple(args, "sK", &seq, &c)) {
- return NULL;
- }
- unsigned long long n_consumed = 0;
- Label * the_label = hb->check_and_allocate_label(c);
-
- hb->consume_sequence_and_tag_with_labels(seq, n_consumed, *the_label);
- return Py_BuildValue("K", n_consumed);
+ delete obj->countgraph;
+ obj->countgraph = NULL;
+ Py_TYPE(obj)->tp_free((PyObject*)obj);
}
-static
-PyObject *
-labelhash_sweep_label_neighborhood(khmer_KGraphLabels_Object * me,
- PyObject * args)
+//
+// khmer_nodegraph_dealloc -- clean up a nodegraph object.
+//
+static void khmer_nodegraph_dealloc(khmer_KNodegraph_Object * obj)
{
- LabelHash * hb = me->labelhash;
-
- const char * seq = NULL;
- int r = 0;
- PyObject * break_on_stop_tags_o = NULL;
- PyObject * stop_big_traversals_o = NULL;
-
- if (!PyArg_ParseTuple(args, "s|iOO", &seq, &r,
- &break_on_stop_tags_o,
- &stop_big_traversals_o)) {
- return NULL;
- }
-
- unsigned int range = (2 * hb->graph->_get_tag_density()) + 1;
- if (r >= 0) {
- range = r;
- }
-
- bool break_on_stop_tags = false;
- if (break_on_stop_tags_o && PyObject_IsTrue(break_on_stop_tags_o)) {
- break_on_stop_tags = true;
- }
- bool stop_big_traversals = false;
- if (stop_big_traversals_o && PyObject_IsTrue(stop_big_traversals_o)) {
- stop_big_traversals = true;
- }
-
- if (strlen(seq) < hb->graph->ksize()) {
- PyErr_SetString(PyExc_ValueError,
- "string length must >= the hashtable k-mer size");
- return NULL;
- }
+ delete obj->nodegraph;
+ obj->nodegraph = NULL;
- //std::pair<TagLabelPtrPair::iterator, TagLabelPtrPair::iterator> ret;
- LabelPtrSet found_labels;
-
- //unsigned int num_traversed = 0;
- //Py_BEGIN_ALLOW_THREADS
- hb->sweep_label_neighborhood(seq, found_labels, range, break_on_stop_tags,
- stop_big_traversals);
- //Py_END_ALLOW_THREADS
-
- //printf("...%u kmers traversed\n", num_traversed);
-
- PyObject * x = PyList_New(found_labels.size());
- LabelPtrSet::const_iterator si;
- unsigned long long i = 0;
- for (si = found_labels.begin(); si != found_labels.end(); ++si) {
- PyList_SET_ITEM(x, i, Py_BuildValue("K", *(*si)));
- i++;
- }
-
- return x;
+ Py_TYPE(obj)->tp_free((PyObject*)obj);
}
-// Similar to find_all_tags, but returns tags in a way actually usable by python
-// need a tags_in_sequence iterator or function in c++ land for reuse in all
-// these functions
-static
-PyObject *
-labelhash_sweep_tag_neighborhood(khmer_KGraphLabels_Object * me,
- PyObject * args)
+//
+// khmer_subset_dealloc -- clean up a subset object.
+//
+
+static void khmer_subset_dealloc(khmer_KSubsetPartition_Object * obj)
{
- LabelHash * labelhash = me->labelhash;
+ delete obj->subset;
+ obj->subset = NULL;
+ Py_TYPE(obj)->tp_free((PyObject*)obj);
+}
- const char * seq = NULL;
- int r = 0;
- PyObject * break_on_stop_tags_o = NULL;
- PyObject * stop_big_traversals_o = NULL;
- if (!PyArg_ParseTuple(args, "s|iOO", &seq, &r,
- &break_on_stop_tags_o,
- &stop_big_traversals_o)) {
- return NULL;
- }
+/***********************************************************************/
- unsigned int range = (2 * labelhash->graph->_get_tag_density()) + 1;
- if (r >= 0) {
- range = r;
- }
+//
+// KHLLCounter object
+//
- bool break_on_stop_tags = false;
- if (break_on_stop_tags_o && PyObject_IsTrue(break_on_stop_tags_o)) {
- break_on_stop_tags = true;
- }
- bool stop_big_traversals = false;
- if (stop_big_traversals_o && PyObject_IsTrue(stop_big_traversals_o)) {
- stop_big_traversals = true;
- }
+typedef struct {
+ PyObject_HEAD
+ HLLCounter * hllcounter;
+} khmer_KHLLCounter_Object;
- if (strlen(seq) < labelhash->graph->ksize()) {
- PyErr_SetString(PyExc_ValueError,
- "string length must >= the hashtable k-mer size");
- return NULL;
- }
+static PyObject* khmer_hllcounter_new(PyTypeObject * type, PyObject * args,
+ PyObject * kwds)
+{
+ khmer_KHLLCounter_Object * self;
+ self = (khmer_KHLLCounter_Object *)type->tp_alloc(type, 0);
- SeenSet tagged_kmers;
+ if (self != NULL) {
+ double error_rate = 0.01;
+ WordLength ksize = 20;
- //Py_BEGIN_ALLOW_THREADS
+ if (!PyArg_ParseTuple(args, "|db", &error_rate, &ksize)) {
+ Py_DECREF(self);
+ return NULL;
+ }
- labelhash->graph->partition->sweep_for_tags(seq, tagged_kmers,
- labelhash->graph->all_tags,
- range, break_on_stop_tags,
- stop_big_traversals);
+ try {
+ self->hllcounter = new HLLCounter(error_rate, ksize);
+ } catch (InvalidValue &e) {
+ Py_DECREF(self);
+ PyErr_SetString(PyExc_ValueError, e.what());
+ return NULL;
+ }
+ }
- //Py_END_ALLOW_THREADS
+ return (PyObject *) self;
+}
- PyObject * x = PyList_New(tagged_kmers.size());
- if (x == NULL) {
- return NULL;
- }
- SeenSet::iterator si;
- unsigned long long i = 0;
- for (si = tagged_kmers.begin(); si != tagged_kmers.end(); ++si) {
- //std::string kmer_s = _revhash(*si, labelhash->ksize());
- // type K for python unsigned long long
- PyList_SET_ITEM(x, i, Py_BuildValue("K", *si));
- i++;
- }
+//
+// khmer_hllcounter_dealloc -- clean up a hllcounter object.
+//
- return x;
+static void khmer_hllcounter_dealloc(khmer_KHLLCounter_Object * obj)
+{
+ delete obj->hllcounter;
+ obj->hllcounter = NULL;
+
+ Py_TYPE(obj)->tp_free((PyObject*)obj);
}
static
PyObject *
-labelhash_get_tag_labels(khmer_KGraphLabels_Object * me, PyObject * args)
+hllcounter_add(khmer_KHLLCounter_Object * me, PyObject * args)
{
- LabelHash * labelhash = me->labelhash;
-
- HashIntoType tag;
+ const char * kmer_str;
- if (!PyArg_ParseTuple(args, "K", &tag)) {
+ if (!PyArg_ParseTuple(args, "s", &kmer_str)) {
return NULL;
}
- LabelPtrSet labels;
-
- labels = labelhash->get_tag_labels(tag);
-
- PyObject * x = PyList_New(labels.size());
- LabelPtrSet::const_iterator si;
- unsigned long long i = 0;
- for (si = labels.begin(); si != labels.end(); ++si) {
- //std::string kmer_s = _revhash(*si, labelhash->ksize());
- PyList_SET_ITEM(x, i, Py_BuildValue("K", *(*si)));
- i++;
+ try {
+ me->hllcounter->add(kmer_str);
+ } catch (khmer_exception &e) {
+ PyErr_SetString(PyExc_ValueError, e.what());
+ return NULL;
}
- return x;
+ Py_RETURN_NONE;
}
static
PyObject *
-labelhash_n_labels(khmer_KGraphLabels_Object * me, PyObject * args)
+hllcounter_estimate_cardinality(khmer_KHLLCounter_Object * me, PyObject * args)
{
- LabelHash * labelhash = me->labelhash;
-
- if (!PyArg_ParseTuple(args, "")) {
+ if (!PyArg_ParseTuple( args, "" )) {
return NULL;
}
- return PyLong_FromSize_t(labelhash->n_labels());
+ return PyLong_FromLong(me->hllcounter->estimate_cardinality());
}
static
PyObject *
-labelhash_save_labels_and_tags(khmer_KGraphLabels_Object * me, PyObject * args)
+hllcounter_consume_string(khmer_KHLLCounter_Object * me, PyObject * args)
{
- const char * filename = NULL;
- LabelHash * labelhash = me->labelhash;
+ const char * kmer_str;
+ unsigned long long n_consumed;
- if (!PyArg_ParseTuple(args, "s", &filename)) {
+ if (!PyArg_ParseTuple(args, "s", &kmer_str)) {
return NULL;
}
try {
- labelhash->save_labels_and_tags(filename);
- } catch (khmer_file_exception &e) {
- PyErr_SetString(PyExc_OSError, e.what());
+ n_consumed = me->hllcounter->consume_string(kmer_str);
+ } catch (khmer_exception &e) {
+ PyErr_SetString(PyExc_ValueError, e.what());
return NULL;
}
- Py_RETURN_NONE;
+ return PyLong_FromLong(n_consumed);
}
-static
-PyObject *
-labelhash_load_labels_and_tags(khmer_KGraphLabels_Object * me, PyObject * args)
+static PyObject * hllcounter_consume_seqfile(khmer_KHLLCounter_Object * me,
+ PyObject * args, PyObject * kwds)
{
- const char * filename = NULL;
- LabelHash * labelhash = me->labelhash;
+ const char * filename;
+ PyObject * stream_records_o = NULL;
- if (!PyArg_ParseTuple(args, "s", &filename)) {
+ static const char* const_kwlist[] = {"filename", "stream_records", NULL};
+ static char** kwlist = const_cast<char**>(const_kwlist);
+
+ bool stream_records = false;
+
+ if (!PyArg_ParseTupleAndKeywords(args, kwds, "s|O", kwlist,
+ &filename, &stream_records_o)) {
return NULL;
}
+ if (stream_records_o != NULL && PyObject_IsTrue(stream_records_o)) {
+ stream_records = true;
+ }
+
+ // call the C++ function, and trap signals => Python
+ unsigned long long n_consumed = 0;
+ unsigned int total_reads = 0;
try {
- labelhash->load_labels_and_tags(filename);
- } catch (khmer_file_exception &e) {
- PyErr_SetString(PyExc_OSError, e.what());
+ me->hllcounter->consume_seqfile<FastxReader>(filename, stream_records,
+ total_reads,
+ n_consumed);
+ } catch (khmer_file_exception &exc) {
+ PyErr_SetString(PyExc_OSError, exc.what());
+ return NULL;
+ } catch (khmer_value_exception &exc) {
+ PyErr_SetString(PyExc_ValueError, exc.what());
return NULL;
}
- Py_RETURN_NONE;
+ return Py_BuildValue("IK", total_reads, n_consumed);
}
-static PyMethodDef khmer_graphlabels_methods[] = {
- { "consume_fasta_and_tag_with_labels", (PyCFunction)labelhash_consume_fasta_and_tag_with_labels, METH_VARARGS, "" },
- { "sweep_label_neighborhood", (PyCFunction)labelhash_sweep_label_neighborhood, METH_VARARGS, "" },
- {"consume_partitioned_fasta_and_tag_with_labels", (PyCFunction)labelhash_consume_partitioned_fasta_and_tag_with_labels, METH_VARARGS, "" },
- {"sweep_tag_neighborhood", (PyCFunction)labelhash_sweep_tag_neighborhood, METH_VARARGS, "" },
- {"get_tag_labels", (PyCFunction)labelhash_get_tag_labels, METH_VARARGS, ""},
- {"consume_sequence_and_tag_with_labels", (PyCFunction)labelhash_consume_sequence_and_tag_with_labels, METH_VARARGS, "" },
- {"n_labels", (PyCFunction)labelhash_n_labels, METH_VARARGS, ""},
- {"get_label_dict", (PyCFunction)labelhash_get_label_dict, METH_VARARGS, "" },
- { "save_labels_and_tags", (PyCFunction)labelhash_save_labels_and_tags, METH_VARARGS, "" },
- { "load_labels_and_tags", (PyCFunction)labelhash_load_labels_and_tags, METH_VARARGS, "" }, {NULL, NULL, 0, NULL} /* sentinel */
-};
+static PyObject * hllcounter_merge(khmer_KHLLCounter_Object * me,
+ PyObject * args);
-static PyTypeObject khmer_KGraphLabels_Type = {
- PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
- "_khmer.LabelHash", /* tp_name */
- sizeof(khmer_KGraphLabels_Object), /* tp_basicsize */
- 0, /* tp_itemsize */
- (destructor)khmer_graphlabels_dealloc, /* tp_dealloc */
- 0, /* tp_print */
- 0, /* tp_getattr */
- 0, /* tp_setattr */
- 0, /* tp_compare */
- 0, /* tp_repr */
- 0, /* tp_as_number */
- 0, /* tp_as_sequence */
- 0, /* tp_as_mapping */
- 0, /* tp_hash */
- 0, /* tp_call */
- 0, /* tp_str */
- 0, /* tp_getattro */
- 0, /* tp_setattro */
- 0, /* tp_as_buffer */
- Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */
- 0, /* tp_doc */
- 0, /* tp_traverse */
- 0, /* tp_clear */
- 0, /* tp_richcompare */
- 0, /* tp_weaklistoffset */
- 0, /* tp_iter */
- 0, /* tp_iternext */
- khmer_graphlabels_methods, /* tp_methods */
- 0, /* tp_members */
- 0, /* tp_getset */
- 0, /* tp_base */
- 0, /* tp_dict */
- 0, /* tp_descr_get */
- 0, /* tp_descr_set */
- 0, /* tp_dictoffset */
- 0, /* tp_init */
- 0, /* tp_alloc */
- khmer_graphlabels_new, /* tp_new */
-};
+static
+PyObject *
+hllcounter_get_erate(khmer_KHLLCounter_Object * me)
+{
+ return PyFloat_FromDouble(me->hllcounter->get_erate());
+}
+
+static
+PyObject *
+hllcounter_get_ksize(khmer_KHLLCounter_Object * me)
+{
+ return PyLong_FromLong(me->hllcounter->get_ksize());
+}
+
+static
+int
+hllcounter_set_ksize(khmer_KHLLCounter_Object * me, PyObject *value,
+ void *closure)
+{
+ if (value == NULL) {
+ PyErr_SetString(PyExc_TypeError, "Cannot delete attribute");
+ return -1;
+ }
+
+ long ksize = 0;
+ if (PyLong_Check(value)) {
+ ksize = PyLong_AsLong(value);
+ } else if (PyInt_Check(value)) {
+ ksize = PyInt_AsLong(value);
+ } else {
+ PyErr_SetString(PyExc_TypeError,
+ "Please use an integer value for k-mer size");
+ return -1;
+ }
+
+ if (ksize <= 0) {
+ PyErr_SetString(PyExc_ValueError, "Please set k-mer size to a value "
+ "greater than zero");
+ return -1;
+ }
+
+ try {
+ me->hllcounter->set_ksize(ksize);
+ } catch (ReadOnlyAttribute &e) {
+ PyErr_SetString(PyExc_AttributeError, e.what());
+ return -1;
+ }
+
+ return 0;
+}
static
-PyObject *
-hashtable_traverse_from_tags(khmer_KHashtable_Object * me, PyObject * args)
+int
+hllcounter_set_erate(khmer_KHLLCounter_Object * me, PyObject *value,
+ void *closure)
{
- Hashtable * hashtable = me->hashtable;
+ if (value == NULL) {
+ PyErr_SetString(PyExc_TypeError, "Cannot delete attribute");
+ return -1;
+ }
- khmer_KCountingHash_Object * counting_o = NULL;
- unsigned int distance, threshold, frequency;
+ if (!PyFloat_Check(value)) {
+ PyErr_SetString(PyExc_TypeError,
+ "Please use a float value for k-mer size");
+ return -1;
+ }
- if (!PyArg_ParseTuple(args, "O!III", &khmer_KCountgraph_Type, &counting_o,
- &distance, &threshold, &frequency)) {
- return NULL;
+ double erate = PyFloat_AsDouble(value);
+ try {
+ me->hllcounter->set_erate(erate);
+ } catch (InvalidValue &e) {
+ PyErr_SetString(PyExc_ValueError, e.what());
+ return -1;
+ } catch (ReadOnlyAttribute &e) {
+ PyErr_SetString(PyExc_AttributeError, e.what());
+ return -1;
}
- hashtable->traverse_from_tags(distance, threshold, frequency,
- * counting_o->counting);
+ return 0;
+}
- Py_RETURN_NONE;
+static
+PyObject *
+hllcounter_getalpha(khmer_KHLLCounter_Object * me)
+{
+ return PyFloat_FromDouble(me->hllcounter->get_alpha());
}
static
PyObject *
-hashtable_repartition_largest_partition(khmer_KHashtable_Object * me,
- PyObject * args)
+hllcounter_getcounters(khmer_KHLLCounter_Object * me)
{
- Hashtable * hashtable = me->hashtable;
- khmer_KCountingHash_Object * counting_o = NULL;
- PyObject * subset_o = NULL;
- SubsetPartition * subset_p;
- unsigned int distance, threshold, frequency;
+ std::vector<int> counters = me->hllcounter->get_M();
- if (!PyArg_ParseTuple(args, "OO!III",
- &subset_o,
- &khmer_KCountgraph_Type, &counting_o,
- &distance, &threshold, &frequency)) {
- return NULL;
+ PyObject * x = PyList_New(counters.size());
+ for (size_t i = 0; i < counters.size(); i++) {
+ PyList_SET_ITEM(x, i, PyLong_FromLong(counters[i]));
}
- if (PyObject_TypeCheck(subset_o, &khmer_KSubsetPartition_Type)) {
- subset_p = ((khmer_KSubsetPartition_Object *) subset_o)->subset;
- } else {
- subset_p = hashtable->partition;
- }
+ return x;
+}
- CountingHash * counting = counting_o->counting;
+static PyMethodDef khmer_hllcounter_methods[] = {
+ {
+ "add", (PyCFunction)hllcounter_add,
+ METH_VARARGS,
+ "Add a k-mer to the counter."
+ },
+ {
+ "estimate_cardinality", (PyCFunction)hllcounter_estimate_cardinality,
+ METH_VARARGS,
+ "Return the current estimation."
+ },
+ {
+ "consume_string", (PyCFunction)hllcounter_consume_string,
+ METH_VARARGS,
+ "Break a sequence into k-mers and add each k-mer to the counter."
+ },
+ {
+ "consume_seqfile", (PyCFunction)hllcounter_consume_seqfile,
+ METH_VARARGS | METH_KEYWORDS,
+ "Read sequences from file, break into k-mers, "
+ "and add each k-mer to the counter. If optional keyword 'stream_out' "
+ "is True, also prints each sequence to stdout."
+ },
+ {
+ "merge", (PyCFunction)hllcounter_merge,
+ METH_VARARGS,
+ "Merge other counter into this one."
+ },
+ {NULL} /* Sentinel */
+};
- unsigned long next_largest;
- try {
- next_largest = subset_p->repartition_largest_partition(distance,
- threshold, frequency, *counting);
- } catch (khmer_exception &e) {
- PyErr_SetString(PyExc_RuntimeError, e.what());
- return NULL;
- }
+static PyGetSetDef khmer_hllcounter_getseters[] = {
+ {
+ (char *)"alpha",
+ (getter)hllcounter_getalpha, NULL,
+ (char *)"alpha constant for this HLL counter.",
+ NULL
+ },
+ {
+ (char *)"error_rate",
+ (getter)hllcounter_get_erate, (setter)hllcounter_set_erate,
+ (char *)"Error rate for this HLL counter. "
+ "Can be changed prior to first counting, but becomes read-only after "
+ "that (raising AttributeError)",
+ NULL
+ },
+ {
+ (char *)"ksize",
+ (getter)hllcounter_get_ksize, (setter)hllcounter_set_ksize,
+ (char *)"k-mer size for this HLL counter."
+ "Can be changed prior to first counting, but becomes read-only after "
+ "that (raising AttributeError)",
+ NULL
+ },
+ {
+ (char *)"counters",
+ (getter)hllcounter_getcounters, NULL,
+ (char *)"Read-only internal counters.",
+ NULL
+ },
+ {NULL} /* Sentinel */
+};
- return PyLong_FromLong(next_largest);
-}
+static PyTypeObject khmer_KHLLCounter_Type = {
+ PyVarObject_HEAD_INIT(NULL, 0)
+ "_khmer.KHLLCounter", /* tp_name */
+ sizeof(khmer_KHLLCounter_Object), /* tp_basicsize */
+ 0, /* tp_itemsize */
+ (destructor)khmer_hllcounter_dealloc, /* tp_dealloc */
+ 0, /* tp_print */
+ 0, /* tp_getattr */
+ 0, /* tp_setattr */
+ 0, /* tp_compare */
+ 0, /* tp_repr */
+ 0, /* tp_as_number */
+ 0, /* tp_as_sequence */
+ 0, /* tp_as_mapping */
+ 0, /* tp_hash */
+ 0, /* tp_call */
+ 0, /* tp_str */
+ 0, /* tp_getattro */
+ 0, /* tp_setattro */
+ 0, /* tp_as_buffer */
+ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */
+ "HyperLogLog counter", /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+ 0, /* tp_iter */
+ 0, /* tp_iternext */
+ khmer_hllcounter_methods, /* tp_methods */
+ 0, /* tp_members */
+ khmer_hllcounter_getseters, /* tp_getset */
+ 0, /* tp_base */
+ 0, /* tp_dict */
+ 0, /* tp_descr_get */
+ 0, /* tp_descr_set */
+ 0, /* tp_dictoffset */
+ 0, /* tp_init */
+ 0, /* tp_alloc */
+ khmer_hllcounter_new, /* tp_new */
+};
-static PyObject * readaligner_align(khmer_ReadAligner_Object * me,
- PyObject * args)
+static PyObject * hllcounter_merge(khmer_KHLLCounter_Object * me,
+ PyObject * args)
{
- const char * read;
+ khmer_KHLLCounter_Object * other;
- if (!PyArg_ParseTuple(args, "s", &read)) {
+ if (!PyArg_ParseTuple(args, "O!", &khmer_KHLLCounter_Type, &other)) {
return NULL;
}
- /*if (strlen(read) < (unsigned int)aligner->ksize()) {
- PyErr_SetString(PyExc_ValueError,
- "string length must >= the hashtable k-mer size");
+ try {
+ me->hllcounter->merge(*(other->hllcounter));
+ } catch (khmer_exception &e) {
+ PyErr_SetString(PyExc_ValueError, e.what());
return NULL;
- }*/
+ }
- Alignment * aln = me->aligner->Align(read);
+ Py_RETURN_NONE;
+}
- const char* alignment = aln->graph_alignment.c_str();
- const char* readAlignment = aln->read_alignment.c_str();
- PyObject * ret = Py_BuildValue("dssO", aln->score, alignment,
- readAlignment, (aln->truncated)? Py_True : Py_False);
- delete aln;
+/********************************
+ * Assembler classes
+ ********************************/
- return ret;
+
+typedef struct {
+ PyObject_HEAD
+ LinearAssembler * assembler;
+} khmer_KLinearAssembler_Object;
+
+static void khmer_linearassembler_dealloc(khmer_KLinearAssembler_Object * obj)
+{
+ delete obj->assembler;
+ obj->assembler = NULL;
+
+ Py_TYPE(obj)->tp_free((PyObject*)obj);
}
-static PyObject * readaligner_align_forward(khmer_ReadAligner_Object * me,
- PyObject * args)
+static PyObject * khmer_linearassembler_new(PyTypeObject *type, PyObject *args,
+ PyObject *kwds)
{
- ReadAligner * aligner = me->aligner;
+ khmer_KLinearAssembler_Object *self;
+ self = (khmer_KLinearAssembler_Object*)type->tp_alloc(type, 0);
- const char * read;
+ if (self != NULL) {
+ PyObject * hashgraph_o;
+ Hashgraph * hashgraph = NULL;
- if (!PyArg_ParseTuple(args, "s", &read)) {
- return NULL;
- }
+ if (!PyArg_ParseTuple(args, "O", &hashgraph_o)) {
+ Py_DECREF(self);
+ return NULL;
+ }
- /*if (strlen(read) < (unsigned int)aligner->ksize()) {
- PyErr_SetString(PyExc_ValueError,
- "string length must >= the hashtable k-mer size");
- return NULL;
- }*/
+ if (PyObject_TypeCheck(hashgraph_o, &khmer_KNodegraph_Type)) {
+ khmer_KNodegraph_Object * kho = (khmer_KNodegraph_Object *) hashgraph_o;
+ hashgraph = kho->nodegraph;
+ } else if (PyObject_TypeCheck(hashgraph_o, &khmer_KCountgraph_Type)) {
+ khmer_KCountgraph_Object * cho = (khmer_KCountgraph_Object *) hashgraph_o;
+ hashgraph = cho->countgraph;
+ } else {
+ PyErr_SetString(PyExc_ValueError,
+ "graph object must be a NodeGraph or CountGraph");
+ Py_DECREF(self);
+ return NULL;
+ }
- Alignment * aln;
- aln = aligner->AlignForward(read);
+ try {
+ self->assembler = new LinearAssembler(hashgraph);
+ } catch (std::bad_alloc &e) {
+ Py_DECREF(self);
+ return PyErr_NoMemory();
+ }
- const char* alignment = aln->graph_alignment.c_str();
- const char* readAlignment = aln->read_alignment.c_str();
- PyObject * x = PyList_New(aln->covs.size());
- for (size_t i = 0; i < aln->covs.size(); i++ ) {
- PyList_SET_ITEM(x, i, PyLong_FromLong(aln->covs[i]));
}
- PyObject * ret = Py_BuildValue("dssOO", aln->score, alignment,
- readAlignment,
- (aln->truncated)? Py_True : Py_False,
- x);
- delete aln;
- Py_DECREF(x);
-
- return ret;
+ return (PyObject *) self;
}
-static PyObject* khmer_ReadAligner_get_scoring_matrix(
- khmer_ReadAligner_Object * me, PyObject * args)
+
+static
+PyObject *
+linearassembler_assemble(khmer_KLinearAssembler_Object * me,
+ PyObject * args, PyObject *kwargs)
{
+ LinearAssembler * assembler= me->assembler;
- if (!PyArg_ParseTuple(args, "")) {
+ PyObject * val_o;
+ khmer_KNodegraph_Object * nodegraph_o = NULL;
+ Nodegraph * stop_bf = NULL;
+ const char * dir_str = NULL;
+ char dir = NULL;
+
+ const char *kwnames[] = {"seed_kmer", "stop_filter", "direction", NULL};
+
+ if (!PyArg_ParseTupleAndKeywords(args, kwargs, "O|O!s",
+ const_cast<char **>(kwnames),
+ &val_o, &khmer_KNodegraph_Type,
+ &nodegraph_o, &dir_str)) {
return NULL;
}
- ScoringMatrix matrix = me->aligner->getScoringMatrix();
+ if (dir_str != NULL) {
+ dir = dir_str[0];
+ } else {
+ dir = 'B';
+ }
- return Py_BuildValue( "dddd", matrix.trusted_match, matrix.trusted_mismatch,
- matrix.untrusted_match, matrix.untrusted_mismatch);
-}
+ Kmer start_kmer;
+ if (!ht_convert_PyObject_to_Kmer(val_o, start_kmer, assembler->graph)) {
+ return NULL;
+ }
-static PyObject* khmer_ReadAligner_get_transition_probabilities(
- khmer_ReadAligner_Object * me, PyObject * args)
-{
+ if (nodegraph_o) {
+ stop_bf = nodegraph_o->nodegraph;
+ }
- if (!PyArg_ParseTuple(args, "")) {
+ std::string contig;
+ if (dir == 'B') {
+ contig = assembler->assemble(start_kmer, stop_bf);
+ } else if (dir == 'L') {
+ contig = assembler->assemble_left(start_kmer, stop_bf);
+ } else if (dir == 'R') {
+ contig = assembler->assemble_right(start_kmer, stop_bf);
+ } else {
+ PyErr_SetString(PyExc_ValueError, "Direction must be B (both), L (left),"
+ " or R (right).");
return NULL;
}
- ScoringMatrix matrix = me->aligner->getScoringMatrix();
- return Py_BuildValue( "(dddddd)(dddd)(dddd)(dddddd)(dddd)(dddd)",
- matrix.tsc[0], matrix.tsc[1], matrix.tsc[2],
- matrix.tsc[3], matrix.tsc[4], matrix.tsc[5],
- matrix.tsc[6], matrix.tsc[7], matrix.tsc[8],
- matrix.tsc[9], matrix.tsc[10], matrix.tsc[11],
- matrix.tsc[12], matrix.tsc[13], matrix.tsc[14],
- matrix.tsc[15], matrix.tsc[16], matrix.tsc[17],
- matrix.tsc[18], matrix.tsc[19], matrix.tsc[20],
- matrix.tsc[21], matrix.tsc[22], matrix.tsc[23],
- matrix.tsc[24], matrix.tsc[25], matrix.tsc[26],
- matrix.tsc[27]);
+ PyObject * ret = Py_BuildValue("s", contig.c_str());
+ return ret;
}
-static PyMethodDef khmer_ReadAligner_methods[] = {
- {"align", (PyCFunction)readaligner_align, METH_VARARGS, ""},
- {"align_forward", (PyCFunction)readaligner_align_forward, METH_VARARGS, ""},
- {
- "get_scoring_matrix", (PyCFunction)khmer_ReadAligner_get_scoring_matrix,
- METH_VARARGS,
- "Get the scoring matrix in use.\n\n\
-Returns a tuple of floats: (trusted_match, trusted_mismatch, untrusted_match, \
-untrusted_mismatch)"
- },
+
+static PyMethodDef khmer_linearassembler_methods[] = {
{
- "get_transition_probabilities",
- (PyCFunction)khmer_ReadAligner_get_transition_probabilities,
- METH_VARARGS,
- "Get the transition probabilties in use.\n\n\
-HMM state notation abbreviations:\n\
- M_t - trusted match; M_u - untrusted match\n\
- Ir_t - trusted read insert; Ir_u - untrusted read insert\n\
- Ig_t - trusted graph insert; Ig_u - untrusted graph insert\n\
-\
-Returns a sparse matrix as a tuple of six tuples.\n\
-The inner tuples contain 6, 4, 4, 6, 4, and 4 floats respectively.\n\
-Transition are notated as 'StartState-NextState':\n\
-(\n\
- ( M_t-M_t, M_t-Ir_t, M_t-Ig_t, M_t-M_u, M_t-Ir_u, M_t-Ig_u),\n\
- (Ir_t-M_t, Ir_t-Ir_t, Ir_t-M_u, Ir_t-Ir_u ),\n\
- (Ig_t-M_t, , Ig_t-Ig_t, Ig_t-M_u, Ig_t-Ig_u),\n\
- ( M_u-M_t, M_u-Ir_t, M_u-Ig_t, M_u-M_u, M_u-Ir_u, M_u-Ig_u),\n\
- (Ir_u-M_t, Ir_u-Ir_t, Ir_u-M_u, Ir_u-Ir_u ),\n\
- (Ig_u-M_t, , Ig_u-Ig_t, Ig_u-M_u, Ig_u-Ig_u)\n\
-)"
+ "assemble",
+ (PyCFunction)linearassembler_assemble, METH_VARARGS | METH_KEYWORDS,
+ "Assemble a path linearly until a branch is reached."
},
- {NULL} /* Sentinel */
+ {NULL, NULL, 0, NULL} /* sentinel */
};
-//
-// khmer_readaligner_dealloc -- clean up readaligner object
-// GRAPHALIGN addition
-//
-static void khmer_readaligner_dealloc(khmer_ReadAligner_Object* obj)
+static PyTypeObject khmer_KLinearAssembler_Type = {
+ PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
+ "_khmer.LinearAssembler", /* tp_name */
+ sizeof(khmer_KLinearAssembler_Object), /* tp_basicsize */
+ 0, /* tp_itemsize */
+ (destructor)khmer_linearassembler_dealloc, /* tp_dealloc */
+ 0, /* tp_print */
+ 0, /* tp_getattr */
+ 0, /* tp_setattr */
+ 0, /* tp_compare */
+ 0, /* tp_repr */
+ 0, /* tp_as_number */
+ 0, /* tp_as_sequence */
+ 0, /* tp_as_mapping */
+ 0, /* tp_hash */
+ 0, /* tp_call */
+ 0, /* tp_str */
+ 0, /* tp_getattro */
+ 0, /* tp_setattro */
+ 0, /* tp_as_buffer */
+ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */
+ 0, /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+ 0, /* tp_iter */
+ 0, /* tp_iternext */
+ khmer_linearassembler_methods, /* tp_methods */
+ 0, /* tp_members */
+ 0, /* tp_getset */
+ 0, /* tp_base */
+ 0, /* tp_dict */
+ 0, /* tp_descr_get */
+ 0, /* tp_descr_set */
+ 0, /* tp_dictoffset */
+ 0, /* tp_init */
+ 0, /* tp_alloc */
+ khmer_linearassembler_new, /* tp_new */
+};
+
+
+
+typedef struct {
+ PyObject_HEAD
+ SimpleLabeledAssembler * assembler;
+} khmer_KSimpleLabeledAssembler_Object;
+
+
+static void khmer_simplelabeledassembler_dealloc(khmer_KLinearAssembler_Object *
+ obj)
{
- delete obj->aligner;
- obj->aligner = NULL;
+ delete obj->assembler;
+ obj->assembler = NULL;
+
Py_TYPE(obj)->tp_free((PyObject*)obj);
}
-//
-// new_readaligner
-//
-static PyObject* khmer_ReadAligner_new(PyTypeObject *type, PyObject * args,
- PyObject *kwds)
+static PyObject * khmer_simplelabeledassembler_new(PyTypeObject *type,
+ PyObject *args,
+ PyObject *kwds)
{
- khmer_ReadAligner_Object * self;
-
- self = (khmer_ReadAligner_Object *)type->tp_alloc(type, 0);
+ khmer_KSimpleLabeledAssembler_Object *self;
+ self = (khmer_KSimpleLabeledAssembler_Object*)type->tp_alloc(type, 0);
if (self != NULL) {
- khmer_KCountingHash_Object * ch = NULL;
- unsigned short int trusted_cov_cutoff = 2;
- double bits_theta = 1;
- double scoring_matrix[] = { 0, 0, 0, 0 };
- double * transitions = new double[28];
+ PyObject * labelhash_o;
+ LabelHash * labelhash = NULL;
- if(!PyArg_ParseTuple(
- args,
- "O!Hd|(dddd)((dddddd)(dddd)(dddd)(dddddd)(dddd)(dddd))",
- &khmer_KCountgraph_Type, &ch, &trusted_cov_cutoff,
- &bits_theta, &scoring_matrix[0], &scoring_matrix[1],
- &scoring_matrix[2], &scoring_matrix[3], &transitions[0],
- &transitions[1], &transitions[2], &transitions[3],
- &transitions[4], &transitions[5], &transitions[6],
- &transitions[7], &transitions[8], &transitions[9],
- &transitions[10], &transitions[11], &transitions[12],
- &transitions[13], &transitions[14], &transitions[15],
- &transitions[16], &transitions[17], &transitions[18],
- &transitions[19], &transitions[20], &transitions[21],
- &transitions[22], &transitions[23], &transitions[24],
- &transitions[25], &transitions[26], &transitions[27])) {
+ if (!PyArg_ParseTuple(args, "O", &labelhash_o)) {
Py_DECREF(self);
return NULL;
}
- self->aligner = new ReadAligner(ch->counting, trusted_cov_cutoff,
- bits_theta, scoring_matrix,
- transitions);
+ if (PyObject_TypeCheck(labelhash_o, &khmer_KGraphLabels_Type)) {
+ khmer_KGraphLabels_Object * klo = (khmer_KGraphLabels_Object *) labelhash_o;
+ labelhash = klo->labelhash;
+ } else {
+ PyErr_SetString(PyExc_ValueError,
+ "SimpleLabeledAssembler needs a GraphLabels object.");
+ Py_DECREF(self);
+ return NULL;
+ }
+
+ try {
+ self->assembler = new SimpleLabeledAssembler(labelhash);
+ } catch (std::bad_alloc &e) {
+ Py_DECREF(self);
+ return PyErr_NoMemory();
+ }
+
}
return (PyObject *) self;
}
-static PyTypeObject khmer_ReadAlignerType = {
- PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
- "_khmer.ReadAligner", /*tp_name*/
- sizeof(khmer_ReadAligner_Object), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- (destructor)khmer_readaligner_dealloc, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- 0, /*tp_compare*/
- 0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
- 0, /*tp_hash */
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/
- "ReadAligner object", /* tp_doc */
- 0, /* tp_traverse */
- 0, /* tp_clear */
- 0, /* tp_richcompare */
- 0, /* tp_weaklistoffset */
- 0, /* tp_iter */
- 0, /* tp_iternext */
- khmer_ReadAligner_methods, /* tp_methods */
- 0, /* tp_members */
- 0, /* tp_getset */
- 0, /* tp_base */
- 0, /* tp_dict */
- 0, /* tp_descr_get */
- 0, /* tp_descr_set */
- 0, /* tp_dictoffset */
- 0, /* tp_init */
- 0, /* tp_alloc */
- khmer_ReadAligner_new, /* tp_new */
-};
static
PyObject *
-hashtable_consume_fasta_and_traverse(khmer_KHashtable_Object * me,
- PyObject * args)
+simplelabeledassembler_assemble(khmer_KSimpleLabeledAssembler_Object * me,
+ PyObject * args, PyObject *kwargs)
{
- Hashtable * hashtable = me->hashtable;
+ SimpleLabeledAssembler * assembler = me->assembler;
- const char * filename;
- unsigned int radius, big_threshold, transfer_threshold;
- khmer_KCountingHash_Object * counting_o = NULL;
+ PyObject * val_o;
+ khmer_KNodegraph_Object * nodegraph_o = NULL;
+ Nodegraph * stop_bf = NULL;
+
+ const char *kwnames[] = {"seed_kmer", "stop_filter", NULL};
- if (!PyArg_ParseTuple(args, "sIIIO!", &filename,
- &radius, &big_threshold, &transfer_threshold,
- &khmer_KCountgraph_Type, &counting_o)) {
+ if (!PyArg_ParseTupleAndKeywords(args, kwargs, "O|O!",
+ const_cast<char **>(kwnames),
+ &val_o, &khmer_KNodegraph_Type,
+ &nodegraph_o)) {
return NULL;
}
- CountingHash * counting = counting_o->counting;
- try {
- hashtable->consume_fasta_and_traverse(filename, radius, big_threshold,
- transfer_threshold, *counting);
- } catch (khmer_file_exception &exc) {
- PyErr_SetString(PyExc_OSError, exc.what());
- return NULL;
- } catch (khmer_value_exception &exc) {
- PyErr_SetString(PyExc_ValueError, exc.what());
+ Kmer start_kmer;
+ if (!ht_convert_PyObject_to_Kmer(val_o, start_kmer, assembler->graph)) {
return NULL;
}
- Py_RETURN_NONE;
+ if (nodegraph_o) {
+ stop_bf = nodegraph_o->nodegraph;
+ }
+
+ std::vector<std::string> contigs = assembler->assemble(start_kmer, stop_bf);
+
+ PyObject * ret = PyList_New(contigs.size());
+ for (unsigned int i = 0; i < contigs.size(); i++) {
+ PyList_SET_ITEM(ret, i, PyUnicode_FromString(contigs[i].c_str()));
+ }
+
+ return ret;
}
-//
-// khmer_counting_dealloc -- clean up a counting hash object.
-//
-static void khmer_counting_dealloc(khmer_KCountingHash_Object * obj)
-{
- delete obj->counting;
- obj->counting = NULL;
- Py_TYPE(obj)->tp_free((PyObject*)obj);
-}
+static PyMethodDef khmer_simplelabeledassembler_methods[] = {
+ {
+ "assemble",
+ (PyCFunction)simplelabeledassembler_assemble, METH_VARARGS | METH_KEYWORDS,
+ "Assemble paths, using labels to jump branches."
+ },
+ {NULL, NULL, 0, NULL} /* sentinel */
+};
+
+static PyTypeObject khmer_KSimpleLabeledAssembler_Type = {
+ PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
+ "_khmer.SimpleLabeledAssembler", /* tp_name */
+ sizeof(khmer_KSimpleLabeledAssembler_Object), /* tp_basicsize */
+ 0, /* tp_itemsize */
+ (destructor)khmer_simplelabeledassembler_dealloc, /* tp_dealloc */
+ 0, /* tp_print */
+ 0, /* tp_getattr */
+ 0, /* tp_setattr */
+ 0, /* tp_compare */
+ 0, /* tp_repr */
+ 0, /* tp_as_number */
+ 0, /* tp_as_sequence */
+ 0, /* tp_as_mapping */
+ 0, /* tp_hash */
+ 0, /* tp_call */
+ 0, /* tp_str */
+ 0, /* tp_getattro */
+ 0, /* tp_setattro */
+ 0, /* tp_as_buffer */
+ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */
+ 0, /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+ 0, /* tp_iter */
+ 0, /* tp_iternext */
+ khmer_simplelabeledassembler_methods, /* tp_methods */
+ 0, /* tp_members */
+ 0, /* tp_getset */
+ 0, /* tp_base */
+ 0, /* tp_dict */
+ 0, /* tp_descr_get */
+ 0, /* tp_descr_set */
+ 0, /* tp_dictoffset */
+ 0, /* tp_init */
+ 0, /* tp_alloc */
+ khmer_simplelabeledassembler_new, /* tp_new */
+};
+
-//
-// khmer_hashbits_dealloc -- clean up a hashbits object.
-//
-static void khmer_hashbits_dealloc(khmer_KHashbits_Object * obj)
-{
- delete obj->hashbits;
- obj->hashbits = NULL;
- Py_TYPE(obj)->tp_free((PyObject*)obj);
-}
+/********************************
+ * JunctionCountAssembler
+ ********************************/
-//
-// khmer_subset_dealloc -- clean up a hashbits object.
-//
+typedef struct {
+ PyObject_HEAD
+ JunctionCountAssembler * assembler;
+} khmer_KJunctionCountAssembler_Object;
-static void khmer_subset_dealloc(khmer_KSubsetPartition_Object * obj)
+static void khmer_junctioncountassembler_dealloc(
+ khmer_KJunctionCountAssembler_Object * obj)
{
- delete obj->subset;
- obj->subset = NULL;
+ delete obj->assembler;
+ obj->assembler = NULL;
+
Py_TYPE(obj)->tp_free((PyObject*)obj);
}
-
-/***********************************************************************/
-
-//
-// KHLLCounter object
-//
-
-typedef struct {
- PyObject_HEAD
- khmer::HLLCounter * hllcounter;
-} khmer_KHLLCounter_Object;
-
-static PyObject* khmer_hllcounter_new(PyTypeObject * type, PyObject * args,
- PyObject * kwds)
+static PyObject * khmer_junctioncountassembler_new(PyTypeObject *type,
+ PyObject *args,
+ PyObject *kwds)
{
- khmer_KHLLCounter_Object * self;
- self = (khmer_KHLLCounter_Object *)type->tp_alloc(type, 0);
+ khmer_KJunctionCountAssembler_Object *self;
+ self = (khmer_KJunctionCountAssembler_Object*)type->tp_alloc(type, 0);
if (self != NULL) {
- double error_rate = 0.01;
- WordLength ksize = 20;
+ PyObject * hashgraph_o;
+ Hashgraph * hashgraph = NULL;
- if (!PyArg_ParseTuple(args, "|db", &error_rate, &ksize)) {
+ if (!PyArg_ParseTuple(args, "O", &hashgraph_o)) {
Py_DECREF(self);
return NULL;
}
- try {
- self->hllcounter = new HLLCounter(error_rate, ksize);
- } catch (InvalidValue &e) {
+ if (PyObject_TypeCheck(hashgraph_o, &khmer_KNodegraph_Type)) {
+ khmer_KNodegraph_Object * kho = (khmer_KNodegraph_Object *) hashgraph_o;
+ hashgraph = kho->nodegraph;
+ } else if (PyObject_TypeCheck(hashgraph_o, &khmer_KCountgraph_Type)) {
+ khmer_KCountgraph_Object * cho = (khmer_KCountgraph_Object *) hashgraph_o;
+ hashgraph = cho->countgraph;
+ } else {
+ PyErr_SetString(PyExc_ValueError,
+ "graph object must be a NodeGraph or CountGraph");
Py_DECREF(self);
- PyErr_SetString(PyExc_ValueError, e.what());
return NULL;
}
+
+ try {
+ self->assembler = new JunctionCountAssembler(hashgraph);
+ } catch (std::bad_alloc &e) {
+ Py_DECREF(self);
+ return PyErr_NoMemory();
+ }
+
}
return (PyObject *) self;
}
-//
-// khmer_hllcounter_dealloc -- clean up a hllcounter object.
-//
-
-static void khmer_hllcounter_dealloc(khmer_KHLLCounter_Object * obj)
-{
- delete obj->hllcounter;
- obj->hllcounter = NULL;
-
- Py_TYPE(obj)->tp_free((PyObject*)obj);
-}
static
PyObject *
-hllcounter_add(khmer_KHLLCounter_Object * me, PyObject * args)
+junctioncountassembler_assemble(khmer_KJunctionCountAssembler_Object * me,
+ PyObject * args, PyObject *kwargs)
{
- const char * kmer_str;
+ JunctionCountAssembler * assembler = me->assembler;
- if (!PyArg_ParseTuple(args, "s", &kmer_str)) {
+ PyObject * val_o;
+ khmer_KNodegraph_Object * nodegraph_o = NULL;
+ Nodegraph * stop_bf = NULL;
+
+ const char *kwnames[] = {"seed_kmer", "stop_filter", NULL};
+
+ if (!PyArg_ParseTupleAndKeywords(args, kwargs, "O|O!",
+ const_cast<char **>(kwnames),
+ &val_o, &khmer_KNodegraph_Type,
+ &nodegraph_o)) {
return NULL;
}
- try {
- me->hllcounter->add(kmer_str);
- } catch (khmer_exception &e) {
- PyErr_SetString(PyExc_ValueError, e.what());
+ Kmer start_kmer;
+ if (!ht_convert_PyObject_to_Kmer(val_o, start_kmer, assembler->graph)) {
return NULL;
}
- Py_RETURN_NONE;
-}
+ if (nodegraph_o) {
+ stop_bf = nodegraph_o->nodegraph;
+ }
-static
-PyObject *
-hllcounter_estimate_cardinality(khmer_KHLLCounter_Object * me, PyObject * args)
-{
- if (!PyArg_ParseTuple( args, "" )) {
- return NULL;
+ std::vector<std::string> contigs = assembler->assemble(start_kmer, stop_bf);
+
+ PyObject * ret = PyList_New(contigs.size());
+ for (unsigned int i = 0; i < contigs.size(); i++) {
+ PyList_SET_ITEM(ret, i, PyUnicode_FromString(contigs[i].c_str()));
}
- return PyLong_FromLong(me->hllcounter->estimate_cardinality());
+ return ret;
}
+
static
PyObject *
-hllcounter_consume_string(khmer_KHLLCounter_Object * me, PyObject * args)
+junctioncountassembler_consume(khmer_KJunctionCountAssembler_Object * me,
+ PyObject * args)
{
- const char * kmer_str;
- unsigned long long n_consumed;
+ JunctionCountAssembler * assembler = me->assembler;
+ const char * long_str;
- if (!PyArg_ParseTuple(args, "s", &kmer_str)) {
+ if (!PyArg_ParseTuple(args, "s", &long_str)) {
return NULL;
}
- try {
- n_consumed = me->hllcounter->consume_string(kmer_str);
- } catch (khmer_exception &e) {
- PyErr_SetString(PyExc_ValueError, e.what());
+ if (strlen(long_str) < assembler->_ksize) {
+ PyErr_SetString(PyExc_ValueError,
+ "string length must >= the hashgraph k-mer size");
return NULL;
}
- return PyLong_FromLong(n_consumed);
-}
-
-static PyObject * hllcounter_consume_fasta(khmer_KHLLCounter_Object * me,
- PyObject * args, PyObject * kwds)
-{
- const char * filename;
- PyObject * stream_records_o = NULL;
-
- static const char* const_kwlist[] = {"filename", "stream_records", NULL};
- static char** kwlist = const_cast<char**>(const_kwlist);
-
- bool stream_records = false;
-
- if (!PyArg_ParseTupleAndKeywords(args, kwds, "s|O", kwlist,
- &filename, &stream_records_o)) {
- return NULL;
- }
+ uint16_t n_junctions = assembler->consume(long_str);
- if (stream_records_o != NULL && PyObject_IsTrue(stream_records_o)) {
- stream_records = true;
- }
+ return PyLong_FromLong((HashIntoType) n_junctions);
+}
- // call the C++ function, and trap signals => Python
- unsigned long long n_consumed = 0;
- unsigned int total_reads = 0;
- try {
- me->hllcounter->consume_fasta(filename, stream_records, total_reads,
- n_consumed);
- } catch (khmer_file_exception &exc) {
- PyErr_SetString(PyExc_OSError, exc.what());
- return NULL;
- } catch (khmer_value_exception &exc) {
- PyErr_SetString(PyExc_ValueError, exc.what());
- return NULL;
- }
- return Py_BuildValue("IK", total_reads, n_consumed);
-}
+static PyMethodDef khmer_junctioncountassembler_methods[] = {
+ {
+ "assemble",
+ (PyCFunction)junctioncountassembler_assemble, METH_VARARGS | METH_KEYWORDS,
+ "Assemble paths, using recorded junctions to jump branches."
+ },
+ {
+ "consume",
+ (PyCFunction)junctioncountassembler_consume, METH_VARARGS,
+ "Consume a string and count its branch junctions."
+ },
+ {NULL, NULL, 0, NULL} /* sentinel */
+};
-static PyObject * hllcounter_merge(khmer_KHLLCounter_Object * me,
- PyObject * args);
+static PyTypeObject khmer_KJunctionCountAssembler_Type = {
+ PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
+ "_khmer.JunctionCountAssembler", /* tp_name */
+ sizeof(khmer_KJunctionCountAssembler_Object), /* tp_basicsize */
+ 0, /* tp_itemsize */
+ (destructor)khmer_junctioncountassembler_dealloc, /* tp_dealloc */
+ 0, /* tp_print */
+ 0, /* tp_getattr */
+ 0, /* tp_setattr */
+ 0, /* tp_compare */
+ 0, /* tp_repr */
+ 0, /* tp_as_number */
+ 0, /* tp_as_sequence */
+ 0, /* tp_as_mapping */
+ 0, /* tp_hash */
+ 0, /* tp_call */
+ 0, /* tp_str */
+ 0, /* tp_getattro */
+ 0, /* tp_setattro */
+ 0, /* tp_as_buffer */
+ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */
+ 0, /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+ 0, /* tp_iter */
+ 0, /* tp_iternext */
+ khmer_junctioncountassembler_methods, /* tp_methods */
+ 0, /* tp_members */
+ 0, /* tp_getset */
+ 0, /* tp_base */
+ 0, /* tp_dict */
+ 0, /* tp_descr_get */
+ 0, /* tp_descr_set */
+ 0, /* tp_dictoffset */
+ 0, /* tp_init */
+ 0, /* tp_alloc */
+ khmer_junctioncountassembler_new, /* tp_new */
+};
-static
-PyObject *
-hllcounter_get_erate(khmer_KHLLCounter_Object * me)
-{
- return PyFloat_FromDouble(me->hllcounter->get_erate());
-}
+////
static
PyObject *
-hllcounter_get_ksize(khmer_KHLLCounter_Object * me)
+hashtable_abundance_distribution_with_reads_parser(khmer_KHashtable_Object * me,
+ PyObject * args)
{
- return PyLong_FromLong(me->hllcounter->get_ksize());
-}
+ Hashtable * hashtable = me->hashtable;
-static
-int
-hllcounter_set_ksize(khmer_KHLLCounter_Object * me, PyObject *value,
- void *closure)
-{
- if (value == NULL) {
- PyErr_SetString(PyExc_TypeError, "Cannot delete attribute");
- return -1;
- }
+ khmer :: python :: khmer_ReadParser_Object * rparser_obj = NULL;
+ khmer_KHashtable_Object * tracking_obj = NULL;
- long ksize = 0;
- if (PyLong_Check(value)) {
- ksize = PyLong_AsLong(value);
- } else if (PyInt_Check(value)) {
- ksize = PyInt_AsLong(value);
- } else {
- PyErr_SetString(PyExc_TypeError,
- "Please use an integer value for k-mer size");
- return -1;
+ if (!PyArg_ParseTuple(args, "O!O!", &python::khmer_ReadParser_Type,
+ &rparser_obj, &khmer_KHashtable_Type, &tracking_obj)) {
+ return NULL;
}
- if (ksize <= 0) {
- PyErr_SetString(PyExc_ValueError, "Please set k-mer size to a value "
- "greater than zero");
- return -1;
- }
+ FastxParserPtr& rparser = rparser_obj->parser;
+ Hashtable *tracking = tracking_obj->hashtable;
+ uint64_t *dist = NULL;
+ const char *value_exception = NULL;
+ const char *file_exception = NULL;
+ std::string exc_string;
+ Py_BEGIN_ALLOW_THREADS
try {
- me->hllcounter->set_ksize(ksize);
- } catch (ReadOnlyAttribute &e) {
- PyErr_SetString(PyExc_AttributeError, e.what());
- return -1;
+ dist = hashtable->abundance_distribution<FastxReader>(rparser, tracking);
+ } catch (khmer_file_exception &exc) {
+ exc_string = exc.what();
+ file_exception = exc_string.c_str();
+ } catch (khmer_value_exception &exc) {
+ exc_string = exc.what();
+ value_exception = exc_string.c_str();
}
+ Py_END_ALLOW_THREADS
- return 0;
-}
-
-static
-int
-hllcounter_set_erate(khmer_KHLLCounter_Object * me, PyObject *value,
- void *closure)
-{
- if (value == NULL) {
- PyErr_SetString(PyExc_TypeError, "Cannot delete attribute");
- return -1;
+ if (file_exception != NULL) {
+ PyErr_SetString(PyExc_OSError, file_exception);
+ return NULL;
}
-
- if (!PyFloat_Check(value)) {
- PyErr_SetString(PyExc_TypeError,
- "Please use a float value for k-mer size");
- return -1;
+ if (value_exception != NULL) {
+ PyErr_SetString(PyExc_ValueError, value_exception);
+ return NULL;
}
- double erate = PyFloat_AsDouble(value);
- try {
- me->hllcounter->set_erate(erate);
- } catch (InvalidValue &e) {
- PyErr_SetString(PyExc_ValueError, e.what());
- return -1;
- } catch (ReadOnlyAttribute &e) {
- PyErr_SetString(PyExc_AttributeError, e.what());
- return -1;
+ PyObject * x = PyList_New(MAX_BIGCOUNT + 1);
+ if (x == NULL) {
+ delete[] dist;
+ return NULL;
+ }
+ for (int i = 0; i < MAX_BIGCOUNT + 1; i++) {
+ PyList_SET_ITEM(x, i, PyLong_FromUnsignedLongLong(dist[i]));
}
- return 0;
-}
-
-static
-PyObject *
-hllcounter_getalpha(khmer_KHLLCounter_Object * me)
-{
- return PyFloat_FromDouble(me->hllcounter->get_alpha());
+ delete[] dist;
+ return x;
}
static
PyObject *
-hllcounter_getcounters(khmer_KHLLCounter_Object * me)
+hashtable_abundance_distribution(khmer_KHashtable_Object * me, PyObject * args)
{
- std::vector<int> counters = me->hllcounter->get_M();
+ Hashtable * hashtable = me->hashtable;
- PyObject * x = PyList_New(counters.size());
- for (size_t i = 0; i < counters.size(); i++) {
- PyList_SET_ITEM(x, i, PyLong_FromLong(counters[i]));
+ const char * filename = NULL;
+ khmer_KHashtable_Object * tracking_obj = NULL;
+ if (!PyArg_ParseTuple(args, "sO!", &filename, &khmer_KHashtable_Type,
+ &tracking_obj)) {
+ return NULL;
}
- return x;
-}
-
-static PyMethodDef khmer_hllcounter_methods[] = {
- {
- "add", (PyCFunction)hllcounter_add,
- METH_VARARGS,
- "Add a k-mer to the counter."
- },
- {
- "estimate_cardinality", (PyCFunction)hllcounter_estimate_cardinality,
- METH_VARARGS,
- "Return the current estimation."
- },
- {
- "consume_string", (PyCFunction)hllcounter_consume_string,
- METH_VARARGS,
- "Break a sequence into k-mers and add each k-mer to the counter."
- },
- {
- "consume_fasta", (PyCFunction)hllcounter_consume_fasta,
- METH_VARARGS | METH_KEYWORDS,
- "Read sequences from file, break into k-mers, "
- "and add each k-mer to the counter. If optional keyword 'stream_out' "
- "is True, also prints each sequence to stdout."
- },
- {
- "merge", (PyCFunction)hllcounter_merge,
- METH_VARARGS,
- "Merge other counter into this one."
- },
- {NULL} /* Sentinel */
-};
-
-static PyGetSetDef khmer_hllcounter_getseters[] = {
- {
- (char *)"alpha",
- (getter)hllcounter_getalpha, NULL,
- (char *)"alpha constant for this HLL counter.",
- NULL
- },
- {
- (char *)"error_rate",
- (getter)hllcounter_get_erate, (setter)hllcounter_set_erate,
- (char *)"Error rate for this HLL counter. "
- "Can be changed prior to first counting, but becomes read-only after "
- "that (raising AttributeError)",
- NULL
- },
- {
- (char *)"ksize",
- (getter)hllcounter_get_ksize, (setter)hllcounter_set_ksize,
- (char *)"k-mer size for this HLL counter."
- "Can be changed prior to first counting, but becomes read-only after "
- "that (raising AttributeError)",
- NULL
- },
- {
- (char *)"counters",
- (getter)hllcounter_getcounters, NULL,
- (char *)"Read-only internal counters.",
- NULL
- },
- {NULL} /* Sentinel */
-};
-
-static PyTypeObject khmer_KHLLCounter_Type = {
- PyVarObject_HEAD_INIT(NULL, 0)
- "_khmer.KHLLCounter", /* tp_name */
- sizeof(khmer_KHLLCounter_Object), /* tp_basicsize */
- 0, /* tp_itemsize */
- (destructor)khmer_hllcounter_dealloc, /* tp_dealloc */
- 0, /* tp_print */
- 0, /* tp_getattr */
- 0, /* tp_setattr */
- 0, /* tp_compare */
- 0, /* tp_repr */
- 0, /* tp_as_number */
- 0, /* tp_as_sequence */
- 0, /* tp_as_mapping */
- 0, /* tp_hash */
- 0, /* tp_call */
- 0, /* tp_str */
- 0, /* tp_getattro */
- 0, /* tp_setattro */
- 0, /* tp_as_buffer */
- Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */
- "HyperLogLog counter", /* tp_doc */
- 0, /* tp_traverse */
- 0, /* tp_clear */
- 0, /* tp_richcompare */
- 0, /* tp_weaklistoffset */
- 0, /* tp_iter */
- 0, /* tp_iternext */
- khmer_hllcounter_methods, /* tp_methods */
- 0, /* tp_members */
- khmer_hllcounter_getseters, /* tp_getset */
- 0, /* tp_base */
- 0, /* tp_dict */
- 0, /* tp_descr_get */
- 0, /* tp_descr_set */
- 0, /* tp_dictoffset */
- 0, /* tp_init */
- 0, /* tp_alloc */
- khmer_hllcounter_new, /* tp_new */
-};
-
-#define is_hllcounter_obj(v) (Py_TYPE(v) == &khmer_KHLLCounter_Type)
+ Hashtable *tracking = tracking_obj->hashtable;
+ uint64_t *dist = NULL;
+ const char *value_exception = NULL;
+ const char *file_exception = NULL;
+ std::string exc_string;
-static PyObject * hllcounter_merge(khmer_KHLLCounter_Object * me,
- PyObject * args)
-{
- khmer_KHLLCounter_Object * other;
+ Py_BEGIN_ALLOW_THREADS
+ try {
+ dist = hashtable->abundance_distribution<FastxReader>(filename, tracking);
+ } catch (khmer_file_exception &exc) {
+ exc_string = exc.what();
+ file_exception = exc_string.c_str();
+ } catch (khmer_value_exception &exc) {
+ exc_string = exc.what();
+ value_exception = exc_string.c_str();
+ }
+ Py_END_ALLOW_THREADS
- if (!PyArg_ParseTuple(args, "O!", &khmer_KHLLCounter_Type, &other)) {
+ if (file_exception != NULL) {
+ PyErr_SetString(PyExc_OSError, file_exception);
+ if (dist != NULL) {
+ delete []dist;
+ }
+ return NULL;
+ }
+ if (value_exception != NULL) {
+ PyErr_SetString(PyExc_ValueError, value_exception);
+ if (dist != NULL) {
+ delete []dist;
+ }
return NULL;
}
- try {
- me->hllcounter->merge(*(other->hllcounter));
- } catch (khmer_exception &e) {
- PyErr_SetString(PyExc_ValueError, e.what());
+ PyObject * x = PyList_New(MAX_BIGCOUNT + 1);
+ if (x == NULL) {
+ if (dist != NULL) {
+ delete []dist;
+ }
return NULL;
}
+ for (int i = 0; i < MAX_BIGCOUNT + 1; i++) {
+ PyList_SET_ITEM(x, i, PyLong_FromUnsignedLongLong(dist[i]));
+ }
- Py_RETURN_NONE;
+ if (dist != NULL) {
+ delete []dist;
+ }
+
+ return x;
}
//////////////////////////////
@@ -4752,12 +4565,18 @@ static PyObject * forward_hash(PyObject * self, PyObject * args)
return NULL;
}
+ if (strlen(kmer) != ksize) {
+ PyErr_Format(PyExc_ValueError, "k-mer size different from ksize");
+ return NULL;
+ }
+
try {
- PyObject * hash;
- hash = PyLong_FromUnsignedLongLong(_hash(kmer, ksize));
+ PyObject * hash = nullptr;
+ const HashIntoType h(_hash(kmer, ksize));
+ convert_HashIntoType_to_PyObject(h, &hash);
return hash;
} catch (khmer_exception &e) {
- PyErr_SetString(PyExc_RuntimeError, e.what());
+ PyErr_SetString(PyExc_ValueError, e.what());
return NULL;
}
@@ -4783,15 +4602,29 @@ static PyObject * forward_hash_no_rc(PyObject * self, PyObject * args)
return NULL;
}
- return PyLong_FromUnsignedLongLong(_hash_forward(kmer, ksize));
+ PyObject * hash = nullptr;
+ const HashIntoType h(_hash_forward(kmer, ksize));
+ convert_HashIntoType_to_PyObject(h, &hash);
+ return hash;
}
static PyObject * reverse_hash(PyObject * self, PyObject * args)
{
- HashIntoType val;
+ PyObject * val;
+ HashIntoType hash;
WordLength ksize;
- if (!PyArg_ParseTuple(args, "Kb", &val, &ksize)) {
+ if (!PyArg_ParseTuple(args, "Ob", &val, &ksize)) {
+ return NULL;
+ }
+
+ if (PyLong_Check(val) || PyInt_Check(val)) {
+ if (!convert_PyLong_to_HashIntoType(val, hash)) {
+ return NULL;
+ }
+ } else {
+ PyErr_SetString(PyExc_TypeError,
+ "Hash value must be an integer.");
return NULL;
}
@@ -4800,7 +4633,7 @@ static PyObject * reverse_hash(PyObject * self, PyObject * args)
return NULL;
}
- return PyUnicode_FromString(_revhash(val, ksize).c_str());
+ return PyUnicode_FromString(_revhash(hash, ksize).c_str());
}
static PyObject * murmur3_forward_hash(PyObject * self, PyObject * args)
@@ -4811,7 +4644,10 @@ static PyObject * murmur3_forward_hash(PyObject * self, PyObject * args)
return NULL;
}
- return PyLong_FromUnsignedLongLong(_hash_murmur(kmer));
+ PyObject * hash = nullptr;
+ const HashIntoType h(_hash_murmur(kmer, strlen(kmer)));
+ convert_HashIntoType_to_PyObject(h, &hash);
+ return hash;
}
static PyObject * murmur3_forward_hash_no_rc(PyObject * self, PyObject * args)
@@ -4822,7 +4658,27 @@ static PyObject * murmur3_forward_hash_no_rc(PyObject * self, PyObject * args)
return NULL;
}
- return PyLong_FromUnsignedLongLong(_hash_murmur_forward(kmer));
+ PyObject * hash = nullptr;
+ const HashIntoType h(_hash_murmur_forward(kmer, strlen(kmer)));
+ convert_HashIntoType_to_PyObject(h, &hash);
+ return hash;
+}
+
+static PyObject * reverse_complement(PyObject * self, PyObject * args)
+{
+ const char * sequence;
+ if (!PyArg_ParseTuple(args, "s", &sequence)) {
+ return NULL;
+ }
+
+ std::string s(sequence);
+ try {
+ s = _revcomp(s);
+ } catch (khmer_exception &e) {
+ PyErr_SetString(PyExc_RuntimeError, e.what());
+ return NULL;
+ }
+ return PyUnicode_FromString(s.c_str());
}
//
@@ -4873,6 +4729,13 @@ static PyMethodDef KhmerMethods[] = {
"(no reverse complement)",
},
{
+ "reverse_complement",
+ reverse_complement,
+ METH_VARARGS,
+ "Calculate the reverse-complement of the DNA sequence "
+ "with alphabet ACGT",
+ },
+ {
"get_version_cpp", get_version_cpp,
METH_VARARGS, "return the VERSION c++ compiler option"
},
@@ -4887,11 +4750,37 @@ MOD_INIT(_khmer)
return MOD_ERROR_VAL;
}
- khmer_KCountgraph_Type.tp_base = &khmer_KHashtable_Type;
+ khmer_KCounttable_Type.tp_base = &khmer_KHashtable_Type;
+ if (PyType_Ready(&khmer_KCounttable_Type) < 0) {
+ return MOD_ERROR_VAL;
+ }
+
+ khmer_KSmallCounttable_Type.tp_base = &khmer_KHashtable_Type;
+ if (PyType_Ready(&khmer_KSmallCounttable_Type) < 0) {
+ return MOD_ERROR_VAL;
+ }
+
+ khmer_KNodetable_Type.tp_base = &khmer_KHashtable_Type;
+ if (PyType_Ready(&khmer_KNodetable_Type) < 0) {
+ return MOD_ERROR_VAL;
+ }
+
+ khmer_KHashgraph_Type.tp_base = &khmer_KHashtable_Type;
+ khmer_KHashgraph_Type.tp_methods = khmer_hashgraph_methods;
+ if (PyType_Ready(&khmer_KHashgraph_Type) < 0) {
+ return MOD_ERROR_VAL;
+ }
+
+ khmer_KCountgraph_Type.tp_base = &khmer_KHashgraph_Type;
if (PyType_Ready(&khmer_KCountgraph_Type) < 0) {
return MOD_ERROR_VAL;
}
+ khmer_KSmallCountgraph_Type.tp_base = &khmer_KHashgraph_Type;
+ if (PyType_Ready(&khmer_KSmallCountgraph_Type) < 0) {
+ return MOD_ERROR_VAL;
+ }
+
if (PyType_Ready(&khmer_PrePartitionInfo_Type) < 0) {
return MOD_ERROR_VAL;
}
@@ -4901,12 +4790,22 @@ MOD_INIT(_khmer)
return MOD_ERROR_VAL;
}
- khmer_KNodegraph_Type.tp_base = &khmer_KHashtable_Type;
- khmer_KNodegraph_Type.tp_methods = khmer_hashbits_methods;
+ khmer_KNodegraph_Type.tp_base = &khmer_KHashgraph_Type;
+ khmer_KNodegraph_Type.tp_methods = khmer_nodegraph_methods;
if (PyType_Ready(&khmer_KNodegraph_Type) < 0) {
return MOD_ERROR_VAL;
}
+ if (PyType_Ready(&khmer_KLinearAssembler_Type) < 0) {
+ return MOD_ERROR_VAL;
+ }
+ if (PyType_Ready(&khmer_KSimpleLabeledAssembler_Type) < 0) {
+ return MOD_ERROR_VAL;
+ }
+ if (PyType_Ready(&khmer_KJunctionCountAssembler_Type) < 0) {
+ return MOD_ERROR_VAL;
+ }
+
khmer_KGraphLabels_Type.tp_base = &khmer_KNodegraph_Type;
khmer_KGraphLabels_Type.tp_methods = khmer_graphlabels_methods;
khmer_KGraphLabels_Type.tp_new = khmer_graphlabels_new;
@@ -4943,18 +4842,60 @@ MOD_INIT(_khmer)
return MOD_ERROR_VAL;
}
+ PyObject * filetype_dict = Py_BuildValue("{s,i,s,i,s,i,s,i,s,i,s,i,s,i}",
+ "COUNTING_HT", SAVED_COUNTING_HT,
+ "HASHBITS", SAVED_HASHBITS,
+ "TAGS", SAVED_TAGS,
+ "STOPTAGS", SAVED_STOPTAGS,
+ "SUBSET", SAVED_SUBSET,
+ "LABELSET", SAVED_LABELSET,
+ "SMALLCOUNT", SAVED_SMALLCOUNT);
+ if (PyModule_AddObject( m, "FILETYPES", filetype_dict ) < 0) {
+ return MOD_ERROR_VAL;
+ }
+
+ Py_INCREF(&khmer_Read_Type);
+ if (PyModule_AddObject( m, "Read",
+ (PyObject *)&khmer_Read_Type ) < 0) {
+ return MOD_ERROR_VAL;
+ }
+
Py_INCREF(&khmer_ReadParser_Type);
if (PyModule_AddObject( m, "ReadParser",
(PyObject *)&khmer_ReadParser_Type ) < 0) {
return MOD_ERROR_VAL;
}
+ Py_INCREF(&khmer_KCounttable_Type);
+ if (PyModule_AddObject( m, "Counttable",
+ (PyObject *)&khmer_KCounttable_Type ) < 0) {
+ return MOD_ERROR_VAL;
+ }
+
+ Py_INCREF(&khmer_KSmallCounttable_Type);
+ if (PyModule_AddObject( m, "SmallCounttable",
+ (PyObject *)&khmer_KSmallCounttable_Type ) < 0) {
+ return MOD_ERROR_VAL;
+ }
+
+ Py_INCREF(&khmer_KNodetable_Type);
+ if (PyModule_AddObject( m, "Nodetable",
+ (PyObject *)&khmer_KNodetable_Type ) < 0) {
+ return MOD_ERROR_VAL;
+ }
+
Py_INCREF(&khmer_KCountgraph_Type);
if (PyModule_AddObject( m, "Countgraph",
(PyObject *)&khmer_KCountgraph_Type ) < 0) {
return MOD_ERROR_VAL;
}
+ Py_INCREF(&khmer_KSmallCountgraph_Type);
+ if (PyModule_AddObject( m, "SmallCountgraph",
+ (PyObject *)&khmer_KSmallCountgraph_Type ) < 0) {
+ return MOD_ERROR_VAL;
+ }
+
Py_INCREF(&khmer_KNodegraph_Type);
if (PyModule_AddObject(m, "Nodegraph",
(PyObject *)&khmer_KNodegraph_Type) < 0) {
@@ -4967,6 +4908,33 @@ MOD_INIT(_khmer)
return MOD_ERROR_VAL;
}
+ Py_INCREF(&khmer_KLinearAssembler_Type);
+ if (PyModule_AddObject(m, "LinearAssembler",
+ (PyObject *)&khmer_KLinearAssembler_Type) < 0) {
+ return MOD_ERROR_VAL;
+ }
+
+ Py_INCREF(&khmer_KSimpleLabeledAssembler_Type);
+ if (PyModule_AddObject(m, "SimpleLabeledAssembler",
+ (PyObject *)&khmer_KSimpleLabeledAssembler_Type) < 0) {
+ return MOD_ERROR_VAL;
+ }
+
+ Py_INCREF(&khmer_KJunctionCountAssembler_Type);
+ if (PyModule_AddObject(m, "JunctionCountAssembler",
+ (PyObject *)&khmer_KJunctionCountAssembler_Type) < 0) {
+ return MOD_ERROR_VAL;
+ }
+
+ if (PyType_Ready(&_HashSet_iter_Type) < 0) {
+ return MOD_ERROR_VAL;
+ }
+
+ khmer_HashSet_Type.tp_new = khmer_HashSet_new;
+ if (PyType_Ready(&khmer_HashSet_Type) < 0) {
+ return MOD_ERROR_VAL;
+ }
+
Py_INCREF(&khmer_KHLLCounter_Type);
if (PyModule_AddObject(m, "HLLCounter",
(PyObject *)&khmer_KHLLCounter_Type) < 0) {
@@ -4979,6 +4947,12 @@ MOD_INIT(_khmer)
return MOD_ERROR_VAL;
}
+ Py_INCREF(&khmer_HashSet_Type);
+ if (PyModule_AddObject(m, "HashSet",
+ (PyObject *)&khmer_HashSet_Type) < 0) {
+ return MOD_ERROR_VAL;
+ }
+
return MOD_SUCCESS_VAL(m);
}
diff --git a/khmer/_version.py b/khmer/_version.py
index b46a20e..aba32a7 100644
--- a/khmer/_version.py
+++ b/khmer/_version.py
@@ -1,4 +1,3 @@
-from __future__ import print_function
# This file helps to compute a version number in source trees obtained from
# git-archive tarball (such as those provided by githubs download-from-tag
@@ -7,7 +6,9 @@ from __future__ import print_function
# that just contains the computed version number.
# This file is released into the public domain. Generated by
-# versioneer-0.14 (https://github.com/warner/python-versioneer)
+# versioneer-0.15+dev (https://github.com/warner/python-versioneer)
+
+"""Git implementation of _version.py."""
import errno
import os
@@ -15,21 +16,65 @@ import re
import subprocess
import sys
-# these strings will be replaced by git during git-archive
-git_refnames = " (HEAD -> master, tag: v2.0)"
-git_full = "c2cc671127b97083e87989c0822ea036dd8202dc"
-# these strings are filled in when 'setup.py versioneer' creates _version.py
-tag_prefix = "v"
-parentdir_prefix = "."
-versionfile_source = "khmer/_version.py"
+def get_keywords():
+ """Get the keywords needed to look up the version information."""
+ # these strings will be replaced by git during git-archive.
+ # setup.py/versioneer.py will grep for the variable names, so they must
+ # each be defined on a line of their own. _version.py will just call
+ # get_keywords().
+ git_refnames = " (HEAD -> master)"
+ git_full = "b2ab51575c2fa4c6bff078387ed8b67c4299df12"
+ keywords = {"refnames": git_refnames, "full": git_full}
+ return keywords
+
+
+class VersioneerConfig:
+
+ """Container for Versioneer configuration parameters."""
+
+
+def get_config():
+ """Create, populate and return the VersioneerConfig() object."""
+ # these strings are filled in when 'setup.py versioneer' creates
+ # _version.py
+ cfg = VersioneerConfig()
+ cfg.VCS = "git"
+ cfg.style = "pep440"
+ cfg.tag_prefix = "v"
+ cfg.parentdir_prefix = "."
+ cfg.versionfile_source = "khmer/_version.py"
+ cfg.verbose = False
+ return cfg
+
+
+class NotThisMethod(Exception):
+
+ """Exception raised if a method is not valid for the current scenario."""
+
+
+LONG_VERSION_PY = {}
+HANDLERS = {}
+
+
+def register_vcs_handler(vcs, method): # decorator
+ """Decorator to mark a method as the handler for a particular VCS."""
+ def decorate(f):
+ """Store f in HANDLERS[vcs][method]."""
+ if vcs not in HANDLERS:
+ HANDLERS[vcs] = {}
+ HANDLERS[vcs][method] = f
+ return f
+ return decorate
def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False):
+ """Call the given command(s)."""
assert isinstance(commands, list)
p = None
for c in commands:
try:
+ dispcmd = str([c] + args)
# remember shell=False, so use git.cmd on windows, not just git
p = subprocess.Popen([c] + args, cwd=cwd, stdout=subprocess.PIPE,
stderr=(subprocess.PIPE if hide_stderr
@@ -40,7 +85,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False):
if e.errno == errno.ENOENT:
continue
if verbose:
- print("unable to run %s" % args[0])
+ print("unable to run %s" % dispcmd)
print(e)
return None
else:
@@ -52,24 +97,31 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False):
stdout = stdout.decode()
if p.returncode != 0:
if verbose:
- print("unable to run %s (error)" % args[0])
+ print("unable to run %s (error)" % dispcmd)
return None
return stdout
-def versions_from_parentdir(parentdir_prefix, root, verbose=False):
- # Source tarballs conventionally unpack into a directory that includes
- # both the project name and a version string.
+def versions_from_parentdir(parentdir_prefix, root, verbose):
+ """Try to determine the version from the parent directory name.
+
+ Source tarballs conventionally unpack into a directory that includes
+ both the project name and a version string.
+ """
dirname = os.path.basename(root)
if not dirname.startswith(parentdir_prefix):
if verbose:
print("guessing rootdir is '%s', but '%s' doesn't start with "
"prefix '%s'" % (root, dirname, parentdir_prefix))
- return None
- return {"version": dirname[len(parentdir_prefix):], "full": ""}
+ raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
+ return {"version": dirname[len(parentdir_prefix):],
+ "full-revisionid": None,
+ "dirty": False, "error": None}
+ at register_vcs_handler("git", "get_keywords")
def git_get_keywords(versionfile_abs):
+ """Extract version information from the given file."""
# the code embedded in _version.py can just fetch the value of these
# keywords. When used from setup.py, we don't want to import _version.py,
# so we do it with a regexp instead. This function is not used from
@@ -92,14 +144,16 @@ def git_get_keywords(versionfile_abs):
return keywords
-def git_versions_from_keywords(keywords, tag_prefix, verbose=False):
+ at register_vcs_handler("git", "keywords")
+def git_versions_from_keywords(keywords, tag_prefix, verbose):
+ """Get version information from git keywords."""
if not keywords:
- return {} # keyword-finding function failed to find keywords
+ raise NotThisMethod("no keywords at all, weird")
refnames = keywords["refnames"].strip()
if refnames.startswith("$Format"):
if verbose:
print("keywords are unexpanded, not using")
- return {} # unexpanded, so not in an unpacked git-archive tarball
+ raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
refs = set([r.strip() for r in refnames.strip("()").split(",")])
# starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
# just "foo-1.0". If we see a "tag: " prefix, prefer those.
@@ -125,116 +179,308 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose=False):
if verbose:
print("picking %s" % r)
return {"version": r,
- "full": keywords["full"].strip()}
+ "full-revisionid": keywords["full"].strip(),
+ "dirty": False, "error": None
+ }
# no suitable tags, so version is "0+unknown", but full hex is still there
if verbose:
print("no suitable tags, using unknown + full revision id")
return {"version": "0+unknown",
- "full": keywords["full"].strip()}
+ "full-revisionid": keywords["full"].strip(),
+ "dirty": False, "error": "no suitable tags"}
+
+ at register_vcs_handler("git", "pieces_from_vcs")
+def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
+ """Get version from 'git describe' in the root of the source tree.
-def git_parse_vcs_describe(git_describe, tag_prefix, verbose=False):
- # TAG-NUM-gHEX[-dirty] or HEX[-dirty] . TAG might have hyphens.
+ This only gets called if the git-archive 'subst' keywords were *not*
+ expanded, and _version.py hasn't already been rewritten with a short
+ version string, meaning we're inside a checked out source tree.
+ """
+ if not os.path.exists(os.path.join(root, ".git")):
+ if verbose:
+ print("no .git in %s" % root)
+ raise NotThisMethod("no .git directory")
- # dirty
+ GITS = ["git"]
+ if sys.platform == "win32":
+ GITS = ["git.cmd", "git.exe"]
+ # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
+ # if there isn't one, this yields HEX[-dirty] (no NUM)
+ describe_out = run_command(GITS, ["describe", "--tags", "--dirty",
+ "--always", "--long",
+ "--match", "%s*" % tag_prefix],
+ cwd=root)
+ # --long was added in git-1.5.5
+ if describe_out is None:
+ raise NotThisMethod("'git describe' failed")
+ describe_out = describe_out.strip()
+ full_out = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
+ if full_out is None:
+ raise NotThisMethod("'git rev-parse' failed")
+ full_out = full_out.strip()
+
+ pieces = {}
+ pieces["long"] = full_out
+ pieces["short"] = full_out[:7] # maybe improved later
+ pieces["error"] = None
+
+ # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
+ # TAG might have hyphens.
+ git_describe = describe_out
+
+ # look for -dirty suffix
dirty = git_describe.endswith("-dirty")
+ pieces["dirty"] = dirty
if dirty:
git_describe = git_describe[:git_describe.rindex("-dirty")]
- dirty_suffix = ".dirty" if dirty else ""
# now we have TAG-NUM-gHEX or HEX
- if "-" not in git_describe: # just HEX
- return "0+untagged.g" + git_describe + dirty_suffix, dirty
+ if "-" in git_describe:
+ # TAG-NUM-gHEX
+ mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
+ if not mo:
+ # unparseable. Maybe git-describe is misbehaving?
+ pieces["error"] = ("unable to parse git-describe output: '%s'"
+ % describe_out)
+ return pieces
+
+ # tag
+ full_tag = mo.group(1)
+ if not full_tag.startswith(tag_prefix):
+ if verbose:
+ fmt = "tag '%s' doesn't start with prefix '%s'"
+ print(fmt % (full_tag, tag_prefix))
+ pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
+ % (full_tag, tag_prefix))
+ return pieces
+ pieces["closest-tag"] = full_tag[len(tag_prefix):]
- # just TAG-NUM-gHEX
- mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
- if not mo:
- # unparseable. Maybe git-describe is misbehaving?
- return "0+unparseable" + dirty_suffix, dirty
+ # distance: number of commits since tag
+ pieces["distance"] = int(mo.group(2))
- # tag
- full_tag = mo.group(1)
- if not full_tag.startswith(tag_prefix):
- if verbose:
- fmt = "tag '%s' doesn't start with prefix '%s'"
- print(fmt % (full_tag, tag_prefix))
- return None, dirty
- tag = full_tag[len(tag_prefix):]
+ # commit: short hex revision ID
+ pieces["short"] = mo.group(3)
- # distance: number of commits since tag
- distance = int(mo.group(2))
+ else:
+ # HEX: no tags
+ pieces["closest-tag"] = None
+ count_out = run_command(GITS, ["rev-list", "HEAD", "--count"],
+ cwd=root)
+ pieces["distance"] = int(count_out) # total number of commits
+
+ return pieces
+
+
+def plus_or_dot(pieces):
+ """Return a + if we don't already have one, else return a ."""
+ if "+" in pieces.get("closest-tag", ""):
+ return "."
+ return "+"
+
+
+def render_pep440(pieces):
+ """Build up version string, with post-release "local version identifier".
+
+ Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
+ get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty
+
+ Exceptions:
+ 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty]
+ """
+ if pieces["closest-tag"]:
+ rendered = pieces["closest-tag"]
+ if pieces["distance"] or pieces["dirty"]:
+ rendered += plus_or_dot(pieces)
+ rendered += "%d.g%s" % (pieces["distance"], pieces["short"])
+ if pieces["dirty"]:
+ rendered += ".dirty"
+ else:
+ # exception #1
+ rendered = "0+untagged.%d.g%s" % (pieces["distance"],
+ pieces["short"])
+ if pieces["dirty"]:
+ rendered += ".dirty"
+ return rendered
+
+
+def render_pep440_pre(pieces):
+ """TAG[.post.devDISTANCE] -- No -dirty.
+
+ Exceptions:
+ 1: no tags. 0.post.devDISTANCE
+ """
+ if pieces["closest-tag"]:
+ rendered = pieces["closest-tag"]
+ if pieces["distance"]:
+ rendered += ".post.dev%d" % pieces["distance"]
+ else:
+ # exception #1
+ rendered = "0.post.dev%d" % pieces["distance"]
+ return rendered
+
+
+def render_pep440_post(pieces):
+ """TAG[.postDISTANCE[.dev0]+gHEX] .
+
+ The ".dev0" means dirty. Note that .dev0 sorts backwards
+ (a dirty tree will appear "older" than the corresponding clean one),
+ but you shouldn't be releasing software with -dirty anyways.
+
+ Exceptions:
+ 1: no tags. 0.postDISTANCE[.dev0]
+ """
+ if pieces["closest-tag"]:
+ rendered = pieces["closest-tag"]
+ if pieces["distance"] or pieces["dirty"]:
+ rendered += ".post%d" % pieces["distance"]
+ if pieces["dirty"]:
+ rendered += ".dev0"
+ rendered += plus_or_dot(pieces)
+ rendered += "g%s" % pieces["short"]
+ else:
+ # exception #1
+ rendered = "0.post%d" % pieces["distance"]
+ if pieces["dirty"]:
+ rendered += ".dev0"
+ rendered += "+g%s" % pieces["short"]
+ return rendered
+
+
+def render_pep440_old(pieces):
+ """TAG[.postDISTANCE[.dev0]] .
+
+ The ".dev0" means dirty.
+
+ Eexceptions:
+ 1: no tags. 0.postDISTANCE[.dev0]
+ """
+ if pieces["closest-tag"]:
+ rendered = pieces["closest-tag"]
+ if pieces["distance"] or pieces["dirty"]:
+ rendered += ".post%d" % pieces["distance"]
+ if pieces["dirty"]:
+ rendered += ".dev0"
+ else:
+ # exception #1
+ rendered = "0.post%d" % pieces["distance"]
+ if pieces["dirty"]:
+ rendered += ".dev0"
+ return rendered
- # commit: short hex revision ID
- commit = mo.group(3)
- # now build up version string, with post-release "local version
- # identifier". Our goal: TAG[+NUM.gHEX[.dirty]] . Note that if you get a
- # tagged build and then dirty it, you'll get TAG+0.gHEX.dirty . So you
- # can always test version.endswith(".dirty").
- version = tag
- if distance or dirty:
- version += "+%d.g%s" % (distance, commit) + dirty_suffix
+def render_git_describe(pieces):
+ """TAG[-DISTANCE-gHEX][-dirty].
- return version, dirty
+ Like 'git describe --tags --dirty --always'.
+ Exceptions:
+ 1: no tags. HEX[-dirty] (note: no 'g' prefix)
+ """
+ if pieces["closest-tag"]:
+ rendered = pieces["closest-tag"]
+ if pieces["distance"]:
+ rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
+ else:
+ # exception #1
+ rendered = pieces["short"]
+ if pieces["dirty"]:
+ rendered += "-dirty"
+ return rendered
-def git_versions_from_vcs(tag_prefix, root, verbose=False):
- # this runs 'git' from the root of the source tree. This only gets called
- # if the git-archive 'subst' keywords were *not* expanded, and
- # _version.py hasn't already been rewritten with a short version string,
- # meaning we're inside a checked out source tree.
- if not os.path.exists(os.path.join(root, ".git")):
- if verbose:
- print("no .git in %s" % root)
- return {} # get_versions() will try next method
+def render_git_describe_long(pieces):
+ """TAG-DISTANCE-gHEX[-dirty].
- GITS = ["git"]
- if sys.platform == "win32":
- GITS = ["git.cmd", "git.exe"]
- # if there is a tag, this yields TAG-NUM-gHEX[-dirty]
- # if there are no tags, this yields HEX[-dirty] (no NUM)
- stdout = run_command(GITS, ["describe", "--tags", "--dirty",
- "--always", "--long"],
- cwd=root)
- # --long was added in git-1.5.5
- if stdout is None:
- return {} # try next method
- version, dirty = git_parse_vcs_describe(stdout, tag_prefix, verbose)
-
- # build "full", which is FULLHEX[.dirty]
- stdout = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
- if stdout is None:
- return {}
- full = stdout.strip()
- if dirty:
- full += ".dirty"
+ Like 'git describe --tags --dirty --always -long'.
+ The distance/hash is unconditional.
- return {"version": version, "full": full}
+ Exceptions:
+ 1: no tags. HEX[-dirty] (note: no 'g' prefix)
+ """
+ if pieces["closest-tag"]:
+ rendered = pieces["closest-tag"]
+ rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
+ else:
+ # exception #1
+ rendered = pieces["short"]
+ if pieces["dirty"]:
+ rendered += "-dirty"
+ return rendered
+
+
+def render(pieces, style):
+ """Render the given version pieces into the requested style."""
+ if pieces["error"]:
+ return {"version": "unknown",
+ "full-revisionid": pieces.get("long"),
+ "dirty": None,
+ "error": pieces["error"]}
+
+ if not style or style == "default":
+ style = "pep440" # the default
+
+ if style == "pep440":
+ rendered = render_pep440(pieces)
+ elif style == "pep440-pre":
+ rendered = render_pep440_pre(pieces)
+ elif style == "pep440-post":
+ rendered = render_pep440_post(pieces)
+ elif style == "pep440-old":
+ rendered = render_pep440_old(pieces)
+ elif style == "git-describe":
+ rendered = render_git_describe(pieces)
+ elif style == "git-describe-long":
+ rendered = render_git_describe_long(pieces)
+ else:
+ raise ValueError("unknown style '%s'" % style)
+ return {"version": rendered, "full-revisionid": pieces["long"],
+ "dirty": pieces["dirty"], "error": None}
-def get_versions(default={"version": "0+unknown", "full": ""}, verbose=False):
+
+def get_versions():
+ """Get version information or return default if unable to do so."""
# I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have
# __file__, we can work backwards from there to the root. Some
# py2exe/bbfreeze/non-CPython implementations don't do __file__, in which
# case we can only use expanded keywords.
- keywords = {"refnames": git_refnames, "full": git_full}
- ver = git_versions_from_keywords(keywords, tag_prefix, verbose)
- if ver:
- return ver
+ cfg = get_config()
+ verbose = cfg.verbose
+
+ try:
+ return git_versions_from_keywords(get_keywords(), cfg.tag_prefix,
+ verbose)
+ except NotThisMethod:
+ pass
try:
root = os.path.realpath(__file__)
# versionfile_source is the relative path from the top of the source
# tree (where the .git directory might live) to this file. Invert
# this to find the root from __file__.
- for i in versionfile_source.split('/'):
+ for i in cfg.versionfile_source.split('/'):
root = os.path.dirname(root)
except NameError:
- return default
+ return {"version": "0+unknown", "full-revisionid": None,
+ "dirty": None,
+ "error": "unable to find root of source tree"}
+
+ try:
+ pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
+ return render(pieces, cfg.style)
+ except NotThisMethod:
+ pass
+
+ try:
+ if cfg.parentdir_prefix:
+ return versions_from_parentdir(cfg.parentdir_prefix, root, verbose)
+ except NotThisMethod:
+ pass
- return (git_versions_from_vcs(tag_prefix, root, verbose)
- or versions_from_parentdir(parentdir_prefix, root, verbose)
- or default)
+ return {"version": "0+unknown", "full-revisionid": None,
+ "dirty": None,
+ "error": "unable to compute version"}
diff --git a/khmer/kfile.py b/khmer/kfile.py
index 5962b8c..9228833 100644
--- a/khmer/kfile.py
+++ b/khmer/kfile.py
@@ -34,7 +34,7 @@
# Contact: khmer-project at idyll.org
"""File handling/checking utilities for command-line scripts."""
-from __future__ import print_function, unicode_literals
+from __future__ import print_function, unicode_literals, division
import os
import sys
@@ -42,7 +42,6 @@ import errno
from stat import S_ISBLK, S_ISFIFO, S_ISCHR
import gzip
import bz2file
-from khmer import khmer_args
def check_input_files(file_path, force):
@@ -152,7 +151,12 @@ def check_space(in_files, force, _testhook_free_space=None):
def check_space_for_graph(outfile_name, hash_size, force,
_testhook_free_space=None):
- """Check that we have enough size to write the specified graph."""
+ """
+ Check that we have enough size to write the specified graph.
+
+ The "hash_size" parameter should equal the total bytes required for the
+ entire data structure.
+ """
dir_path = os.path.dirname(os.path.realpath(outfile_name))
target = os.statvfs(dir_path)
@@ -163,18 +167,19 @@ def check_space_for_graph(outfile_name, hash_size, force,
size_diff = hash_size - free_space
if size_diff > 0:
- print("ERROR: Not enough free space on disk "
- "for saved graph files;"
- " Need at least %.1f GB more."
- % (float(size_diff) / 1e9,), file=sys.stderr)
- print(" Table size: %.1f GB"
- % (float(hash_size) / 1e9,), file=sys.stderr)
- print(" Free space: %.1f GB"
- % (float(free_space) / 1e9,), file=sys.stderr)
- if not force:
- print("NOTE: This can be overridden using the --force argument",
- file=sys.stderr)
- sys.exit(1)
+ mem_needed = '{:.1f} GB'.format(size_diff / 1e9)
+ mem_requested = '{:.1f} GB'.format(hash_size / 1e9)
+ mem_available = '{:.1f} GB'.format(free_space / 1e9)
+ message = 'Not enough free space on disk for saved graph files;'
+ message += '\n Need at least {:s} more.'.format(mem_needed)
+ message += '\n Table size: {:s}'.format(mem_requested)
+ message += '\n Free space: {:s}'.format(mem_available)
+ if force:
+ print('WARNING:', message, file=sys.stderr)
+ else:
+ message = 'ERROR: ' + message + \
+ '\nNOTE: This can be overridden using the --force argument'
+ raise SystemExit(message)
def check_valid_file_exists(in_files):
@@ -210,6 +215,7 @@ def is_block(fthing):
def describe_file_handle(fthing):
+ """Return the name of file or a description."""
if is_block(fthing):
return "block device"
else:
@@ -230,7 +236,7 @@ def get_file_writer(file_handle, do_gzip, do_bzip):
ofile = None
if do_gzip and do_bzip:
- raise Exception("Cannot specify both bzip and gzip compression!")
+ raise ValueError("Cannot specify both bzip and gzip compression!")
if do_gzip:
ofile = gzip.GzipFile(fileobj=file_handle, mode='w')
diff --git a/khmer/khmer_args.py b/khmer/khmer_args.py
index d8e43df..6f00e01 100644
--- a/khmer/khmer_args.py
+++ b/khmer/khmer_args.py
@@ -1,7 +1,7 @@
# vim: set encoding=utf-8
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2011-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -33,21 +33,25 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
+"""Common argparse constructs."""
from __future__ import unicode_literals
from __future__ import print_function
import sys
-import os
import argparse
import math
import textwrap
from argparse import _VersionAction
from collections import namedtuple
+try:
+ from StringIO import StringIO
+except ImportError:
+ from io import StringIO
import screed
import khmer
-from khmer import extract_countgraph_info, extract_nodegraph_info
+from khmer import extract_countgraph_info
from khmer import __version__
from .utils import print_error
from .khmer_logger import log_info, log_warn, configure_logging
@@ -58,10 +62,50 @@ DEFAULT_N_TABLES = 4
DEFAULT_MAX_TABLESIZE = 1e6
DEFAULT_N_THREADS = 1
+ALGORITHMS = {
+ 'software': 'MR Crusoe et al., '
+ '2015. http://dx.doi.org/10.12688/f1000research.6924.1',
+ 'diginorm': 'CT Brown et al., arXiv:1203.4802 [q-bio.GN]',
+ 'streaming': 'Q Zhang, S Awad, CT Brown, '
+ 'https://dx.doi.org/10.7287/peerj.preprints.890v1',
+ 'graph': 'J Pell et al., http://dx.doi.org/10.1073/pnas.1121464109',
+ 'counting': 'Q Zhang et al., '
+ 'http://dx.doi.org/10.1371/journal.pone.0101271',
+ 'sweep': 'C Scott, MR Crusoe, and CT Brown, unpublished',
+ 'SeqAn': 'A. Döring et al. http://dx.doi.org:80/10.1186/1471-2105-9-11',
+ 'hll': 'Irber and Brown. http://dx.doi.org/10.1101/056846'
+}
+
+
+class CitationAction(argparse.Action):
+ # pylint: disable=too-few-public-methods
+ """Output citation information and exit."""
+
+ def __init__(self, *args, **kwargs):
+ self.citations = kwargs.pop('citations')
+ super(CitationAction, self).__init__(*args, nargs=0, **kwargs)
+
+ def __call__(self, parser, namespace, values, option_string=None):
+ info(parser.prog, self.citations)
+ parser.exit()
+
+
+class _HelpAction(argparse._HelpAction):
+ # pylint: disable=too-few-public-methods, protected-access
+ def __call__(self, parser, namespace, values, option_string=None):
+ info(parser.prog, parser._citations)
+ super(_HelpAction, self).__call__(parser, namespace, values,
+ option_string=option_string)
+
class _VersionStdErrAction(_VersionAction):
+ # pylint: disable=too-few-public-methods, protected-access
+ """Force output to StdErr."""
def __call__(self, parser, namespace, values, option_string=None):
+ # have to call info() directly as the version action exits
+ # which means parse_args() does not get a chance to run
+ info(parser.prog, parser._citations)
version = self.version
if version is None:
version = parser.version
@@ -73,12 +117,97 @@ class _VersionStdErrAction(_VersionAction):
class ComboFormatter(argparse.ArgumentDefaultsHelpFormatter,
argparse.RawDescriptionHelpFormatter):
+ """Both ArgumentDefaults and RawDescription formatters."""
+
pass
+class KhmerArgumentParser(argparse.ArgumentParser):
+ """Specialize ArgumentParser with khmer defaults.
+
+ Take care of common arguments and setup printing of citation information.
+ """
+
+ def __init__(self, citations=None, formatter_class=ComboFormatter,
+ **kwargs):
+ super(KhmerArgumentParser, self).__init__(
+ formatter_class=formatter_class, add_help=False, **kwargs)
+ self._citations = citations
+
+ self.add_argument('--version', action=_VersionStdErrAction,
+ version='khmer {v}'.format(v=__version__))
+ self.add_argument('--info', action=CitationAction,
+ citations=self._citations)
+ self.add_argument('-h', '--help', action=_HelpAction,
+ default=argparse.SUPPRESS,
+ help='show this help message and exit')
+
+ def parse_args(self, args=None, namespace=None):
+ args = super(KhmerArgumentParser, self).parse_args(args=args,
+ namespace=namespace)
+
+ # some scripts do not have a quiet flag, assume quiet=False for those
+ if 'quiet' not in args or not args.quiet:
+ info(self.prog, self._citations)
+
+ return args
+
+
+# Temporary fix to argparse FileType which ignores the
+# binary mode flag. Upstream bug tracked in https://bugs.python.org/issue14156
+# pylint: disable=too-few-public-methods,missing-docstring
+class FileType(argparse.FileType):
+ def __call__(self, fname):
+ # detect if stdout is being faked (StringIO during unit tests) in
+ # which case we do not have to do anything
+ if (fname == '-' and
+ sys.version_info.major == 3 and
+ not isinstance(sys.stdout, StringIO)):
+ if 'r' in self._mode:
+ fname = sys.stdin.fileno()
+ elif 'w' in self._mode:
+ fname = sys.stdout.fileno()
+
+ return super(FileType, self).__call__(fname)
+
+
+def memory_setting(label):
+ """
+ Parse user-supplied memory setting.
+
+ Converts strings into floats, representing a number of bytes. Supports the
+ following notations.
+ - raw integers: 1, 1000, 1000000000
+ - scientific notation: 1, 1e3, 1e9
+ - "common" notation: 1, 1K, 1G
+
+ Suffixes supported: K/k, M/m, G/g, T/t. Do not include a trailing B/b.
+ """
+ suffixes = {
+ 'K': 1000.0,
+ 'M': 1000.0 ** 2,
+ 'G': 1000.0 ** 3,
+ 'T': 1000.0 ** 4,
+ }
+ try:
+ mem = float(label)
+ return mem
+ except ValueError:
+ prefix = label[:-1]
+ suffix = label[-1:].upper()
+ if suffix not in suffixes.keys():
+ raise ValueError('cannot parse memory setting "{}"'.format(label))
+ try:
+ multiplier = float(prefix)
+ return multiplier * suffixes[suffix]
+ except ValueError:
+ raise ValueError('cannot parse memory setting "{}"'.format(label))
+
+
def optimal_size(num_kmers, mem_cap=None, fp_rate=None):
"""
- Utility function for estimating optimal countgraph args where:
+ Utility function for estimating optimal countgraph args.
+
- num_kmers: number of unique kmers [required]
- mem_cap: the allotted amount of memory [optional, conflicts with f]
- fp_rate: the desired false positive rate [optional, conflicts with M]
@@ -94,10 +223,10 @@ def optimal_size(num_kmers, mem_cap=None, fp_rate=None):
def check_conflicting_args(args, hashtype):
"""
- Utility function that takes in an args object and checks if there's things
- that conflict, e.g. --loadgraph and --ksize being set.
- """
+ Check argparse args object for conflicts.
+ e.g. --loadgraph and --ksize being set.
+ """
if getattr(args, "quiet", None):
configure_logging(args.quiet)
@@ -129,23 +258,42 @@ def check_conflicting_args(args, hashtype):
break # no repeat warnings
infoset = None
- if hashtype == 'countgraph':
+ if hashtype in ('countgraph', 'smallcountgraph'):
infoset = extract_countgraph_info(args.loadgraph)
- if info:
- ksize = infoset[0]
- max_tablesize = infoset[1]
- n_tables = infoset[2]
+ if infoset is not None:
+ ksize = infoset.ksize
+ max_tablesize = infoset.table_size
+ n_tables = infoset.n_tables
args.ksize = ksize
args.n_tables = n_tables
args.max_tablesize = max_tablesize
+ if infoset.ht_type == khmer.FILETYPES['SMALLCOUNT']:
+ args.small_count = True
+
+
+def check_argument_range(low, high, parameter_name):
+ """Check if parameter value is in the range `low` to `high`."""
+ def _in_range(value):
+ value = int(value)
+ if not low <= value < high:
+ print_error("\n** ERROR: khmer only supports "
+ "%i <= %s < %i.\n" % (low, parameter_name, high))
+ sys.exit(1)
+
+ else:
+ return value
+ return _in_range
+
+# pylint: disable=invalid-name
def estimate_optimal_with_K_and_M(num_kmers, mem_cap):
"""
- Utility function for estimating optimal countgraph args where num_kmers
- is the number of unique kmer and mem_cap is the allotted amount of memory
- """
+ Estimate optimal countgraph args.
+ - num_kmers: number of unique kmer
+ - mem_cap: the allotted amount of memory
+ """
n_tables = math.log(2) * (mem_cap / float(num_kmers))
int_n_tables = int(n_tables)
if int_n_tables == 0:
@@ -158,10 +306,13 @@ def estimate_optimal_with_K_and_M(num_kmers, mem_cap):
return res(int_n_tables, ht_size, mem_cap, fp_rate)
+# pylint: disable=invalid-name
def estimate_optimal_with_K_and_f(num_kmers, des_fp_rate):
"""
- Utility function for estimating optimal memory where num_kmers is the
- number of unique kmers and des_fp_rate is the desired false positive rate
+ Estimate optimal memory.
+
+ - num_kmers: the number of unique kmers
+ - des_fp_rate: the desired false positive rate
"""
n_tables = math.log(des_fp_rate, 0.5)
int_n_tables = int(n_tables)
@@ -180,8 +331,10 @@ def estimate_optimal_with_K_and_f(num_kmers, des_fp_rate):
def graphsize_args_report(unique_kmers, fp_rate):
"""
- Assembles output string for optimal arg sandbox scripts
- takes in unique_kmers and desired fp_rate
+ Assemble output string for optimal arg sandbox scripts.
+
+ - unique_kmers: number of uniqe k-mers
+ - fp_rate: desired false positive rate
"""
to_print = []
@@ -220,10 +373,11 @@ def graphsize_args_report(unique_kmers, fp_rate):
def _check_fp_rate(args, desired_max_fp):
"""
- Function to check if the desired_max_fp rate makes sense given specified
- number of unique kmers and max_memory restrictions present in the args.
+ Check if the desired_max_fp rate makes sense.
- Takes in args object and desired_max_fp
+ - args: argparse args object, possible members: fp_rate, max_memory_usage,
+ unique_kmers, force, max_tablesize
+ - desired_max_fp: desired maximum false positive rate
"""
if not args.unique_kmers:
return args
@@ -275,15 +429,11 @@ def _check_fp_rate(args, desired_max_fp):
return args
-def build_graph_args(descr=None, epilog=None, parser=None):
+def build_graph_args(descr=None, epilog=None, parser=None, citations=None):
"""Build an ArgumentParser with args for bloom filter based scripts."""
-
if parser is None:
- parser = argparse.ArgumentParser(description=descr, epilog=epilog,
- formatter_class=ComboFormatter)
-
- parser.add_argument('--version', action=_VersionStdErrAction,
- version='khmer {v}'.format(v=__version__))
+ parser = KhmerArgumentParser(description=descr, epilog=epilog,
+ citations=citations)
parser.add_argument('--ksize', '-k', type=int, default=DEFAULT_K,
help='k-mer size to use')
@@ -302,46 +452,52 @@ def build_graph_args(descr=None, epilog=None, parser=None):
group.add_argument('--max-tablesize', '-x', type=float,
default=DEFAULT_MAX_TABLESIZE,
help='upper bound on tablesize to use; overrides ' +
- '--max-memory-usage/-M.')
- group.add_argument('-M', '--max-memory-usage', type=float,
+ '--max-memory-usage/-M')
+ group.add_argument('-M', '--max-memory-usage', type=memory_setting,
help='maximum amount of memory to use for data ' +
- 'structure.')
+ 'structure')
return parser
-def build_counting_args(descr=None, epilog=None):
+def build_counting_args(descr=None, epilog=None, citations=None):
"""Build an ArgumentParser with args for countgraph based scripts."""
- parser = build_graph_args(descr=descr, epilog=epilog)
+ parser = build_graph_args(descr=descr, epilog=epilog, citations=citations)
+
+ parser.add_argument('--small-count', default=False, action='store_true',
+ help='Reduce memory usage by using a smaller counter'
+ ' for individual kmers.')
return parser
-def build_nodegraph_args(descr=None, epilog=None, parser=None):
+def build_nodegraph_args(descr=None, epilog=None, parser=None, citations=None):
"""Build an ArgumentParser with args for nodegraph based scripts."""
- parser = build_graph_args(descr=descr, epilog=epilog, parser=parser)
+ parser = build_graph_args(descr=descr, epilog=epilog, parser=parser,
+ citations=citations)
return parser
-# add an argument for loadgraph with warning about parameters
-
def add_loadgraph_args(parser):
+ """Common loadgraph argument."""
parser.add_argument('-l', '--loadgraph', metavar="filename", default=None,
help='load a precomputed k-mer graph from disk')
def calculate_graphsize(args, graphtype, multiplier=1.0):
- if graphtype not in ('countgraph', 'nodegraph'):
- raise ValueError("unknown graph type: %s" % (graphtype,))
+ """
+ Transform the table parameters into a size.
+
+ The return value refers to the target size (in buckets, not bytes) of each
+ individual table in the graph.
+ """
+ if graphtype not in khmer._buckets_per_byte:
+ raise ValueError('unknown graph type: ' + graphtype)
if args.max_memory_usage:
- if graphtype == 'countgraph':
- tablesize = args.max_memory_usage / args.n_tables / \
- float(multiplier)
- elif graphtype == 'nodegraph':
- tablesize = 8. * args.max_memory_usage / args.n_tables / \
- float(multiplier)
+ tablesize = (khmer._buckets_per_byte[graphtype] *
+ args.max_memory_usage / args.n_tables / float(multiplier))
else:
tablesize = args.max_tablesize
@@ -349,8 +505,20 @@ def calculate_graphsize(args, graphtype, multiplier=1.0):
def create_nodegraph(args, ksize=None, multiplier=1.0, fp_rate=0.01):
- """Creates and returns a nodegraph"""
+ """Create and return a nodegraph."""
args = _check_fp_rate(args, fp_rate)
+
+ if hasattr(args, 'force'):
+ if args.n_tables > 20:
+ if not args.force:
+ print_error(
+ "\n** ERROR: khmer only supports number "
+ "of tables <= 20.\n")
+ sys.exit(1)
+ else:
+ log_warn("\n*** Warning: Maximum recommended number of "
+ "tables is 20, discarded by force nonetheless!\n")
+
if ksize is None:
ksize = args.ksize
if ksize > 32:
@@ -362,16 +530,35 @@ def create_nodegraph(args, ksize=None, multiplier=1.0, fp_rate=0.01):
def create_countgraph(args, ksize=None, multiplier=1.0, fp_rate=0.1):
- """Creates and returns a countgraph"""
+ """Create and return a countgraph."""
args = _check_fp_rate(args, fp_rate)
+
+ if hasattr(args, 'force'):
+ if args.n_tables > 20:
+ if not args.force:
+ print_error(
+ "\n** ERROR: khmer only supports number "
+ "of tables <= 20.\n")
+ sys.exit(1)
+ else:
+ if args.n_tables > 20:
+ log_warn("\n*** Warning: Maximum recommended number of "
+ "tables is 20, discarded by force nonetheless!\n")
+
if ksize is None:
ksize = args.ksize
if ksize > 32:
print_error("\n** ERROR: khmer only supports k-mer sizes <= 32.\n")
sys.exit(1)
- tablesize = calculate_graphsize(args, 'countgraph', multiplier=multiplier)
- return khmer.Countgraph(ksize, tablesize, args.n_tables)
+ if args.small_count:
+ tablesize = calculate_graphsize(args, 'smallcountgraph',
+ multiplier=multiplier)
+ return khmer.SmallCountgraph(ksize, tablesize, args.n_tables)
+ else:
+ tablesize = calculate_graphsize(args, 'countgraph',
+ multiplier=multiplier)
+ return khmer.Countgraph(ksize, tablesize, args.n_tables)
def report_on_config(args, graphtype='countgraph'):
@@ -381,31 +568,23 @@ def report_on_config(args, graphtype='countgraph'):
made available by this module.
"""
check_conflicting_args(args, graphtype)
- if graphtype not in ('countgraph', 'nodegraph'):
- raise ValueError("unknown graph type: %s" % (graphtype,))
+ if graphtype not in khmer._buckets_per_byte:
+ raise ValueError('unknown graph type: ' + graphtype)
tablesize = calculate_graphsize(args, graphtype)
-
+ maxmem = args.n_tables * tablesize / khmer._buckets_per_byte[graphtype]
log_info("\nPARAMETERS:")
- log_info(" - kmer size = {ksize} \t\t(-k)", ksize=args.ksize)
- log_info(" - n tables = {ntables} \t\t(-N)", ntables=args.n_tables)
+ log_info(" - kmer size = {ksize} \t\t(-k)", ksize=args.ksize)
+ log_info(" - n tables = {ntables} \t\t(-N)", ntables=args.n_tables)
log_info(" - max tablesize = {tsize:5.2g} \t(-x)", tsize=tablesize)
- log_info("")
- if graphtype == 'countgraph':
- log_info(
- "Estimated memory usage is {0:.2g} bytes "
- "(n_tables x max_tablesize)".format(
- args.n_tables * tablesize))
- elif graphtype == 'nodegraph':
- log_info(
- "Estimated memory usage is {0:.2g} bytes "
- "(n_tables x max_tablesize / 8)".format(args.n_tables *
- tablesize / 8)
- )
-
+ log_info("Estimated memory usage is {mem:.1f} Gb "
+ "({bytes:.2g} bytes = {ntables} bytes x {tsize:5.2g} entries "
+ "/ {div:d} entries per byte)", bytes=maxmem, mem=maxmem / 1e9,
+ div=khmer._buckets_per_byte[graphtype], ntables=args.n_tables,
+ tsize=tablesize)
log_info("-" * 8)
- if DEFAULT_MAX_TABLESIZE == tablesize and \
+ if tablesize == DEFAULT_MAX_TABLESIZE and \
not getattr(args, 'loadgraph', None):
log_warn('''\
@@ -441,25 +620,9 @@ def sanitize_help(parser):
parser.epilog = newlog
return parser
-_algorithms = {
- 'software': 'MR Crusoe et al., '
- '2015. http://dx.doi.org/10.12688/f1000research.6924.1',
- 'diginorm': 'CT Brown et al., arXiv:1203.4802 [q-bio.GN]',
- 'streaming': 'Q Zhang, S Awad, CT Brown, '
- 'https://dx.doi.org/10.7287/peerj.preprints.890v1',
- 'graph': 'J Pell et al., http://dx.doi.org/10.1073/pnas.1121464109',
- 'counting': 'Q Zhang et al., '
- 'http://dx.doi.org/10.1371/journal.pone.0101271',
- 'sweep': 'C Scott, MR Crusoe, and CT Brown, unpublished',
- 'SeqAn': 'A. Döring et al. http://dx.doi.org:80/10.1186/1471-2105-9-11',
- 'hll': 'Irber and Brown, unpublished'
-}
-
def info(scriptname, algorithm_list=None):
"""Print version and project info to stderr."""
- import khmer
-
log_info("\n|| This is the script {name} in khmer.\n"
"|| You are running khmer version {version}",
name=scriptname, version=khmer.__version__)
@@ -475,14 +638,15 @@ def info(scriptname, algorithm_list=None):
algorithm_list.insert(0, 'software')
for alg in algorithm_list:
- algstr = "|| * " + _algorithms[alg].encode(
+ algstr = "|| * " + ALGORITHMS[alg].encode(
'utf-8', 'surrogateescape').decode('utf-8', 'replace')
try:
log_info(algstr)
except UnicodeEncodeError:
log_info(algstr.encode(sys.getfilesystemencoding(), 'replace'))
- log_info("||\n|| Please see http://khmer.readthedocs.org/en/"
+ log_info("||\n|| Please see http://khmer.readthedocs.io/en/"
"latest/citations.html for details.\n")
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
+# vim: set filetype=python tabstop=4 softtabstop=4 shiftwidth=4 expandtab:
+# vim: set textwidth=79:
diff --git a/khmer/khmer_logger.py b/khmer/khmer_logger.py
index 9644869..bfe64b4 100644
--- a/khmer/khmer_logger.py
+++ b/khmer/khmer_logger.py
@@ -31,23 +31,22 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
-'''Lightweight logging framework for khmer'''
+"""Lightweight logging framework for khmer."""
from __future__ import print_function, unicode_literals
import sys
-global __QUIET__
__QUIET__ = False
def configure_logging(quiet):
- global __QUIET__
+ """Set the logging level."""
+ global __QUIET__ # pylint: disable=global-statement
__QUIET__ = quiet
def log_info(message, **kwargs):
"""For non-critical informative/status output to stderr."""
- global __QUIET__
if not __QUIET__:
if kwargs:
message = message.format(**kwargs)
@@ -61,9 +60,8 @@ def log_error(message, **kwargs):
print(message, file=sys.stderr)
-def log_debug(message, **kwagrs):
+def log_debug(message, **kwargs):
"""For non-critical debug output to stderr."""
- global __QUIET__
if not __QUIET__:
if kwargs:
message = message.format(**kwargs)
@@ -77,4 +75,5 @@ def log_warn(message, **kwargs):
print(message, file=sys.stderr)
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
+# vim: set filetype=python tabstop=4 softtabstop=4 shiftwidth=4 expandtab:
+# vim: set textwidth=79:
diff --git a/khmer/thread_utils.py b/khmer/thread_utils.py
index f71efc1..63b8e8d 100644
--- a/khmer/thread_utils.py
+++ b/khmer/thread_utils.py
@@ -1,6 +1,6 @@
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2011-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -32,6 +32,7 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
+# pylint: disable=missing-docstring,too-few-public-methods
"""Utilities for dealing with multithreaded processing of short reads."""
from __future__ import print_function, unicode_literals
@@ -39,7 +40,9 @@ from __future__ import print_function, unicode_literals
import threading
import sys
import screed
+import khmer
from khmer.utils import write_record, check_is_pair
+from khmer.khmer_logger import log_info
# stdlib queue module was renamed on Python 3
try:
import queue
@@ -51,14 +54,13 @@ DEFAULT_GROUPSIZE = 100
def verbose_loader(filename):
- """Screed iterator that additionally prints progress info to stderr."""
- screed_iter = screed.open(filename)
- for n, record in enumerate(screed_iter):
- if n % 100000 == 0:
- print('... filtering', n, file=sys.stderr)
+ """Read iterator that additionally prints progress info to stderr."""
+ for num, record in enumerate(khmer.ReadParser(filename)):
+ if num % 100000 == 0:
+ log_info('... filtering {num}', num=num)
yield record
-verbose_fasta_iter = verbose_loader
+verbose_fasta_iter = verbose_loader # pylint: disable=invalid-name
class SequenceGroup(object):
@@ -69,6 +71,7 @@ class SequenceGroup(object):
class ThreadedSequenceProcessor(object):
+ # pylint: disable=too-many-instance-attributes
QUEUESIZE = 50
def __init__(self, process_fn, n_workers=DEFAULT_WORKER_THREADS,
@@ -97,15 +100,15 @@ class ThreadedSequenceProcessor(object):
try:
for _ in range(self.n_workers):
- t = threading.Thread(target=self.do_process)
+ thread = threading.Thread(target=self.do_process)
self.worker_count += 1
- t.start()
+ thread.start()
if self.verbose:
print('starting writer', file=sys.stderr)
- w = threading.Thread(target=self.do_write, args=(outfp,))
- w.start()
+ writer = threading.Thread(target=self.do_write, args=(outfp,))
+ writer.start()
if self.verbose:
print('loading...', file=sys.stderr)
@@ -116,7 +119,7 @@ class ThreadedSequenceProcessor(object):
print('done loading in sequences', file=sys.stderr)
self.done = True
- w.join()
+ writer.join()
except Exception:
self.done = True
raise
@@ -130,13 +133,13 @@ class ThreadedSequenceProcessor(object):
# keep pairs together in batches, to retain the interleaving.
if check_is_pair(last_record, record):
batch.append(record)
- g = SequenceGroup(0, batch)
- self.inqueue.put(g)
+ grouping = SequenceGroup(0, batch)
+ self.inqueue.put(grouping)
batch = []
else:
- g = SequenceGroup(0, batch)
- self.inqueue.put(g)
+ grouping = SequenceGroup(0, batch)
+ self.inqueue.put(grouping)
batch = [record]
i = 0
@@ -148,15 +151,15 @@ class ThreadedSequenceProcessor(object):
# submit last set of sequences
if batch:
- g = SequenceGroup(0, batch)
- self.inqueue.put(g)
+ grouping = SequenceGroup(0, batch)
+ self.inqueue.put(grouping)
def do_process(self):
inq = self.inqueue
while not self.done or not inq.empty():
try:
- g = inq.get(True, 1)
+ grouping = inq.get(True, 1)
except queue.Empty:
continue
@@ -164,13 +167,13 @@ class ThreadedSequenceProcessor(object):
bp_written = 0
keep = []
- for record in g.seqlist:
+ for record in grouping.seqlist:
name, sequence = self.process_fn(record)
- bp_processed += len(record['sequence'])
+ bp_processed += len(record.sequence)
if name:
- quality = record.get('quality')
- if quality:
- quality = quality[:len(sequence)]
+ quality = None
+ if hasattr(record, 'quality'):
+ quality = record.quality[:len(sequence)]
bp_written += len(sequence)
keep.append((name, sequence, quality))
@@ -179,7 +182,7 @@ class ThreadedSequenceProcessor(object):
# the tallies are shared among workers, hence we lock
with self.tallies_lock:
- self.n_processed += len(g.seqlist)
+ self.n_processed += len(grouping.seqlist)
self.n_written += len(keep)
self.bp_processed += bp_processed
self.bp_written += bp_written
@@ -193,8 +196,8 @@ class ThreadedSequenceProcessor(object):
self.bp_processed - self.bp_written),
file=sys.stderr)
discarded = self.bp_processed - self.bp_written
- f = float(discarded) / float(self.bp_processed) * 100
- print("discarded %.1f%%" % f, file=sys.stderr)
+ percent = float(discarded) / float(self.bp_processed) * 100
+ print("discarded %.1f%%" % percent, file=sys.stderr)
# end of thread; exit, decrement worker count.
with self.worker_count_lock:
@@ -204,11 +207,11 @@ class ThreadedSequenceProcessor(object):
outq = self.outqueue
while self.worker_count > 0 or not outq.empty():
try:
- g = outq.get(True, 1)
+ grouping = outq.get(True, 1)
except queue.Empty:
continue
- for name, seq, qual in g.seqlist:
+ for name, seq, qual in grouping.seqlist:
if qual:
record = screed.Record(name=name, sequence=seq,
quality=qual)
@@ -224,7 +227,8 @@ class ThreadedSequenceProcessor(object):
(self.bp_processed, self.bp_written,
self.bp_processed - self.bp_written), file=sys.stderr)
discarded = self.bp_processed - self.bp_written
- f = float(discarded) / float(self.bp_processed) * 100
- print("discarded %.1f%%" % f, file=sys.stderr)
+ percent = float(discarded) / float(self.bp_processed) * 100
+ print("discarded %.1f%%" % percent, file=sys.stderr)
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
+# vim: set filetype=python tabstop=4 softtabstop=4 shiftwidth=4 expandtab:
+# vim: set textwidth=79:
diff --git a/khmer/khmer_logger.py b/khmer/trimming.py
similarity index 61%
copy from khmer/khmer_logger.py
copy to khmer/trimming.py
index 9644869..e23679b 100644
--- a/khmer/khmer_logger.py
+++ b/khmer/trimming.py
@@ -1,5 +1,5 @@
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -31,50 +31,38 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
-'''Lightweight logging framework for khmer'''
-
+"""Common methods for trimming short reads on k-mer abundance."""
from __future__ import print_function, unicode_literals
-import sys
-
-global __QUIET__
-__QUIET__ = False
-
-
-def configure_logging(quiet):
- global __QUIET__
- __QUIET__ = quiet
-
-
-def log_info(message, **kwargs):
- """For non-critical informative/status output to stderr."""
- global __QUIET__
- if not __QUIET__:
- if kwargs:
- message = message.format(**kwargs)
- print(message, file=sys.stderr)
+import screed
-def log_error(message, **kwargs):
- """For critical error output to stderr."""
- if kwargs:
- message = message.format(**kwargs)
- print(message, file=sys.stderr)
+def trim_record(countgraph, record, cutoff, variable_coverage=False,
+ normalize_to=None):
+ name = record.name
+ seq = record.sequence
+ seqN = record.cleaned_seq
+ if variable_coverage: # only trim when sequence has high enough C
+ if not countgraph.median_at_least(seqN, normalize_to):
+ return record, False # return unmodified
-def log_debug(message, **kwagrs):
- """For non-critical debug output to stderr."""
- global __QUIET__
- if not __QUIET__:
- if kwargs:
- message = message.format(**kwargs)
- print(message, file=sys.stderr)
+ _, trim_at = countgraph.trim_on_abundance(seqN, cutoff)
+ # too short? eliminate read
+ if trim_at < countgraph.ksize():
+ return None, True
-def log_warn(message, **kwargs):
- """For critical warning output to stderr."""
- if kwargs:
- message = message.format(**kwargs)
- print(message, file=sys.stderr)
+ # would we trim? if not, return unmodified.
+ if trim_at == len(seq):
+ return record, False
+ # construct new record
+ trim_seq = seq[:trim_at]
+ if hasattr(record, 'quality'):
+ trim_qual = record.quality[:trim_at]
+ trim_rec = screed.Record(name=name, sequence=trim_seq,
+ quality=trim_qual)
+ else:
+ trim_rec = screed.Record(name=name, sequence=trim_seq)
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
+ return trim_rec, True
diff --git a/khmer/utils.py b/khmer/utils.py
index 7d37a33..d318417 100644
--- a/khmer/utils.py
+++ b/khmer/utils.py
@@ -1,6 +1,6 @@
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2013-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -32,9 +32,7 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
-'''Convenience functions for performing common argument-checking tasks in
-scripts.'''
-
+"""Helpful methods for performing common argument-checking tasks in scripts."""
from __future__ import print_function, unicode_literals
@@ -136,10 +134,20 @@ def check_is_right(name):
class UnpairedReadsError(ValueError):
+ """ValueError with refs to the read pair in question."""
+
def __init__(self, msg, r1, r2):
- super(ValueError, self).__init__(msg)
- self.r1 = r1
- self.r2 = r2
+ r1_name = "<no read>"
+ r2_name = "<no read>"
+ if r1:
+ r1_name = r1.name
+ if r2:
+ r2_name = r2.name
+
+ msg = msg + '\n"{0}"\n"{1}"'.format(r1_name, r2_name)
+ ValueError.__init__(self, msg)
+ self.read1 = r1
+ self.read2 = r2
def broken_paired_reader(screed_iter, min_length=None,
@@ -169,30 +177,36 @@ def broken_paired_reader(screed_iter, min_length=None,
"""
record = None
prev_record = None
- n = 0
+ num = 0
if force_single and require_paired:
raise ValueError("force_single and require_paired cannot both be set!")
# handle the majority of the stream.
for record in screed_iter:
- # ignore short reads
- if min_length and len(record.sequence) < min_length:
- record = None
- continue
-
if prev_record:
if check_is_pair(prev_record, record) and not force_single:
- yield n, True, prev_record, record # it's a pair!
- n += 2
- record = None
+ if min_length and (len(prev_record.sequence) < min_length or
+ len(record.sequence) < min_length):
+ if require_paired:
+ record = None
+ else:
+ yield num, True, prev_record, record # it's a pair!
+ num += 2
+ record = None
else: # orphan.
if require_paired:
- e = UnpairedReadsError("Unpaired reads when require_paired"
- " is set!", prev_record, record)
- raise e
- yield n, False, prev_record, None
- n += 1
+ err = UnpairedReadsError(
+ "Unpaired reads when require_paired is set!",
+ prev_record, record)
+ raise err
+
+ # ignore short reads
+ if min_length and len(prev_record.sequence) < min_length:
+ pass
+ else:
+ yield num, False, prev_record, None
+ num += 1
prev_record = record
record = None
@@ -202,7 +216,10 @@ def broken_paired_reader(screed_iter, min_length=None,
if require_paired:
raise UnpairedReadsError("Unpaired reads when require_paired "
"is set!", prev_record, None)
- yield n, False, prev_record, None
+ if min_length and len(prev_record.sequence) < min_length:
+ pass
+ else:
+ yield num, False, prev_record, None
def write_record(record, fileobj):
@@ -218,17 +235,63 @@ def write_record(record, fileobj):
sequence=record.sequence)
try:
- fileobj.write(bytes(recstr, 'utf-8'))
+ fileobj.write(bytes(recstr, 'ascii'))
except TypeError:
fileobj.write(recstr)
def write_record_pair(read1, read2, fileobj):
"""Write a pair of sequence records to 'fileobj' in FASTA/FASTQ format."""
+ _rec_pair = '@%s\n%s\n+\n%s\n' * 2
+ _rec_pair_no_qual = '>%s\n%s\n' * 2
+
if hasattr(read1, 'quality'):
assert hasattr(read2, 'quality')
- write_record(read1, fileobj)
- write_record(read2, fileobj)
+ recstr = _rec_pair % (read1.name, read1.sequence, read1.quality,
+ read2.name, read2.sequence, read2.quality)
+
+ else:
+ recstr = _rec_pair_no_qual % (read1.name, read1.sequence,
+ read2.name, read2.sequence)
+
+ try:
+ fileobj.write(bytes(recstr, 'ascii'))
+ except TypeError:
+ fileobj.write(recstr)
+
+
+def clean_input_reads(records):
+ """Add a cleaned_seq attribute to records that do not have one
+
+ Use this to convert a stream of records that might not have a
+ `cleaned_seq` attribute to one that does. Use this to extend
+ Records loaded by `screed.open()`. It is a mistake to apply
+ this to a `ReadParser` stream.
+ """
+ for record in records:
+ record.cleaned_seq = record.sequence.upper().replace('N', 'A')
+ yield record
+
+
+class ReadBundle(object):
+ def __init__(self, *raw_records):
+ self.reads = [i for i in raw_records if i]
+
+ def coverages(self, graph):
+ return [graph.get_median_count(r.cleaned_seq)[0] for r in self.reads]
+
+ def coverages_at_least(self, graph, coverage):
+ return all(graph.median_at_least(r.cleaned_seq, coverage)
+ for r in self.reads)
+
+ @property
+ def num_reads(self):
+ return len(self.reads)
+
+ @property
+ def total_length(self):
+ return sum([len(r.sequence) for r in self.reads])
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
+# vim: set filetype=python tabstop=4 softtabstop=4 shiftwidth=4 expandtab:
+# vim: set textwidth=79:
diff --git a/ChangeLog b/legacy/ChangeLog
similarity index 83%
rename from ChangeLog
rename to legacy/ChangeLog
index 40e0967..fc495c9 100644
--- a/ChangeLog
+++ b/legacy/ChangeLog
@@ -1,3 +1,533 @@
+2016-11-15 Nicole Kingsley <nbkingsley at ucdavis.edu>
+
+ * tests/{test_normalize_by_median.py,test_scripts.py}:
+ Replaced two lines that created a file and stored test data with one
+ line that calls the utils.copy_test_data function to complete the
+ same task.
+
+2016-11-15 Daniel Standage <daniel.standage at gmail.com>
+
+ * docs/dev/scripts-and-sandbox.rst: Added documentation for reserved flags
+ for command line scripts.
+
+2016-11-15 Titus Brown <titus at idyll.org>
+
+ * khmer/{_cpy_counttable,_cpy_hashgraph.hh,cpy_nodetable.hh,_khmer.cc,
+ khmer/__init__.py}: new Counttable and Nodetable CPython types, plus
+ renaming of CountingHash to CountGraph and Hashbits to Nodegraph;
+ refactoring of CPython hierarchy to separate graph methods from table
+ methods.
+ * lib/hashtable.{cc,hh}: pull some more CountingHash/Counttable methods
+ back to base class; rename.
+ * lib/hashgraph.{cc,hh}: create new files containing the Countgraph
+ and Nodegraph classes.
+ * Makefile, setup.py: updated dependencies for added and removed files.
+ * lib/Makefile: eliminated lib/counting.{cc,hh} and lib/hashbits.{cc,hh}.
+ * lib/{labelhash.cc,read_aligner.hh,storage.cc,storage.hh,subset.cc,
+ subset.hh,test-Colors.cc,test-compile.cc},
+ examples/c++-api/count-demo.cc - renamed CountingHash and Hashbits.
+ * tests/test_cpython_hierarchy.py - some preliminary tests for new CPython
+ inheritance hierarchy.
+ * tests/{test_nodegraph,test_countgraph}.py - added creation tests of
+ 'tablesizes' passed into Nodegraph and Countgraph constructors.
+
+2016-11-15 Luiz Irber <khmer at luizirber.org>
+
+ * khmer/__init__.py,tests/test_functions.py: Fix get_n_primes_near_x to
+ always return integers.
+
+2016-11-14 Tim Head <betatim at gmail.com>
+
+ * khmer/_khmer.cc,lib/read_parsers.hh: Expose khmer's Read type fully to
+ the python side.
+ * scripts/{extract-paired-reads.py,filter-abund-single.py,filter-abund.py,
+ sample-reads-randomly.py,split-paired-reads.py,trim-low-abund.py}: Switch to
+ using ReadParser to speed up scripts.
+ * tests/test_read_handling.py,tests/test_scripts.py: Remove streaming tests
+ that use a FIFO.
+
+2016-11-14 Shannon EK Joslin <sejoslin at ucdavis.edu>
+ *khmer/tests/test_countgraph.py: Refactor test code to use load_countgraph #1474
+ *khmer/tests/test_nodegraph.py: Refactor test code to use load_nodegraph and load_countgraph #1474
+
+2016-11-14 Tim Head <betatim at gmail.com>
+
+ * .travis.yml: whitelist `master` branch to allow build-on-push without
+ building every push for a PR twice.
+
+2016-11-11 Titus Brown <titus at idyll.org>
+
+ * doc/requirements.txt: set autoprogram version requirements to something
+ that works on python 2.7, in order to fix ReadTheDocs builds.
+
+2016-11-10 Camille Scott <camille.scott.w at gmail.com>
+
+ * lib/assembler.{hh,cc}: add JunctionCountAssembler implementation.
+ * lib/kmer_filters.{hh,cc}: add get junction_count_filter function.
+ * khmer/{__init__.py,_khmer.cc}: add LinearAssembler,
+ SimpleLabeledAssembler, and JunctionCountAssembler to CPython interface.
+ * tests/test_assembly.py: minor refactoring, & tests for
+ JunctionCountAssembler and newly exposed C++ functions.
+ * sandbox/streaming-assembly-simple.py: demo script for streaming assembly.
+ * Makefile: update debug flags.
+ * lib/{counting.hh,hashtable.{hh,cc},hllcounter.hh,labelhash.hh,
+ read_aligner.hh,subset.{hh,cc}}: minor cleanup.
+ * tests/test_sandbox_scripts.py: minor cleanup.
+
+2016-11-07 Luiz Irber <khmer at luizirber.org>
+
+ * Makefile: add --ignore-installed flag to pip install (fix installation
+ on conda environments.
+ * doc/requirements.txt: change hard requirement to 'newer than', avoid
+ installing a quite old setuptools version.
+
+2016-11-04 Tim Head <betatim at gmail.com>
+
+ * Make khmer's Read type accessible from the python API.
+
+2016-11-03 Titus Brown <titus at idyll.org>
+
+ * lib/{counting.cc,counting.hh,hashbits.cc,hashbits.hh,hashtable.cc,
+ hashtable.hh,storage.cc,storage.hh}: extracted in-memory storage details
+ into Storage/Bitstorage/ByteStorage classes.
+ * khmer/_khmer.cc,lib/{assembler.cc,assembler.hh,subset.cc,
+ subset.hh,labelhash.cc,labelhash.hh,traversal.cc,traversal.hh}: renamed
+ Hashtable to Hashgraph.
+ * setup.py,lib/Makefile: added storage.{cc,hh} to build.
+
+2016-10-31 Titus Brown <titus at idyll.org>
+
+ * lib/{counting.hh,hashbits.hh,hashtable.hh}: factor out global functions
+ _hash and _revhash into Hashtable methods hash_dna and unhash_dna.
+ * khmer/_khmer.cc, lib/{hashtable.cc,read_aligner.cc,subset.cc}: update
+ Hashtable code to use new hash_dna and unhash_dna methods.
+
+2016-10-31 Camille Scott <camille.scott.w at gmail.com>
+
+ * khmer/__init__.py, khmer/_khmer.cc, tests/test_functions.py: Expose
+ reverse_complement to Python.
+ * lib/{traversal.cc, traversal.hh}: Add two new Traverser classes,
+ AssemblerTraverser and NonloopingAT, to do the traversal portions of
+ assembly.
+ * lib/{assembler.cc, assembler.hh}, khmer/_khmer.cc: New code files
+ containing the LinearAssembler and LabeledLinearAssembler classes which wrap
+ AssemblerTraverser and NonloopingAT, respectively, and expose a contig
+ assembly interface.
+ * lib/{hashtable.cc, hashtable.hh, labelhash.cc, labelhash.hh}: Move
+ assembler API to the new assembler.hh.
+ * lib/{kmer_filters.hh, kmer_filters.cc}: Helper filter-functions for the
+ AssemblerTraversers.
+ * lib/kmer_hash.hh: Helper functions for the Kmer class.
+ * lib/{alphabets.hh, alphabets.cc}: Global DNA alphabets.
+ * tests/test_assembly.py: Tests for the assembler API.
+
+2016-10-28 Daniel Standage <daniel.standage at gmail.com>
+
+ * lib/hashtable.cc,tests/test_nodegraph.py: fix bug in assemble_linear_path
+ that returns seed k-mer even if it is not present in the DBG.
+
+2016-10-13 Camille Scott <camille.scott.w at gmail.com>
+
+ * Wrap IO functions in with an extra catch to handle the gcc
+ basic_ios_failure bug.
+
+2016-10-03 Tim Head <betatim at gmail.com>
+
+ * .travis.yml: adjust setup for exclusive use of travis (jenkins is retiring)
+
+2016-10-02 Titus Brown <titus at idyll.org>
+
+ * khmer/{utils.py,thread_utils.py,trimming.py}: introduce new function,
+ clean_input_reads, that does consistent read cleaning; update ReadBundle
+ and trimming to make use of new cleaned_seq attribute.
+ * scripts/{normalize-by-median.py,trim-low-abund.py}: refactor to use
+ cleaned_seq attribute properly; this fixed a bug in normalize-by-median.py
+ that led to ignoring lowercase 'actgn'.
+ * doc/dev/development.rst: update developer documentation for new
+ cleaned_seq attribute and ReadBundle behavior.
+ * tests/test_script_output.py: update md5 signatures for output to reflect
+ corrected behavior.
+ * tests/test_functions.py: add test for broken_paired_iter uppercase
+ behavior.
+ * tests/test_read_handling.py: update tests for ReadBundle.
+
+2016-10-01 Titus Brown <titus at idyll.org>
+
+ * khmer/trimming.py,scripts/{filter-abund-single.py,filter-abund.py,
+ trim-low-abund.py}: extracted similar trimming code and refactored.
+ * khmer/utils.py,tests/test_read_handling.py: change ReadBundle.trimmed_reads
+ to trimmed_seqs; fix associated tests.
+ * tests/test_functions.py: updated tests to use screed.Record instead of
+ namedtuple classes.
+
+2016-10-01 Titus Brown <titus at idyll.org>
+
+ * lib/hashtable.{cc,hh}: added assemble_linear_path function & helpers.
+ * khmer/_khmer.cc: CPython API for assemble_linear_path.
+ * tests/test_nodegraph.py: tests for new assemble_linear_path behavior.
+ * khmer/khmer_args.py, tests/test_script_arguments.py: fix some lingering
+ PEP 8 errors.
+ * lib/kmer_hash.hh: added string -> string _revcomp function.
+
+2016-09-30 Daniel Standage <daniel.standage at gmail.com>
+
+ * scripts/trim-low-abund.py, khmer/utils.py, doc/dev/development.rst: moved
+ ReadBundle class to utils
+ * tests/test_read_handling.py, tests/test-data/unclean-reads.fastq: tests
+ related to ReadBundle
+
+2016-09-29 Tim Head <betatim at gmail.com>
+
+ * khmer/khmer_args.py, tests/test_functions.py,
+ tests/test_script_arguments.py: fix up formatting
+
+2016-09-26 Ali Aliyari <aaliyari at ucdavis.edu>
+
+ * khmer/khmer_args.py: prevent -N from being set to more than 20 (override by -f)
+ * tests/test_script_arguments.py added test functions for the above change
+
+2016-09-26 Luiz Irber <khmer at luizirber.org>
+
+ * khmer/khmer_args.py: Update HLL citation to point to preprint.
+
+2016-09-23 Tim Head <betatim at gmail.com>
+
+ * khmer/_khmer.cc, lib/counting.{cc,hh}, lib/hashbits.{cc,hh},
+ lib/hashtable.hh, lib/hllcounter.{cc,hh}, lib/kmer_hash.cc,
+ tests/khmer_tst_utils.py, tests/test_functions.py: move away from using
+ HashIntoType as synonym to uint64.
+
+2016-09-21 Tim Head <betatim at gmail.com>
+
+ * .travis.yml: add python 3.5 to the build matrix and allow fast finishing
+
+2016-09-20 Titus Brown <titus at idyll.org>
+
+ * khmer/utils.py: fixed bug in broken_paired_reader when short reads
+ are discarded and require_paired is set; improved read pair error reporting.
+ * tests/test_functions.py: added tests for broken_paired_reader fix.
+ * tests/khmer_tst_utils.py: de-nested exceptions for better error reporting
+ from tests.
+
+2016-09-09 Daniel Standage <daniel.standage at gmail.com>
+
+ * lib/read_parsers.{cc,hh}: rename SeqAnParser to FastxParser.
+
+2016-09-09 Tim Head <betatim at gmail.com>
+
+ * tests/test_filter_abund.py: remove for loops introduce to the test suite.
+
+2016-09-01 Tim Head <betatim at gmail.com>
+
+ * khmer/khmer_args.py: added check_argument_range to check an integer
+ command-line argument is within a given range.
+ * scripts/{normalize-by-median.py, filter-abund.py, filter-abund-single.py}
+ now use check_argument_range for the cutoff parameter.
+ * tests/test_normalize_by_median.py: modified
+ test_normalize_by_median_no_bigcount.
+
+2016-09-01 Tim Head <betatim at gmail.com>
+
+ * scripts/filter-abund-single.py: Add support for variable coverage trimming
+
+2016-08-31 Tim Head <betatim at gmail.com>
+
+ * Fixed several source code style issues in python and cpp.
+ * Makefile: removed setup.py from the list of files passed to astyle
+
+2016-08-30 Tim Head <betatim at gmail.com>
+
+ * Fix coverage reporting on OSX and rename nosetests.xml to pytests.xml
+
+2016-08-29 Daniel Standage <daniel.standage at gmail.com>
+
+ * doc/dev/getting-started.rst: updated dev environment setup instructions to
+ include installation of 'enchant' library, and dropped Arch linux install
+ instructions.
+
+2016-08-26 Daniel Standage <daniel.standage at gmail.com>
+
+ * tests/test_scripts.py: fix PEP8 errors missed with previous PR (due to CI
+ issues)
+ * Makefile: make the pep8 target less verbose by removing the --show-pep8
+ option
+
+2016-08-26 Ryan Shean <rcs333 at uw.edu>
+
+ * tests/{test_countergraph.py, test_filter_abund.py,
+ test_normalize_by_median.py, test_read_handling.py,
+ test_sandbox_scripts.py, test_scripts.py}: updated to use
+ copy_test_data function
+
+2016-07-18 Titus Brown <titus at idyll.org>
+
+ * khmer/_khmer.cc: fixed ReadPairIterator exception return error messages.
+
+2016-07-03 Titus Brown <titus at idyll.org>
+
+ * lib/{hashtable.cc, hashtable.hh}: added get_kmer_hashes_as_hashset to
+ graphs.
+ * khmer/_khmer.cc: updated CPython API to add get_kmer_hashes_as_hashset.
+ * tests/test_countgraph.py: added test for get_kmer_hashes_as_hashset.
+
+2016-06-27 Titus Brown <titus at idyll.org>
+
+ * doc/requirements.txt: updated sphinx-autoprogram requirement for building
+ documentation, to point at released version.
+
+2016-06-26 Titus Brown <titus at idyll.org>
+
+ * khmer/_khmer.cc, tests/test_nodegraph.py: 'add' is now a synonym for
+ graph.count(kmer).
+ * khmer/thread_utils.py: update verbose_loader function to take 'verbose'
+ argument.
+ * scripts/{abundance-dist-single.py, abundance-dist.py,
+ filter-abund-single.py, filter-abund.py, load-into-counting.py,
+ normalize-by-median.py,trim-low-abund.py}: updated to
+ respect -q/--quiet.
+ * tests/test_filter_abund.py: tests for '-q'.
+ * scripts/partition-graph.py: fix typo in args help message.
+
+2016-06-26 Titus Brown <titus at idyll.org>
+
+ * khmer/_khmer.cc, lib/{hashtable.cc, hashtable.hh},
+ tests/test-data/simple-genome.fa, tests/test_nodegraph.py: added functions
+ 'find_high_degree_nodes' and 'traverse_linear_path' to hashtables/graphs.
+ * lib/kmer_hash.cc: minor change to use object member _seq instead of
+ constructor argument seq in KmerIterator.
+ * lib/kmer_hash.hh: added const to Kmer::get_string_rep(...) signature.
+ * sandbox/extract-compact-dbg.py: new sandbox script to
+ extract compact De Bruijn graphs (with linear paths contracted).
+ * tests/test_sandbox_scripts.py: added tests for the extract-compact-dbg.py
+ script.
+
+2016-06-26 Titus Brown <titus at idyll.org>
+
+ * lib/khmer.hh,lib/{labelhash.cc,labelhash.hh}: removed label pointer-based
+ indirection from labelhash code.
+ * khmer/_khmer.cc: updated CPython API to match new behavior.
+ * tests/test_labelhash.py: renamed to match new API; no changes in test
+ logic.
+
+2016-06-17 Daniel Standage <daniel.standage at gmail.com>
+
+ * scripts/filter-abund-single.py: add -o/--outfile option.
+ * tests/test_script_output.py: move `_calc_md5` function for calculating
+ file MD5 hashes to test utils module (tests/khmer_tst_utils.py).
+ * tests/{test_filter_abund.py,test_scripts.py): move filter_abund tests to
+ dedicated test script, add minimal test for new -o option.
+ * tests/test-data/paired-mixed-witherror.fa.pe: add data file in support of
+ new test.
+ * .gitignore: add .cache/ directory, which appears to be an artifact of the
+ py.test framework.
+
+2016-06-17 Daniel Standage <daniel.standage at gmail.com>
+
+ * scripts/filter-abund-single.py: add -o/--outfile option.
+ * tests/test_script_output.py: move `_calc_md5` function for calculating file
+ MD5 hashes to test utils module (tests/khmer_tst_utils.py).
+ * tests/{test_filter_abund.py,test_scripts.py): move filter_abund tests to
+ dedicated test script, add minimal test for new -o option.
+ * tests/test-data/paired-mixed-witherror.fa.pe: add data file in support of
+ new test.
+ * .gitignore: add .cache/ directory, which appears to be an artifact of the
+ py.test framework.
+
+2016-05-25 Titus Brown <titus at idyll.org>
+
+ * scripts/trim-low-abund.py: switched to watermark-based reporting to
+ isolate a hard-to-trigger undefined variable error in reporting.
+ * tests/test_scripts.py: added a test for basic reporting functionality.
+
+2016-05-16 Titus Brown <titus at idyll.org>
+
+ * khmer/_khmer.cc: define new khmer_HashSet_Type and khmer_HashSet_Object;
+ lots of associated cleanup of k-mer <-> C++ interface; added
+ Hashtable::neighbors; added Hashtable::hash and Hashtable::reverse_hash;
+ CPython 'hashtable.count(...)' function now takes either hash or string.
+ * lib/{kmer_hash.cc, kmer_hash.hh}: added some function overloads so that
+ _hash(...) could take strings as arguments without conversion; added
+ Kmer::set_from_unique_hash convenience function.
+ * lib/{hashtable.cc, hashtable.hh}: minor cleanup;
+ * lib/{read_aligner.cc, subset.cc}: minor refactoring.
+ * lib/{traversal.cc, traversal.hh}: made 'filter' argument to traverse*
+ functions optional; added 'traverse' function for combine traversal.
+ * tests/test_hashset.py: tests for new HashSet class.
+ * tests/test_countgraph.py: tests for new hash/reverse_hash functions,
+ and 'count' behavior.
+ * tests/test_nodegraph.py: tests for new neighbors function.
+ * khmer/__init__.py: import new HashSet type from _khmer.
+ * scripts/{do-partition.py, make-initial-stoptags.py,
+ partition-graph.py},tests/{test_labelhash.py, test_subset_graph.py}:
+ refactor existing code to use HashSet object.
+ * tests/test_counting_single.py: add printout to assert.
+
+2016-05-16 Luiz Irber <khmer at luizirber.org>
+
+ * Makefile,jenkins-build.sh,setup.cfg,tests/khmer_tst_utils.py,
+ tests/test_{countgraph,counting_single,hll,labelhash,nodegraph,
+ normalize_by_median,read_aligner,read_handling,read_parsers,sandbox_scripts,
+ scripts,version}.py: replace nose with pytest, update configuration.
+
+2016-05-16 Luiz Irber <khmer at luizirber.org>
+
+ * lib/hashtable.cc: fix bug with substr
+ * tests/test_countgraph.py: add test to trigger the substr bug.
+
+2016-05-11 Titus Brown <titus at idyll.org>
+
+ * scripts/trim-low-abund.py: refactor to use generators; add --diginorm
+ option to include digital normalization in trim-low-abund functionality.
+ * tests/test_script_output.py: added md5sum hashing tests to pin down
+ functionality in trim-low-abund.py and normalize-by-median.py; verified
+ that refactoring does not alter existing functionality.
+ * tests/test-data/simple-genome-reads.fa: supporting file for md5sum
+ tests.
+ * tests/test-data/README.rst: a new README for describing test files,
+ how to generate them, and their uses.
+ * tests/test_scripts.py: added additional tests for trim-low-abund.py
+ functionality and error cases.
+
+2016-05-11 Titus Brown <titus at idyll.org>
+
+ * tests/test_read_parsers.py: fixed syntax error introduced by previous
+ merge.
+
+2016-05-08 Michael R. Crusoe <crusoe at ucdavis.edu>
+
+ * scripts/{do-partition,partition-graph}.py,oxli/partition.py: pulled up
+ duplicate `worker` partition function into a reusable place.
+
+2016-05-08 Michael R. Crusoe <michael.crusoe at gmail.com>
+
+ * .dictionary, pylintrc: added `pylint` configuration that checks spelling
+ in Python files. Added dictionary of project specific words.
+ * khmer/__init__.py, scripts/readstats.py, setup.py: Fixed typos.
+ * Makefile: line-wrapped; bumped up `pep8` version; beefed up `cppcheck`
+ target to correctly list the defines and includes for the current platform
+ which eliminates false positives; `*.pyc` files are now cleaned from the
+ `sandbox` as well as the `dist` directory. Added `cppcheck-long` target to
+ also examine the seqan headers. Fed the dynamically constucted list of
+ includes to Doxygen. Added simultaneous OS X, Debian, and Ubuntu
+ compatibility to many targets. Added helper target to print the value of
+ any variable via `make print-VARNAME`. Fixed the `make coverage-report`
+ target. pep257 is now called pydocstyle
+ * third-party/seqan/core/include/seqan/basic/debug_test_system.h,
+ third-party/seqan/ChangeLog: silenced bogus import
+ * doc/dev/coding-guidelines-and-review.rst,.github/PULL_REQUEST_TEMPLATE.md:
+ reformulated checklist to list action followed by a motivating question.
+ * doc/dev/release.rst: added author management to release checklist
+ * lib/counting.{cc,hh},sandbox/find-high-abund-kmers.py,
+ sandbox/README.rsr: removed the unused function
+ CountingHash::collect_high_abundance_kmers and the nonfunctional sandbox
+ script that called it.
+ * lib/kmer_hash.hh: make KmerFactory's default contrustor explicit to avoid
+ auto-casting optimizations.
+ * */*.py: a multitude of pylint inspired cleanups and bug fixes. Some
+ checks silenced in place.
+
+2016-05-08 Michael R. Crusoe <michael.crusoe at gmail.com>
+
+ * README.rst: add depsy badge
+
+2016-05-08 Michael R. Crusoe <michael.crusoe at gmail.com>
+
+ * setup.py,sandbox/{readaligner_pairhmm_train.py,
+ Makefile.read_aligner_training}: switch to BAM parsing using simplesam
+
+2016-05-06 Titus Brown <titus at idyll.org>
+
+ * khmer/_khmer.cc, lib/{counting.cc,counting.hh,hashbits.cc,hashbits.hh,
+ hashtable.cc,hashtable.hh,subset.cc,subset.hh},
+ sandbox/{fasta-to-abundance-hist.py,find-high-abund-kmers.py
+ hi-lo-abundance-by-position.py,stoptag-abundance-hist.py,
+ abundance-hist-by-position.py},
+ tests/{test_countgraph.py,test_counting_single.py,test_filter.py,
+ test_nodegraph.py,test_subset_graph.py}: removed unused functions,
+ sandbox scripts, and tests for many functions. Specifically,
+ consume_fasta_and_tag_with_stoptags, identify_stop_tags_by_position and
+ identify_stoptags_by_position,
+ count_and_transfer_to_stoptags, traverse_from_tags,
+ filter_if_present, consume_fasta_and_traverse,
+ collect_high_abundance_kmers, fasta_dump_kmers_by_abundance,
+ fasta_count_kmers_by_position, output_fasta_kmer_pos_freq,
+ compare_partitions/compare_to_partition, join_partitions_by_path,
+ is_single_partition, and find_unpart function.
+
+ * sandbox/README.rst: updated for removed sandbox scripts.
+
+2016-04-29 Luiz Irber <khmer at luizirber.org>
+
+ * jenkins-build.sh: add codecov coverage upload tool.
+
+2016-02-17 Daniel Standage <daniel.standage at gmail.com>
+
+ * ./github/CONTRIBUTING.md,.github/PULL_REQUEST_TEMPLATE.md: auto-populate
+ pull requests with checklist using GitHub's new template feature
+ * doc/dev/coding-guidelines-and-review.rst: update developer docs with
+ compensatory changes
+
+2016-02-15 Kevin Murray <spam at kdmurray.id.au>
+
+ * scripts/load-into-counting.py: Insert khmer's version into .info files
+
+2015-11-30 Luiz Irber <khmer at luizirber.org>
+
+ * lib/Makefile: add missing hllcounter.hh header to KHMER_HEADERS.
+
+2015-11-14 Luiz Irber <khmer at luizirber.org>
+
+ * lib/subset.cc: check iterator before decrementing in
+ repartition_largest_partition
+
+2015-10-25 Titus Brown <titus at idyll.org>
+
+ * scripts/normalize-by-median.py,tests/test_normalize_by_median.py: test
+ and fix for close of --output file after first input file.
+
+2015-10-19 Michael R. Crusoe <crusoe at ucdavis.edu>
+
+ * versioneer.py,khmer/_version.py,setup.py,setup.cfg: upgrade Versioneer to
+ version 0.15+dev, Mon Jun 29 2015 99d5d9341830945f7080537ddd3bbd79c4aa1732
+ * doc/conf.py, lib/Makefile: update method of retrieving current version
+ * lib/get_version.py: no longer needed, removed
+
+2015-10-05 Michael R. Crusoe <crusoe at ucdavis.edu>
+
+ * lib/magic: add file extensions, one media type, and a better comment
+ * khmer/__init__.py: Replace an errant 'Presence table' with 'node graph'
+
+2015-09-28 Lisa Cohen <ljcohen at ucdavis.edu>
+
+ * tests/test_read_handling.py: created new file with interleave-reads,
+ split-paired-reads, and extract-paired-reads functions
+ * tests/test_scripts.py: removed functions mentioned above
+
+2015-09-19 Titus Brown <titus at idyll.org>
+
+ * scripts/filter-abund.py: fixed bug with -o and --gzip used together.
+ * tests/test_scripts.py: added test for fixed bug.
+ * sandbox/count-kmers.py: added executable bit.
+
+2015-09-17 Camille Scott <camille.scott.w at gmail.com>
+
+ * scripts/interleave-reads.py: Added --no-reformat flag
+ to disable format checking and renaming of headers
+ * tests/{test_scripts.py, test-data/paired.malformat*}: Tests
+ and test data for --no-reformat flag.
+
+2015-09-11 Russell Y. Neches <ryneches at ucdavis.edu>
+
+ * lib/hashbits.hh: added get_raw_tables to Hashbits
+ * khmer/_khmer.cc: added get_raw_tables to Hashbits
+ * tests/test_nodegraph.py: added test for Nodegraph.get_raw_tables
+
+2015-09-11 Camille Scott <camille.scott.w at gmail.com>
+
+ * lib/hashbits.cc: Make hasbits::update_from() correctly update
+ _occupied_bins.
+ * lib/test_nodegraph.py: Test Nodegraph.n_occupied() after update.
+
2015-09-07 Michael R. Crusoe <crusoe at ucdavis.edu>
* doc/roadmap.rst: Updated for 2.0 release.
@@ -140,6 +670,12 @@
* tests/test_streaming_io.py: Fix unique-kmers tests, use new option.
* khmer/_khmer.cc, lib/hllcounter.cc: Rename some variables for consistency.
+2015-08-13 Jacob Fenton <bocajnotnef at gmail.com>
+
+ * scripts/extract-partitions.py: refactored much of the processing into
+ generators
+ * tests/test_scripts.py: added test
+
2015-08-12 Jacob Fenton <bocajnotnef at gmail.com>
* doc/dev/{codebase-guide,coding-guidelines-and-review,development,
@@ -151,7 +687,7 @@
* scripts/*.py, khmer/khmer_args.py: added epilog sanitation
* scripts/{load-into-counting,load-graph,load-into-countgraph,
load-into-nodegraph}.py, tests/{test_scripts,test_normalize_by_median,
- test_streaming_io,test_countgraph}: renamed load-into-counting ->
+ test_streaming_io,test_countgraph}: renamed load-into-counting ->
load-into-countgraph, load-graph -> load-into-nodegraph, fixed tests to not
bork
@@ -164,7 +700,7 @@
* CITATION, doc/{index,introduction,user/scripts}.rst, khmer/khmer_args.py:
formatting fixes and new citation for the software as a whole
* Makefile: PDF building hints, tweaked dependencies, update coverity URL,
- new target to generate author list for the paper citation
+ new target to generate author list for the paper citation
* sort-authors-list.py: helper script for the above
* doc/conf.py: don't generate a module index
* doc/contributors.rst: formatting, remove references to old lab
@@ -196,18 +732,18 @@
and KmerIterator, respectively.
* lib/Makefile: Add -std=c++11 flag.
* Makefile: Update -std=c++11 flag in libtest target.
- * lib/hashtable.{cc,hh}: Update calc_connected_graph_size to use Traverser.
+ * lib/hashtable.{cc,hh}: Update calc_connected_graph_size to use Traverser.
Change kmer_degree to use functions from traversal.cc. Remove redundant
count_kmers_with_radius in favor of calc_connected_graph_size. Update
traverse_from_kmer to use Traverser. Hashtable subclasses KmerFactory.
* lib/{hashtable.hh,kmer_hash.{cc,hh}}: Move KmerIterator from hashtable.hh
to kmer_hash.{cc,hh}. Add Kmer class to store forward, reverse, and
uniqified integer representations of k-mers, and to handle string
- conversion. Update KmerIterator to emit objects of type Kmer and to subclass
+ conversion. Update KmerIterator to emit objects of type Kmer and to subclass
KmerFactory; add doxygen markup.
* lib/khmer.hh: Forward declare Kmer and typedef new Kmer data structures.
* lib/subset.{cc,hh}: Move constructor definition to .cc file. Remove
- queue_neighbors in favor of new traversal machinery. Update find_all_tags,
+ queue_neighbors in favor of new traversal machinery. Update find_all_tags,
sweep_for_tags, and find_all_tags_truncate_on_abundance to use Traverser.
* setup.py: Add traversal.{cc,hh} to deps.
@@ -273,9 +809,9 @@
2015-08-04 Jacob Fenton <bocajnotnef at gmail.com>
- * khmer/khmer_args.py, oxli/functions.py: migrated estimation functions out
+ * khmer/khmer_args.py, oxli/functions.py: migrated estimation functions out
oxli and into khmer_args
- * oxli/build_graph.py, tests/test_oxli_functions.py,
+ * oxli/build_graph.py, tests/test_oxli_functions.py,
sandbox/{estimate_optimal_hash,optimal_args_hashbits}.py,
scripts/{normalize-by-median,unique-kmers}.py: changed to not break on
location change
@@ -500,7 +1036,7 @@
abundance-dist}.py,tests/test_{normalize_by_median,subset_graph,hashbits,
oxli_function}.py: pylint cleanup.
-2015-07-17 Michael R. Crusoe <crusoe at ucdavis.edu>
+2015-07-17 Michael R. Crusoe <crusoe at ucdavis.edu>
* Makefile, tests/test_read_aligner.py: import khmer when pylinting.
@@ -552,7 +1088,7 @@
2015-07-05 Jacob Fenton <bocajnotnef at gmail.com>
- * doc/whats-new-2.0.rst: added in normalize-by-median.py broken paired
+ * doc/whats-new-2.0.rst: added in normalize-by-median.py broken paired
updates.
2015-07-05 Michael R. Crusoe <crusoe at ucdavis.edu>
@@ -629,7 +1165,7 @@
2015-06-28 Qingpeng Zhang <qingpeng at msu.edu>
- * sandbox/{estimate_optimal_hash,optimal_args_hashbits}.py: added sandbox
+ * sandbox/{estimate_optimal_hash,optimal_args_hashbits}.py: added sandbox
methods for estimating memory usage based on desired fp rate, etc.
2015-06-27 Kevin Murray <spam at kdmurray.id.au>
@@ -967,7 +1503,7 @@
2015-04-17 Jessica Mizzi <mizzijes at msu.edu>
- * tests/test_scripts.py: split test_extract_long_sequences
+ * tests/test_scripts.py: split test_extract_long_sequences
into test_extract_long_sequences_fa and test_extract_long_sequences_fq
2015-04-15 Elmar Bucher <buchere at ohsu.edu>
@@ -1003,7 +1539,7 @@
2015-04-15 Sarah Guermond <sarah.guermond at gmail.com>
* scripts/trim-low-abund.py: implemented STDOUT output, redirected
- existing print statements to STDERR, fixed existing & new PEP 8 issues
+ existing print statements to STDERR, fixed existing & new PEP 8 issues
* tests/test_scripts.py: added test for above changes
2014-04-15 Andreas Härpfer <ahaerpfer at gmail.com>
@@ -1017,25 +1553,25 @@
2015-04-15 Susan Steinman <steinman.tutoring at gmail.com>
- * khmer/scripts/normalize-by-median.py: pass individual arg values to
+ * khmer/scripts/normalize-by-median.py: pass individual arg values to
functions instead of ArgParse object
2015-04-15 Thomas Fenzl <thomas.fenzl at gmx.net>
- * scripts/{count-overlap.py,readstats.py},tests/test_scripts.py:
+ * scripts/{count-overlap.py,readstats.py},tests/test_scripts.py:
added a --csv option to readstats
updated documentation for count-overlap
- * khmer/_khmermodule.cc: fixed missing error handling
+ * khmer/_khmermodule.cc: fixed missing error handling
for hashbits_count_overlap
2015-04-15 en zyme <en_zyme at outlook.com>
* khmer/khmer/kfile.py: check_file_status() -> check_input_files()
- * khmer/sandbox/{collect-reads, khmer/sandbox/sweep-reads}.py
+ * khmer/sandbox/{collect-reads, khmer/sandbox/sweep-reads}.py
khmer/scripts/{abundance-dist-single, abundance-dist, annotate-partitions,
- count-median, count-overlap, do-partition, extract-paired-reads,
+ count-median, count-overlap, do-partition, extract-paired-reads,
extract-partitions, filter-abund-single, filter-abund, filter-stoptags,
- find-knots, interleave-reads, load-graph, load-into-counting,
+ find-knots, interleave-reads, load-graph, load-into-counting,
make-initial-stoptags, merge-partitions, partition-graph,
sample-reads-randomly, split-paired-reads}.py:
check_file_status() -> check_input_files()
@@ -1111,7 +1647,7 @@
2015-04-13 Thomas Fenzl <thomas.fenzl at gmx.net>
- * lib/{khmer_exception.hh,{counting,hashbits,hashtable,subset}.cc}: changed
+ * lib/{khmer_exception.hh,{counting,hashbits,hashtable,subset}.cc}: changed
khmer_exception to use std::string to fix memory management.
2015-04-13 Elmar Bucher <buchere at ohsu.edu>
@@ -1138,7 +1674,7 @@
2015-04-13 David Lin
- * scripts/abundance-dist.py: disambiguate documentation for force and
+ * scripts/abundance-dist.py: disambiguate documentation for force and
squash options
2015-04-13 Michael R. Crusoe <mcrusoe at msu.edu>
@@ -1158,7 +1694,7 @@
2015-04-10 Jacob Fenton <bocajnotnef at gmail.com>
- * scripts/test-{scripts.py}: added test for check_file_writable using
+ * scripts/test-{scripts.py}: added test for check_file_writable using
load_into_counting
2015-04-10 Phillip Garland <pgarland at gmail.com>
@@ -1324,7 +1860,7 @@
* scripts/abundance-dist-single.py: Use CSV format for the histogram.
* scripts/count-overlap.py: Use CSV format for the curve file output.
Includes column headers.
- * scripts/abundance-dist-single.py: Use CSV format for the histogram.
+ * scripts/abundance-dist-single.py: Use CSV format for the histogram.
Includes column headers.
* tests/test_scripts.py: add test functions for the --csv option in
abundance-dist-single.py and count-overlap.py
@@ -1336,9 +1872,9 @@
2015-02-25 Aditi Gupta <agupta at msu.edu>
- * sandbox/{collect-reads.py, correct-errors.py,
- normalize-by-median-pct.py, slice-reads-by-coverage.py,
- sweep-files.py, sweep-reads3.py, to-casava-1.8-fastq.py}:
+ * sandbox/{collect-reads.py, correct-errors.py,
+ normalize-by-median-pct.py, slice-reads-by-coverage.py,
+ sweep-files.py, sweep-reads3.py, to-casava-1.8-fastq.py}:
Replaced 'accuracy' with 'quality'. Fixes #787.
2015-02-25 Tamer A. Mansour <drtamermansour at gmail.com>
@@ -1568,7 +2104,7 @@
* khmer/utils.py: Added single write_record fuction to write FASTA/Q
* scripts/{abundance-dist,extract-long-sequences,extract-partitions,
- interleave-reads,normalize-by-median,sample-reads-randomly}.py:
+ interleave-reads,normalize-by-median,sample-reads-randomly}.py:
Replaced FASTA/Q writing method with write_record
2015-01-23 Michael R. Crusoe <mcrusoe at msu.edu>
@@ -1636,13 +2172,13 @@
2015-01-09 Rhys Kidd <rhyskidd at gmail.com>
* lib/khmer.hh: implement generic NONCOPYABLE() macro guard
- * lib/hashtable.hh: apply NONCOPYABLE macro guard in case of future
- modifications to Hashtable that might exposure potential memory corruption
+ * lib/hashtable.hh: apply NONCOPYABLE macro guard in case of future
+ modifications to Hashtable that might exposure potential memory corruption
with default copy constructor
2014-12-30 Michael Wright <wrig517 at msu.edu>
- * tests/test_scripts.py: Attained complete testing coverage for
+ * tests/test_scripts.py: Attained complete testing coverage for
scripts/filter_abund.py
2014-12-30 Brian Wyss <wyssbria at msu.edu>
@@ -1704,8 +2240,8 @@
filter-stoptags,interleave-reads,load-graph,load-into-counting,
make-initial-stoptags,merge-partitions,normalize-by-median,partition-graph,
sample-reads-randomly,split-paired-reads}.py,setup.cfg,
- tests/{test_script_arguments,test_scripts}.py: Added force option to all
- scripts to script IO sanity checks and updated tests to match.
+ tests/{test_script_arguments,test_scripts}.py: Added force option to all
+ scripts to script IO sanity checks and updated tests to match.
2014-12-17 Michael R. Crusoe <mcrusoe at msu.edu>
@@ -1834,7 +2370,7 @@
2014-11-11 Jacob Fenton <bocajnotnef at gmail.com>
- * do-partition.py: replaced threading args in scripts with things from
+ * do-partition.py: replaced threading args in scripts with things from
khmer_args
* khmer/theading_args.py: removed as it has been deprecated
@@ -1862,7 +2398,7 @@
annotate-partitions, count-median, count-overlap, do-partition,
extract-paired-reads, extract-partitions, filter-abund, filter-abund-single,
filter-stoptags, find-knots, load-graph, load-into-counting,
- make-initial-stoptags, merge-partitions, normalize-by-median,
+ make-initial-stoptags, merge-partitions, normalize-by-median,
partition-graph, sample-reads-randomly}.py:
changed stdout output in scripts to go to stderr.
@@ -1893,11 +2429,11 @@
* scripts/{abundance-dist-single, abundance-dist, count-median,
count-overlap, extract-paired-reads, filter-abund-single,
load-graph, load-into-counting, make-initial-stoptags,
- partition-graph, split-paired-reads}.py:
+ partition-graph, split-paired-reads}.py:
added output file listing at end of file
* scripts/extract-long-sequences.py: refactored to set write_out to
sys.stdout by default; added output location listing.
- * scripts/{fastq-to-fasta, interleave-reads}.py:
+ * scripts/{fastq-to-fasta, interleave-reads}.py:
added output file listing sensitive to optional -o argument
* tests/test_scripts.py: added test for scripts/make-initial-stoptags.py
@@ -1913,7 +2449,7 @@
.empty() instead of .size()
2014-09-19 Ben Taylor <taylo886 at msu.edu>
-
+
* Makefile: Add astyle, format targets
* doc/dev/coding-guidelines-and-review.txt: Add reference to `make format`
target
@@ -1926,7 +2462,7 @@
average cutoff.
* sandbox/slice-reads-by-coverage.py: added script to extract reads with
a specific coverage slice (based on median k-mer abundance).
-
+
2014-09-09 Titus Brown <titus at idyll.org>
* Added sandbox/README.rst to describe/reference removed files,
@@ -2058,7 +2594,7 @@
* khmer/thread_utils.py, sandbox/filter-below-abund.py,
scripts/{extract-long-sequences,load-graph,load-into-counting,
normalize-by-median,split-paired-reads}.py,
- scripts/galaxy/gedlab.py: fix minor PyLint issues
+ scripts/galaxy/gedlab.py: fix minor PyLint issues
2014-08-20 Michael R. Crusoe <mcrusoe at msu.edu>
@@ -2066,7 +2602,7 @@
2014-08-20 Rhys Kidd <rhyskidd at gmail.com>
- * setup.py,README.rst,doc/user/install.txt: Test requirement for a
+ * setup.py,README.rst,doc/user/install.txt: Test requirement for a
64-bit operating system, documentation changes. Fixes #529
2014-08-19 Michael R. Crusoe <mcrusoe at msu.edu>
@@ -2153,7 +2689,7 @@
2014-07-23 Qingpeng Zhang <qingpeng at gmail.com>
- * scripts/load-graph.py: write fp rate into *.info file with option
+ * scripts/load-graph.py: write fp rate into *.info file with option
to switch on
* tests/test_scripts.py: add test_load_graph_write_fp
@@ -2163,16 +2699,16 @@
2014-07-23 Leonor Garcia-Gutierrez <l.garcia-gutierrez at warwick.ac.uk>
- * tests/test_hashbits.py, tests/test_graph.py,
+ * tests/test_hashbits.py, tests/test_graph.py,
tests/test_lump.py: reduced memory requirement
-
+
2014-07-23 Heather L. Wiencko <wienckhl at tcd.ie>
* khmer_tst_utils.py: added import traceback
* test_scripts.py: added test for normalize_by_median.py for fpr rate
2014-07-22 Justin Lippi <jlippi at gmail.com>
-
+
* khmer/_khmermodule.cc: removed unused assignment
* lib/read_aligner.cc,lib/read_aligner.hh: wrapped function declarations
in the same compiler options that the only invocations are in to avoid
@@ -2195,7 +2731,7 @@
* scripts/filter-abund.py: no longer asks for parameters that are unused,
issue #524
-2014-07-22 Justin Lippi <jlippi at gmail.com>
+2014-07-22 Justin Lippi <jlippi at gmail.com>
* tests/khmer_tst_utils.py: put runscript here
* tests/test_sandbox_scripts.py: remove 'runsandbox', renamed to runscript
@@ -2209,11 +2745,11 @@
2014-07-22 Rodney Picett <pickett.rodney at gmail.com>
* lib/scoringmatrix.{cc,hh}: removed assign function, issue #502
-
+
2014-07-22 Leonor Garcia-Gutierrez <l.garcia-gutierrez at warwick.ac.uk>
* tests/test_counting_single.py: reduced memory requirements
-
+
2014-07-21 Titus Brown <t at idyll.org>
* sandbox/saturate-by-median.py: introduce new sandbox script for
@@ -2234,7 +2770,7 @@
2014-06-20 Chuck Pepe-Ranney <chuck.peperanney at gmail.com>
- * scripts/extract-partitions.py: added epilog documentation for
+ * scripts/extract-partitions.py: added epilog documentation for
<base>.dist columns.
2014-06-20 Michael R. Crusoe <mcrusoe at msu.edu>
@@ -2323,7 +2859,7 @@
2014-06-11 Michael Wright <wrigh517 at msu.edu>
- * scripts/load-into-counting: Fixed docstring misnomer to
+ * scripts/load-into-counting: Fixed docstring misnomer to
load-into-counting.py
2014-06-10 Michael R. Crusoe <mcrusoe at msu.edu>
@@ -2347,7 +2883,7 @@
2014-06-10 Michael Wright <wrigh517 at msu.edu>
- * scripts/extract-long-sequences: Moved from sandbox, added argparse and
+ * scripts/extract-long-sequences: Moved from sandbox, added argparse and
FASTQ support.
* scripts/fastq-to-fasta: Fixed outdated argparse oversight.
* tests/test_scripts.py: Added tests for extract-long-sequences.py
@@ -2365,7 +2901,7 @@
2014-06-03 Chuck Pepe-Ranney <chuck.peperanney at gmail.com>
- * scripts/abundance-dist.py: removed call to check_space on infiles.
+ * scripts/abundance-dist.py: removed call to check_space on infiles.
2014-05-31 Michael R. Crusoe <mcrusoe at msu.edu>
@@ -2398,10 +2934,10 @@
2014-05-22 Michael Wright <wrigh517 at msu.edu>
- * scripts/fastq-to-fasta: Moved and improved fastq-to-fasta.py into scripts
+ * scripts/fastq-to-fasta: Moved and improved fastq-to-fasta.py into scripts
from sandbox
* tests/test_scripts.py: Added tests for fastq-to-fasta.py
- * tests/test-data: Added test-fastq-n-to-fasta.py file with N's in
+ * tests/test-data: Added test-fastq-n-to-fasta.py file with N's in
sequence for testing
2014-05-19 Michael R. Crusoe <mcrusoe at msu.edu>
@@ -2451,7 +2987,7 @@
* sandbox/calc-best-assembly.py: added script to calculate best
assembly from a list of contig/scaffold files
-
+
2014-04-23 Titus Brown <titus at idyll.org>
* scripts/abundance-dist-single.py: fixed problem where ReadParser was
@@ -2591,7 +3127,7 @@
* test_scripts.py: add test code for count-overlap.py
* count-overlap.py: (fix a bug because of a typo and hashsize was replaced
by min_hashsize)
- * count-overlap.py: needs hashbits table generated by load-graph.py.
+ * count-overlap.py: needs hashbits table generated by load-graph.py.
This information is added to the "usage:" line.
* count-overlap.py: fix minor PyLint issues
@@ -2674,7 +3210,7 @@
2014-03-03 Michael R. Crusoe <mcrusoe at msu.edu>
* lib/trace_logger.{cc,hh}: fix for Coverity CID 1063852: Uninitialized
- scalar field (UNINIT_CTOR)
+ scalar field (UNINIT_CTOR)
* lib/node.cc: fix for Coverity CID 1173035: Uninitialized scalar field
(UNINIT_CTOR)
* lib/hashbits.hh: fix for Coverity CID 1153101: Resource leak in object
@@ -2704,7 +3240,7 @@ users without root access to install virtualenv instead of pip.
* Added support for sparse graph labeling
-* Added script to reinflate partitions from read files using the
+* Added script to reinflate partitions from read files using the
labeling system, called sweep-reads-by-partition-buffered.py
* Implemented __new__ methods for Hashbits, enforced inheritance
@@ -2772,14 +3308,14 @@ clarified and simplified.
* khmer/_khmermodule.cc has gotten a once-over with cpychecker. Type errors
were eliminated and the error checking has improved.
-* Several fixes motivated by the results of a Coverity C/C++ scan.
+* Several fixes motivated by the results of a Coverity C/C++ scan.
* Tests that require greater than 0.5 gigabytes of memory are now annotated as
being 'highmem' and be skipped by changing two lines in setup.cfg
* warnings about -Wstrict-prototypes will no longer appear
-* contributors to this release are: ctb, mr-c and camillescott.
+* contributors to this release are: ctb, mr-c and camillescott.
2013-10-15 Michael R. Crusoe <mcrusoe at msu.edu>
@@ -2902,7 +3438,7 @@ project to conform to the standard layout
* test_scripts.py: add test code for count-overlap.py
* count-overlap.py: (fix a bug because of a typo and hashsize was replaced
by min_hashsize)
- * count-overlap.py: needs hashbits table generated by load-graph.py.
+ * count-overlap.py: needs hashbits table generated by load-graph.py.
This information is added to the "usage:" line.
* count-overlap.py: fix minor PyLint issues
@@ -2985,7 +3521,7 @@ project to conform to the standard layout
2014-03-03 Michael R. Crusoe <mcrusoe at msu.edu>
* lib/trace_logger.{cc,hh}: fix for Coverity CID 1063852: Uninitialized
- scalar field (UNINIT_CTOR)
+ scalar field (UNINIT_CTOR)
* lib/node.cc: fix for Coverity CID 1173035: Uninitialized scalar field
(UNINIT_CTOR)
* lib/hashbits.hh: fix for Coverity CID 1153101: Resource leak in object
@@ -3015,7 +3551,7 @@ users without root access to install virtualenv instead of pip.
* Added support for sparse graph labeling
-* Added script to reinflate partitions from read files using the
+* Added script to reinflate partitions from read files using the
labeling system, called sweep-reads-by-partition-buffered.py
* Implemented __new__ methods for Hashbits, enforced inheritance
@@ -3083,14 +3619,14 @@ clarified and simplified.
* khmer/_khmermodule.cc has gotten a once-over with cpychecker. Type errors
were eliminated and the error checking has improved.
-* Several fixes motivated by the results of a Coverity C/C++ scan.
+* Several fixes motivated by the results of a Coverity C/C++ scan.
* Tests that require greater than 0.5 gigabytes of memory are now annotated as
being 'highmem' and be skipped by changing two lines in setup.cfg
* warnings about -Wstrict-prototypes will no longer appear
-* contributors to this release are: ctb, mr-c and camillescott.
+* contributors to this release are: ctb, mr-c and camillescott.
2013-10-15 Michael R. Crusoe <mcrusoe at msu.edu>
diff --git a/jenkins-build.sh b/legacy/jenkins-build.sh
similarity index 91%
rename from jenkins-build.sh
rename to legacy/jenkins-build.sh
index dc5ce1d..8f17704 100755
--- a/jenkins-build.sh
+++ b/legacy/jenkins-build.sh
@@ -1,7 +1,7 @@
#!/bin/bash
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2013-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -68,18 +68,18 @@ then
export CFLAGS="-pg -fprofile-arcs -ftest-coverage"
python setup.py build_ext --build-temp $PWD --debug --inplace \
--libraries gcov develop
- make coverage-gcovr.xml coverage.xml TESTATTR='!known_failing,!huge'
+ make coverage-gcovr.xml coverage.xml TESTATTR='"not known_failing and not huge"'
./setup.py install
else
echo "gcov was not found (or we are on OSX), skipping coverage check"
./setup.py install
./setup.py develop
- make nosetests.xml
+ make pytests.xml
fi
if type cppcheck >/dev/null 2>&1
then
- make cppcheck-result.xml
+ make cppcheck-result.xml SHELL=bash
fi
if type doxygen >/dev/null 2>&1
then
@@ -113,3 +113,7 @@ unset CXXFLAGS
# Don't do lib too, as we already compile as part of libtest
make libtest
+
+# Upload code coverage to codecov.io
+pip install codecov
+codecov -X pycov search gcov -f coverage.xml coverage-gcovr.xml &> /dev/null
diff --git a/lib/.gitignore b/lib/.gitignore
index ca5f8e1..983d7ce 100644
--- a/lib/.gitignore
+++ b/lib/.gitignore
@@ -8,3 +8,4 @@ chkomp
*.so
*.so.*
*.a
+*.dylib*
diff --git a/lib/Makefile b/lib/Makefile
index 7797f34..d05c18c 100644
--- a/lib/Makefile
+++ b/lib/Makefile
@@ -150,7 +150,7 @@ endif
ifneq ($(PACKAGE_VERSION),)
VERSION = $(PACKAGE_VERSION)
else
-VERSION = $(shell ./get_version.py)
+VERSION = $(./setup.py version | grep Version | awk '{print $2}')
endif
# The ABI version of liboxli
@@ -222,9 +222,8 @@ BZIP2_OBJS=$(addprefix $(BZIP2_DIR)/, $(BZIP2_OBJS_BASE))
#### oxli proper below here ####
LIBKHMER_OBJS= \
- counting.o \
- hashbits.o \
hashtable.o \
+ hashgraph.o \
hllcounter.o \
kmer_hash.o \
labelhash.o \
@@ -232,7 +231,11 @@ LIBKHMER_OBJS= \
read_aligner.o \
read_parsers.o \
subset.o \
- murmur3.o
+ kmer_filters.o \
+ assembler.o \
+ alphabets.o \
+ murmur3.o \
+ storage.o
PRECOMILE_OBJS ?=
PRECLEAN_TARGS ?=
@@ -250,9 +253,8 @@ PRECLEAN_TARGS += libbz2clean
endif
KHMER_HEADERS= \
- counting.hh \
- hashbits.hh \
hashtable.hh \
+ hllcounter.hh \
khmer_exception.hh \
khmer.hh \
kmer_hash.hh \
@@ -261,6 +263,10 @@ KHMER_HEADERS= \
read_aligner.hh \
read_parsers.hh \
subset.hh \
+ kmer_filters.hh \
+ assembler.hh \
+ alphabets.hh \
+ storage.hh
# START OF RULES #
diff --git a/lib/test-compile.cc b/lib/alphabets.cc
similarity index 84%
copy from lib/test-compile.cc
copy to lib/alphabets.cc
index 124ac9a..8b0a2c0 100644
--- a/lib/test-compile.cc
+++ b/lib/alphabets.cc
@@ -1,7 +1,6 @@
/*
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-Copyright (C) 2015, Michigan State University.
-Copyright (C) 2015, The Regents of the University of California.
+Copyright (C) 2015-2016, The Regents of the University of California.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
@@ -36,13 +35,17 @@ LICENSE (END)
Contact: khmer-project at idyll.org
*/
-// This file is used to test compilation with libkhmer.a/libkhmer.so, after
-// installation
+#include <string>
-#include <oxli/counting.hh>
-
-int main()
+namespace khmer
+{
+namespace alphabets
{
- khmer::CountingHash test(1,1);
- return 0;
+
+std::string DNA_SIMPLE = "ACGT";
+std::string DNAN_SIMPLE = "ACGTN";
+std::string IUPAC_NUCL = "ACGTURYSWKMBDHVN.-";
+std::string IUPAC_AA = "ACDEFGHIKLMNPQRSTVWY";
+
+}
}
diff --git a/lib/test-compile.cc b/lib/alphabets.hh
similarity index 84%
copy from lib/test-compile.cc
copy to lib/alphabets.hh
index 124ac9a..58b7129 100644
--- a/lib/test-compile.cc
+++ b/lib/alphabets.hh
@@ -1,7 +1,6 @@
/*
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-Copyright (C) 2015, Michigan State University.
-Copyright (C) 2015, The Regents of the University of California.
+Copyright (C) 2015-2016, The Regents of the University of California.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
@@ -35,14 +34,19 @@ LICENSE (END)
Contact: khmer-project at idyll.org
*/
+#ifndef SYMBOLS_HH
+#define SYMBOLS_HH
-// This file is used to test compilation with libkhmer.a/libkhmer.so, after
-// installation
+namespace khmer
+{
+namespace alphabets
+{
-#include <oxli/counting.hh>
+extern std::string DNA_SIMPLE;
+extern std::string DNAN_SIMPLE;
+extern std::string IUPAC_NUCL;
+extern std::string IUPAC_AA;
-int main()
-{
- khmer::CountingHash test(1,1);
- return 0;
}
+}
+#endif
diff --git a/lib/assembler.cc b/lib/assembler.cc
new file mode 100644
index 0000000..464cec8
--- /dev/null
+++ b/lib/assembler.cc
@@ -0,0 +1,523 @@
+/*
+This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+Copyright (C) 2015-2016, The Regents of the University of California.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following
+ disclaimer in the documentation and/or other materials provided
+ with the distribution.
+
+ * Neither the name of the Michigan State University nor the names
+ of its contributors may be used to endorse or promote products
+ derived from this software without specific prior written
+ permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+LICENSE (END)
+
+Contact: khmer-project at idyll.org
+*/
+
+#include "assembler.hh"
+
+#include <algorithm>
+#include <iostream>
+
+using namespace std;
+
+namespace khmer
+{
+
+/********************************
+ * Simple Linear Assembly
+ ********************************/
+
+LinearAssembler::LinearAssembler(const Hashgraph * ht) :
+ graph(ht), _ksize(ht->ksize())
+{
+
+}
+
+// Starting from the given seed k-mer, assemble the maximal linear path in
+// both directions.
+std::string LinearAssembler::assemble(const Kmer seed_kmer,
+ const Hashgraph * stop_bf)
+const
+{
+ if (graph->get_count(seed_kmer) == 0) {
+ // If the seed k-mer is not in the de Bruijn graph, stop trying to make
+ // something happen. It's not going to happen!
+ return "";
+ }
+ std::string right_contig = assemble_right(seed_kmer, stop_bf);
+ std::string left_contig = assemble_left(seed_kmer, stop_bf);
+
+#if DEBUG_ASSEMBLY
+ std::cout << "Left: " << left_contig << std::endl;
+ std::cout << "Right: " << right_contig << std::endl;
+#endif
+
+ right_contig = right_contig.substr(_ksize);
+ return left_contig + right_contig;
+}
+
+
+std::string LinearAssembler::assemble_right(const Kmer seed_kmer,
+ const Hashgraph * stop_bf)
+const
+{
+ std::list<KmerFilter> node_filters;
+ if (stop_bf) {
+ node_filters.push_back(get_stop_bf_filter(stop_bf));
+ }
+
+ AssemblerTraverser<TRAVERSAL_RIGHT> cursor(graph, seed_kmer, node_filters);
+ return _assemble_directed<TRAVERSAL_RIGHT>(cursor);
+}
+
+
+std::string LinearAssembler::assemble_left(const Kmer seed_kmer,
+ const Hashgraph * stop_bf)
+const
+{
+ std::list<KmerFilter> node_filters;
+ if (stop_bf) {
+ node_filters.push_back(get_stop_bf_filter(stop_bf));
+ }
+
+ AssemblerTraverser<TRAVERSAL_LEFT> cursor(graph, seed_kmer, node_filters);
+ return _assemble_directed<TRAVERSAL_LEFT>(cursor);
+}
+
+template <>
+std::string LinearAssembler::_assemble_directed<TRAVERSAL_LEFT>(AssemblerTraverser<TRAVERSAL_LEFT>&
+ cursor)
+const
+{
+ std::string contig = cursor.cursor.get_string_rep(_ksize);
+ if (!cursor.cursor.is_forward()) {
+ contig = _revcomp(contig);
+ }
+
+#if DEBUG_ASSEMBLY
+ std::cout << "## assemble_linear_left[start] at " << contig << std::endl;
+#endif
+
+ reverse(contig.begin(), contig.end());
+ char next_base;
+ unsigned int found = 0;
+
+ while ((next_base = cursor.next_symbol()) != '\0') {
+ contig += next_base;
+ found++;
+ }
+
+ reverse(contig.begin(), contig.end());
+#if DEBUG_ASSEMBLY
+ std::cout << "## assemble_linear_left[end] found " << found << std::endl;
+#endif
+
+ return contig;
+}
+
+template<>
+std::string LinearAssembler::_assemble_directed<TRAVERSAL_RIGHT>
+(AssemblerTraverser<TRAVERSAL_RIGHT>& cursor)
+const
+{
+ std::string contig = cursor.cursor.get_string_rep(_ksize);
+ if (!cursor.cursor.is_forward()) {
+ contig = _revcomp(contig);
+ }
+ char next_base;
+ unsigned int found = 0;
+
+#if DEBUG_ASSEMBLY
+ std::cout << "## assemble_linear_right[start] at " << contig << std::endl;
+#endif
+
+ while ((next_base = cursor.next_symbol()) != '\0') {
+ contig += next_base;
+ found++;
+ }
+#if DEBUG_ASSEMBLY
+ std::cout << "## assemble_linear_right[end] found " << found << std::endl;
+#endif
+ return contig;
+}
+
+
+/********************************
+ * Labeled Assembly
+ ********************************/
+
+SimpleLabeledAssembler::SimpleLabeledAssembler(const LabelHash * lh) :
+ graph(lh->graph), lh(lh), _ksize(lh->graph->ksize())
+{
+ linear_asm = new LinearAssembler(graph);
+}
+
+SimpleLabeledAssembler::~SimpleLabeledAssembler()
+{
+ delete this->linear_asm;
+}
+
+
+// Starting from the given seed k-mer, assemble all maximal linear paths in
+// both directions, using labels to skip over tricky bits.
+StringVector SimpleLabeledAssembler::assemble(const Kmer seed_kmer,
+ const Hashgraph * stop_bf)
+const
+{
+#if DEBUG_ASSEMBLY
+ std::cout << "Assemble Labeled: " << seed_kmer.repr(_ksize) << std::endl;
+#endif
+
+ KmerFilterList node_filters;
+ if (stop_bf) {
+ node_filters.push_back(get_stop_bf_filter(stop_bf));
+ }
+
+ SeenSet visited;
+
+#if DEBUG_ASSEMBLY
+ std::cout << "Assemble Labeled RIGHT: " << seed_kmer.repr(_ksize) << std::endl;
+#endif
+ StringVector right_paths;
+ NonLoopingAT<TRAVERSAL_RIGHT> rcursor(graph, seed_kmer, node_filters, &visited);
+ _assemble_directed<TRAVERSAL_RIGHT>(rcursor, right_paths);
+
+#if DEBUG_ASSEMBLY
+ std::cout << "Assemble Labeled LEFT: " << seed_kmer.repr(_ksize) << std::endl;
+#endif
+ StringVector left_paths;
+ NonLoopingAT<TRAVERSAL_LEFT> lcursor(graph, seed_kmer, node_filters, &visited);
+ _assemble_directed<TRAVERSAL_LEFT>(lcursor, left_paths);
+
+ StringVector paths;
+ for (unsigned int i = 0; i < left_paths.size(); i++) {
+ for (unsigned int j = 0; j < right_paths.size(); j++) {
+ std::string right = right_paths[j];
+ right = right.substr(_ksize);
+ std::string contig = left_paths[i] + right;
+ paths.push_back(contig);
+ }
+ }
+
+ visited.clear();
+ return paths;
+}
+
+template <bool direction>
+void SimpleLabeledAssembler::_assemble_directed(NonLoopingAT<direction>&
+ start_cursor,
+ StringVector& paths)
+const
+{
+#if DEBUG_ASSEMBLY
+ std::cout << "## assemble_labeled_directed_" << direction << " [start] at " <<
+ start_cursor.cursor.repr(_ksize) << std::endl;
+#endif
+
+ // prime the traversal with the first linear segment
+ std::string root_contig = linear_asm->_assemble_directed<direction>
+ (start_cursor);
+#if DEBUG_ASSEMBLY
+ std::cout << "Primed: " << root_contig << std::endl;
+ std::cout << "Cursor: " << start_cursor.cursor.repr(_ksize) << std::endl;
+#endif
+ StringVector segments;
+ std::vector< NonLoopingAT<direction> > cursors;
+
+ segments.push_back(root_contig);
+ cursors.push_back(start_cursor);
+
+ while(segments.size() != 0) {
+
+ std::string segment = segments.back();
+ NonLoopingAT<direction> cursor = cursors.back();
+#if DEBUG_ASSEMBLY
+ std::cout << "Pop: " << segments.size() << " segments on stack." << std::endl;
+ std::cout << "Segment: " << segment << std::endl;
+ std::cout << "Cursor: " << cursor.cursor.repr(_ksize) << std::endl;
+ std::cout << "n_filters: " << cursor.n_filters() << std::endl;
+#endif
+ segments.pop_back();
+ cursors.pop_back();
+
+ // check if the cursor has hit a HDN or reached a dead end
+ if (cursor.cursor_degree() > 1) {
+
+ LabelSet labels;
+ lh->get_tag_labels(cursor.cursor, labels);
+
+ if(labels.size() == 0) {
+ // if no labels are found we can do nothing; gather this contig
+#if DEBUG_ASSEMBLY
+ std::cout << "no-label dead-end" << std::endl;
+#endif
+ paths.push_back(segment);
+ continue;
+ } else {
+ // if there are labels, try to hop the HDN.
+ // first, get a label filter
+ cursor.push_filter(get_simple_label_intersect_filter(labels, lh));
+ KmerQueue branch_starts;
+ // now get neighbors that pass the filter
+ cursor.neighbors(branch_starts);
+ // remove the filter
+ cursor.pop_filter();
+
+ // no neighbors found; done with this path
+ if (branch_starts.empty()) {
+#if DEBUG_ASSEMBLY
+ std::cout << "no-neighbors dead-end" << std::endl;
+#endif
+ paths.push_back(segment);
+ continue;
+ }
+
+ // found some neighbors; extend them
+ while(!branch_starts.empty()) {
+ // spin off a cursor for the new branch
+ NonLoopingAT<direction> branch_cursor(cursor);
+ branch_cursor.cursor = branch_starts.front();
+ branch_starts.pop();
+
+#if DEBUG_ASSEMBLY
+ std::cout << "Branch cursor: " << branch_cursor.cursor.repr(
+ _ksize) << std::endl;
+#endif
+
+ // assemble linearly as far as possible
+ std::string branch = linear_asm->_assemble_directed<direction>(branch_cursor);
+ // create a new segment with the branch
+ std::string new_segment = branch_cursor.join_contigs(segment, branch, 1);
+#if DEBUG_ASSEMBLY
+ std::cout << "Push segment: " << new_segment << std::endl;
+ std::cout << "Push cursor: " << branch_cursor.cursor.repr(_ksize) << std::endl;
+#endif
+ segments.push_back(new_segment);
+ cursors.push_back(branch_cursor);
+ }
+ }
+ } else {
+ // this segment is a dead-end; keep the contig
+#if DEBUG_ASSEMBLY
+ std::cout << "degree-1 dead-end" << std::endl;
+#endif
+ paths.push_back(segment);
+ continue;
+ }
+ }
+}
+
+/***************************************
+ * Junction-counting assembler
+ ***************************************/
+
+JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) :
+ graph(ht), _ksize(ht->ksize()), traverser(ht), linear_asm(ht)
+{
+ std::vector<uint64_t> table_sizes = graph->get_tablesizes();
+ junctions = new Countgraph(_ksize, table_sizes);
+}
+
+
+JunctionCountAssembler::~JunctionCountAssembler()
+{
+ delete this->junctions;
+}
+
+uint16_t JunctionCountAssembler::consume(std::string sequence)
+{
+ // first we need to put the sequence in the graph
+ graph->consume_string(sequence);
+ // now we find its high degree nodes and count the
+ // branch junctions
+ KmerIterator kmers(sequence.c_str(), _ksize);
+ Kmer kmer = kmers.next();
+ if (kmers.done()) {
+ return 0;
+ }
+ Kmer next_kmer = kmers.next();
+ if (kmers.done()) {
+ return 0;
+ }
+ uint16_t d = this->traverser.degree(kmer);
+ uint16_t next_d = this->traverser.degree(next_kmer);
+ uint16_t n_junctions = 0;
+
+ while(!kmers.done()) {
+ if (d > 2 || next_d > 2) {
+ count_junction(kmer, next_kmer);
+ n_junctions++;
+#if DEBUG_ASSEMBLY
+ std::cout << "Junction: " << kmer.repr(_ksize) << ", " << next_kmer.repr(
+ _ksize) << std::endl;
+ std::cout << "Junction Count: " << get_junction_count(kmer,
+ next_kmer) << std::endl;
+#endif
+ }
+ kmer = next_kmer;
+ d = next_d;
+ next_kmer = kmers.next();
+ next_d = this->traverser.degree(next_kmer);
+ }
+
+ return n_junctions / 2;
+}
+
+void JunctionCountAssembler::count_junction(Kmer kmer_a, Kmer kmer_b)
+{
+ junctions->count(kmer_a.kmer_u ^ kmer_b.kmer_u);
+}
+
+BoundedCounterType JunctionCountAssembler::get_junction_count(Kmer kmer_a,
+ Kmer kmer_b)
+const
+{
+ return junctions->get_count(kmer_a.kmer_u ^ kmer_b.kmer_u);
+}
+
+// Starting from the given seed k-mer, assemble all maximal linear paths in
+// both directions, using junction counts to skip over tricky bits.
+StringVector JunctionCountAssembler::assemble(const Kmer seed_kmer,
+ const Hashtable * stop_bf)
+const
+{
+#if DEBUG_ASSEMBLY
+ std::cout << "Assemble Junctions: " << seed_kmer.repr(_ksize) << std::endl;
+#endif
+
+ KmerFilterList node_filters;
+ if (stop_bf) {
+ node_filters.push_back(get_stop_bf_filter(stop_bf));
+ }
+
+ SeenSet visited;
+
+#if DEBUG_ASSEMBLY
+ std::cout << "Assemble Junctions RIGHT: " << seed_kmer.repr(
+ _ksize) << std::endl;
+#endif
+ StringVector right_paths;
+ NonLoopingAT<TRAVERSAL_RIGHT> rcursor(graph, seed_kmer, node_filters, &visited);
+ _assemble_directed<TRAVERSAL_RIGHT>(rcursor, right_paths);
+
+#if DEBUG_ASSEMBLY
+ std::cout << "Assemble Junctions LEFT: " << seed_kmer.repr(_ksize) << std::endl;
+#endif
+ StringVector left_paths;
+ NonLoopingAT<TRAVERSAL_LEFT> lcursor(graph, seed_kmer, node_filters, &visited);
+ _assemble_directed<TRAVERSAL_LEFT>(lcursor, left_paths);
+
+ StringVector paths;
+ for (unsigned int i = 0; i < left_paths.size(); i++) {
+ for (unsigned int j = 0; j < right_paths.size(); j++) {
+ std::string right = right_paths[j];
+ right = right.substr(_ksize);
+ std::string contig = left_paths[i] + right;
+ paths.push_back(contig);
+ }
+ }
+
+ visited.clear();
+ return paths;
+}
+
+template <bool direction>
+void JunctionCountAssembler::_assemble_directed(NonLoopingAT<direction>&
+ start_cursor,
+ StringVector& paths)
+const
+{
+#if DEBUG_ASSEMBLY
+ std::cout << "## assemble_junctions_directed_" << direction << " [start] at " <<
+ start_cursor.cursor.repr(_ksize) << std::endl;
+#endif
+
+ // prime the traversal with the first linear segment
+ std::string root_contig = linear_asm._assemble_directed<direction>
+ (start_cursor);
+#if DEBUG_ASSEMBLY
+ std::cout << "Primed: " << root_contig << std::endl;
+ std::cout << "Cursor: " << start_cursor.cursor.repr(_ksize) << std::endl;
+#endif
+ StringVector segments;
+ std::vector< NonLoopingAT<direction> > cursors;
+
+ segments.push_back(root_contig);
+ cursors.push_back(start_cursor);
+
+ while(segments.size() != 0) {
+
+ std::string segment = segments.back();
+ NonLoopingAT<direction> cursor = cursors.back();
+#if DEBUG_ASSEMBLY
+ std::cout << "Pop: " << segments.size() << " segments on stack." << std::endl;
+ std::cout << "Segment: " << segment << std::endl;
+ std::cout << "Cursor: " << cursor.cursor.repr(_ksize) << std::endl;
+ std::cout << "n_filters: " << cursor.n_filters() << std::endl;
+#endif
+ segments.pop_back();
+ cursors.pop_back();
+
+ // check if the cursor has hit a HDN or reached a dead end
+ if (cursor.cursor_degree() > 1) {
+
+ cursor.push_filter(get_junction_count_filter(cursor.cursor, this->junctions));
+ KmerQueue branch_starts;
+ // now get neighbors that pass the filter
+ cursor.neighbors(branch_starts);
+ // remove the filter
+ cursor.pop_filter();
+
+ // no neighbors found; done with this path
+ if (branch_starts.empty()) {
+ paths.push_back(segment);
+ continue;
+ }
+
+ // found some neighbors; extend them
+ while(!branch_starts.empty()) {
+ // spin off a cursor for the new branch
+ NonLoopingAT<direction> branch_cursor(cursor);
+
+ branch_cursor.cursor = branch_starts.front();
+ branch_starts.pop();
+
+ // assemble linearly as far as possible
+ std::string branch = linear_asm._assemble_directed<direction>(branch_cursor);
+ // create a new segment with the branch
+ std::string new_segment = branch_cursor.join_contigs(segment, branch, 1);
+
+ segments.push_back(new_segment);
+ cursors.push_back(branch_cursor);
+ }
+ } else {
+ // this segment is a dead-end; keep the contig
+ paths.push_back(segment);
+ continue;
+ }
+ }
+}
+
+}
diff --git a/lib/assembler.hh b/lib/assembler.hh
new file mode 100644
index 0000000..fa02cc5
--- /dev/null
+++ b/lib/assembler.hh
@@ -0,0 +1,177 @@
+/*
+This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+Copyright (C) 2015-2016, The Regents of the University of California.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following
+ disclaimer in the documentation and/or other materials provided
+ with the distribution.
+
+ * Neither the name of the Michigan State University nor the names
+ of its contributors may be used to endorse or promote products
+ derived from this software without specific prior written
+ permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+LICENSE (END)
+
+Contact: khmer-project at idyll.org
+*/
+#ifndef ASSEMBLER_HH
+#define ASSEMBLER_HH
+
+#include <functional>
+
+#include "khmer.hh"
+#include "kmer_hash.hh"
+#include "hashgraph.hh"
+#include "kmer_filters.hh"
+#include "traversal.hh"
+#include "labelhash.hh"
+
+
+namespace khmer
+{
+
+class Hashgraph;
+class LabelHash;
+
+/**
+ * \class LinearAssembler
+ *
+ * \brief Naively assemble linear paths.
+ *
+ * The LinearAssember is the basic building block of general assembly.
+ * The core function, _assemble_directed, takes a direction and branch-specialiazed
+ * AssemblerTraverser and gathers a contig up until any branch points. The behavior
+ * of this function can be modified by passing it a cursor with varying
+ * filtering functions.
+ *
+ * The assemble, assemble_right, and assemble_left functions are for convenience.
+ * They take care of building the filters and creating the contig strings.
+ *
+ * \author Camille Scott
+ *
+ * Contact: camille.scott.w at gmail.com
+ *
+ */
+class LinearAssembler
+{
+public:
+
+ WordLength _ksize;
+ const Hashgraph * graph;
+
+ explicit LinearAssembler(const Hashgraph * ht);
+
+ std::string assemble(const Kmer seed_kmer,
+ const Hashgraph * stop_bf = 0) const;
+
+ std::string assemble_right(const Kmer seed_kmer,
+ const Hashgraph * stop_bf = 0) const;
+
+ std::string assemble_left(const Kmer seed_kmer,
+ const Hashgraph * stop_bf = 0) const;
+
+ template <bool direction>
+ std::string _assemble_directed(AssemblerTraverser<direction>& cursor) const;
+};
+
+// The explicit specializations need to be declared in the same translation unit
+// as their unspecialized declaration.
+template<>
+std::string LinearAssembler::_assemble_directed<TRAVERSAL_LEFT>(AssemblerTraverser<TRAVERSAL_LEFT>
+ &cursor) const;
+
+template<>
+std::string LinearAssembler::_assemble_directed<TRAVERSAL_RIGHT>(AssemblerTraverser<TRAVERSAL_RIGHT>
+ &cursor) const;
+
+
+/**
+ * \class SimpleLabeledAssembler
+ *
+ * \brief Assemble linear paths using labels to span high degree nodes.
+ *
+ * Shares a common API (namely, the assemble and templated _assemble_directed functions) with
+ * LinearAssembler, though does not inherit. High degree nodes (nodes with degree > 2) are spanned
+ * using labeling formation: if there is a matching label on two sides of the HDN, we can keep
+ * traverse across. Internally, this is performed by pushing a new filter to search for the label on to
+ * the Traverser's filter stack and popping it on the other side of the HDN. This implementation also
+ * does a simple check to guess whether a branch is an error: if the HDN has label coverage great than 5, and
+ * the branch has only a single label spanning, it is guessed to be a tip and ignored.
+ *
+ * \author Camille Scott
+ *
+ * Contact: camille.scott.w at gmail.com
+ *
+ */
+class SimpleLabeledAssembler
+{
+ const LinearAssembler * linear_asm;
+
+public:
+
+ const Hashgraph * graph;
+ const LabelHash * lh;
+ WordLength _ksize;
+
+ explicit SimpleLabeledAssembler(const LabelHash * lh);
+ ~SimpleLabeledAssembler();
+
+ StringVector assemble(const Kmer seed_kmer,
+ const Hashgraph * stop_bf=0) const;
+
+ template <bool direction>
+ void _assemble_directed(NonLoopingAT<direction>& start_cursor,
+ StringVector& paths) const;
+
+};
+
+
+class JunctionCountAssembler
+{
+ LinearAssembler linear_asm;
+ Countgraph * junctions;
+ Traverser traverser;
+
+public:
+
+ Hashgraph * graph;
+ WordLength _ksize;
+
+ explicit JunctionCountAssembler(Hashgraph * ht);
+ ~JunctionCountAssembler();
+
+
+ StringVector assemble(const Kmer seed_kmer,
+ const Hashtable * stop_bf=0) const;
+
+ uint16_t consume(std::string sequence);
+ void count_junction(Kmer kmer_a, Kmer kmer_b);
+ BoundedCounterType get_junction_count(Kmer kmer_a, Kmer kmer_b) const;
+
+ template <bool direction>
+ void _assemble_directed(NonLoopingAT<direction>& start_cursor,
+ StringVector& paths) const;
+
+};
+} //namespace khmer
+#endif
diff --git a/lib/counting.cc b/lib/counting.cc
deleted file mode 100644
index 1b7736c..0000000
--- a/lib/counting.cc
+++ /dev/null
@@ -1,1041 +0,0 @@
-/*
-This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-Copyright (C) 2010-2015, Michigan State University.
-Copyright (C) 2015, The Regents of the University of California.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are
-met:
-
- * Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
-
- * Redistributions in binary form must reproduce the above
- copyright notice, this list of conditions and the following
- disclaimer in the documentation and/or other materials provided
- with the distribution.
-
- * Neither the name of the Michigan State University nor the names
- of its contributors may be used to endorse or promote products
- derived from this software without specific prior written
- permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
-DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
-THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-LICENSE (END)
-
-Contact: khmer-project at idyll.org
-*/
-
-#include <errno.h>
-#include <algorithm>
-#include <iostream>
-#include <sstream> // IWYU pragma: keep
-
-#include "counting.hh"
-#include "hashbits.hh"
-#include "hashtable.hh"
-#include "khmer_exception.hh"
-#include "kmer_hash.hh"
-#include "read_parsers.hh"
-#include "zlib.h"
-
-using namespace std;
-using namespace khmer;
-using namespace khmer:: read_parsers;
-
-///
-/// output_fasta_kmer_pos_freq: outputs the kmer frequencies for each read
-///
-
-void CountingHash::output_fasta_kmer_pos_freq(
- const std::string &inputfile,
- const std::string &outputfile)
-{
- IParser* parser = IParser::get_parser(inputfile.c_str());
- ofstream outfile;
- outfile.open(outputfile.c_str());
- string seq;
- Read read;
-
- while(!parser->is_complete()) {
- try {
- read = parser->get_next_read();
- } catch (NoMoreReadsAvailable &exc) {
- break;
- }
- seq = read.sequence;
-
- long numPos = seq.length() - _ksize + 1;
-
- for (long i = 0; i < numPos; i++) {
- string kmer = seq.substr(i, _ksize);
- outfile << (int)get_count(kmer.c_str()) << " ";
- }
- outfile << endl;
- }
-
- delete parser;
- if (outfile.fail()) {
- throw khmer_file_exception(strerror(errno));
- }
-
- outfile.close();
-}
-
-BoundedCounterType CountingHash::get_min_count(const std::string &s)
-{
- KmerIterator kmers(s.c_str(), _ksize);
-
- BoundedCounterType min_count = MAX_KCOUNT;
-
- while(!kmers.done()) {
- HashIntoType kmer = kmers.next();
-
- BoundedCounterType count = this->get_count(kmer);
-
- if (this->get_count(kmer) < min_count) {
- min_count = count;
- }
- }
- return min_count;
-}
-
-BoundedCounterType CountingHash::get_max_count(const std::string &s)
-{
- KmerIterator kmers(s.c_str(), _ksize);
-
- BoundedCounterType max_count = 0;
-
- while(!kmers.done()) {
- HashIntoType kmer = kmers.next();
-
- BoundedCounterType count = this->get_count(kmer);
-
- if (count > max_count) {
- max_count = count;
- }
- }
- return max_count;
-}
-
-HashIntoType *
-CountingHash::abundance_distribution(
- read_parsers::IParser * parser,
- Hashbits * tracking)
-{
- HashIntoType * dist = new HashIntoType[MAX_BIGCOUNT + 1];
- HashIntoType i;
-
- for (i = 0; i <= MAX_BIGCOUNT; i++) {
- dist[i] = 0;
- }
-
- Read read;
-
- string name;
- string seq;
-
- // if not, could lead to overflow.
- if (sizeof(BoundedCounterType) != 2) {
- delete[] dist;
- throw khmer_exception();
- }
-
- while(!parser->is_complete()) {
- try {
- read = parser->get_next_read();
- } catch (NoMoreReadsAvailable &exc) {
- break;
- }
- seq = read.sequence;
-
- if (check_and_normalize_read(seq)) {
- KmerIterator kmers(seq.c_str(), _ksize);
-
- while(!kmers.done()) {
- HashIntoType kmer = kmers.next();
-
- if (!tracking->get_count(kmer)) {
- tracking->count(kmer);
-
- BoundedCounterType n = get_count(kmer);
- dist[n]++;
- }
- }
-
- name.clear();
- seq.clear();
- }
- }
- return dist;
-}
-
-
-HashIntoType * CountingHash::abundance_distribution(
- std::string filename,
- Hashbits * tracking)
-{
- IParser* parser = IParser::get_parser(filename.c_str());
-
- HashIntoType * distribution = abundance_distribution(parser, tracking);
- delete parser;
- return distribution;
-}
-
-HashIntoType * CountingHash::fasta_count_kmers_by_position(
- const std::string &inputfile,
- const unsigned int max_read_len,
- BoundedCounterType limit_by_count,
- CallbackFn callback,
- void * callback_data)
-{
- unsigned long long *counts = new unsigned long long[max_read_len];
-
- for (unsigned int i = 0; i < max_read_len; i++) {
- counts[i] = 0;
- }
-
- Read read;
- IParser* parser = IParser::get_parser(inputfile.c_str());
- string name;
- string seq;
- unsigned long long read_num = 0;
-
- while(!parser->is_complete()) {
- try {
- read = parser->get_next_read();
- } catch (NoMoreReadsAvailable &exc) {
- break;
- }
-
- seq = read.sequence;
- bool valid_read = check_and_normalize_read(seq);
-
- if (valid_read) {
- for (unsigned int i = 0; i < seq.length() - _ksize + 1; i++) {
- string kmer = seq.substr(i, i + _ksize);
- BoundedCounterType n = get_count(kmer.c_str());
-
- if (limit_by_count == 0 || n == limit_by_count) {
- if (i < max_read_len) {
- counts[i]++;
- }
- }
- }
- }
-
- name.clear();
- seq.clear();
-
- read_num += 1;
-
- // run callback, if specified
- if (read_num % CALLBACK_PERIOD == 0 && callback) {
- try {
- callback("fasta_file_count_kmers_by_position", callback_data,
- read_num, 0);
- } catch (...) {
- throw;
- }
- }
- } // while reads
-
- delete parser;
-
- return counts;
-}
-
-void CountingHash::fasta_dump_kmers_by_abundance(
- const std::string &inputfile,
- BoundedCounterType limit_by_count,
- CallbackFn callback,
- void * callback_data)
-{
- Read read;
- IParser* parser = IParser::get_parser(inputfile.c_str());
- string name;
- string seq;
- unsigned long long read_num = 0;
-
- while(!parser->is_complete()) {
- try {
- read = parser->get_next_read();
- } catch (NoMoreReadsAvailable &exc) {
- break;
- }
- bool valid_read = check_and_normalize_read(seq);
- seq = read.sequence;
-
- if (valid_read) {
- for (unsigned int i = 0; i < seq.length() - _ksize + 1; i++) {
- string kmer = seq.substr(i, i + _ksize);
- BoundedCounterType n = get_count(kmer.c_str());
- char * ss = new char[_ksize + 1];
- strncpy(ss, kmer.c_str(), _ksize);
- ss[_ksize] = 0;
-
- if (n == limit_by_count) {
- cout << *ss << endl;
- }
- delete[] ss;
- }
- }
-
- name.clear();
- seq.clear();
-
- read_num += 1;
-
- // run callback, if specified
- if (read_num % CALLBACK_PERIOD == 0 && callback) {
- try {
- callback("fasta_file_dump_kmers_by_abundance", callback_data,
- read_num, 0);
- } catch (...) {
- throw;
- }
- }
- } // while reads
-
- delete parser;
-}
-
-void CountingHash::save(std::string outfilename)
-{
- CountingHashFile::save(outfilename, *this);
-}
-
-void CountingHash::load(std::string infilename)
-{
- CountingHashFile::load(infilename, *this);
-}
-
-unsigned long CountingHash::trim_on_abundance(
- std::string seq,
- BoundedCounterType min_abund)
-const
-{
- if (!check_and_normalize_read(seq)) {
- return 0;
- }
-
- KmerIterator kmers(seq.c_str(), _ksize);
-
- HashIntoType kmer;
-
- if (kmers.done()) {
- return 0;
- }
- kmer = kmers.next();
-
- if (kmers.done() || get_count(kmer) < min_abund) {
- return 0;
- }
-
- unsigned long i = _ksize;
- while (!kmers.done()) {
- kmer = kmers.next();
-
- if (get_count(kmer) < min_abund) {
- return i;
- }
- i++;
- }
-
- return seq.length();
-}
-
-unsigned long CountingHash::trim_below_abundance(
- std::string seq,
- BoundedCounterType max_abund)
-const
-{
- if (!check_and_normalize_read(seq)) {
- return 0;
- }
-
- KmerIterator kmers(seq.c_str(), _ksize);
-
- HashIntoType kmer;
-
- if (kmers.done()) {
- return 0;
- }
- kmer = kmers.next();
-
- if (kmers.done() || get_count(kmer) > max_abund) {
- return 0;
- }
-
- unsigned long i = _ksize;
- while (!kmers.done()) {
- kmer = kmers.next();
-
- if (get_count(kmer) > max_abund) {
- return i;
- }
- i++;
- }
-
- return seq.length();
-}
-
-std::vector<unsigned int> CountingHash::find_spectral_error_positions(
- std::string seq,
- BoundedCounterType max_abund)
-const
-{
- std::vector<unsigned int> posns;
- if (!check_and_normalize_read(seq)) {
- throw khmer_exception("invalid read");
- }
-
- KmerIterator kmers(seq.c_str(), _ksize);
-
- HashIntoType kmer = kmers.next();
- if (kmers.done()) {
- return posns;
- }
-
- // find the first trusted k-mer
- while (!kmers.done()) {
- if (get_count(kmer) > max_abund) {
- break;
- }
- kmer = kmers.next();
- }
-
- if (kmers.done()) {
- return posns;
- }
-
- // did we bypass some erroneous k-mers? call the last one.
- if (kmers.get_start_pos() > 0) {
- // if we are well past the first k, forget the whole thing (!? @CTB)
- if (kmers.get_start_pos() >= _ksize && 0) {
- return posns;
- }
- posns.push_back(kmers.get_start_pos() - 1);
- }
-
- while (!kmers.done()) {
- kmer = kmers.next();
- if (get_count(kmer) <= max_abund) { // error!
- posns.push_back(kmers.get_end_pos() - 1);
-
- // find next good
- while (!kmers.done()) {
- kmer = kmers.next();
- if (get_count(kmer) > max_abund) { // a good stretch again.
- break;
- }
- }
- }
- }
-
- return posns;
-}
-
-
-void CountingHashFile::load(
- const std::string &infilename,
- CountingHash &ht)
-{
- std::string filename(infilename);
- size_t found = filename.find_last_of(".");
- std::string type = filename.substr(found + 1);
-
- if (type == "gz") {
- CountingHashGzFileReader(filename, ht);
- } else {
- CountingHashFileReader(filename, ht);
- }
-}
-
-
-void CountingHashFile::save(
- const std::string &outfilename,
- const CountingHash &ht)
-{
- std::string filename(outfilename);
- size_t found = filename.find_last_of(".");
- std::string type = filename.substr(found + 1);
-
- if (type == "gz") {
- CountingHashGzFileWriter(filename, ht);
- } else {
- CountingHashFileWriter(filename, ht);
- }
-}
-
-
-CountingHashFileReader::CountingHashFileReader(
- const std::string &infilename,
- CountingHash &ht)
-{
- ifstream infile;
- // configure ifstream to raise exceptions for everything.
- infile.exceptions(std::ifstream::failbit | std::ifstream::badbit |
- std::ifstream::eofbit);
-
- try {
- infile.open(infilename.c_str(), ios::binary);
- } catch (std::ifstream::failure &e) {
- std::string err;
- if (!infile.is_open()) {
- err = "Cannot open k-mer count file: " + infilename;
- } else {
- err = "Unknown error in opening file: " + infilename;
- }
- throw khmer_file_exception(err + " " + strerror(errno));
- }
-
- if (ht._counts) {
- for (unsigned int i = 0; i < ht._n_tables; i++) {
- delete[] ht._counts[i];
- ht._counts[i] = NULL;
- }
- delete[] ht._counts;
- ht._counts = NULL;
- }
- ht._tablesizes.clear();
-
- try {
- unsigned int save_ksize = 0;
- unsigned char save_n_tables = 0;
- unsigned long long save_tablesize = 0;
- unsigned long long save_occupied_bins = 0;
- char signature [4];
- unsigned char version = 0, ht_type = 0, use_bigcount = 0;
-
- infile.read(signature, 4);
- infile.read((char *) &version, 1);
- infile.read((char *) &ht_type, 1);
- if (!(std::string(signature, 4) == SAVED_SIGNATURE)) {
- std::ostringstream err;
- err << "Does not start with signature for a khmer file: 0x";
- for(size_t i=0; i < 4; ++i) {
- err << std::hex << (int) signature[i];
- }
- err << " Should be: " << SAVED_SIGNATURE;
- throw khmer_file_exception(err.str());
- } else if (!(version == SAVED_FORMAT_VERSION)) {
- std::ostringstream err;
- err << "Incorrect file format version " << (int) version
- << " while reading k-mer count file from " << infilename
- << "; should be " << (int) SAVED_FORMAT_VERSION;
- throw khmer_file_exception(err.str());
- } else if (!(ht_type == SAVED_COUNTING_HT)) {
- std::ostringstream err;
- err << "Incorrect file format type " << (int) ht_type
- << " while reading k-mer count file from " << infilename;
- throw khmer_file_exception(err.str());
- }
-
- infile.read((char *) &use_bigcount, 1);
- infile.read((char *) &save_ksize, sizeof(save_ksize));
- infile.read((char *) &save_n_tables, sizeof(save_n_tables));
- infile.read((char *) &save_occupied_bins, sizeof(save_occupied_bins));
-
- ht._ksize = (WordLength) save_ksize;
- ht._n_tables = (unsigned int) save_n_tables;
- ht._occupied_bins = save_occupied_bins;
- ht._init_bitstuff();
-
- ht._use_bigcount = use_bigcount;
-
- ht._counts = new Byte*[ht._n_tables];
- for (unsigned int i = 0; i < ht._n_tables; i++) {
- ht._counts[i] = NULL;
- }
-
- for (unsigned int i = 0; i < ht._n_tables; i++) {
- HashIntoType tablesize;
-
- infile.read((char *) &save_tablesize, sizeof(save_tablesize));
-
- tablesize = (HashIntoType) save_tablesize;
- ht._tablesizes.push_back(tablesize);
-
- ht._counts[i] = new Byte[tablesize];
-
- unsigned long long loaded = 0;
- while (loaded != tablesize) {
- infile.read((char *) ht._counts[i], tablesize - loaded);
- loaded += infile.gcount();
- }
- }
-
- HashIntoType n_counts = 0;
- infile.read((char *) &n_counts, sizeof(n_counts));
-
- if (n_counts) {
- ht._bigcounts.clear();
-
- HashIntoType kmer;
- BoundedCounterType count;
-
- for (HashIntoType n = 0; n < n_counts; n++) {
- infile.read((char *) &kmer, sizeof(kmer));
- infile.read((char *) &count, sizeof(count));
- ht._bigcounts[kmer] = count;
- }
- }
-
- infile.close();
- } catch (std::ifstream::failure &e) {
- std::string err;
- if (infile.eof()) {
- err = "Unexpected end of k-mer count file: " + infilename;
- } else {
- err = "Error reading from k-mer count file: " + infilename + " "
- + strerror(errno);
- }
- throw khmer_file_exception(err);
- }
-}
-
-CountingHashGzFileReader::CountingHashGzFileReader(
- const std::string &infilename,
- CountingHash &ht)
-{
- gzFile infile = gzopen(infilename.c_str(), "rb");
- if (infile == Z_NULL) {
- std::string err = "Cannot open k-mer count file: " + infilename;
- throw khmer_file_exception(err);
- }
-
- if (ht._counts) {
- for (unsigned int i = 0; i < ht._n_tables; i++) {
- delete[] ht._counts[i];
- ht._counts[i] = NULL;
- }
- delete[] ht._counts;
- ht._counts = NULL;
- }
- ht._tablesizes.clear();
-
- unsigned int save_ksize = 0;
- unsigned char save_n_tables = 0;
- unsigned long long save_tablesize = 0;
- unsigned long long save_occupied_bins = 0;
- char signature [4];
- unsigned char version, ht_type, use_bigcount;
-
- int read_s = gzread(infile, signature, 4);
- int read_v = gzread(infile, (char *) &version, 1);
- int read_t = gzread(infile, (char *) &ht_type, 1);
- if (read_s <= 0 || read_v <= 0 || read_t <= 0) {
- std::string err = "K-mer count file read error: " + infilename + " "
- + strerror(errno);
- gzclose(infile);
- throw khmer_file_exception(err);
- } else if (!(std::string(signature, 4) == SAVED_SIGNATURE)) {
- std::ostringstream err;
- err << "Does not start with signature for a khmer " <<
- "file: " << signature << " Should be: " <<
- SAVED_SIGNATURE;
- throw khmer_file_exception(err.str());
- } else if (!(version == SAVED_FORMAT_VERSION)
- || !(ht_type == SAVED_COUNTING_HT)) {
- if (!(version == SAVED_FORMAT_VERSION)) {
- std::ostringstream err;
- err << "Incorrect file format version " << (int) version
- << " while reading k-mer count file from " << infilename
- << "; should be " << (int) SAVED_FORMAT_VERSION;
- gzclose(infile);
- throw khmer_file_exception(err.str());
- } else if (!(ht_type == SAVED_COUNTING_HT)) {
- std::ostringstream err;
- err << "Incorrect file format type " << (int) ht_type
- << " while reading k-mer count file from " << infilename;
- gzclose(infile);
- throw khmer_file_exception(err.str());
- }
- }
-
- int read_b = gzread(infile, (char *) &use_bigcount, 1);
- int read_k = gzread(infile, (char *) &save_ksize, sizeof(save_ksize));
- int read_nt = gzread(infile, (char *) &save_n_tables,
- sizeof(save_n_tables));
- int read_ob = gzread(infile, (char *) &save_occupied_bins,
- sizeof(save_occupied_bins));
-
- if (read_b <= 0 || read_k <= 0 || read_nt <= 0 || read_ob <= 0) {
- std::string err = "K-mer count file header read error: " + infilename
- + " " + strerror(errno);
- gzclose(infile);
- throw khmer_file_exception(err);
- }
-
- ht._ksize = (WordLength) save_ksize;
- ht._occupied_bins = save_occupied_bins;
- ht._n_tables = (unsigned int) save_n_tables;
- ht._init_bitstuff();
-
- ht._use_bigcount = use_bigcount;
-
- ht._counts = new Byte*[ht._n_tables];
- for (unsigned int i = 0; i < ht._n_tables; i++) {
- HashIntoType tablesize;
-
- read_b = gzread(infile, (char *) &save_tablesize,
- sizeof(save_tablesize));
-
- if (read_b <= 0) {
- std::string gzerr = gzerror(infile, &read_b);
- std::string err = "K-mer count file header read error: "
- + infilename;
- if (read_b == Z_ERRNO) {
- err = err + " " + strerror(errno);
- } else {
- err = err + " " + gzerr;
- }
- gzclose(infile);
- throw khmer_file_exception(err);
- }
-
- tablesize = (HashIntoType) save_tablesize;
- ht._tablesizes.push_back(tablesize);
-
- ht._counts[i] = new Byte[tablesize];
-
- HashIntoType loaded = 0;
- while (loaded != tablesize) {
- unsigned long long to_read_ll = tablesize - loaded;
- unsigned int to_read_int;
- // Zlib can only read chunks of at most INT_MAX bytes.
- if (to_read_ll > INT_MAX) {
- to_read_int = INT_MAX;
- } else {
- to_read_int = (unsigned int) to_read_ll;
- }
- read_b = gzread(infile, (char *) ht._counts[i], to_read_int);
-
- if (read_b <= 0) {
- std::string gzerr = gzerror(infile, &read_b);
- std::string err = "K-mer count file read error: " + infilename;
- if (read_b == Z_ERRNO) {
- err = err + " " + strerror(errno);
- } else {
- err = err + " " + gzerr;
- }
- gzclose(infile);
- throw khmer_file_exception(err);
- }
-
- loaded += read_b;
- }
- }
-
- HashIntoType n_counts = 0;
- read_b = gzread(infile, (char *) &n_counts, sizeof(n_counts));
- if (read_b <= 0) {
- std::string gzerr = gzerror(infile, &read_b);
- std::string err = "K-mer count header read error: " + infilename;
- if (read_b == Z_ERRNO) {
- err = err + " " + strerror(errno);
- } else {
- err = err + " " + gzerr;
- }
- gzclose(infile);
- throw khmer_file_exception(err);
- }
-
- if (n_counts) {
- ht._bigcounts.clear();
-
- HashIntoType kmer;
- BoundedCounterType count;
-
- for (HashIntoType n = 0; n < n_counts; n++) {
- int read_k = gzread(infile, (char *) &kmer, sizeof(kmer));
- int read_c = gzread(infile, (char *) &count, sizeof(count));
-
- if (read_k <= 0 || read_c <= 0) {
- std::string gzerr = gzerror(infile, &read_b);
- std::string err = "K-mer count read error: " + infilename;
- if (read_b == Z_ERRNO) {
- err = err + " " + strerror(errno);
- } else {
- err = err + " " + gzerr;
- }
- gzclose(infile);
- throw khmer_file_exception(err);
- }
-
- ht._bigcounts[kmer] = count;
- }
- }
-
- gzclose(infile);
-}
-
-CountingHashFileWriter::CountingHashFileWriter(
- const std::string &outfilename,
- const CountingHash &ht)
-{
- if (!ht._counts[0]) {
- throw khmer_exception();
- }
-
- unsigned int save_ksize = ht._ksize;
- unsigned char save_n_tables = ht._n_tables;
- unsigned long long save_tablesize;
- unsigned long long save_occupied_bins = ht._occupied_bins;
-
- ofstream outfile(outfilename.c_str(), ios::binary);
-
- outfile.write(SAVED_SIGNATURE, 4);
- unsigned char version = SAVED_FORMAT_VERSION;
- outfile.write((const char *) &version, 1);
-
- unsigned char ht_type = SAVED_COUNTING_HT;
- outfile.write((const char *) &ht_type, 1);
-
- unsigned char use_bigcount = 0;
- if (ht._use_bigcount) {
- use_bigcount = 1;
- }
- outfile.write((const char *) &use_bigcount, 1);
-
- outfile.write((const char *) &save_ksize, sizeof(save_ksize));
- outfile.write((const char *) &save_n_tables, sizeof(save_n_tables));
- outfile.write((const char *) &save_occupied_bins,
- sizeof(save_occupied_bins));
-
- for (unsigned int i = 0; i < save_n_tables; i++) {
- save_tablesize = ht._tablesizes[i];
-
- outfile.write((const char *) &save_tablesize, sizeof(save_tablesize));
- outfile.write((const char *) ht._counts[i], save_tablesize);
- }
-
- HashIntoType n_counts = ht._bigcounts.size();
- outfile.write((const char *) &n_counts, sizeof(n_counts));
-
- if (n_counts) {
- KmerCountMap::const_iterator it = ht._bigcounts.begin();
-
- for (; it != ht._bigcounts.end(); ++it) {
- outfile.write((const char *) &it->first, sizeof(it->first));
- outfile.write((const char *) &it->second, sizeof(it->second));
- }
- }
- if (outfile.fail()) {
- throw khmer_file_exception(strerror(errno));
- }
- outfile.close();
-}
-
-CountingHashGzFileWriter::CountingHashGzFileWriter(
- const std::string &outfilename,
- const CountingHash &ht)
-{
- if (!ht._counts[0]) {
- throw khmer_exception();
- }
-
- int errnum = 0;
- unsigned int save_ksize = ht._ksize;
- unsigned char save_n_tables = ht._n_tables;
- unsigned long long save_tablesize;
- unsigned long long save_occupied_bins = ht._occupied_bins;
-
- gzFile outfile = gzopen(outfilename.c_str(), "wb");
- if (outfile == NULL) {
- const char * error = gzerror(outfile, &errnum);
- if (errnum == Z_ERRNO) {
- throw khmer_file_exception(strerror(errno));
- } else {
- throw khmer_file_exception(error);
- }
- }
-
- gzwrite(outfile, SAVED_SIGNATURE, 4);
- unsigned char version = SAVED_FORMAT_VERSION;
- gzwrite(outfile, (const char *) &version, 1);
-
- unsigned char ht_type = SAVED_COUNTING_HT;
- gzwrite(outfile, (const char *) &ht_type, 1);
-
- unsigned char use_bigcount = 0;
- if (ht._use_bigcount) {
- use_bigcount = 1;
- }
- gzwrite(outfile, (const char *) &use_bigcount, 1);
-
- gzwrite(outfile, (const char *) &save_ksize, sizeof(save_ksize));
- gzwrite(outfile, (const char *) &save_n_tables, sizeof(save_n_tables));
- gzwrite(outfile, (const char *) &save_occupied_bins,
- sizeof(save_occupied_bins));
-
- for (unsigned int i = 0; i < save_n_tables; i++) {
- save_tablesize = ht._tablesizes[i];
-
- gzwrite(outfile, (const char *) &save_tablesize,
- sizeof(save_tablesize));
- unsigned long long written = 0;
- while (written != save_tablesize) {
- unsigned long long to_write_ll = save_tablesize - written;
- unsigned int to_write_int;
- int gz_result;
- // Zlib can only write chunks of at most INT_MAX bytes.
- if (to_write_ll > INT_MAX) {
- to_write_int = INT_MAX;
- } else {
- to_write_int = (unsigned int) to_write_ll;
- }
- gz_result = gzwrite(outfile, (const char *) ht._counts[i],
- to_write_int);
- // Zlib returns 0 on error
- if (gz_result == 0) {
- int errcode = 0;
- const char *err_msg;
- std::ostringstream msg;
-
- msg << "gzwrite failed while writing counting hash: ";
- // Get zlib error
- err_msg = gzerror(outfile, &errcode);
- if (errcode != Z_ERRNO) {
- // Zlib error, not stdlib
- msg << err_msg;
- gzclearerr(outfile);
- } else {
- // stdlib error
- msg << strerror(errno);
- }
- gzclose(outfile);
- throw khmer_file_exception(msg.str());
- }
- written += gz_result;
- }
- }
-
- HashIntoType n_counts = ht._bigcounts.size();
- gzwrite(outfile, (const char *) &n_counts, sizeof(n_counts));
-
- if (n_counts) {
- KmerCountMap::const_iterator it = ht._bigcounts.begin();
-
- for (; it != ht._bigcounts.end(); ++it) {
- gzwrite(outfile, (const char *) &it->first, sizeof(it->first));
- gzwrite(outfile, (const char *) &it->second, sizeof(it->second));
- }
- }
- const char * error = gzerror(outfile, &errnum);
- if (errnum == Z_ERRNO) {
- throw khmer_file_exception(strerror(errno));
- } else if (errnum != Z_OK) {
- throw khmer_file_exception(error);
- }
- gzclose(outfile);
-}
-
-void CountingHash::collect_high_abundance_kmers(
- const std::string &filename,
- unsigned int lower_count,
- unsigned int upper_count,
- SeenSet& found_kmers)
-{
- unsigned long long total_reads = 0;
-
- IParser* parser = IParser::get_parser(filename.c_str());
- Read read;
-
- string currSeq = "";
-
- //
- // iterate through the FASTA file & consume the reads, until we hit
- // upper_count.
- //
-
- bool done = false;
- while(!parser->is_complete() && !done) {
- try {
- read = parser->get_next_read();
- } catch (NoMoreReadsAvailable &exc) {
- break;
- }
- currSeq = read.sequence;
-
- // do we want to process it?
- if (check_and_normalize_read(currSeq)) {
- const char * sp = currSeq.c_str();
-
- KmerIterator kmers(sp, _ksize);
-
- while(!kmers.done()) {
- HashIntoType kmer = kmers.next();
-
- count(kmer);
- if (get_count(kmer) >= upper_count) {
- done = true;
- }
- }
- }
-
- // increment read number
- total_reads++;
-
- if (total_reads % 100000 == 0) {
- std::cout << "..." << total_reads << "\n";
- }
- }
-
- delete parser;
-
- unsigned long long stop_at_read = total_reads;
-
- //
- // go back through the file again, and store all k-mers >= lower_count
- //
-
- parser = IParser::get_parser(filename.c_str());
-
- total_reads = 0;
- while(!parser->is_complete() && total_reads != stop_at_read) {
- try {
- read = parser->get_next_read();
- } catch (NoMoreReadsAvailable &exc) {
- break;
- }
- currSeq = read.sequence;
-
- // do we want to process it?
- if (check_and_normalize_read(currSeq)) {
- const char * sp = currSeq.c_str();
-
- KmerIterator kmers(sp, _ksize);
-
- while(!kmers.done()) {
- HashIntoType kmer = kmers.next();
-
- if (get_count(kmer) >= lower_count) {
- found_kmers.insert(kmer);
- }
- }
- }
-
- // increment read number
- total_reads++;
-
- if (total_reads % 100000 == 0) {
- std::cout << "... x 2 " << total_reads << "\n";
- }
- }
- delete parser;
- parser = NULL;
-}
-
-/* vim: set ft=cpp ts=8 sts=4 sw=4 et tw=79 */
diff --git a/lib/counting.hh b/lib/counting.hh
deleted file mode 100644
index 779755b..0000000
--- a/lib/counting.hh
+++ /dev/null
@@ -1,348 +0,0 @@
-/*
-This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-Copyright (C) 2010-2015, Michigan State University.
-Copyright (C) 2015, The Regents of the University of California.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are
-met:
-
- * Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
-
- * Redistributions in binary form must reproduce the above
- copyright notice, this list of conditions and the following
- disclaimer in the documentation and/or other materials provided
- with the distribution.
-
- * Neither the name of the Michigan State University nor the names
- of its contributors may be used to endorse or promote products
- derived from this software without specific prior written
- permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
-DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
-THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-LICENSE (END)
-
-Contact: khmer-project at idyll.org
-*/
-#ifndef COUNTING_HH
-#define COUNTING_HH
-
-#include <stddef.h>
-#include <stdint.h>
-#include <string.h>
-#include <map>
-#include <string>
-#include <utility>
-#include <vector>
-
-#include "hashtable.hh"
-#include "khmer.hh"
-#include "kmer_hash.hh"
-
-namespace khmer
-{
-class Hashbits;
-
-namespace read_parsers
-{
-struct IParser;
-} // namespace read_parsers
-} // namespace khmer
-
-namespace khmer
-{
-typedef std::map<HashIntoType, BoundedCounterType> KmerCountMap;
-
-class CountingHashFile;
-class CountingHashFileReader;
-class CountingHashFileWriter;
-class CountingHashGzFileReader;
-class CountingHashGzFileWriter;
-class CountingHashIntersect;
-
-class CountingHash : public khmer::Hashtable
-{
- friend class CountingHashIntersect;
- friend class CountingHashFile;
- friend class CountingHashFileReader;
- friend class CountingHashFileWriter;
- friend class CountingHashGzFileReader;
- friend class CountingHashGzFileWriter;
-
-protected:
- bool _use_bigcount; // keep track of counts > Bloom filter hash count threshold?
- uint32_t _bigcount_spin_lock;
- std::vector<HashIntoType> _tablesizes;
- size_t _n_tables;
- HashIntoType _n_unique_kmers;
- HashIntoType _occupied_bins;
-
- Byte ** _counts;
-
- virtual void _allocate_counters()
- {
- _n_tables = _tablesizes.size();
-
- _counts = new Byte*[_n_tables];
- for (size_t i = 0; i < _n_tables; i++) {
- _counts[i] = new Byte[_tablesizes[i]];
- memset(_counts[i], 0, _tablesizes[i]);
- }
- }
-public:
- KmerCountMap _bigcounts;
-
- CountingHash( WordLength ksize, HashIntoType single_tablesize ) :
- khmer::Hashtable(ksize), _use_bigcount(false),
- _bigcount_spin_lock(false), _n_unique_kmers(0), _occupied_bins(0)
- {
- _tablesizes.push_back(single_tablesize);
-
- _allocate_counters();
- }
-
- CountingHash( WordLength ksize, std::vector<HashIntoType>& tablesizes ) :
- khmer::Hashtable(ksize), _use_bigcount(false),
- _bigcount_spin_lock(false), _tablesizes(tablesizes),
- _n_unique_kmers(0), _occupied_bins(0)
- {
-
- _allocate_counters();
- }
-
- virtual ~CountingHash()
- {
- if (_counts) {
- for (size_t i = 0; i < _n_tables; i++) {
- if (_counts[i]) {
- delete[] _counts[i];
- _counts[i] = NULL;
- }
- }
-
- delete[] _counts;
- _counts = NULL;
-
- _n_tables = 0;
- }
- }
-
- // Writing to the tables outside of defined methods has undefined behavior!
- // As such, this should only be used to return read-only interfaces
- Byte ** get_raw_tables()
- {
- return _counts;
- }
-
- virtual BoundedCounterType test_and_set_bits(const char * kmer)
- {
- BoundedCounterType x = get_count(kmer); // @CTB just hash it, yo.
- count(kmer);
- return !x;
- }
-
- virtual BoundedCounterType test_and_set_bits(HashIntoType khash)
- {
- BoundedCounterType x = get_count(khash);
- count(khash);
- return !x;
- }
-
- std::vector<HashIntoType> get_tablesizes() const
- {
- return _tablesizes;
- }
-
- virtual const HashIntoType n_unique_kmers() const
- {
- return _n_unique_kmers;
- }
-
- void set_use_bigcount(bool b)
- {
- _use_bigcount = b;
- }
- bool get_use_bigcount()
- {
- return _use_bigcount;
- }
-
- virtual void save(std::string);
- virtual void load(std::string);
-
- const size_t n_tables() const
- {
- return _n_tables;
- }
-
- // count number of occupied bins
- virtual const HashIntoType n_occupied() const
- {
- return _occupied_bins;
- }
-
- virtual void count(const char * kmer)
- {
- HashIntoType hash = _hash(kmer, _ksize);
- count(hash);
- }
-
- virtual void count(HashIntoType khash)
- {
- bool is_new_kmer = false;
- unsigned int n_full = 0;
-
- for (unsigned int i = 0; i < _n_tables; i++) {
- const HashIntoType bin = khash % _tablesizes[i];
- Byte current_count = _counts[ i ][ bin ];
- if (!is_new_kmer) {
- if (current_count == 0) {
- is_new_kmer = true;
- if (i == 0) {
- __sync_add_and_fetch(&_occupied_bins, 1);
- }
- }
- }
- // NOTE: Technically, multiple threads can cause the bin to spill
- // over max_count a little, if they all read it as less than
- // max_count before any of them increment it.
- // However, do we actually care if there is a little
- // bit of slop here? It can always be trimmed off later, if
- // that would help with stats.
- if ( _max_count > current_count ) {
- __sync_add_and_fetch( *(_counts + i) + bin, 1 );
- } else {
- n_full++;
- }
- } // for each table
-
- if (n_full == _n_tables && _use_bigcount) {
- while (!__sync_bool_compare_and_swap( &_bigcount_spin_lock, 0, 1 ));
- if (_bigcounts[khash] == 0) {
- _bigcounts[khash] = _max_count + 1;
- } else {
- if (_bigcounts[khash] < _max_bigcount) {
- _bigcounts[khash] += 1;
- }
- }
- __sync_bool_compare_and_swap( &_bigcount_spin_lock, 1, 0 );
- }
-
- if (is_new_kmer) {
- __sync_add_and_fetch(&_n_unique_kmers, 1);
- }
-
- } // count
-
- // get the count for the given k-mer.
- virtual const BoundedCounterType get_count(const char * kmer) const
- {
- HashIntoType hash = _hash(kmer, _ksize);
- return get_count(hash);
- }
-
- // get the count for the given k-mer hash.
- virtual const BoundedCounterType get_count(HashIntoType khash) const
- {
- unsigned int max_count = _max_count;
- BoundedCounterType min_count = max_count;
- for (unsigned int i = 0; i < _n_tables; i++) {
- BoundedCounterType the_count = _counts[i][khash % _tablesizes[i]];
- if (the_count < min_count) {
- min_count = the_count;
- }
- }
- if (min_count == max_count && _use_bigcount) {
- KmerCountMap::const_iterator it = _bigcounts.find(khash);
- if (it != _bigcounts.end()) {
- min_count = it->second;
- }
- }
- return min_count;
- }
-
- void output_fasta_kmer_pos_freq(const std::string &inputfile,
- const std::string &outputfile);
-
- BoundedCounterType get_min_count(const std::string &s);
-
- BoundedCounterType get_max_count(const std::string &s);
-
- HashIntoType * abundance_distribution(read_parsers::IParser * parser,
- Hashbits * tracking);
- HashIntoType * abundance_distribution(std::string filename,
- Hashbits * tracking);
-
- HashIntoType * fasta_count_kmers_by_position(const std::string &inputfile,
- const unsigned int max_read_len,
- BoundedCounterType limit_by_count=0,
- CallbackFn callback = NULL,
- void * callback_data = NULL);
-
- void fasta_dump_kmers_by_abundance(const std::string &inputfile,
- BoundedCounterType limit_by_count,
- CallbackFn callback = NULL,
- void * callback_data = NULL);
-
- unsigned long trim_on_abundance(std::string seq,
- BoundedCounterType min_abund) const;
- unsigned long trim_below_abundance(std::string seq,
- BoundedCounterType max_abund) const;
- std::vector<unsigned int> find_spectral_error_positions(std::string seq,
- BoundedCounterType min_abund) const;
-
- void collect_high_abundance_kmers(const std::string &infilename,
- unsigned int lower_count,
- unsigned int upper_count,
- SeenSet& kmers);
-};
-
-
-class CountingHashFile
-{
-public:
- static void load(const std::string &infilename, CountingHash &ht);
- static void save(const std::string &outfilename, const CountingHash &ht);
-};
-
-class CountingHashFileReader : public CountingHashFile
-{
-public:
- CountingHashFileReader(const std::string &infilename, CountingHash &ht);
-};
-
-class CountingHashGzFileReader : public CountingHashFile
-{
-public:
- CountingHashGzFileReader(const std::string &infilename, CountingHash &ht);
-};
-
-
-class CountingHashFileWriter : public CountingHashFile
-{
-public:
- CountingHashFileWriter(const std::string &outfilename, const CountingHash &ht);
-};
-
-class CountingHashGzFileWriter : public CountingHashFile
-{
-public:
- CountingHashGzFileWriter(const std::string &outfilename,
- const CountingHash &ht);
-};
-}
-
-#endif // COUNTING_HH
-
-// vim: set sts=2 sw=2:
diff --git a/lib/get_version.py b/lib/get_version.py
deleted file mode 100755
index 8d69266..0000000
--- a/lib/get_version.py
+++ /dev/null
@@ -1,52 +0,0 @@
-#!/usr/bin/env python
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) 2014-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are
-# met:
-#
-# * Redistributions of source code must retain the above copyright
-# notice, this list of conditions and the following disclaimer.
-#
-# * Redistributions in binary form must reproduce the above
-# copyright notice, this list of conditions and the following
-# disclaimer in the documentation and/or other materials provided
-# with the distribution.
-#
-# * Neither the name of the Michigan State University nor the names
-# of its contributors may be used to endorse or promote products
-# derived from this software without specific prior written
-# permission.
-#
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
-# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
-# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-#
-# Contact: khmer-project at idyll.org
-
-from __future__ import print_function
-import sys
-import os
-sys.path.insert(
- 0, os.path.abspath(os.path.join(
- os.path.dirname(os.path.abspath(__file__)),
- os.pardir)))
-import versioneer
-
-versioneer.VCS = 'git'
-versioneer.versionfile_source = '../khmer/_version.py'
-versioneer.versionfile_build = '../khmer/_version.py'
-versioneer.tag_prefix = 'v' # tags are like v1.2.0
-versioneer.parentdir_prefix = '..'
-
-print(versioneer.get_version())
diff --git a/lib/hashbits.cc b/lib/hashbits.cc
deleted file mode 100644
index 7feae6d..0000000
--- a/lib/hashbits.cc
+++ /dev/null
@@ -1,215 +0,0 @@
-/*
-This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-Copyright (C) 2010-2015, Michigan State University.
-Copyright (C) 2015, The Regents of the University of California.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are
-met:
-
- * Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
-
- * Redistributions in binary form must reproduce the above
- copyright notice, this list of conditions and the following
- disclaimer in the documentation and/or other materials provided
- with the distribution.
-
- * Neither the name of the Michigan State University nor the names
- of its contributors may be used to endorse or promote products
- derived from this software without specific prior written
- permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
-DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
-THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-LICENSE (END)
-
-Contact: khmer-project at idyll.org
-*/
-#include <errno.h>
-#include <sstream> // IWYU pragma: keep
-
-#include "hashbits.hh"
-#include "hashtable.hh"
-#include "khmer_exception.hh"
-#include "read_parsers.hh"
-
-using namespace std;
-using namespace khmer;
-using namespace khmer:: read_parsers;
-
-void Hashbits::save(std::string outfilename)
-{
- if (!_counts[0]) {
- throw khmer_exception();
- }
-
- unsigned int save_ksize = _ksize;
- unsigned char save_n_tables = _n_tables;
- unsigned long long save_tablesize;
- unsigned long long save_occupied_bins = _occupied_bins;
-
- ofstream outfile(outfilename.c_str(), ios::binary);
-
- outfile.write(SAVED_SIGNATURE, 4);
- unsigned char version = SAVED_FORMAT_VERSION;
- outfile.write((const char *) &version, 1);
-
- unsigned char ht_type = SAVED_HASHBITS;
- outfile.write((const char *) &ht_type, 1);
-
- outfile.write((const char *) &save_ksize, sizeof(save_ksize));
- outfile.write((const char *) &save_n_tables, sizeof(save_n_tables));
- outfile.write((const char *) &save_occupied_bins,
- sizeof(save_occupied_bins));
-
- for (unsigned int i = 0; i < _n_tables; i++) {
- save_tablesize = _tablesizes[i];
- unsigned long long tablebytes = save_tablesize / 8 + 1;
-
- outfile.write((const char *) &save_tablesize, sizeof(save_tablesize));
-
- outfile.write((const char *) _counts[i], tablebytes);
- }
- if (outfile.fail()) {
- throw khmer_file_exception(strerror(errno));
- }
- outfile.close();
-}
-
-/**
- * Loads @param infilename into Hashbits, with error checking on
- * file type and file version. Populates _counts internally.
- */
-void Hashbits::load(std::string infilename)
-{
- ifstream infile;
-
- // configure ifstream to raise exceptions for everything.
- infile.exceptions(std::ifstream::failbit | std::ifstream::badbit |
- std::ifstream::eofbit);
-
- try {
- infile.open(infilename.c_str(), ios::binary);
- } catch (std::ifstream::failure &e) {
- std::string err;
- if (!infile.is_open()) {
- err = "Cannot open k-mer graph file: " + infilename;
- } else {
- err = "Unknown error in opening file: " + infilename;
- }
- throw khmer_file_exception(err);
- }
-
- if (_counts) {
- for (unsigned int i = 0; i < _n_tables; i++) {
- delete[] _counts[i];
- _counts[i] = NULL;
- }
- delete[] _counts;
- _counts = NULL;
- }
- _tablesizes.clear();
-
- try {
- unsigned int save_ksize = 0;
- unsigned char save_n_tables = 0;
- unsigned long long save_tablesize = 0;
- unsigned long long save_occupied_bins = 0;
- char signature[4];
- unsigned char version, ht_type;
-
- infile.read(signature, 4);
- infile.read((char *) &version, 1);
- infile.read((char *) &ht_type, 1);
- if (!(std::string(signature, 4) == SAVED_SIGNATURE)) {
- std::ostringstream err;
- err << "Does not start with signature for a khmer file: 0x";
- for(size_t i=0; i < 4; ++i) {
- err << std::hex << (int) signature[i];
- }
- err << " Should be: " << SAVED_SIGNATURE;
- throw khmer_file_exception(err.str());
- } else if (!(version == SAVED_FORMAT_VERSION)) {
- std::ostringstream err;
- err << "Incorrect file format version " << (int) version
- << " while reading k-mer graph from " << infilename
- << "; should be " << (int) SAVED_FORMAT_VERSION;
- throw khmer_file_exception(err.str());
- } else if (!(ht_type == SAVED_HASHBITS)) {
- std::ostringstream err;
- err << "Incorrect file format type " << (int) ht_type
- << " while reading k-mer graph from " << infilename;
- throw khmer_file_exception(err.str());
- }
-
- infile.read((char *) &save_ksize, sizeof(save_ksize));
- infile.read((char *) &save_n_tables, sizeof(save_n_tables));
- infile.read((char *) &save_occupied_bins, sizeof(save_occupied_bins));
-
- _ksize = (WordLength) save_ksize;
- _n_tables = (unsigned int) save_n_tables;
- _occupied_bins = save_occupied_bins;
- _init_bitstuff();
-
- _counts = new Byte*[_n_tables];
- for (unsigned int i = 0; i < _n_tables; i++) {
- HashIntoType tablesize;
- unsigned long long tablebytes;
-
- infile.read((char *) &save_tablesize, sizeof(save_tablesize));
-
- tablesize = (HashIntoType) save_tablesize;
- _tablesizes.push_back(tablesize);
-
- tablebytes = tablesize / 8 + 1;
- _counts[i] = new Byte[tablebytes];
-
- unsigned long long loaded = 0;
- while (loaded != tablebytes) {
- infile.read((char *) _counts[i], tablebytes - loaded);
- loaded += infile.gcount();
- }
- }
- infile.close();
- } catch (std::ifstream::failure &e) {
- std::string err;
- if (infile.eof()) {
- err = "Unexpected end of k-mer graph file: " + infilename;
- } else {
- err = "Error reading from k-mer graph file: " + infilename;
- }
- throw khmer_file_exception(err);
- }
-}
-
-void Hashbits::update_from(const Hashbits &other)
-{
- if (_ksize != other._ksize) {
- throw khmer_exception("both nodegraphs must have same k size");
- }
- if (_tablesizes != other._tablesizes) {
- throw khmer_exception("both nodegraphs must have same table sizes");
- }
- for (unsigned int table_num = 0; table_num < _n_tables; table_num++) {
- Byte * me = _counts[table_num];
- Byte * ot = other._counts[table_num];
- HashIntoType tablesize = _tablesizes[table_num];
- HashIntoType tablebytes = tablesize / 8 + 1;
-
- for (HashIntoType index = 0; index < tablebytes; index++) {
- me[index] |= ot[index]; // bitwise or
- }
- }
-}
-
-// vim: set sts=2 sw=2:
diff --git a/lib/hashbits.hh b/lib/hashbits.hh
deleted file mode 100644
index c20ad6e..0000000
--- a/lib/hashbits.hh
+++ /dev/null
@@ -1,215 +0,0 @@
-/*
-This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-Copyright (C) 2010-2015, Michigan State University.
-Copyright (C) 2015, The Regents of the University of California.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are
-met:
-
- * Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
-
- * Redistributions in binary form must reproduce the above
- copyright notice, this list of conditions and the following
- disclaimer in the documentation and/or other materials provided
- with the distribution.
-
- * Neither the name of the Michigan State University nor the names
- of its contributors may be used to endorse or promote products
- derived from this software without specific prior written
- permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
-DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
-THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-LICENSE (END)
-
-Contact: khmer-project at idyll.org
-*/
-#ifndef HASHBITS_HH
-#define HASHBITS_HH
-
-#include <stddef.h>
-#include <string.h>
-#include <string>
-#include <vector>
-
-#include "hashtable.hh"
-#include "khmer.hh"
-#include "kmer_hash.hh"
-
-namespace khmer
-{
-class CountingHash;
-class LabelHash;
-
-class Hashbits : public khmer::Hashtable
-{
-protected:
- std::vector<HashIntoType> _tablesizes;
- size_t _n_tables;
- HashIntoType _occupied_bins;
- HashIntoType _n_unique_kmers;
- Byte ** _counts;
-
- virtual void _allocate_counters()
- {
- _n_tables = _tablesizes.size();
-
- _counts = new Byte*[_n_tables];
-
- for (size_t i = 0; i < _n_tables; i++) {
- HashIntoType tablesize = _tablesizes[i];
- HashIntoType tablebytes = tablesize / 8 + 1;
-
- _counts[i] = new Byte[tablebytes];
- memset(_counts[i], 0, tablebytes);
- }
- }
-
-public:
- Hashbits(WordLength ksize, std::vector<HashIntoType>& tablesizes)
- : khmer::Hashtable(ksize),
- _tablesizes(tablesizes)
- {
- _occupied_bins = 0;
- _n_unique_kmers = 0;
-
- _allocate_counters();
- }
-
- ~Hashbits()
- {
- if (_counts) {
- for (size_t i = 0; i < _n_tables; i++) {
- delete[] _counts[i];
- _counts[i] = NULL;
- }
- delete[] _counts;
- _counts = NULL;
-
- _n_tables = 0;
- }
-
- }
-
- // Accessors for protected/private table info members
- std::vector<HashIntoType> get_tablesizes() const
- {
- return _tablesizes;
- }
-
- const size_t n_tables() const
- {
- return _n_tables;
- }
-
- virtual void save(std::string);
- virtual void load(std::string);
-
- // count number of occupied bins
- virtual const HashIntoType n_occupied() const
- {
- return _occupied_bins;
- }
-
- virtual const HashIntoType n_unique_kmers() const
- {
- return _n_unique_kmers;
- }
-
- // Get and set the hashbits for the given kmer.
- inline
- virtual
- BoundedCounterType
- test_and_set_bits(const char * kmer)
- {
- HashIntoType hash = _hash(kmer, _ksize);
- return test_and_set_bits(hash);
- }
-
- // Get and set the hashbits for the given kmer hash.
- // Generally, it is better to keep tests and mutations separate,
- // but, in the interests of efficiency and thread safety,
- // tests and mutations are being blended here against conventional
- // software engineering wisdom.
- inline
- virtual
- BoundedCounterType
- test_and_set_bits( HashIntoType khash )
- {
- bool is_new_kmer = false;
-
- for (size_t i = 0; i < _n_tables; i++) {
- HashIntoType bin = khash % _tablesizes[i];
- HashIntoType byte = bin / 8;
- unsigned char bit = (unsigned char)(1 << (bin % 8));
-
- unsigned char bits_orig = __sync_fetch_and_or( *(_counts + i) + byte, bit );
- if (!(bits_orig & bit)) {
- if (i == 0) {
- __sync_add_and_fetch( &_occupied_bins, 1 );
- }
- is_new_kmer = true;
- }
- } // iteration over hashtables
-
- if (is_new_kmer) {
- __sync_add_and_fetch( &_n_unique_kmers, 1 );
- return 1; // kmer not seen before
- }
-
- return 0; // kmer already seen
- } // test_and_set_bits
-
- virtual void count(const char * kmer)
- {
- HashIntoType hash = _hash(kmer, _ksize);
- count(hash);
- }
-
- virtual void count(HashIntoType khash)
- {
- test_and_set_bits(khash);
- }
-
- // get the count for the given k-mer.
- virtual const BoundedCounterType get_count(const char * kmer) const
- {
- HashIntoType hash = _hash(kmer, _ksize);
- return get_count(hash);
- }
-
- // get the count for the given k-mer hash.
- virtual const BoundedCounterType get_count(HashIntoType khash) const
- {
- for (size_t i = 0; i < _n_tables; i++) {
- HashIntoType bin = khash % _tablesizes[i];
- HashIntoType byte = bin / 8;
- unsigned char bit = bin % 8;
-
- if (!(_counts[i][byte] & (1 << bit))) {
- return 0;
- }
- }
- return 1;
- }
-
- void update_from(const Hashbits &other);
-};
-}
-
-#include "counting.hh"
-#include "labelhash.hh"
-#endif // HASHBITS_HH
-
-// vim: set sts=2 sw=2:
diff --git a/lib/hashtable.cc b/lib/hashgraph.cc
similarity index 55%
copy from lib/hashtable.cc
copy to lib/hashgraph.cc
index aefddcf..888b8f6 100644
--- a/lib/hashtable.cc
+++ b/lib/hashgraph.cc
@@ -1,7 +1,6 @@
/*
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-Copyright (C) 2010-2015, Michigan State University.
-Copyright (C) 2015, The Regents of the University of California.
+Copyright (C) 2016, The Regents of the University of California.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
@@ -15,7 +14,7 @@ met:
disclaimer in the documentation and/or other materials provided
with the distribution.
- * Neither the name of the Michigan State University nor the names
+ * Neither the name of the University of California nor the names
of its contributors may be used to endorse or promote products
derived from this software without specific prior written
permission.
@@ -45,8 +44,7 @@ Contact: khmer-project at idyll.org
#include <queue>
#include <set>
-#include "counting.hh"
-#include "hashtable.hh"
+#include "hashgraph.hh"
#include "khmer.hh"
#include "read_parsers.hh"
@@ -54,194 +52,7 @@ using namespace std;
using namespace khmer;
using namespace khmer:: read_parsers;
-//
-// check_and_process_read: checks for non-ACGT characters before consuming
-//
-
-unsigned int Hashtable::check_and_process_read(std::string &read,
- bool &is_valid)
-{
- is_valid = check_and_normalize_read(read);
-
- if (!is_valid) {
- return 0;
- }
-
- return consume_string(read);
-}
-
-//
-// check_and_normalize_read: checks for non-ACGT characters
-// converts lowercase characters to uppercase one
-// Note: Usually it is desirable to keep checks and mutations separate.
-// However, in the interests of efficiency (we are potentially working
-// with TB of data), a check and mutation have been placed inside the
-// same loop. Potentially trillions fewer fetches from memory would
-// seem to be a worthwhile goal.
-//
-
-bool Hashtable::check_and_normalize_read(std::string &read) const
-{
- bool rc = true;
-
- if (read.length() < _ksize) {
- return false;
- }
-
- for (unsigned int i = 0; i < read.length(); i++) {
- read[ i ] &= 0xdf; // toupper - knock out the "lowercase bit"
- if (!is_valid_dna( read[ i ] )) {
- rc = false;
- break;
- }
- }
-
- return rc;
-}
-
-//
-// consume_fasta: consume a FASTA file of reads
-//
-
-// TODO? Inline in header.
-void
-Hashtable::
-consume_fasta(
- std:: string const &filename,
- unsigned int &total_reads, unsigned long long &n_consumed
-)
-{
- IParser * parser =
- IParser::get_parser( filename );
-
- consume_fasta(
- parser,
- total_reads, n_consumed
- );
-
- delete parser;
-}
-
-void
-Hashtable::
-consume_fasta(
- read_parsers:: IParser * parser,
- unsigned int &total_reads, unsigned long long &n_consumed
-)
-{
- Read read;
-
- // Iterate through the reads and consume their k-mers.
- while (!parser->is_complete( )) {
- bool is_valid;
- try {
- read = parser->get_next_read( );
- } catch (NoMoreReadsAvailable) {
- break;
- }
-
- unsigned int this_n_consumed =
- check_and_process_read(read.sequence, is_valid);
-
- __sync_add_and_fetch( &n_consumed, this_n_consumed );
- __sync_add_and_fetch( &total_reads, 1 );
-
- } // while reads left for parser
-
-} // consume_fasta
-
-//
-// consume_string: run through every k-mer in the given string, & hash it.
-//
-
-unsigned int Hashtable::consume_string(const std::string &s)
-{
- const char * sp = s.c_str();
- unsigned int n_consumed = 0;
-
- KmerIterator kmers(sp, _ksize);
-
- while(!kmers.done()) {
- HashIntoType kmer = kmers.next();
-
- count(kmer);
- n_consumed++;
- }
-
- return n_consumed;
-}
-
-// technically, get medioid count... our "median" is always a member of the
-// population.
-
-void Hashtable::get_median_count(const std::string &s,
- BoundedCounterType &median,
- float &average,
- float &stddev)
-{
- std::vector<BoundedCounterType> counts;
- this->get_kmer_counts(s, counts);
-
- if (!counts.size()) {
- throw khmer_exception("no k-mer counts for this string; too short?");
- }
-
- average = 0;
- for (std::vector<BoundedCounterType>::const_iterator i = counts.begin();
- i != counts.end(); ++i) {
- average += *i;
- }
- average /= float(counts.size());
-
- stddev = 0;
- for (std::vector<BoundedCounterType>::const_iterator i = counts.begin();
- i != counts.end(); ++i) {
- stddev += (float(*i) - average) * (float(*i) - average);
- }
- stddev /= float(counts.size());
- stddev = sqrt(stddev);
-
- sort(counts.begin(), counts.end());
- median = counts[counts.size() / 2]; // rounds down
-}
-
-//
-// Optimized filter function for normalize-by-median
-//
-bool Hashtable::median_at_least(const std::string &s,
- unsigned int cutoff)
-{
- KmerIterator kmers(s.c_str(), _ksize);
- unsigned int min_req = 0.5 + float(s.size() - _ksize + 1) / 2;
- unsigned int num_cutoff_kmers = 0;
-
- // first loop:
- // accumulate at least min_req worth of counts before checking to see
- // if we have enough high-abundance k-mers to indicate success.
- for (unsigned int i = 0; i < min_req; ++i) {
- HashIntoType kmer = kmers.next();
- if (this->get_count(kmer) >= cutoff) {
- ++num_cutoff_kmers;
- }
- }
-
- // second loop: now check to see if we pass the threshold for each k-mer.
- if (num_cutoff_kmers >= min_req) {
- return true;
- }
- while(!kmers.done()) {
- HashIntoType kmer = kmers.next();
- if (this->get_count(kmer) >= cutoff) {
- ++num_cutoff_kmers;
- if (num_cutoff_kmers >= min_req) {
- return true;
- }
- }
- }
- return false;
-}
-
-void Hashtable::save_tagset(std::string outfilename)
+void Hashgraph::save_tagset(std::string outfilename)
{
ofstream outfile(outfilename.c_str(), ios::binary);
const size_t tagset_size = n_tags();
@@ -276,7 +87,7 @@ void Hashtable::save_tagset(std::string outfilename)
delete[] buf;
}
-void Hashtable::load_tagset(std::string infilename, bool clear_tags)
+void Hashgraph::load_tagset(std::string infilename, bool clear_tags)
{
ifstream infile;
@@ -294,6 +105,12 @@ void Hashtable::load_tagset(std::string infilename, bool clear_tags)
err = "Unknown error in opening file: " + infilename;
}
throw khmer_file_exception(err);
+ } catch (const std::exception &e) {
+ // Catching std::exception is a stopgap for
+ // https://gcc.gnu.org/bugzilla/show_bug.cgi?id=66145
+ std::string err = "Unknown error opening file: " + infilename + " "
+ + strerror(errno);
+ throw khmer_file_exception(err);
}
if (clear_tags) {
@@ -359,10 +176,28 @@ void Hashtable::load_tagset(std::string infilename, bool clear_tags)
delete[] buf;
}
throw khmer_file_exception(err);
+ /* Yes, this is boneheaded. Unfortunately, there is a bug in gcc > 5
+ * regarding the basic_ios::failure that makes it impossible to catch
+ * with more specificty. So, we catch *all* exceptions after trying to
+ * get the ifstream::failure, and assume it must have been the buggy one.
+ * Unfortunately, this would also cause us to catch the
+ * khmer_file_exceptions thrown above, so we catch them again first and
+ * rethrow them :) If this is understandably irritating to you, please
+ * bother the gcc devs at:
+ * https://gcc.gnu.org/bugzilla/show_bug.cgi?id=66145
+ *
+ * See also: http://media4.giphy.com/media/3o6UBpHgaXFDNAuttm/giphy.gif
+ */
+ } catch (khmer_file_exception &e) {
+ throw e;
+ } catch (const std::exception &e) {
+ std::string err = "Unknown error opening file: " + infilename + " "
+ + strerror(errno);
+ throw khmer_file_exception(err);
}
}
-void Hashtable::consume_sequence_and_tag(const std::string& seq,
+void Hashgraph::consume_sequence_and_tag(const std::string& seq,
unsigned long long& n_consumed,
SeenSet * found_tags)
{
@@ -382,7 +217,7 @@ void Hashtable::consume_sequence_and_tag(const std::string& seq,
// This is probably better than first testing and then setting the bits,
// as a failed test essentially results in doing the same amount of work
// twice.
- if ((is_new_kmer = test_and_set_bits( kmer ))) {
+ if ((is_new_kmer = store->test_and_set_bits( kmer ))) {
++n_consumed;
}
@@ -436,34 +271,27 @@ void Hashtable::consume_sequence_and_tag(const std::string& seq,
}
//
-// consume_fasta_and_tag: consume a FASTA file of reads, tagging reads every
-// so often.
+// consume_seqfile_and_tag: consume a file containing reads, tagging reads every
+// so often
//
// TODO? Inline in header.
-void
-Hashtable::
-consume_fasta_and_tag(
- std:: string const &filename,
- unsigned int &total_reads, unsigned long long &n_consumed
+template<typename SeqIO>
+void Hashgraph::consume_seqfile_and_tag(
+ std::string const &filename,
+ unsigned int &total_reads,
+ unsigned long long &n_consumed
)
{
- IParser * parser =
- IParser::get_parser( filename );
-
- consume_fasta_and_tag(
- parser,
- total_reads, n_consumed
- );
-
- delete parser;
+ ReadParserPtr<SeqIO> parser = get_parser<SeqIO>(filename);
+ consume_seqfile_and_tag<SeqIO>(parser, total_reads, n_consumed);
}
-void
-Hashtable::
-consume_fasta_and_tag(
- read_parsers:: IParser * parser,
- unsigned int &total_reads, unsigned long long &n_consumed
+template<typename SeqIO>
+void Hashgraph::consume_seqfile_and_tag(
+ ReadParserPtr<SeqIO>& parser,
+ unsigned int &total_reads,
+ unsigned long long &n_consumed
)
{
Read read;
@@ -474,7 +302,6 @@ consume_fasta_and_tag(
// Iterate through the reads and consume their k-mers.
while (!parser->is_complete( )) {
-
try {
read = parser->get_next_read( );
} catch (NoMoreReadsAvailable &e) {
@@ -494,116 +321,11 @@ consume_fasta_and_tag(
}
//
-// consume_fasta_and_tag_with_stoptags: consume a FASTA file of reads,
-// tagging reads every so often. Do not insert matches to stoptags,
-// and join the tags across those gaps.
-//
-
-void Hashtable::consume_fasta_and_tag_with_stoptags(const std::string &filename,
- unsigned int &total_reads,
- unsigned long long &n_consumed)
-{
- total_reads = 0;
- n_consumed = 0;
-
- IParser* parser = IParser::get_parser(filename.c_str());
- Read read;
-
- string seq = "";
-
- SeenSet read_tags;
-
- //
- // iterate through the FASTA file & consume the reads.
- //
-
- while(!parser->is_complete()) {
- try {
- read = parser->get_next_read();
- } catch (NoMoreReadsAvailable &exc) {
- break;
- }
- seq = read.sequence;
-
- read_tags.clear();
-
- // n_consumed += this_n_consumed;
-
- if (check_and_normalize_read(seq)) { // process?
- bool is_new_kmer;
- KmerIterator kmers(seq.c_str(), _ksize);
-
- HashIntoType kmer, last_kmer;
- bool is_first_kmer = true;
-
- unsigned int since = _tag_density / 2 + 1;
- while (!kmers.done()) {
- kmer = kmers.next();
-
- if (!set_contains(stop_tags, kmer)) { // NOT a stop tag... ok.
- is_new_kmer = (bool) !get_count(kmer);
- if (is_new_kmer) {
- count(kmer);
- n_consumed++;
- }
-
- if (!is_new_kmer && set_contains(all_tags, kmer)) {
- read_tags.insert(kmer);
- since = 1;
- } else {
- since++;
- }
-
- if (since >= _tag_density) {
- all_tags.insert(kmer);
- read_tags.insert(kmer);
- since = 1;
- }
- } else { // stop tag! do not insert, but connect.
- // before first tag insertion; insert last kmer.
- if (!is_first_kmer && read_tags.empty()) {
- read_tags.insert(last_kmer);
- all_tags.insert(last_kmer);
- }
-
- since = _tag_density - 1; // insert next kmer, too.
- }
-
- last_kmer = kmer;
- is_first_kmer = false;
- }
-
- if (!set_contains(stop_tags, kmer)) { // NOT a stop tag... ok.
- is_new_kmer = (bool) !get_count(kmer);
- if (is_new_kmer) {
- count(kmer);
- n_consumed++;
- }
-
- if (since >= _tag_density/2 - 1) {
- all_tags.insert(kmer); // insert the last k-mer, too.
- read_tags.insert(kmer);
- }
- }
- }
-
- if (read_tags.size() > 1) {
- partition->assign_partition_id(*(read_tags.begin()), read_tags);
- }
-
- // reset the sequence info, increment read number
- total_reads++;
-
- }
- delete parser;
-}
-
-//
// divide_tags_into_subsets - take all of the tags in 'all_tags', and
// divide them into subsets (based on starting tag) of <= given size.
//
-void Hashtable::divide_tags_into_subsets(unsigned int subset_size,
+void Hashgraph::divide_tags_into_subsets(unsigned int subset_size,
SeenSet& divvy)
{
unsigned int i = 0;
@@ -622,14 +344,17 @@ void Hashtable::divide_tags_into_subsets(unsigned int subset_size,
// consume_partitioned_fasta: consume a FASTA file of reads
//
-void Hashtable::consume_partitioned_fasta(const std::string &filename,
+template<typename SeqIO>
+void Hashgraph::consume_partitioned_fasta(
+ const std::string &filename,
unsigned int &total_reads,
- unsigned long long &n_consumed)
+ unsigned long long &n_consumed
+)
{
total_reads = 0;
n_consumed = 0;
- IParser* parser = IParser::get_parser(filename.c_str());
+ ReadParserPtr<SeqIO> parser = get_parser<SeqIO>(filename);
Read read;
string seq = "";
@@ -658,7 +383,7 @@ void Hashtable::consume_partitioned_fasta(const std::string &filename,
n_consumed += consume_string(seq); // @CTB why are we doing this?
// Next, compute the tag & set the partition, if nonzero
- HashIntoType kmer = _hash(seq.c_str(), _ksize);
+ HashIntoType kmer = hash_dna(seq.c_str());
all_tags.insert(kmer);
if (p > 0) {
partition->set_partition_id(kmer, p);
@@ -668,81 +393,12 @@ void Hashtable::consume_partitioned_fasta(const std::string &filename,
// reset the sequence info, increment read number
total_reads++;
}
-
- delete parser;
-}
-
-//
-// consume_fasta: consume a FASTA file of reads
-//
-
-void Hashtable::consume_fasta_and_traverse(const std::string &filename,
- unsigned int radius,
- unsigned int big_threshold,
- unsigned int transfer_threshold,
- CountingHash &counting)
-{
- unsigned long long total_reads = 0;
-
- IParser* parser = IParser::get_parser(filename.c_str());
- Read read;
-
- string seq = "";
-
- //
- // iterate through the FASTA file & consume the reads.
- //
-
- while(!parser->is_complete()) {
- try {
- read = parser->get_next_read();
- } catch (NoMoreReadsAvailable &exc) {
- break;
- }
- seq = read.sequence;
-
- if (check_and_normalize_read(seq)) { // process?
- KmerIterator kmers(seq.c_str(), _ksize);
-
- bool is_first_kmer = true;
- Kmer kmer(0,0,0);
- while (!kmers.done()) {
- kmer = kmers.next();
-
- if (set_contains(stop_tags, kmer)) {
- break;
- }
- count(kmer);
- is_first_kmer = false;
- }
-
- if (!is_first_kmer) { // traverse
- KmerSet keeper;
- unsigned int n = traverse_from_kmer(kmer, radius, keeper);
- if (n >= big_threshold) {
-#if VERBOSE_REPARTITION
- std::cout << "lmp: " << n << "; added: " << stop_tags.size() << "\n";
-#endif // VERBOSE_REPARTITION
- count_and_transfer_to_stoptags(keeper, transfer_threshold, counting);
- }
- }
- }
-
- // reset the sequence info, increment read number
- total_reads++;
-
- // run callback, if specified
- if (total_reads % CALLBACK_PERIOD == 0) {
- std::cout << "n reads: " << total_reads << "\n";
- }
- }
- delete parser;
}
//////////////////////////////////////////////////////////////////////
// graph stuff
-void Hashtable::calc_connected_graph_size(Kmer start,
+void Hashgraph::calc_connected_graph_size(Kmer start,
unsigned long long& count,
KmerSet& keeper,
const unsigned long long threshold,
@@ -755,15 +411,16 @@ const
return;
}
- Traverser traverser(this);
KmerQueue node_q;
node_q.push(start);
// Avoid high-circumference k-mers
- auto filter = [&] (Kmer& n) {
- return !(break_on_circum &&
- traverser.degree(n) > 4);
+ Traverser traverser(this);
+
+ KmerFilter filter = [&] (const Kmer& n) {
+ return break_on_circum && traverser.degree(n) > 4;
};
+ traverser.push_filter(filter);
while(!node_q.empty()) {
Kmer node = node_q.front();
@@ -790,76 +447,25 @@ const
}
// otherwise, explore in all directions.
- traverser.traverse_right(node, node_q, filter);
- traverser.traverse_left(node, node_q, filter);
+ traverser.traverse(node, node_q);
}
}
-unsigned int Hashtable::kmer_degree(HashIntoType kmer_f, HashIntoType kmer_r)
+unsigned int Hashgraph::kmer_degree(HashIntoType kmer_f, HashIntoType kmer_r)
{
Traverser traverser(this);
Kmer node = build_kmer(kmer_f, kmer_r);
return traverser.degree(node);
}
-unsigned int Hashtable::kmer_degree(const char * kmer_s)
+unsigned int Hashgraph::kmer_degree(const char * kmer_s)
{
Traverser traverser(this);
Kmer node = build_kmer(kmer_s);
return traverser.degree(node);
}
-void Hashtable::filter_if_present(const std::string &infilename,
- const std::string &outputfile)
-{
- IParser* parser = IParser::get_parser(infilename);
- ofstream outfile(outputfile.c_str());
-
- unsigned int total_reads = 0;
- unsigned int reads_kept = 0;
-
- Read read;
- string seq;
-
- HashIntoType kmer;
-
- while(!parser->is_complete()) {
- try {
- read = parser->get_next_read();
- } catch (NoMoreReadsAvailable &exc) {
- break;
- }
- seq = read.sequence;
-
- if (check_and_normalize_read(seq)) {
- KmerIterator kmers(seq.c_str(), _ksize);
- bool keep = true;
-
- while (!kmers.done()) {
- kmer = kmers.next();
- if (get_count(kmer)) {
- keep = false;
- break;
- }
- }
-
- if (keep) {
- outfile << ">" << read.name;
- outfile << "\n" << seq << "\n";
- reads_kept++;
- }
-
- total_reads++;
- }
- }
-
- delete parser;
- parser = NULL;
-
- return;
-}
-
-size_t Hashtable::trim_on_stoptags(std::string seq) const
+size_t Hashgraph::trim_on_stoptags(std::string seq) const
{
if (!check_and_normalize_read(seq)) {
return 0;
@@ -879,71 +485,23 @@ size_t Hashtable::trim_on_stoptags(std::string seq) const
return seq.length();
}
-void Hashtable::traverse_from_tags(unsigned int distance,
- unsigned int threshold,
- unsigned int frequency,
- CountingHash &counting)
-{
- unsigned int i = 0;
- unsigned int n = 0;
- unsigned int n_big = 0;
- KmerSet keeper;
-
-#if VERBOSE_REPARTITION
- std::cout << all_tags.size() << " tags...\n";
-#endif // 0
-
- for (SeenSet::const_iterator si = all_tags.begin(); si != all_tags.end();
- ++si, i++) {
-
- n++;
- Kmer tag = build_kmer(*si);
- unsigned int count = traverse_from_kmer(tag, distance, keeper);
-
- if (count >= threshold) {
- n_big++;
-
- KmerSet::const_iterator ti;
- for (ti = keeper.begin(); ti != keeper.end(); ++ti) {
- if (counting.get_count(*ti) > frequency) {
- stop_tags.insert(*ti);
- } else {
- counting.count(*ti);
- }
- }
-#if VERBOSE_REPARTITION
- std::cout << "traversed from " << n << " tags total; "
- << n_big << " big; " << keeper.size() << "\n";
-#endif // 0
- }
- keeper.clear();
-
- if (n % 100 == 0) {
-#if VERBOSE_REPARTITION
- std::cout << "traversed " << n << " " << n_big << " " <<
- all_tags.size() << " " << stop_tags.size() << "\n";
-#endif // 0
- }
- }
-}
-
-unsigned int Hashtable::traverse_from_kmer(Kmer start,
+unsigned int Hashgraph::traverse_from_kmer(Kmer start,
unsigned int radius,
KmerSet &keeper,
unsigned int max_count)
const
{
- Traverser traverser(this);
KmerQueue node_q;
std::queue<unsigned int> breadth_q;
unsigned int cur_breadth = 0;
unsigned int total = 0;
unsigned int nfound = 0;
- auto filter = [&] (Kmer& n) {
- return !set_contains(keeper, n);
+ KmerFilter filter = [&] (const Kmer& n) {
+ return set_contains(keeper, n);
};
+ Traverser traverser(this, filter);
node_q.push(start);
breadth_q.push(0);
@@ -982,12 +540,12 @@ const
cur_breadth = breadth;
}
- nfound = traverser.traverse_right(node, node_q, filter);
+ nfound = traverser.traverse_right(node, node_q);
for (unsigned int i = 0; i<nfound; ++i) {
breadth_q.push(breadth + 1);
}
- nfound = traverser.traverse_left(node, node_q, filter);
+ nfound = traverser.traverse_left(node, node_q);
for (unsigned int i = 0; i<nfound; ++i) {
breadth_q.push(breadth + 1);
}
@@ -996,7 +554,7 @@ const
return total;
}
-void Hashtable::load_stop_tags(std::string infilename, bool clear_tags)
+void Hashgraph::load_stop_tags(std::string infilename, bool clear_tags)
{
ifstream infile;
@@ -1014,6 +572,12 @@ void Hashtable::load_stop_tags(std::string infilename, bool clear_tags)
err = "Unknown error in opening file: " + infilename;
}
throw khmer_file_exception(err);
+ } catch (const std::exception &e) {
+ // Catching std::exception is a stopgap for
+ // https://gcc.gnu.org/bugzilla/show_bug.cgi?id=66145
+ std::string err = "Unknown error opening file: " + infilename + " "
+ + strerror(errno);
+ throw khmer_file_exception(err);
}
if (clear_tags) {
@@ -1072,10 +636,18 @@ void Hashtable::load_stop_tags(std::string infilename, bool clear_tags)
} catch (std::ifstream::failure &e) {
std::string err = "Error reading stoptags from: " + infilename;
throw khmer_file_exception(err);
+ } catch (khmer_file_exception &e) {
+ throw e;
+ } catch (const std::exception &e) {
+ // Catching std::exception is a stopgap for
+ // https://gcc.gnu.org/bugzilla/show_bug.cgi?id=66145
+ std::string err = "Unknown error opening file: " + infilename + " "
+ + strerror(errno);
+ throw khmer_file_exception(err);
}
}
-void Hashtable::save_stop_tags(std::string outfilename)
+void Hashgraph::save_stop_tags(std::string outfilename)
{
ofstream outfile(outfilename.c_str(), ios::binary);
size_t tagset_size = stop_tags.size();
@@ -1105,7 +677,7 @@ void Hashtable::save_stop_tags(std::string outfilename)
delete[] buf;
}
-void Hashtable::print_stop_tags(std::string infilename)
+void Hashgraph::print_stop_tags(std::string infilename)
{
ofstream printfile(infilename.c_str());
@@ -1119,7 +691,7 @@ void Hashtable::print_stop_tags(std::string infilename)
printfile.close();
}
-void Hashtable::print_tagset(std::string infilename)
+void Hashgraph::print_tagset(std::string infilename)
{
ofstream printfile(infilename.c_str());
@@ -1133,49 +705,7 @@ void Hashtable::print_tagset(std::string infilename)
printfile.close();
}
-unsigned int Hashtable::count_and_transfer_to_stoptags(KmerSet &keeper,
- unsigned int threshold,
- CountingHash &counting)
-{
- unsigned int n_inserted = 0;
-
- KmerSet::const_iterator ti;
- for (ti = keeper.begin(); ti != keeper.end(); ++ti) {
- if (counting.get_count(*ti) >= threshold) {
- stop_tags.insert(*ti);
- n_inserted++;
- } else {
- counting.count(*ti);
- }
- }
-
- return n_inserted;
-}
-
-void Hashtable::identify_stop_tags_by_position(std::string seq,
- std::vector<unsigned int> &posns)
-const
-{
- if (!check_and_normalize_read(seq)) {
- return;
- }
-
- KmerIterator kmers(seq.c_str(), _ksize);
-
- unsigned int i = 0;
- while(!kmers.done()) {
- HashIntoType kmer = kmers.next();
-
- if (set_contains(stop_tags, kmer)) {
- posns.push_back(i);
- }
- i++;
- }
-
- return;
-}
-
-void Hashtable::extract_unique_paths(std::string seq,
+void Hashgraph::extract_unique_paths(std::string seq,
unsigned int min_length,
float min_unique_f,
std::vector<std::string> &results)
@@ -1272,41 +802,107 @@ void Hashtable::extract_unique_paths(std::string seq,
}
-void Hashtable::get_kmers(const std::string &s,
- std::vector<std::string> &kmers_vec) const
+void Hashgraph::find_high_degree_nodes(const char * s,
+ SeenSet& high_degree_nodes)
+const
{
- if (s.length() < _ksize) {
- return;
- }
- for (unsigned int i = 0; i < s.length() - _ksize + 1; i++) {
- std::string sub = s.substr(i, i + _ksize);
- kmers_vec.push_back(sub);
+ Traverser traverser(this);
+ KmerIterator kmers(s, _ksize);
+
+ unsigned long n = 0;
+ while(!kmers.done()) {
+ n++;
+ if (n % 10000 == 0) {
+ std::cout << "... find_high_degree_nodes: " << n << "\n";
+ std::cout << std::flush;
+ }
+ Kmer kmer = kmers.next();
+ if ((traverser.degree(kmer)) > 2) {
+ high_degree_nodes.insert(kmer);
+ }
}
}
-
-void Hashtable::get_kmer_hashes(const std::string &s,
- std::vector<HashIntoType> &kmers_vec) const
+unsigned int Hashgraph::traverse_linear_path(const Kmer seed_kmer,
+ SeenSet &adjacencies,
+ SeenSet &visited, Hashtable &bf,
+ SeenSet &high_degree_nodes)
+const
{
- KmerIterator kmers(s.c_str(), _ksize);
+ unsigned int size = 0;
- while(!kmers.done()) {
- HashIntoType kmer = kmers.next();
- kmers_vec.push_back(kmer);
+ Traverser traverser(this);
+
+ // if this k-mer is in the Bloom filter, truncate search.
+ // This prevents paths from being traversed in two directions.
+ if (bf.get_count(seed_kmer)) {
+ return 0;
}
-}
+ std::vector<Kmer> to_be_visited;
+ to_be_visited.push_back(seed_kmer);
+
+ while (to_be_visited.size()) {
+ Kmer kmer = to_be_visited.back();
+ to_be_visited.pop_back();
+
+ visited.insert(kmer);
+ size += 1;
+
+ KmerQueue node_q;
+ traverser.traverse(kmer, node_q);
-void Hashtable::get_kmer_counts(const std::string &s,
- std::vector<BoundedCounterType> &counts) const
+ while (node_q.size()) {
+ Kmer node = node_q.front();
+ node_q.pop();
+
+ if (set_contains(high_degree_nodes, node)) {
+ // if there are any adjacent high degree nodes, record;
+ adjacencies.insert(node);
+ // also, add this to the stop Bloom filter.
+ bf.count(kmer);
+ } else if (set_contains(visited, node)) {
+ // do nothing - already visited
+ ;
+ } else {
+ to_be_visited.push_back(node);
+ }
+ }
+ }
+ return size;
+}
+
+void Nodegraph::update_from(const Nodegraph &otherBASE)
{
- KmerIterator kmers(s.c_str(), _ksize);
+ if (_ksize != otherBASE._ksize) {
+ throw khmer_exception("both nodegraphs must have same k size");
+ }
+ BitStorage * myself = dynamic_cast<BitStorage *>(this->store);
+ const BitStorage * other;
+ other = dynamic_cast<const BitStorage*>(otherBASE.store);
- while(!kmers.done()) {
- HashIntoType kmer = kmers.next();
- BoundedCounterType c = this->get_count(kmer);
- counts.push_back(c);
+ // if dynamic_cast worked, then the pointers will be not null.
+ if (myself && other) {
+ myself->update_from(*other);
+ } else {
+ throw khmer_exception("update_from failed with incompatible objects");
}
}
-// vim: set sts=2 sw=2:
+template void Hashgraph::consume_seqfile_and_tag<read_parsers::FastxReader>(
+ std::string const &filename,
+ unsigned int &total_reads,
+ unsigned long long &n_consumed
+);
+
+template void Hashgraph::consume_seqfile_and_tag<read_parsers::FastxReader>(
+ FastxParserPtr& parser,
+ unsigned int &total_reads,
+ unsigned long long &n_consumed
+);
+
+template void Hashgraph::consume_partitioned_fasta<read_parsers::FastxReader>(
+ const std::string &filename,
+ unsigned int &total_reads,
+ unsigned long long &n_consumed
+);
diff --git a/lib/hashgraph.hh b/lib/hashgraph.hh
new file mode 100644
index 0000000..b8bb805
--- /dev/null
+++ b/lib/hashgraph.hh
@@ -0,0 +1,298 @@
+/*
+This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+Copyright (C) 2016, The Regents of the University of California.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following
+ disclaimer in the documentation and/or other materials provided
+ with the distribution.
+
+ * Neither the name of the University of California nor the names
+ of its contributors may be used to endorse or promote products
+ derived from this software without specific prior written
+ permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+LICENSE (END)
+
+Contact: khmer-project at idyll.org
+*/
+#ifndef HASHGRAPH_HH
+#define HASHGRAPH_HH
+
+#include <stddef.h>
+#include <stdint.h>
+#include <string.h>
+#include <fstream>
+#include <iostream>
+#include <list>
+#include <map>
+#include <queue>
+#include <set>
+#include <string>
+#include <vector>
+
+#include "hashtable.hh"
+#include "traversal.hh"
+#include "subset.hh"
+
+namespace khmer
+{
+ namespace read_parsers
+ {
+ template<typename SeqIO> class ReadParser;
+ class FastxReader;
+ }
+}
+
+#define MAX_KEEPER_SIZE int(1e6)
+
+#define next_f(kmer_f, ch) ((((kmer_f) << 2) & bitmask) | (twobit_repr(ch)))
+#define next_r(kmer_r, ch) (((kmer_r) >> 2) | (twobit_comp(ch) << rc_left_shift))
+
+#define prev_f(kmer_f, ch) ((kmer_f) >> 2 | twobit_repr(ch) << rc_left_shift)
+#define prev_r(kmer_r, ch) ((((kmer_r) << 2) & bitmask) | (twobit_comp(ch)))
+
+#define set_contains(s, e) ((s).find(e) != (s).end())
+
+#define CALLBACK_PERIOD 100000
+
+namespace khmer
+{
+//
+// Hashgraph: Extension of Hashtable to support graph operations.
+//
+
+class Hashgraph: public Hashtable
+{
+
+ friend class SubsetPartition;
+ friend class LabelHash;
+ friend class Traverser;
+
+protected:
+ unsigned int _tag_density;
+
+ explicit Hashgraph(WordLength ksize, Storage * s)
+ : Hashtable(ksize, s)
+ {
+ _tag_density = DEFAULT_TAG_DENSITY;
+ if (!(_tag_density % 2 == 0)) {
+ throw khmer_exception();
+ }
+ partition = new SubsetPartition(this);
+ _all_tags_spin_lock = 0;
+ }
+
+ // clean up the partition structure.
+ virtual ~Hashgraph( )
+ {
+ delete partition;
+ }
+
+ // empty the partition structure
+ void _clear_all_partitions()
+ {
+ if (partition != NULL) {
+ partition->_clear_all_partitions();
+ }
+ }
+
+ uint32_t _all_tags_spin_lock;
+public:
+ // default master partitioning
+ SubsetPartition * partition;
+
+ // tags for sparse graph implementation
+ SeenSet all_tags;
+
+ // tags at which to stop traversal
+ SeenSet stop_tags;
+
+ // tags used in repartitioning
+ SeenSet repart_small_tags;
+
+ // set the minimum density of tagging.
+ void _set_tag_density(unsigned int d)
+ {
+ // must be odd; can't be set if tags exist.
+ if (!(d % 2 == 0) || !all_tags.empty()) {
+ throw khmer_exception();
+ }
+ _tag_density = d;
+ }
+
+ unsigned int _get_tag_density() const
+ {
+ return _tag_density;
+ }
+
+ void add_tag(HashIntoType tag)
+ {
+ all_tags.insert(tag);
+ }
+ void add_stop_tag(HashIntoType tag)
+ {
+ stop_tags.insert(tag);
+ }
+
+ size_t n_tags() const
+ {
+ return all_tags.size();
+ }
+
+ void divide_tags_into_subsets(unsigned int subset_size, SeenSet& divvy);
+
+ void add_kmer_to_tags(HashIntoType kmer)
+ {
+ all_tags.insert(kmer);
+ }
+
+ void clear_tags()
+ {
+ all_tags.clear();
+ }
+
+ // Consume reads & build sparse graph.
+ template<typename SeqIO>
+ void consume_seqfile_and_tag(
+ std::string const &filename,
+ unsigned int &total_reads,
+ unsigned long long &n_consumed
+ );
+
+ // Count every k-mer from a stream of FASTA or FASTQ reads,
+ // using the supplied parser.
+ // Tag certain ones on the connectivity graph.
+ template<typename SeqIO>
+ void consume_seqfile_and_tag(
+ read_parsers::ReadParserPtr<SeqIO>& parser,
+ unsigned int &total_reads,
+ unsigned long long &n_consumed
+ );
+
+ // consume a string & add sparse graph nodes.
+ void consume_sequence_and_tag(const std::string& seq,
+ unsigned long long& n_consumed,
+ SeenSet * new_tags = 0);
+
+
+ // consume an already-partitioned file & load in the partition IDs
+ template<typename SeqIO>
+ void consume_partitioned_fasta(const std::string &filename,
+ unsigned int &total_reads,
+ unsigned long long &n_consumed);
+
+ // trim the given sequence on stoptags
+ size_t trim_on_stoptags(std::string sequence) const;
+
+ // @@
+ unsigned int traverse_from_kmer(Kmer start,
+ unsigned int radius,
+ KmerSet &keeper,
+ unsigned int max_count = MAX_KEEPER_SIZE)
+ const;
+
+ // print, save, and load the set of tags.
+ void print_tagset(std::string);
+ void save_tagset(std::string);
+ void load_tagset(std::string, bool clear_tags=true);
+
+ // print, save and load the set of stop tags.
+ void print_stop_tags(std::string);
+ void save_stop_tags(std::string);
+ void load_stop_tags(std::string filename, bool clear_tags=true);
+
+ // @@
+ void extract_unique_paths(std::string seq,
+ unsigned int min_length,
+ float min_unique_f,
+ std::vector<std::string> &results);
+
+ // @@
+ void calc_connected_graph_size(Kmer node,
+ unsigned long long& count,
+ KmerSet& keeper,
+ const unsigned long long threshold=0,
+ bool break_on_circum=false) const;
+
+ // Calculate the graph degree of the given k-mer.
+ unsigned int kmer_degree(HashIntoType kmer_f, HashIntoType kmer_r);
+ unsigned int kmer_degree(const char * kmer_s);
+
+ // Find all nodes with a degree > 2.
+ void find_high_degree_nodes(const char * sequence,
+ SeenSet& high_degree_nodes) const;
+
+ // Find the maximal linear path (nodes degree <= 2)
+ unsigned int traverse_linear_path(const Kmer start_kmer,
+ SeenSet &adjacencies,
+ SeenSet &nodes, Hashtable& bf,
+ SeenSet &high_degree_nodes) const;
+
+ //
+ // for debugging/testing purposes only!
+ //
+
+ // check partition map validity.
+ void _validate_pmap()
+ {
+ if (partition) {
+ partition->_validate_pmap();
+ }
+ }
+
+};
+
+// Hashgraph-derived class with ByteStorage.
+class Countgraph : public khmer::Hashgraph
+{
+public:
+ explicit Countgraph(WordLength ksize, std::vector<uint64_t> sizes)
+ : Hashgraph(ksize, new ByteStorage(sizes)) { } ;
+};
+
+// Hashgraph-derived class with NibbleStorage.
+class SmallCountgraph : public khmer::Hashgraph
+{
+public:
+ explicit SmallCountgraph(WordLength ksize, std::vector<uint64_t> sizes)
+ : Hashgraph(ksize, new NibbleStorage(sizes)) { } ;
+};
+
+// Hashgraph-derived class with BitStorage.
+class Nodegraph : public Hashgraph
+{
+public:
+ explicit Nodegraph(WordLength ksize, std::vector<uint64_t> sizes)
+ : Hashgraph(ksize, new BitStorage(sizes)) { } ;
+
+ void update_from(const Nodegraph &other);
+};
+
+}
+
+#define ACQUIRE_ALL_TAGS_SPIN_LOCK \
+ while (!__sync_bool_compare_and_swap( &_all_tags_spin_lock, 0, 1 ));
+
+#define RELEASE_ALL_TAGS_SPIN_LOCK \
+ __sync_bool_compare_and_swap( &_all_tags_spin_lock, 1, 0 );
+
+#endif // HASHGRAPH_HH
diff --git a/lib/hashtable.cc b/lib/hashtable.cc
index aefddcf..c68009a 100644
--- a/lib/hashtable.cc
+++ b/lib/hashtable.cc
@@ -1,7 +1,7 @@
/*
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2010-2015, Michigan State University.
-Copyright (C) 2015, The Regents of the University of California.
+Copyright (C) 2015-2016, The Regents of the University of California.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
@@ -44,15 +44,20 @@ Contact: khmer-project at idyll.org
#include <sstream> // IWYU pragma: keep
#include <queue>
#include <set>
+#include <memory>
-#include "counting.hh"
#include "hashtable.hh"
#include "khmer.hh"
+#include "traversal.hh"
#include "read_parsers.hh"
+#include "kmer_hash.hh"
using namespace std;
using namespace khmer;
-using namespace khmer:: read_parsers;
+using namespace khmer::read_parsers;
+
+namespace khmer
+{
//
// check_and_process_read: checks for non-ACGT characters before consuming
@@ -100,33 +105,26 @@ bool Hashtable::check_and_normalize_read(std::string &read) const
}
//
-// consume_fasta: consume a FASTA file of reads
+// consume_seqfile: consume a file of reads
//
// TODO? Inline in header.
-void
-Hashtable::
-consume_fasta(
- std:: string const &filename,
- unsigned int &total_reads, unsigned long long &n_consumed
+template<typename SeqIO>
+void Hashtable::consume_seqfile(
+ std::string const &filename,
+ unsigned int &total_reads,
+ unsigned long long &n_consumed
)
{
- IParser * parser =
- IParser::get_parser( filename );
-
- consume_fasta(
- parser,
- total_reads, n_consumed
- );
-
- delete parser;
+ ReadParserPtr<SeqIO> parser = get_parser<SeqIO>(filename);
+ consume_seqfile<SeqIO>(parser, total_reads, n_consumed);
}
-void
-Hashtable::
-consume_fasta(
- read_parsers:: IParser * parser,
- unsigned int &total_reads, unsigned long long &n_consumed
+template<typename SeqIO>
+void Hashtable::consume_seqfile(
+ ReadParserPtr<SeqIO>& parser,
+ unsigned int &total_reads,
+ unsigned long long &n_consumed
)
{
Read read;
@@ -148,7 +146,7 @@ consume_fasta(
} // while reads left for parser
-} // consume_fasta
+} // consume_seqfile
//
// consume_string: run through every k-mer in the given string, & hash it.
@@ -156,13 +154,12 @@ consume_fasta(
unsigned int Hashtable::consume_string(const std::string &s)
{
- const char * sp = s.c_str();
unsigned int n_consumed = 0;
- KmerIterator kmers(sp, _ksize);
+ KmerHashIteratorPtr kmers = new_kmer_iterator(s);
- while(!kmers.done()) {
- HashIntoType kmer = kmers.next();
+ while(!kmers->done()) {
+ HashIntoType kmer = kmers->next();
count(kmer);
n_consumed++;
@@ -211,7 +208,7 @@ void Hashtable::get_median_count(const std::string &s,
bool Hashtable::median_at_least(const std::string &s,
unsigned int cutoff)
{
- KmerIterator kmers(s.c_str(), _ksize);
+ KmerHashIteratorPtr kmers = new_kmer_iterator(s);
unsigned int min_req = 0.5 + float(s.size() - _ksize + 1) / 2;
unsigned int num_cutoff_kmers = 0;
@@ -219,7 +216,7 @@ bool Hashtable::median_at_least(const std::string &s,
// accumulate at least min_req worth of counts before checking to see
// if we have enough high-abundance k-mers to indicate success.
for (unsigned int i = 0; i < min_req; ++i) {
- HashIntoType kmer = kmers.next();
+ HashIntoType kmer = kmers->next();
if (this->get_count(kmer) >= cutoff) {
++num_cutoff_kmers;
}
@@ -229,8 +226,8 @@ bool Hashtable::median_at_least(const std::string &s,
if (num_cutoff_kmers >= min_req) {
return true;
}
- while(!kmers.done()) {
- HashIntoType kmer = kmers.next();
+ while(!kmers->done()) {
+ HashIntoType kmer = kmers->next();
if (this->get_count(kmer) >= cutoff) {
++num_cutoff_kmers;
if (num_cutoff_kmers >= min_req) {
@@ -241,459 +238,115 @@ bool Hashtable::median_at_least(const std::string &s,
return false;
}
-void Hashtable::save_tagset(std::string outfilename)
+void Hashtable::get_kmers(const std::string &s,
+ std::vector<std::string> &kmers_vec) const
{
- ofstream outfile(outfilename.c_str(), ios::binary);
- const size_t tagset_size = n_tags();
- unsigned int save_ksize = _ksize;
-
- HashIntoType * buf = new HashIntoType[tagset_size];
-
- outfile.write(SAVED_SIGNATURE, 4);
- unsigned char version = SAVED_FORMAT_VERSION;
- outfile.write((const char *) &version, 1);
-
- unsigned char ht_type = SAVED_TAGS;
- outfile.write((const char *) &ht_type, 1);
-
- outfile.write((const char *) &save_ksize, sizeof(save_ksize));
- outfile.write((const char *) &tagset_size, sizeof(tagset_size));
- outfile.write((const char *) &_tag_density, sizeof(_tag_density));
-
- unsigned int i = 0;
- for (SeenSet::iterator pi = all_tags.begin(); pi != all_tags.end();
- ++pi, i++) {
- buf[i] = *pi;
+ if (s.length() < _ksize) {
+ return;
}
-
- outfile.write((const char *) buf, sizeof(HashIntoType) * tagset_size);
- if (outfile.fail()) {
- delete[] buf;
- throw khmer_file_exception(strerror(errno));
+ for (unsigned int i = 0; i < s.length() - _ksize + 1; i++) {
+ std::string sub = s.substr(i, _ksize);
+ kmers_vec.push_back(sub);
}
- outfile.close();
-
- delete[] buf;
}
-void Hashtable::load_tagset(std::string infilename, bool clear_tags)
-{
- ifstream infile;
-
- // configure ifstream to raise exceptions for everything.
- infile.exceptions(std::ifstream::failbit | std::ifstream::badbit |
- std::ifstream::eofbit);
-
- try {
- infile.open(infilename.c_str(), ios::binary);
- } catch (std::ifstream::failure &e) {
- std::string err;
- if (!(infile.is_open())) {
- err = "Cannot open tagset file: " + infilename;
- } else {
- err = "Unknown error in opening file: " + infilename;
- }
- throw khmer_file_exception(err);
- }
-
- if (clear_tags) {
- all_tags.clear();
- }
-
- unsigned char version, ht_type;
- unsigned int save_ksize = 0;
-
- size_t tagset_size = 0;
- HashIntoType * buf = NULL;
-
- try {
- char signature[4];
- infile.read(signature, 4);
- infile.read((char *) &version, 1);
- infile.read((char *) &ht_type, 1);
- if (!(std::string(signature, 4) == SAVED_SIGNATURE)) {
- std::ostringstream err;
- err << "Incorrect file signature 0x";
- for(size_t i=0; i < 4; ++i) {
- err << std::hex << (int) signature[i];
- }
- err << " while reading tagset from " << infilename
- << "; should be " << SAVED_SIGNATURE;
- throw khmer_file_exception(err.str());
- } else if (!(version == SAVED_FORMAT_VERSION)) {
- std::ostringstream err;
- err << "Incorrect file format version " << (int) version
- << " while reading tagset from " << infilename
- << "; should be " << (int) SAVED_FORMAT_VERSION;
- throw khmer_file_exception(err.str());
- } else if (!(ht_type == SAVED_TAGS)) {
- std::ostringstream err;
- err << "Incorrect file format type " << (int) ht_type
- << " while reading tagset from " << infilename;
- throw khmer_file_exception(err.str());
- }
-
- infile.read((char *) &save_ksize, sizeof(save_ksize));
- if (!(save_ksize == _ksize)) {
- std::ostringstream err;
- err << "Incorrect k-mer size " << save_ksize
- << " while reading tagset from " << infilename;
- throw khmer_file_exception(err.str());
- }
- infile.read((char *) &tagset_size, sizeof(tagset_size));
- infile.read((char *) &_tag_density, sizeof(_tag_density));
-
- buf = new HashIntoType[tagset_size];
-
- infile.read((char *) buf, sizeof(HashIntoType) * tagset_size);
-
- for (unsigned int i = 0; i < tagset_size; i++) {
- all_tags.insert(buf[i]);
- }
+void Hashtable::get_kmer_hashes(const std::string &s,
+ std::vector<HashIntoType> &kmers_vec) const
+{
+ KmerHashIteratorPtr kmers = new_kmer_iterator(s);
- delete[] buf;
- } catch (std::ifstream::failure &e) {
- std::string err = "Error reading data from: " + infilename;
- if (buf != NULL) {
- delete[] buf;
- }
- throw khmer_file_exception(err);
+ while(!kmers->done()) {
+ HashIntoType kmer = kmers->next();
+ kmers_vec.push_back(kmer);
}
}
-void Hashtable::consume_sequence_and_tag(const std::string& seq,
- unsigned long long& n_consumed,
- SeenSet * found_tags)
-{
- bool kmer_tagged;
-
- KmerIterator kmers(seq.c_str(), _ksize);
- HashIntoType kmer;
-
- unsigned int since = _tag_density / 2 + 1;
-
- while(!kmers.done()) {
- kmer = kmers.next();
- bool is_new_kmer;
-
- // Set the bits for the kmer in the various hashtables,
- // and report on whether or not they had already been set.
- // This is probably better than first testing and then setting the bits,
- // as a failed test essentially results in doing the same amount of work
- // twice.
- if ((is_new_kmer = test_and_set_bits( kmer ))) {
- ++n_consumed;
- }
-#if (1)
- if (is_new_kmer) {
- ++since;
- } else {
- ACQUIRE_ALL_TAGS_SPIN_LOCK
- kmer_tagged = set_contains(all_tags, kmer);
- RELEASE_ALL_TAGS_SPIN_LOCK
- if (kmer_tagged) {
- since = 1;
- if (found_tags) {
- found_tags->insert(kmer);
- }
- } else {
- ++since;
- }
- }
-#else
- if (!is_new_kmer && set_contains(all_tags, kmer)) {
- since = 1;
- if (found_tags) {
- found_tags->insert(kmer);
- }
- } else {
- since++;
- }
-#endif
-
- if (since >= _tag_density) {
- ACQUIRE_ALL_TAGS_SPIN_LOCK
- all_tags.insert(kmer);
- RELEASE_ALL_TAGS_SPIN_LOCK
- if (found_tags) {
- found_tags->insert(kmer);
- }
- since = 1;
- }
-
- } // iteration over kmers
+void Hashtable::get_kmer_hashes_as_hashset(const std::string &s,
+ SeenSet& hashes) const
+{
+ KmerHashIteratorPtr kmers = new_kmer_iterator(s);
- if (since >= _tag_density/2 - 1) {
- ACQUIRE_ALL_TAGS_SPIN_LOCK
- all_tags.insert(kmer); // insert the last k-mer, too.
- RELEASE_ALL_TAGS_SPIN_LOCK
- if (found_tags) {
- found_tags->insert(kmer);
- }
+ while(!kmers->done()) {
+ HashIntoType kmer = kmers->next();
+ hashes.insert(kmer);
}
}
-//
-// consume_fasta_and_tag: consume a FASTA file of reads, tagging reads every
-// so often.
-//
-// TODO? Inline in header.
-void
-Hashtable::
-consume_fasta_and_tag(
- std:: string const &filename,
- unsigned int &total_reads, unsigned long long &n_consumed
-)
+void Hashtable::get_kmer_counts(const std::string &s,
+ std::vector<BoundedCounterType> &counts) const
{
- IParser * parser =
- IParser::get_parser( filename );
-
- consume_fasta_and_tag(
- parser,
- total_reads, n_consumed
- );
+ KmerHashIteratorPtr kmers = new_kmer_iterator(s);
- delete parser;
+ while(!kmers->done()) {
+ HashIntoType kmer = kmers->next();
+ BoundedCounterType c = this->get_count(kmer);
+ counts.push_back(c);
+ }
}
-void
-Hashtable::
-consume_fasta_and_tag(
- read_parsers:: IParser * parser,
- unsigned int &total_reads, unsigned long long &n_consumed
-)
+BoundedCounterType Hashtable::get_min_count(const std::string &s)
{
- Read read;
+ KmerHashIteratorPtr kmers = new_kmer_iterator(s);
- // TODO? Delete the following assignments.
- total_reads = 0;
- n_consumed = 0;
+ BoundedCounterType min_count = MAX_KCOUNT;
- // Iterate through the reads and consume their k-mers.
- while (!parser->is_complete( )) {
+ while(!kmers->done()) {
+ HashIntoType kmer = kmers->next();
- try {
- read = parser->get_next_read( );
- } catch (NoMoreReadsAvailable &e) {
- // Bail out if this error is raised
- break;
- }
-
- if (check_and_normalize_read( read.sequence )) {
- unsigned long long this_n_consumed = 0;
- consume_sequence_and_tag( read.sequence, this_n_consumed );
+ BoundedCounterType count = this->get_count(kmer);
- __sync_add_and_fetch( &n_consumed, this_n_consumed );
- __sync_add_and_fetch( &total_reads, 1 );
+ if (this->get_count(kmer) < min_count) {
+ min_count = count;
}
- } // while reads left for parser
-
+ }
+ return min_count;
}
-//
-// consume_fasta_and_tag_with_stoptags: consume a FASTA file of reads,
-// tagging reads every so often. Do not insert matches to stoptags,
-// and join the tags across those gaps.
-//
-
-void Hashtable::consume_fasta_and_tag_with_stoptags(const std::string &filename,
- unsigned int &total_reads,
- unsigned long long &n_consumed)
+BoundedCounterType Hashtable::get_max_count(const std::string &s)
{
- total_reads = 0;
- n_consumed = 0;
-
- IParser* parser = IParser::get_parser(filename.c_str());
- Read read;
-
- string seq = "";
-
- SeenSet read_tags;
-
- //
- // iterate through the FASTA file & consume the reads.
- //
-
- while(!parser->is_complete()) {
- try {
- read = parser->get_next_read();
- } catch (NoMoreReadsAvailable &exc) {
- break;
- }
- seq = read.sequence;
+ BoundedCounterType max_count = 0;
- read_tags.clear();
-
- // n_consumed += this_n_consumed;
-
- if (check_and_normalize_read(seq)) { // process?
- bool is_new_kmer;
- KmerIterator kmers(seq.c_str(), _ksize);
-
- HashIntoType kmer, last_kmer;
- bool is_first_kmer = true;
-
- unsigned int since = _tag_density / 2 + 1;
- while (!kmers.done()) {
- kmer = kmers.next();
-
- if (!set_contains(stop_tags, kmer)) { // NOT a stop tag... ok.
- is_new_kmer = (bool) !get_count(kmer);
- if (is_new_kmer) {
- count(kmer);
- n_consumed++;
- }
-
- if (!is_new_kmer && set_contains(all_tags, kmer)) {
- read_tags.insert(kmer);
- since = 1;
- } else {
- since++;
- }
-
- if (since >= _tag_density) {
- all_tags.insert(kmer);
- read_tags.insert(kmer);
- since = 1;
- }
- } else { // stop tag! do not insert, but connect.
- // before first tag insertion; insert last kmer.
- if (!is_first_kmer && read_tags.empty()) {
- read_tags.insert(last_kmer);
- all_tags.insert(last_kmer);
- }
-
- since = _tag_density - 1; // insert next kmer, too.
- }
+ KmerHashIteratorPtr kmers = new_kmer_iterator(s);
- last_kmer = kmer;
- is_first_kmer = false;
- }
+ while(!kmers->done()) {
+ HashIntoType kmer = kmers->next();
- if (!set_contains(stop_tags, kmer)) { // NOT a stop tag... ok.
- is_new_kmer = (bool) !get_count(kmer);
- if (is_new_kmer) {
- count(kmer);
- n_consumed++;
- }
+ BoundedCounterType count = this->get_count(kmer);
- if (since >= _tag_density/2 - 1) {
- all_tags.insert(kmer); // insert the last k-mer, too.
- read_tags.insert(kmer);
- }
- }
+ if (count > max_count) {
+ max_count = count;
}
-
- if (read_tags.size() > 1) {
- partition->assign_partition_id(*(read_tags.begin()), read_tags);
- }
-
- // reset the sequence info, increment read number
- total_reads++;
-
}
- delete parser;
+ return max_count;
}
-//
-// divide_tags_into_subsets - take all of the tags in 'all_tags', and
-// divide them into subsets (based on starting tag) of <= given size.
-//
-
-void Hashtable::divide_tags_into_subsets(unsigned int subset_size,
- SeenSet& divvy)
+template<typename SeqIO>
+uint64_t * Hashtable::abundance_distribution(
+ ReadParserPtr<SeqIO>& parser,
+ Hashtable * tracking)
{
- unsigned int i = 0;
+ uint64_t * dist = new uint64_t[MAX_BIGCOUNT + 1];
+ uint64_t i;
- for (SeenSet::const_iterator si = all_tags.begin(); si != all_tags.end();
- ++si) {
- if (i % subset_size == 0) {
- divvy.insert(*si);
- i = 0;
- }
- i++;
+ for (i = 0; i <= MAX_BIGCOUNT; i++) {
+ dist[i] = 0;
}
-}
-//
-// consume_partitioned_fasta: consume a FASTA file of reads
-//
-
-void Hashtable::consume_partitioned_fasta(const std::string &filename,
- unsigned int &total_reads,
- unsigned long long &n_consumed)
-{
- total_reads = 0;
- n_consumed = 0;
-
- IParser* parser = IParser::get_parser(filename.c_str());
Read read;
- string seq = "";
-
- // reset the master subset partition
- delete partition;
- partition = new SubsetPartition(this);
-
- //
- // iterate through the FASTA file & consume the reads.
- //
-
- while(!parser->is_complete()) {
- try {
- read = parser->get_next_read();
- } catch (NoMoreReadsAvailable &exc) {
- break;
- }
- seq = read.sequence;
-
- if (check_and_normalize_read(seq)) {
- // First, figure out what the partition is (if non-zero), and save that.
- PartitionID p = _parse_partition_id(read.name);
-
- // Then consume the sequence
- n_consumed += consume_string(seq); // @CTB why are we doing this?
-
- // Next, compute the tag & set the partition, if nonzero
- HashIntoType kmer = _hash(seq.c_str(), _ksize);
- all_tags.insert(kmer);
- if (p > 0) {
- partition->set_partition_id(kmer, p);
- }
- }
+ string name;
+ string seq;
- // reset the sequence info, increment read number
- total_reads++;
+ // if not, could lead to overflow.
+ if (sizeof(BoundedCounterType) != 2) {
+ delete[] dist;
+ throw khmer_exception();
}
- delete parser;
-}
-
-//
-// consume_fasta: consume a FASTA file of reads
-//
-
-void Hashtable::consume_fasta_and_traverse(const std::string &filename,
- unsigned int radius,
- unsigned int big_threshold,
- unsigned int transfer_threshold,
- CountingHash &counting)
-{
- unsigned long long total_reads = 0;
-
- IParser* parser = IParser::get_parser(filename.c_str());
- Read read;
-
- string seq = "";
-
- //
- // iterate through the FASTA file & consume the reads.
- //
-
- while(!parser->is_complete()) {
+ while(!parser->is_complete()) {
try {
read = parser->get_next_read();
} catch (NoMoreReadsAvailable &exc) {
@@ -701,176 +354,63 @@ void Hashtable::consume_fasta_and_traverse(const std::string &filename,
}
seq = read.sequence;
- if (check_and_normalize_read(seq)) { // process?
- KmerIterator kmers(seq.c_str(), _ksize);
+ if (check_and_normalize_read(seq)) {
+ KmerHashIteratorPtr kmers = new_kmer_iterator(seq);
- bool is_first_kmer = true;
- Kmer kmer(0,0,0);
- while (!kmers.done()) {
- kmer = kmers.next();
+ while(!kmers->done()) {
+ HashIntoType kmer = kmers->next();
- if (set_contains(stop_tags, kmer)) {
- break;
- }
- count(kmer);
- is_first_kmer = false;
- }
+ if (!tracking->get_count(kmer)) {
+ tracking->count(kmer);
- if (!is_first_kmer) { // traverse
- KmerSet keeper;
- unsigned int n = traverse_from_kmer(kmer, radius, keeper);
- if (n >= big_threshold) {
-#if VERBOSE_REPARTITION
- std::cout << "lmp: " << n << "; added: " << stop_tags.size() << "\n";
-#endif // VERBOSE_REPARTITION
- count_and_transfer_to_stoptags(keeper, transfer_threshold, counting);
+ BoundedCounterType n = get_count(kmer);
+ dist[n]++;
}
}
- }
-
- // reset the sequence info, increment read number
- total_reads++;
-
- // run callback, if specified
- if (total_reads % CALLBACK_PERIOD == 0) {
- std::cout << "n reads: " << total_reads << "\n";
- }
- }
- delete parser;
-}
-
-//////////////////////////////////////////////////////////////////////
-// graph stuff
-
-void Hashtable::calc_connected_graph_size(Kmer start,
- unsigned long long& count,
- KmerSet& keeper,
- const unsigned long long threshold,
- bool break_on_circum)
-const
-{
- const BoundedCounterType val = get_count(start);
-
- if (val == 0) {
- return;
- }
-
- Traverser traverser(this);
- KmerQueue node_q;
- node_q.push(start);
-
- // Avoid high-circumference k-mers
- auto filter = [&] (Kmer& n) {
- return !(break_on_circum &&
- traverser.degree(n) > 4);
- };
- while(!node_q.empty()) {
- Kmer node = node_q.front();
- node_q.pop();
-
- // have we already seen me? don't count; exit.
- if (set_contains(keeper, node)) {
- continue;
- }
-
- // is this in stop_tags?
- if (set_contains(stop_tags, node)) {
- continue;
- }
-
- // keep track of both seen kmers, and counts.
- keeper.insert(node);
-
- count += 1;
-
- // are we past the threshold? truncate search.
- if (threshold && count >= threshold) {
- return;
+ name.clear();
+ seq.clear();
}
-
- // otherwise, explore in all directions.
- traverser.traverse_right(node, node_q, filter);
- traverser.traverse_left(node, node_q, filter);
}
+ return dist;
}
-unsigned int Hashtable::kmer_degree(HashIntoType kmer_f, HashIntoType kmer_r)
+template<typename SeqIO>
+uint64_t * Hashtable::abundance_distribution(
+ std::string filename,
+ Hashtable * tracking)
{
- Traverser traverser(this);
- Kmer node = build_kmer(kmer_f, kmer_r);
- return traverser.degree(node);
+ ReadParserPtr<SeqIO> parser = get_parser<SeqIO>(filename);
+ return abundance_distribution(parser, tracking);
}
-unsigned int Hashtable::kmer_degree(const char * kmer_s)
-{
- Traverser traverser(this);
- Kmer node = build_kmer(kmer_s);
- return traverser.degree(node);
-}
-
-void Hashtable::filter_if_present(const std::string &infilename,
- const std::string &outputfile)
+unsigned long Hashtable::trim_on_abundance(
+ std::string seq,
+ BoundedCounterType min_abund)
+const
{
- IParser* parser = IParser::get_parser(infilename);
- ofstream outfile(outputfile.c_str());
+ if (!check_and_normalize_read(seq)) {
+ return 0;
+ }
- unsigned int total_reads = 0;
- unsigned int reads_kept = 0;
-
- Read read;
- string seq;
+ KmerHashIteratorPtr kmers = new_kmer_iterator(seq);
HashIntoType kmer;
- while(!parser->is_complete()) {
- try {
- read = parser->get_next_read();
- } catch (NoMoreReadsAvailable &exc) {
- break;
- }
- seq = read.sequence;
-
- if (check_and_normalize_read(seq)) {
- KmerIterator kmers(seq.c_str(), _ksize);
- bool keep = true;
-
- while (!kmers.done()) {
- kmer = kmers.next();
- if (get_count(kmer)) {
- keep = false;
- break;
- }
- }
-
- if (keep) {
- outfile << ">" << read.name;
- outfile << "\n" << seq << "\n";
- reads_kept++;
- }
-
- total_reads++;
- }
+ if (kmers->done()) {
+ return 0;
}
+ kmer = kmers->next();
- delete parser;
- parser = NULL;
-
- return;
-}
-
-size_t Hashtable::trim_on_stoptags(std::string seq) const
-{
- if (!check_and_normalize_read(seq)) {
+ if (kmers->done() || get_count(kmer) < min_abund) {
return 0;
}
- KmerIterator kmers(seq.c_str(), _ksize);
+ unsigned long i = _ksize;
+ while (!kmers->done()) {
+ kmer = kmers->next();
- size_t i = _ksize - 2;
- while (!kmers.done()) {
- HashIntoType kmer = kmers.next();
- if (set_contains(stop_tags, kmer)) {
+ if (get_count(kmer) < min_abund) {
return i;
}
i++;
@@ -879,434 +419,158 @@ size_t Hashtable::trim_on_stoptags(std::string seq) const
return seq.length();
}
-void Hashtable::traverse_from_tags(unsigned int distance,
- unsigned int threshold,
- unsigned int frequency,
- CountingHash &counting)
-{
- unsigned int i = 0;
- unsigned int n = 0;
- unsigned int n_big = 0;
- KmerSet keeper;
-
-#if VERBOSE_REPARTITION
- std::cout << all_tags.size() << " tags...\n";
-#endif // 0
-
- for (SeenSet::const_iterator si = all_tags.begin(); si != all_tags.end();
- ++si, i++) {
-
- n++;
- Kmer tag = build_kmer(*si);
- unsigned int count = traverse_from_kmer(tag, distance, keeper);
-
- if (count >= threshold) {
- n_big++;
-
- KmerSet::const_iterator ti;
- for (ti = keeper.begin(); ti != keeper.end(); ++ti) {
- if (counting.get_count(*ti) > frequency) {
- stop_tags.insert(*ti);
- } else {
- counting.count(*ti);
- }
- }
-#if VERBOSE_REPARTITION
- std::cout << "traversed from " << n << " tags total; "
- << n_big << " big; " << keeper.size() << "\n";
-#endif // 0
- }
- keeper.clear();
-
- if (n % 100 == 0) {
-#if VERBOSE_REPARTITION
- std::cout << "traversed " << n << " " << n_big << " " <<
- all_tags.size() << " " << stop_tags.size() << "\n";
-#endif // 0
- }
- }
-}
-
-unsigned int Hashtable::traverse_from_kmer(Kmer start,
- unsigned int radius,
- KmerSet &keeper,
- unsigned int max_count)
+unsigned long Hashtable::trim_below_abundance(
+ std::string seq,
+ BoundedCounterType max_abund)
const
{
-
- Traverser traverser(this);
- KmerQueue node_q;
- std::queue<unsigned int> breadth_q;
- unsigned int cur_breadth = 0;
- unsigned int total = 0;
- unsigned int nfound = 0;
-
- auto filter = [&] (Kmer& n) {
- return !set_contains(keeper, n);
- };
-
- node_q.push(start);
- breadth_q.push(0);
-
- while(!node_q.empty()) {
- Kmer node = node_q.front();
- node_q.pop();
-
- unsigned int breadth = breadth_q.front();
- breadth_q.pop();
-
- if (breadth > radius) {
- break;
- }
-
- if (max_count && total > max_count) {
- break;
- }
-
- if (set_contains(keeper, node)) {
- continue;
- }
-
- if (set_contains(stop_tags, node)) {
- continue;
- }
-
- // keep track of seen kmers
- keeper.insert(node);
- total++;
-
- if (!(breadth >= cur_breadth)) { // keep track of watermark, for debugging.
- throw khmer_exception();
- }
- if (breadth > cur_breadth) {
- cur_breadth = breadth;
- }
-
- nfound = traverser.traverse_right(node, node_q, filter);
- for (unsigned int i = 0; i<nfound; ++i) {
- breadth_q.push(breadth + 1);
- }
-
- nfound = traverser.traverse_left(node, node_q, filter);
- for (unsigned int i = 0; i<nfound; ++i) {
- breadth_q.push(breadth + 1);
- }
- }
-
- return total;
-}
-
-void Hashtable::load_stop_tags(std::string infilename, bool clear_tags)
-{
- ifstream infile;
-
- // configure ifstream to raise exceptions for everything.
- infile.exceptions(std::ifstream::failbit | std::ifstream::badbit |
- std::ifstream::eofbit);
-
- try {
- infile.open(infilename.c_str(), ios::binary);
- } catch (std::ifstream::failure &e) {
- std::string err;
- if (!(infile.is_open())) {
- err = "Cannot open stoptags file: " + infilename;
- } else {
- err = "Unknown error in opening file: " + infilename;
- }
- throw khmer_file_exception(err);
- }
-
- if (clear_tags) {
- stop_tags.clear();
- }
-
- unsigned char version, ht_type;
- unsigned int save_ksize = 0;
-
- size_t tagset_size = 0;
-
- try {
- char signature[4];
- infile.read(signature, 4);
- infile.read((char *) &version, 1);
- infile.read((char *) &ht_type, 1);
- if (!(std::string(signature, 4) == SAVED_SIGNATURE)) {
- std::ostringstream err;
- err << "Incorrect file signature 0x";
- for(size_t i=0; i < 4; ++i) {
- err << std::hex << (int) signature[i];
- }
- err << " while reading stoptags from " << infilename
- << "; should be " << SAVED_SIGNATURE;
- throw khmer_file_exception(err.str());
- } else if (!(version == SAVED_FORMAT_VERSION)) {
- std::ostringstream err;
- err << "Incorrect file format version " << (int) version
- << " while reading stoptags from " << infilename
- << "; should be " << (int) SAVED_FORMAT_VERSION;
- throw khmer_file_exception(err.str());
- } else if (!(ht_type == SAVED_STOPTAGS)) {
- std::ostringstream err;
- err << "Incorrect file format type " << (int) ht_type
- << " while reading stoptags from " << infilename;
- throw khmer_file_exception(err.str());
- }
-
- infile.read((char *) &save_ksize, sizeof(save_ksize));
- if (!(save_ksize == _ksize)) {
- std::ostringstream err;
- err << "Incorrect k-mer size " << save_ksize
- << " while reading stoptags from " << infilename;
- throw khmer_file_exception(err.str());
- }
- infile.read((char *) &tagset_size, sizeof(tagset_size));
-
- HashIntoType * buf = new HashIntoType[tagset_size];
-
- infile.read((char *) buf, sizeof(HashIntoType) * tagset_size);
-
- for (unsigned int i = 0; i < tagset_size; i++) {
- stop_tags.insert(buf[i]);
- }
- delete[] buf;
- } catch (std::ifstream::failure &e) {
- std::string err = "Error reading stoptags from: " + infilename;
- throw khmer_file_exception(err);
- }
-}
-
-void Hashtable::save_stop_tags(std::string outfilename)
-{
- ofstream outfile(outfilename.c_str(), ios::binary);
- size_t tagset_size = stop_tags.size();
-
- HashIntoType * buf = new HashIntoType[tagset_size];
-
- outfile.write(SAVED_SIGNATURE, 4);
- unsigned char version = SAVED_FORMAT_VERSION;
- outfile.write((const char *) &version, 1);
-
- unsigned char ht_type = SAVED_STOPTAGS;
- outfile.write((const char *) &ht_type, 1);
-
- unsigned int save_ksize = _ksize;
- outfile.write((const char *) &save_ksize, sizeof(save_ksize));
- outfile.write((const char *) &tagset_size, sizeof(tagset_size));
-
- unsigned int i = 0;
- for (SeenSet::iterator pi = stop_tags.begin(); pi != stop_tags.end();
- ++pi, i++) {
- buf[i] = *pi;
+ if (!check_and_normalize_read(seq)) {
+ return 0;
}
- outfile.write((const char *) buf, sizeof(HashIntoType) * tagset_size);
- outfile.close();
-
- delete[] buf;
-}
+ KmerHashIteratorPtr kmers = new_kmer_iterator(seq);
-void Hashtable::print_stop_tags(std::string infilename)
-{
- ofstream printfile(infilename.c_str());
+ HashIntoType kmer;
- unsigned int i = 0;
- for (SeenSet::iterator pi = stop_tags.begin(); pi != stop_tags.end();
- ++pi, i++) {
- std::string kmer = _revhash(*pi, _ksize);
- printfile << kmer << "\n";
+ if (kmers->done()) {
+ return 0;
}
+ kmer = kmers->next();
- printfile.close();
-}
-
-void Hashtable::print_tagset(std::string infilename)
-{
- ofstream printfile(infilename.c_str());
-
- unsigned int i = 0;
- for (SeenSet::iterator pi = all_tags.begin(); pi != all_tags.end();
- ++pi, i++) {
- std::string kmer = _revhash(*pi, _ksize);
- printfile << kmer << "\n";
+ if (kmers->done() || get_count(kmer) > max_abund) {
+ return 0;
}
- printfile.close();
-}
+ unsigned long i = _ksize;
+ while (!kmers->done()) {
+ kmer = kmers->next();
-unsigned int Hashtable::count_and_transfer_to_stoptags(KmerSet &keeper,
- unsigned int threshold,
- CountingHash &counting)
-{
- unsigned int n_inserted = 0;
-
- KmerSet::const_iterator ti;
- for (ti = keeper.begin(); ti != keeper.end(); ++ti) {
- if (counting.get_count(*ti) >= threshold) {
- stop_tags.insert(*ti);
- n_inserted++;
- } else {
- counting.count(*ti);
+ if (get_count(kmer) > max_abund) {
+ return i;
}
+ i++;
}
- return n_inserted;
+ return seq.length();
}
-void Hashtable::identify_stop_tags_by_position(std::string seq,
- std::vector<unsigned int> &posns)
+std::vector<unsigned int> Hashtable::find_spectral_error_positions(
+ std::string seq,
+ BoundedCounterType max_abund)
const
{
+ std::vector<unsigned int> posns;
if (!check_and_normalize_read(seq)) {
- return;
+ throw khmer_exception("invalid read");
}
- KmerIterator kmers(seq.c_str(), _ksize);
+ KmerHashIteratorPtr kmers = new_kmer_iterator(seq);
- unsigned int i = 0;
- while(!kmers.done()) {
- HashIntoType kmer = kmers.next();
+ HashIntoType kmer = kmers->next();
+ if (kmers->done()) {
+ return posns;
+ }
- if (set_contains(stop_tags, kmer)) {
- posns.push_back(i);
+ // find the first trusted k-mer
+ while (!kmers->done()) {
+ if (get_count(kmer) > max_abund) {
+ break;
}
- i++;
+ kmer = kmers->next();
}
- return;
-}
-
-void Hashtable::extract_unique_paths(std::string seq,
- unsigned int min_length,
- float min_unique_f,
- std::vector<std::string> &results)
-{
- if (seq.size() < min_length) {
- return;
+ if (kmers->done()) {
+ return posns;
}
- float max_seen = 1.0 - min_unique_f;
-
- min_length = min_length - _ksize + 1; // adjust for k-mer size.
-
- KmerIterator kmers(seq.c_str(), _ksize);
-
- std::deque<bool> seen_queue;
- unsigned int n_already_seen = 0;
- unsigned int n_kmers = 0;
-
- // first, put together an array for presence/absence of the k-mer
- // at each given position.
- while (!kmers.done()) {
- HashIntoType kmer = kmers.next();
-
- if (get_count(kmer)) {
- seen_queue.push_back(true);
- n_already_seen++;
- } else {
- seen_queue.push_back(false);
- }
- n_kmers++;
+ // did we bypass some erroneous k-mers? call the last one.
+ if (kmers->get_start_pos() > 0) {
+ // if this is not the *first* k-mer, save.
+ posns.push_back(kmers->get_start_pos() - 1);
}
- // next, run through this array with 'i'.
-
- unsigned int i = 0;
- while (i < n_kmers - min_length) {
- unsigned int seen_counter, j;
-
- // For each starting 'i', count the number of 'seen' k-mers in the
- // given window.
+ while (!kmers->done()) {
+ kmer = kmers->next();
+ if (get_count(kmer) <= max_abund) { // error!
+ posns.push_back(kmers->get_end_pos() - 1);
- // yes, inefficient n^2 algorithm. sue me.
- for (seen_counter = 0, j = 0; j < min_length; j++) {
- if (seen_queue[i + j]) {
- seen_counter++;
- }
- }
-
- // If the fraction seen is small enough to be interesting, suggesting
- // that this, in fact, a "new" window -- extend until it isn't, and
- // then extract.
-
- if (!(j == min_length)) {
- throw khmer_exception();
- }
- if ( ((float)seen_counter / (float) j) <= max_seen) {
- unsigned int start = i;
-
- // extend the window until the end of the sequence...
- while ((start + min_length) < n_kmers) {
- if (seen_queue[start]) {
- seen_counter--;
- }
- if (seen_queue[start + min_length]) {
- seen_counter++;
- }
- start++;
-
- // ...or until we've seen too many of the k-mers.
- if (((float)seen_counter / (float) min_length) > max_seen) {
+ // find next good
+ while (!kmers->done()) {
+ kmer = kmers->next();
+ if (get_count(kmer) > max_abund) { // a good stretch again.
break;
}
}
-
- // adjust for ending point.
- if (start + min_length == n_kmers) { // potentially decrement twice at end
- if (((float)seen_counter / (float) min_length) > max_seen) {
- start--;
- }
- start--;
- } else {
- start -= 2;
- }
-
- // ...and now extract the relevant portion of the sequence, and adjust
- // starting pos'n.
- results.push_back(seq.substr(i, start + min_length + _ksize - i));
-
- i = start + min_length + 1;
- } else {
- i++;
}
}
-}
+ return posns;
+}
-void Hashtable::get_kmers(const std::string &s,
- std::vector<std::string> &kmers_vec) const
+class MurmurKmerHashIterator : public KmerHashIterator
{
- if (s.length() < _ksize) {
- return;
- }
- for (unsigned int i = 0; i < s.length() - _ksize + 1; i++) {
- std::string sub = s.substr(i, i + _ksize);
- kmers_vec.push_back(sub);
- }
-}
+ const char * _seq;
+ const char _ksize;
+ unsigned int index;
+ unsigned int length;
+ bool _initialized;
+public:
+ MurmurKmerHashIterator(const char * seq, unsigned char k) :
+ _seq(seq), _ksize(k), index(0), _initialized(false) {
+ length = strlen(_seq);
+ };
+ HashIntoType first() { _initialized = true; return next(); }
-void Hashtable::get_kmer_hashes(const std::string &s,
- std::vector<HashIntoType> &kmers_vec) const
-{
- KmerIterator kmers(s.c_str(), _ksize);
+ HashIntoType next() {
+ if (!_initialized) { _initialized = true; }
- while(!kmers.done()) {
- HashIntoType kmer = kmers.next();
- kmers_vec.push_back(kmer);
- }
-}
+ if (done()) {
+ throw khmer_exception("past end of iterator");
+ }
+ std::string kmer;
+ kmer.assign(_seq + index, _ksize);
+ index += 1;
+ return _hash_murmur(kmer, _ksize);
+ }
-void Hashtable::get_kmer_counts(const std::string &s,
- std::vector<BoundedCounterType> &counts) const
-{
- KmerIterator kmers(s.c_str(), _ksize);
+ bool done() const {
+ return (index + _ksize > length);
+ }
- while(!kmers.done()) {
- HashIntoType kmer = kmers.next();
- BoundedCounterType c = this->get_count(kmer);
- counts.push_back(c);
+ unsigned int get_start_pos() const {
+ if (!_initialized) { return 0; }
+ return index - 1;
+ }
+ unsigned int get_end_pos() const {
+ if (!_initialized) { return _ksize; }
+ return index + _ksize - 1;
}
+};
+
+KmerHashIteratorPtr Counttable::new_kmer_iterator(const char * sp) const {
+ KmerHashIterator * ki = new MurmurKmerHashIterator(sp, _ksize);
+ return unique_ptr<KmerHashIterator>(ki);
}
-// vim: set sts=2 sw=2:
+template void Hashtable::consume_seqfile<FastxReader>(
+ std::string const &filename,
+ unsigned int &total_reads,
+ unsigned long long &n_consumed
+);
+template void Hashtable::consume_seqfile<FastxReader>(
+ ReadParserPtr<FastxReader>& parser,
+ unsigned int &total_reads,
+ unsigned long long &n_consumed
+);
+template uint64_t * Hashtable::abundance_distribution<FastxReader>(
+ ReadParserPtr<FastxReader>& parser,
+ Hashtable * tracking
+);
+template uint64_t * Hashtable::abundance_distribution<FastxReader>(
+ std::string filename,
+ Hashtable * tracking
+);
+
+} // namespace khmer
diff --git a/lib/hashtable.hh b/lib/hashtable.hh
index 22d8e84..b8b8a04 100644
--- a/lib/hashtable.hh
+++ b/lib/hashtable.hh
@@ -1,7 +1,7 @@
/*
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2010-2015, Michigan State University.
-Copyright (C) 2015, The Regents of the University of California.
+Copyright (C) 2015-2016, The Regents of the University of California.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
@@ -38,7 +38,6 @@ Contact: khmer-project at idyll.org
#ifndef HASHTABLE_HH
#define HASHTABLE_HH
-
#include <stddef.h>
#include <stdint.h>
#include <string.h>
@@ -47,54 +46,45 @@ Contact: khmer-project at idyll.org
#include <list>
#include <map>
#include <queue>
-#include <queue>
#include <set>
#include <string>
#include <vector>
+#include <memory>
+#include "MurmurHash3.h"
#include "khmer.hh"
#include "khmer_exception.hh"
#include "kmer_hash.hh"
#include "read_parsers.hh"
-#include "traversal.hh"
+#include "storage.hh"
#include "subset.hh"
-namespace khmer
-{
-class CountingHash;
-class Hashtable;
+using namespace std;
-namespace read_parsers
+namespace khmer
{
-struct IParser;
-} // namespace read_parsers
-} // namespace khmer
-
-#define MAX_KEEPER_SIZE int(1e6)
-
-#define next_f(kmer_f, ch) ((((kmer_f) << 2) & bitmask) | (twobit_repr(ch)))
-#define next_r(kmer_r, ch) (((kmer_r) >> 2) | (twobit_comp(ch) << rc_left_shift))
-
-#define prev_f(kmer_f, ch) ((kmer_f) >> 2 | twobit_repr(ch) << rc_left_shift)
-#define prev_r(kmer_r, ch) ((((kmer_r) << 2) & bitmask) | (twobit_comp(ch)))
-
-#define set_contains(s, e) ((s).find(e) != (s).end())
+ namespace read_parsers
+ {
+ template<typename SeqIO> class ReadParser;
+ class FastxReader;
+ }
+}
#define CALLBACK_PERIOD 100000
namespace khmer
{
+typedef std::unique_ptr<KmerHashIterator> KmerHashIteratorPtr;
+
class Hashtable: public
KmerFactory // Base class implementation of a Bloom ht.
{
friend class SubsetPartition;
friend class LabelHash;
- friend class Traverser;
protected:
- unsigned int _tag_density;
-
+ Storage * store;
unsigned int _max_count;
unsigned int _max_bigcount;
@@ -102,23 +92,17 @@ protected:
HashIntoType bitmask;
unsigned int _nbits_sub_1;
- explicit Hashtable( WordLength ksize )
- : KmerFactory( ksize ),
+ explicit Hashtable( WordLength ksize, Storage * s)
+ : KmerFactory( ksize ), store(s),
_max_count( MAX_KCOUNT ),
_max_bigcount( MAX_BIGCOUNT )
{
- _tag_density = DEFAULT_TAG_DENSITY;
- if (!(_tag_density % 2 == 0)) {
- throw khmer_exception();
- }
_init_bitstuff();
- partition = new SubsetPartition(this);
- _all_tags_spin_lock = 0;
}
virtual ~Hashtable( )
{
- delete partition;
+ delete store;
}
void _init_bitstuff()
@@ -130,57 +114,98 @@ protected:
_nbits_sub_1 = (_ksize*2 - 2);
}
- HashIntoType _next_hash(char ch, HashIntoType &h, HashIntoType &r) const
- {
- // left-shift the previous hash over
- h = h << 2;
-
- // 'or' in the current nt
- h |= twobit_repr(ch);
-
- // mask off the 2 bits we shifted over.
- h &= bitmask;
+ explicit Hashtable(const Hashtable&);
+ Hashtable& operator=(const Hashtable&);
- // now handle reverse complement
- r = r >> 2;
- r |= (twobit_comp(ch) << _nbits_sub_1);
+ virtual KmerHashIteratorPtr new_kmer_iterator(const char * sp) const {
+ KmerHashIterator * ki = new TwoBitKmerHashIterator(sp, _ksize);
+ return unique_ptr<KmerHashIterator>(ki);
+ }
- return uniqify_rc(h, r);
+ virtual KmerHashIteratorPtr new_kmer_iterator(const std::string& s) const {
+ return new_kmer_iterator(s.c_str());
}
- void _clear_all_partitions()
+public:
+ // accessor to get 'k'
+ const WordLength ksize() const
{
- if (partition != NULL) {
- partition->_clear_all_partitions();
- }
+ return _ksize;
}
- uint32_t _all_tags_spin_lock;
+ // various hash functions.
+ inline
+ virtual
+ HashIntoType
+ hash_dna(const char * kmer) const
+ {
+ return _hash(kmer, _ksize);
+ }
- explicit Hashtable(const Hashtable&);
- Hashtable& operator=(const Hashtable&);
+ inline
+ virtual
+ HashIntoType
+ hash_dna_top_strand(const char * kmer) const
+ {
+ HashIntoType f = 0, r = 0;
+ _hash(kmer, _ksize, f, r);
+ return f;
+ }
-public:
- SubsetPartition * partition;
- SeenSet all_tags;
- SeenSet stop_tags;
- SeenSet repart_small_tags;
+ inline
+ virtual
+ HashIntoType
+ hash_dna_bottom_strand(const char * kmer) const
+ {
+ HashIntoType f = 0, r = 0;
+ _hash(kmer, _ksize, f, r);
+ return r;
+ }
- // accessor to get 'k'
- const WordLength ksize() const
+ inline
+ virtual
+ std::string
+ unhash_dna(HashIntoType hashval) const
{
- return _ksize;
+ return _revhash(hashval, _ksize);
}
- virtual void count(const char * kmer) = 0;
- virtual void count(HashIntoType khash) = 0;
+ void count(const char * kmer)
+ {
+ store->add(hash_dna(kmer));
+ }
+ void count(HashIntoType khash)
+ {
+ store->add(khash);
+ }
+ void add(const char * kmer)
+ {
+ store->add(hash_dna(kmer));
+ }
+ void add(HashIntoType khash)
+ {
+ store->add(khash);
+ }
// get the count for the given k-mer.
- virtual const BoundedCounterType get_count(const char * kmer) const = 0;
- virtual const BoundedCounterType get_count(HashIntoType khash) const = 0;
+ const BoundedCounterType get_count(const char * kmer) const
+ {
+ return store->get_count(hash_dna(kmer));
+ }
+ const BoundedCounterType get_count(HashIntoType khash) const
+ {
+ return store->get_count(khash);
+ }
- virtual void save(std::string) = 0;
- virtual void load(std::string) = 0;
+ void save(std::string filename)
+ {
+ store->save(filename, _ksize);
+ }
+ void load(std::string filename)
+ {
+ store->load(filename, _ksize);
+ _init_bitstuff();
+ }
// count every k-mer in the string.
unsigned int consume_string(const std::string &s);
@@ -192,23 +217,32 @@ public:
unsigned int check_and_process_read(std::string &read,
bool &is_valid);
- // Count every k-mer in a FASTA or FASTQ file.
- // Note: Yes, the name 'consume_fasta' is a bit misleading,
- // but the FASTA format is effectively a subset of the FASTQ format
- // and the FASTA portion is what we care about in this case.
- void consume_fasta(
- std::string const &filename,
- unsigned int &total_reads,
- unsigned long long &n_consumed
+ // Count every k-mer in a file containing nucleotide sequences.
+ template<typename SeqIO>
+ void consume_seqfile(
+ std::string const &filename,
+ unsigned int &total_reads,
+ unsigned long long &n_consumed
);
- // Count every k-mer from a stream of FASTA or FASTQ reads,
+
+ // Count every k-mer in a file containing nucleotide sequences,
// using the supplied parser.
- void consume_fasta(
- read_parsers:: IParser * parser,
- unsigned int &total_reads,
- unsigned long long &n_consumed
+ template<typename SeqIO>
+ void consume_seqfile(
+ read_parsers::ReadParserPtr<SeqIO>& parser,
+ unsigned int &total_reads,
+ unsigned long long &n_consumed
);
+ void set_use_bigcount(bool b)
+ {
+ store->set_use_bigcount(b);
+ }
+ bool get_use_bigcount()
+ {
+ return store->get_use_bigcount();
+ }
+
bool median_at_least(const std::string &s,
unsigned int cutoff);
@@ -218,171 +252,131 @@ public:
float &stddev);
// number of unique k-mers
- virtual const HashIntoType n_unique_kmers() const = 0;
-
- // count number of occupied bins
- virtual const HashIntoType n_occupied() const = 0;
-
- // partitioning stuff
- void _validate_pmap()
+ const uint64_t n_unique_kmers() const
{
- if (partition) {
- partition->_validate_pmap();
- }
+ return store->n_unique_kmers();
}
- virtual void save_tagset(std::string);
- virtual void load_tagset(std::string, bool clear_tags=true);
-
- // for debugging/testing purposes only!
- void _set_tag_density(unsigned int d)
- {
- if (!(d % 2 == 0) || !all_tags.empty()) { // must be even and tags must exist
- throw khmer_exception();
- }
- _tag_density = d;
- }
-
- unsigned int _get_tag_density() const
+ // count number of occupied bins
+ const uint64_t n_occupied() const
{
- return _tag_density;
+ return store->n_occupied();
}
- void add_tag(HashIntoType tag)
+ // table information
+ std::vector<uint64_t> get_tablesizes() const
{
- all_tags.insert(tag);
+ return store->get_tablesizes();
}
- void add_stop_tag(HashIntoType tag)
+ const size_t n_tables() const
{
- stop_tags.insert(tag);
+ return store->n_tables();
}
- // Partitioning stuff.
+ // return all k-mer substrings, on the forward strand.
+ void get_kmers(const std::string &s, std::vector<std::string> &kmers)
+ const;
- size_t n_tags() const
- {
- return all_tags.size();
- }
+ // return hash values for all k-mer substrings
+ void get_kmer_hashes(const std::string &s,
+ std::vector<HashIntoType> &kmers) const;
- void divide_tags_into_subsets(unsigned int subset_size, SeenSet& divvy);
+ // return hash values for all k-mer substrings in a SeenSet
+ void get_kmer_hashes_as_hashset(const std::string &s,
+ SeenSet& hashes) const;
- void add_kmer_to_tags(HashIntoType kmer)
- {
- all_tags.insert(kmer);
- }
+ // return counts of all k-mers in this string.
+ void get_kmer_counts(const std::string &s,
+ std::vector<BoundedCounterType> &counts) const;
- void clear_tags()
+ // get access to raw tables.
+ Byte ** get_raw_tables()
{
- all_tags.clear();
+ return store->get_raw_tables();
}
- // Count every k-mer in a FASTA or FASTQ file.
- // Tag certain ones on the connectivity graph.
- void consume_fasta_and_tag(
- std::string const &filename,
- unsigned int &total_reads,
- unsigned long long &n_consumed
- );
-
- // Count every k-mer from a stream of FASTA or FASTQ reads,
- // using the supplied parser.
- // Tag certain ones on the connectivity graph.
- void consume_fasta_and_tag(
- read_parsers:: IParser * parser,
- unsigned int &total_reads,
- unsigned long long &n_consumed
- );
-
- void consume_sequence_and_tag(const std::string& seq,
- unsigned long long& n_consumed,
- SeenSet * new_tags = 0);
-
-
- void consume_fasta_and_tag_with_stoptags(const std::string &filename,
- unsigned int &total_reads,
- unsigned long long &n_consumed);
- void consume_fasta_and_traverse(const std::string &filename,
- unsigned int distance,
- unsigned int big_threshold,
- unsigned int transfer_threshold,
- CountingHash &counting);
-
- void consume_partitioned_fasta(const std::string &filename,
- unsigned int &total_reads,
- unsigned long long &n_consumed);
-
- virtual BoundedCounterType test_and_set_bits(const char * kmer) = 0;
- virtual BoundedCounterType test_and_set_bits(HashIntoType khash) = 0;
-
- virtual std::vector<HashIntoType> get_tablesizes() const = 0;
- virtual const size_t n_tables() const = 0;
-
- void filter_if_present(const std::string &infilename,
- const std::string &outputfilename);
-
- size_t trim_on_stoptags(std::string sequence) const;
-
- void traverse_from_tags(unsigned int distance,
- unsigned int threshold,
- unsigned int num_high_todo,
- CountingHash &counting);
-
- unsigned int traverse_from_kmer(Kmer start,
- unsigned int radius,
- KmerSet &keeper,
- unsigned int max_count = MAX_KEEPER_SIZE)
- const;
+ // find the minimum k-mer count in the given sequence
+ BoundedCounterType get_min_count(const std::string &s);
- unsigned int count_and_transfer_to_stoptags(KmerSet &keeper,
- unsigned int threshold,
- CountingHash &counting);
+ // find the maximum k-mer count in the given sequence
+ BoundedCounterType get_max_count(const std::string &s);
- virtual void print_tagset(std::string);
- virtual void print_stop_tags(std::string);
- virtual void save_stop_tags(std::string);
- void load_stop_tags(std::string filename, bool clear_tags=true);
-
- void identify_stop_tags_by_position(std::string sequence,
- std::vector<unsigned int> &posns)
- const;
-
- void extract_unique_paths(std::string seq,
- unsigned int min_length,
- float min_unique_f,
- std::vector<std::string> &results);
-
- void calc_connected_graph_size(Kmer node,
- unsigned long long& count,
- KmerSet& keeper,
- const unsigned long long threshold=0,
- bool break_on_circum=false) const;
-
- typedef void (*kmer_cb)(const char * k, unsigned int n_reads, void *data);
+ // calculate the abundance distribution of kmers in the given file.
+ template<typename SeqIO>
+ uint64_t * abundance_distribution(
+ read_parsers::ReadParserPtr<SeqIO>& parser,
+ Hashtable * tracking
+ );
+ template<typename SeqIO>
+ uint64_t * abundance_distribution(std::string filename,
+ Hashtable * tracking);
+
+ // return the index of the first position in the sequence with k-mer
+ // abundance below min_abund.
+ unsigned long trim_on_abundance(std::string seq,
+ BoundedCounterType min_abund) const;
+
+ // return the index of the first position in the sequence with k-mer
+ // abundance above max_abund.
+ unsigned long trim_below_abundance(std::string seq,
+ BoundedCounterType max_abund) const;
+
+ // detect likely positions of errors
+ std::vector<unsigned int> find_spectral_error_positions(std::string seq,
+ BoundedCounterType min_abund) const;
+};
+// Hashtable-derived class with ByteStorage.
+class Counttable : public khmer::Hashtable
+{
+public:
+ explicit Counttable(WordLength ksize, std::vector<uint64_t> sizes)
+ : Hashtable(ksize, new ByteStorage(sizes)) { } ;
+
+ inline
+ virtual
+ HashIntoType
+ hash_dna(const char * kmer) const {
+ if (!(strlen(kmer) >= _ksize)) {
+ throw khmer_exception("Supplied kmer string doesn't match the underlying k-size.");
+ }
+ return _hash_murmur(kmer, _ksize);
+ }
- unsigned int kmer_degree(HashIntoType kmer_f, HashIntoType kmer_r);
- unsigned int kmer_degree(const char * kmer_s);
+ inline virtual HashIntoType
+ hash_dna_top_strand(const char * kmer) const {
+ throw khmer_exception("not implemented");
+ }
- // return all k-mer substrings, on the forward strand.
- void get_kmers(const std::string &s, std::vector<std::string> &kmers)
- const;
+ inline virtual HashIntoType
+ hash_dna_bottom_strand(const char * kmer) const {
+ throw khmer_exception("not implemented");
+ }
- // return hash values for all k-mer substrings
- void get_kmer_hashes(const std::string &s,
- std::vector<HashIntoType> &kmers) const;
+ inline virtual std::string
+ unhash_dna(HashIntoType hashval) const {
+ throw khmer_exception("not implemented");
+ }
- // return counts of all k-mers in this string.
- void get_kmer_counts(const std::string &s,
- std::vector<BoundedCounterType> &counts) const;
+ virtual KmerHashIteratorPtr new_kmer_iterator(const char * sp) const;
};
-}
-
+// Hashtable-derived class with NibbleStorage.
+class SmallCounttable : public khmer::Hashtable
+{
+public:
+ explicit SmallCounttable(WordLength ksize, std::vector<uint64_t> sizes)
+ : Hashtable(ksize, new NibbleStorage(sizes)) { } ;
+};
-#define ACQUIRE_ALL_TAGS_SPIN_LOCK \
- while (!__sync_bool_compare_and_swap( &_all_tags_spin_lock, 0, 1 ));
+// Hashtable-derived class with BitStorage.
+class Nodetable : public Hashtable
+{
+public:
+ explicit Nodetable(WordLength ksize, std::vector<uint64_t> sizes)
+ : Hashtable(ksize, new BitStorage(sizes)) { } ;
+};
-#define RELEASE_ALL_TAGS_SPIN_LOCK \
- __sync_bool_compare_and_swap( &_all_tags_spin_lock, 1, 0 );
+}
#endif // HASHTABLE_HH
diff --git a/lib/hllcounter.cc b/lib/hllcounter.cc
index 47abb1c..176c195 100644
--- a/lib/hllcounter.cc
+++ b/lib/hllcounter.cc
@@ -1,7 +1,7 @@
/*
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2014-2015, Michigan State University.
-Copyright (C) 2015, The Regents of the University of California.
+Copyright (C) 2015-2016, The Regents of the University of California.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
@@ -58,6 +58,7 @@ Contact: khmer-project at idyll.org
#define arr_len(a) (a + sizeof a / sizeof a[0])
using namespace khmer;
+using namespace khmer::read_parsers;
std::map<int, std::vector<double> > rawEstimateData;
std::map<int, std::vector<double> > biasData;
@@ -332,7 +333,7 @@ double HLLCounter::_Ep()
return E;
}
-HashIntoType HLLCounter::estimate_cardinality()
+uint64_t HLLCounter::estimate_cardinality()
{
long V = count(this->M.begin(), this->M.end(), 0);
@@ -347,8 +348,8 @@ HashIntoType HLLCounter::estimate_cardinality()
void HLLCounter::add(const std::string &value)
{
- HashIntoType x = khmer::_hash_murmur(value);
- HashIntoType j = x & (this->m - 1);
+ HashIntoType x = khmer::_hash_murmur(value, value.length());
+ uint64_t j = x & (this->m - 1);
this->M[j] = std::max(this->M[j], get_rho(x >> this->p, 64 - this->p));
}
@@ -375,21 +376,20 @@ unsigned int HLLCounter::consume_string(const std::string &inp)
return n_consumed;
}
-void HLLCounter::consume_fasta(
+template<typename SeqIO>
+void HLLCounter::consume_seqfile(
std::string const &filename,
bool stream_records,
unsigned int &total_reads,
unsigned long long &n_consumed)
{
- read_parsers::IParser * parser = read_parsers::IParser::get_parser(filename);
-
- consume_fasta(parser, stream_records, total_reads, n_consumed);
-
- delete parser;
+ ReadParserPtr<SeqIO> parser = get_parser<SeqIO>(filename);
+ consume_seqfile<SeqIO>(parser, stream_records, total_reads, n_consumed);
}
-void HLLCounter::consume_fasta(
- read_parsers::IParser *parser,
+template<typename SeqIO>
+void HLLCounter::consume_seqfile(
+ ReadParserPtr<SeqIO>& parser,
bool stream_records,
unsigned int & total_reads,
unsigned long long & n_consumed)
@@ -429,7 +429,7 @@ void HLLCounter::consume_fasta(
}
if (stream_records) {
- read.write_to(std::cout);
+ read.write_fastx(std::cout);
}
#pragma omp task default(none) firstprivate(read) \
@@ -508,3 +508,16 @@ void HLLCounter::merge(HLLCounter &other)
this->M[i] = std::max(other.M[i], this->M[i]);
}
}
+
+template void HLLCounter::consume_seqfile<FastxReader>(
+ std::string const &,
+ bool,
+ unsigned int &,
+ unsigned long long &
+);
+template void HLLCounter::consume_seqfile<FastxReader>(
+ ReadParserPtr<FastxReader>&,
+ bool,
+ unsigned int &,
+ unsigned long long &
+);
diff --git a/lib/hllcounter.hh b/lib/hllcounter.hh
index 92f450d..8720f6f 100644
--- a/lib/hllcounter.hh
+++ b/lib/hllcounter.hh
@@ -1,7 +1,7 @@
/*
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2014-2015, Michigan State University.
-Copyright (C) 2015, The Regents of the University of California.
+Copyright (C) 2015-2016, The Regents of the University of California.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
@@ -46,15 +46,12 @@ Contact: khmer-project at idyll.org
namespace khmer
{
-namespace read_parsers
-{
-struct IParser;
-} // namespace read_parsers
-} // namespace khmer
-
-namespace khmer
+namespace read_parsers
{
+ template<typename SeqIO> class ReadParser;
+ class FastxReader;
+}
class HLLCounter
{
@@ -64,18 +61,20 @@ public:
void add(const std::string &);
unsigned int consume_string(const std::string &);
- void consume_fasta(std::string const &,
- bool,
- unsigned int &,
- unsigned long long &);
- void consume_fasta(read_parsers::IParser *,
- bool,
- unsigned int &,
- unsigned long long &);
+ template<typename SeqIO>
+ void consume_seqfile(std::string const &,
+ bool,
+ unsigned int &,
+ unsigned long long &);
+ template<typename SeqIO>
+ void consume_seqfile(read_parsers::ReadParserPtr<SeqIO>&,
+ bool,
+ unsigned int &,
+ unsigned long long &);
unsigned int check_and_process_read(std::string &,
bool &);
bool check_and_normalize_read(std::string &) const;
- HashIntoType estimate_cardinality();
+ uint64_t estimate_cardinality();
void merge(HLLCounter &);
virtual ~HLLCounter() {}
diff --git a/lib/khmer.hh b/lib/khmer.hh
index 68cab2b..0dcefe3 100644
--- a/lib/khmer.hh
+++ b/lib/khmer.hh
@@ -1,7 +1,7 @@
/*
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2010-2015, Michigan State University.
-Copyright (C) 2015, The Regents of the University of California.
+Copyright (C) 2015-2016, The Regents of the University of California.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
@@ -72,6 +72,8 @@ private:\
#include <set>
#include <map>
#include <queue>
+#include <list>
+#include <functional>
#include "khmer_exception.hh"
@@ -91,6 +93,11 @@ private:\
# define SAVED_STOPTAGS 4
# define SAVED_SUBSET 5
# define SAVED_LABELSET 6
+# define SAVED_SMALLCOUNT 7
+
+
+# define TRAVERSAL_LEFT 0
+# define TRAVERSAL_RIGHT 1
# define VERBOSE_REPARTITION 0
@@ -99,6 +106,7 @@ private:\
namespace khmer
{
+
// largest number we can count up to, exactly. (8 bytes)
typedef unsigned long long int ExactCounterType;
@@ -135,13 +143,13 @@ PartitionCountDistribution;
// types used in @camillescott's sparse labeling extension
typedef unsigned long long int Label;
-typedef std::multimap<HashIntoType, Label*> TagLabelPtrMap;
+typedef std::multimap<HashIntoType, Label> TagLabelMap;
typedef std::multimap<Label, HashIntoType> LabelTagMap;
-typedef std::pair<HashIntoType, Label*> TagLabelPtrPair;
+typedef std::pair<HashIntoType, Label> TagLabelPair;
typedef std::pair<Label, HashIntoType> LabelTagPair;
-typedef std::set<Label*> LabelPtrSet;
+typedef std::set<Label> LabelSet;
typedef std::set<HashIntoType> TagSet;
-typedef std::map<Label, Label*> LabelPtrMap;
+
template <typename T>
void deallocate_ptr_set(T& s)
@@ -155,6 +163,11 @@ class Kmer;
typedef std::queue<Kmer> KmerQueue;
typedef std::set<Kmer> KmerSet;
+// A function which takes a Kmer and returns true if it
+// is to be filtered / ignored
+typedef std::function<bool (const Kmer&)> KmerFilter;
+typedef std::list<KmerFilter> KmerFilterList;
+typedef std::vector<std::string> StringVector;
}
#endif // KHMER_HH
diff --git a/lib/kmer_filters.cc b/lib/kmer_filters.cc
new file mode 100644
index 0000000..ba65b25
--- /dev/null
+++ b/lib/kmer_filters.cc
@@ -0,0 +1,159 @@
+/*
+This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+Copyright (C) 2015-2016, The Regents of the University of California.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following
+ disclaimer in the documentation and/or other materials provided
+ with the distribution.
+
+ * Neither the name of the Michigan State University nor the names
+ of its contributors may be used to endorse or promote products
+ derived from this software without specific prior written
+ permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+LICENSE (END)
+
+Contact: khmer-project at idyll.org
+*/
+#include <algorithm>
+
+#include "khmer.hh"
+#include "hashtable.hh"
+#include "labelhash.hh"
+#include "kmer_filters.hh"
+
+
+namespace khmer
+{
+
+bool apply_kmer_filters(const Kmer& node, const std::list<KmerFilter>& filters)
+{
+ if (!filters.size()) {
+ return false;
+ }
+
+ for(auto filter : filters) {
+ if (filter(node)) {
+ return true;
+ }
+ }
+
+ return false;
+}
+
+
+KmerFilter get_label_filter(const Label label, const LabelHash * lh)
+{
+ KmerFilter filter = [=] (const Kmer& node) {
+ LabelSet ls;
+ lh->get_tag_labels(node, ls);
+#if DEBUG_FILTERS
+ if (ls.size() == 0) {
+ // this should never happen
+ std::cout << "no labels to jump to!" << std::endl;
+ }
+#endif
+
+ return !set_contains(ls, label);
+
+ };
+
+ return filter;
+}
+
+
+KmerFilter get_simple_label_intersect_filter(const LabelSet& src_labels,
+ const LabelHash * lh,
+ const unsigned int min_cov)
+{
+ auto src_begin = src_labels.begin();
+ auto src_end = src_labels.end();
+ unsigned int src_size = src_labels.size();
+
+ KmerFilter filter = [=] (const Kmer& node) {
+ LabelSet dst_labels;
+ lh->get_tag_labels(node, dst_labels);
+
+ LabelSet intersect;
+ std::set_intersection(src_begin, src_end,
+ dst_labels.begin(), dst_labels.end(),
+ std::inserter(intersect, intersect.begin()));
+
+ if ((intersect.size() == 1)
+ && (dst_labels.size() == 1)
+ && (src_size >= min_cov)) {
+#if DEBUG_FILTERS
+ std::cout << "TIP: " << intersect.size() << ", " <<
+ dst_labels.size() << ", " << src_size << std::endl;
+#endif
+ // putative error / tip
+ return true;
+ } else if (intersect.size() > 0) {
+ // there's at least one spanning read
+ return false;
+ } else {
+ return true;
+ }
+ };
+
+ return filter;
+}
+
+
+KmerFilter get_junction_count_filter(const Kmer& src_node,
+ Countgraph * junctions,
+ const unsigned int min_cov)
+{
+ KmerFilter filter = [=] (const Kmer& dst_node) {
+ unsigned int jc = junctions->get_count(src_node.kmer_u ^ dst_node.kmer_u);
+#if DEBUG_FILTERS
+ std::cout << "Junction Count: " << jc << std::endl;
+#endif
+ return jc < min_cov;
+ };
+
+ return filter;
+}
+
+
+KmerFilter get_stop_bf_filter(const Hashtable * stop_bf)
+{
+ KmerFilter filter = [=] (const Kmer& n) {
+ return stop_bf->get_count(n);
+ };
+ return filter;
+}
+
+
+KmerFilter get_visited_filter(const SeenSet * visited)
+{
+#if DEBUG_FILTERS
+ std::cout << "Create new visited filter with " << visited <<
+ " containing " << visited->size() << " nodes" << std::endl;
+#endif
+ KmerFilter filter = [=] (const Kmer& node) {
+ return set_contains(*visited, node);
+ };
+ return filter;
+}
+
+}
diff --git a/lib/test-Colors.cc b/lib/kmer_filters.hh
similarity index 67%
copy from lib/test-Colors.cc
copy to lib/kmer_filters.hh
index bcafd84..b40b831 100644
--- a/lib/test-Colors.cc
+++ b/lib/kmer_filters.hh
@@ -1,7 +1,6 @@
/*
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-Copyright (C) 2013-2015, Michigan State University.
-Copyright (C) 2015, The Regents of the University of California.
+Copyright (C) 2015-2016, The Regents of the University of California.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
@@ -35,25 +34,38 @@ LICENSE (END)
Contact: khmer-project at idyll.org
*/
+#ifndef FILTER_HH
+#define FILTER_HH
+
+#include <functional>
+
#include "khmer.hh"
-#include "hashtable.hh"
-#include "hashbits.hh"
+#include "kmer_hash.hh"
#include "labelhash.hh"
-#include <iostream>
-using namespace khmer;
-int main()
+namespace khmer
{
- HashIntoType sizes[] = { 100000003, 100000004, 100000007, 10000000011};
- std::vector<HashIntoType> sizes_vec (sizes,
- sizes + sizeof(sizes) / sizeof(HashIntoType) );
- khmer::LabelHash * lh_pointer = new khmer::LabelHash(20, sizes_vec);
- khmer::Hashbits * hb_pointer = (khmer::Hashbits *)lh_pointer;
+class Hashtable;
+class LabelHash;
+
+
+bool apply_kmer_filters(const Kmer& node, const KmerFilterList& filters);
+
+KmerFilter get_label_filter(const Label label, const LabelHash * lh);
+
+KmerFilter get_simple_label_intersect_filter(const LabelSet& src_labels,
+ const LabelHash * lh,
+ const unsigned int min_cov = 5);
+
+KmerFilter get_stop_bf_filter(const Hashtable * stop_bf);
+
+KmerFilter get_visited_filter(const SeenSet * visited);
- std::cout << "lh_pointer n_tags: " << lh_pointer->n_tags() << std::endl;
- std::cout << "hb_pointer n_tags: " << hb_pointer->n_tags() << std::endl;
+KmerFilter get_junction_count_filter(const Kmer& src_node,
+ Countgraph * junctions,
+ const unsigned int min_cov = 2);
- return 0;
}
+#endif
diff --git a/lib/kmer_hash.cc b/lib/kmer_hash.cc
index 03702fb..c94016c 100644
--- a/lib/kmer_hash.cc
+++ b/lib/kmer_hash.cc
@@ -1,7 +1,7 @@
/*
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2010-2015, Michigan State University.
-Copyright (C) 2015, The Regents of the University of California.
+Copyright (C) 2015-2016, The Regents of the University of California.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
@@ -40,6 +40,7 @@ Contact: khmer-project at idyll.org
#include <string.h>
#include <algorithm>
#include <string>
+#include <assert.h>
#include "MurmurHash3.h"
#include "khmer.hh"
@@ -59,10 +60,14 @@ HashIntoType _hash(const char * kmer, const WordLength k,
HashIntoType& _h, HashIntoType& _r)
{
// sizeof(HashIntoType) * 8 bits / 2 bits/base
- if (!(k <= sizeof(HashIntoType)*4) || !(strlen(kmer) >= k)) {
+ if (k > sizeof(HashIntoType)*4) {
throw khmer_exception("Supplied kmer string doesn't match the underlying k-size.");
}
+ if (strlen(kmer) < k) {
+ throw khmer_exception("k-mer is too short to hash.");
+ }
+
HashIntoType h = 0, r = 0;
h |= twobit_repr(kmer[0]);
@@ -104,6 +109,17 @@ HashIntoType _hash_forward(const char * kmer, WordLength k)
return h; // return forward only
}
+HashIntoType _hash(const std::string kmer, const WordLength k)
+{
+ return _hash(kmer.c_str(), k);
+}
+
+HashIntoType _hash(const std::string kmer, const WordLength k,
+ HashIntoType& h, HashIntoType& r)
+{
+ return _hash(kmer.c_str(), k, h, r);
+}
+
//
// _revhash: given an unsigned int, return the associated k-mer.
//
@@ -148,7 +164,7 @@ std::string _revcomp(const std::string& kmer)
complement = 'A';
break;
default:
- throw khmer::khmer_exception("Invalid base in read");
+ complement = kmer[i]; // leave alone.
break;
}
out[ksize - i - 1] = complement;
@@ -156,35 +172,42 @@ std::string _revcomp(const std::string& kmer)
return out;
}
-HashIntoType _hash_murmur(const std::string& kmer)
+HashIntoType _hash_murmur(const std::string& kmer, const WordLength k)
{
HashIntoType h = 0;
HashIntoType r = 0;
- return khmer::_hash_murmur(kmer, h, r);
+ return khmer::_hash_murmur(kmer, k, h, r);
}
-HashIntoType _hash_murmur(const std::string& kmer,
+HashIntoType _hash_murmur(const std::string& kmer, const WordLength k,
HashIntoType& h, HashIntoType& r)
{
- HashIntoType out[2];
+ uint64_t out[2];
uint32_t seed = 0;
- MurmurHash3_x64_128((void *)kmer.c_str(), kmer.size(), seed, &out);
+ MurmurHash3_x64_128((void *)kmer.c_str(), k, seed, &out);
h = out[0];
+ assert(kmer.length() == k); // an assumption of the below code
std::string rev = khmer::_revcomp(kmer);
- MurmurHash3_x64_128((void *)rev.c_str(), rev.size(), seed, &out);
+ if (rev == kmer) {
+ // self complement kmer, can't use bitwise XOR
+ r = out[0];
+ return h;
+ }
+
+ MurmurHash3_x64_128((void *)rev.c_str(), k, seed, &out);
r = out[0];
return h ^ r;
}
-HashIntoType _hash_murmur_forward(const std::string& kmer)
+HashIntoType _hash_murmur_forward(const std::string& kmer, const WordLength k)
{
HashIntoType h = 0;
HashIntoType r = 0;
- khmer::_hash_murmur(kmer, h, r);
+ khmer::_hash_murmur(kmer, k, h, r);
return h;
}
@@ -199,7 +222,7 @@ KmerIterator::KmerIterator(const char * seq,
_nbits_sub_1 = (_ksize*2 - 2);
index = _ksize - 1;
- length = strlen(seq);
+ length = strlen(_seq);
_kmer_f = 0;
_kmer_r = 0;
diff --git a/lib/kmer_hash.hh b/lib/kmer_hash.hh
index f601cdc..caf98a6 100644
--- a/lib/kmer_hash.hh
+++ b/lib/kmer_hash.hh
@@ -1,7 +1,7 @@
/*
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2010-2015, Michigan State University.
-Copyright (C) 2015, The Regents of the University of California.
+Copyright (C) 2015-2016, The Regents of the University of California.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
@@ -100,15 +100,20 @@ namespace khmer
HashIntoType _hash(const char * kmer, const WordLength k);
HashIntoType _hash(const char * kmer, const WordLength k,
HashIntoType& h, HashIntoType& r);
+HashIntoType _hash(const std::string kmer, const WordLength k);
+HashIntoType _hash(const std::string kmer, const WordLength k,
+ HashIntoType& h, HashIntoType& r);
HashIntoType _hash_forward(const char * kmer, WordLength k);
std::string _revhash(HashIntoType hash, WordLength k);
+std::string _revcomp(const std::string& kmer);
// two-way hash functions, MurmurHash3.
-HashIntoType _hash_murmur(const std::string& kmer);
-HashIntoType _hash_murmur(const std::string& kmer,
+HashIntoType _hash_murmur(const std::string& kmer, const WordLength k);
+HashIntoType _hash_murmur(const std::string& kmer, const WordLength k,
HashIntoType& h, HashIntoType& r);
-HashIntoType _hash_murmur_forward(const std::string& kmer);
+HashIntoType _hash_murmur_forward(const std::string& kmer,
+ const WordLength k);
/**
* \class Kmer
@@ -149,12 +154,26 @@ public:
kmer_u = u;
}
+ /** @param[in] s DNA k-mer
+ @param[in] ksize k-mer size
+ */
+ Kmer(const std::string s, WordLength ksize)
+ {
+ kmer_u = _hash(s.c_str(), ksize, kmer_f, kmer_r);
+ }
+
/// @warning The default constructor builds an invalid k-mer.
Kmer()
{
kmer_f = kmer_r = kmer_u = 0;
}
+ void set_from_unique_hash(HashIntoType h, WordLength ksize)
+ {
+ std::string s = _revhash(h, ksize);
+ kmer_u = _hash(s.c_str(), ksize, kmer_f, kmer_r);
+ }
+
/// Allows complete backwards compatibility
operator HashIntoType() const
{
@@ -166,13 +185,32 @@ public:
return kmer_u < other.kmer_u;
}
- std::string get_string_rep(WordLength K)
+ std::string get_string_rep(WordLength K) const
{
return _revhash(kmer_u, K);
}
+ char get_last_base() const
+ {
+ return revtwobit_repr(kmer_f & 3);
+ }
+
+ std::string repr(WordLength K) const
+ {
+ std::string s = "<Us=" + _revhash(kmer_u, K) + ", Fs=" +
+ _revhash(kmer_f, K) + ", Rs=" + _revhash(kmer_r, K) + ">";
+ //", U=" + std::to_string(kmer_u) + ", F=" + std::to_string(kmer_f) +
+ //", R=" + std::to_string(kmer_r) + ">";
+ return s;
+ }
+
+ bool is_forward() const
+ {
+ return kmer_f == kmer_u;
+ }
};
+
/**
* \class KmerFactory
*
@@ -200,12 +238,13 @@ protected:
public:
- KmerFactory(WordLength K): _ksize(K) {}
+ explicit KmerFactory(WordLength K): _ksize(K) {}
/** @param[in] kmer_u Uniqified hash value.
* @return A complete Kmer object.
*/
Kmer build_kmer(HashIntoType kmer_u)
+ const
{
HashIntoType kmer_f, kmer_r;
std:: string kmer_s = _revhash(kmer_u, _ksize);
@@ -220,6 +259,7 @@ public:
* @return A complete Kmer object.
*/
Kmer build_kmer(HashIntoType kmer_f, HashIntoType kmer_r)
+ const
{
HashIntoType kmer_u = uniqify_rc(kmer_f, kmer_r);
return Kmer(kmer_f, kmer_r, kmer_u);
@@ -231,7 +271,7 @@ public:
* @param[in] kmer_s String representation of a k-mer.
* @return A complete Kmer object hashed from the given string.
*/
- Kmer build_kmer(std::string kmer_s)
+ Kmer build_kmer(std::string kmer_s) const
{
HashIntoType kmer_f, kmer_r, kmer_u;
kmer_u = _hash(kmer_s.c_str(), _ksize, kmer_f, kmer_r);
@@ -244,7 +284,7 @@ public:
* @param[in] kmer_c The character array representation of a k-mer.
* @return A complete Kmer object hashed from the given char array.
*/
- Kmer build_kmer(const char * kmer_c)
+ Kmer build_kmer(const char * kmer_c) const
{
HashIntoType kmer_f, kmer_r, kmer_u;
kmer_u = _hash(kmer_c, _ksize, kmer_f, kmer_r);
@@ -309,7 +349,7 @@ public:
}
/// @return Whether or not the iterator has completed.
- bool done()
+ bool done() const
{
return index >= length;
}
@@ -325,6 +365,46 @@ public:
}
}; // class KmerIterator
+//
+// KmerHashIterator - analogous to KmerIterator classes, but returns only
+// HashIntoType hashes, not full Kmer objects. This supports irreversible
+// hashing.
+//
+
+class KmerHashIterator {
+public:
+ virtual HashIntoType first() = 0;
+ virtual HashIntoType next() = 0;
+ virtual bool done() const = 0;
+ virtual unsigned int get_start_pos() const = 0;
+ virtual unsigned int get_end_pos() const = 0;
+ virtual ~KmerHashIterator() { };
+};
+
+// TwoBitKmerHashIterator -- just wrap KmerIterator.
+
+class TwoBitKmerHashIterator : public KmerHashIterator {
+protected:
+ KmerIterator iter;
+public:
+ TwoBitKmerHashIterator(const char * seq, WordLength k) :
+ iter(seq, k) { } ;
+
+ HashIntoType first() { return iter.first(); }
+
+ HashIntoType next() { return iter.next(); }
+
+ bool done() const { return iter.done(); }
+
+ virtual unsigned int get_start_pos() const {
+ return iter.get_start_pos();
+ }
+
+ virtual unsigned int get_end_pos() const {
+ return iter.get_end_pos();
+ }
+};
+
}
#endif // KMER_HASH_HH
diff --git a/lib/labelhash.cc b/lib/labelhash.cc
index 23d88d8..3fad2ab 100644
--- a/lib/labelhash.cc
+++ b/lib/labelhash.cc
@@ -1,7 +1,7 @@
/*
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2013-2015, Michigan State University.
-Copyright (C) 2015, The Regents of the University of California.
+Copyright (C) 2015-2016, The Regents of the University of California.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
@@ -41,8 +41,7 @@ Contact: khmer-project at idyll.org
#include <sstream> // IWYU pragma: keep
#include <set>
-#include "hashbits.hh"
-#include "hashtable.hh"
+#include "hashgraph.hh"
#include "khmer_exception.hh"
#include "labelhash.hh"
#include "read_parsers.hh"
@@ -53,38 +52,39 @@ Contact: khmer-project at idyll.org
#define LABEL_DBG 0
#define printdbg(m) if(LABEL_DBG) std::cout << #m << std::endl;
+#define DEBUG 0
+
using namespace std;
using namespace khmer;
-using namespace khmer:: read_parsers;
+using namespace khmer::read_parsers;
+
+namespace khmer
+{
/*
* @camillescott
- * Might be time for a refactor: could do a general consume_fasta
+ * Might be time for a refactor: could do a general consume_seqfile
* function which accepts a consume_sequence function pointer as a parameter
*/
-void
-LabelHash::consume_fasta_and_tag_with_labels(
+template<typename SeqIO>
+void LabelHash::consume_seqfile_and_tag_with_labels(
std:: string const &filename,
unsigned int &total_reads, unsigned long long &n_consumed,
CallbackFn callback, void * callback_data
)
{
- IParser * parser =
- IParser::get_parser( filename );
-
- consume_fasta_and_tag_with_labels(
+ ReadParserPtr<SeqIO> parser = get_parser<SeqIO>(filename);
+ consume_seqfile_and_tag_with_labels<SeqIO>(
parser,
total_reads, n_consumed,
callback, callback_data
);
-
- delete parser;
}
-void
-LabelHash::consume_fasta_and_tag_with_labels(
- read_parsers:: IParser * parser,
+template<typename SeqIO>
+void LabelHash::consume_seqfile_and_tag_with_labels(
+ ReadParserPtr<SeqIO>& parser,
unsigned int &total_reads, unsigned long long &n_consumed,
CallbackFn callback, void * callback_data
)
@@ -98,9 +98,8 @@ LabelHash::consume_fasta_and_tag_with_labels(
total_reads = 0;
n_consumed = 0;
- Label _tag_label = 0;
+ Label the_label = 0;
- Label * the_label;
// Iterate through the reads and consume their k-mers.
while (!parser->is_complete( )) {
try {
@@ -112,11 +111,10 @@ LabelHash::consume_fasta_and_tag_with_labels(
if (graph->check_and_normalize_read( read.sequence )) {
// TODO: make threadsafe!
unsigned long long this_n_consumed = 0;
- the_label = check_and_allocate_label(_tag_label);
consume_sequence_and_tag_with_labels( read.sequence,
this_n_consumed,
- *the_label );
- _tag_label++;
+ the_label );
+ the_label++;
#if (0) // Note: Used with callback - currently disabled.
n_consumed_LOCAL = __sync_add_and_fetch( &n_consumed, this_n_consumed );
@@ -133,7 +131,7 @@ LabelHash::consume_fasta_and_tag_with_labels(
if (total_reads_TL % CALLBACK_PERIOD == 0 && callback) {
std::cout << "n tags: " << graph->all_tags.size() << "\n";
try {
- callback("consume_fasta_and_tag_with_labels", callback_data,
+ callback("consume_seqfile_and_tag_with_labels", callback_data,
total_reads_TL,
n_consumed);
} catch (...) {
@@ -147,6 +145,7 @@ LabelHash::consume_fasta_and_tag_with_labels(
}
+template<typename SeqIO>
void LabelHash::consume_partitioned_fasta_and_tag_with_labels(
const std::string &filename,
unsigned int &total_reads,
@@ -157,7 +156,7 @@ void LabelHash::consume_partitioned_fasta_and_tag_with_labels(
total_reads = 0;
n_consumed = 0;
- IParser* parser = IParser::get_parser(filename.c_str());
+ ReadParserPtr<SeqIO> parser = get_parser<SeqIO>(filename);
Read read;
std::string seq = "";
@@ -169,7 +168,6 @@ void LabelHash::consume_partitioned_fasta_and_tag_with_labels(
//
// iterate through the FASTA file & consume the reads.
//
- Label * c;
PartitionID p;
while(!parser->is_complete()) {
read = parser->get_next_read();
@@ -180,13 +178,10 @@ void LabelHash::consume_partitioned_fasta_and_tag_with_labels(
// save that.
printdbg(parsing partition id)
p = _parse_partition_id(read.name);
- printdbg(checking label and allocating if necessary) {
- c = check_and_allocate_label(p);
- }
printdbg(consuming sequence and tagging)
consume_sequence_and_tag_with_labels( seq,
n_consumed,
- *c );
+ p );
printdbg(back in consume_partitioned)
}
@@ -199,32 +194,28 @@ void LabelHash::consume_partitioned_fasta_and_tag_with_labels(
callback("consume_partitioned_fasta_and_tag_with_labels", callback_data,
total_reads, n_consumed);
} catch (...) {
- delete parser;
throw;
}
}
}
printdbg(done with while loop in consume_partitioned)
-
- // @cswelcher TODO: check that deallocate LabelPtrMap is correct
- {
- delete parser;
- }
printdbg(deleted parser and exiting)
}
// @cswelcher: double-check -- is it valid to pull the address from a reference?
-void LabelHash::link_tag_and_label(HashIntoType& kmer, Label& kmer_label)
+void LabelHash::link_tag_and_label(const HashIntoType kmer,
+ const Label kmer_label)
{
printdbg(linking tag and label)
- tag_labels.insert(TagLabelPtrPair(kmer, &kmer_label));
- label_tag_ptrs.insert(LabelTagPair(kmer_label, kmer));
+ tag_labels.insert(TagLabelPair(kmer, kmer_label));
+ label_tag.insert(LabelTagPair(kmer_label, kmer));
+ all_labels.insert(kmer_label);
printdbg(done linking tag and label)
}
void LabelHash::consume_sequence_and_tag_with_labels(const std::string& seq,
unsigned long long& n_consumed,
- Label& current_label,
+ Label current_label,
SeenSet * found_tags)
{
@@ -242,11 +233,10 @@ void LabelHash::consume_sequence_and_tag_with_labels(const std::string& seq,
kmer = kmers.next();
bool is_new_kmer;
- if ((is_new_kmer = graph->test_and_set_bits( kmer ))) {
+ if ((is_new_kmer = graph->store->test_and_set_bits( kmer ))) {
++n_consumed;
printdbg(test_and_set_bits)
}
-#if (1)
if (is_new_kmer) {
printdbg(new kmer...)
++since;
@@ -277,16 +267,6 @@ void LabelHash::consume_sequence_and_tag_with_labels(const std::string& seq,
++since;
}
}
-#else
- if (!is_new_kmer && set_contains(graph->all_tags, kmer)) {
- since = 1;
- if (found_tags) {
- found_tags->insert(kmer);
- }
- } else {
- since++;
- }
-#endif
//
if (since >= graph->_tag_density) {
printdbg(exceeded tag density: drop a tag and label --
@@ -327,7 +307,7 @@ void LabelHash::consume_sequence_and_tag_with_labels(const std::string& seq,
}
unsigned int LabelHash::sweep_label_neighborhood(const std::string& seq,
- LabelPtrSet& found_labels,
+ LabelSet& found_labels,
unsigned int range,
bool break_on_stoptags,
bool stop_big_traversals)
@@ -349,16 +329,24 @@ unsigned int LabelHash::sweep_label_neighborhood(const std::string& seq,
return num_traversed;
}
-LabelPtrSet LabelHash::get_tag_labels(const HashIntoType& tag)
+void LabelHash::get_tag_labels(const HashIntoType tag,
+ LabelSet& labels) const
+{
+ if (set_contains(graph->all_tags, tag)) {
+ _get_tag_labels(tag, tag_labels, labels);
+ }
+}
+
+void LabelHash::get_tags_from_label(const Label label,
+ TagSet& tags) const
{
- LabelPtrSet labels;
- //unsigned int num_labels;
- _get_tag_labels(tag, tag_labels, labels);
- return labels;
+ if(set_contains(all_labels, label)) {
+ _get_tags_from_label(label, label_tag, tags);
+ }
}
-void LabelHash::traverse_labels_and_resolve(const SeenSet& tagged_kmers,
- LabelPtrSet& found_labels)
+void LabelHash::traverse_labels_and_resolve(const SeenSet tagged_kmers,
+ LabelSet& found_labels)
{
SeenSet::const_iterator si;
@@ -375,10 +363,7 @@ void LabelHash::traverse_labels_and_resolve(const SeenSet& tagged_kmers,
LabelHash::~LabelHash()
{
- for (LabelPtrMap::iterator itr=label_ptrs.begin();
- itr!=label_ptrs.end(); ++itr) {
- delete itr->second;
- }
+ ;
}
@@ -410,14 +395,14 @@ void LabelHash::save_labels_and_tags(std::string filename)
// For each tag in the partition map, save the tag and the associated
// partition ID.
- TagLabelPtrMap::const_iterator pi = tag_labels.begin();
+ TagLabelMap::const_iterator pi = tag_labels.begin();
for (; pi != tag_labels.end(); ++pi) {
HashIntoType *k_p = (HashIntoType *) (buf + n_bytes);
*k_p = pi->first;
n_bytes += sizeof(HashIntoType);
Label * l_p = (Label *) (buf + n_bytes);
- *l_p = *(pi->second);
+ *l_p = pi->second;
n_bytes += sizeof(Label);
// flush to disk
@@ -457,6 +442,12 @@ void LabelHash::load_labels_and_tags(std::string filename)
err = "Unknown error in opening file: " + filename;
}
throw khmer_file_exception(err);
+ } catch (const std::exception &e) {
+ // Catching std::exception is a stopgap for
+ // https://gcc.gnu.org/bugzilla/show_bug.cgi?id=66145
+ std::string err = "Unknown error opening file: " + filename + " "
+ + strerror(errno);
+ throw khmer_file_exception(err);
}
unsigned long n_labeltags = 1;
@@ -502,6 +493,12 @@ void LabelHash::load_labels_and_tags(std::string filename)
std::string err;
err = "Unknown error reading header info from: " + filename;
throw khmer_file_exception(err);
+ } catch (khmer_file_exception &e) {
+ throw e;
+ } catch (const std::exception &e) {
+ std::string err = "Unknown error opening file: " + filename + " "
+ + strerror(errno);
+ throw khmer_file_exception(err);
}
char * buf = new char[IO_BUF_SIZE];
@@ -520,7 +517,7 @@ void LabelHash::load_labels_and_tags(std::string filename)
try {
infile.read(buf + remainder, IO_BUF_SIZE - remainder);
- } catch (std::ifstream::failure &e) {
+ } catch (std::exception &e) {
// We may get an exception here if we fail to read all the
// expected bytes due to EOF -- only pass it up if we read
@@ -548,11 +545,9 @@ void LabelHash::load_labels_and_tags(std::string filename)
labelp = (Label *) (buf + i);
i += sizeof(Label);
- Label * labelp2;
-
graph->all_tags.insert(*kmer_p);
- labelp2 = check_and_allocate_label(*labelp);
- link_tag_and_label(*kmer_p, *labelp2);
+ all_labels.insert(*labelp);
+ link_tag_and_label(*kmer_p, *labelp);
loaded++;
}
@@ -575,3 +570,68 @@ void LabelHash::load_labels_and_tags(std::string filename)
delete[] buf;
}
+
+// tag & label k-mers on either side of an HDN.
+
+void LabelHash::label_across_high_degree_nodes(const char * s,
+ SeenSet& high_degree_nodes,
+ const Label label)
+{
+ KmerIterator kmers(s, graph->_ksize);
+
+ unsigned long n = 0;
+
+ Kmer prev_kmer = kmers.next();
+ if (kmers.done()) {
+ return;
+ }
+ Kmer kmer = kmers.next();
+ if (kmers.done()) {
+ return;
+ }
+ Kmer next_kmer = kmers.next();
+
+ // ignore any situation where HDN is at beginning or end of sequence
+ // @CTB testme :)
+ while(!kmers.done()) {
+ n++;
+ if (n % 10000 == 0) {
+ std::cout << "... label_across_hdn: " << n << "\n";
+ }
+ if (set_contains(high_degree_nodes, kmer)) {
+ graph->add_tag(prev_kmer);
+ graph->add_tag(kmer);
+ graph->add_tag(next_kmer);
+ link_tag_and_label(prev_kmer, label);
+ link_tag_and_label(kmer, label);
+ link_tag_and_label(next_kmer, label);
+ }
+ prev_kmer = kmer;
+ kmer = next_kmer;
+ next_kmer = kmers.next();
+ }
+}
+
+template void LabelHash::consume_seqfile_and_tag_with_labels<FastxReader>(
+ std:: string const &filename,
+ unsigned int &total_reads,
+ unsigned long long &n_consumed,
+ CallbackFn callback,
+ void * callback_data
+);
+template void LabelHash::consume_seqfile_and_tag_with_labels<FastxReader>(
+ ReadParserPtr<FastxReader>& parser,
+ unsigned int &total_reads,
+ unsigned long long &n_consumed,
+ CallbackFn callback,
+ void * callback_data
+);
+template void LabelHash::consume_partitioned_fasta_and_tag_with_labels<FastxReader>(
+ const std::string &filename,
+ unsigned int &total_reads,
+ unsigned long long &n_consumed,
+ CallbackFn callback = NULL,
+ void * callback_datac = NULL
+);
+
+} // namespace khmer
diff --git a/lib/labelhash.hh b/lib/labelhash.hh
index 6a4d96a..3fe371b 100644
--- a/lib/labelhash.hh
+++ b/lib/labelhash.hh
@@ -1,7 +1,7 @@
/*
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2013-2015, Michigan State University.
-Copyright (C) 2015, The Regents of the University of California.
+Copyright (C) 2015-2016, The Regents of the University of California.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
@@ -44,36 +44,33 @@ Contact: khmer-project at idyll.org
#include <string>
#include <utility>
-#include "hashbits.hh"
-#include "hashtable.hh"
+#include "hashgraph.hh"
#include "khmer.hh"
#include "read_parsers.hh"
namespace khmer
{
-class Hashtable;
+ class Hashgraph;
-namespace read_parsers
-{
-struct IParser;
-} // namespace read_parsers
-} // namespace khmer
-
-namespace khmer
-{
+ using read_parsers::ReadParser;
+ namespace read_parsers
+ {
+ template<typename SeqIO> class ReadParser;
+ class FastxReader;
+ }
class LabelHash
{
protected:
// Does the given tag already have the given label?
- bool _cmap_contains_label(const TagLabelPtrMap& cmap,
- HashIntoType& kmer,
- Label& the_label)
+ bool _cmap_contains_label(const TagLabelMap& cmap,
+ const HashIntoType kmer,
+ const Label the_label)
{
- std::pair<TagLabelPtrMap::const_iterator, TagLabelPtrMap::const_iterator> ret;
+ std::pair<TagLabelMap::const_iterator, TagLabelMap::const_iterator> ret;
ret = cmap.equal_range(kmer);
- for (TagLabelPtrMap::const_iterator it=ret.first; it!=ret.second; ++it) {
- if (*(it->second) == the_label) {
+ for (TagLabelMap::const_iterator it=ret.first; it!=ret.second; ++it) {
+ if (it->second == the_label) {
return true;
}
}
@@ -95,14 +92,14 @@ protected:
return false;
}
- unsigned int _get_tag_labels(const HashIntoType& tag,
- const TagLabelPtrMap& cmap,
- LabelPtrSet& found_labels)
+ unsigned int _get_tag_labels(const HashIntoType tag,
+ const TagLabelMap cmap,
+ LabelSet& found_labels) const
{
unsigned int num_labels = 0;
- std::pair<TagLabelPtrMap::const_iterator, TagLabelPtrMap::const_iterator> ret;
+ std::pair<TagLabelMap::const_iterator, TagLabelMap::const_iterator> ret;
ret = cmap.equal_range(tag);
- for (TagLabelPtrMap::const_iterator it=ret.first; it!=ret.second; ++it) {
+ for (TagLabelMap::const_iterator it=ret.first; it!=ret.second; ++it) {
found_labels.insert(it->second);
++num_labels;
}
@@ -111,7 +108,7 @@ protected:
unsigned int _get_tags_from_label(const Label& label,
const LabelTagMap& cmap,
- TagSet& labeled_tags)
+ TagSet& labeled_tags) const
{
unsigned int num_tags = 0;
std::pair<LabelTagMap::const_iterator, LabelTagMap::const_iterator> ret;
@@ -126,9 +123,9 @@ protected:
uint32_t _tag_labels_spin_lock;
public:
- khmer::Hashtable * graph;
+ khmer::Hashgraph * graph;
- explicit LabelHash(Hashtable * ht) : graph(ht)
+ explicit LabelHash(Hashgraph * ht) : graph(ht)
{
_tag_labels_spin_lock = 0;
@@ -136,70 +133,69 @@ public:
~LabelHash();
- TagLabelPtrMap tag_labels;
- LabelTagMap label_tag_ptrs;
- LabelPtrMap label_ptrs;
+ TagLabelMap tag_labels;
+ LabelTagMap label_tag;
+ LabelSet all_labels;
size_t n_labels() const
{
- return label_ptrs.size();
+ return all_labels.size();
}
-
- Label * check_and_allocate_label(Label new_label)
- {
- Label * c;
- if (label_ptrs.count(new_label)) {
- c = label_ptrs[new_label];
- } else {
- c = new Label(new_label);
- label_ptrs[*c] = c;
- }
- return c;
- }
- void consume_fasta_and_tag_with_labels(
+ template<typename SeqIO>
+ void consume_seqfile_and_tag_with_labels(
std::string const &filename,
unsigned int &total_reads,
unsigned long long &n_consumed,
CallbackFn callback = NULL,
void * callback_data = NULL);
- void consume_fasta_and_tag_with_labels(
- read_parsers:: IParser * parser,
+ template<typename SeqIO>
+ void consume_seqfile_and_tag_with_labels(
+ read_parsers::ReadParserPtr<SeqIO>& parser,
unsigned int &total_reads,
unsigned long long &n_consumed,
CallbackFn callback = NULL,
void * callback_data = NULL);
- void consume_partitioned_fasta_and_tag_with_labels(const std::string &filename,
- unsigned int &total_reads,
- unsigned long long &n_consumed,
- CallbackFn callback = NULL,
- void * callback_datac = NULL);
+ template<typename SeqIO>
+ void consume_partitioned_fasta_and_tag_with_labels(
+ const std::string &filename,
+ unsigned int &total_reads,
+ unsigned long long &n_consumed,
+ CallbackFn callback = NULL,
+ void * callback_datac = NULL);
void consume_sequence_and_tag_with_labels(const std::string& seq,
unsigned long long& n_consumed,
- Label& current_label,
+ Label current_label,
SeenSet * new_tags = 0);
- LabelPtrSet get_tag_labels(const HashIntoType& tag);
+ void get_tag_labels(const HashIntoType tag,
+ LabelSet& labels) const;
+ void get_tags_from_label(const Label label,
+ TagSet& tags) const;
- void link_tag_and_label(HashIntoType& kmer, Label& label);
+ void link_tag_and_label(const HashIntoType kmer, const Label label);
unsigned int sweep_label_neighborhood(const std::string & seq,
- LabelPtrSet& found_labels,
+ LabelSet& found_labels,
unsigned int range,
bool break_on_stoptags,
bool stop_big_traversals);
- void traverse_labels_and_resolve(const SeenSet& tagged_kmers,
- LabelPtrSet& found_labels);
+ void traverse_labels_and_resolve(const SeenSet tagged_kmers,
+ LabelSet& found_labels);
void save_labels_and_tags(std::string);
void load_labels_and_tags(std::string);
+ void label_across_high_degree_nodes(const char * sequence,
+ SeenSet& high_degree_nodes,
+ const Label label);
};
-}
+
+} // namespace khmer
#define ACQUIRE_TAG_COLORS_SPIN_LOCK \
while(!__sync_bool_compare_and_swap( &_tag_labels_spin_lock, 0, 1));
diff --git a/lib/magic b/lib/magic
index 1ab0707..ee2e026 100644
--- a/lib/magic
+++ b/lib/magic
@@ -1,11 +1,67 @@
+#! /usr/bin/env python
+# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# Copyright (C) 2015, The Regents of the University of California.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+#
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# * Redistributions in binary form must reproduce the above
+# copyright notice, this list of conditions and the following
+# disclaimer in the documentation and/or other materials provided
+# with the distribution.
+#
+# * Neither the name of the Michigan State University nor the names
+# of its contributors may be used to endorse or promote products
+# derived from this software without specific prior written
+# permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Contact: khmer-project at idyll.org
+
# Magic descriptions of khmer file types for file(1) command.
# Format is described in magic(5).
+#
+# Example:
+#
+# $ file --magic-file lib/magic tests/test-data/normC20k20.ct
+# tests/test-data/normC20k20.ct: Binary from the khmer project, file format version 4, k-mer countgraph
+#
+# $ file --magic-file lib/magic --mime-type tests/test-data/normC20k20.ct
+# tests/test-data/normC20k20.ct: application/vnd.oxli.countgraph
+#
+# $ file --magic-file lib/magic --extension tests/test-data/normC20k20.ct
+# tests/test-data/normC20k20.ct: oxlicg
+#
+# See also:
+# http://www.iana.org/assignments/media-types/application/vnd.oxli.countgraph
0 string OXLI Binary from the khmer project,
>4 byte x file format version %u,
->5 byte 1 k-mer count table
->5 byte 2 k-mer presence table
+>5 byte 1 k-mer countgraph
+!:ext oxlicg
+!:mime application/vnd.oxli.countgraph
+>5 byte 2 k-mer nodegraph
+!:ext oxling
>5 byte 3 k-mer tagset
+!:ext oxlits
>5 byte 4 k-mer partition stoptags
+!:ext oxlist
>5 byte 5 k-mer partition subset
->5 byte 6 labels/tags for implicit k-mer De Bruijn graph
+!:ext oxliss
+>5 byte 6 k-mer graphlabels
+!:ext oxligl
diff --git a/lib/oxli.pc.in b/lib/oxli.pc.in
index 6cf09fb..523d395 100644
--- a/lib/oxli.pc.in
+++ b/lib/oxli.pc.in
@@ -6,9 +6,11 @@ includedir=${prefix}/include
Name: oxli
Description: The unsupported core C++ library from the khmer project
-URL: http://khmer.readthedocs.org/
+URL: http://khmer.readthedocs.io/
Version: @VERSION@
Requires:
+Requires.private: zlib
Libs: -L${libdir} -L${sharedlibdir} -loxli
+Libs.private: -lbz2
Cflags: -I${includedir}
diff --git a/lib/read_aligner.cc b/lib/read_aligner.cc
index fd65dd3..db44109 100644
--- a/lib/read_aligner.cc
+++ b/lib/read_aligner.cc
@@ -1,7 +1,7 @@
/*
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2013-2015, Michigan State University.
-Copyright (C) 2015, The Regents of the University of California.
+Copyright (C) 2015-2016, The Regents of the University of California.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
@@ -317,8 +317,8 @@ void ReadAligner::WriteNode(AlignmentNode* curr)
{
std::cerr << "curr: " << curr << " "
<< curr->prev << " " << " state=" << curr->state << " "
- << _revhash(curr->fwd_hash, m_ch->ksize()) << " "
- << _revhash(curr->rc_hash, m_ch->ksize())
+ << m_ch->unhash_dna(curr->fwd_hash) << " "
+ << m_ch->unhash_dna(curr->rc_hash)
<< " cov="
<< m_ch->get_count(uniqify_rc(curr->fwd_hash, curr->rc_hash))
<< " emission=" << curr->base
@@ -463,8 +463,8 @@ Alignment* ReadAligner::ExtractAlignment(AlignmentNode* node,
<< node->f_score << "\t" << node->length << "\t"
<< node->state << "\t" << node->trusted << "\t"
<< node->seq_idx << "\t"
- << _revhash(node->fwd_hash, m_ch->ksize()) << "\t"
- << _revhash(node->rc_hash, m_ch->ksize()) << std::endl;
+ << m_ch->unhash_dna(node->fwd_hash) << "\t"
+ << m_ch->unhash_dna(node->rc_hash) << std::endl;
#endif
if(forward) {
@@ -532,12 +532,13 @@ Alignment* ReadAligner::Align(const std::string& read)
}
HashIntoType fhash = 0, rhash = 0;
- _hash(start.kmer.c_str(), k, fhash, rhash);
+ fhash = m_ch->hash_dna_top_strand(start.kmer.c_str());
+ rhash = m_ch->hash_dna_bottom_strand(start.kmer.c_str());
#if READ_ALIGNER_DEBUG
std::cerr << "Starting kmer: " << start.kmer << " "
- << _revhash(fhash, m_ch->ksize()) << " "
- << _revhash(rhash, m_ch->ksize())
+ << m_ch->unhash_dna(fhash) << " "
+ << m_ch->unhash_dna(rhash)
<< " cov: " << start.k_cov << " idx: " << start.kmer_idx << ", "
<< start.kmer_idx + k - 1
<< " emission: " << start.kmer[k - 1] << std::endl;
@@ -610,12 +611,13 @@ Alignment* ReadAligner::AlignForward(const std::string& read)
}
HashIntoType fhash = 0, rhash = 0;
- _hash(start.kmer.c_str(), k, fhash, rhash);
+ fhash = m_ch->hash_dna_top_strand(start.kmer.c_str());
+ rhash = m_ch->hash_dna_bottom_strand(start.kmer.c_str());
#if READ_ALIGNER_DEBUG
std::cerr << "Starting kmer: " << start.kmer << " "
- << _revhash(fhash, m_ch->ksize()) << " "
- << _revhash(rhash, m_ch->ksize())
+ << m_ch->unhash_dna(fhash) << " "
+ << m_ch->unhash_dna(rhash)
<< " cov: " << start.k_cov << " idx: " << start.kmer_idx << ", "
<< start.kmer_idx + k - 1
<< " emission: " << start.kmer[k - 1] << std::endl;
diff --git a/lib/read_aligner.hh b/lib/read_aligner.hh
index eb03d04..cb0c456 100644
--- a/lib/read_aligner.hh
+++ b/lib/read_aligner.hh
@@ -48,8 +48,8 @@ Contact: khmer-project at idyll.org
#include <string>
#include <vector>
-#include "counting.hh"
#include "khmer.hh"
+#include "hashgraph.hh"
#include "kmer_hash.hh"
#define READ_ALIGNER_DEBUG 0
@@ -226,7 +226,7 @@ private:
const HashIntoType bitmask;
const size_t rc_left_shift;
- khmer::CountingHash* m_ch;
+ khmer::Countgraph* m_ch;
ScoringMatrix m_sm;
size_t m_trusted_cutoff;
@@ -244,7 +244,7 @@ public:
Alignment* Align(const std::string&);
Alignment* AlignForward(const std::string&);
- ReadAligner(khmer::CountingHash* ch,
+ ReadAligner(khmer::Countgraph* ch,
BoundedCounterType trusted_cutoff, double bits_theta)
: bitmask(comp_bitmask(ch->ksize())),
rc_left_shift(ch->ksize() * 2 - 2),
@@ -265,7 +265,7 @@ public:
#endif
}
- ReadAligner(khmer::CountingHash* ch,
+ ReadAligner(khmer::Countgraph* ch,
BoundedCounterType trusted_cutoff, double bits_theta,
double* scoring_matrix, double* transitions)
: bitmask(comp_bitmask(ch->ksize())),
diff --git a/lib/read_parsers.cc b/lib/read_parsers.cc
index b74448c..f22dbc1 100644
--- a/lib/read_parsers.cc
+++ b/lib/read_parsers.cc
@@ -1,7 +1,7 @@
/*
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2012-2015, Michigan State University.
-Copyright (C) 2015, The Regents of the University of California.
+Copyright (C) 2015-2016, The Regents of the University of California.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
@@ -35,128 +35,36 @@ LICENSE (END)
Contact: khmer-project at idyll.org
*/
-#include <seqan/seq_io.h> // IWYU pragma: keep
-#include <seqan/sequence.h> // IWYU pragma: keep
-#include <seqan/stream.h> // IWYU pragma: keep
#include <fstream>
-
#include "khmer_exception.hh"
#include "read_parsers.hh"
namespace khmer
{
-
namespace read_parsers
{
-void
-Read::write_to(std::ostream& output)
-{
- if (quality.length() != 0) {
- output << "@" << name << std::endl
- << sequence << std::endl
- << "+" << std::endl
- << quality << std::endl;
- } else {
- output << ">" << name << std::endl
- << sequence << std::endl;
- }
-}
-
-
-struct SeqAnParser::Handle {
- seqan::SequenceStream stream;
- uint32_t seqan_spin_lock;
-};
-
-SeqAnParser::SeqAnParser( char const * filename ) : IParser( )
+unsigned char _to_valid_dna(const unsigned char c)
{
- _private = new SeqAnParser::Handle();
- seqan::open(_private->stream, filename);
- if (!seqan::isGood(_private->stream)) {
- std::string message = "Could not open ";
- message = message + filename + " for reading.";
- throw InvalidStream(message);
- } else if (seqan::atEnd(_private->stream)) {
- std::string message = "File ";
- message = message + filename + " does not contain any sequences!";
- throw InvalidStream(message);
- }
- __asm__ __volatile__ ("" ::: "memory");
- _private->seqan_spin_lock = 0;
-}
-
-bool SeqAnParser::is_complete()
-{
- return !seqan::isGood(_private->stream) || seqan::atEnd(_private->stream);
-}
-
-void SeqAnParser::imprint_next_read(Read &the_read)
-{
- the_read.reset();
- int ret = -1;
- const char *invalid_read_exc = NULL;
- while (!__sync_bool_compare_and_swap(& _private->seqan_spin_lock, 0, 1));
- bool atEnd = seqan::atEnd(_private->stream);
- if (!atEnd) {
- ret = seqan::readRecord(the_read.name, the_read.sequence,
- the_read.quality, _private->stream);
- if (ret == 0) {
- // Detect if we're parsing something w/ qualities on the first read
- // only
- if (_num_reads == 0 && the_read.quality.length() != 0) {
- _have_qualities = true;
- }
-
- // Handle error cases, or increment number of reads on success
- if (the_read.sequence.length() == 0) {
- invalid_read_exc = "Sequence is empty";
- } else if (_have_qualities && (the_read.sequence.length() != \
- the_read.quality.length())) {
- invalid_read_exc = "Sequence and quality lengths differ";
- } else {
- _num_reads++;
- }
- }
- }
- __asm__ __volatile__ ("" ::: "memory");
- _private->seqan_spin_lock = 0;
- // Throw any error in the read, even if we're at the end
- if (invalid_read_exc != NULL) {
- throw InvalidRead(invalid_read_exc);
- }
- // Throw NoMoreReadsAvailable if none of the above errors were raised, even
- // if ret == 0
- if (atEnd) {
- throw NoMoreReadsAvailable();
- }
- // Catch-all error in readRecord that isn't one of the above
- if (ret != 0) {
- throw StreamReadError();
+ switch(c) {
+ case 'A':
+ case 'C':
+ case 'G':
+ case 'T':
+ return c;
+ case 'a':
+ case 'c':
+ case 'g':
+ case 't':
+ return toupper(c);
+ default:
+ return 'A';
}
}
-SeqAnParser::~SeqAnParser()
-{
- seqan::close(_private->stream);
- delete _private;
-}
-
-IParser * const
-IParser::
-get_parser(
- std:: string const &ifile_name
-)
-{
-
- return new SeqAnParser(ifile_name.c_str());
-}
-
-
-IParser::
-IParser(
-)
+template<typename SeqIO>
+void ReadParser<SeqIO>::_init()
{
int regex_rc =
regcomp(
@@ -184,61 +92,13 @@ IParser(
if (regex_rc) {
throw khmer_exception("Could not compile R2 regex");
}
- _num_reads = 0;
- _have_qualities = false;
}
-IParser::
-~IParser( )
+template<typename SeqIO>
+ReadPair ReadParser<SeqIO>::_get_next_read_pair_in_ignore_mode()
{
- regfree( &_re_read_2_nosub );
- regfree( &_re_read_1 );
- regfree( &_re_read_2 );
-}
-
-void
-IParser::
-imprint_next_read_pair( ReadPair &the_read_pair, uint8_t mode )
-{
- switch (mode) {
-#if (0)
- case IParser:: PAIR_MODE_ALLOW_UNPAIRED:
- _imprint_next_read_pair_in_allow_mode( the_read_pair );
- break;
-#endif
- case IParser:: PAIR_MODE_IGNORE_UNPAIRED:
- _imprint_next_read_pair_in_ignore_mode( the_read_pair );
- break;
- case IParser:: PAIR_MODE_ERROR_ON_UNPAIRED:
- _imprint_next_read_pair_in_error_mode( the_read_pair );
- break;
- default:
- std::ostringstream oss;
- oss << "Unknown pair reading mode: " << mode;
- throw UnknownPairReadingMode(oss.str());
- }
-}
-
-
-#if (0)
-void
-IParser::
-_imprint_next_read_pair_in_allow_mode( ReadPair &the_read_pair )
-{
- // TODO: Implement.
- // Probably need caching of reads between invocations
- // and the ability to return pairs which are half empty.
-}
-#endif
-
-
-void
-IParser::
-_imprint_next_read_pair_in_ignore_mode( ReadPair &the_read_pair )
-{
- Read &read_1 = the_read_pair.first;
- Read &read_2 = the_read_pair.second;
- regmatch_t match_1, match_2;
+ ReadPair pair;
+ regmatch_t match_1, match_2;
// Hunt for a read pair until one is found or end of reads is reached.
while (true) {
@@ -247,9 +107,9 @@ _imprint_next_read_pair_in_ignore_mode( ReadPair &the_read_pair )
// Note: We let any exception, which flies out of the following,
// pass through unhandled.
while (true) {
- imprint_next_read( read_1 );
+ pair.first = get_next_read();
if (!regexec(
- &_re_read_1, read_1.name.c_str( ), 1, &match_1, 0
+ &_re_read_1, pair.first.name.c_str( ), 1, &match_1, 0
)) {
break;
}
@@ -259,57 +119,54 @@ _imprint_next_read_pair_in_ignore_mode( ReadPair &the_read_pair )
// If not found, then restart search for pair.
// If found, then validate match.
// If invalid pair, then restart search for pair.
- imprint_next_read( read_2 );
+ pair.second = get_next_read();
if (!regexec(
- &_re_read_2, read_2.name.c_str( ), 1, &match_2, 0
+ &_re_read_2, pair.second.name.c_str( ), 1, &match_2, 0
)) {
- if (_is_valid_read_pair( the_read_pair, match_1, match_2 )) {
+ if (_is_valid_read_pair(pair, match_1, match_2)) {
break;
}
}
} // while pair not found
-} // _imprint_next_read_pair_in_ignore_mode
-
+ return pair;
+} // _get_next_read_pair_in_ignore_mode
-void
-IParser::
-_imprint_next_read_pair_in_error_mode( ReadPair &the_read_pair )
+template<typename SeqIO>
+ReadPair ReadParser<SeqIO>::_get_next_read_pair_in_error_mode()
{
- Read &read_1 = the_read_pair.first;
- Read &read_2 = the_read_pair.second;
- regmatch_t match_1, match_2;
+ ReadPair pair;
+ regmatch_t match_1, match_2;
// Note: We let any exception, which flies out of the following,
// pass through unhandled.
- imprint_next_read( read_1 );
- imprint_next_read( read_2 );
+ pair.first = get_next_read();
+ pair.second = get_next_read();
// Is the first read really the first member of a pair?
if (REG_NOMATCH == regexec(
- &_re_read_1, read_1.name.c_str( ), 1, &match_1, 0
+ &_re_read_1, pair.first.name.c_str( ), 1, &match_1, 0
)) {
throw InvalidReadPair( );
}
// Is the second read really the second member of a pair?
if (REG_NOMATCH == regexec(
- &_re_read_2, read_2.name.c_str( ), 1, &match_2, 0
+ &_re_read_2, pair.second.name.c_str( ), 1, &match_2, 0
)) {
throw InvalidReadPair( );
}
// Is the pair valid?
- if (!_is_valid_read_pair( the_read_pair, match_1, match_2 )) {
+ if (!_is_valid_read_pair(pair, match_1, match_2)) {
throw InvalidReadPair( );
}
-} // _imprint_next_read_pair_in_error_mode
+ return pair;
+} // _get_next_read_pair_in_error_mode
-
-bool
-IParser::
-_is_valid_read_pair(
+template<typename SeqIO>
+bool ReadParser<SeqIO>::_is_valid_read_pair(
ReadPair &the_read_pair, regmatch_t &match_1, regmatch_t &match_2
)
{
@@ -319,9 +176,184 @@ _is_valid_read_pair(
== the_read_pair.second.name.substr( 0, match_1.rm_so ));
}
-} // namespace read_parsers
+template<typename SeqIO>
+ReadParser<SeqIO>::ReadParser(std::unique_ptr<SeqIO> pf)
+{
+ _parser = std::move(pf);
+ _init();
+}
+template<typename SeqIO>
+ReadParser<SeqIO>::ReadParser(ReadParser& other)
+{
+ _parser = std::move(other._parser);
+ _init();
+}
-} // namespace khmer
+template<typename SeqIO>
+ReadParser<SeqIO>::~ReadParser()
+{
+ regfree(&_re_read_2_nosub);
+ regfree(&_re_read_1);
+ regfree(&_re_read_2);
+}
-// vim: set ft=cpp sts=4 sw=4 tw=80:
+template<typename SeqIO>
+Read ReadParser<SeqIO>::get_next_read()
+{
+ return _parser->get_next_read();
+}
+
+template<typename SeqIO>
+ReadPair ReadParser<SeqIO>::get_next_read_pair(uint8_t mode)
+{
+ if (mode == ReadParser<SeqIO>::PAIR_MODE_IGNORE_UNPAIRED) {
+ return _get_next_read_pair_in_ignore_mode();
+ } else if (mode == ReadParser<SeqIO>::PAIR_MODE_ERROR_ON_UNPAIRED) {
+ return _get_next_read_pair_in_error_mode();
+ } else {
+ std::ostringstream oss;
+ oss << "Unknown pair reading mode: " << mode;
+ throw UnknownPairReadingMode(oss.str());
+ }
+}
+
+template<typename SeqIO>
+size_t ReadParser<SeqIO>::get_num_reads()
+{
+ return _parser->get_num_reads();
+}
+
+template<typename SeqIO>
+bool ReadParser<SeqIO>::is_complete()
+{
+ return _parser->is_complete();
+}
+
+template<typename SeqIO>
+void ReadParser<SeqIO>::close()
+{
+ _parser->close();
+}
+
+void FastxReader::_init()
+{
+ seqan::open(_stream, _filename.c_str());
+ if (!seqan::isGood(_stream)) {
+ std::string message = "Could not open ";
+ message = message + _filename + " for reading.";
+ throw InvalidStream(message);
+ } else if (seqan::atEnd(_stream)) {
+ std::string message = "File ";
+ message = message + _filename + " does not contain any sequences!";
+ throw InvalidStream(message);
+ }
+ __asm__ __volatile__ ("" ::: "memory");
+}
+
+FastxReader::FastxReader()
+ : _filename("-"), _spin_lock(0), _num_reads(0), _have_qualities(false)
+{
+ _init();
+}
+
+FastxReader::FastxReader(const std::string& infile)
+ : _filename(infile),
+ _spin_lock(0),
+ _num_reads(0),
+ _have_qualities(false)
+{
+ _init();
+}
+
+FastxReader::FastxReader(FastxReader& other)
+ : _filename(other._filename),
+ _spin_lock(other._spin_lock),
+ _num_reads(other._num_reads),
+ _have_qualities(other._have_qualities)
+{
+ _stream = std::move(other._stream);
+}
+
+FastxReader::~FastxReader()
+{
+ seqan::close(_stream);
+}
+
+bool FastxReader::is_complete()
+{
+ return !seqan::isGood(_stream) || seqan::atEnd(_stream);
+}
+
+size_t FastxReader::get_num_reads()
+{
+ return _num_reads;
+}
+
+void FastxReader::close()
+{
+ seqan::close(_stream);
+}
+
+Read FastxReader::get_next_read()
+{
+ Read read;
+ int ret = -1;
+ const char *invalid_read_exc = NULL;
+ while (!__sync_bool_compare_and_swap(&_spin_lock, 0, 1));
+ bool atEnd = seqan::atEnd(_stream);
+ if (!atEnd) {
+ ret = seqan::readRecord(read.name, read.sequence, read.quality, _stream);
+ if (ret == 0) {
+ // Detect if we're parsing something w/ qualities on the first read
+ // only
+ if (_num_reads == 0 && read.quality.length() != 0) {
+ _have_qualities = true;
+ }
+
+ // Handle error cases, or increment number of reads on success
+ if (read.sequence.length() == 0) {
+ invalid_read_exc = "Sequence is empty";
+ } else if (_have_qualities && (read.sequence.length() != \
+ read.quality.length())) {
+ invalid_read_exc = "Sequence and quality lengths differ";
+ } else {
+ _num_reads++;
+ }
+ }
+ }
+ __asm__ __volatile__ ("" ::: "memory");
+ _spin_lock = 0;
+ // Throw any error in the read, even if we're at the end
+ if (invalid_read_exc != NULL) {
+ throw InvalidRead(invalid_read_exc);
+ }
+ // Throw NoMoreReadsAvailable if none of the above errors were raised, even
+ // if ret == 0
+ if (atEnd) {
+ throw NoMoreReadsAvailable();
+ }
+ // Catch-all error in readRecord that isn't one of the above
+ if (ret != 0) {
+ throw StreamReadError();
+ }
+ return read;
+}
+
+template<typename SeqIO>
+ReadParserPtr<SeqIO> get_parser(const std::string& filename)
+{
+ return ReadParserPtr<SeqIO>(
+ new ReadParser<SeqIO>(
+ std::unique_ptr<SeqIO>(new SeqIO(filename))
+ )
+ );
+}
+
+// All template instantiations used in the codebase must be declared here.
+template class ReadParser<FastxReader>;
+template FastxParserPtr get_parser<FastxReader>(const std::string& filename);
+
+} // namespace read_parsers
+
+} // namespace khmer
diff --git a/lib/read_parsers.hh b/lib/read_parsers.hh
index 932d5f8..2773b1f 100644
--- a/lib/read_parsers.hh
+++ b/lib/read_parsers.hh
@@ -1,7 +1,7 @@
/*
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2012-2015, Michigan State University.
-Copyright (C) 2015, The Regents of the University of California.
+Copyright (C) 2015-2016, The Regents of the University of California.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
@@ -38,13 +38,19 @@ Contact: khmer-project at idyll.org
#ifndef READ_PARSERS_HH
#define READ_PARSERS_HH
+#include <seqan/seq_io.h> // IWYU pragma: keep
+#include <seqan/sequence.h> // IWYU pragma: keep
+#include <seqan/stream.h> // IWYU pragma: keep
+
#include <regex.h>
#include <stddef.h>
#include <stdint.h>
+#include <algorithm>
#include <cstdlib>
#include <iostream>
#include <string>
#include <utility>
+#include <memory>
#include "khmer.hh"
#include "khmer_exception.hh"
@@ -52,8 +58,6 @@ Contact: khmer-project at idyll.org
namespace khmer
{
-
-
namespace read_parsers
{
@@ -85,109 +89,109 @@ struct InvalidReadPair : public khmer_value_exception {
khmer_value_exception("Invalid read pair detected.") {}
};
+
+unsigned char _to_valid_dna(const unsigned char c);
+
+
struct Read {
- std:: string name;
- std:: string annotations;
- std:: string sequence;
- std:: string quality;
- // TODO? Add description field.
+ std::string name;
+ std::string description;
+ std::string sequence;
+ std::string quality;
+ std::string cleaned_seq;
- inline void reset ( )
+ inline void reset()
{
- name.clear( );
- annotations.clear( );
- sequence.clear( );
- quality.clear( );
+ name.clear();
+ description.clear();
+ sequence.clear();
+ quality.clear();
+ cleaned_seq.clear();
}
- void write_to(std::ostream&);
+ inline void write_fastx(std::ostream& output)
+ {
+ if (quality.length() != 0) {
+ output << "@" << name << '\n'
+ << sequence << '\n'
+ << "+" << '\n'
+ << quality << '\n';
+ } else {
+ output << ">" << name << '\n'
+ << sequence << '\n';
+ }
+ }
+
+ // Compute cleaned_seq from sequence. Call this after changing sequence.
+ inline void set_clean_seq()
+ {
+ cleaned_seq = std::string(sequence.size(), 0);
+ std::transform(sequence.begin(), sequence.end(), cleaned_seq.begin(),
+ _to_valid_dna);
+ }
};
+typedef std::pair<Read, Read> ReadPair;
-typedef std:: pair< Read, Read > ReadPair;
-struct IParser {
+template<typename SeqIO>
+class ReadParser
+{
+protected:
+ std::unique_ptr<SeqIO> _parser;
+ regex_t _re_read_2_nosub;
+ regex_t _re_read_1;
+ regex_t _re_read_2;
+ void _init();
+
+ ReadPair _get_next_read_pair_in_ignore_mode();
+ ReadPair _get_next_read_pair_in_error_mode();
+ bool _is_valid_read_pair(
+ ReadPair &the_read_pair,
+ regmatch_t &match_1,
+ regmatch_t &match_2
+ );
+public:
enum {
- PAIR_MODE_ALLOW_UNPAIRED = 0,
PAIR_MODE_IGNORE_UNPAIRED,
PAIR_MODE_ERROR_ON_UNPAIRED
};
- static IParser * const get_parser(
- std:: string const &ifile_name
- );
-
- IParser( );
- virtual ~IParser( );
-
- virtual bool is_complete( ) = 0;
-
- // Note: 'get_next_read' exists for legacy reasons.
- // In the long term, it should be eliminated in favor of direct use of
- // 'imprint_next_read'. A potentially costly copy-by-value happens
- // upon return.
- // TODO: Eliminate all calls to 'get_next_read'.
- // Or switch to C++11 w/ move constructors
- inline Read get_next_read( )
- {
- Read the_read;
- imprint_next_read( the_read );
- return the_read;
- }
- virtual void imprint_next_read( Read &the_read ) = 0;
-
- virtual void imprint_next_read_pair(
- ReadPair &the_read_pair,
- uint8_t mode = PAIR_MODE_ERROR_ON_UNPAIRED
- );
+ explicit ReadParser(std::unique_ptr<SeqIO> pf);
+ explicit ReadParser(ReadParser& other);
+ virtual ~ReadParser();
- size_t get_num_reads()
- {
- return _num_reads;
- }
+ Read get_next_read();
+ ReadPair get_next_read_pair(uint8_t mode = PAIR_MODE_ERROR_ON_UNPAIRED);
-protected:
-
- size_t _num_reads;
- bool _have_qualities;
- regex_t _re_read_2_nosub;
- regex_t _re_read_1;
- regex_t _re_read_2;
-
-#if (0)
- void _imprint_next_read_pair_in_allow_mode(
- ReadPair &the_read_pair
- );
-#endif
-
- void _imprint_next_read_pair_in_ignore_mode(
- ReadPair &the_read_pair
- );
- void _imprint_next_read_pair_in_error_mode(
- ReadPair &the_read_pair
- );
- bool _is_valid_read_pair(
- ReadPair &the_read_pair, regmatch_t &match_1, regmatch_t &match_2
- );
+ size_t get_num_reads();
+ bool is_complete();
+ void close();
+}; // class ReadParser
-}; // struct IParser
-class SeqAnParser : public IParser
+class FastxReader
{
+private:
+ std::string _filename;
+ seqan::SequenceStream _stream;
+ uint32_t _spin_lock;
+ size_t _num_reads;
+ bool _have_qualities;
+ void _init();
public:
- explicit SeqAnParser( const char * filename );
- ~SeqAnParser( );
+ FastxReader();
+ FastxReader(const std::string& infile);
+ FastxReader(FastxReader& other);
+ ~FastxReader();
- bool is_complete( );
- void imprint_next_read(Read &the_read);
+ Read get_next_read();
+ bool is_complete();
+ size_t get_num_reads();
+ void close();
+}; // class FastxReader
-private:
- struct Handle;
-
- Handle* _private;
-
-};
inline PartitionID _parse_partition_id(std::string name)
{
@@ -204,21 +208,26 @@ inline PartitionID _parse_partition_id(std::string name)
if (*s == '\t') {
p = (PartitionID) atoi(s + 1);
} else {
- std::cerr << "consume_partitioned_fasta barfed on read " << name << "\n";
+ std::cerr << "consume_partitioned_fasta barfed on read "
+ << name << "\n";
throw khmer_exception();
}
return p;
}
+// Alias for generic/templated ReadParser pointer
+template<typename T> using ReadParserPtr = std::unique_ptr<ReadParser<T>>;
+// Convenience function
+template<typename SeqIO>
+ReadParserPtr<SeqIO> get_parser(const std::string& filename);
-} // namespace read_parsers
+// Alias for instantiated ReadParsers
+typedef std::unique_ptr<ReadParser<FastxReader>> FastxParserPtr;
+} // namespace read_parsers
} // namespace khmer
-
#endif // READ_PARSERS_HH
-
-// vim: set ft=cpp sts=4 sw=4 tw=80:
diff --git a/lib/storage.cc b/lib/storage.cc
new file mode 100644
index 0000000..488aebc
--- /dev/null
+++ b/lib/storage.cc
@@ -0,0 +1,916 @@
+/*
+This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+Copyright (C) 2016, The Regents of the University of California.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following
+ disclaimer in the documentation and/or other materials provided
+ with the distribution.
+
+ * Neither the name of the University of California nor the names
+ of its contributors may be used to endorse or promote products
+ derived from this software without specific prior written
+ permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+LICENSE (END)
+
+Contact: khmer-project at idyll.org
+*/
+
+#include <errno.h>
+#include <sstream> // IWYU pragma: keep
+#include <fstream>
+#include <iostream>
+
+#include "khmer_exception.hh"
+#include "hashtable.hh"
+#include "zlib.h"
+
+using namespace khmer;
+using namespace std;
+
+void Storage::set_use_bigcount(bool b)
+{
+ if (!_supports_bigcount) {
+ throw khmer_exception("bigcount is not supported for this storage.");
+ }
+ _use_bigcount = b;
+}
+
+bool Storage::get_use_bigcount()
+{
+ return _use_bigcount;
+}
+
+void BitStorage::update_from(const BitStorage& other)
+{
+ if (_tablesizes != other._tablesizes) {
+ throw khmer_exception("both nodegraphs must have same table sizes");
+ }
+
+ Byte tmp = 0;
+ for (unsigned int table_num = 0; table_num < _n_tables; table_num++) {
+ Byte * me = _counts[table_num];
+ Byte * ot = other._counts[table_num];
+ uint64_t tablesize = _tablesizes[table_num];
+ uint64_t tablebytes = tablesize / 8 + 1;
+
+ for (uint64_t index = 0; index < tablebytes; index++) {
+ // Bloom filters can be unioned with bitwise OR.
+ // First, get the new value
+ tmp = me[index] | ot[index];
+ if (table_num == 0) {
+ // We'd like for the merged filter to have an accurate
+ // count of occupied bins. First, observe that
+ // HammingDistance(x,y) is equivalent to
+ // HammingWeight(x^y). Then, observe that the number
+ // of additional occupied bins from the update is the
+ // hamming distance between the original bin and the
+ // OR'd bin. Thus, we can use the builtin popcountll
+ // function, which calls a hardware instruction for
+ // hamming weight, with the original and merged bin,
+ // to find the number of additional occupied bins.
+ _occupied_bins += __builtin_popcountll(me[index] ^ tmp);
+ }
+ me[index] = tmp;
+ }
+ }
+}
+
+
+void BitStorage::save(std::string outfilename, WordLength ksize)
+{
+ if (!_counts[0]) {
+ throw khmer_exception();
+ }
+
+ unsigned int save_ksize = ksize;
+ unsigned char save_n_tables = _n_tables;
+ unsigned long long save_tablesize;
+ unsigned long long save_occupied_bins = _occupied_bins;
+
+ ofstream outfile(outfilename.c_str(), ios::binary);
+
+ outfile.write(SAVED_SIGNATURE, 4);
+ unsigned char version = SAVED_FORMAT_VERSION;
+ outfile.write((const char *) &version, 1);
+
+ unsigned char ht_type = SAVED_HASHBITS;
+ outfile.write((const char *) &ht_type, 1);
+
+ outfile.write((const char *) &save_ksize, sizeof(save_ksize));
+ outfile.write((const char *) &save_n_tables, sizeof(save_n_tables));
+ outfile.write((const char *) &save_occupied_bins,
+ sizeof(save_occupied_bins));
+
+ for (unsigned int i = 0; i < _n_tables; i++) {
+ save_tablesize = _tablesizes[i];
+ unsigned long long tablebytes = save_tablesize / 8 + 1;
+
+ outfile.write((const char *) &save_tablesize, sizeof(save_tablesize));
+
+ outfile.write((const char *) _counts[i], tablebytes);
+ }
+ if (outfile.fail()) {
+ throw khmer_file_exception(strerror(errno));
+ }
+ outfile.close();
+}
+
+/**
+ * Loads @param infilename into BitStorage, with error checking on
+ * file type and file version. Populates _counts internally.
+ */
+void BitStorage::load(std::string infilename, WordLength &ksize)
+{
+ ifstream infile;
+
+ // configure ifstream to raise exceptions for everything.
+ infile.exceptions(std::ifstream::failbit | std::ifstream::badbit |
+ std::ifstream::eofbit);
+
+ try {
+ infile.open(infilename.c_str(), ios::binary);
+ } catch (std::ifstream::failure &e) {
+ std::string err;
+ if (!infile.is_open()) {
+ err = "Cannot open k-mer graph file: " + infilename;
+ } else {
+ err = "Unknown error in opening file: " + infilename;
+ }
+ throw khmer_file_exception(err);
+ } catch (const std::exception &e) {
+ // Catching std::exception is a stopgap for
+ // https://gcc.gnu.org/bugzilla/show_bug.cgi?id=66145
+ std::string err = "Unknown error opening file: " + infilename + " "
+ + strerror(errno);
+ throw khmer_file_exception(err);
+ }
+
+ if (_counts) {
+ for (unsigned int i = 0; i < _n_tables; i++) {
+ delete[] _counts[i];
+ _counts[i] = NULL;
+ }
+ delete[] _counts;
+ _counts = NULL;
+ }
+ _tablesizes.clear();
+
+ try {
+ unsigned int save_ksize = 0;
+ unsigned char save_n_tables = 0;
+ unsigned long long save_tablesize = 0;
+ unsigned long long save_occupied_bins = 0;
+ char signature[4];
+ unsigned char version, ht_type;
+
+ infile.read(signature, 4);
+ infile.read((char *) &version, 1);
+ infile.read((char *) &ht_type, 1);
+ if (!(std::string(signature, 4) == SAVED_SIGNATURE)) {
+ std::ostringstream err;
+ err << "Does not start with signature for a khmer file: 0x";
+ for(size_t i=0; i < 4; ++i) {
+ err << std::hex << (int) signature[i];
+ }
+ err << " Should be: " << SAVED_SIGNATURE;
+ throw khmer_file_exception(err.str());
+ } else if (!(version == SAVED_FORMAT_VERSION)) {
+ std::ostringstream err;
+ err << "Incorrect file format version " << (int) version
+ << " while reading k-mer graph from " << infilename
+ << "; should be " << (int) SAVED_FORMAT_VERSION;
+ throw khmer_file_exception(err.str());
+ } else if (!(ht_type == SAVED_HASHBITS)) {
+ std::ostringstream err;
+ err << "Incorrect file format type " << (int) ht_type
+ << " while reading k-mer graph from " << infilename;
+ throw khmer_file_exception(err.str());
+ }
+
+ infile.read((char *) &save_ksize, sizeof(save_ksize));
+ infile.read((char *) &save_n_tables, sizeof(save_n_tables));
+ infile.read((char *) &save_occupied_bins, sizeof(save_occupied_bins));
+
+ ksize = (WordLength) save_ksize;
+ _n_tables = (unsigned int) save_n_tables;
+ _occupied_bins = save_occupied_bins;
+
+ _counts = new Byte*[_n_tables];
+ for (unsigned int i = 0; i < _n_tables; i++) {
+ uint64_t tablesize;
+ unsigned long long tablebytes;
+
+ infile.read((char *) &save_tablesize, sizeof(save_tablesize));
+
+ tablesize = save_tablesize;
+ _tablesizes.push_back(tablesize);
+
+ tablebytes = tablesize / 8 + 1;
+ _counts[i] = new Byte[tablebytes];
+
+ unsigned long long loaded = 0;
+ while (loaded != tablebytes) {
+ infile.read((char *) _counts[i], tablebytes - loaded);
+ loaded += infile.gcount();
+ }
+ }
+ infile.close();
+ } catch (std::ifstream::failure &e) {
+ std::string err;
+ if (infile.eof()) {
+ err = "Unexpected end of k-mer graph file: " + infilename;
+ } else {
+ err = "Error reading from k-mer graph file: " + infilename;
+ }
+ throw khmer_file_exception(err);
+ } catch (const std::exception &e) {
+ // Catching std::exception is a stopgap for
+ // https://gcc.gnu.org/bugzilla/show_bug.cgi?id=66145
+ std::string err = "Unknown error opening file: " + infilename + " "
+ + strerror(errno);
+ throw khmer_file_exception(err);
+ }
+}
+
+void ByteStorageFile::save(
+ const std::string &outfilename,
+ WordLength ksize,
+ const ByteStorage &store)
+{
+ std::string filename(outfilename);
+ size_t found = filename.find_last_of(".");
+ std::string type = filename.substr(found + 1);
+
+ if (type == "gz") {
+ ByteStorageGzFileWriter(filename, ksize, store);
+ } else {
+ ByteStorageFileWriter(filename, ksize, store);
+ }
+}
+
+
+ByteStorageFileReader::ByteStorageFileReader(
+ const std::string &infilename,
+ WordLength& ksize,
+ ByteStorage &store)
+{
+ ifstream infile;
+ // configure ifstream to raise exceptions for everything.
+ infile.exceptions(std::ifstream::failbit | std::ifstream::badbit |
+ std::ifstream::eofbit);
+
+ try {
+ infile.open(infilename.c_str(), ios::binary);
+ } catch (std::ifstream::failure &e) {
+ std::string err;
+ if (!infile.is_open()) {
+ err = "Cannot open k-mer count file: " + infilename;
+ } else {
+ err = "Unknown error in opening file: " + infilename;
+ }
+ throw khmer_file_exception(err + " " + strerror(errno));
+ } catch (const std::exception &e) {
+ std::string err = "Unknown error opening file: " + infilename + " "
+ + strerror(errno);
+ throw khmer_file_exception(err);
+ }
+
+ if (store._counts) {
+ for (unsigned int i = 0; i < store._n_tables; i++) {
+ delete[] store._counts[i];
+ store._counts[i] = NULL;
+ }
+ delete[] store._counts;
+ store._counts = NULL;
+ }
+ store._tablesizes.clear();
+
+ try {
+ unsigned int save_ksize = 0;
+ unsigned char save_n_tables = 0;
+ unsigned long long save_tablesize = 0;
+ unsigned long long save_occupied_bins = 0;
+ char signature [4];
+ unsigned char version = 0, ht_type = 0, use_bigcount = 0;
+
+ infile.read(signature, 4);
+ infile.read((char *) &version, 1);
+ infile.read((char *) &ht_type, 1);
+ if (!(std::string(signature, 4) == SAVED_SIGNATURE)) {
+ std::ostringstream err;
+ err << "Does not start with signature for a khmer file: 0x";
+ for(size_t i=0; i < 4; ++i) {
+ err << std::hex << (int) signature[i];
+ }
+ err << " Should be: " << SAVED_SIGNATURE;
+ throw khmer_file_exception(err.str());
+ } else if (!(version == SAVED_FORMAT_VERSION)) {
+ std::ostringstream err;
+ err << "Incorrect file format version " << (int) version
+ << " while reading k-mer count file from " << infilename
+ << "; should be " << (int) SAVED_FORMAT_VERSION;
+ throw khmer_file_exception(err.str());
+ } else if (!(ht_type == SAVED_COUNTING_HT)) {
+ std::ostringstream err;
+ err << "Incorrect file format type " << (int) ht_type
+ << " while reading k-mer count file from " << infilename;
+ throw khmer_file_exception(err.str());
+ }
+
+ infile.read((char *) &use_bigcount, 1);
+ infile.read((char *) &save_ksize, sizeof(save_ksize));
+ infile.read((char *) &save_n_tables, sizeof(save_n_tables));
+ infile.read((char *) &save_occupied_bins, sizeof(save_occupied_bins));
+
+ ksize = (WordLength) save_ksize;
+ store._n_tables = (unsigned int) save_n_tables;
+ store._occupied_bins = save_occupied_bins;
+
+ store._use_bigcount = use_bigcount;
+
+ store._counts = new Byte*[store._n_tables];
+ for (unsigned int i = 0; i < store._n_tables; i++) {
+ store._counts[i] = NULL;
+ }
+
+ for (unsigned int i = 0; i < store._n_tables; i++) {
+ uint64_t tablesize;
+
+ infile.read((char *) &save_tablesize, sizeof(save_tablesize));
+
+ tablesize = save_tablesize;
+ store._tablesizes.push_back(tablesize);
+
+ store._counts[i] = new Byte[tablesize];
+
+ unsigned long long loaded = 0;
+ while (loaded != tablesize) {
+ infile.read((char *) store._counts[i], tablesize - loaded);
+ loaded += infile.gcount();
+ }
+ }
+
+ uint64_t n_counts = 0;
+ infile.read((char *) &n_counts, sizeof(n_counts));
+
+ if (n_counts) {
+ store._bigcounts.clear();
+
+ HashIntoType kmer;
+ BoundedCounterType count;
+
+ for (uint64_t n = 0; n < n_counts; n++) {
+ infile.read((char *) &kmer, sizeof(kmer));
+ infile.read((char *) &count, sizeof(count));
+ store._bigcounts[kmer] = count;
+ }
+ }
+
+ infile.close();
+ } catch (std::ifstream::failure &e) {
+ std::string err;
+ if (infile.eof()) {
+ err = "Unexpected end of k-mer count file: " + infilename;
+ } else {
+ err = "Error reading from k-mer count file: " + infilename + " "
+ + strerror(errno);
+ }
+ throw khmer_file_exception(err);
+ } catch (const std::exception &e) {
+ std::string err = "Error reading from k-mer count file: " + infilename + " "
+ + strerror(errno);
+ throw khmer_file_exception(err);
+ }
+}
+
+ByteStorageGzFileReader::ByteStorageGzFileReader(
+ const std::string &infilename,
+ WordLength &ksize,
+ ByteStorage &store)
+{
+ gzFile infile = gzopen(infilename.c_str(), "rb");
+ if (infile == Z_NULL) {
+ std::string err = "Cannot open k-mer count file: " + infilename;
+ throw khmer_file_exception(err);
+ }
+
+ if (store._counts) {
+ for (unsigned int i = 0; i < store._n_tables; i++) {
+ delete[] store._counts[i];
+ store._counts[i] = NULL;
+ }
+ delete[] store._counts;
+ store._counts = NULL;
+ }
+ store._tablesizes.clear();
+
+ unsigned int save_ksize = 0;
+ unsigned char save_n_tables = 0;
+ unsigned long long save_tablesize = 0;
+ unsigned long long save_occupied_bins = 0;
+ char signature [4];
+ unsigned char version, ht_type, use_bigcount;
+
+ int read_s = gzread(infile, signature, 4);
+ int read_v = gzread(infile, (char *) &version, 1);
+ int read_t = gzread(infile, (char *) &ht_type, 1);
+ if (read_s <= 0 || read_v <= 0 || read_t <= 0) {
+ std::string err = "K-mer count file read error: " + infilename + " "
+ + strerror(errno);
+ gzclose(infile);
+ throw khmer_file_exception(err);
+ } else if (!(std::string(signature, 4) == SAVED_SIGNATURE)) {
+ std::ostringstream err;
+ err << "Does not start with signature for a khmer " <<
+ "file: " << signature << " Should be: " <<
+ SAVED_SIGNATURE;
+ throw khmer_file_exception(err.str());
+ } else if (!(version == SAVED_FORMAT_VERSION)
+ || !(ht_type == SAVED_COUNTING_HT)) {
+ if (!(version == SAVED_FORMAT_VERSION)) {
+ std::ostringstream err;
+ err << "Incorrect file format version " << (int) version
+ << " while reading k-mer count file from " << infilename
+ << "; should be " << (int) SAVED_FORMAT_VERSION;
+ gzclose(infile);
+ throw khmer_file_exception(err.str());
+ } else if (!(ht_type == SAVED_COUNTING_HT)) {
+ std::ostringstream err;
+ err << "Incorrect file format type " << (int) ht_type
+ << " while reading k-mer count file from " << infilename;
+ gzclose(infile);
+ throw khmer_file_exception(err.str());
+ }
+ }
+
+ int read_b = gzread(infile, (char *) &use_bigcount, 1);
+ int read_k = gzread(infile, (char *) &save_ksize, sizeof(save_ksize));
+ int read_nt = gzread(infile, (char *) &save_n_tables,
+ sizeof(save_n_tables));
+ int read_ob = gzread(infile, (char *) &save_occupied_bins,
+ sizeof(save_occupied_bins));
+
+ if (read_b <= 0 || read_k <= 0 || read_nt <= 0 || read_ob <= 0) {
+ std::string err = "K-mer count file header read error: " + infilename
+ + " " + strerror(errno);
+ gzclose(infile);
+ throw khmer_file_exception(err);
+ }
+
+ ksize = (WordLength) save_ksize;
+ store._occupied_bins = save_occupied_bins;
+ store._n_tables = (unsigned int) save_n_tables;
+
+ store._use_bigcount = use_bigcount;
+
+ store._counts = new Byte*[store._n_tables];
+ for (unsigned int i = 0; i < store._n_tables; i++) {
+ uint64_t tablesize;
+
+ read_b = gzread(infile, (char *) &save_tablesize,
+ sizeof(save_tablesize));
+
+ if (read_b <= 0) {
+ std::string gzerr = gzerror(infile, &read_b);
+ std::string err = "K-mer count file header read error: "
+ + infilename;
+ if (read_b == Z_ERRNO) {
+ err = err + " " + strerror(errno);
+ } else {
+ err = err + " " + gzerr;
+ }
+ gzclose(infile);
+ throw khmer_file_exception(err);
+ }
+
+ tablesize = save_tablesize;
+ store._tablesizes.push_back(tablesize);
+
+ store._counts[i] = new Byte[tablesize];
+
+ uint64_t loaded = 0;
+ while (loaded != tablesize) {
+ unsigned long long to_read_ll = tablesize - loaded;
+ unsigned int to_read_int;
+ // Zlib can only read chunks of at most INT_MAX bytes.
+ if (to_read_ll > INT_MAX) {
+ to_read_int = INT_MAX;
+ } else {
+ to_read_int = (unsigned int) to_read_ll;
+ }
+ read_b = gzread(infile, (char *) store._counts[i], to_read_int);
+
+ if (read_b <= 0) {
+ std::string gzerr = gzerror(infile, &read_b);
+ std::string err = "K-mer count file read error: " + infilename;
+ if (read_b == Z_ERRNO) {
+ err = err + " " + strerror(errno);
+ } else {
+ err = err + " " + gzerr;
+ }
+ gzclose(infile);
+ throw khmer_file_exception(err);
+ }
+
+ loaded += read_b;
+ }
+ }
+
+ uint64_t n_counts = 0;
+ read_b = gzread(infile, (char *) &n_counts, sizeof(n_counts));
+ if (read_b <= 0) {
+ std::string gzerr = gzerror(infile, &read_b);
+ std::string err = "K-mer count header read error: " + infilename;
+ if (read_b == Z_ERRNO) {
+ err = err + " " + strerror(errno);
+ } else {
+ err = err + " " + gzerr;
+ }
+ gzclose(infile);
+ throw khmer_file_exception(err);
+ }
+
+ if (n_counts) {
+ store._bigcounts.clear();
+
+ HashIntoType kmer;
+ BoundedCounterType count;
+
+ for (uint64_t n = 0; n < n_counts; n++) {
+ int read_k = gzread(infile, (char *) &kmer, sizeof(kmer));
+ int read_c = gzread(infile, (char *) &count, sizeof(count));
+
+ if (read_k <= 0 || read_c <= 0) {
+ std::string gzerr = gzerror(infile, &read_b);
+ std::string err = "K-mer count read error: " + infilename;
+ if (read_b == Z_ERRNO) {
+ err = err + " " + strerror(errno);
+ } else {
+ err = err + " " + gzerr;
+ }
+ gzclose(infile);
+ throw khmer_file_exception(err);
+ }
+
+ store._bigcounts[kmer] = count;
+ }
+ }
+
+ gzclose(infile);
+}
+
+ByteStorageFileWriter::ByteStorageFileWriter(
+ const std::string &outfilename,
+ const WordLength ksize,
+ const ByteStorage& store)
+{
+ if (!store._counts[0]) {
+ throw khmer_exception();
+ }
+
+ unsigned int save_ksize = ksize;
+ unsigned char save_n_tables = store._n_tables;
+ unsigned long long save_tablesize;
+ unsigned long long save_occupied_bins = store._occupied_bins;
+
+ ofstream outfile(outfilename.c_str(), ios::binary);
+
+ outfile.write(SAVED_SIGNATURE, 4);
+ unsigned char version = SAVED_FORMAT_VERSION;
+ outfile.write((const char *) &version, 1);
+
+ unsigned char ht_type = SAVED_COUNTING_HT;
+ outfile.write((const char *) &ht_type, 1);
+
+ unsigned char use_bigcount = 0;
+ if (store._use_bigcount) {
+ use_bigcount = 1;
+ }
+ outfile.write((const char *) &use_bigcount, 1);
+
+ outfile.write((const char *) &save_ksize, sizeof(save_ksize));
+ outfile.write((const char *) &save_n_tables, sizeof(save_n_tables));
+ outfile.write((const char *) &save_occupied_bins,
+ sizeof(save_occupied_bins));
+
+ for (unsigned int i = 0; i < save_n_tables; i++) {
+ save_tablesize = store._tablesizes[i];
+
+ outfile.write((const char *) &save_tablesize, sizeof(save_tablesize));
+ outfile.write((const char *) store._counts[i], save_tablesize);
+ }
+
+ uint64_t n_counts = store._bigcounts.size();
+ outfile.write((const char *) &n_counts, sizeof(n_counts));
+
+ if (n_counts) {
+ KmerCountMap::const_iterator it = store._bigcounts.begin();
+
+ for (; it != store._bigcounts.end(); ++it) {
+ outfile.write((const char *) &it->first, sizeof(it->first));
+ outfile.write((const char *) &it->second, sizeof(it->second));
+ }
+ }
+ if (outfile.fail()) {
+ throw khmer_file_exception(strerror(errno));
+ }
+ outfile.close();
+}
+
+ByteStorageGzFileWriter::ByteStorageGzFileWriter(
+ const std::string &outfilename,
+ const WordLength ksize,
+ const ByteStorage &store)
+{
+ if (!store._counts[0]) {
+ throw khmer_exception();
+ }
+
+ int errnum = 0;
+ unsigned int save_ksize = ksize;
+ unsigned char save_n_tables = store._n_tables;
+ unsigned long long save_tablesize;
+ unsigned long long save_occupied_bins = store._occupied_bins;
+
+ gzFile outfile = gzopen(outfilename.c_str(), "wb");
+ if (outfile == NULL) {
+ const char * error = gzerror(outfile, &errnum);
+ if (errnum == Z_ERRNO) {
+ throw khmer_file_exception(strerror(errno));
+ } else {
+ throw khmer_file_exception(error);
+ }
+ }
+
+ gzwrite(outfile, SAVED_SIGNATURE, 4);
+ unsigned char version = SAVED_FORMAT_VERSION;
+ gzwrite(outfile, (const char *) &version, 1);
+
+ unsigned char ht_type = SAVED_COUNTING_HT;
+ gzwrite(outfile, (const char *) &ht_type, 1);
+
+ unsigned char use_bigcount = 0;
+ if (store._use_bigcount) {
+ use_bigcount = 1;
+ }
+ gzwrite(outfile, (const char *) &use_bigcount, 1);
+
+ gzwrite(outfile, (const char *) &save_ksize, sizeof(save_ksize));
+ gzwrite(outfile, (const char *) &save_n_tables, sizeof(save_n_tables));
+ gzwrite(outfile, (const char *) &save_occupied_bins,
+ sizeof(save_occupied_bins));
+
+ for (unsigned int i = 0; i < save_n_tables; i++) {
+ save_tablesize = store._tablesizes[i];
+
+ gzwrite(outfile, (const char *) &save_tablesize,
+ sizeof(save_tablesize));
+ unsigned long long written = 0;
+ while (written != save_tablesize) {
+ unsigned long long to_write_ll = save_tablesize - written;
+ unsigned int to_write_int;
+ int gz_result;
+ // Zlib can only write chunks of at most INT_MAX bytes.
+ if (to_write_ll > INT_MAX) {
+ to_write_int = INT_MAX;
+ } else {
+ to_write_int = (unsigned int) to_write_ll;
+ }
+ gz_result = gzwrite(outfile, (const char *) store._counts[i],
+ to_write_int);
+ // Zlib returns 0 on error
+ if (gz_result == 0) {
+ int errcode = 0;
+ const char *err_msg;
+ std::ostringstream msg;
+
+ msg << "gzwrite failed while writing counting hash: ";
+ // Get zlib error
+ err_msg = gzerror(outfile, &errcode);
+ if (errcode != Z_ERRNO) {
+ // Zlib error, not stdlib
+ msg << err_msg;
+ gzclearerr(outfile);
+ } else {
+ // stdlib error
+ msg << strerror(errno);
+ }
+ gzclose(outfile);
+ throw khmer_file_exception(msg.str());
+ }
+ written += gz_result;
+ }
+ }
+
+ uint64_t n_counts = store._bigcounts.size();
+ gzwrite(outfile, (const char *) &n_counts, sizeof(n_counts));
+
+ if (n_counts) {
+ KmerCountMap::const_iterator it = store._bigcounts.begin();
+
+ for (; it != store._bigcounts.end(); ++it) {
+ gzwrite(outfile, (const char *) &it->first, sizeof(it->first));
+ gzwrite(outfile, (const char *) &it->second, sizeof(it->second));
+ }
+ }
+ const char * error = gzerror(outfile, &errnum);
+ if (errnum == Z_ERRNO) {
+ throw khmer_file_exception(strerror(errno));
+ } else if (errnum != Z_OK) {
+ throw khmer_file_exception(error);
+ }
+ gzclose(outfile);
+}
+
+void ByteStorageFile::load(
+ const std::string &infilename,
+ WordLength &ksize,
+ ByteStorage &store)
+{
+ std::string filename(infilename);
+ size_t found = filename.find_last_of(".");
+ std::string type = filename.substr(found + 1);
+
+ if (type == "gz") {
+ ByteStorageGzFileReader(filename, ksize, store);
+ } else {
+ ByteStorageFileReader(filename, ksize, store);
+ }
+}
+
+void ByteStorage::save(std::string outfilename, WordLength ksize)
+{
+ ByteStorageFile::save(outfilename, ksize, *this);
+}
+
+void ByteStorage::load(std::string infilename, WordLength& ksize)
+{
+ ByteStorageFile::load(infilename, ksize, *this);
+}
+
+
+void NibbleStorage::save(std::string outfilename, WordLength ksize)
+{
+ if (!_counts[0]) {
+ throw khmer_exception();
+ }
+
+ unsigned int save_ksize = ksize;
+ unsigned char save_n_tables = _n_tables;
+ unsigned long long save_tablesize;
+ unsigned long long save_occupied_bins = _occupied_bins;
+
+ ofstream outfile(outfilename.c_str(), ios::binary);
+
+ outfile.write(SAVED_SIGNATURE, 4);
+ unsigned char version = SAVED_FORMAT_VERSION;
+ outfile.write((const char *) &version, 1);
+
+ unsigned char ht_type = SAVED_SMALLCOUNT;
+ outfile.write((const char *) &ht_type, 1);
+
+ outfile.write((const char *) &save_ksize, sizeof(save_ksize));
+ outfile.write((const char *) &save_n_tables, sizeof(save_n_tables));
+ outfile.write((const char *) &save_occupied_bins,
+ sizeof(save_occupied_bins));
+
+ for (unsigned int i = 0; i < save_n_tables; i++) {
+ save_tablesize = _tablesizes[i];
+
+ outfile.write((const char *) &save_tablesize, sizeof(save_tablesize));
+ outfile.write((const char *) _counts[i], save_tablesize / 2 + 1);
+ }
+}
+
+void NibbleStorage::load(std::string infilename, WordLength& ksize)
+{
+ ifstream infile;
+ // configure ifstream to raise exceptions for everything.
+ infile.exceptions(std::ifstream::failbit | std::ifstream::badbit |
+ std::ifstream::eofbit);
+
+ try {
+ infile.open(infilename.c_str(), ios::binary);
+ } catch (std::ifstream::failure &e) {
+ std::string err;
+ if (!infile.is_open()) {
+ err = "Cannot open k-mer count file: " + infilename;
+ } else {
+ err = "Unknown error in opening file: " + infilename;
+ }
+ throw khmer_file_exception(err + " " + strerror(errno));
+ } catch (const std::exception &e) {
+ std::string err = "Unknown error opening file: " + infilename + " "
+ + strerror(errno);
+ throw khmer_file_exception(err);
+ }
+
+ if (_counts) {
+ for (unsigned int i = 0; i < _n_tables; i++) {
+ delete[] _counts[i];
+ _counts[i] = NULL;
+ }
+ delete[] _counts;
+ _counts = NULL;
+ }
+ _tablesizes.clear();
+
+ try {
+ unsigned int save_ksize = 0;
+ unsigned char save_n_tables = 0;
+ unsigned long long save_tablesize = 0;
+ unsigned long long save_occupied_bins = 0;
+ char signature [4];
+ unsigned char version = 0, ht_type = 0;
+
+ infile.read(signature, 4);
+ infile.read((char *) &version, 1);
+ infile.read((char *) &ht_type, 1);
+ if (!(std::string(signature, 4) == SAVED_SIGNATURE)) {
+ std::ostringstream err;
+ err << "Does not start with signature for a khmer file: 0x";
+ for(size_t i=0; i < 4; ++i) {
+ err << std::hex << (int) signature[i];
+ }
+ err << " Should be: " << SAVED_SIGNATURE;
+ throw khmer_file_exception(err.str());
+ } else if (!(version == SAVED_FORMAT_VERSION)) {
+ std::ostringstream err;
+ err << "Incorrect file format version " << (int) version
+ << " while reading k-mer count file from " << infilename
+ << "; should be " << (int) SAVED_FORMAT_VERSION;
+ throw khmer_file_exception(err.str());
+ } else if (!(ht_type == SAVED_SMALLCOUNT)) {
+ std::ostringstream err;
+ err << "Incorrect file format type " << (int) ht_type
+ << " while reading k-mer count file from " << infilename;
+ throw khmer_file_exception(err.str());
+ }
+
+ infile.read((char *) &save_ksize, sizeof(save_ksize));
+ infile.read((char *) &save_n_tables, sizeof(save_n_tables));
+ infile.read((char *) &save_occupied_bins, sizeof(save_occupied_bins));
+
+ ksize = (WordLength) save_ksize;
+ _n_tables = (unsigned int) save_n_tables;
+ _occupied_bins = save_occupied_bins;
+
+ _counts = new Byte*[_n_tables];
+ for (unsigned int i = 0; i < _n_tables; i++) {
+ _counts[i] = NULL;
+ }
+
+ for (unsigned int i = 0; i < _n_tables; i++) {
+ uint64_t tablesize;
+ uint64_t tablebytes;
+
+ infile.read((char *) &save_tablesize, sizeof(save_tablesize));
+
+ tablebytes = save_tablesize / 2 + 1;
+ tablesize = save_tablesize;
+ _tablesizes.push_back(tablesize);
+
+ _counts[i] = new Byte[tablebytes];
+
+ unsigned long long loaded = 0;
+ while (loaded != tablebytes) {
+ infile.read((char *) _counts[i], tablebytes - loaded);
+ loaded += infile.gcount();
+ }
+ }
+ infile.close();
+ } catch (std::ifstream::failure &e) {
+ std::string err;
+ if (infile.eof()) {
+ err = "Unexpected end of k-mer count file: " + infilename;
+ } else {
+ err = "Error reading from k-mer count file: " + infilename + " "
+ + strerror(errno);
+ }
+ throw khmer_file_exception(err);
+ } catch (const std::exception &e) {
+ std::string err = "Error reading from k-mer count file: " + infilename + " "
+ + strerror(errno);
+ throw khmer_file_exception(err);
+ }
+}
diff --git a/lib/storage.hh b/lib/storage.hh
new file mode 100644
index 0000000..4228a35
--- /dev/null
+++ b/lib/storage.hh
@@ -0,0 +1,651 @@
+/*
+This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+Copyright (C) 2016, The Regents of the University of California.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following
+ disclaimer in the documentation and/or other materials provided
+ with the distribution.
+
+ * Neither the name of the University of California nor the names
+ of its contributors may be used to endorse or promote products
+ derived from this software without specific prior written
+ permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+LICENSE (END)
+
+Contact: khmer-project at idyll.org
+*/
+
+#ifndef STORAGE_HH
+#define STORAGE_HH
+
+#include <cassert>
+#include <array>
+#include <mutex>
+using MuxGuard = std::lock_guard<std::mutex>;
+
+namespace khmer
+{
+typedef std::map<HashIntoType, BoundedCounterType> KmerCountMap;
+
+//
+// base Storage class for hashtable-related storage of information in memory.
+//
+
+class Storage
+{
+protected:
+ bool _supports_bigcount;
+ bool _use_bigcount;
+
+public:
+ Storage() : _supports_bigcount(false), _use_bigcount(false) { } ;
+ virtual ~Storage() { }
+ virtual std::vector<uint64_t> get_tablesizes() const = 0;
+ virtual const size_t n_tables() const = 0;
+ virtual void save(std::string, WordLength) = 0;
+ virtual void load(std::string, WordLength&) = 0;
+ virtual const uint64_t n_occupied() const = 0;
+ virtual const uint64_t n_unique_kmers() const = 0;
+ virtual BoundedCounterType test_and_set_bits( HashIntoType khash ) = 0;
+ virtual void add(HashIntoType khash) = 0;
+ virtual const BoundedCounterType get_count(HashIntoType khash) const = 0;
+ virtual Byte ** get_raw_tables() = 0;
+
+ void set_use_bigcount(bool b);
+ bool get_use_bigcount();
+};
+
+
+/*
+ * \class BitStorage
+ *
+ * \brief A Bloom filter implementation.
+ *
+ * BitStorage is used to track presence/absence of k-mers by Hashtable
+ * and derived classes. It contains 'n_tables' different tables of
+ * bitsizes specified in 'tablesizes' (so 1/8 for bytesizes).
+ *
+ * Like other Storage classes, BitStorage manages setting the bits and
+ * tracking statistics, as well as save/load, and not much else.
+ *
+ */
+
+class BitStorage : public Storage
+{
+protected:
+ std::vector<uint64_t> _tablesizes;
+ size_t _n_tables;
+ uint64_t _occupied_bins;
+ uint64_t _n_unique_kmers;
+ Byte ** _counts;
+
+public:
+ BitStorage(std::vector<uint64_t>& tablesizes) :
+ _tablesizes(tablesizes)
+ {
+ _occupied_bins = 0;
+ _n_unique_kmers = 0;
+
+ _allocate_counters();
+ }
+ ~BitStorage()
+ {
+ if (_counts) {
+ for (size_t i = 0; i < _n_tables; i++) {
+ delete[] _counts[i];
+ _counts[i] = NULL;
+ }
+ delete[] _counts;
+ _counts = NULL;
+
+ _n_tables = 0;
+ }
+ }
+
+ void _allocate_counters()
+ {
+ _n_tables = _tablesizes.size();
+
+ _counts = new Byte*[_n_tables];
+
+ for (size_t i = 0; i < _n_tables; i++) {
+ uint64_t tablesize = _tablesizes[i];
+ uint64_t tablebytes = tablesize / 8 + 1;
+
+ _counts[i] = new Byte[tablebytes];
+ memset(_counts[i], 0, tablebytes);
+ }
+ }
+
+ // Accessors for protected/private table info members
+ std::vector<uint64_t> get_tablesizes() const
+ {
+ return _tablesizes;
+ }
+
+ const size_t n_tables() const
+ {
+ return _n_tables;
+ }
+
+ void save(std::string, WordLength ksize);
+ void load(std::string, WordLength& ksize);
+
+ // count number of occupied bins
+ const uint64_t n_occupied() const
+ {
+ return _occupied_bins;
+ }
+
+ const uint64_t n_unique_kmers() const
+ {
+ return _n_unique_kmers;
+ }
+
+ // Get and set the hashbits for the given kmer hash.
+ // Generally, it is better to keep tests and mutations separate,
+ // but, in the interests of efficiency and thread safety,
+ // tests and mutations are being blended here against conventional
+ // software engineering wisdom.
+ inline
+ BoundedCounterType
+ test_and_set_bits( HashIntoType khash )
+ {
+ bool is_new_kmer = false;
+
+ for (size_t i = 0; i < _n_tables; i++) {
+ uint64_t bin = khash % _tablesizes[i];
+ uint64_t byte = bin / 8;
+ unsigned char bit = (unsigned char)(1 << (bin % 8));
+
+ unsigned char bits_orig = __sync_fetch_and_or( *(_counts + i) +
+ byte, bit );
+ if (!(bits_orig & bit)) {
+ if (i == 0) {
+ __sync_add_and_fetch( &_occupied_bins, 1 );
+ }
+ is_new_kmer = true;
+ }
+ } // iteration over hashtables
+
+ if (is_new_kmer) {
+ __sync_add_and_fetch( &_n_unique_kmers, 1 );
+ return 1; // kmer not seen before
+ }
+
+ return 0; // kmer already seen
+ } // test_and_set_bits
+
+ inline void add(HashIntoType khash)
+ {
+ test_and_set_bits(khash);
+ }
+
+ // get the count for the given k-mer hash.
+ inline const BoundedCounterType get_count(HashIntoType khash) const
+ {
+ for (size_t i = 0; i < _n_tables; i++) {
+ uint64_t bin = khash % _tablesizes[i];
+ uint64_t byte = bin / 8;
+ unsigned char bit = bin % 8;
+
+ if (!(_counts[i][byte] & (1 << bit))) {
+ return 0;
+ }
+ }
+ return 1;
+ }
+
+ // Writing to the tables outside of defined methods has undefined behavior!
+ // As such, this should only be used to return read-only interfaces
+ Byte ** get_raw_tables()
+ {
+ return _counts;
+ }
+
+ void update_from(const BitStorage&);
+};
+
+
+/*
+ * \class NibbleStorage
+ *
+ * \brief A A CountMin sketch implementation using 4bit counters.
+ *
+ * NibbleStorage is used to track counts of k-mers by Hashtable
+ * and derived classes. It contains 'n_tables' different tables of
+ * 'tablesizes' entries. It allocates half a byte per table entry.
+ *
+ * Like other Storage classes, NibbleStorage manages setting the bits and
+ * tracking statistics, as well as save/load, and not much else.
+ *
+ */
+class NibbleStorage : public Storage
+{
+protected:
+ // table size is measured in number of entries in the table, not in bytes
+ std::vector<uint64_t> _tablesizes;
+ size_t _n_tables;
+ uint64_t _occupied_bins;
+ uint64_t _n_unique_kmers;
+ std::array<std::mutex, 32> mutexes;
+ static constexpr uint8_t _max_count{15};
+ Byte ** _counts;
+
+ // Compute index into the table, this retrieves the correct byte
+ // which you then need to select the correct nibble from
+ uint64_t _table_index(const HashIntoType k, const uint64_t tablesize) const
+ {
+ return (k % tablesize) / 2;
+ }
+ // Compute which half of the byte to use for this hash value
+ uint8_t _mask(const HashIntoType k, const uint64_t tablesize) const
+ {
+ return (k%tablesize)%2 ? 15 : 240;
+ }
+ // Compute which half of the byte to use for this hash value
+ uint8_t _shift(const HashIntoType k, const uint64_t tablesize) const
+ {
+ return (k%tablesize)%2 ? 0 : 4;
+ }
+
+public:
+ NibbleStorage(std::vector<uint64_t>& tablesizes) :
+ _tablesizes{tablesizes},
+ _occupied_bins{0}, _n_unique_kmers{0}
+ {
+ // to allow more than 32 tables increase the size of mutex pool
+ assert(_n_tables <= 32);
+ _allocate_counters();
+ }
+
+ ~NibbleStorage()
+ {
+ if (_counts) {
+ for (size_t i = 0; i < _n_tables; i++) {
+ delete[] _counts[i];
+ _counts[i] = NULL;
+ }
+ delete[] _counts;
+ _counts = NULL;
+ _n_tables = 0;
+ }
+ }
+
+ void _allocate_counters()
+ {
+ _n_tables = _tablesizes.size();
+
+ _counts = new Byte*[_n_tables];
+
+ for (size_t i = 0; i < _n_tables; i++) {
+ const uint64_t tablesize = _tablesizes[i];
+ const uint64_t tablebytes = tablesize / 2 + 1;
+
+ _counts[i] = new Byte[tablebytes];
+ memset(_counts[i], 0, tablebytes);
+ }
+ }
+
+
+ BoundedCounterType test_and_set_bits(HashIntoType khash)
+ {
+ BoundedCounterType x = get_count(khash);
+ add(khash);
+ return !x;
+ }
+
+ void add(HashIntoType khash)
+ {
+ bool is_new_kmer = false;
+
+ for (unsigned int i = 0; i < _n_tables; i++) {
+ MuxGuard g(mutexes[i]);
+ Byte* const table(_counts[i]);
+ const uint64_t idx = _table_index(khash, _tablesizes[i]);
+ const uint8_t mask = _mask(khash, _tablesizes[i]);
+ const uint8_t shift = _shift(khash, _tablesizes[i]);
+ const uint8_t current_count = (table[idx] & mask) >> shift;
+
+ if (!is_new_kmer) {
+ if (current_count == 0) {
+ is_new_kmer = true;
+
+ // track occupied bins in the first table only, as proxy
+ // for all.
+ if (i == 0) {
+ __sync_add_and_fetch(&_occupied_bins, 1);
+ }
+ }
+ }
+ // if we have reached the maximum count stop incrementing the
+ // counter. This avoids overflowing it.
+ if (current_count == _max_count) {
+ continue;
+ }
+
+ // increase count, no checking for overflow
+ const uint8_t new_count = (current_count + 1) << shift;
+ table[idx] = (table[idx] & ~mask) | (new_count & mask);
+ }
+
+ if (is_new_kmer) {
+ __sync_add_and_fetch(&_n_unique_kmers, 1);
+ }
+ }
+
+ // get the count for the given k-mer hash.
+ const BoundedCounterType get_count(HashIntoType khash) const
+ {
+ uint8_t min_count = _max_count; // bound count by maximum
+
+ // get the minimum count across all tables
+ for (unsigned int i = 0; i < _n_tables; i++) {
+ const Byte* table(_counts[i]);
+ const uint64_t idx = _table_index(khash, _tablesizes[i]);
+ const uint8_t mask = _mask(khash, _tablesizes[i]);
+ const uint8_t shift = _shift(khash, _tablesizes[i]);
+ const uint8_t the_count = (table[idx] & mask) >> shift;
+
+ if (the_count < min_count) {
+ min_count = the_count;
+ }
+ }
+ return min_count;
+ }
+
+ // Accessors for protected/private table info members
+ std::vector<uint64_t> get_tablesizes() const
+ {
+ return _tablesizes;
+ }
+ const size_t n_tables() const
+ {
+ return _n_tables;
+ }
+ const uint64_t n_unique_kmers() const
+ {
+ return _n_unique_kmers;
+ }
+ const uint64_t n_occupied() const
+ {
+ return _occupied_bins;
+ }
+ void save(std::string outfilename, WordLength ksize);
+ void load(std::string infilename, WordLength& ksize);
+
+ Byte ** get_raw_tables()
+ {
+ return _counts;
+ }
+};
+
+
+/*
+ * \class ByteStorage
+ *
+ * \brief A CountMin sketch implementation.
+ *
+ * ByteStorage is used to track counts of k-mers by Hashtable
+ * and derived classes. It contains 'n_tables' different tables of
+ * bytesizes specified in 'tablesizes'.
+ *
+ * Like other Storage classes, ByteStorage manages setting the bits and
+ * tracking statistics, as well as save/load, and not much else.
+ *
+ */
+
+class ByteStorageFile;
+class ByteStorageFileReader;
+class ByteStorageFileWriter;
+class ByteStorageGzFileReader;
+class ByteStorageGzFileWriter;
+
+class ByteStorage : public Storage
+{
+ friend class ByteStorageFile;
+ friend class ByteStorageFileReader;
+ friend class ByteStorageFileWriter;
+ friend class ByteStorageGzFileReader;
+ friend class ByteStorageGzFileWriter;
+ friend class CountGraph;
+protected:
+ unsigned int _max_count;
+ unsigned int _max_bigcount;
+
+ uint32_t _bigcount_spin_lock;
+ std::vector<uint64_t> _tablesizes;
+ size_t _n_tables;
+ uint64_t _n_unique_kmers;
+ uint64_t _occupied_bins;
+
+ Byte ** _counts;
+
+ // initialize counts with empty hashtables.
+ void _allocate_counters()
+ {
+ _n_tables = _tablesizes.size();
+
+ _counts = new Byte*[_n_tables];
+ for (size_t i = 0; i < _n_tables; i++) {
+ _counts[i] = new Byte[_tablesizes[i]];
+ memset(_counts[i], 0, _tablesizes[i]);
+ }
+ }
+public:
+ KmerCountMap _bigcounts;
+
+ // constructor: create an empty CountMin sketch.
+ ByteStorage(std::vector<uint64_t>& tablesizes ) :
+ _max_count(MAX_KCOUNT), _max_bigcount(MAX_BIGCOUNT),
+ _bigcount_spin_lock(false), _tablesizes(tablesizes),
+ _n_unique_kmers(0), _occupied_bins(0)
+ {
+ _supports_bigcount = true;
+ _allocate_counters();
+ }
+
+ // destructor: clear out the memory.
+ ~ByteStorage()
+ {
+ if (_counts) {
+ for (size_t i = 0; i < _n_tables; i++) {
+ if (_counts[i]) {
+ delete[] _counts[i];
+ _counts[i] = NULL;
+ }
+ }
+
+ delete[] _counts;
+ _counts = NULL;
+
+ _n_tables = 0;
+ }
+ }
+
+ std::vector<uint64_t> get_tablesizes() const
+ {
+ return _tablesizes;
+ }
+
+ const uint64_t n_unique_kmers() const
+ {
+ return _n_unique_kmers;
+ }
+ const size_t n_tables() const
+ {
+ return _n_tables;
+ }
+ const uint64_t n_occupied() const
+ {
+ return _occupied_bins;
+ }
+
+ void save(std::string, WordLength);
+ void load(std::string, WordLength&);
+
+ inline BoundedCounterType test_and_set_bits(HashIntoType khash)
+ {
+ BoundedCounterType x = get_count(khash);
+ add(khash);
+ return !x;
+ }
+
+ inline void add(HashIntoType khash)
+ {
+ bool is_new_kmer = false;
+ unsigned int n_full = 0;
+
+ // add one to each entry in each table.
+ for (unsigned int i = 0; i < _n_tables; i++) {
+ const uint64_t bin = khash % _tablesizes[i];
+ Byte current_count = _counts[ i ][ bin ];
+
+ if (!is_new_kmer) {
+ if (current_count == 0) {
+ is_new_kmer = true;
+
+ // track occupied bins in the first table only, as proxy
+ // for all.
+ if (i == 0) {
+ __sync_add_and_fetch(&_occupied_bins, 1);
+ }
+ }
+ }
+ // NOTE: Technically, multiple threads can cause the bin to spill
+ // over max_count a little, if they all read it as less than
+ // max_count before any of them increment it.
+ // However, do we actually care if there is a little
+ // bit of slop here? It can always be trimmed off later, if
+ // that would help with stats.
+
+ if ( _max_count > current_count ) {
+ __sync_add_and_fetch( *(_counts + i) + bin, 1 );
+ } else {
+ n_full++;
+ }
+ } // for each table
+
+ // if all tables are full for this position, then add in bigcounts.
+ if (n_full == _n_tables && _use_bigcount) {
+ while (!__sync_bool_compare_and_swap(&_bigcount_spin_lock, 0, 1));
+ if (_bigcounts[khash] == 0) {
+ _bigcounts[khash] = _max_count + 1;
+ } else {
+ if (_bigcounts[khash] < _max_bigcount) {
+ _bigcounts[khash] += 1;
+ }
+ }
+ __sync_bool_compare_and_swap( &_bigcount_spin_lock, 1, 0 );
+ }
+
+ if (is_new_kmer) {
+ __sync_add_and_fetch(&_n_unique_kmers, 1);
+ }
+
+ }
+
+ // get the count for the given k-mer hash.
+ inline const BoundedCounterType get_count(HashIntoType khash) const
+ {
+ unsigned int max_count = _max_count;
+ BoundedCounterType min_count = max_count; // bound count by max.
+
+ // first, get the min count across all tables (standard CMS).
+ for (unsigned int i = 0; i < _n_tables; i++) {
+ BoundedCounterType the_count = _counts[i][khash % _tablesizes[i]];
+ if (the_count < min_count) {
+ min_count = the_count;
+ }
+ }
+
+ // if the count is saturated, check in the bigcount structure to
+ // see if we've accumulated more counts.
+ if (min_count == max_count && _use_bigcount) {
+ KmerCountMap::const_iterator it = _bigcounts.find(khash);
+ if (it != _bigcounts.end()) {
+ min_count = it->second;
+ }
+ }
+ return min_count;
+ }
+ // Get direct access to the counts.
+ //
+ // Note:
+ // Writing to the tables outside of defined methods has undefined behavior!
+ // As such, this should only be used to return read-only interfaces
+ Byte ** get_raw_tables()
+ {
+ return _counts;
+ }
+
+};
+
+// Helper classes for saving ByteStorage objs to disk & loading them.
+
+class ByteStorageFile
+{
+public:
+ static void load(const std::string &infilename,
+ WordLength &ksize,
+ ByteStorage &store);
+ static void save(const std::string &outfilename,
+ const WordLength ksize,
+ const ByteStorage &store);
+};
+
+class ByteStorageFileReader : public ByteStorageFile
+{
+public:
+ ByteStorageFileReader(const std::string &infilename,
+ WordLength &ksize,
+ ByteStorage &store);
+};
+
+class ByteStorageGzFileReader : public ByteStorageFile
+{
+public:
+ ByteStorageGzFileReader(const std::string &infilename,
+ WordLength &ksize,
+ ByteStorage &store);
+};
+
+
+class ByteStorageFileWriter : public ByteStorageFile
+{
+public:
+ ByteStorageFileWriter(const std::string &outfilename,
+ const WordLength ksize,
+ const ByteStorage &store);
+};
+
+class ByteStorageGzFileWriter : public ByteStorageFile
+{
+public:
+ ByteStorageGzFileWriter(const std::string &outfilename,
+ const WordLength ksize,
+ const ByteStorage &store);
+};
+}
+
+#endif // STORAGE_HH
diff --git a/lib/subset.cc b/lib/subset.cc
index 254c468..1384923 100644
--- a/lib/subset.cc
+++ b/lib/subset.cc
@@ -1,7 +1,7 @@
/*
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2010-2015, Michigan State University.
-Copyright (C) 2015, The Regents of the University of California.
+Copyright (C) 2015-2016, The Regents of the University of California.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
@@ -44,12 +44,11 @@ Contact: khmer-project at idyll.org
#include <set>
#include <utility>
-#include "counting.hh"
-#include "hashtable.hh"
+#include "hashgraph.hh"
#include "khmer_exception.hh"
-#include "kmer_hash.hh"
#include "read_parsers.hh"
#include "subset.hh"
+#include "traversal.hh"
#define IO_BUF_SIZE 250*1000*1000
#define BIG_TRAVERSALS_ARE 200
@@ -82,7 +81,7 @@ static void print_tag_set(SeenSet& p)
#endif //0
-SubsetPartition::SubsetPartition(Hashtable * ht) :
+SubsetPartition::SubsetPartition(Hashgraph * ht) :
next_partition_id(2), _ht(ht)
{
}
@@ -120,7 +119,7 @@ size_t SubsetPartition::output_partitioned_file(
CallbackFn callback,
void * callback_data)
{
- IParser* parser = IParser::get_parser(infilename);
+ auto parser = read_parsers::get_parser<FastxReader>(infilename);
ofstream outfile(outputfile.c_str());
unsigned int total_reads = 0;
@@ -155,7 +154,7 @@ size_t SubsetPartition::output_partitioned_file(
bool found_tag = false;
for (unsigned int i = 0; i < seq.length() - ksize + 1; i++) {
- kmer = _hash(kmer_s + i, ksize);
+ kmer = _ht->hash_dna(kmer_s + i);
// is this a known tag?
if (set_contains(partition_map, kmer)) {
@@ -191,12 +190,6 @@ size_t SubsetPartition::output_partitioned_file(
outfile << "\n" << seq << "\n";
}
}
-#ifdef VALIDATE_PARTITIONS
- std::cout << "checking: " << read.name << "\n";
- if (!is_single_partition(seq)) {
- throw khmer_exception();
- }
-#endif // VALIDATE_PARTITIONS
total_reads++;
@@ -206,8 +199,6 @@ size_t SubsetPartition::output_partitioned_file(
callback("output_partitions", callback_data,
total_reads, reads_kept);
} catch (...) {
- delete parser;
- parser = NULL;
outfile.close();
throw;
}
@@ -215,154 +206,9 @@ size_t SubsetPartition::output_partitioned_file(
}
}
- delete parser;
- parser = NULL;
-
return partitions.size() + n_singletons;
}
-unsigned int SubsetPartition::find_unpart(
- const std::string &infilename,
- bool traverse,
- bool stop_big_traversals,
- CallbackFn callback,
- void * callback_data)
-{
- IParser* parser = IParser::get_parser(infilename);
-
- unsigned int total_reads = 0;
- unsigned int reads_kept = 0;
- unsigned int n_singletons = 0;
-
- Read read;
- string seq;
-
- SeenSet tags_todo;
-
- //
- // go through all the new reads, and consume & tag them. keep track
- // of all waypoints in the read in 'found_tags', and then check to
- // see if we've found either tags with no partition, or tags from
- // different partitions, or, heck, anything new. if we did, then
- // we have "new stuff" from the perspective of the graph.
- //
- // so, we can either traverse the graph, or just merge the partitions.
- // the former is exact, the latter is inexact but way faster :)
- //
-
- while(!parser->is_complete()) {
- try {
- read = parser->get_next_read();
- } catch (NoMoreReadsAvailable &exc) {
- break;
- }
- seq = read.sequence;
-
- if (_ht->check_and_normalize_read(seq)) {
- unsigned long long n_consumed = 0;
- SeenSet found_tags;
- _ht->consume_sequence_and_tag(seq, n_consumed, &found_tags);
-
- PartitionSet pset;
- bool found_zero = false;
-
- for (SeenSet::iterator si = found_tags.begin();
- si != found_tags.end(); ++si) {
- PartitionMap::iterator pi = partition_map.find(*si);
- PartitionID partition_id = 0;
- if (pi != partition_map.end() && pi->second != NULL) {
- partition_id = *(pi->second);
- }
- if (partition_id == 0) {
- found_zero = true;
- } else {
- pset.insert(partition_id);
- }
- }
-
- if (pset.size() > 1 || found_zero || n_consumed) {
-
- // ok, we found something unaccounted for by the current
- // partitioning. We can either
- // (1) redo the partitioning of this area from scratch;
- // (2) just join tags that are on the same sequence (incl 0-tags);
- // 1 is "perfect", 2 is imperfect but really fast.
-
- // note, in the case of #2, we can dispense with the hashtable,
- // and just use the tagset/partition map.
-
- if (traverse) {
- // go with behavior #1
-
- if (n_consumed || found_zero) {
- for (SeenSet::iterator si = found_tags.begin(); si !=
- found_tags.end(); ++si) {
- tags_todo.insert(*si);
- }
- } else {
- assign_partition_id(*(found_tags.begin()), found_tags);
- }
- } else {
- assign_partition_id(*(found_tags.begin()), found_tags);
- }
-
- // std::cout << "got one! " << read.name << "\n";
- // std::cout << pset.size() << " " << found_zero << " "
- // << n_consumed << "\n";
- }
-
- total_reads++;
-
- // run callback, if specified
- if (total_reads % CALLBACK_PERIOD == 0 && callback) {
- try {
- callback("find_unpart", callback_data,
- total_reads, reads_kept);
- } catch (...) {
- delete parser;
- parser = NULL;
- throw;
- }
- }
- }
- }
-
- if (traverse) {
- // std::cout << "new tags size: " << tags_todo.size() << "\n";
-
- unsigned int n = 0;
- SeenSet tagged_kmers;
- for (SeenSet::iterator si = tags_todo.begin(); si != tags_todo.end();
- ++si) {
- n += 1;
-
- Kmer kmer = _ht->build_kmer(*si);
-
- // find all tagged kmers within range.
- tagged_kmers.clear();
- find_all_tags(kmer, tagged_kmers, _ht->all_tags,
- true, stop_big_traversals);
-
- // std::cout << "found " << tagged_kmers.size() << "\n";
-
- // assign the partition ID
- // std::cout << next_partition_id << "\n";
- assign_partition_id(kmer, tagged_kmers);
-
- // print out
- if (n % 1000 == 0) {
- cout << "unpart-part " << n << " " << next_partition_id
- << "\n";
- }
- }
- }
-
- delete parser;
- parser = NULL;
-
- return n_singletons;
-}
-
// find_all_tags: the core of the partitioning code. finds all tagged k-mers
// connected to kmer_f/kmer_r in the graph.
@@ -384,12 +230,11 @@ void SubsetPartition::find_all_tags(
unsigned int total = 0;
unsigned int nfound = 0;
- Traverser traverser(_ht);
KmerSet keeper; // keep track of traversed kmers
-
- auto filter = [&] (Kmer& n) -> bool {
- return !set_contains(keeper, n);
+ KmerFilter filter = [&] (const Kmer& n) -> bool {
+ return set_contains(keeper, n);
};
+ Traverser traverser(_ht, filter);
node_q.push(start_kmer);
breadth_q.push(0);
@@ -441,12 +286,12 @@ void SubsetPartition::find_all_tags(
continue; // truncate search @CTB exit?
}
- nfound = traverser.traverse_right(node, node_q, filter);
+ nfound = traverser.traverse_right(node, node_q);
for (unsigned int i = 0; i<nfound; ++i) {
breadth_q.push(breadth + 1);
}
- nfound = traverser.traverse_left(node, node_q, filter);
+ nfound = traverser.traverse_left(node, node_q);
for (unsigned int i = 0; i<nfound; ++i) {
breadth_q.push(breadth + 1);
}
@@ -456,10 +301,9 @@ void SubsetPartition::find_all_tags(
}
}
-
-
// Perform a breadth-first search starting from the k-mers in the given
-// sequence
+// sequence.
+
unsigned int SubsetPartition::sweep_for_tags(
const std::string& seq,
SeenSet& tagged_kmers,
@@ -469,7 +313,6 @@ unsigned int SubsetPartition::sweep_for_tags(
bool stop_big_traversals)
{
- Traverser traverser(_ht);
KmerSet traversed_nodes;
KmerQueue node_q;
std::queue<unsigned int> breadth_q;
@@ -478,9 +321,10 @@ unsigned int SubsetPartition::sweep_for_tags(
unsigned int total = 0;
unsigned int nfound = 0;
- auto filter = [&] (Kmer& n) -> bool {
- return !set_contains(traversed_nodes, n);
+ KmerFilter filter = [&] (const Kmer& n) -> bool {
+ return set_contains(traversed_nodes, n);
};
+ Traverser traverser(_ht, filter);
// Queue up all the sequence's k-mers at breadth zero
// We are searching around the perimeter of the known k-mers
@@ -537,12 +381,12 @@ unsigned int SubsetPartition::sweep_for_tags(
return total;
}
- nfound = traverser.traverse_right(node, node_q, filter);
+ nfound = traverser.traverse_right(node, node_q);
for (unsigned int i = 0; i<nfound; ++i) {
breadth_q.push(breadth + 1);
}
- nfound = traverser.traverse_left(node, node_q, filter);
+ nfound = traverser.traverse_left(node, node_q);
for (unsigned int i = 0; i<nfound; ++i) {
breadth_q.push(breadth + 1);
}
@@ -551,8 +395,8 @@ unsigned int SubsetPartition::sweep_for_tags(
return total;
}
-// find_all_tags: the core of the partitioning code. finds all tagged k-mers
-// connected to kmer_f/kmer_r in the graph.
+// find_all_tags_truncate_on_abundance: experimental code for streaming
+// partitioning.
void SubsetPartition::find_all_tags_truncate_on_abundance(
Kmer start_kmer,
@@ -574,13 +418,13 @@ void SubsetPartition::find_all_tags_truncate_on_abundance(
unsigned int total = 0;
unsigned int nfound = 0;
- Traverser traverser(_ht);
KmerSet keeper; // keep track of traversed kmers
-
- auto filter = [&] (Kmer& n) -> bool {
- return !set_contains(keeper, n);
+ KmerFilter filter = [&] (const Kmer& n) -> bool {
+ return set_contains(keeper, n);
};
+ Traverser traverser(_ht, filter);
+
node_q.push(start_kmer);
breadth_q.push(0);
@@ -640,12 +484,12 @@ void SubsetPartition::find_all_tags_truncate_on_abundance(
continue; // truncate search @CTB exit?
}
- nfound = traverser.traverse_right(node, node_q, filter);
+ nfound = traverser.traverse_right(node, node_q);
for (unsigned int i = 0; i<nfound; ++i) {
breadth_q.push(breadth + 1);
}
- nfound = traverser.traverse_left(node, node_q, filter);
+ nfound = traverser.traverse_left(node, node_q);
for (unsigned int i = 0; i<nfound; ++i) {
breadth_q.push(breadth + 1);
}
@@ -654,7 +498,7 @@ void SubsetPartition::find_all_tags_truncate_on_abundance(
}
}
-///////////////////////////////////////////////////////////////////////
+// do_partition: Main partitioning code, to find components in large graphs.
void SubsetPartition::do_partition(
HashIntoType first_kmer,
@@ -710,6 +554,8 @@ void SubsetPartition::do_partition(
}
}
+// do_partition with abundance: Experimental code to do streaming partitioning.
+
void SubsetPartition::do_partition_with_abundance(
HashIntoType first_kmer,
HashIntoType last_kmer,
@@ -779,7 +625,7 @@ void SubsetPartition::set_partition_id(
if (!(kmer_s.length() >= _ht->ksize())) {
throw khmer_exception();
}
- kmer = _hash(kmer_s.c_str(), _ht->ksize());
+ kmer = _ht->hash_dna(kmer_s.c_str());
set_partition_id(kmer, p);
}
@@ -928,8 +774,8 @@ PartitionID SubsetPartition::join_partitions(
return 0;
}
- if (reverse_pmap.find(orig) == reverse_pmap.end() ||
- reverse_pmap.find(join) == reverse_pmap.end() ||
+ if (!set_contains(reverse_pmap, orig) ||
+ !set_contains(reverse_pmap, join) ||
reverse_pmap[orig] == NULL ||
reverse_pmap[join] == NULL) {
return 0;
@@ -949,14 +795,14 @@ PartitionID SubsetPartition::get_partition_id(std::string kmer_s)
if (!(kmer_s.length() >= _ht->ksize())) {
throw khmer_exception();
}
- kmer = _hash(kmer_s.c_str(), _ht->ksize());
+ kmer = _ht->hash_dna(kmer_s.c_str());
return get_partition_id(kmer);
}
PartitionID SubsetPartition::get_partition_id(HashIntoType kmer)
{
- if (partition_map.find(kmer) != partition_map.end()) {
+ if (set_contains(partition_map, kmer)) {
PartitionID * pp = partition_map[kmer];
if (pp == NULL) {
return 0;
@@ -1055,7 +901,22 @@ void SubsetPartition::merge_from_disk(string other_filename)
err = "Unknown error in opening file: " + other_filename;
}
throw khmer_file_exception(err);
+ } catch (const std::exception &e) {
+ // Catching std::exception is a stopgap for
+ // https://gcc.gnu.org/bugzilla/show_bug.cgi?id=66145
+ std::string err = "Unknown error opening file: " + other_filename + " "
+ + strerror(errno);
+ throw khmer_file_exception(err);
}
+ infile.seekg(0, infile.end);
+ const int length = infile.tellg();
+ infile.seekg(0, infile.beg);
+ if (length == 18) {
+ std::string err;
+ err = other_filename + " contains only a header and no partition IDs.";
+ throw khmer_file_exception(err);
+ }
+
try {
unsigned int save_ksize = 0;
@@ -1099,8 +960,13 @@ void SubsetPartition::merge_from_disk(string other_filename)
std::string err;
err = "Unknown error reading header info from: " + other_filename;
throw khmer_file_exception(err);
+ } catch (khmer_file_exception &e) {
+ throw e;
+ } catch (const std::exception &e) {
+ std::string err = "Unknown error opening file: " + other_filename + " "
+ + strerror(errno);
+ throw khmer_file_exception(err);
}
-
char * buf = new char[IO_BUF_SIZE];
unsigned int loaded = 0;
@@ -1124,7 +990,7 @@ void SubsetPartition::merge_from_disk(string other_filename)
try {
infile.read(buf + remainder, IO_BUF_SIZE - remainder);
- } catch (std::ifstream::failure &e) {
+ } catch (std::exception &e) {
// We may get an exception here if we fail to read all the
// expected bytes due to EOF -- only pass it up if we read
@@ -1295,51 +1161,6 @@ void SubsetPartition::_clear_all_partitions()
}
-bool SubsetPartition::is_single_partition(std::string seq)
-{
- if (!_ht->check_and_normalize_read(seq)) {
- return 0;
- }
-
- PartitionSet partitions;
- PartitionID *pp;
-
- KmerIterator kmers(seq.c_str(), _ht->ksize());
- while (!kmers.done()) {
- HashIntoType kmer = kmers.next();
-
- if (partition_map.find(kmer) != partition_map.end()) {
- pp = partition_map[kmer];
- if (pp) {
- partitions.insert(*pp);
- }
- }
- }
-
- if (partitions.size() > 1) {
- return false;
- }
-
- return true;
-}
-
-void SubsetPartition::join_partitions_by_path(std::string seq)
-{
- SeenSet tagged_kmers;
-
- KmerIterator kmers(seq.c_str(), _ht->ksize());
-
- while(!kmers.done()) {
- HashIntoType kmer = kmers.next();
- if (_ht->all_tags.find(kmer) != _ht->all_tags.end()) {
- tagged_kmers.insert(kmer);
- }
- }
-
- // assert(tagged_kmers.size());
- assign_partition_id(*(tagged_kmers.begin()), tagged_kmers);
-}
-
void SubsetPartition::partition_size_distribution(
PartitionCountDistribution &d,
unsigned int &n_unassigned)
@@ -1375,7 +1196,7 @@ const
void SubsetPartition::partition_average_coverages(
PartitionCountMap &cm,
- CountingHash * ht) const
+ Countgraph * ht) const
{
PartitionCountMap csum;
PartitionCountMap cN;
@@ -1400,7 +1221,7 @@ unsigned long long SubsetPartition::repartition_largest_partition(
unsigned int distance,
unsigned int threshold,
unsigned int frequency,
- CountingHash &counting)
+ Countgraph &counting)
{
PartitionCountMap cm;
unsigned int n_unassigned = 0;
@@ -1431,11 +1252,11 @@ unsigned long long SubsetPartition::repartition_largest_partition(
// find biggest.
PartitionCountDistribution::const_iterator di = d.end();
- --di;
if (d.empty()) {
throw khmer_exception();
}
+ --di;
for (PartitionCountMap::const_iterator cmi = cm.begin(); cmi != cm.end();
++cmi) {
@@ -1450,13 +1271,15 @@ unsigned long long SubsetPartition::repartition_largest_partition(
#if VERBOSE_REPARTITION
std::cout << "biggest partition: " << di->first << "\n";
#endif // 0
- --di;
#if VERBOSE_REPARTITION
std::cout << "biggest partition ID: " << biggest_p << "\n";
#endif // 0
- next_largest = di->first;
+ if (di != d.begin()) {
+ --di;
+ next_largest = di->first;
+ }
#if VERBOSE_REPARTITION
std::cout << "next biggest partition: " << di->first << "\n";
@@ -1610,7 +1433,7 @@ void SubsetPartition::report_on_partitions()
for (SeenSet::iterator ti = _ht->all_tags.begin();
ti != _ht->all_tags.end(); ++ti) {
- std::cout << "TAG: " << _revhash(*ti, _ht->ksize()) << "\n";
+ std::cout << "TAG: " << _ht->unhash_dna(*ti) << "\n";
PartitionID *pid = partition_map[*ti];
if (pid) {
std::cout << "partition: " << *(partition_map[*ti]) << "\n";
@@ -1620,37 +1443,3 @@ void SubsetPartition::report_on_partitions()
std::cout << "--\n";
}
}
-
-void SubsetPartition::compare_to_partition(
- PartitionID pid1,
- SubsetPartition *p2,
- PartitionID pid2,
- unsigned int &n_only1,
- unsigned int &n_only2,
- unsigned int &n_shared)
-{
- SubsetPartition * p1 = this;
-
- for (PartitionMap::iterator pi = p1->partition_map.begin();
- pi != p1->partition_map.end(); ++pi) {
- PartitionID * pid = pi->second;
- if (pid && *pid == pid1) {
- PartitionID * pp2 = p2->partition_map[pi->first];
- if (pp2 && *pp2 == pid2) {
- n_shared++;
- } else {
- n_only1++;
- }
- }
- }
-
- for (PartitionMap::iterator pi = p2->partition_map.begin();
- pi != p2->partition_map.end(); ++pi) {
- PartitionID * pid = pi->second;
- if (pid && *pid == pid2) {
- n_only2++;
- }
- }
-
- n_only2 -= n_shared;
-}
diff --git a/lib/subset.hh b/lib/subset.hh
index 92df78f..02a710b 100644
--- a/lib/subset.hh
+++ b/lib/subset.hh
@@ -43,13 +43,11 @@ Contact: khmer-project at idyll.org
#include <string>
#include "khmer.hh"
-#include "traversal.hh"
namespace khmer
{
-class CountingHash;
-class Hashbits;
-class Hashtable;
+class Countgraph;
+class Hashgraph;
struct pre_partition_info {
HashIntoType kmer;
@@ -60,10 +58,10 @@ struct pre_partition_info {
class SubsetPartition
{
- friend class Hashtable;
+ friend class Hashgraph;
protected:
unsigned int next_partition_id;
- Hashtable * _ht;
+ Hashgraph * _ht;
PartitionMap partition_map;
ReversePartitionMap reverse_pmap;
@@ -75,7 +73,7 @@ protected:
const HashIntoType kmer);
public:
- explicit SubsetPartition(Hashtable * ht);
+ explicit SubsetPartition(Hashgraph * ht);
~SubsetPartition()
{
@@ -151,16 +149,6 @@ public:
CallbackFn callback=0,
void * callback_data=0);
- unsigned int find_unpart(const std::string &infilename,
- bool traverse,
- bool stop_big_traversals,
- CallbackFn callback=0,
- void * callback_data=0);
-
- bool is_single_partition(std::string sequence);
-
- void join_partitions_by_path(std::string sequence);
-
void partition_sizes(PartitionCountMap &cm,
unsigned int& n_unassigned) const;
@@ -168,10 +156,10 @@ public:
unsigned int& n_unassigned) const;
void partition_average_coverages(PartitionCountMap &cm,
- CountingHash * ht) const;
+ Countgraph * ht) const;
unsigned long long repartition_largest_partition(unsigned int, unsigned int,
- unsigned int, CountingHash&);
+ unsigned int, Countgraph&);
void repartition_a_partition(const SeenSet& partition_tags);
void _clear_partition(PartitionID, SeenSet& partition_tags);
@@ -181,11 +169,6 @@ public:
PartitionPtrMap& diskp_to_pp);
void report_on_partitions();
-
- void compare_to_partition(PartitionID, SubsetPartition *, PartitionID,
- unsigned int &n_only1,
- unsigned int &n_only2,
- unsigned int &n_shared);
};
}
diff --git a/lib/test-Colors.cc b/lib/test-Colors.cc
index bcafd84..28e06a0 100644
--- a/lib/test-Colors.cc
+++ b/lib/test-Colors.cc
@@ -50,7 +50,7 @@ int main()
sizes + sizeof(sizes) / sizeof(HashIntoType) );
khmer::LabelHash * lh_pointer = new khmer::LabelHash(20, sizes_vec);
- khmer::Hashbits * hb_pointer = (khmer::Hashbits *)lh_pointer;
+ khmer::Nodegraph * hb_pointer = (khmer::Hashbits *)lh_pointer;
std::cout << "lh_pointer n_tags: " << lh_pointer->n_tags() << std::endl;
std::cout << "hb_pointer n_tags: " << hb_pointer->n_tags() << std::endl;
diff --git a/lib/test-compile.cc b/lib/test-compile.cc
index 124ac9a..d272613 100644
--- a/lib/test-compile.cc
+++ b/lib/test-compile.cc
@@ -39,10 +39,10 @@ Contact: khmer-project at idyll.org
// This file is used to test compilation with libkhmer.a/libkhmer.so, after
// installation
-#include <oxli/counting.hh>
+#include <oxli/hashtable.hh>
int main()
{
- khmer::CountingHash test(1,1);
+ khmer::Countgraph test(1,1);
return 0;
}
diff --git a/lib/traversal.cc b/lib/traversal.cc
index f4693be..152c5fe 100644
--- a/lib/traversal.cc
+++ b/lib/traversal.cc
@@ -1,6 +1,6 @@
/*
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-Copyright (C) 2015, The Regents of the University of California.
+Copyright (C) 2015-2016, The Regents of the University of California.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
@@ -34,14 +34,25 @@ LICENSE (END)
Contact: khmer-project at idyll.org
*/
+#include "khmer.hh"
#include "hashtable.hh"
#include "traversal.hh"
+#include "alphabets.hh"
+#include "kmer_hash.hh"
-using namespace khmer;
using namespace std;
-Traverser::Traverser(const Hashtable * ht) :
- KmerFactory(ht->ksize()), graph(ht)
+namespace khmer
+{
+
+/******************************************
+ * NodeGatherer
+ ******************************************/
+
+template <bool direction>
+NodeGatherer<direction>::NodeGatherer(const Hashgraph * ht,
+ KmerFilterList filters) :
+ KmerFactory(ht->ksize()), graph(ht), filters(filters)
{
bitmask = 0;
for (unsigned int i = 0; i < _ksize; i++) {
@@ -50,8 +61,29 @@ Traverser::Traverser(const Hashtable * ht) :
rc_left_shift = _ksize * 2 - 2;
}
-Kmer Traverser::get_left(Kmer& node, const char ch)
+
+template <bool direction>
+NodeGatherer<direction>::NodeGatherer(const Hashgraph * ht) :
+ NodeGatherer(ht, KmerFilterList())
{
+}
+
+
+template <bool direction>
+NodeGatherer<direction>::NodeGatherer(const Hashgraph * ht,
+ KmerFilter filter) :
+ NodeGatherer(ht, KmerFilterList())
+{
+ filters.push_back(filter);
+}
+
+
+template<>
+Kmer NodeGatherer<TRAVERSAL_LEFT>::get_neighbor(const Kmer& node, const char ch)
+const
+{
+ // optimized bit-foo to check for LEFT neighbors in both forward and
+ // reverse-complemented directions
HashIntoType kmer_f, kmer_r;
kmer_f = ((node.kmer_f) >> 2 | twobit_repr(ch) << rc_left_shift);
kmer_r = (((node.kmer_r) << 2) & bitmask) | (twobit_comp(ch));
@@ -59,26 +91,33 @@ Kmer Traverser::get_left(Kmer& node, const char ch)
}
-Kmer Traverser::get_right(Kmer& node, const char ch)
+template<>
+Kmer NodeGatherer<TRAVERSAL_RIGHT>::get_neighbor(const Kmer& node,
+ const char ch)
+const
{
+ // optimized bit-foo to check for LEFT neighbors in both forward and
+ // reverse-complemented directions
HashIntoType kmer_f, kmer_r;
kmer_f = (((node.kmer_f) << 2) & bitmask) | (twobit_repr(ch));
kmer_r = ((node.kmer_r) >> 2) | (twobit_comp(ch) << rc_left_shift);
return build_kmer(kmer_f, kmer_r);
}
-unsigned int Traverser::traverse_left(Kmer& node,
- KmerQueue & node_q,
- std::function<bool (Kmer&)> filter)
+
+template<bool direction>
+unsigned int NodeGatherer<direction>::neighbors(const Kmer& node,
+ KmerQueue & node_q)
+const
{
unsigned int found = 0;
- char bases[] = "ACGT";
- char * base = bases;
- while(*base != '\0') {
- Kmer prev_node = get_left(node, *base);
- if (graph->get_count(prev_node) && filter(prev_node)) {
- node_q.push(prev_node);
+ for (auto base : alphabets::DNA_SIMPLE) {
+ // Get the putative neighboring Kmer
+ Kmer neighbor = get_neighbor(node, base);
+ // Now check if it's in the graph and passes the filters
+ if (graph->get_count(neighbor) && !(apply_kmer_filters(neighbor, filters))) {
+ node_q.push(neighbor);
++found;
}
++base;
@@ -87,61 +126,222 @@ unsigned int Traverser::traverse_left(Kmer& node,
return found;
}
-unsigned int Traverser::traverse_right(Kmer& node,
- KmerQueue & node_q,
- std::function<bool (Kmer&)> filter)
+
+template<bool direction>
+unsigned int NodeGatherer<direction>::degree(const Kmer& node)
+const
{
- unsigned int found = 0;
+ unsigned int degree = 0;
- char bases[] = "ACGT";
- char * base = bases;
- while(*base != '\0') {
- Kmer next_node = get_right(node, *base);
- if (graph->get_count(next_node) && filter(next_node)) {
- node_q.push(next_node);
- ++found;
+ for (auto base : alphabets::DNA_SIMPLE) {
+ if (graph->get_count(get_neighbor(node, base))) {
+ ++degree;
}
++base;
}
- return found;
+ return degree;
}
-unsigned int Traverser::degree_left(Kmer& node)
+/******************************************
+ * NodeCursor
+ ******************************************/
+
+template<bool direction>
+NodeCursor<direction>::NodeCursor(const Hashgraph * ht,
+ Kmer start_kmer,
+ KmerFilterList filters) :
+ NodeGatherer<direction>(ht, filters)
{
- unsigned int degree = 0;
+ cursor = start_kmer;
+}
- char bases[] = "ACGT";
- char * base = bases;
- while(*base != '\0') {
- Kmer prev_node = get_left(node, *base);
- if (graph->get_count(prev_node)) {
- ++degree;
- }
- ++base;
- }
- return degree;
+template<bool direction>
+NodeCursor<direction>::NodeCursor(const Hashgraph * ht,
+ Kmer start_kmer) :
+ NodeCursor<direction>(ht, start_kmer, KmerFilterList())
+{
}
-unsigned int Traverser::degree_right(Kmer& node)
+
+template<bool direction>
+NodeCursor<direction>::NodeCursor(const Hashgraph * ht,
+ Kmer start_kmer,
+ KmerFilter filter) :
+ NodeCursor<direction>(ht, start_kmer)
{
- unsigned int degree = 0;
+ push_filter(filter);
+}
- char bases[] = "ACGT";
- char * base = bases;
- while(*base != '\0') {
- Kmer next_node = get_right(node, *base);
- if (graph->get_count(next_node)) {
- ++degree;
+
+template<bool direction>
+unsigned int NodeCursor<direction>::cursor_degree()
+const
+{
+ return this->degree(this->cursor);
+}
+
+
+
+/******************************************
+ * Traverser
+ ******************************************/
+
+Traverser::Traverser(const Hashgraph * ht,
+ KmerFilterList filters) :
+ KmerFactory(ht->ksize()),
+ graph(ht),
+ left_gatherer(ht, filters),
+ right_gatherer(ht, filters)
+{
+}
+
+Traverser::Traverser(const Hashgraph * ht,
+ KmerFilter filter) :
+ KmerFactory(ht->ksize()),
+ graph(ht),
+ left_gatherer(ht, filter),
+ right_gatherer(ht, filter)
+{
+}
+
+
+void Traverser::push_filter(KmerFilter filter)
+{
+ left_gatherer.push_filter(filter);
+ right_gatherer.push_filter(filter);
+}
+
+
+unsigned int Traverser::traverse(const Kmer& node,
+ KmerQueue& node_q) const
+{
+ return left_gatherer.neighbors(node, node_q) +
+ right_gatherer.neighbors(node, node_q);
+}
+
+
+unsigned int Traverser::traverse_left(const Kmer& node,
+ KmerQueue& node_q) const
+{
+ return left_gatherer.neighbors(node, node_q);
+}
+
+
+unsigned int Traverser::traverse_right(const Kmer& node,
+ KmerQueue& node_q) const
+{
+ return right_gatherer.neighbors(node, node_q);
+}
+
+
+unsigned int Traverser::degree(const Kmer& node) const
+{
+ return left_gatherer.degree(node) + right_gatherer.degree(node);
+}
+
+
+unsigned int Traverser::degree_left(const Kmer& node) const
+{
+ return left_gatherer.degree(node);
+}
+
+
+unsigned int Traverser::degree_right(const Kmer& node) const
+{
+ return right_gatherer.degree(node);
+}
+
+
+
+
+/******************************************
+ * AssemblerTraverser
+ ******************************************/
+
+template <>
+std::string AssemblerTraverser<TRAVERSAL_RIGHT>::join_contigs(std::string& contig_a,
+ std::string& contig_b, WordLength offset)
+const
+{
+ return contig_a + contig_b.substr(_ksize - offset);
+}
+
+template <>
+std::string AssemblerTraverser<TRAVERSAL_LEFT>::join_contigs(std::string& contig_a,
+ std::string& contig_b, WordLength offset)
+const
+{
+ return contig_b + contig_a.substr(_ksize - offset);
+}
+
+template<bool direction>
+char AssemblerTraverser<direction>::next_symbol()
+{
+ short found = 0;
+ char found_base = '\0';
+ Kmer neighbor;
+ Kmer cursor_next;
+
+ for (auto base : alphabets::DNA_SIMPLE) {
+ // Get the putative neighbor for this base at the cursor position
+ neighbor = NodeCursor<direction>::get_neighbor(this->cursor, base);
+
+ // Now check that the putative neighbor is in the graph and passes the filters
+ if (this->graph->get_count(neighbor) &&
+ !apply_kmer_filters(neighbor, this->filters)) {
+
+ found++;
+ // This naive traverser stops on high degree nodes
+ if (found > 1) {
+ return '\0';
+ }
+ found_base = base;
+ cursor_next = neighbor;
}
- ++base;
}
- return degree;
+ if (!found) {
+ return '\0';
+ } else {
+ this->cursor = cursor_next;
+ return found_base;
+ }
+}
+
+/******************************************
+ * NonLoopingAT
+ ******************************************/
+
+template<bool direction>
+NonLoopingAT<direction>::NonLoopingAT(const Hashgraph * ht,
+ Kmer start_kmer,
+ KmerFilterList filters,
+ SeenSet * visited) :
+ AssemblerTraverser<direction>(ht, start_kmer, filters), visited(visited)
+{
+ AssemblerTraverser<direction>::push_filter(get_visited_filter(visited));
}
-unsigned int Traverser::degree(Kmer& node)
+template<bool direction>
+char NonLoopingAT<direction>::next_symbol()
{
- return degree_right(node) + degree_left(node);
+#if DEBUG_TRAVERSAL
+ std::cout << "Insert cursor to visited filter" << std::endl;
+#endif
+ visited->insert(this->cursor);
+ return AssemblerTraverser<direction>::next_symbol();
}
+
+template class NodeGatherer<TRAVERSAL_LEFT>;
+template class NodeGatherer<TRAVERSAL_RIGHT>;
+template class NodeCursor<TRAVERSAL_LEFT>;
+template class NodeCursor<TRAVERSAL_RIGHT>;
+template class AssemblerTraverser<TRAVERSAL_RIGHT>;
+template class AssemblerTraverser<TRAVERSAL_LEFT>;
+template class NonLoopingAT<TRAVERSAL_RIGHT>;
+template class NonLoopingAT<TRAVERSAL_LEFT>;
+
+
+} // namespace khmer
diff --git a/lib/traversal.hh b/lib/traversal.hh
index 8f41e75..f79cdbf 100644
--- a/lib/traversal.hh
+++ b/lib/traversal.hh
@@ -1,6 +1,6 @@
/*
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-Copyright (C) 2015, The Regents of the University of California.
+Copyright (C) 2015-2016, The Regents of the University of California.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
@@ -41,45 +41,262 @@ Contact: khmer-project at idyll.org
#include <functional>
#include "khmer.hh"
-
-#include "khmer_exception.hh"
-#include "read_parsers.hh"
-#include "kmer_hash.hh"
#include "hashtable.hh"
+#include "kmer_hash.hh"
+#include "kmer_filters.hh"
namespace khmer
{
-class Hashtable;
+#ifndef TRAVERSAL_LEFT
+#define TRAVERSAL_LEFT 0
+#endif
+#ifndef TRAVERSAL_RIGHT
+#define TRAVERSAL_RIGHT 1
+#endif
+
+class Hashgraph;
+class LabelHash;
-class Traverser: public KmerFactory
+/**
+ * @brief Gather neighbors from a given node.
+ *
+ * The most basic traversal utility. Stores a list of KmerFilter functions, and given
+ * a Kmer, finds all its neighbors that pass the filter function.s
+ *
+ * @tparam direction The direction in the graph to gather nodes from.
+ */
+template<bool direction>
+class NodeGatherer: public KmerFactory
{
- friend class Hashtable;
+ friend class Hashgraph;
protected:
+ KmerFilterList filters;
HashIntoType bitmask;
unsigned int rc_left_shift;
+ const Hashgraph * graph;
public:
- const Hashtable * graph;
+ explicit NodeGatherer(const Hashgraph * ht,
+ KmerFilterList filters);
+
+ explicit NodeGatherer(const Hashgraph * ht);
- explicit Traverser(const Hashtable * ht);
+ explicit NodeGatherer(const Hashgraph * ht, KmerFilter filter);
- Kmer get_left(Kmer& node, const char ch);
- Kmer get_right(Kmer& node, const char ch);
+ /**
+ * @brief Push a new filter on to the filter stack.
+ */
+ void push_filter(KmerFilter filter)
+ {
+ filters.push_back(filter);
+ }
- unsigned int traverse_left(Kmer& node,
- KmerQueue &node_q,
- std::function<bool (Kmer&)> filter);
- unsigned int traverse_right(Kmer& node,
- KmerQueue &node_q,
- std::function<bool (Kmer&)> filter);
+ /**
+ * @brief Pop a filter off the stack.
+ *
+ * @return The filter.
+ */
+ KmerFilter pop_filter()
+ {
+ KmerFilter back = this->filters.back();
+ this->filters.pop_back();
+ return back;
+ }
+
+ unsigned int n_filters()
+ {
+ return filters.size();
+ }
+
+ /**
+ * @brief Build the Kmer for the potential neighbor node of the given Kmer.
+ *
+ * When templated for RIGHT, will return the Kmer built from the length K-1 suffix of the
+ * input Kmer with the new base appended; when LEFT, the length K-1 prefix of the input Kmer
+ * with the new base prepended.
+ *
+ * @param node The starting node.
+ * @param ch The new base to build from.
+ *
+ * @return The new Kmer.
+ */
+ Kmer get_neighbor(const Kmer& node, const char ch) const;
+
+ /**
+ * @brief Get all neighbors which are present in the graph and pass the filters.
+ *
+ * @param node The Kmer to start at.
+ * @param node_q To collect the results.
+ *
+ * @return Number of neighbors found.
+ */
+ unsigned int neighbors(const Kmer& node,
+ KmerQueue &node_q) const;
+
+ /**
+ * @brief Get the degree of the given Kmer in the templated direction.
+ *
+ * @param node The Kmer to check.
+ *
+ * @return The degree.
+ */
+ unsigned int degree(const Kmer& node) const;
+};
+
+
+/**
+ * @brief A stateful NodeGatherer. Stores its current position.
+ *
+ * @tparam direction The direction to gather nodes from.
+ */
+template <bool direction>
+class NodeCursor: public NodeGatherer<direction>
+{
+
+public:
+
+ // The current position.
+ Kmer cursor;
+ using NodeGatherer<direction>::push_filter;
+
+ explicit NodeCursor(const Hashgraph * ht,
+ Kmer start_kmer,
+ KmerFilterList filters);
+
+ explicit NodeCursor(const Hashgraph * ht,
+ Kmer start_kmer);
+
+ explicit NodeCursor(const Hashgraph * ht,
+ Kmer start_kmer,
+ KmerFilter filter);
+
+ /**
+ * @brief Get the neighbors for the current position.
+
+ *
+ * @param node_q To collection the results.
+ *
+ * @return Number of neighbors found.
+ */
+ unsigned int neighbors(KmerQueue& node_q) const
+ {
+ return NodeGatherer<direction>::neighbors(cursor, node_q);
+ }
+
+ /**
+ * @return Degree of the current cursor position and direction.
+ */
+ unsigned int cursor_degree() const;
+
+};
+
+
+/**
+ * @brief Wraps a LEFT and RIGHT NodeGatherer.
+ */
+class Traverser: public KmerFactory
+{
+
+protected:
+
+ const Hashgraph * graph;
+ NodeGatherer<TRAVERSAL_LEFT> left_gatherer;
+ NodeGatherer<TRAVERSAL_RIGHT> right_gatherer;
+
+public:
+
+ explicit Traverser(const Hashgraph * ht,
+ KmerFilterList filters);
+
+ explicit Traverser(const Hashgraph * ht) : Traverser(ht, KmerFilterList()) {}
+
+ explicit Traverser(const Hashgraph * ht,
+ KmerFilter filter);
+
+ void push_filter(KmerFilter filter);
+
+ unsigned int traverse(const Kmer& node,
+ KmerQueue& node_q) const;
+
+ unsigned int traverse_left(const Kmer& node,
+ KmerQueue& node_q) const;
+
+ unsigned int traverse_right(const Kmer& node,
+ KmerQueue& node_q) const;
+
+ unsigned int degree(const Kmer& node) const;
+ unsigned int degree_left(const Kmer& node) const;
+ unsigned int degree_right(const Kmer& node) const;
+
+};
+
+
+/**
+ * @brief A NodeCursor specialized for assembling contigs.
+ *
+ * @tparam direction The direction to assemble.
+ */
+template <bool direction>
+class AssemblerTraverser: public NodeCursor<direction>
+{
+
+public:
+ using NodeCursor<direction>::NodeCursor;
+
+ /**
+ * @brief Get the next symbol.
+ *
+ * Finds the next symbol which passes the filters, so long as there is only
+ * one branch. Does not return a new symbol if there are multiple potential neighbors.
+ *
+ * @return A member of alphabets::DNA_SIMPLE if a neighbor is found; '\0' otherwise.
+ */
+ virtual char next_symbol();
+
+ /**
+ * @brief Utility function to join two overlapping contigs with proper directionality.
+ *
+ * By default, assumes the two contigs overlap by length K. This can be reduced via the
+ * offset parameter.
+ *
+ * @param contig_a
+ * @param contig_b
+ * @param offset Number of bases to subtract from K when joining.
+ *
+ * @return The joined contig.
+ */
+ std::string join_contigs(std::string& contig_a,
+ std::string& contig_b,
+ WordLength offset = 0) const;
+};
+
+
+/**
+ * @brief An AssemblerTraverser which does not traverse to Kmers it has already encountered.
+ *
+ * Simply adds a new filter to check if the Kmer has been seen, and adds the Kmer to the set
+ * of seen Kmers after calling ::next_symbol.
+ *
+ * @tparam direction The direction to assemble.
+ */
+template<bool direction>
+class NonLoopingAT: public AssemblerTraverser<direction>
+{
+protected:
+
+ SeenSet * visited;
+
+public:
- unsigned int degree_left(Kmer& node);
- unsigned int degree_right(Kmer& node);
- unsigned int degree(Kmer& node);
+ explicit NonLoopingAT(const Hashgraph * ht,
+ Kmer start_kmer,
+ KmerFilterList filters,
+ SeenSet * visited);
+ virtual char next_symbol();
};
}
diff --git a/oxli/__init__.py b/oxli/__init__.py
index 821703b..caf0e99 100755
--- a/oxli/__init__.py
+++ b/oxli/__init__.py
@@ -34,9 +34,7 @@
#
# Contact: khmer-project at idyll.org
-"""
-Single entry point script for khmer
-"""
+"""Single entry point script for khmer."""
import argparse
import sys
@@ -46,10 +44,7 @@ from oxli import build_graph
def get_parser():
- """
- returns the parser object for the oxli subcommand handler
- """
-
+ """Return the parser object for the oxli subcommand handler."""
parser = argparse.ArgumentParser(
description='Single entry point script for khmer',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
@@ -71,10 +66,8 @@ def get_parser():
def main():
- """
- main function; does the parsing and kicks off the subcommand
- """
- if (len(sys.argv) < 2):
+ """Parse the command line and kick off the subcommand."""
+ if len(sys.argv) < 2:
args = get_parser().parse_args(['--help'])
else:
args = get_parser().parse_args()
diff --git a/oxli/build_graph.py b/oxli/build_graph.py
old mode 100644
new mode 100755
index 119fb92..2cd12df
--- a/oxli/build_graph.py
+++ b/oxli/build_graph.py
@@ -51,7 +51,7 @@ import khmer
from khmer import khmer_args
from khmer.khmer_args import (report_on_config, info, add_threading_args,
calculate_graphsize)
-from khmer.kfile import check_input_files, check_space
+from khmer.kfile import check_input_files
from khmer.kfile import check_space_for_graph
from oxli import functions as oxfuncs
@@ -72,15 +72,18 @@ def build_parser(parser):
def main(args):
- report_on_config(args, graphtype='nodegraph')
+ graph_type = 'nodegraph'
+ report_on_config(args, graphtype=graph_type)
base = args.output_filename
filenames = args.input_filenames
for fname in args.input_filenames:
check_input_files(fname, args.force)
- graphsize = calculate_graphsize(args, 'nodegraph')
- check_space_for_graph(args.output_filename, graphsize, args.force)
+ graphsize = calculate_graphsize(args, graph_type)
+ space_needed = (args.n_tables * graphsize /
+ khmer._buckets_per_byte[graph_type])
+ check_space_for_graph(args.output_filename, space_needed, args.force)
print('Saving k-mer nodegraph to %s' % base, file=sys.stderr)
print('Loading kmers from sequences in %s' %
@@ -129,4 +132,5 @@ def main(args):
if __name__ == '__main__':
main(None)
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
+# vim: set filetype=python tabstop=4 softtabstop=4 shiftwidth=4 expandtab:
+# vim: set textwidth=79:
diff --git a/oxli/functions.py b/oxli/functions.py
old mode 100644
new mode 100755
index de06475..e3608f6
--- a/oxli/functions.py
+++ b/oxli/functions.py
@@ -33,29 +33,26 @@
#
# Contact: khmer-project at idyll.org
-"""
-A collection of functions for use throughout khmer/oxli
-"""
+"""A collection of functions for use throughout khmer/oxli."""
from __future__ import print_function
-from collections import namedtuple
import threading
-import math
import khmer.utils
-import sys
def build_graph(ifilenames, graph, num_threads=1, tags=False):
"""
- Algorithm to construct a counting graph from a set of input files
- takes in list of input files, existing graph
- optionally, number of threads and if there should be tags
- """
+ Construct a counting graph from a set of input files.
+ - ifilenames: list of input files
+ - graph: existing graph
+ - num_threads: number of threads (optional)
+ - tags: should there be tags
+ """
if tags:
- eat = graph.consume_fasta_and_tag_with_reads_parser
+ eat = graph.consume_seqfile_and_tag_with_reads_parser
else:
- eat = graph.consume_fasta_with_reads_parser
+ eat = graph.consume_seqfile_with_reads_parser
for _, ifile in enumerate(ifilenames):
rparser = khmer.ReadParser(ifile)
diff --git a/oxli/partition.py b/oxli/partition.py
new file mode 100755
index 0000000..7d5dcc4
--- /dev/null
+++ b/oxli/partition.py
@@ -0,0 +1,49 @@
+#! /usr/bin/env python
+#
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# the three-clause BSD license; see doc/LICENSE.txt.
+# Contact: khmer-project at idyll.org
+#
+# pylint: disable=missing-docstring,no-member
+"""Common functions for partitioning."""
+from __future__ import print_function, absolute_import, unicode_literals
+
+import sys
+import gc
+import os.path
+
+# stdlib queue module was renamed on Python 3
+try:
+ import queue
+except ImportError:
+ import Queue as queue
+
+
+def worker(que, basename, stop_big_traversals):
+ while True:
+ try:
+ (nodegraph, index, start, stop) = que.get(False)
+ except queue.Empty:
+ print('exiting', file=sys.stderr)
+ return
+
+ outfile = basename + '.subset.%d.pmap' % (index,)
+ if os.path.exists(outfile):
+ print('SKIPPING', outfile, ' -- already exists', file=sys.stderr)
+ continue
+
+ print('starting:', basename, index, file=sys.stderr)
+
+ # pay attention to stoptags when partitioning; take command line
+ # direction on whether or not to exhaustively traverse.
+ subset = nodegraph.do_subset_partition(start, stop, True,
+ stop_big_traversals)
+
+ print('saving:', basename, index, file=sys.stderr)
+ nodegraph.save_subset_partitionmap(subset, outfile)
+ del subset
+ gc.collect()
+
+# vim: set filetype=python tabstop=4 softtabstop=4 shiftwidth=4 expandtab:
+# vim: set textwidth=79:
diff --git a/pylintrc b/pylintrc
new file mode 100644
index 0000000..b156d66
--- /dev/null
+++ b/pylintrc
@@ -0,0 +1,384 @@
+[MASTER]
+
+# Specify a configuration file.
+#rcfile=
+
+# Python code to execute, usually for sys.path manipulation such as
+# pygtk.require().
+#init-hook=
+
+# Profiled execution.
+#profile=no
+
+# Add files or directories to the blacklist. They should be base names, not
+# paths.
+#ignore=CVS
+
+# Pickle collected data for later comparisons.
+#persistent=yes
+
+# List of plugins (as comma separated values of python modules names) to load,
+# usually to register additional checkers.
+#load-plugins=
+
+# Use multiple processes to speed up Pylint.
+#jobs=1
+
+# Allow loading of arbitrary C extensions. Extensions are imported into the
+# active Python interpreter and may run arbitrary code.
+unsafe-load-any-extension=yes
+
+# A comma-separated list of package or module names from where C extensions may
+# be loaded. Extensions are loading into the active Python interpreter and may
+# run arbitrary code
+extension-pkg-whitelist=khmer,_khmer,khmer._khmer,pytest,distutils
+
+# Allow optimization of some AST trees. This will activate a peephole AST
+# optimizer, which will apply various small optimizations. For instance, it can
+# be used to obtain the result of joining multiple strings with the addition
+# operator. Joining a lot of strings can lead to a maximum recursion error in
+# Pylint and this flag can prevent that. It has one side effect, the resulting
+# AST will be different than the one from reality.
+#optimize-ast=no
+
+
+[MESSAGES CONTROL]
+
+# Only show warnings with the listed confidence levels. Leave empty to show
+# all. Valid levels: HIGH, INFERENCE, INFERENCE_FAILURE, UNDEFINED
+#confidence=
+
+# Enable the message, report, category or checker with the given id(s). You can
+# either give multiple identifier separated by comma (,) or put this option
+# multiple time. See also the "--disable" option for examples.
+#enable=
+
+# Disable the message, report, category or checker with the given id(s). You
+# can either give multiple identifiers separated by comma (,) or put this
+# option multiple times (only on the command line, not in the configuration
+# file where it should appear only once).You can also use "--disable=all" to
+# disable everything first and then reenable specific checks. For example, if
+# you want to run only the similarities checker, you can use "--disable=all
+# --enable=similarities". If you want to run only the classes checker, but have
+# no Warning level messages displayed, use"--disable=all --enable=classes
+# --disable=W"
+#disable=E1608,W1627,E1601,E1603,E1602,E1605,E1604,E1607,E1606,W1621,W1620,W1623,W1622,W1625,W1624,W1609,W1608,W1607,W1606,W1605,W1604,W1603,W1602,W1601,W1639,W1640,I0021,W1638,I0020,W1618,W1619,W1630,W1626,W1637,W1634,W1635,W1610,W1611,W1612,W1613,W1614,W1615,W1616,W1617,W1632,W1633,W0704,W1628,W1629,W1636
+
+
+[REPORTS]
+
+# Set the output format. Available formats are text, parseable, colorized, msvs
+# (visual studio) and html. You can also give a reporter class, eg
+# mypackage.mymodule.MyReporterClass.
+#output-format=text
+
+# Put messages in a separate file for each module / package specified on the
+# command line instead of printing them on stdout. Reports (if any) will be
+# written in a file name "pylint_global.[txt|html]".
+#files-output=no
+
+# Tells whether to display a full report or only the messages
+#reports=yes
+
+# Python expression which should return a note less than 10 (10 is the highest
+# note). You have access to the variables errors warning, statement which
+# respectively contain the number of errors / warnings messages and the total
+# number of statements analyzed. This is used by the global evaluation report
+# (RP0004).
+#evaluation=10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10)
+
+# Add a comment according to your evaluation note. This is used by the global
+# evaluation report (RP0004).
+#comment=no
+
+# Template used to display messages. This is a python new-style format string
+# used to format the message information. See doc for all details
+#msg-template=
+
+
+[SPELLING]
+
+# Spelling dictionary name. Available dictionaries: none. To make it working
+# install pyenchant package.
+# sudo apt-get install python-enchant hunspell-en-us iamerican-large
+# wamerican-large python-enchant python3-enchant
+spelling-dict=en_US
+
+# List of comma separated words that should not be checked.
+#spelling-ignore-words=
+
+# A path to a file that contains private dictionary; one word per line.
+spelling-private-dict-file=.dictionary
+
+# Tells whether to store unknown words to indicated private dictionary in
+# --spelling-private-dict-file option instead of raising a message.
+#spelling-store-unknown-words=yes
+
+
+[SIMILARITIES]
+
+# Minimum lines number of a similarity.
+#min-similarity-lines=4
+
+# Ignore comments when computing similarities.
+#ignore-comments=yes
+
+# Ignore docstrings when computing similarities.
+#ignore-docstrings=yes
+
+# Ignore imports when computing similarities.
+#ignore-imports=no
+
+
+[TYPECHECK]
+
+# Tells whether missing members accessed in mixin class should be ignored. A
+# mixin class is detected if its name ends with "mixin" (case insensitive).
+#ignore-mixin-members=yes
+
+# List of module names for which member attributes should not be checked
+# (useful for modules/projects where namespaces are manipulated during runtime
+# and thus existing member attributes cannot be deduced by static analysis
+#ignored-modules=
+
+# List of classes names for which member attributes should not be checked
+# (useful for classes with attributes dynamically set).
+#ignored-classes=SQLObject
+
+# When zope mode is activated, add a predefined set of Zope acquired attributes
+# to generated-members.
+#zope=no
+
+# List of members which are set dynamically and missed by pylint inference
+# system, and so shouldn't trigger E0201 when accessed. Python regular
+# expressions are accepted.
+#generated-members=REQUEST,acl_users,aq_parent
+
+
+[LOGGING]
+
+# Logging modules to check that the string format arguments are in logging
+# function parameter format
+#logging-modules=logging
+
+
+[BASIC]
+
+# Required attributes for module, separated by a comma
+#required-attributes=
+
+# List of builtins function names that should not be used, separated by a comma
+#bad-functions=map,filter,input
+
+# Good variable names which should always be accepted, separated by a comma
+#good-names=i,j,k,ex,Run,_
+
+# Bad variable names which should always be refused, separated by a comma
+#bad-names=foo,bar,baz,toto,tutu,tata
+
+# Colon-delimited sets of names that determine each other's naming style when
+# the name regexes allow several styles.
+#name-group=
+
+# Include a hint for the correct naming format with invalid-name
+#include-naming-hint=no
+
+# Regular expression matching correct function names
+#function-rgx=[a-z_][a-z0-9_]{2,30}$
+
+# Naming hint for function names
+#function-name-hint=[a-z_][a-z0-9_]{2,30}$
+
+# Regular expression matching correct variable names
+#variable-rgx=[a-z_][a-z0-9_]{2,30}$
+
+# Naming hint for variable names
+#variable-name-hint=[a-z_][a-z0-9_]{2,30}$
+
+# Regular expression matching correct constant names
+#const-rgx=(([A-Z_][A-Z0-9_]*)|(__.*__))$
+
+# Naming hint for constant names
+#const-name-hint=(([A-Z_][A-Z0-9_]*)|(__.*__))$
+
+# Regular expression matching correct attribute names
+#attr-rgx=[a-z_][a-z0-9_]{2,30}$
+
+# Naming hint for attribute names
+#attr-name-hint=[a-z_][a-z0-9_]{2,30}$
+
+# Regular expression matching correct argument names
+#argument-rgx=[a-z_][a-z0-9_]{2,30}$
+
+# Naming hint for argument names
+#argument-name-hint=[a-z_][a-z0-9_]{2,30}$
+
+# Regular expression matching correct class attribute names
+#class-attribute-rgx=([A-Za-z_][A-Za-z0-9_]{2,30}|(__.*__))$
+
+# Naming hint for class attribute names
+#class-attribute-name-hint=([A-Za-z_][A-Za-z0-9_]{2,30}|(__.*__))$
+
+# Regular expression matching correct inline iteration names
+#inlinevar-rgx=[A-Za-z_][A-Za-z0-9_]*$
+
+# Naming hint for inline iteration names
+#inlinevar-name-hint=[A-Za-z_][A-Za-z0-9_]*$
+
+# Regular expression matching correct class names
+#class-rgx=[A-Z_][a-zA-Z0-9]+$
+
+# Naming hint for class names
+#class-name-hint=[A-Z_][a-zA-Z0-9]+$
+
+# Regular expression matching correct module names
+#module-rgx=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
+
+# Naming hint for module names
+#module-name-hint=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
+
+# Regular expression matching correct method names
+#method-rgx=[a-z_][a-z0-9_]{2,30}$
+
+# Naming hint for method names
+#method-name-hint=[a-z_][a-z0-9_]{2,30}$
+
+# Regular expression which should only match function or class names that do
+# not require a docstring.
+#no-docstring-rgx=__.*__
+
+# Minimum line length for functions/classes that require docstrings, shorter
+# ones are exempt.
+#docstring-min-length=-1
+
+
+[MISCELLANEOUS]
+
+# List of note tags to take in consideration, separated by a comma.
+#notes=FIXME,XXX,TODO
+
+
+[FORMAT]
+
+# Maximum number of characters on a single line.
+#max-line-length=100
+
+# Regexp for a line that is allowed to be longer than the limit.
+#ignore-long-lines=^\s*(# )?<?https?://\S+>?$
+
+# Allow the body of an if to be on the same line as the test if there is no
+# else.
+#single-line-if-stmt=no
+
+# List of optional constructs for which whitespace checking is disabled
+#no-space-check=trailing-comma,dict-separator
+
+# Maximum number of lines in a module
+#max-module-lines=1000
+
+# String used as indentation unit. This is usually " " (4 spaces) or "\t" (1
+# tab).
+#indent-string=' '
+
+# Number of spaces of indent required inside a hanging or continued line.
+#indent-after-paren=4
+
+# Expected format of line ending, e.g. empty (any line ending), LF or CRLF.
+#expected-line-ending-format=
+
+
+[VARIABLES]
+
+# Tells whether we should check for unused import in __init__ files.
+#init-import=no
+
+# A regular expression matching the name of dummy variables (i.e. expectedly
+# not used).
+#dummy-variables-rgx=_$|dummy
+
+# List of additional names supposed to be defined in builtins. Remember that
+# you should avoid to define new builtins when possible.
+#additional-builtins=
+
+# List of strings which can identify a callback function by name. A callback
+# name must start or end with one of those strings.
+#callbacks=cb_,_cb
+
+
+[IMPORTS]
+
+# Deprecated modules which should not be used, separated by a comma
+#deprecated-modules=regsub,TERMIOS,Bastion,rexec
+
+# Create a graph of every (i.e. internal and external) dependencies in the
+# given file (report RP0402 must not be disabled)
+#import-graph=
+
+# Create a graph of external dependencies in the given file (report RP0402 must
+# not be disabled)
+#ext-import-graph=
+
+# Create a graph of internal dependencies in the given file (report RP0402 must
+# not be disabled)
+#int-import-graph=
+
+
+[CLASSES]
+
+# List of interface methods to ignore, separated by a comma. This is used for
+# instance to not check methods defines in Zope's Interface base class.
+#ignore-iface-methods=isImplementedBy,deferred,extends,names,namesAndDescriptions,queryDescriptionFor,getBases,getDescriptionFor,getDoc,getName,getTaggedValue,getTaggedValueTags,isEqualOrExtendedBy,setTaggedValue,isImplementedByInstancesOf,adaptWith,is_implemented_by
+
+# List of method names used to declare (i.e. assign) instance attributes.
+#defining-attr-methods=__init__,__new__,setUp
+
+# List of valid names for the first argument in a class method.
+#valid-classmethod-first-arg=cls
+
+# List of valid names for the first argument in a metaclass class method.
+#valid-metaclass-classmethod-first-arg=mcs
+
+# List of member names, which should be excluded from the protected access
+# warning.
+#exclude-protected=_asdict,_fields,_replace,_source,_make
+
+
+[DESIGN]
+
+# Maximum number of arguments for function / method
+#max-args=5
+
+# Argument names that match this expression will be ignored. Default to name
+# with leading underscore
+#ignored-argument-names=_.*
+
+# Maximum number of locals for function / method body
+#max-locals=15
+
+# Maximum number of return / yield for function / method body
+#max-returns=6
+
+# Maximum number of branch for function / method body
+#max-branches=12
+
+# Maximum number of statements in function / method body
+#max-statements=50
+
+# Maximum number of parents for a class (see R0901).
+#max-parents=7
+
+# Maximum number of attributes for a class (see R0902).
+#max-attributes=7
+
+# Minimum number of public methods for a class (see R0903).
+#min-public-methods=2
+
+# Maximum number of public methods for a class (see R0904).
+#max-public-methods=20
+
+
+[EXCEPTIONS]
+
+# Exceptions that will emit a warning when being caught. Defaults to
+# "Exception"
+#overgeneral-exceptions=Exception
diff --git a/pytest.ini b/pytest.ini
new file mode 100644
index 0000000..81ba721
--- /dev/null
+++ b/pytest.ini
@@ -0,0 +1,4 @@
+[pytest]
+addopts = -m "not known_failing and not jenkins and not huge" -v
+norecursedirs = third-party
+testpaths = tests
diff --git a/sandbox/Makefile.read_aligner_training b/sandbox/Makefile.read_aligner_training
index f793ff6..dde83c6 100644
--- a/sandbox/Makefile.read_aligner_training
+++ b/sandbox/Makefile.read_aligner_training
@@ -1,6 +1,6 @@
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -33,7 +33,7 @@
#
# Contact: khmer-project at idyll.org
-KHMER= ../khmer
+KHMER=..
KSIZE= 30
HASH_SIZE= 4e8
@@ -41,21 +41,25 @@ N_HASHES= 4
all: estimated_probabilities.${KSIZE}.json
-mockRefG.fa:
- wget https://github.com/dib-lab/khmer-testdata/raw/master/mockRefG.fa
+my_mock.fa:
+ wget https://github.com/dib-lab/khmer-testdata/raw/master/my_mock.fa
%.fastq.gz:
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR172/SRR172903/SRR172903.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR172/SRR172902/SRR172902.fastq.gz
combined_reads.ht: SRR172902.fastq.gz SRR172903.fastq.gz
- python $(KHMER)/scripts/load-into-counting.py --ksize $(KSIZE) -x $(HASH_SIZE) -N $(N_HASHES) $@ $^
+ python $(KHMER)/scripts/load-into-counting.py --ksize $(KSIZE) \
+ -x $(HASH_SIZE) -N $(N_HASHES) $@ $^
-mockRefG.1.bt1: mockRefG.fa
- bowtie2-build mockRefG.fa
+my_mock.1.bt1: my_mock.fa
+ bowtie2-build my_mock.fa my_mock
-combined_reads_mapping.bam: SRR172902.fastq.gz SRR172903.fastq.gz mockRefG.1.bt1
- bowtie2 -x mockRefG -U SRR172902.fastq.gz -U SRR172903.fastq.gz | samtools view -S -F4 -b - > combined_reads_mapping.bam
+combined_reads_mapping.bam: SRR172902.fastq.gz SRR172903.fastq.gz my_mock.1.bt1
+ bowtie2 -x my_mock -U SRR172902.fastq.gz -U SRR172903.fastq.gz \
+ | samtools view -S -F4 -b - > combined_reads_mapping.bam
-estimated_probabilities.${KSIZE}.json: combined_reads.ht combined_reads_mapping.bam
- python readaligner_pairhmm_train.py --json combined_reads.ht combined_reads_mapping.bam > estimated_probabilities.${KSIZE}.json
+estimated_probabilities.$(KSIZE).json: combined_reads.ht combined_reads_mapping.bam
+ python readaligner_pairhmm_train.py --json combined_reads.ht \
+ combined_reads_mapping.bam \
+ > estimated_probabilities.${KSIZE}.json
diff --git a/sandbox/README.rst b/sandbox/README.rst
index 9735ea5..41d9ea1 100644
--- a/sandbox/README.rst
+++ b/sandbox/README.rst
@@ -65,20 +65,16 @@ Scripts with recipes:
To keep, document, and build recipes for:
-* `make-coverage.py - RPKM calculation script
-* abundance-hist-by-position.py - look at abundance of k-mers by position within read; use with fasta-to-abundance-hist.py
+* make-coverage.py - RPKM calculation script
* assemstats3.py - print out assembly statistics
* build-sparse-graph.py - code for building a sparse graph (by Camille Scott)
* calc-best-assembly.py - calculate the "best assembly" - used in metagenome protocol
* collect-variants.py - used in a `gist <https://gist.github.com/ctb/6eaef7971ea429ab348d>`__
* extract-single-partition.py - extract all the sequences that belong to a specific partition, from a file with multiple partitions
-* fasta-to-abundance-hist.py - generate abundance of k-mers by position within reads; use with abundance-hist-by-position.py
* filter-below-abund.py - like filter-abund, but trim off high-abundance k-mers
* filter-median-and-pct.py - see blog post on Trinity in silico norm (http://ivory.idyll.org/blog/trinity-in-silico-normalize.html)
* filter-median.py - see blog post on Trinity in silico norm (http://ivory.idyll.org/blog/trinity-in-silico-normalize.html)
-* find-high-abund-kmers.py - extract high-abundance k-mers into a list
* graph-size.py - filter reads based on size of connected graph
-* hi-lo-abundance-by-position.py - look at high and low-abundance k-mers by position within read
* memusg - memory usage analysis
* multi-rename.py - rename sequences from multiple files with a common prefix
* normalize-by-median-pct.py - see blog post on Trinity in silico norm (http://ivory.idyll.org/blog/trinity-in-silico-normalize.html)
@@ -87,7 +83,6 @@ To keep, document, and build recipes for:
* renumber-partitions.py - systematically renumber partitions
* shuffle-reverse-rotary.py - FASTA file shuffler for larger FASTA files
* split-fasta.py - break a FASTA file up into smaller chunks
-* stoptag-abundance-hist.py - print out abundance histogram of stoptags
* stoptags-by-position.py - print out where stoptags tend to occur
* strip-partition.py - clear off partition information
* subset-report.py - report stats on pmap files
@@ -107,6 +102,15 @@ Good ideas to rewrite using newer tools/approaches:
----
+Present in commit ff7f047b5b0d9acb6c1eb73d54cfd39c9e3d1393 but removed
+thereafter:
+
+* abundance-hist-by-position.py - look at abundance of k-mers by position within read; use with fasta-to-abundance-hist.py
+* fasta-to-abundance-hist.py - generate abundance of k-mers by position within reads; use with abundance-hist-by-position.py
+* find-high-abund-kmers.py - extract high-abundance k-mers into a list
+* hi-lo-abundance-by-position.py - look at high and low-abundance k-mers by position within read
+* stoptag-abundance-hist.py - print out abundance histogram of stoptags
+
Present in commit 19b0a09353cddc45070edcf1283cae2c83c13b0e but removed
thereafter:
diff --git a/sandbox/abundance-hist-by-position.py b/sandbox/abundance-hist-by-position.py
deleted file mode 100755
index 43c5768..0000000
--- a/sandbox/abundance-hist-by-position.py
+++ /dev/null
@@ -1,70 +0,0 @@
-#! /usr/bin/env python
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) 2010-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are
-# met:
-#
-# * Redistributions of source code must retain the above copyright
-# notice, this list of conditions and the following disclaimer.
-#
-# * Redistributions in binary form must reproduce the above
-# copyright notice, this list of conditions and the following
-# disclaimer in the documentation and/or other materials provided
-# with the distribution.
-#
-# * Neither the name of the Michigan State University nor the names
-# of its contributors may be used to endorse or promote products
-# derived from this software without specific prior written
-# permission.
-#
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
-# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
-# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-#
-# Contact: khmer-project at idyll.org
-from __future__ import division
-from __future__ import print_function
-import sys
-
-def main():
- n = 0
- countSum = [0] * 255
- countN = [0] * 255
-
- freqfile = sys.argv[1]
-
- print('opening .freq file:', freqfile, file=sys.stderr)
- fd = open(freqfile)
- for n, line in enumerate(fd):
- if n % 100000 == 0:
- print('...', n, file=sys.stderr)
-
- tok = line.split()
-
- for i in range(len(tok)):
- countSum[i] += int(tok[i])
- countN[i] += 1
-
- print('summarizing.', file=sys.stderr)
- y = [0.0] * len(countSum)
-
- for i in range(len(countSum)):
- if countN[i]:
- y[i] = float(countSum[i]) / float(countN[i])
-
- for n, i in enumerate(y):
- print(n, i)
-
-if __name__ == '__main__':
- main()
diff --git a/sandbox/assemble-and-track.py b/sandbox/assemble-and-track.py
new file mode 100755
index 0000000..429bce6
--- /dev/null
+++ b/sandbox/assemble-and-track.py
@@ -0,0 +1,139 @@
+#! /usr/bin/env python
+from __future__ import print_function
+import csv
+import screed
+import khmer
+from khmer.khmer_args import build_counting_args, create_countgraph
+import argparse
+import sys
+
+
+DEFAULT_COV = 20
+THRESH2 = 30
+
+
+dna_to_aa={'TTT':'F','TTC':'F', 'TTA':'L','TTG':'L',
+ 'TCT':'S','TCC':'S','TCA':'S','TCG':'S',
+ 'TAT':'Y','TAC':'Y', 'TAA':'*','TAG':'*','TGA':'*',
+ 'TGT':'C','TGC':'C', 'TGG':'W',
+ 'CTT':'L','CTC':'L','CTA':'L','CTG':'L',
+ 'CCT':'P','CCC':'P','CCA':'P','CCG':'P',
+ 'CAT':'H','CAC':'H', 'CAA':'Q','CAG':'Q',
+ 'CGT':'R','CGC':'R','CGA':'R','CGG':'R',
+ 'ATT':'I','ATC':'I','ATA':'I', 'ATG':'M',
+ 'ACT':'T','ACC':'T','ACA':'T','ACG':'T',
+ 'AAT':'N','AAC':'N', 'AAA':'K','AAG':'K',
+ 'AGT':'S','AGC':'S', 'AGA':'R','AGG':'R',
+ 'GTT':'V','GTC':'V','GTA':'V','GTG':'V',
+ 'GCT':'A','GCC':'A','GCA':'A','GCG':'A',
+ 'GAT':'D','GAC':'D', 'GAA':'E','GAG':'E',
+ 'GGT':'G','GGC':'G','GGA':'G','GGG':'G'}
+
+
+__complementTranslation = { "A": "T", "C": "G", "G": "C", "T": "A", "N": "N" }
+def complement(s):
+ """
+ Return complement of 's'.
+ """
+ c = "".join(__complementTranslation[n] for n in s)
+ return c
+
+
+def reverse(s):
+ """
+ Return reverse of 's'.
+ """
+ r = "".join(reversed(s))
+ return r
+
+
+def peptides(seq, start):
+ for i in range(start, len(seq), 3):
+ yield dna_to_aa.get(seq[i:i+3], "X")
+
+
+def translate(seq):
+ for i in range(3):
+ pep = peptides(seq, i)
+ yield "".join(pep)
+
+ revcomp = reverse(complement((seq)))
+ for i in range(3):
+ pep = peptides(revcomp, i)
+ yield "".join(pep)
+
+
+def extract_orfs(pepseq, min_length=99):
+ peplist = [ x for x in pepseq.split('*') if len(x) >= min_length ]
+ for x in peplist:
+ yield x
+
+
+def main():
+ p = build_counting_args(descr='Streaming assembly with tracking info')
+ p.add_argument('fastq_files', nargs='+')
+ p.add_argument('-o', type=argparse.FileType('w'),
+ default='assembly-stats.csv')
+ args = p.parse_args()
+
+ cg = create_countgraph(args)
+
+ kept = 0
+ hdn = khmer.HashSet(args.ksize)
+ lh = khmer._GraphLabels(cg)
+ next_label = 1
+ next_orf = 1
+ output = set()
+ statswriter = csv.DictWriter(args.o, delimiter=',',
+ fieldnames=['read_n', 'action', 'cov', 'n_hdn',
+ 'contig_n', 'orf_n', 'new'])
+
+ for filename in args.fastq_files:
+ for n, record in enumerate(screed.open(filename)):
+ if n and n % 10000 == 0:
+ print('...', n, file=sys.stderr)
+
+ if len(record.sequence) < args.ksize:
+ continue
+
+ cov, _, _ = cg.get_median_count(record.sequence)
+ if cov < 20:
+ kept += 1
+ cg.consume(record.sequence)
+ statswriter.writerow({'read_n': n, 'action': 'c', 'cov': cov,
+ 'n_hdn': None, 'contig_n': None,
+ 'orf_n': None, 'new': None})
+ elif cov < 30:
+ #print('intermediate', next_label, file=sys.stderr)
+ seq, pos = cg.trim_on_abundance(record.sequence, 3)
+ if len(seq) < args.ksize:
+ continue
+
+ cg.consume(seq)
+ hdn = cg.find_high_degree_nodes(seq)
+ lh.label_across_high_degree_nodes(seq, hdn, next_label)
+ next_label += 1
+ statswriter.writerow({'read_n': n, 'action': 'l', 'cov': cov,
+ 'n_hdn': len(hdn), 'contig_n': None,
+ 'orf_n': None, 'new': None})
+ elif cov == 30:
+ contigs = lh.assemble_labeled_path(record.sequence[:args.ksize])
+ for contig_n, contig in enumerate(contigs):
+ statswriter.writerow({'read_n': n, 'action': 'a', 'cov': cov,
+ 'n_hdn': None, 'contig_n': contig_n,
+ 'orf_n': None, 'new': None})
+ for t in translate(contig):
+ for orf_n, o in enumerate(extract_orfs(t)):
+ if hash(o) not in output:
+ new = True
+ output.add(hash(o))
+ print('>orf%d\n%s' % (next_orf, o))
+ next_orf += 1
+ else:
+ new = False
+ statswriter.writerow({'read_n': n, 'action': 'a', 'cov': cov,
+ 'n_hdn': None, 'contig_n': contig_n,
+ 'orf_n': orf_n, 'new': new})
+
+if __name__ == '__main__':
+ main()
diff --git a/sandbox/assemble-on-the-go.py b/sandbox/assemble-on-the-go.py
new file mode 100755
index 0000000..6e5f882
--- /dev/null
+++ b/sandbox/assemble-on-the-go.py
@@ -0,0 +1,118 @@
+#! /usr/bin/env python
+from __future__ import print_function
+import screed
+import khmer
+import argparse
+import sys
+
+
+DEFAULT_COV = 20
+K = 21
+THRESH2 = 30
+
+
+dna_to_aa={'TTT':'F','TTC':'F', 'TTA':'L','TTG':'L',
+ 'TCT':'S','TCC':'S','TCA':'S','TCG':'S',
+ 'TAT':'Y','TAC':'Y', 'TAA':'*','TAG':'*','TGA':'*',
+ 'TGT':'C','TGC':'C', 'TGG':'W',
+ 'CTT':'L','CTC':'L','CTA':'L','CTG':'L',
+ 'CCT':'P','CCC':'P','CCA':'P','CCG':'P',
+ 'CAT':'H','CAC':'H', 'CAA':'Q','CAG':'Q',
+ 'CGT':'R','CGC':'R','CGA':'R','CGG':'R',
+ 'ATT':'I','ATC':'I','ATA':'I', 'ATG':'M',
+ 'ACT':'T','ACC':'T','ACA':'T','ACG':'T',
+ 'AAT':'N','AAC':'N', 'AAA':'K','AAG':'K',
+ 'AGT':'S','AGC':'S', 'AGA':'R','AGG':'R',
+ 'GTT':'V','GTC':'V','GTA':'V','GTG':'V',
+ 'GCT':'A','GCC':'A','GCA':'A','GCG':'A',
+ 'GAT':'D','GAC':'D', 'GAA':'E','GAG':'E',
+ 'GGT':'G','GGC':'G','GGA':'G','GGG':'G'}
+
+
+__complementTranslation = { "A": "T", "C": "G", "G": "C", "T": "A", "N": "N" }
+def complement(s):
+ """
+ Return complement of 's'.
+ """
+ c = "".join(__complementTranslation[n] for n in s)
+ return c
+
+
+def reverse(s):
+ """
+ Return reverse of 's'.
+ """
+ r = "".join(reversed(s))
+ return r
+
+
+def peptides(seq, start):
+ for i in range(start, len(seq), 3):
+ yield dna_to_aa.get(seq[i:i+3], "X")
+
+
+def translate(seq):
+ for i in range(3):
+ pep = peptides(seq, i)
+ yield "".join(pep)
+
+ revcomp = reverse(complement((seq)))
+ for i in range(3):
+ pep = peptides(revcomp, i)
+ yield "".join(pep)
+
+
+def extract_orfs(pepseq, min_length=99):
+ peplist = [ x for x in pepseq.split('*') if len(x) >= min_length ]
+ for x in peplist:
+ yield x
+
+
+def main():
+ p = argparse.ArgumentParser()
+ p.add_argument('fastq_files', nargs='+')
+ args = p.parse_args()
+
+ cg = khmer.Countgraph(K, 1e8, 4)
+
+ kept = 0
+ hdn = khmer.HashSet(K)
+ lh = khmer._GraphLabels(cg)
+ next_label = 1
+ next_orf = 1
+ output = set()
+
+ for filename in args.fastq_files:
+ for n, record in enumerate(screed.open(filename)):
+ if n and n % 10000 == 0:
+ print('...', n, file=sys.stderr)
+
+ if len(record.sequence) < K:
+ continue
+
+ cov, _, _ = cg.get_median_count(record.sequence)
+ if cov < 20:
+ kept += 1
+ cg.consume(record.sequence)
+ elif cov < 30:
+ #print('intermediate', next_label, file=sys.stderr)
+ seq, pos = cg.trim_on_abundance(record.sequence, 3)
+ if len(seq) < K:
+ continue
+
+ cg.consume(seq)
+ hdn = cg.find_high_degree_nodes(seq)
+ lh.label_across_high_degree_nodes(seq, hdn, next_label)
+ next_label += 1
+ elif cov == 30:
+ contigs = lh.assemble_labeled_path(record.sequence[:K])
+ for contig in contigs:
+ for t in translate(contig):
+ for o in extract_orfs(t):
+ if hash(o) not in output:
+ output.add(hash(o))
+ print('>orf%d\n%s' % (next_orf, o))
+ next_orf += 1
+
+if __name__ == '__main__':
+ main()
diff --git a/sandbox/assembly-diff.py b/sandbox/assembly-diff.py
index 501c774..4c19d7f 100755
--- a/sandbox/assembly-diff.py
+++ b/sandbox/assembly-diff.py
@@ -55,9 +55,9 @@ def main():
paths = sys.argv[3]
kh1 = khmer.Nodegraph(K, HASHTABLE_SIZE, N_HT)
- kh1.consume_fasta(filename1)
+ kh1.consume_seqfile(filename1)
kh2 = khmer.Nodegraph(K, HASHTABLE_SIZE, N_HT)
- kh2.consume_fasta(filename2)
+ kh2.consume_seqfile(filename2)
for record in screed.open(paths):
n = 0
diff --git a/sandbox/assemstats3.py b/sandbox/assemstats3.py
index 7100927..6104231 100755
--- a/sandbox/assemstats3.py
+++ b/sandbox/assemstats3.py
@@ -152,4 +152,5 @@ def main():
main()
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
+# vim: set filetype=python tabstop=4 softtabstop=4 shiftwidth=4 expandtab:
+# vim: set textwidth=79:
diff --git a/sandbox/bloom-count.py b/sandbox/bloom-count.py
index 622356b..7feefca 100755
--- a/sandbox/bloom-count.py
+++ b/sandbox/bloom-count.py
@@ -33,7 +33,10 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
+# pylint: disable=missing-docstring,no-member
from __future__ import print_function
+from __future__ import absolute_import
+
import khmer
import sys
import screed
diff --git a/sandbox/collect-reads.py b/sandbox/collect-reads.py
index 007be70..6d8e397 100755
--- a/sandbox/collect-reads.py
+++ b/sandbox/collect-reads.py
@@ -175,4 +175,5 @@ def main():
if __name__ == '__main__':
main()
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
+# vim: set filetype=python tabstop=4 softtabstop=4 shiftwidth=4 expandtab:
+# vim: set textwidth=79:
diff --git a/sandbox/collect-variants.py b/sandbox/collect-variants.py
index 990c0f9..339e276 100755
--- a/sandbox/collect-variants.py
+++ b/sandbox/collect-variants.py
@@ -180,4 +180,5 @@ def main():
if __name__ == '__main__':
main()
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
+# vim: set filetype=python tabstop=4 softtabstop=4 shiftwidth=4 expandtab:
+# vim: set textwidth=79:
diff --git a/sandbox/count-kmers-single.py b/sandbox/count-kmers-single.py
index 7fc929f..480f249 100755
--- a/sandbox/count-kmers-single.py
+++ b/sandbox/count-kmers-single.py
@@ -103,7 +103,7 @@ def main():
for _ in range(args.threads):
thread = \
threading.Thread(
- target=countgraph.consume_fasta_with_reads_parser,
+ target=countgraph.consume_seqfile_with_reads_parser,
args=(rparser, )
)
threads.append(thread)
@@ -127,4 +127,5 @@ def main():
if __name__ == '__main__':
main()
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
+# vim: set filetype=python tabstop=4 softtabstop=4 shiftwidth=4 expandtab:
+# vim: set textwidth=79:
diff --git a/sandbox/count-kmers.py b/sandbox/count-kmers.py
old mode 100644
new mode 100755
index d17a762..ca33983
--- a/sandbox/count-kmers.py
+++ b/sandbox/count-kmers.py
@@ -104,4 +104,5 @@ def main():
if __name__ == '__main__':
main()
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
+# vim: set filetype=python tabstop=4 softtabstop=4 shiftwidth=4 expandtab:
+# vim: set textwidth=79:
diff --git a/sandbox/extract-compact-dbg.py b/sandbox/extract-compact-dbg.py
new file mode 100755
index 0000000..e6abdd5
--- /dev/null
+++ b/sandbox/extract-compact-dbg.py
@@ -0,0 +1,230 @@
+#! /usr/bin/env python
+from __future__ import print_function
+import khmer
+import screed
+import argparse
+from collections import OrderedDict
+import sys
+
+# graph settings
+DEFAULT_KSIZE=31
+NODEGRAPH_SIZE=8e8
+
+# minhash settings
+MH_SIZE_DIVISOR=50
+MH_MIN_SIZE=5
+MH_PRIME=9999999967
+
+class Pathfinder(object):
+ "Track segment IDs & adjacency lists."
+ def __init__(self, ksize):
+ self.ksize = ksize
+
+ self.segment_counter = 1
+ self.segments = {}
+ self.segments_r = {}
+ self.adjacencies = {}
+
+ def new_segment(self, kmer):
+ if kmer in self.segments_r:
+ return self.segments_r[kmer]
+
+ this_id = self.segment_counter
+ self.segment_counter += 1
+
+ self.segments[this_id] = self.ksize
+ self.segments_r[kmer] = this_id
+
+ return this_id
+
+ def new_linear_segment(self, size):
+ this_id = self.segment_counter
+ self.segment_counter += 1
+ self.segments[this_id] = size
+ return this_id
+
+ def add_adjacency(self, node_id, adj):
+ node_id, adj = min(node_id, adj), max(node_id, adj)
+
+ x = self.adjacencies.get(node_id, set())
+ x.add(adj)
+ self.adjacencies[node_id] = x
+
+
+def traverse_and_mark_linear_paths(graph, nk, stop_bf, pathy, degree_nodes):
+ size, conns, visited = graph.traverse_linear_path(nk, degree_nodes,
+ stop_bf)
+ if not size:
+ return
+
+ # give it a segment ID
+ path_id = pathy.new_linear_segment(size)
+
+ # for all adjacencies, add.
+ for conn in conns:
+ conn_id = pathy.segments_r.get(conn)
+ pathy.add_adjacency(path_id, conn_id)
+
+
+def main():
+ parser = argparse.ArgumentParser()
+ parser.add_argument('seqfiles', nargs='+')
+ parser.add_argument('-o', '--output', default=None)
+ parser.add_argument('-k', '--ksize', default=DEFAULT_KSIZE, type=int)
+ parser.add_argument('-x', '--tablesize', default=NODEGRAPH_SIZE,
+ type=float)
+ parser.add_argument('--force', action='store_true')
+ args = parser.parse_args()
+
+ assert args.ksize % 2, "ksize must be odd"
+ assert args.output, "you probably want an output file"
+
+ print('building graphs and loading files')
+
+ # Create graph, and two stop bloom filters - one for loading, one for
+ # traversing. Create them all here so that we can error out quickly
+ # if memory is a problem.
+
+ graph = khmer.Nodegraph(args.ksize, args.tablesize, 2)
+ stop_bf = khmer.Nodegraph(args.ksize, args.tablesize, 2)
+ stop_bf2 = khmer.Nodegraph(args.ksize, args.tablesize, 2)
+ n = 0
+
+ # load in all of the input sequences, one file at a time.
+ for seqfile in args.seqfiles:
+ for record in screed.open(seqfile):
+ n += 1
+ if n % 10000 == 0:
+ print('...', seqfile, n)
+ graph.consume(record.sequence)
+
+ # complain if too small set of graphs was used.
+ fp_rate = khmer.calc_expected_collisions(graph,
+ args.force, max_false_pos=.05)
+
+ # initialize the object that will track information for us.
+ pathy = Pathfinder(args.ksize)
+
+ print('finding high degree nodes')
+ degree_nodes = khmer.HashSet(args.ksize)
+ n = 0
+ for seqfile in args.seqfiles:
+ for record in screed.open(seqfile):
+ n += 1
+ if n % 10000 == 0:
+ print('...2', seqfile, n)
+ # walk across sequences, find all high degree nodes,
+ # name them and cherish them. Don't do this on identical sequences.
+ if min(stop_bf2.get_kmer_counts(record.sequence)) == 0:
+ stop_bf2.consume(record.sequence)
+ degree_nodes += graph.find_high_degree_nodes(record.sequence)
+ del stop_bf2
+
+ if not len(degree_nodes):
+ print('no high degree nodes; exiting.')
+ sys.exit(0)
+
+ # get all of the degree > 2 nodes and give them IDs.
+ for node in degree_nodes:
+ pathy.new_segment(node)
+
+ print('traversing linear segments from', len(degree_nodes), 'nodes')
+
+ # now traverse from each high degree nodes into all neighboring nodes,
+ # seeking adjacencies. if neighbor is high degree node, add it to
+ # adjacencies; if neighbor is not, then traverse the linear path. also
+ # track minhashes while we're at it.
+ for n, k in enumerate(degree_nodes):
+ if n % 10000 == 0:
+ print('...', n, 'of', len(degree_nodes))
+
+ # retrieve the segment ID of the primary node.
+ k_id = pathy.segments_r[k]
+
+ # find all the neighbors of this high-degree node.
+ nbh = graph.neighbors(k)
+ for nk in nbh:
+ # neighbor is high degree? fine, mark its adjacencies.
+ if nk in degree_nodes:
+ nk_id = pathy.segments_r[nk]
+ pathy.add_adjacency(k_id, nk_id)
+ else:
+ # linear! walk it.
+ traverse_and_mark_linear_paths(graph, nk, stop_bf, pathy,
+ degree_nodes)
+
+ print(len(pathy.segments), 'segments, containing',
+ sum(pathy.segments.values()), 'nodes')
+
+ # save to GML
+ if args.output:
+ print('saving to', args.output)
+ fp = open(args.output, 'w')
+ w = GmlWriter(fp, [], [])
+
+ for k, v in pathy.segments.items():
+ w.add_vertex(k, v, [])
+
+ for k, v in pathy.adjacencies.items():
+ for edge in v:
+ w.add_edge(k, edge, [])
+
+
+# Author of the below code: Dominik Moritz, originally for spacegraphcats.
+
+class GmlWriter:
+ """Similar to the writer for gxt above but for gml."""
+
+ def __init__(self, file, vertex_attributes=None, edge_attributes=None, directed=False):
+ """Initialize graph writer."""
+ self.file = file
+
+ if vertex_attributes is not None:
+ self.vertex_attributes = vertex_attributes
+ if edge_attributes is not None:
+ self.edge_attributes = edge_attributes
+
+ if directed:
+ self._write('graph [\n directed 1\n')
+ else:
+ self._write('graph [\n directed 0\n')
+
+ def _write(self, string):
+ self.file.write(string)
+
+ def _quote(self, value):
+ if isinstance(value, str):
+ return '"{}"'.format(value)
+ return value
+
+ def add_vertex(self, id, size, attribute_values=[], vertex_attributes=None):
+ """Add a vertex to the output."""
+ if not hasattr(self, 'vertex_attributes'):
+ self.vertex_attributes = vertex_attributes
+
+ self._write(' node [\n')
+ self._write(' id {}\n'.format(id))
+ self._write(' size {}\n'.format(size))
+ for k, v in zip(self.vertex_attributes, attribute_values):
+ self._write(' {} {}\n'.format(k, self._quote(v)))
+ self._write(' ]\n')
+
+ def add_edge(self, src, dest, attribute_values=[], edge_attributes=None):
+ """Add an edge to the output."""
+ if not hasattr(self, 'edge_attributes'):
+ self.edge_attributes = edge_attributes
+
+ self._write(' edge [\n')
+ self._write(' source {}\n'.format(src))
+ self._write(' target {}\n'.format(dest))
+ for k, v in zip(self.edge_attributes, attribute_values):
+ self._write(' {} {}\n'.format(k, self._quote(v)))
+ self._write(' ]\n')
+
+ def done(self):
+ """Call when done."""
+ self._write(']\n')
+
+
+if __name__ == '__main__':
+ main()
diff --git a/sandbox/extract-unassembled-reads-2.py b/sandbox/extract-unassembled-reads-2.py
new file mode 100755
index 0000000..56095e0
--- /dev/null
+++ b/sandbox/extract-unassembled-reads-2.py
@@ -0,0 +1,72 @@
+#! /usr/bin/env python
+"""
+This script differs from extract-unassembled-reads.py in that it only tags
+the assembly, not the reads. This is more efficient (and streaming for
+the reads!) but it will erroneously extract some small fraction of reads
+because they miss the tags for reasons of length or errors.
+
+Procedure:
+
+* hard trim the reads at an abundance of ~5 (to avoid low abundance, and
+ eliminate erroneous paths)
+* and/or variable-coverage trim the reads at an abundance of 3, to eliminate
+ erroneous paths from super-high-abundance data
+* run this script with the assembly & the remaining reads.
+"""
+from __future__ import print_function
+import sys
+import os.path
+import khmer, khmer.utils
+import screed
+import argparse
+
+
+DEFAULT_KSIZE=31
+NODEGRAPH_SIZE=1e8
+
+
+def main():
+ p = argparse.ArgumentParser()
+ p.add_argument('assembly')
+ p.add_argument('readfiles', nargs='+')
+ p.add_argument('-o', '--output', default=None)
+ p.add_argument('-k', '--ksize', default=DEFAULT_KSIZE, type=int)
+ p.add_argument('-x', '--tablesize', default=NODEGRAPH_SIZE,
+ type=float)
+ args = p.parse_args()
+
+ ng = khmer.Nodegraph(args.ksize, args.tablesize, 4)
+ ng._set_tag_density(20)
+
+ print('loading & tagging assembly from:', args.assembly)
+ ng.consume_seqfile_and_tag(args.assembly)
+
+ if args.output:
+ outfp = open(args.output, 'w')
+
+ n = 0
+ m = 0
+ for readfile in args.readfiles:
+ print('loading reads from:', readfile)
+ if not args.output:
+ outfile = os.path.basename(readfile) + '.leftover'
+ outfp = open(outfile, 'w')
+ print('writing to:', outfile, file=sys.stderr)
+
+ for record in screed.open(readfile):
+ if n % 100000 == 0 and n:
+ print('...', readfile, n, m, file=sys.stderr)
+ x = ng.get_tags_and_positions(record.sequence)
+ if not x:
+ khmer.utils.write_record(record, outfp)
+ m += 1
+ n += 1
+
+ if not args.output:
+ outfp.close()
+
+ print('%d left out of assembly, of %d reads' % (m, n), file=sys.stderr)
+
+
+if __name__ == '__main__':
+ main()
diff --git a/sandbox/extract-unassembled-reads.py b/sandbox/extract-unassembled-reads.py
new file mode 100755
index 0000000..3fc7842
--- /dev/null
+++ b/sandbox/extract-unassembled-reads.py
@@ -0,0 +1,86 @@
+#! /usr/bin/env python
+"""
+Procedure:
+
+* hard trim the reads at an abundance of ~5 (to avoid low abundance, and
+ eliminate erroneous paths)
+* and/or variable-coverage trim the reads at an abundance of 3, to eliminate
+ erroneous paths from super-high-abundance data
+* run this script with the assembly & the remaining reads.
+"""
+from __future__ import print_function
+import sys
+import os.path
+import khmer, khmer.utils
+import screed
+import argparse
+
+
+DEFAULT_KSIZE=31
+NODEGRAPH_SIZE=1e8
+
+
+def main():
+ p = argparse.ArgumentParser()
+ p.add_argument('assembly')
+ p.add_argument('readfiles', nargs='+')
+ p.add_argument('-o', '--output', default=None)
+ p.add_argument('-k', '--ksize', default=DEFAULT_KSIZE, type=int)
+ p.add_argument('-x', '--tablesize', default=NODEGRAPH_SIZE,
+ type=float)
+ args = p.parse_args()
+
+ ng = khmer.Nodegraph(args.ksize, args.tablesize, 4)
+
+ # first, consume & tag the reads
+
+ for readfile in args.readfiles:
+ print('loading & tagging reads from:', readfile)
+ ng.consume_seqfile_and_tag(readfile)
+
+ ## next, consume & label the assembly
+
+ print('loading & tagging assembly from:', args.assembly)
+ lh = khmer._GraphLabels(ng)
+ lh.consume_seqfile_and_tag_with_labels(args.assembly)
+
+ if args.output:
+ outfp = open(args.output, 'w')
+
+ ## finally, walk across the reads & find those with no labels
+
+ n = 0
+ m = 0
+
+ for readfile in args.readfiles:
+ print('loading reads from:', readfile)
+ if not args.output:
+ outfile = os.path.basename(readfile) + '.leftover2'
+ outfp = open(outfile, 'w')
+ print('writing to:', outfile, file=sys.stderr)
+
+ for record in screed.open(readfile):
+ if n % 100000 == 0 and n:
+ print('...', readfile, n, m, file=sys.stderr)
+ x = ng.get_tags_and_positions(record.sequence)
+
+ do_extract = False
+ for (pos, tag) in x:
+ if not lh.get_tag_labels(tag):
+ do_extract = True
+ break
+
+ if do_extract:
+ khmer.utils.write_record(record, outfp)
+ m += 1
+
+ n += 1
+
+ if not args.output:
+ outfp.close()
+
+ print('%d left out of assembly, of %d reads' % (m, n), file=sys.stderr)
+
+
+if __name__ == '__main__':
+ main()
diff --git a/sandbox/find-high-abund-kmers.py b/sandbox/find-high-abund-kmers.py
deleted file mode 100755
index 07ed044..0000000
--- a/sandbox/find-high-abund-kmers.py
+++ /dev/null
@@ -1,107 +0,0 @@
-#! /usr/bin/env python
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) 2011-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are
-# met:
-#
-# * Redistributions of source code must retain the above copyright
-# notice, this list of conditions and the following disclaimer.
-#
-# * Redistributions in binary form must reproduce the above
-# copyright notice, this list of conditions and the following
-# disclaimer in the documentation and/or other materials provided
-# with the distribution.
-#
-# * Neither the name of the Michigan State University nor the names
-# of its contributors may be used to endorse or promote products
-# derived from this software without specific prior written
-# permission.
-#
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
-# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
-# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-#
-# Contact: khmer-project at idyll.org
-from __future__ import print_function
-
-import sys
-import screed
-import khmer
-from khmer.khmer_args import build_counting_args, DEFAULT_MAX_TABLESIZE
-
-DEFAULT_LOWER_CUTOFF = 2000
-DEFAULT_UPPER_CUTOFF = 65535
-
-###
-
-
-def main():
- parser = build_construct_args()
- parser.add_argument('-l', '--lower-cutoff', type=int, dest='lower_cutoff',
- default=DEFAULT_LOWER_CUTOFF)
- parser.add_argument('-u', '--upper-cutoff', type=int, dest='upper_cutoff',
- default=DEFAULT_UPPER_CUTOFF)
-
- parser.add_argument('output_filename')
- parser.add_argument('input_filename')
-
- args = parser.parse_args()
-
- if not args.quiet:
- if args.min_hashsize == DEFAULT_MAX_TABLESIZE:
- print("** WARNING: hashsize is default! " \
- "You absodefly want to increase this!\n** " \
- "Please read the docs!", file=sys.stderr)
-
- print('\nPARAMETERS:', file=sys.stderr)
- print(' - kmer size = %d \t\t(-k)' % args.ksize, file=sys.stderr)
- print(' - n hashes = %d \t\t(-N)' % args.n_hashes, file=sys.stderr)
- print(' - min hashsize = %-5.2g \t(-x)' % \
- args.min_hashsize, file=sys.stderr)
- print('', file=sys.stderr)
- print('Estimated memory usage is %.2g bytes " \
- "(n_hashes x min_hashsize)' % (
- args.n_hashes * args.min_hashsize), file=sys.stderr)
- print('-' * 8, file=sys.stderr)
-
- K = args.ksize
- HT_SIZE = args.min_hashsize
- N_HT = args.n_hashes
-
- output = args.output_filename
- input = args.input_filename
-
- print('lower cutoff:', args.lower_cutoff)
- print('upper cutoff:', args.upper_cutoff)
- print('Saving stoptags to %s' % output)
- print('Loading sequences in %s' % input)
-
- ###
-
- print('making hashtable')
- ht = khmer.Countgraph(K, HT_SIZE, N_HT)
- ht.set_use_bigcount(True)
-
- print('consuming input', input)
- hb = ht.collect_high_abundance_kmers(input,
- args.lower_cutoff,
- args.upper_cutoff)
-
- print('saving stoptags', output)
- hb.save_stop_tags(output)
-
-if __name__ == '__main__':
- main()
-
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
diff --git a/sandbox/graph-size.py b/sandbox/graph-size.py
index 1c981ba..f9b9553 100755
--- a/sandbox/graph-size.py
+++ b/sandbox/graph-size.py
@@ -72,7 +72,7 @@ def main():
print('creating ht')
ht = khmer.Nodegraph(K, HASHTABLE_SIZE, N_HT)
print('eating fa', infile)
- total_reads, n_consumed = ht.consume_fasta(infile)
+ total_reads, n_consumed = ht.consume_seqfile(infile)
outfp = open(outfile, 'w')
###
diff --git a/sandbox/link-compact-dbg.py b/sandbox/link-compact-dbg.py
new file mode 100755
index 0000000..65372e7
--- /dev/null
+++ b/sandbox/link-compact-dbg.py
@@ -0,0 +1,198 @@
+#! /usr/bin/env python
+from __future__ import print_function
+import khmer
+import screed
+import argparse
+from collections import OrderedDict
+import sys
+
+# graph settings
+DEFAULT_KSIZE=31
+NODEGRAPH_SIZE=8e8 # small, big is 2e8
+
+# minhash settings
+MH_SIZE_DIVISOR=50
+MH_MIN_SIZE=5
+MH_PRIME=9999999967
+
+class Pathfinder(object):
+ "Track segment IDs & adjacency lists."
+ def __init__(self, ksize):
+ self.ksize = ksize
+
+ self.segment_counter = 1
+ self.segments = {}
+ self.segments_r = {}
+ self.adjacencies = {}
+
+ def new_segment(self, kmer):
+ if kmer in self.segments_r:
+ return self.segments_r[kmer]
+
+ this_id = self.segment_counter
+ self.segment_counter += 1
+
+ self.segments[this_id] = self.ksize
+ self.segments_r[kmer] = this_id
+
+ return this_id
+
+ def new_linear_segment(self, size):
+ this_id = self.segment_counter
+ self.segment_counter += 1
+ self.segments[this_id] = size
+ return this_id
+
+ def add_adjacency(self, node_id, adj):
+ node_id, adj = min(node_id, adj), max(node_id, adj)
+
+ x = self.adjacencies.get(node_id, set())
+ x.add(adj)
+ self.adjacencies[node_id] = x
+
+
+def traverse_and_mark_linear_paths(graph, nk, stop_bf, pathy, degree_nodes,
+ lh):
+ size, conns, visited = graph.traverse_linear_path(nk, degree_nodes,
+ stop_bf)
+ if not size:
+ return
+
+ linear_path_labels = set()
+ for node in visited:
+ linear_path_labels.update(lh.get_tag_labels(node))
+
+ # TODO: do something graph-y with these, like split paths across HDNs
+ # or simply omit HDNs altogether with traversal.
+
+ # give it a segment ID
+ path_id = pathy.new_linear_segment(size)
+
+ # for all adjacencies, add.
+ for conn in conns:
+ conn_id = pathy.segments_r.get(conn)
+ pathy.add_adjacency(path_id, conn_id)
+
+
+def main():
+ parser = argparse.ArgumentParser()
+ parser.add_argument('seqfiles', nargs='+')
+ parser.add_argument('-o', '--output', default=None)
+ parser.add_argument('-k', '--ksize', default=DEFAULT_KSIZE, type=int)
+ parser.add_argument('-x', '--tablesize', default=NODEGRAPH_SIZE,
+ type=float)
+ parser.add_argument('--force', action='store_true')
+ #parser.add_argument('--gml', action='store_true')
+ args = parser.parse_args()
+
+ assert args.ksize % 2, "ksize must be odd"
+ assert args.output, "you probably want an output file"
+
+ print('building graphs and loading files')
+
+ # Create graph, and two stop bloom filters - one for loading, one for
+ # traversing. Create them all here so that we can error out quickly
+ # if memory is a problem.
+
+ graph = khmer.Nodegraph(args.ksize, args.tablesize, 2)
+ stop_bf = khmer.Nodegraph(args.ksize, args.tablesize, 2)
+ stop_bf2 = khmer.Nodegraph(args.ksize, args.tablesize, 2)
+ n = 0
+
+ # load in all of the input sequences, one file at a time.
+ for seqfile in args.seqfiles:
+ for record in screed.open(seqfile):
+ n += 1
+ if n % 10000 == 0:
+ print('...', seqfile, n)
+ graph.consume(record.sequence)
+
+ # complain if too small set of graphs was used.
+ fp_rate = khmer.calc_expected_collisions(graph,
+ args.force, max_false_pos=.05)
+
+ # initialize the object that will track information for us.
+ pathy = Pathfinder(args.ksize)
+
+ print('finding high degree nodes')
+ degree_nodes = khmer.HashSet(args.ksize)
+ n = 0
+ for seqfile in args.seqfiles:
+ for record in screed.open(seqfile):
+ n += 1
+ if n % 10000 == 0:
+ print('...2', seqfile, n)
+ # walk across sequences, find all high degree nodes,
+ # name them and cherish them. Don't do this on identical sequences.
+ if min(stop_bf2.get_kmer_counts(record.sequence)) == 0:
+ stop_bf2.consume(record.sequence)
+ degree_nodes += graph.find_high_degree_nodes(record.sequence)
+ del stop_bf2
+
+ if not len(degree_nodes):
+ print('no high degree nodes; exiting.')
+ sys.exit(0)
+
+ ####
+
+ lh = khmer._GraphLabels(graph)
+ n = 0
+ for seqfile in args.seqfiles:
+ for record in screed.open(seqfile):
+ n += 1
+ if n % 10000 == 0:
+ print('...2', seqfile, n)
+ lh.label_across_high_degree_nodes(record.sequence, degree_nodes, n)
+
+ print('num labels:', lh.n_labels())
+
+ # get all of the degree > 2 nodes and give them IDs.
+ for node in degree_nodes:
+ pathy.new_segment(node)
+
+ print('traversing linear segments from', len(degree_nodes), 'nodes')
+
+ # now traverse from each high degree nodes into all neighboring nodes,
+ # seeking adjacencies. if neighbor is high degree node, add it to
+ # adjacencies; if neighbor is not, then traverse the linear path. also
+ # track minhashes while we're at it.
+ for n, k in enumerate(degree_nodes):
+ if n % 10000 == 0:
+ print('...', n, 'of', len(degree_nodes))
+
+ # retrieve the segment ID of the primary node.
+ k_id = pathy.segments_r[k]
+
+ # find all the neighbors of this high-degree node.
+ nbh = graph.neighbors(k)
+ for nk in nbh:
+ # neighbor is high degree? fine, mark its adjacencies.
+ if nk in degree_nodes:
+ nk_id = pathy.segments_r[nk]
+ pathy.add_adjacency(k_id, nk_id)
+ else:
+ # linear! walk it.
+ traverse_and_mark_linear_paths(graph, nk, stop_bf, pathy,
+ degree_nodes, lh)
+
+ print(len(pathy.segments), 'segments, containing',
+ sum(pathy.segments.values()), 'nodes')
+
+ # save to GML
+ if args.output:
+ import graph_writer
+
+ print('saving to', args.output)
+ fp = open(args.output, 'w')
+ w = graph_writer.GmlWriter(fp, [], [])
+
+ for k, v in pathy.segments.items():
+ w.add_vertex(k, v, [])
+
+ for k, v in pathy.adjacencies.items():
+ for edge in v:
+ w.add_edge(k, edge, [])
+
+
+if __name__ == '__main__':
+ main()
diff --git a/sandbox/memusg b/sandbox/memusg
new file mode 100755
index 0000000..9044a99
--- /dev/null
+++ b/sandbox/memusg
@@ -0,0 +1,46 @@
+#!/usr/bin/env bash
+# memusg -- Measure memory usage of processes
+# Usage: memusg COMMAND [ARGS]...
+#
+# Author: Jaeho Shin <netj at sparcs.org>
+# Created: 2010-08-16
+set -um
+
+# check input
+[ $# -gt 0 ] || { sed -n '2,/^#$/ s/^# //p' <"$0"; exit 1; }
+
+# TODO support more options: peak, footprint, sampling rate, etc.
+
+pgid=`ps -o pgid= $$`
+# make sure we're in a separate process group
+if [ $pgid = $(ps -o pgid= $(ps -o ppid= $$)) ]; then
+ cmd=
+ set -- "$0" "$@"
+ for a; do cmd+="'${a//"'"/"'\\''"}' "; done
+ exec bash -i -c "$cmd"
+fi
+
+# detect operating system and prepare measurement
+case `uname` in
+ Darwin|*BSD) sizes() { /bin/ps -o rss= -g $1; } ;;
+ Linux) sizes() { /bin/ps -o rss= -$1; } ;;
+ *) echo "`uname`: unsupported operating system" >&2; exit 2 ;;
+esac
+
+# monitor the memory usage in the background.
+(
+peak=0
+while sizes=`sizes $pgid`
+do
+ set -- $sizes
+ sample=$((${@/#/+}))
+ let peak="sample > peak ? sample : peak"
+ sleep 0.1
+done
+echo "memusg: peak=$peak" >&2
+) &
+monpid=$!
+
+
+# run the given command
+exec "$@"
diff --git a/sandbox/optimal_args_hashbits.py b/sandbox/optimal_args_hashbits.py
old mode 100644
new mode 100755
index 4aae527..794ad26
--- a/sandbox/optimal_args_hashbits.py
+++ b/sandbox/optimal_args_hashbits.py
@@ -81,7 +81,7 @@ def main():
file=sys.stderr)
htable = khmer.new_nodegraph(args.ksize, args.max_tablesize, args.n_tables)
- target_method = htable.consume_fasta_with_reads_parser
+ target_method = htable.consume_seqfile_with_reads_parser
for _, filename in enumerate(filenames):
rparser = khmer.ReadParser(filename)
@@ -122,4 +122,5 @@ def main():
if __name__ == '__main__':
main()
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
+# vim: set filetype=python tabstop=4 softtabstop=4 shiftwidth=4 expandtab:
+# vim: set textwidth=79:
diff --git a/sandbox/readaligner_pairhmm_train.py b/sandbox/readaligner_pairhmm_train.py
old mode 100644
new mode 100755
index 45658f7..e761c40
--- a/sandbox/readaligner_pairhmm_train.py
+++ b/sandbox/readaligner_pairhmm_train.py
@@ -1,7 +1,7 @@
#!/usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -41,18 +41,18 @@ import collections
from math import log
import json
try:
- import pysam
+ from simplesam import Reader
except:
pass
-cigar_to_state = {0: 'M', 1: 'Ir', 2: 'Ig'}
+CIGAR_TO_STATE = {'M': 'M', 'I': 'Ir', 'D': 'Ig'}
def extract_cigar(cigar):
ret = []
- for t, length in cigar:
+ for length, cig in cigar:
for i in range(length):
- ret.append(cigar_to_state[t])
+ ret.append(CIGAR_TO_STATE[cig])
return ret
@@ -75,7 +75,7 @@ def main():
args = parser.parse_args()
ht = khmer.load_countgraph(args.ht)
- samfile = pysam.Samfile(args.bam_file)
+ samfile = Reader(open(args.bam_file, 'r'))
k = ht.ksize()
seq_cnt = 0
@@ -95,7 +95,7 @@ def main():
dropped_seqs += 1
continue
- states = extract_cigar(cigar)
+ states = extract_cigar(rec.cigars)
kmer = seq[:k]
state = states[k] + trusted_str(ht.count(kmer), args.trusted_cutoff)
diff --git a/sandbox/reassemble-contigs.py b/sandbox/reassemble-contigs.py
new file mode 100755
index 0000000..d968b25
--- /dev/null
+++ b/sandbox/reassemble-contigs.py
@@ -0,0 +1,51 @@
+#! /usr/bin/env python
+from __future__ import print_function
+import argparse
+import screed
+import khmer
+
+K = 31
+
+
+def main():
+ p = argparse.ArgumentParser()
+ p.add_argument('contig_files', nargs='+')
+ args = p.parse_args()
+
+ ng = khmer.Nodegraph(K, 1e8, 4)
+ starts = []
+
+ for filename in args.contig_files:
+ for n, record in enumerate(screed.open(filename)):
+ if n and n % 10000 == 0:
+ print('...', n)
+ ng.consume(record.sequence)
+ starts.append(record.sequence[:K])
+
+ hdn = khmer.HashSet(K)
+ for filename in args.contig_files:
+ for n, record in enumerate(screed.open(filename)):
+ if n and n % 10000 == 0:
+ print('...', n)
+ hdn += ng.find_high_degree_nodes(record.sequence)
+
+ lh = khmer._GraphLabels(ng)
+ for filename in args.contig_files:
+ for n, record in enumerate(screed.open(filename)):
+ if n and n % 10000 == 0:
+ print('...', n)
+ lh.label_across_high_degree_nodes(record.sequence, hdn, n)
+
+
+ counter = 0
+ for k in starts:
+ contigs = lh.assemble_labeled_path(k)
+ if not contigs:
+ print('nada...')
+ for c in contigs:
+ print('>%d\n%s' % (counter, c))
+ counter += 1
+
+
+if __name__ == '__main__':
+ main()
diff --git a/sandbox/saturate-by-median.py b/sandbox/saturate-by-median.py
index 9c04719..64c1375 100755
--- a/sandbox/saturate-by-median.py
+++ b/sandbox/saturate-by-median.py
@@ -283,4 +283,5 @@ def main(): # pylint: disable=too-many-branches,too-many-statements
if __name__ == '__main__':
main()
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
+# vim: set filetype=python tabstop=4 softtabstop=4 shiftwidth=4 expandtab:
+# vim: set textwidth=79:
diff --git a/sandbox/stoptag-abundance-hist.py b/sandbox/stoptag-abundance-hist.py
index a43a484..61ee329 100755
--- a/sandbox/stoptag-abundance-hist.py
+++ b/sandbox/stoptag-abundance-hist.py
@@ -38,6 +38,8 @@ import sys
import khmer
import os
try:
+ import matplotlib
+ matplotlib.use('Agg')
from pylab import *
except ImportError:
pass
diff --git a/sandbox/streaming-assembly-simple.py b/sandbox/streaming-assembly-simple.py
new file mode 100755
index 0000000..ea68f71
--- /dev/null
+++ b/sandbox/streaming-assembly-simple.py
@@ -0,0 +1,145 @@
+#! /usr/bin/env python
+from __future__ import print_function
+import csv
+import screed
+import khmer
+from khmer.khmer_args import build_counting_args, create_countgraph
+import argparse
+import sys
+
+
+DEFAULT_COV = 20
+THRESH2 = 30
+
+
+dna_to_aa={'TTT':'F','TTC':'F', 'TTA':'L','TTG':'L',
+ 'TCT':'S','TCC':'S','TCA':'S','TCG':'S',
+ 'TAT':'Y','TAC':'Y', 'TAA':'*','TAG':'*','TGA':'*',
+ 'TGT':'C','TGC':'C', 'TGG':'W',
+ 'CTT':'L','CTC':'L','CTA':'L','CTG':'L',
+ 'CCT':'P','CCC':'P','CCA':'P','CCG':'P',
+ 'CAT':'H','CAC':'H', 'CAA':'Q','CAG':'Q',
+ 'CGT':'R','CGC':'R','CGA':'R','CGG':'R',
+ 'ATT':'I','ATC':'I','ATA':'I', 'ATG':'M',
+ 'ACT':'T','ACC':'T','ACA':'T','ACG':'T',
+ 'AAT':'N','AAC':'N', 'AAA':'K','AAG':'K',
+ 'AGT':'S','AGC':'S', 'AGA':'R','AGG':'R',
+ 'GTT':'V','GTC':'V','GTA':'V','GTG':'V',
+ 'GCT':'A','GCC':'A','GCA':'A','GCG':'A',
+ 'GAT':'D','GAC':'D', 'GAA':'E','GAG':'E',
+ 'GGT':'G','GGC':'G','GGA':'G','GGG':'G'}
+
+
+__complementTranslation = { "A": "T", "C": "G", "G": "C", "T": "A", "N": "N" }
+def complement(s):
+ """
+ Return complement of 's'.
+ """
+ c = "".join(__complementTranslation[n] for n in s)
+ return c
+
+
+def reverse(s):
+ """
+ Return reverse of 's'.
+ """
+ r = "".join(reversed(s))
+ return r
+
+
+def peptides(seq, start):
+ for i in range(start, len(seq), 3):
+ yield dna_to_aa.get(seq[i:i+3], "X")
+
+
+def translate(seq):
+ for i in range(3):
+ pep = peptides(seq, i)
+ yield "".join(pep)
+
+ revcomp = reverse(complement((seq)))
+ for i in range(3):
+ pep = peptides(revcomp, i)
+ yield "".join(pep)
+
+
+def extract_orfs(pepseq, min_length=99):
+ peplist = [ x for x in pepseq.split('*') if len(x) >= min_length ]
+ for x in peplist:
+ yield x
+
+
+def main():
+ p = build_counting_args(descr='Streaming assembly with tracking info')
+ p.add_argument('fastq_files', nargs='+')
+ p.add_argument('--prefix', default='transcriptome')
+ args = p.parse_args()
+
+ cg = create_countgraph(args)
+ asm = khmer.JunctionCountAssembler(cg)
+
+ tr_fn = '{0}.transcripts.fa'.format(args.prefix)
+ orf_fn = '{0}.orfs.fa'.format(args.prefix)
+ stats_fn = '{0}.stats.fa'.format(args.prefix)
+
+ with open(tr_fn, 'w') as tr_fp,\
+ open(orf_fn, 'w') as orf_fp,\
+ open(stats_fn, 'w') as stats_fp:
+
+ kept = 0
+ next_contig = 1
+ next_orf = 1
+ output = set()
+ statswriter = csv.DictWriter(stats_fp, delimiter=',',
+ fieldnames=['read_n', 'action', 'cov',
+ 'n_junctions', 'contig_n'])
+
+ for filename in args.fastq_files:
+ for n, record in enumerate(screed.open(filename)):
+ if n and n % 10000 == 0:
+ print('...', n, file=sys.stderr)
+
+ if len(record.sequence) < args.ksize:
+ continue
+
+ cov, _, _ = cg.get_median_count(record.sequence)
+ if cov < 20:
+ kept += 1
+ cg.consume(record.sequence)
+ statswriter.writerow({'read_n': n, 'action': 'c', 'cov': cov,
+ 'n_junctions': None,
+ 'contig_n': None})
+ elif cov < 30:
+ seq, pos = cg.trim_on_abundance(record.sequence, 3)
+ if len(seq) < args.ksize:
+ continue
+
+ n_junctions = asm.consume(seq)
+ statswriter.writerow({'read_n': n, 'action': 't', 'cov': cov,
+ 'n_junctions': n_junctions,
+ 'contig_n': None})
+ elif cov == 30:
+ contigs = asm.assemble(record.sequence[:args.ksize])
+ for contig_n, contig in enumerate(contigs):
+ statswriter.writerow({'read_n': n, 'action': 'a', 'cov': cov,
+ 'n_junctions': None,
+ 'contig_n': (next_contig, contig_n)})
+ tr_fp.write('>contig%d\n%s\n' % (next_contig, contig))
+ next_contig += 1
+
+ for t in translate(contig):
+ for orf_n, o in enumerate(extract_orfs(t)):
+ if hash(o) not in output:
+ new = True
+ output.add(hash(o))
+ orf_fp.write('>orf%d\n%s\n' % (next_orf, o))
+ next_orf += 1
+ else:
+ new = False
+ else:
+ statswriter.writerow({'read_n': n, 'action': 's', 'cov': cov,
+ 'n_junctions': None,
+ 'contig_n': None})
+
+if __name__ == '__main__':
+ main()
diff --git a/sandbox/sweep-out-reads-with-contigs.py b/sandbox/sweep-out-reads-with-contigs.py
index 4f74758..0673ddc 100755
--- a/sandbox/sweep-out-reads-with-contigs.py
+++ b/sandbox/sweep-out-reads-with-contigs.py
@@ -58,7 +58,7 @@ def main():
# load contigs, connect into N partitions
print('loading contigs from', contigfile)
- ht.consume_fasta_and_tag(contigfile)
+ ht.consume_seqfile_and_tag(contigfile)
subset = ht.do_subset_partition(0, 0)
ht.merge_subset(subset)
diff --git a/sandbox/sweep-reads2.py b/sandbox/sweep-reads2.py
index 943b735..f1a2d8e 100755
--- a/sandbox/sweep-reads2.py
+++ b/sandbox/sweep-reads2.py
@@ -1,4 +1,4 @@
-#! /usr/bin/env python
+#!/usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2012-2015, Michigan State University.
# Copyright (C) 2015, The Regents of the University of California.
@@ -48,68 +48,59 @@ import sys
import khmer
import os.path
import screed
+from khmer import khmer_args
from khmer.khmer_args import (build_nodegraph_args, DEFAULT_MAX_TABLESIZE)
+from khmer.utils import broken_paired_reader, write_record
def main():
- parser = build_construct_args()
+ parser = build_nodegraph_args()
+ parser.add_argument('-o', '--outfile',
+ help='output file; default is "infile".sweep2')
+ parser.add_argument('-q', '--quiet')
parser.add_argument('input_filename')
parser.add_argument('read_filename')
args = parser.parse_args()
- if not args.quiet:
- if args.min_hashsize == DEFAULT_MAX_TABLESIZE:
- print("** WARNING: hashsize is default! " \
- "You absodefly want to increase this!\n** " \
- "Please read the docs!", file=sys.stderr)
-
- print('\nPARAMETERS:', file=sys.stderr)
- print(' - kmer size = %d \t\t(-k)' % args.ksize, file=sys.stderr)
- print(' - n hashes = %d \t\t(-N)' % args.n_hashes, file=sys.stderr)
- print(' - min hashsize = %-5.2g \t(-x)' % \
- args.min_hashsize, file=sys.stderr)
- print('', file=sys.stderr)
- print('Estimated memory usage is %.2g bytes ' \
- '(n_hashes x min_hashsize / 8)' % (
- args.n_hashes * args.min_hashsize / 8.), file=sys.stderr)
- print('-' * 8, file=sys.stderr)
-
- K = args.ksize
- HT_SIZE = args.min_hashsize
- N_HT = args.n_hashes
-
inp = args.input_filename
readsfile = args.read_filename
outfile = os.path.basename(readsfile) + '.sweep2'
+ if args.outfile:
+ outfile = args.outfile
outfp = open(outfile, 'w')
# create a nodegraph data structure
- ht = khmer.Nodegraph(K, HT_SIZE, N_HT)
+ ht = khmer_args.create_countgraph(args)
# load contigs, connect into N partitions
print('loading input reads from', inp)
- ht.consume_fasta(inp)
+ ht.consume_seqfile(inp)
print('starting sweep.')
- n = 0
m = 0
- for record in screed.open(readsfile):
- if len(record.sequence) < K:
- continue
-
+ K = ht.ksize()
+ instream = screed.open(readsfile)
+ for n, is_pair, read1, read2 in broken_paired_reader(instream):
if n % 10000 == 0:
print('...', n, m)
- count = ht.get_median_count(record.sequence)[0]
- if count:
- m += 1
- outfp.write('>%s\n%s\n' % (record.name, record.sequence))
- n += 1
+ if is_pair:
+ count1 = ht.get_median_count(read1.sequence)[0]
+ count2 = ht.get_median_count(read2.sequence)[0]
+ if count1 or count2:
+ m += 1
+ write_record_pair(read1, read2, outfp)
+ else:
+ count = ht.get_median_count(read1.sequence)[0]
+ if count:
+ m += 1
+ write_record(read1, outfp)
if __name__ == '__main__':
main()
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
+# vim: set filetype=python tabstop=4 softtabstop=4 shiftwidth=4 expandtab:
+# vim: set textwidth=79:
diff --git a/sandbox/sweep-reads3.py b/sandbox/sweep-reads3.py
index 0fa7571..942c207 100755
--- a/sandbox/sweep-reads3.py
+++ b/sandbox/sweep-reads3.py
@@ -103,7 +103,7 @@ def main():
# load contigs, connect into N partitions
print('loading input reads from', inp_name)
- ht.consume_fasta(inp_name)
+ ht.consume_seqfile(inp_name)
print('starting sweep.')
@@ -124,4 +124,5 @@ def main():
if __name__ == '__main__':
main()
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
+# vim: set filetype=python tabstop=4 softtabstop=4 shiftwidth=4 expandtab:
+# vim: set textwidth=79:
diff --git a/scripts/abundance-dist-single.py b/scripts/abundance-dist-single.py
index 4bbf991..cb10e82 100755
--- a/scripts/abundance-dist-single.py
+++ b/scripts/abundance-dist-single.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2010-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -52,9 +52,11 @@ import threading
import textwrap
from khmer import khmer_args
from khmer.khmer_args import (build_counting_args, add_threading_args,
- report_on_config, info, calculate_graphsize,
+ report_on_config, calculate_graphsize,
sanitize_help)
from khmer.kfile import (check_input_files, check_space_for_graph)
+from khmer.khmer_logger import (configure_logging, log_info, log_error,
+ log_warn)
def get_parser():
@@ -74,7 +76,8 @@ def get_parser():
'''
parser = build_counting_args(
descr="Calculate the abundance distribution of k-mers from a "
- "single sequence file.", epilog=textwrap.dedent(epilog))
+ "single sequence file.", epilog=textwrap.dedent(epilog),
+ citations=['counting', 'SeqAn'])
add_threading_args(parser)
parser.add_argument('input_sequence_filename', help='The name of the input'
@@ -97,22 +100,26 @@ def get_parser():
"filename.")
parser.add_argument('-f', '--force', default=False, action='store_true',
help='Overwrite output file if it exists')
+ parser.add_argument('-q', '--quiet', dest='quiet', default=False,
+ action='store_true')
return parser
def main(): # pylint: disable=too-many-locals,too-many-branches
- info('abundance-dist-single.py', ['counting', 'SeqAn'])
args = sanitize_help(get_parser()).parse_args()
- report_on_config(args)
+ graph_type = 'smallcountgraph' if args.small_count else 'countgraph'
+
+ configure_logging(args.quiet)
+ report_on_config(args, graph_type)
check_input_files(args.input_sequence_filename, args.force)
if args.savegraph:
- graphsize = calculate_graphsize(args, 'countgraph')
+ graphsize = calculate_graphsize(args, graph_type)
check_space_for_graph(args.savegraph, graphsize, args.force)
if (not args.squash_output and
os.path.exists(args.output_histogram_filename)):
- print('ERROR: %s exists; not squashing.' %
- args.output_histogram_filename, file=sys.stderr)
+ log_error('ERROR: {output} exists; not squashing.',
+ output=args.output_histogram_filename)
sys.exit(1)
else:
hist_fp = open(args.output_histogram_filename, 'w')
@@ -121,27 +128,26 @@ def main(): # pylint: disable=too-many-locals,too-many-branches
hist_fp_csv.writerow(['abundance', 'count', 'cumulative',
'cumulative_fraction'])
- print('making countgraph', file=sys.stderr)
+ log_info('making countgraph')
countgraph = khmer_args.create_countgraph(args, multiplier=1.1)
countgraph.set_use_bigcount(args.bigcount)
- print('building k-mer tracking graph', file=sys.stderr)
+ log_info('building k-mer tracking graph')
tracking = khmer_args.create_nodegraph(args, multiplier=1.1)
- print('kmer_size:', countgraph.ksize(), file=sys.stderr)
- print('k-mer countgraph sizes:',
- countgraph.hashsizes(), file=sys.stderr)
- print('outputting to', args.output_histogram_filename, file=sys.stderr)
+ log_info('kmer_size: {ksize}', ksize=countgraph.ksize())
+ log_info('k-mer countgraph sizes: {sizes}', sizes=countgraph.hashsizes())
+ log_info('outputting to {output}', output=args.output_histogram_filename)
# start loading
rparser = khmer.ReadParser(args.input_sequence_filename)
threads = []
- print('consuming input, round 1 --',
- args.input_sequence_filename, file=sys.stderr)
+ log_info('consuming input, round 1 -- {input}',
+ input=args.input_sequence_filename)
for _ in range(args.threads):
thread = \
threading.Thread(
- target=countgraph.consume_fasta_with_reads_parser,
+ target=countgraph.consume_seqfile_with_reads_parser,
args=(rparser, )
)
threads.append(thread)
@@ -150,8 +156,8 @@ def main(): # pylint: disable=too-many-locals,too-many-branches
for thread in threads:
thread.join()
- print('Total number of unique k-mers: {0}'.format(
- countgraph.n_unique_kmers()), file=sys.stderr)
+ log_info('Total number of unique k-mers: {nk}',
+ nk=countgraph.n_unique_kmers())
abundance_lists = []
@@ -160,12 +166,12 @@ def main(): # pylint: disable=too-many-locals,too-many-branches
read_parser, tracking)
abundance_lists.append(abundances)
- print('preparing hist from %s...' %
- args.input_sequence_filename, file=sys.stderr)
+ log_info('preparing hist from {seqfile}...',
+ seqfile=args.input_sequence_filename)
rparser = khmer.ReadParser(args.input_sequence_filename)
threads = []
- print('consuming input, round 2 --',
- args.input_sequence_filename, file=sys.stderr)
+ log_info('consuming input, round 2 -- {filename}',
+ filename=args.input_sequence_filename)
for _ in range(args.threads):
thread = \
threading.Thread(
@@ -187,10 +193,9 @@ def main(): # pylint: disable=too-many-locals,too-many-branches
total = sum(abundance.values())
if 0 == total:
- print("ERROR: abundance distribution is uniformly zero; "
- "nothing to report.", file=sys.stderr)
- print(
- "\tPlease verify that the input files are valid.", file=sys.stderr)
+ log_error("ERROR: abundance distribution is uniformly zero; "
+ "nothing to report.")
+ log_error("\tPlease verify that the input files are valid.")
sys.exit(1)
sofar = 0
@@ -207,13 +212,15 @@ def main(): # pylint: disable=too-many-locals,too-many-branches
break
if args.savegraph:
- print('Saving k-mer countgraph ', args.savegraph, file=sys.stderr)
- print('...saving to', args.savegraph, file=sys.stderr)
+ log_info('Saving k-mer countgraph to {savegraph}',
+ savegraph=args.savegraph)
countgraph.save(args.savegraph)
- print('wrote to: ' + args.output_histogram_filename, file=sys.stderr)
+ log_info('wrote to: {output}', output=args.output_histogram_filename)
+
if __name__ == '__main__':
main()
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
+# vim: set filetype=python tabstop=4 softtabstop=4 shiftwidth=4 expandtab:
+# vim: set textwidth=79:
diff --git a/scripts/abundance-dist.py b/scripts/abundance-dist.py
index 001d54d..c482948 100755
--- a/scripts/abundance-dist.py
+++ b/scripts/abundance-dist.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2010-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -37,7 +37,7 @@
"""
Produce the k-mer abundance distribution for the given file.
-% python scripts/abundance-dist.py [ -z -s ] <htname> <data> <histout>
+% python scripts/abundance-dist.py [ -z -s ] <countgraph> <data> <histout>
Use '-h' for parameter help.
"""
@@ -46,27 +46,26 @@ from __future__ import print_function
import sys
import csv
import khmer
-import argparse
import textwrap
import os
-from khmer import __version__
from khmer.kfile import check_input_files
-from khmer.khmer_args import (info, sanitize_help, ComboFormatter,
- _VersionStdErrAction)
+from khmer.khmer_args import (sanitize_help, KhmerArgumentParser)
+from khmer.khmer_logger import (configure_logging, log_info, log_error,
+ log_warn)
def get_parser():
epilog = """\
Example::
- load-into-countgraph.py -x 1e7 -N 2 -k 17 counts \\
+ load-into-counting.py -x 1e7 -N 2 -k 17 counts \\
tests/test-data/test-abund-read-2.fa
abundance-dist.py counts tests/test-data/test-abund-read-2.fa test-dist
"""
- parser = argparse.ArgumentParser(
+ parser = KhmerArgumentParser(
description="Calculate abundance distribution of the k-mers in "
"the sequence file using a pre-made k-mer countgraph.",
- formatter_class=ComboFormatter, epilog=textwrap.dedent(epilog))
+ epilog=textwrap.dedent(epilog), citations=['counting'])
parser.add_argument('input_count_graph_filename', help='The name of the'
' input k-mer countgraph file.')
@@ -84,33 +83,33 @@ def get_parser():
parser.add_argument('-b', '--no-bigcount', dest='bigcount', default=True,
action='store_false',
help='Do not count k-mers past 255')
- parser.add_argument('--version', action=_VersionStdErrAction,
- version='khmer {v}'.format(v=__version__))
parser.add_argument('-f', '--force', default=False, action='store_true',
help='Continue even if specified input files '
'do not exist or are empty.')
+ parser.add_argument('-q', '--quiet', dest='quiet', default=False,
+ action='store_true')
return parser
def main():
- info('abundance-dist.py', ['counting'])
args = sanitize_help(get_parser()).parse_args()
+ configure_logging(args.quiet)
+
infiles = [args.input_count_graph_filename,
args.input_sequence_filename]
for infile in infiles:
check_input_files(infile, False)
- print('Counting graph from', args.input_count_graph_filename,
- file=sys.stderr)
+ log_info('Loading counting graph from {graph}',
+ graph=args.input_count_graph_filename)
countgraph = khmer.load_countgraph(
args.input_count_graph_filename)
if not countgraph.get_use_bigcount() and args.bigcount:
- print("WARNING: The loaded graph has bigcount DISABLED while bigcount"
- " reporting is ENABLED--counts higher than 255 will not be "
- "reported.",
- file=sys.stderr)
+ log_warn("WARNING: The loaded graph has bigcount DISABLED while "
+ "bigcount reporting is ENABLED--counts higher than 255 will "
+ "not be reported.")
countgraph.set_use_bigcount(args.bigcount)
@@ -119,31 +118,29 @@ def main():
tracking = khmer._Nodegraph( # pylint: disable=protected-access
kmer_size, hashsizes)
- print('K:', kmer_size, file=sys.stderr)
- print('outputting to', args.output_histogram_filename, file=sys.stderr)
+ log_info('K: {ksize}', ksize=kmer_size)
+ log_info('outputting to {output}', output=args.output_histogram_filename)
if args.output_histogram_filename in ('-', '/dev/stdout'):
pass
elif os.path.exists(args.output_histogram_filename):
if not args.squash_output:
- print('ERROR: %s exists; not squashing.' %
- args.output_histogram_filename,
- file=sys.stderr)
+ log_error('ERROR: {output} exists; not squashing.',
+ output=args.output_histogram_filename)
sys.exit(1)
- print('** squashing existing file %s' %
- args.output_histogram_filename, file=sys.stderr)
+ log_info('** squashing existing file {output}',
+ output=args.output_histogram_filename)
- print('preparing hist...', file=sys.stderr)
+ log_info('preparing hist...')
abundances = countgraph.abundance_distribution(
args.input_sequence_filename, tracking)
total = sum(abundances)
if 0 == total:
- print("ERROR: abundance distribution is uniformly zero; "
- "nothing to report.", file=sys.stderr)
- print("\tPlease verify that the input files are valid.",
- file=sys.stderr)
+ log_error("ERROR: abundance distribution is uniformly zero; "
+ "nothing to report.")
+ log_error("\tPlease verify that the input files are valid.")
sys.exit(1)
if args.output_histogram_filename in ('-', '/dev/stdout'):
@@ -172,4 +169,5 @@ def main():
if __name__ == '__main__':
main()
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
+# vim: set filetype=python tabstop=4 softtabstop=4 shiftwidth=4 expandtab:
+# vim: set textwidth=79:
diff --git a/scripts/annotate-partitions.py b/scripts/annotate-partitions.py
index 88cd669..cb20ab9 100755
--- a/scripts/annotate-partitions.py
+++ b/scripts/annotate-partitions.py
@@ -46,13 +46,11 @@ Use '-h' for parameter help.
from __future__ import print_function
import os
-import argparse
import textwrap
import sys
from khmer import __version__, Nodegraph
from khmer.kfile import check_input_files, check_space
-from khmer.khmer_args import (info, sanitize_help, ComboFormatter,
- _VersionStdErrAction)
+from khmer.khmer_args import (sanitize_help, KhmerArgumentParser)
DEFAULT_K = 32
@@ -71,9 +69,9 @@ def get_parser():
merge-partitions.py -k 20 example
annotate-partitions.py -k 20 example tests/test-data/random-20-a.fa
"""
- parser = argparse.ArgumentParser(
+ parser = KhmerArgumentParser(
description="Annotate sequences with partition IDs.",
- epilog=textwrap.dedent(epilog), formatter_class=ComboFormatter)
+ epilog=textwrap.dedent(epilog))
parser.add_argument('--ksize', '-k', type=int, default=DEFAULT_K,
help="k-mer size (default: %d)" % DEFAULT_K)
@@ -82,15 +80,12 @@ def get_parser():
parser.add_argument('input_filenames', metavar='input_sequence_filename',
nargs='+', help='input FAST[AQ] sequences to '
'annotate.')
- parser.add_argument('--version', action=_VersionStdErrAction,
- version='khmer {v}'.format(v=__version__))
parser.add_argument('-f', '--force', default=False, action='store_true',
help='Overwrite output file if it exists')
return parser
def main():
- info('annotate-partitions.py', ['graph'])
args = sanitize_help(get_parser()).parse_args()
ksize = args.ksize
diff --git a/scripts/count-median.py b/scripts/count-median.py
index 8f41ae1..ab3a4cc 100755
--- a/scripts/count-median.py
+++ b/scripts/count-median.py
@@ -41,7 +41,7 @@ The abundance is based on the k-mer counts in the given k-mer countgraph.
Can be used to estimate expression levels (mRNAseq) or coverage
(genomic/metagenomic).
-% scripts/count-median.py <htname> <input seqs> <output counts>
+% scripts/count-median.py <countgraph> <input seqs> <output counts>
Use '-h' for parameter help.
@@ -50,16 +50,15 @@ The output file contains sequence id, median, average, stddev, and seq length.
NOTE: All 'N's in the input sequences are converted to 'A's.
"""
from __future__ import print_function
-import screed
import argparse
+import screed
import sys
import csv
import textwrap
from khmer import __version__, load_countgraph
from khmer.kfile import check_input_files, check_space
-from khmer.khmer_args import (info, sanitize_help, ComboFormatter,
- _VersionStdErrAction)
+from khmer.khmer_args import (sanitize_help, KhmerArgumentParser)
def get_parser():
@@ -73,14 +72,14 @@ def get_parser():
Example::
- load-into-countgraph.py counts tests/test-data/test-reads.fq.gz
+ load-into-counting.py counts tests/test-data/test-reads.fq.gz
count-median.py counts tests/test-data/test-reads.fq.gz medians.txt
NOTE: All 'N's in the input sequences are converted to 'A's.
"""
- parser = argparse.ArgumentParser(
+ parser = KhmerArgumentParser(
description='Count k-mers summary stats for sequences',
- epilog=textwrap.dedent(epilog), formatter_class=ComboFormatter)
+ epilog=textwrap.dedent(epilog))
parser.add_argument('countgraph', metavar='input_count_graph_filename',
help='input k-mer countgraph filename')
@@ -89,15 +88,12 @@ def get_parser():
parser.add_argument('output', metavar='output_summary_filename',
help='output summary filename',
type=argparse.FileType('w'))
- parser.add_argument('--version', action=_VersionStdErrAction,
- version='khmer {v}'.format(v=__version__))
parser.add_argument('-f', '--force', default=False, action='store_true',
help='Overwrite output file if it exists')
return parser
def main():
- info('count-median.py', ['diginorm'])
args = sanitize_help(get_parser()).parse_args()
htfile = args.countgraph
diff --git a/scripts/do-partition.py b/scripts/do-partition.py
index e21584b..f3275f6 100755
--- a/scripts/do-partition.py
+++ b/scripts/do-partition.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2011-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -46,17 +46,16 @@ from __future__ import print_function
import khmer
import sys
import threading
-import gc
import os.path
import os
+import gc
import textwrap
from khmer import khmer_args
-from khmer.khmer_args import (build_nodegraph_args, report_on_config, info,
+from khmer.khmer_args import (build_nodegraph_args, report_on_config,
add_threading_args, sanitize_help)
import glob
from khmer.kfile import check_input_files, check_space
-import re
-import platform
+from oxli.partition import worker
# stdlib queue module was renamed on Python 3
try:
@@ -69,32 +68,6 @@ DEFAULT_N_THREADS = 4
DEFAULT_K = 32
-def worker(tasks, basename, stop_big_traversals):
- while True:
- try:
- (nodegraph, index, start, stop) = tasks.get(False)
- except queue.Empty:
- print('exiting', file=sys.stderr)
- return
-
- outfile = basename + '.subset.%d.pmap' % (index,)
- if os.path.exists(outfile):
- print('SKIPPING', outfile, ' -- already exists', file=sys.stderr)
- continue
-
- print('starting:', basename, index, file=sys.stderr)
-
- # pay attention to stoptags when partitioning; take command line
- # direction on whether or not to exhaustively traverse.
- subset = nodegraph.do_subset_partition(start, stop, True,
- stop_big_traversals)
-
- print('saving:', basename, index, file=sys.stderr)
- nodegraph.save_subset_partitionmap(subset, outfile)
- del subset
- gc.collect()
-
-
def get_parser():
epilog = """\
Load in a set of sequences, partition them, merge the partitions, and
@@ -113,7 +86,7 @@ def get_parser():
"""
parser = build_nodegraph_args(
descr='Load, partition, and annotate FAST[AQ] sequences',
- epilog=textwrap.dedent(epilog))
+ epilog=textwrap.dedent(epilog), citations=['graph'])
add_threading_args(parser)
parser.add_argument('--subset-size', '-s', default=DEFAULT_SUBSET_SIZE,
dest='subset_size', type=float,
@@ -134,7 +107,6 @@ def get_parser():
# pylint: disable=too-many-branches
def main(): # pylint: disable=too-many-locals,too-many-statements
- info('do-partition.py', ['graph'])
args = sanitize_help(get_parser()).parse_args()
report_on_config(args, graphtype='nodegraph')
@@ -160,7 +132,7 @@ def main(): # pylint: disable=too-many-locals,too-many-statements
for _, filename in enumerate(args.input_filenames):
print('consuming input', filename, file=sys.stderr)
- nodegraph.consume_fasta_and_tag(filename)
+ nodegraph.consume_seqfile_and_tag(filename)
# 0.18 is ACTUAL MAX. Do not change.
fp_rate = \
@@ -185,6 +157,7 @@ def main(): # pylint: disable=too-many-locals,too-many-statements
# divide the tags up into subsets
divvy = nodegraph.divide_tags_into_subsets(int(args.subset_size))
+ divvy = list(divvy)
n_subsets = len(divvy)
divvy.append(0)
@@ -216,8 +189,6 @@ def main(): # pylint: disable=too-many-locals,too-many-statements
threads.append(cur_thread)
cur_thread.start()
- assert threading.active_count() == args.threads + 1
-
print('done starting threads', file=sys.stderr)
# wait for threads
@@ -259,4 +230,5 @@ def main(): # pylint: disable=too-many-locals,too-many-statements
if __name__ == '__main__':
main()
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
+# vim: set filetype=python tabstop=4 softtabstop=4 shiftwidth=4 expandtab:
+# vim: set textwidth=79:
diff --git a/scripts/extract-long-sequences.py b/scripts/extract-long-sequences.py
index 0656c48..7de3f68 100755
--- a/scripts/extract-long-sequences.py
+++ b/scripts/extract-long-sequences.py
@@ -54,8 +54,7 @@ import sys
from khmer import __version__
from khmer.utils import write_record
from khmer.kfile import add_output_compression_type, get_file_writer
-from khmer.khmer_args import (ComboFormatter, sanitize_help, info,
- _VersionStdErrAction)
+from khmer.khmer_args import sanitize_help, KhmerArgumentParser
def get_parser():
@@ -64,10 +63,10 @@ def get_parser():
extract-long-sequences.py --length 10 tests/test-data/paired-mixed.fa
"""
- parser = argparse.ArgumentParser(
+ parser = KhmerArgumentParser(
description='Extract FASTQ or FASTA sequences longer than'
' specified length (default: 200 bp).',
- formatter_class=ComboFormatter, epilog=textwrap.dedent(epilog))
+ epilog=textwrap.dedent(epilog))
parser.add_argument('input_filenames', help='Input FAST[AQ]'
' sequence filename.', nargs='+')
@@ -77,14 +76,11 @@ def get_parser():
parser.add_argument('-l', '--length', help='The minimum length of'
' the sequence file.',
type=int, default=200)
- parser.add_argument('--version', action=_VersionStdErrAction,
- version='khmer {v}'.format(v=__version__))
add_output_compression_type(parser)
return parser
def main():
- info('extract-long-sequences.py')
args = sanitize_help(get_parser()).parse_args()
outfp = get_file_writer(args.output, args.gzip, args.bzip)
for filename in args.input_filenames:
@@ -93,5 +89,6 @@ def main():
write_record(record, outfp)
print('wrote to: ' + args.output.name, file=sys.stderr)
+
if __name__ == '__main__':
main()
diff --git a/scripts/extract-paired-reads.py b/scripts/extract-paired-reads.py
index 0f3ff9a..1e82441 100755
--- a/scripts/extract-paired-reads.py
+++ b/scripts/extract-paired-reads.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2013-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -45,16 +45,14 @@ extract them into separate files (.pe and .se).
Reads FASTQ and FASTA input, retains format for output.
"""
from __future__ import print_function
-import screed
import sys
import os.path
import textwrap
-import argparse
-from khmer import __version__
+from khmer import ReadParser
from khmer.kfile import check_input_files, check_space
-from khmer.khmer_args import (info, sanitize_help, ComboFormatter,
- _VersionStdErrAction)
+from khmer.khmer_args import sanitize_help, KhmerArgumentParser
+from khmer.khmer_args import FileType as khFileType
from khmer.kfile import add_output_compression_type
from khmer.kfile import get_file_writer
@@ -89,22 +87,19 @@ def get_parser():
extract-paired-reads.py tests/test-data/paired.fq
"""
- parser = argparse.ArgumentParser(
+ parser = KhmerArgumentParser(
description='Take a mixture of reads and split into pairs and '
- 'orphans.', epilog=textwrap.dedent(epilog),
- formatter_class=ComboFormatter)
+ 'orphans.', epilog=textwrap.dedent(epilog))
parser.add_argument('infile', nargs='?', default='/dev/stdin')
- parser.add_argument('--version', action=_VersionStdErrAction,
- version='khmer {v}'.format(v=__version__))
parser.add_argument('-d', '--output-dir', default='', help='Output '
'split reads to specified directory. Creates '
'directory if necessary')
parser.add_argument('--output-paired', '-p', metavar="filename",
- type=argparse.FileType('wb'),
+ type=khFileType('wb'),
default=None, help='Output paired reads to this '
'file')
parser.add_argument('--output-single', '-s', metavar="filename",
- type=argparse.FileType('wb'), default=None,
+ type=khFileType('wb'), default=None,
help='Output orphaned reads to this file')
parser.add_argument('-f', '--force', default=False, action='store_true',
help='Overwrite output file if it exists')
@@ -113,7 +108,6 @@ def get_parser():
def main():
- info('extract-paired-reads.py')
args = sanitize_help(get_parser()).parse_args()
infile = args.infile
@@ -122,6 +116,8 @@ def main():
# decide where to put output files - specific directory? or just default?
if infile in ('/dev/stdin', '-'):
+ # seqan only treats '-' as "read from stdin"
+ infile = '-'
if not (args.output_paired and args.output_single):
print("Accepting input from stdin; output filenames must be "
"provided.", file=sys.stderr)
@@ -156,8 +152,8 @@ def main():
n_pe = 0
n_se = 0
- screed_iter = screed.open(infile)
- for index, is_pair, read1, read2 in broken_paired_reader(screed_iter):
+ reads = ReadParser(infile)
+ for index, is_pair, read1, read2 in broken_paired_reader(reads):
if index % 100000 == 0 and index > 0:
print('...', index, file=sys.stderr)
diff --git a/scripts/extract-partitions.py b/scripts/extract-partitions.py
index 000cb3a..a404b41 100755
--- a/scripts/extract-partitions.py
+++ b/scripts/extract-partitions.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2010-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -50,14 +50,14 @@ from __future__ import print_function
import sys
import screed
-import argparse
import textwrap
-from khmer import __version__
+from contextlib import contextmanager
+import khmer
+
from khmer.kfile import (check_input_files, check_space,
add_output_compression_type,
get_file_writer)
-from khmer.khmer_args import (info, sanitize_help, ComboFormatter,
- _VersionStdErrAction)
+from khmer.khmer_args import sanitize_help, KhmerArgumentParser
from khmer.utils import write_record
DEFAULT_MAX_SIZE = int(1e6)
@@ -65,13 +65,15 @@ DEFAULT_THRESHOLD = 5
def read_partition_file(filename):
+ """Utility function to get partitioned reads from file."""
for record_index, record in enumerate(screed.open(filename)):
_, partition_id = record.name.rsplit('\t', 1)
yield record_index, record, int(partition_id)
def get_parser():
- epilog = """\
+ """Create parser for extract-partitions.py."""
+ epilog = """
Example (results will be in ``example.group0000.fa``)::
load-graph.py -k 20 example tests/test-data/random-20-a.fa
@@ -85,10 +87,10 @@ def get_parser():
(2) count of partitions with n reads, (3) cumulative sum of partitions,
(4) cumulative sum of reads.)
"""
- parser = argparse.ArgumentParser(
+ parser = KhmerArgumentParser(
description="Separate sequences that are annotated with partitions "
"into grouped files.", epilog=textwrap.dedent(epilog),
- formatter_class=ComboFormatter)
+ citations=['graph'])
parser.add_argument('prefix', metavar='output_filename_prefix')
parser.add_argument('part_filenames', metavar='input_partition_filename',
nargs='+')
@@ -104,23 +106,154 @@ def get_parser():
parser.add_argument('--output-unassigned', '-U', default=False,
action='store_true',
help='Output unassigned sequences, too')
- parser.add_argument('--version', action=_VersionStdErrAction,
- version='khmer {v}'.format(v=__version__))
parser.add_argument('-f', '--force', default=False, action='store_true',
help='Overwrite output file if it exists')
add_output_compression_type(parser)
return parser
-# pylint: disable=too-many-statements
-def main(): # pylint: disable=too-many-locals,too-many-branches
- info('extract-partitions.py', ['graph'])
+ at contextmanager
+def PartitionedReader(filename_list, quiet=False, single=False):
+ yield PartitionedReadIterator(filename_list, quiet, single)
+
+
+def PartitionedReadIterator(filename_list, quiet=False, single=False):
+ """
+ Generator to do boilerplate output of statistics.
+
+ Uses a list of input files and verbosity
+ Returns reads and partition IDs
+ """
+ for filename in filename_list:
+ for index, read, pid in read_partition_file(filename):
+ if not quiet:
+ if index % 100000 == 0:
+ print('...x2', index, file=sys.stderr)
+ yield read, pid
+ if single:
+ break # only yield a single read from each file
+
+
+class PartitionExtractor(object):
+ """
+ Does extraction, processing and accounting of partitioned reads.
+
+ Contains methods for self_maintenance and output production
+ """
+
+ def __init__(self, file_list, min_size, max_size):
+ # We'll make our own generator! With files! And...
+ self.file_list = file_list
+ self.n_unassigned = 0
+ self.count = {}
+
+ self.divvy = None
+ self.group_n = 0
+ self.group_d = {}
+ self.min_size = min_size
+ self.max_size = max_size
+
+ def process_unassigned(self, outfp=None):
+ """
+ Process unassigned reads.
+
+ Can optionally output said reads if outfp is given
+ Also develops counts of partition IDs--necessary for further processing
+ """
+ with PartitionedReader(self.file_list) as reader:
+ for read, pid in reader:
+ self.count[pid] = self.count.get(pid, 0) + 1
+
+ if pid == 0:
+ self.n_unassigned += 1
+ if outfp:
+ write_record(read, outfp)
+
+ def output_histogram(self, dist_filename):
+ """Output histogram of partition counts to the given filename."""
+ # develop histogram of partition sizes
+ dist = {}
+ for _, size in list(self.count.items()):
+ dist[size] = dist.get(size, 0) + 1
+
+ # output histogram
+ distfp = open(dist_filename, 'w')
+
+ total = 0
+ wtotal = 0
+ for counter, index in sorted(dist.items()):
+ total += index
+ wtotal += counter * index
+ distfp.write('%d %d %d %d\n' % (counter, index, total, wtotal))
+ distfp.close()
+
+ def develop_groups(self):
+ """Processing method that divides up the partitions into groups."""
+ if 0 in self.count: # eliminate unpartitioned sequences
+ del self.count[0]
+
+ # sort groups by size
+ self.divvy = sorted(list(self.count.items()), key=lambda y: y[1])
+ self.divvy = [y for y in self.divvy if y[1] > self.min_size]
+
+ # divvy up into different groups, based on having max_size sequences
+ # in each group.
+ total = 0
+ group = set()
+ for partition_id, n_reads in self.divvy:
+ group.add(partition_id)
+ total += n_reads
+
+ if total > self.max_size:
+ for partition_id in group:
+ self.group_d[partition_id] = self.group_n
+
+ self.group_n += 1
+ group = set()
+ total = 0
+
+ if group:
+ for partition_id in group:
+ self.group_d[partition_id] = self.group_n
+ self.group_n += 1
+
+ class ReadGroupGenerator(object):
+ """
+ Generator that yields partitioned reads and their group.
+
+ Takes PartitionExtractor and PartitionedReadIterator objects
+ """
+
+ def __init__(self, extractor):
+ self.extractor = extractor
+
+ self.total_seqs = 0
+ self.part_seqs = 0
+ self.toosmall_parts = 0
+
+ def __call__(self, reader):
+ for read, partition_id in reader:
+ self.total_seqs += 1
+ if partition_id == 0:
+ continue
+
+ try:
+ group_n = self.extractor.group_d[partition_id]
+ except KeyError:
+ assert self.extractor.count[partition_id] <=\
+ self.extractor.min_size
+ self.toosmall_parts += 1
+ continue
+
+ yield read, group_n
+ self.part_seqs += 1
+
+
+def main():
args = sanitize_help(get_parser()).parse_args()
distfilename = args.prefix + '.dist'
- n_unassigned = 0
-
for infile in args.part_filenames:
check_input_files(infile, args.force)
@@ -147,143 +280,72 @@ def main(): # pylint: disable=too-many-locals,too-many-branches
#
- suffix = 'fa'
- is_fastq = False
+ suffix = None
+ is_fastq = None
- for index, read, pid in read_partition_file(args.part_filenames[0]):
- if hasattr(read, 'quality'):
- suffix = 'fq'
- is_fastq = True
- break
-
- for filename in args.part_filenames:
- for index, read, pid in read_partition_file(filename):
- if is_fastq:
- assert hasattr(read, 'quality'), \
- "all input files must be FASTQ if the first one is"
+ with PartitionedReader(args.part_filenames, True, True) as reader:
+ for read, _ in reader:
+ if is_fastq is None:
+ is_fastq = hasattr(read, 'quality')
else:
- assert not hasattr(read, 'quality'), \
- "all input files must be FASTA if the first one is"
+ assert hasattr(read, 'quality') == is_fastq,\
+ "Input files must have consistent format."
- break
+ if is_fastq:
+ suffix = "fq"
+ else:
+ suffix = "fa"
+
+ # remember folks, generators exhaust themseleves
+ extractor = PartitionExtractor(args.part_filenames,
+ args.min_part_size,
+ args.max_size)
if args.output_unassigned:
ofile = open('%s.unassigned.%s' % (args.prefix, suffix), 'wb')
unassigned_fp = get_file_writer(ofile, args.gzip, args.bzip)
- count = {}
- for filename in args.part_filenames:
- for index, read, pid in read_partition_file(filename):
- if index % 100000 == 0:
- print('...', index, file=sys.stderr)
-
- count[pid] = count.get(pid, 0) + 1
-
- if pid == 0:
- n_unassigned += 1
- if args.output_unassigned:
- write_record(read, unassigned_fp)
-
- if args.output_unassigned:
+ extractor.process_unassigned(unassigned_fp)
unassigned_fp.close()
+ else:
+ extractor.process_unassigned()
- if 0 in count: # eliminate unpartitioned sequences
- del count[0]
-
- # develop histogram of partition sizes
- dist = {}
- for pid, size in list(count.items()):
- dist[size] = dist.get(size, 0) + 1
-
- # output histogram
- distfp = open(distfilename, 'w')
-
- total = 0
- wtotal = 0
- for counter, index in sorted(dist.items()):
- total += index
- wtotal += counter * index
- distfp.write('%d %d %d %d\n' % (counter, index, total, wtotal))
- distfp.close()
+ extractor.output_histogram(distfilename)
if not args.output_groups:
sys.exit(0)
- # sort groups by size
- divvy = sorted(list(count.items()), key=lambda y: y[1])
- divvy = [y for y in divvy if y[1] > args.min_part_size]
-
- # divvy up into different groups, based on having max_size sequences
- # in each group.
- total = 0
- group = set()
- group_n = 0
- group_d = {}
- for partition_id, n_reads in divvy:
- group.add(partition_id)
- total += n_reads
-
- if total > args.max_size:
- for partition_id in group:
- group_d[partition_id] = group_n
- # print 'group_d', partition_id, group_n
-
- group_n += 1
- group = set()
- total = 0
-
- if group:
- for partition_id in group:
- group_d[partition_id] = group_n
- # print 'group_d', partition_id, group_n
- group_n += 1
+ extractor.develop_groups()
- print('%d groups' % group_n, file=sys.stderr)
- if group_n == 0:
+ print('%d groups' % extractor.group_n, file=sys.stderr)
+ if extractor.group_n == 0:
print('nothing to output; exiting!', file=sys.stderr)
return
# open a bunch of output files for the different groups
group_fps = {}
- for index in range(group_n):
+ for index in range(extractor.group_n):
fname = '%s.group%04d.%s' % (args.prefix, index, suffix)
group_fp = get_file_writer(open(fname, 'wb'), args.gzip,
args.bzip)
group_fps[index] = group_fp
# write 'em all out!
+ # refresh the generator
+ read_generator = PartitionExtractor.ReadGroupGenerator(extractor)
- total_seqs = 0
- part_seqs = 0
- toosmall_parts = 0
- for filename in args.part_filenames:
- for index, read, partition_id in read_partition_file(filename):
- total_seqs += 1
- if index % 100000 == 0:
- print('...x2', index, file=sys.stderr)
-
- if partition_id == 0:
- continue
-
- try:
- group_n = group_d[partition_id]
- except KeyError:
- assert count[partition_id] <= args.min_part_size
- toosmall_parts += 1
- continue
-
+ with PartitionedReader(args.part_filenames) as reader:
+ for read, group_n in read_generator(reader):
outfp = group_fps[group_n]
-
write_record(read, outfp)
- part_seqs += 1
print('---', file=sys.stderr)
- print('Of %d total seqs,' % total_seqs, file=sys.stderr)
+ print('Of %d total seqs,' % read_generator.total_seqs, file=sys.stderr)
print('extracted %d partitioned seqs into group files,' %
- part_seqs, file=sys.stderr)
+ read_generator.part_seqs, file=sys.stderr)
print('discarded %d sequences from small partitions (see -m),' %
- toosmall_parts, file=sys.stderr)
+ read_generator.toosmall_parts, file=sys.stderr)
print('and found %d unpartitioned sequences (see -U).' %
- n_unassigned, file=sys.stderr)
+ extractor.n_unassigned, file=sys.stderr)
print('', file=sys.stderr)
print('Created %d group files named %s.groupXXXX.%s' %
(len(group_fps),
diff --git a/scripts/fastq-to-fasta.py b/scripts/fastq-to-fasta.py
index 349f4b5..6e61b37 100755
--- a/scripts/fastq-to-fasta.py
+++ b/scripts/fastq-to-fasta.py
@@ -44,42 +44,37 @@ Use '-h' for parameter help.
"""
from __future__ import print_function, unicode_literals
import sys
-import argparse
import screed
from khmer import __version__
from khmer.kfile import (add_output_compression_type, get_file_writer,
- is_block, describe_file_handle)
+ describe_file_handle)
from khmer.utils import write_record
-from khmer.khmer_args import (sanitize_help, ComboFormatter, info,
- _VersionStdErrAction)
+from khmer.khmer_args import sanitize_help, KhmerArgumentParser
+from khmer.khmer_args import FileType as khFileType
def get_parser():
- parser = argparse.ArgumentParser(
- description='Converts FASTQ format (.fq) files to FASTA format (.fa).',
- formatter_class=ComboFormatter)
+ parser = KhmerArgumentParser(
+ description='Converts FASTQ format (.fq) files to FASTA format (.fa).')
parser.add_argument('input_sequence', help='The name of the input'
' FASTQ sequence file.')
parser.add_argument('-o', '--output', metavar="filename",
- type=argparse.FileType('wb'),
+ type=khFileType('wb'),
help='The name of the output'
' FASTA sequence file.',
default=sys.stdout)
parser.add_argument('-n', '--n_keep', default=False, action='store_true',
help='Option to keep reads containing \'N\'s in '
'input_sequence file. Default is to drop reads')
- parser.add_argument('--version', action=_VersionStdErrAction,
- version='khmer {v}'.format(v=__version__))
add_output_compression_type(parser)
return parser
def main():
- info('fastq-to-fasta.py')
args = sanitize_help(get_parser()).parse_args()
- print(('fastq from ', args.input_sequence), file=sys.stderr)
+ print('fastq from ', args.input_sequence, file=sys.stderr)
outfp = get_file_writer(args.output, args.gzip, args.bzip)
n_count = 0
for n, record in enumerate(screed.open(args.input_sequence)):
@@ -87,7 +82,6 @@ def main():
print('...', n, file=sys.stderr)
sequence = record['sequence']
- name = record['name']
if 'N' in sequence:
if not args.n_keep:
diff --git a/scripts/filter-abund-single.py b/scripts/filter-abund-single.py
index b6790ca..4dcc966 100755
--- a/scripts/filter-abund-single.py
+++ b/scripts/filter-abund-single.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2013-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -48,19 +48,25 @@ Use '-h' for parameter help.
from __future__ import print_function
import os
import sys
-import khmer
import threading
import textwrap
-from khmer.thread_utils import ThreadedSequenceProcessor, verbose_loader
+import khmer
+
+from khmer import ReadParser
+from khmer.utils import broken_paired_reader, write_record
from khmer import khmer_args
from khmer.khmer_args import (build_counting_args, report_on_config,
- add_threading_args, info, calculate_graphsize,
- sanitize_help)
+ add_threading_args, calculate_graphsize,
+ sanitize_help, check_argument_range)
from khmer.kfile import (check_input_files, check_space,
check_space_for_graph,
add_output_compression_type,
get_file_writer)
+from khmer.khmer_logger import (configure_logging, log_info, log_error,
+ log_warn)
+from khmer.trimming import (trim_record)
+DEFAULT_NORMALIZE_LIMIT = 20
DEFAULT_CUTOFF = 2
@@ -80,26 +86,42 @@ def get_parser():
"""
parser = build_counting_args(
descr="Trims sequences at a minimum k-mer abundance "
- "(in memory version).", epilog=textwrap.dedent(epilog))
+ "(in memory version).", epilog=textwrap.dedent(epilog),
+ citations=['counting', 'SeqAn'])
add_threading_args(parser)
- parser.add_argument('--cutoff', '-C', default=DEFAULT_CUTOFF, type=int,
+ parser.add_argument('--cutoff', '-C', default=DEFAULT_CUTOFF,
+ type=check_argument_range(0, 256, "cutoff"),
help="Trim at k-mers below this abundance.")
+ parser.add_argument('--variable-coverage', '-V', action='store_true',
+ dest='variable_coverage', default=False,
+ help='Only trim low-abundance k-mers from sequences '
+ 'that have high coverage.')
+ parser.add_argument('--normalize-to', '-Z', type=int, dest='normalize_to',
+ help='Base the variable-coverage cutoff on this median'
+ ' k-mer abundance.',
+ default=DEFAULT_NORMALIZE_LIMIT)
parser.add_argument('--savegraph', metavar="filename", default='',
help="If present, the name of the file to save the "
"k-mer countgraph to")
+ parser.add_argument('-o', '--outfile', metavar='optional_output_filename',
+ default=None, help='Override default output filename '
+ 'and output trimmed sequences into a file with the '
+ 'given filename.')
parser.add_argument('datafile', metavar='input_sequence_filename',
help="FAST[AQ] sequence file to trim")
parser.add_argument('-f', '--force', default=False, action='store_true',
help='Overwrite output file if it exists')
+ parser.add_argument('-q', '--quiet', dest='quiet', default=False,
+ action='store_true')
add_output_compression_type(parser)
return parser
def main():
- info('filter-abund-single.py', ['counting', 'SeqAn'])
args = sanitize_help(get_parser()).parse_args()
+ configure_logging(args.quiet)
check_input_files(args.datafile, args.force)
check_space([args.datafile], args.force)
@@ -109,17 +131,17 @@ def main():
report_on_config(args)
- print('making countgraph', file=sys.stderr)
+ log_info('making countgraph')
graph = khmer_args.create_countgraph(args)
# first, load reads into graph
rparser = khmer.ReadParser(args.datafile)
threads = []
- print('consuming input, round 1 --', args.datafile, file=sys.stderr)
+ log_info('consuming input, round 1 -- {datafile}', datafile=args.datafile)
for _ in range(args.threads):
cur_thread = \
threading.Thread(
- target=graph.consume_fasta_with_reads_parser,
+ target=graph.consume_seqfile_with_reads_parser,
args=(rparser, )
)
threads.append(cur_thread)
@@ -128,43 +150,40 @@ def main():
for _ in threads:
_.join()
- print('Total number of unique k-mers: {0}'.format(
- graph.n_unique_kmers()), file=sys.stderr)
+ log_info('Total number of unique k-mers: {nk}', nk=graph.n_unique_kmers())
fp_rate = khmer.calc_expected_collisions(graph, args.force)
- print('fp rate estimated to be %1.3f' % fp_rate, file=sys.stderr)
-
- # now, trim.
-
- # the filtering function.
- def process_fn(record):
- name = record.name
- seq = record.sequence
- seqN = seq.replace('N', 'A')
-
- _, trim_at = graph.trim_on_abundance(seqN, args.cutoff)
-
- if trim_at >= args.ksize:
- # be sure to not to change the 'N's in the trimmed sequence -
- # so, return 'seq' and not 'seqN'.
- return name, seq[:trim_at]
-
- return None, None
+ log_info('fp rate estimated to be {fpr:1.3f}', fpr=fp_rate)
# the filtering loop
- print('filtering', args.datafile, file=sys.stderr)
- outfile = os.path.basename(args.datafile) + '.abundfilt'
- outfile = open(outfile, 'wb')
- outfp = get_file_writer(outfile, args.gzip, args.bzip)
-
- tsp = ThreadedSequenceProcessor(process_fn)
- tsp.start(verbose_loader(args.datafile), outfp)
-
- print('output in', outfile.name, file=sys.stderr)
+ log_info('filtering {datafile}', datafile=args.datafile)
+ if args.outfile is None:
+ outfile = os.path.basename(args.datafile) + '.abundfilt'
+ else:
+ outfile = args.outfile
+ outfp = open(outfile, 'wb')
+ outfp = get_file_writer(outfp, args.gzip, args.bzip)
+
+ paired_iter = broken_paired_reader(ReadParser(args.datafile),
+ min_length=graph.ksize(),
+ force_single=True)
+
+ for n, is_pair, read1, read2 in paired_iter:
+ assert not is_pair
+ assert read2 is None
+
+ trimmed_record, _ = trim_record(graph, read1, args.cutoff,
+ args.variable_coverage,
+ args.normalize_to)
+ if trimmed_record:
+ print((trimmed_record,))
+ write_record(trimmed_record, outfp)
+
+ log_info('output in {outfile}', outfile=outfile)
if args.savegraph:
- print('Saving k-mer countgraph filename',
- args.savegraph, file=sys.stderr)
+ log_info('Saving k-mer countgraph filename {graph}',
+ graph=args.savegraph)
graph.save(args.savegraph)
if __name__ == '__main__':
diff --git a/scripts/filter-abund.py b/scripts/filter-abund.py
index 9d9b764..a400a5b 100755
--- a/scripts/filter-abund.py
+++ b/scripts/filter-abund.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2011-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -45,17 +45,22 @@ Output sequences will be placed in 'infile.abundfilt'.
Use '-h' for parameter help.
"""
from __future__ import print_function
+import sys
import os
-import khmer
import textwrap
-import argparse
-import sys
-from khmer.thread_utils import ThreadedSequenceProcessor, verbose_loader
-from khmer.khmer_args import (ComboFormatter, add_threading_args, info,
- sanitize_help, _VersionStdErrAction)
+import khmer
+
+from khmer import __version__
+from khmer import ReadParser
+from khmer.utils import (broken_paired_reader, write_record)
+from khmer.khmer_args import (add_threading_args, KhmerArgumentParser,
+ sanitize_help, check_argument_range)
+from khmer.khmer_args import FileType as khFileType
from khmer.kfile import (check_input_files, check_space,
add_output_compression_type, get_file_writer)
-from khmer import __version__
+from khmer.khmer_logger import (configure_logging, log_info, log_error,
+ log_warn)
+from khmer.trimming import (trim_record)
DEFAULT_NORMALIZE_LIMIT = 20
DEFAULT_CUTOFF = 2
@@ -73,17 +78,18 @@ def get_parser():
load-into-counting.py -k 20 -x 5e7 countgraph data/100k-filtered.fa
filter-abund.py -C 2 countgraph data/100k-filtered.fa
"""
- parser = argparse.ArgumentParser(
+ parser = KhmerArgumentParser(
description='Trim sequences at a minimum k-mer abundance.',
epilog=textwrap.dedent(epilog),
- formatter_class=ComboFormatter)
+ citations=['counting'])
parser.add_argument('input_graph', metavar='input_count_graph_filename',
help='The input k-mer countgraph filename')
parser.add_argument('input_filename', metavar='input_sequence_filename',
help='Input FAST[AQ] sequence filename', nargs='+')
add_threading_args(parser)
parser.add_argument('--cutoff', '-C', dest='cutoff',
- default=DEFAULT_CUTOFF, type=int,
+ default=DEFAULT_CUTOFF,
+ type=check_argument_range(0, 256, 'cutoff'),
help="Trim at k-mers below this abundance.")
parser.add_argument('--variable-coverage', '-V', action='store_true',
dest='variable_coverage', default=False,
@@ -94,29 +100,29 @@ def get_parser():
' k-mer abundance.',
default=DEFAULT_NORMALIZE_LIMIT)
parser.add_argument('-o', '--output', dest='single_output_file',
- type=argparse.FileType('wb'),
+ type=khFileType('wb'),
metavar="optional_output_filename",
help='Output the trimmed sequences into a single file '
'with the given filename instead of creating a new '
'file for each input file.')
- parser.add_argument('--version', action=_VersionStdErrAction,
- version='khmer {v}'.format(v=__version__))
parser.add_argument('-f', '--force', default=False, action='store_true',
help='Overwrite output file if it exists')
+ parser.add_argument('-q', '--quiet', dest='quiet', default=False,
+ action='store_true')
add_output_compression_type(parser)
return parser
def main():
- info('filter-abund.py', ['counting'])
args = sanitize_help(get_parser()).parse_args()
- check_input_files(args.input_graph, args.force)
+ configure_logging(args.quiet)
+
infiles = args.input_filename
if ('-' in infiles or '/dev/stdin' in infiles) and not \
args.single_output_file:
- print("Accepting input from stdin; output filename must "
- "be provided with -o.", file=sys.stderr)
+ log_error("Accepting input from stdin; output filename must "
+ "be provided with -o.")
sys.exit(1)
for filename in infiles:
@@ -124,53 +130,39 @@ def main():
check_space(infiles, args.force)
- print('loading countgraph:', args.input_graph,
- file=sys.stderr)
+ log_info('loading countgraph: {graph}', graph=args.input_graph)
countgraph = khmer.load_countgraph(args.input_graph)
ksize = countgraph.ksize()
- print("K:", ksize, file=sys.stderr)
-
- # the filtering function.
- def process_fn(record):
- name = record.name
- seq = record.sequence
- seqN = seq.replace('N', 'A')
-
- if args.variable_coverage: # only trim when sequence has high enough C
- med, _, _ = countgraph.get_median_count(seqN)
- if med < args.normalize_to:
- return name, seq
-
- _, trim_at = countgraph.trim_on_abundance(seqN, args.cutoff)
-
- if trim_at >= ksize:
- # be sure to not to change the 'N's in the trimmed sequence -
- # so, return 'seq' and not 'seqN'.
- return name, seq[:trim_at]
-
- return None, None
+ log_info("K: {ksize}", ksize=ksize)
if args.single_output_file:
outfile = args.single_output_file.name
- outfp = get_file_writer(outfile, args.gzip, args.bzip)
+ outfp = get_file_writer(args.single_output_file, args.gzip, args.bzip)
# the filtering loop
for infile in infiles:
- print('filtering', infile, file=sys.stderr)
- if args.single_output_file:
- outfile = args.single_output_file.name
- outfp = get_file_writer(args.single_output_file, args.gzip,
- args.bzip)
- else:
+ log_info('filtering {infile}', infile=infile)
+ if not args.single_output_file:
outfile = os.path.basename(infile) + '.abundfilt'
outfp = open(outfile, 'wb')
outfp = get_file_writer(outfp, args.gzip, args.bzip)
- tsp = ThreadedSequenceProcessor(process_fn, n_workers=args.threads)
- tsp.start(verbose_loader(infile), outfp)
+ paired_iter = broken_paired_reader(ReadParser(infile),
+ min_length=ksize,
+ force_single=True)
+
+ for n, is_pair, read1, read2 in paired_iter:
+ assert not is_pair
+ assert read2 is None
+
+ trimmed_record, _ = trim_record(countgraph, read1, args.cutoff,
+ args.variable_coverage,
+ args.normalize_to)
+ if trimmed_record:
+ write_record(trimmed_record, outfp)
- print('output in', outfile, file=sys.stderr)
+ log_info('output in {outfile}', outfile=outfile)
if __name__ == '__main__':
diff --git a/scripts/filter-stoptags.py b/scripts/filter-stoptags.py
index 4472ab9..85689bb 100755
--- a/scripts/filter-stoptags.py
+++ b/scripts/filter-stoptags.py
@@ -47,14 +47,12 @@ Use '-h' for parameter help.
from __future__ import print_function
import os
-import argparse
import textwrap
import sys
from khmer import __version__, Nodegraph
from khmer.thread_utils import ThreadedSequenceProcessor, verbose_loader
from khmer.kfile import check_input_files, check_space
-from khmer.khmer_args import (info, sanitize_help, ComboFormatter,
- _VersionStdErrAction)
+from khmer.khmer_args import sanitize_help, KhmerArgumentParser
# @CTB K should be loaded from file...
DEFAULT_K = 32
@@ -66,23 +64,20 @@ def get_parser():
or remove the sequences in `<file1-N>`. Trimmed sequences will be placed
in `<fileN>.stopfilt`.
"""
- parser = argparse.ArgumentParser(
+ parser = KhmerArgumentParser(
description="Trim sequences at stoptags.",
- epilog=textwrap.dedent(epilog), formatter_class=ComboFormatter)
+ epilog=textwrap.dedent(epilog), citations=['graph'])
parser.add_argument('--ksize', '-k', default=DEFAULT_K, type=int,
help='k-mer size')
parser.add_argument('stoptags_file', metavar='input_stoptags_filename')
parser.add_argument('input_filenames', metavar='input_sequence_filename',
nargs='+')
- parser.add_argument('--version', action=_VersionStdErrAction,
- version='khmer {v}'.format(v=__version__))
parser.add_argument('-f', '--force', default=False, action='store_true',
help='Overwrite output file if it exists')
return parser
def main():
- info('filter-stoptags.py', ['graph'])
args = sanitize_help(get_parser()).parse_args()
stoptags = args.stoptags_file
infiles = args.input_filenames
@@ -97,8 +92,8 @@ def main():
nodegraph.load_stop_tags(stoptags)
def process_fn(record):
- name = record['name']
- seq = record['sequence']
+ name = record.name
+ seq = record.sequence
if 'N' in seq:
return None, None
diff --git a/scripts/find-knots.py b/scripts/find-knots.py
index 96c75db..59495c6 100755
--- a/scripts/find-knots.py
+++ b/scripts/find-knots.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2010-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -43,7 +43,6 @@ k-mers are output into a .stoptags file, for later use in partitioning.
"""
from __future__ import print_function
-import argparse
import glob
import os
import textwrap
@@ -51,9 +50,7 @@ import khmer
import sys
from khmer.kfile import check_input_files, check_space
from khmer import khmer_args
-from khmer.khmer_args import (build_counting_args, info, add_loadgraph_args,
- report_on_config, sanitize_help,
- ComboFormatter)
+from khmer.khmer_args import (build_counting_args, sanitize_help)
# counting hash parameters.
DEFAULT_COUNTING_HT_SIZE = 3e6 # number of bytes
@@ -97,7 +94,8 @@ def get_parser():
"""
parser = build_counting_args(
descr="Find all highly connected k-mers.",
- epilog=textwrap.dedent(epilog))
+ epilog=textwrap.dedent(epilog),
+ citations=['graph'])
parser.add_argument('graphbase', help='Basename for the input and output '
'files.')
@@ -107,11 +105,10 @@ def get_parser():
def main():
- info('find-knots.py', ['graph'])
parser = get_parser()
parser.epilog = parser.epilog.replace(
":doc:`partitioning-big-data`",
- "http://khmer.readthedocs.org/en/stable/user/"
+ "http://khmer.readthedocs.io/en/stable/user/"
"partitioning-big-data.html"
)
args = sanitize_help(parser).parse_args()
diff --git a/scripts/interleave-reads.py b/scripts/interleave-reads.py
index a96b03e..ece85e8 100755
--- a/scripts/interleave-reads.py
+++ b/scripts/interleave-reads.py
@@ -48,13 +48,11 @@ from __future__ import print_function
import screed
import sys
-import os
import textwrap
-import argparse
from khmer import __version__
-from khmer.kfile import check_input_files, check_space, is_block
-from khmer.khmer_args import (info, sanitize_help, ComboFormatter,
- _VersionStdErrAction)
+from khmer.kfile import check_input_files, check_space
+from khmer.khmer_args import sanitize_help, KhmerArgumentParser
+from khmer.khmer_args import FileType as khFileType
from khmer.kfile import (add_output_compression_type, get_file_writer,
describe_file_handle)
from khmer.utils import (write_record_pair, check_is_left, check_is_right,
@@ -75,22 +73,25 @@ def get_parser():
As a "bonus", this file ensures that if read names are not already
formatted properly, they are reformatted consistently, such that
they look like the pre-1.8 Casava format (`@name/1`, `@name/2`).
+ This reformatting can be switched off with the
+ :option:`--no-reformat` flag.
Example::
interleave-reads.py tests/test-data/paired.fq.1 \\
tests/test-data/paired.fq.2 -o paired.fq"""
- parser = argparse.ArgumentParser(
+ parser = KhmerArgumentParser(
description='Produce interleaved files from R1/R2 paired files',
- epilog=textwrap.dedent(epilog), formatter_class=ComboFormatter)
+ epilog=textwrap.dedent(epilog))
parser.add_argument('left')
parser.add_argument('right')
parser.add_argument('-o', '--output', metavar="filename",
- type=argparse.FileType('wb'),
+ type=khFileType('wb'),
default=sys.stdout)
- parser.add_argument('--version', action=_VersionStdErrAction,
- version='khmer {v}'.format(v=__version__))
+ parser.add_argument('--no-reformat', default=False, action='store_true',
+ help='Do not reformat read names or enforce\
+ consistency')
parser.add_argument('-f', '--force', default=False, action='store_true',
help='Overwrite output file if it exists')
add_output_compression_type(parser)
@@ -98,7 +99,6 @@ def get_parser():
def main():
- info('interleave-reads.py')
args = sanitize_help(get_parser()).parse_args()
check_input_files(args.left, args.force)
@@ -108,8 +108,6 @@ def main():
s1_file = args.left
s2_file = args.right
- fail = False
-
print("Interleaving:\n\t%s\n\t%s" % (s1_file, s2_file), file=sys.stderr)
outfp = get_file_writer(args.output, args.gzip, args.bzip)
@@ -128,19 +126,21 @@ def main():
counter += 1
name1 = read1.name
- if not check_is_left(name1):
- name1 += '/1'
name2 = read2.name
- if not check_is_right(name2):
- name2 += '/2'
- read1.name = name1
- read2.name = name2
+ if not args.no_reformat:
+ if not check_is_left(name1):
+ name1 += '/1'
+ if not check_is_right(name2):
+ name2 += '/2'
- if not check_is_pair(read1, read2):
- print("ERROR: This doesn't look like paired data! "
- "%s %s" % (read1.name, read2.name), file=sys.stderr)
- sys.exit(1)
+ read1.name = name1
+ read2.name = name2
+
+ if not check_is_pair(read1, read2):
+ print("ERROR: This doesn't look like paired data! "
+ "%s %s" % (read1.name, read2.name), file=sys.stderr)
+ sys.exit(1)
write_record_pair(read1, read2, outfp)
diff --git a/scripts/load-graph.py b/scripts/load-graph.py
index 0e74729..3f47426 100755
--- a/scripts/load-graph.py
+++ b/scripts/load-graph.py
@@ -44,20 +44,20 @@ Use '-h' for parameter help.
import sys
-from khmer.khmer_args import build_nodegraph_args, info
+from khmer.khmer_args import build_nodegraph_args
from oxli import build_graph
def get_parser():
parser = build_nodegraph_args(descr="Load sequences into the compressible "
- "graph format plus optional tagset.")
+ "graph format plus optional tagset.",
+ citations=['graph', 'SeqAn'])
parser = build_graph.build_parser(parser)
return parser
if __name__ == '__main__':
- info('load-graph.py', ['graph', 'SeqAn'])
build_graph.main(get_parser().parse_args())
# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
diff --git a/scripts/load-into-counting.py b/scripts/load-into-counting.py
index c616d5a..4797aec 100755
--- a/scripts/load-into-counting.py
+++ b/scripts/load-into-counting.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2011-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -33,11 +33,11 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
-# pylint: disable=missing-docstring,invalid-name
+# pylint: disable=missing-docstring,invalid-name,no-member
"""
-Build a counting Bloom filter from the given sequences, save in <htname>.
+Build a counting Bloom filter from the given sequences, save in <countgraph>.
-% load-into-counting.py <htname> <data1> [ <data2> <...> ]
+% load-into-counting.py <countgraph> <data1> [ <data2> <...> ]
Use '-h' for parameter help.
"""
@@ -56,6 +56,8 @@ from khmer.khmer_args import (build_counting_args, report_on_config, info,
from khmer.kfile import check_file_writable
from khmer.kfile import check_input_files
from khmer.kfile import check_space_for_graph
+from khmer.khmer_logger import (configure_logging, log_info, log_error,
+ log_warn)
def get_parser():
@@ -79,7 +81,8 @@ def get_parser():
"""
parser = build_counting_args("Build a k-mer countgraph from the given"
- " sequences.", epilog=textwrap.dedent(epilog))
+ " sequences.", epilog=textwrap.dedent(epilog),
+ citations=['counting', 'SeqAn'])
add_threading_args(parser)
parser.add_argument('output_countgraph_filename', help="The name of the"
" file to write the k-mer countgraph to.")
@@ -97,14 +100,16 @@ def get_parser():
" default)")
parser.add_argument('-f', '--force', default=False, action='store_true',
help='Overwrite output file if it exists')
+ parser.add_argument('-q', '--quiet', dest='quiet', default=False,
+ action='store_true')
return parser
def main():
- info('load-into-counting.py', ['counting', 'SeqAn'])
-
args = sanitize_help(get_parser()).parse_args()
+
+ configure_logging(args.quiet)
report_on_config(args)
base = args.output_countgraph_filename
@@ -117,18 +122,19 @@ def main():
check_space_for_graph(args.output_countgraph_filename, tablesize,
args.force)
+ info_filename = base + ".info"
check_file_writable(base)
- check_file_writable(base + ".info")
+ check_file_writable(info_filename)
- print('Saving k-mer countgraph to %s' % base, file=sys.stderr)
- print('Loading kmers from sequences in %s' %
- repr(filenames), file=sys.stderr)
+ log_info('Saving k-mer countgraph to {base}', base=base)
+ log_info('Loading kmers from sequences in {filenames}',
+ filenames=repr(filenames))
# clobber the '.info' file now, as we always open in append mode below
- if os.path.exists(base + '.info'):
- os.remove(base + '.info')
+ with open(info_filename, 'w') as info_fp:
+ print('khmer version:', khmer.__version__, file=info_fp)
- print('making countgraph', file=sys.stderr)
+ log_info('making countgraph')
countgraph = khmer_args.create_countgraph(args)
countgraph.set_use_bigcount(args.bigcount)
@@ -140,11 +146,11 @@ def main():
rparser = khmer.ReadParser(filename)
threads = []
- print('consuming input', filename, file=sys.stderr)
+ log_info('consuming input {input}', input=filename)
for _ in range(args.threads):
cur_thrd = \
threading.Thread(
- target=countgraph.consume_fasta_with_reads_parser,
+ target=countgraph.consume_seqfile_with_reads_parser,
args=(rparser, )
)
threads.append(cur_thrd)
@@ -156,19 +162,19 @@ def main():
if index > 0 and index % 10 == 0:
tablesize = calculate_graphsize(args, 'countgraph')
check_space_for_graph(base, tablesize, args.force)
- print('mid-save', base, file=sys.stderr)
+ log_info('mid-save {base}', base=base)
countgraph.save(base)
- with open(base + '.info', 'a') as info_fh:
+ with open(info_filename, 'a') as info_fh:
print('through', filename, file=info_fh)
total_num_reads += rparser.num_reads
n_kmers = countgraph.n_unique_kmers()
- print('Total number of unique k-mers:', n_kmers, file=sys.stderr)
- with open(base + '.info', 'a') as info_fp:
+ log_info('Total number of unique k-mers: {nk}', nk=n_kmers)
+ with open(info_filename, 'a') as info_fp:
print('Total number of unique k-mers:', n_kmers, file=info_fp)
- print('saving', base, file=sys.stderr)
+ log_info('saving {base}', base=base)
countgraph.save(base)
# Change max_false_pos=0.2 only if you really grok it. HINT: You don't
@@ -176,13 +182,13 @@ def main():
khmer.calc_expected_collisions(
countgraph, args.force, max_false_pos=.2)
- with open(base + '.info', 'a') as info_fp:
+ with open(info_filename, 'a') as info_fp:
print('fp rate estimated to be %1.3f\n' % fp_rate, file=info_fp)
if args.summary_info:
mr_fmt = args.summary_info.lower()
mr_file = base + '.info.' + mr_fmt
- print("Writing summmary info to", mr_file, file=sys.stderr)
+ log_info("Writing summmary info to {mr_file}", mr_file=mr_file)
with open(mr_file, 'w') as mr_fh:
if mr_fmt == 'json':
mr_data = {
@@ -206,12 +212,13 @@ def main():
]
mr_fh.write("\t".join(vals) + "\n")
- print('fp rate estimated to be %1.3f' % fp_rate, file=sys.stderr)
+ log_info('fp rate estimated to be {fpr:1.3f}', fpr=fp_rate)
- print('DONE.', file=sys.stderr)
- print('wrote to:', base + '.info', file=sys.stderr)
+ log_info('DONE.')
+ log_info('wrote to: {filename}', filename=info_filename)
if __name__ == '__main__':
main()
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
+# vim: set filetype=python tabstop=4 softtabstop=4 shiftwidth=4 expandtab:
+# vim: set textwidth=79:
diff --git a/scripts/make-initial-stoptags.py b/scripts/make-initial-stoptags.py
index 04fa92b..765ffe5 100755
--- a/scripts/make-initial-stoptags.py
+++ b/scripts/make-initial-stoptags.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2011-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -45,7 +45,7 @@ import sys
import textwrap
import khmer
from khmer import khmer_args
-from khmer.khmer_args import (build_counting_args, info, sanitize_help)
+from khmer.khmer_args import (build_counting_args, sanitize_help)
from khmer.kfile import check_input_files
DEFAULT_SUBSET_SIZE = int(1e4)
@@ -85,7 +85,8 @@ def get_parser():
"""
parser = build_counting_args(
descr="Find an initial set of highly connected k-mers.",
- epilog=textwrap.dedent(epilog))
+ epilog=textwrap.dedent(epilog),
+ citations=['graph'])
parser.add_argument('--subset-size', '-s', default=DEFAULT_SUBSET_SIZE,
dest='subset_size', type=float,
help='Set subset size (default 1e4 is prob ok)')
@@ -99,8 +100,6 @@ def get_parser():
def main():
-
- info('make-initial-stoptags.py', ['graph'])
args = sanitize_help(get_parser()).parse_args()
graphbase = args.graphbase
@@ -127,6 +126,7 @@ def main():
# divide up into SUBSET_SIZE fragments
divvy = nodegraph.divide_tags_into_subsets(args.subset_size)
+ divvy = list(divvy)
# pick off the first one
if len(divvy) == 1:
diff --git a/scripts/merge-partitions.py b/scripts/merge-partitions.py
index 21cc193..5d7ed72 100755
--- a/scripts/merge-partitions.py
+++ b/scripts/merge-partitions.py
@@ -44,16 +44,13 @@ merged pmap file will be in <base>.pmap.merged.
"""
from __future__ import print_function
-import argparse
import glob
import os
import textwrap
import khmer
import sys
-from khmer import __version__
from khmer.kfile import check_input_files, check_space
-from khmer.khmer_args import (info, sanitize_help, ComboFormatter,
- _VersionStdErrAction)
+from khmer.khmer_args import sanitize_help, KhmerArgumentParser
DEFAULT_K = 32
@@ -64,9 +61,10 @@ def get_parser():
single ``${graphbase}.pmap.merged`` file for
:program:`annotate-partitions.py` to use.
"""
- parser = argparse.ArgumentParser(
+ parser = KhmerArgumentParser(
description="Merge partition map '.pmap' files.",
- epilog=textwrap.dedent(epilog), formatter_class=ComboFormatter)
+ epilog=textwrap.dedent(epilog),
+ citations=['graph'])
parser.add_argument('--ksize', '-k', type=int, default=DEFAULT_K,
help="k-mer size (default: %d)" % DEFAULT_K)
parser.add_argument('--keep-subsets', dest='remove_subsets',
@@ -74,15 +72,12 @@ def get_parser():
help='Keep individual subsets (default: False)')
parser.add_argument('graphbase', help='basename for input and output '
'files')
- parser.add_argument('--version', action=_VersionStdErrAction,
- version='khmer {v}'.format(v=__version__))
parser.add_argument('-f', '--force', default=False, action='store_true',
help='Overwrite output file if it exists')
return parser
def main():
- info('merge-partitions.py', ['graph'])
args = sanitize_help(get_parser()).parse_args()
output_file = args.graphbase + '.pmap.merged'
diff --git a/scripts/normalize-by-median.py b/scripts/normalize-by-median.py
index 9be0a13..8b1d7ba 100755
--- a/scripts/normalize-by-median.py
+++ b/scripts/normalize-by-median.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2011-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -56,12 +56,14 @@ from khmer import khmer_args
from contextlib import contextmanager
from khmer.khmer_args import (build_counting_args, add_loadgraph_args,
report_on_config, info, calculate_graphsize,
- sanitize_help)
+ sanitize_help, check_argument_range)
+from khmer.khmer_args import FileType as khFileType
import argparse
from khmer.kfile import (check_space, check_space_for_graph,
check_valid_file_exists, add_output_compression_type,
get_file_writer, is_block, describe_file_handle)
-from khmer.utils import write_record, broken_paired_reader
+from khmer.utils import (write_record, broken_paired_reader, ReadBundle,
+ clean_input_reads)
from khmer.khmer_logger import (configure_logging, log_info, log_error)
@@ -152,7 +154,6 @@ class WithDiagnostics(object):
class Normalizer(object):
-
"""Digital normalization algorithm."""
def __init__(self, desired_coverage, countgraph):
@@ -169,24 +170,13 @@ class Normalizer(object):
* if any read's median k-mer count is below desired coverage, keep all;
* consume and yield kept reads.
"""
+ batch = ReadBundle(read0, read1)
desired_coverage = self.desired_coverage
- passed_filter = False
-
- batch = []
- batch.append(read0)
- if read1 is not None:
- batch.append(read1)
-
- for record in batch:
- seq = record.sequence.replace('N', 'A')
- if not self.countgraph.median_at_least(seq, desired_coverage):
- passed_filter = True
-
- if passed_filter:
- for record in batch:
- seq = record.sequence.replace('N', 'A')
- self.countgraph.consume(seq)
+ # if any in batch have coverage below desired coverage, consume &yield
+ if not batch.coverages_at_least(self.countgraph, desired_coverage):
+ for record in batch.reads:
+ self.countgraph.consume(record.cleaned_seq)
yield record
@@ -265,12 +255,14 @@ def get_parser():
tests/test-data/test-fastq-reads.fq"""
parser = build_counting_args(
descr="Do digital normalization (remove mostly redundant sequences)",
- epilog=textwrap.dedent(epilog))
+ epilog=textwrap.dedent(epilog),
+ citations=['diginorm'])
parser.add_argument('-q', '--quiet', dest='quiet', default=False,
action='store_true')
- parser.add_argument('-C', '--cutoff', type=int, help="when the median "
- "k-mer coverage level above is above this numer the "
+ parser.add_argument('-C', '--cutoff', help="when the median "
+ "k-mer coverage level is above this number the "
"read is not kept.",
+ type=check_argument_range(0, 256, "cutoff"),
default=DEFAULT_DESIRED_COVERAGE)
parser.add_argument('-p', '--paired', action='store_true',
help='require that all sequences be properly paired')
@@ -293,7 +285,7 @@ def get_parser():
help='continue past file reading errors',
action='store_true')
parser.add_argument('-o', '--output', metavar="filename",
- type=argparse.FileType('wb'),
+ type=khFileType('wb'),
default=None, dest='single_output_file',
help='only output a single file with '
'the specified filename; use a single dash "-" to '
@@ -307,9 +299,9 @@ def get_parser():
def main(): # pylint: disable=too-many-branches,too-many-statements
- info('normalize-by-median.py', ['diginorm'])
parser = sanitize_help(get_parser())
args = parser.parse_args()
+
configure_logging(args.quiet)
report_on_config(args)
@@ -388,8 +380,7 @@ def main(): # pylint: disable=too-many-branches,too-many-statements
# failsafe context manager in case an input file breaks
with catch_io_errors(filename, outfp, args.single_output_file,
args.force, corrupt_files):
-
- screed_iter = screed.open(filename)
+ screed_iter = clean_input_reads(screed.open(filename))
reader = broken_paired_reader(screed_iter, min_length=args.ksize,
force_single=force_single,
require_paired=require_paired)
@@ -400,7 +391,7 @@ def main(): # pylint: disable=too-many-branches,too-many-statements
write_record(record, outfp)
log_info('output in {name}', name=describe_file_handle(outfp))
- if not is_block(outfp):
+ if not args.single_output_file:
outfp.close()
# finished - print out some diagnostics.
@@ -427,4 +418,5 @@ def main(): # pylint: disable=too-many-branches,too-many-statements
if __name__ == '__main__':
main()
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
+# vim: set filetype=python tabstop=4 softtabstop=4 shiftwidth=4 expandtab:
+# vim: set textwidth=79:
diff --git a/scripts/partition-graph.py b/scripts/partition-graph.py
index 0b0a676..fc14c7a 100755
--- a/scripts/partition-graph.py
+++ b/scripts/partition-graph.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2011-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -46,16 +46,16 @@ Use '-h' for parameter help.
from __future__ import print_function
import threading
-import gc
-import os.path
-import argparse
import textwrap
import sys
+import gc
+import os.path
from khmer import __version__, load_nodegraph
-from khmer.khmer_args import (add_threading_args, info, sanitize_help,
- ComboFormatter, _VersionStdErrAction)
+from khmer.khmer_args import (add_threading_args, sanitize_help,
+ KhmerArgumentParser)
from khmer.kfile import check_input_files
+from oxli.partition import worker
# stdlib queue module was renamed on Python 3
try:
@@ -67,43 +67,17 @@ DEFAULT_SUBSET_SIZE = int(1e5)
DEFAULT_N_THREADS = 4
-def worker(tasks, basename, stop_big_traversals):
- while True:
- try:
- (nodegraph, index, start, stop) = tasks.get(False)
- except queue.Empty:
- print('exiting', file=sys.stderr)
- return
-
- outfile = basename + '.subset.%d.pmap' % (index,)
- if os.path.exists(outfile):
- print('SKIPPING', outfile, ' -- already exists', file=sys.stderr)
- continue
-
- print('starting:', basename, index, file=sys.stderr)
-
- # pay attention to stoptags when partitioning; take command line
- # direction on whether or not to exhaustively traverse.
- subset = nodegraph.do_subset_partition(start, stop, True,
- stop_big_traversals)
-
- print('saving:', basename, index, file=sys.stderr)
- nodegraph.save_subset_partitionmap(subset, outfile)
- del subset
- gc.collect()
-
-
def get_parser():
epilog = """\
The resulting partition maps are saved as ``${basename}.subset.#.pmap``
files.
"""
- parser = argparse.ArgumentParser(
+ parser = KhmerArgumentParser(
description="Partition a sequence graph based upon waypoint "
"connectivity", epilog=textwrap.dedent(epilog),
- formatter_class=ComboFormatter)
+ citations=['graph'])
- parser.add_argument('basename', help="basename of the input k-mer"
+ parser.add_argument('basename', help="basename of the input k-mer "
"nodegraph + tagset files")
parser.add_argument('--stoptags', '-S', metavar='filename', default='',
help="Use stoptags in this file during partitioning")
@@ -113,8 +87,6 @@ def get_parser():
parser.add_argument('--no-big-traverse', action='store_true',
default=False, help='Truncate graph joins at big '
'traversals')
- parser.add_argument('--version', action=_VersionStdErrAction,
- version='khmer {v}'.format(v=__version__))
parser.add_argument('-f', '--force', default=False, action='store_true',
help='Overwrite output file if it exists')
add_threading_args(parser)
@@ -122,7 +94,6 @@ def get_parser():
def main():
- info('partition-graph.py', ['graph'])
args = sanitize_help(get_parser()).parse_args()
basename = args.basename
@@ -161,6 +132,7 @@ def main():
# divide the tags up into subsets
divvy = nodegraph.divide_tags_into_subsets(int(args.subset_size))
+ divvy = list(divvy)
n_subsets = len(divvy)
divvy.append(0)
diff --git a/scripts/readstats.py b/scripts/readstats.py
index 24ebebd..f3887d0 100755
--- a/scripts/readstats.py
+++ b/scripts/readstats.py
@@ -33,6 +33,7 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
+# pylint: disable=missing-docstring
"""
Display summary statistics for one or more FASTA/FASTQ files.
@@ -42,15 +43,14 @@ Use '-h' for parameter help.
"""
from __future__ import print_function
+import argparse
import sys
import csv
import screed
-import argparse
import textwrap
from khmer import __version__
-from khmer.khmer_args import (sanitize_help, ComboFormatter, info,
- _VersionStdErrAction)
+from khmer.khmer_args import sanitize_help, KhmerArgumentParser
def get_parser():
@@ -67,9 +67,9 @@ def get_parser():
readstats.py tests/test-data/test-abund-read-2.fa
"""
- parser = argparse.ArgumentParser(
- description=descr, formatter_class=ComboFormatter,
- epilog=textwrap.dedent(epilog),)
+ parser = KhmerArgumentParser(
+ description=descr,
+ epilog=textwrap.dedent(epilog))
parser.add_argument('filenames', nargs='+')
parser.add_argument('-o', '--output', dest='outfp', metavar="filename",
help="output file for statistics; defaults to stdout.",
@@ -77,13 +77,10 @@ def get_parser():
parser.add_argument('--csv', default=False, action='store_true',
help='Use the CSV format for the statistics, '
'including column headers.')
- parser.add_argument('--version', action=_VersionStdErrAction,
- version='khmer {v}'.format(v=__version__))
return parser
class StatisticsOutput(object): # pylint: disable=too-few-public-methods
-
"""
Output statistics for several data files.
@@ -95,6 +92,7 @@ class StatisticsOutput(object): # pylint: disable=too-few-public-methods
self.formatter = formatter
def __enter__(self):
+ """Write header upon entry."""
self.formatter.write_header()
return self
@@ -104,13 +102,13 @@ class StatisticsOutput(object): # pylint: disable=too-few-public-methods
basepairs, seqs, basepairs / float(seqs), filename)
def __exit__(self, exc_type, exc_value, traceback):
+ """No exception? Finalize the formatter on exit."""
if exc_type is None:
self.formatter.finalize()
class CsvFormatter(object):
-
- """Format the statistis information as CSV."""
+ """Format the statistics information as CSV."""
headers = ['bp', 'seqs', 'avg_len', 'filename']
@@ -131,7 +129,6 @@ class CsvFormatter(object):
class StdFormatter(object):
-
"""Format the statistics in a human readable string."""
def __init__(self, underlying_file):
@@ -176,12 +173,8 @@ def analyze_file(filename):
def main():
"""Main function - run when executed as a script."""
- info('readstats.py')
args = sanitize_help(get_parser()).parse_args()
- total_bp = 0
- total_seqs = 0
-
statistics = []
for filename in args.filenames:
diff --git a/scripts/sample-reads-randomly.py b/scripts/sample-reads-randomly.py
index b346091..5d1fa6e 100755
--- a/scripts/sample-reads-randomly.py
+++ b/scripts/sample-reads-randomly.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2013-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -48,17 +48,16 @@ Reads FASTQ and FASTA input, retains format for output.
from __future__ import print_function
import argparse
-import screed
import os.path
import random
import textwrap
import sys
from khmer import __version__
+from khmer import ReadParser
from khmer.kfile import (check_input_files, add_output_compression_type,
get_file_writer)
-from khmer.khmer_args import (info, sanitize_help, ComboFormatter,
- _VersionStdErrAction)
+from khmer.khmer_args import sanitize_help, KhmerArgumentParser
from khmer.utils import write_record, broken_paired_reader
DEFAULT_NUM_READS = int(1e5)
@@ -82,9 +81,9 @@ def get_parser():
<http://en.wikipedia.org/wiki/Reservoir_sampling>`__ algorithm.
"""
- parser = argparse.ArgumentParser(
+ parser = KhmerArgumentParser(
description="Uniformly subsample sequences from a collection of files",
- formatter_class=ComboFormatter, epilog=textwrap.dedent(epilog))
+ epilog=textwrap.dedent(epilog))
parser.add_argument('filenames', nargs='+')
parser.add_argument('-N', '--num_reads', type=int, dest='num_reads',
@@ -100,8 +99,6 @@ def get_parser():
parser.add_argument('-o', '--output', dest='output_file',
type=argparse.FileType('wb'),
metavar="filename", default=None)
- parser.add_argument('--version', action=_VersionStdErrAction,
- version='khmer {v}'.format(v=__version__))
parser.add_argument('-f', '--force', default=False, action='store_true',
help='Overwrite output file if it exits')
add_output_compression_type(parser)
@@ -109,7 +106,6 @@ def get_parser():
def main():
- info('sample-reads-randomly.py')
parser = get_parser()
parser.epilog = parser.epilog.replace(
"`reservoir sampling\n"
@@ -118,8 +114,8 @@ def main():
"http://en.wikipedia.org/wiki/Reservoir_sampling")
args = sanitize_help(parser).parse_args()
- for _ in args.filenames:
- check_input_files(_, args.force)
+ for name in args.filenames:
+ check_input_files(name, args.force)
# seed the random number generator?
if args.random_seed:
@@ -148,6 +144,11 @@ def main():
sys.exit(1)
output_filename = os.path.basename(filename) + '.subset'
+ filename = args.filenames[0]
+ if filename in ('/dev/stdin', '-'):
+ # seqan only treats '-' as "read from stdin"
+ filename = '-'
+
if num_samples == 1:
print('Subsampling %d reads using reservoir sampling.' %
args.num_reads, file=sys.stderr)
@@ -163,17 +164,15 @@ def main():
print('', file=sys.stderr)
reads = []
- for n in range(num_samples):
+ for _ in range(num_samples):
reads.append([])
# read through all the sequences and load/resample the reservoir
for filename in args.filenames:
print('opening', filename, 'for reading', file=sys.stderr)
- screed_iter = screed.open(filename)
- for count, (_, ispair, rcrd1, rcrd2) in enumerate(broken_paired_reader(
- screed_iter,
- force_single=args.force_single)):
+ for count, (_, _, rcrd1, rcrd2) in enumerate(broken_paired_reader(
+ ReadParser(filename), force_single=args.force_single)):
if count % 10000 == 0:
print('...', count, 'reads scanned', file=sys.stderr)
if count >= args.max_reads:
@@ -183,10 +182,11 @@ def main():
# collect first N reads
if count < args.num_reads:
- for n in range(num_samples):
- reads[n].append((rcrd1, rcrd2))
+ for sample in range(num_samples):
+ reads[sample].append((rcrd1, rcrd2))
else:
- assert len(reads[n]) <= count
+ for sample in range(num_samples):
+ assert len(reads[sample]) <= count
# use reservoir sampling to replace reads at random
# see http://en.wikipedia.org/wiki/Reservoir_sampling
diff --git a/scripts/split-paired-reads.py b/scripts/split-paired-reads.py
index 8120808..6efa4f9 100755
--- a/scripts/split-paired-reads.py
+++ b/scripts/split-paired-reads.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2013-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -35,7 +35,7 @@
# Contact: khmer-project at idyll.org
# pylint: disable=invalid-name,missing-docstring
"""
-De-interleave a file.
+Deinterleave a file.
Take an interleaved set of reads (/1 and /2), and extract them into separate
files (.1 and .2).
@@ -45,19 +45,19 @@ files (.1 and .2).
Reads FASTQ and FASTA input, retains format for output.
"""
from __future__ import print_function
-import screed
import sys
import os
import textwrap
-import argparse
+
from khmer import __version__
-from khmer.khmer_args import (info, sanitize_help, ComboFormatter,
- _VersionStdErrAction)
+from khmer import ReadParser
+from khmer.khmer_args import sanitize_help, KhmerArgumentParser
+from khmer.khmer_args import FileType as khFileType
from khmer.utils import (write_record, broken_paired_reader,
UnpairedReadsError)
from khmer.kfile import (check_input_files, check_space,
add_output_compression_type,
- get_file_writer, is_block, describe_file_handle)
+ get_file_writer, describe_file_handle)
def get_parser():
@@ -90,10 +90,9 @@ def get_parser():
split-paired-reads.py -1 reads.1 -2 reads.2 tests/test-data/paired.fq
"""
- parser = argparse.ArgumentParser(
+ parser = KhmerArgumentParser(
description='Split interleaved reads into two files, left and right.',
- epilog=textwrap.dedent(epilog),
- formatter_class=ComboFormatter)
+ epilog=textwrap.dedent(epilog))
parser.add_argument('infile', nargs='?', default='/dev/stdin')
@@ -104,15 +103,13 @@ def get_parser():
parser.add_argument('-0', '--output-orphaned', metavar='output_orphaned',
help='Allow "orphaned" reads and extract them to ' +
'this file',
- type=argparse.FileType('wb'))
+ type=khFileType('wb'))
parser.add_argument('-1', '--output-first', metavar='output_first',
default=None, help='Output "left" reads to this '
- 'file', type=argparse.FileType('wb'))
+ 'file', type=khFileType('wb'))
parser.add_argument('-2', '--output-second', metavar='output_second',
default=None, help='Output "right" reads to this '
- 'file', type=argparse.FileType('wb'))
- parser.add_argument('--version', action=_VersionStdErrAction,
- version='khmer {v}'.format(v=__version__))
+ 'file', type=khFileType('wb'))
parser.add_argument('-f', '--force', default=False, action='store_true',
help='Overwrite output file if it exists')
add_output_compression_type(parser)
@@ -120,7 +117,6 @@ def get_parser():
def main():
- info('split-paired-reads.py')
args = sanitize_help(get_parser()).parse_args()
infile = args.infile
@@ -133,6 +129,8 @@ def main():
# decide where to put output files - specific directory? or just default?
if infile in ('/dev/stdin', '-'):
+ # seqan only treats '-' as "read from stdin"
+ infile = '-'
if not (args.output_first and args.output_second):
print("Accepting input from stdin; "
"output filenames must be provided.", file=sys.stderr)
@@ -170,10 +168,8 @@ def main():
counter3 = 0
index = None
- screed_iter = screed.open(infile)
-
# walk through all the reads in broken-paired mode.
- paired_iter = broken_paired_reader(screed_iter,
+ paired_iter = broken_paired_reader(ReadParser(infile),
require_paired=not args.output_orphaned)
try:
@@ -191,7 +187,7 @@ def main():
counter3 += 1
except UnpairedReadsError as e:
print("Unpaired reads found starting at {name}; exiting".format(
- name=e.r1.name), file=sys.stderr)
+ name=e.read1.name), file=sys.stderr)
sys.exit(1)
print("DONE; split %d sequences (%d left, %d right, %d orphans)" %
diff --git a/scripts/trim-low-abund.py b/scripts/trim-low-abund.py
index 5ce0e3c..2246f5c 100755
--- a/scripts/trim-low-abund.py
+++ b/scripts/trim-low-abund.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2012-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -33,6 +33,7 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
+# pylint: disable=invalid-name,missing-docstring,no-member
"""
Trim sequences at k-mers of the given abundance, using a streaming algorithm.
@@ -44,37 +45,31 @@ Use -h for parameter help.
"""
from __future__ import print_function
import sys
-import screed
import os
import khmer
import tempfile
import shutil
import textwrap
-import argparse
-from screed import Record
from khmer import khmer_args
+from khmer import ReadParser
-from khmer.khmer_args import (build_counting_args, info, add_loadgraph_args,
+from khmer.khmer_args import (build_counting_args, add_loadgraph_args,
report_on_config, calculate_graphsize,
sanitize_help)
-from khmer.utils import write_record, write_record_pair, broken_paired_reader
+from khmer.khmer_args import FileType as khFileType
+from khmer.utils import write_record, broken_paired_reader, ReadBundle
from khmer.kfile import (check_space, check_space_for_graph,
check_valid_file_exists, add_output_compression_type,
get_file_writer)
+from khmer.khmer_logger import configure_logging, log_info, log_error
+from khmer.trimming import trim_record
-DEFAULT_NORMALIZE_LIMIT = 20
+DEFAULT_TRIM_AT_COVERAGE = 20
DEFAULT_CUTOFF = 2
+DEFAULT_DIGINORM_COVERAGE = 20
-
-def trim_record(read, trim_at):
- new_read = Record()
- new_read.name = read.name
- new_read.sequence = read.sequence[:trim_at]
- if hasattr(read, 'quality'):
- new_read.quality = read.quality[:trim_at]
-
- return new_read
+REPORT_EVERY_N_READS = 10000
def get_parser():
@@ -90,7 +85,7 @@ def get_parser():
Note that the output reads will not necessarily be in the same order
as the reads in the input files; if this is an important consideration,
- use :program:`load-into-countgraph.py` and :program:`filter-abund.py`.
+ use :program:`load-into-counting.py` and :program:`filter-abund.py`.
However, read pairs will be kept together, in "broken-paired" format; you
can use :program:`extract-paired-reads.py` to extract read pairs and
orphans.
@@ -102,7 +97,8 @@ def get_parser():
parser = build_counting_args(
descr='Trim low-abundance k-mers using a streaming algorithm.',
- epilog=textwrap.dedent(epilog))
+ epilog=textwrap.dedent(epilog),
+ citations=['streaming'])
parser.add_argument('input_filenames', nargs='+')
@@ -110,12 +106,13 @@ def get_parser():
help='remove k-mers below this abundance',
default=DEFAULT_CUTOFF)
- parser.add_argument('--normalize-to', '-Z', type=int,
- help='base cutoff on this median k-mer abundance',
- default=DEFAULT_NORMALIZE_LIMIT)
+ parser.add_argument('--trim-at-coverage', '-Z', '--normalize-to',
+ type=int,
+ help='trim reads when entire read above this coverage',
+ default=DEFAULT_TRIM_AT_COVERAGE)
parser.add_argument('-o', '--output', metavar="output_filename",
- type=argparse.FileType('wb'),
+ type=khFileType('wb'),
help='only output a single file with '
'the specified filename; use a single dash "-" to '
'specify that output should go to STDOUT (the '
@@ -130,250 +127,360 @@ def get_parser():
parser.add_argument('-s', '--savegraph', metavar="filename", default='',
help='save the k-mer countgraph to disk after all'
'reads are loaded.')
+ parser.add_argument('-q', '--quiet', dest='quiet', default=False,
+ action='store_true')
# expert options
parser.add_argument('--force', default=False, action='store_true')
parser.add_argument('--ignore-pairs', default=False, action='store_true')
- parser.add_argument('--tempdir', '-T', type=str, default='./')
+ parser.add_argument('--tempdir', '-T', type=str, default='./',
+ help="Set location of temporary directory for "
+ "second pass")
add_output_compression_type(parser)
+ parser.add_argument('--diginorm', default=False, action='store_true',
+ help="Eliminate high-coverage reads altogether "
+ "(digital normalization).")
+ parser.add_argument('--diginorm-coverage', type=int,
+ default=DEFAULT_DIGINORM_COVERAGE,
+ help="Coverage threshold for --diginorm")
+ parser.add_argument('--single-pass', default=False, action='store_true',
+ help="Do not do a second pass across the low coverage "
+ "data")
+
return parser
+class Trimmer(object):
+ """
+ Core trimming object.
+
+ The two utility functions are 'pass1' and 'pass2',
+ which execute the first and second pass across the data, respectively.
+ """
+
+ def __init__(self, graph, do_trim_low_abund, cutoff, trim_at_coverage):
+ self.graph = graph
+ self.do_trim_low_abund = do_trim_low_abund
+ self.cutoff = cutoff
+ self.trim_at_coverage = trim_at_coverage
+
+ self.n_reads = 0
+ self.n_bp = 0
+ self.trimmed_reads = 0
+ self.n_saved = 0
+ self.n_skipped = 0
+ self.bp_skipped = 0
+
+ self.do_normalize = False
+ self.diginorm_coverage = None
+
+ def set_diginorm(self, coverage):
+ self.do_normalize = True
+ self.diginorm_coverage = coverage
+
+ def pass1(self, reader, saver):
+ """
+ The first pass across the read data.
+
+ It does the following:
+
+ 1. If do_normalize is set, discard all read pairs with coverage
+ above DIGINORM_COVERAGE.
+
+ 2. For each remaining read pair, check if the read pair is above
+ the coverage necessary for trimming (TRIM_AT_COVERAGE). If so,
+ k-mer trim the reads at CUTOFF, and yield them.
+
+ 3. If the read pair is not at the coverage necessary for trimming,
+ consume the read pair with the graph and save the read pair for the
+ second pass.
+ """
+ graph = self.graph
+ TRIM_AT_COVERAGE = self.trim_at_coverage
+ CUTOFF = self.cutoff
+ DIGINORM_COVERAGE = self.diginorm_coverage
+
+ for n, is_pair, read1, read2 in reader:
+ bundle = ReadBundle(read1, read2)
+
+ # clean up the sequences for examination.
+ self.n_reads += bundle.num_reads
+ self.n_bp += bundle.total_length
+
+ min_coverage = min(bundle.coverages(graph))
+
+ if self.do_normalize and min_coverage >= DIGINORM_COVERAGE:
+ # skip reads if normalizing
+ continue
+
+ # trim?
+ if min_coverage >= TRIM_AT_COVERAGE:
+ for read in bundle.reads:
+ record, did_trim = trim_record(graph, read, CUTOFF)
+ if did_trim:
+ self.trimmed_reads += 1
+ if record:
+ yield record
+ # no, too low coverage to trim; consume & set aside for 2nd pass.
+ else:
+ for read in bundle.reads:
+ graph.consume(read.cleaned_seq)
+ write_record(read, saver)
+ self.n_saved += 1
+
+ def pass2(self, reader):
+ """
+ The second pass across the data does the following.
+
+ 1. For each read, evaluate the coverage. If the coverage is
+ sufficient to trim, OR we are trimming low-abundance reads (-V not
+ set), do trimming.
+
+ 2. Otherwise, return the untrimmed read pair.
+ """
+ graph = self.graph
+ TRIM_AT_COVERAGE = self.trim_at_coverage
+ CUTOFF = self.cutoff
+
+ for n, is_pair, read1, read2 in reader:
+ bundle = ReadBundle(read1, read2)
+
+ # clean up the sequences for examination.
+ self.n_reads += bundle.num_reads
+ self.n_bp += bundle.total_length
+
+ if self.do_trim_low_abund or \
+ bundle.coverages_at_least(graph, TRIM_AT_COVERAGE):
+
+ for read in bundle.reads:
+ trimmed_record, did_trim = trim_record(graph, read, CUTOFF)
+
+ if did_trim:
+ self.trimmed_reads += 1
+ if trimmed_record:
+ yield trimmed_record
+ else:
+ for read in bundle.reads:
+ self.n_skipped += 1
+ self.bp_skipped += 1
+ yield read
+
+
def main():
- info('trim-low-abund.py', ['streaming'])
parser = sanitize_help(get_parser())
args = parser.parse_args()
+ configure_logging(args.quiet)
+
###
if len(set(args.input_filenames)) != len(args.input_filenames):
- print("Error: Cannot input the same filename multiple times.",
- file=sys.stderr)
+ log_error("Error: Cannot input the same filename multiple times.")
+ sys.exit(1)
+
+ if args.trim_at_coverage != DEFAULT_TRIM_AT_COVERAGE and \
+ not args.variable_coverage:
+ log_error("Error: --trim-at-coverage/-Z given, but "
+ "--variable-coverage/-V not specified.")
+ sys.exit(1)
+
+ if args.diginorm_coverage != DEFAULT_DIGINORM_COVERAGE and \
+ not args.diginorm:
+ log_error("Error: --diginorm-coverage given, but "
+ "--diginorm not specified.")
+ sys.exit(1)
+
+ if args.diginorm and args.single_pass:
+ log_error("Error: --diginorm and --single-pass are incompatible!\n"
+ "You probably want to use normalize-by-median.py instead.")
sys.exit(1)
###
- report_on_config(args)
+ graphtype = 'countgraph' if not args.small_count else 'smallcountgraph'
+ report_on_config(args, graphtype=graphtype)
check_valid_file_exists(args.input_filenames)
check_space(args.input_filenames, args.force)
if args.savegraph:
- graphsize = calculate_graphsize(args, 'countgraph')
+ graphsize = calculate_graphsize(args, graphtype)
check_space_for_graph(args.savegraph, graphsize, args.force)
if ('-' in args.input_filenames or '/dev/stdin' in args.input_filenames) \
and not args.output:
- print("Accepting input from stdin; output filename must "
- "be provided with -o.", file=sys.stderr)
+ log_error("Accepting input from stdin; output filename must "
+ "be provided with -o.")
sys.exit(1)
if args.loadgraph:
- print('loading countgraph from', args.loadgraph, file=sys.stderr)
- ct = khmer.load_countgraph(args.loadgraph)
+ log_info('loading countgraph from {graph}', graph=args.loadgraph)
+ ct = khmer.load_countgraph(args.loadgraph, args.small_count)
else:
- print('making countgraph', file=sys.stderr)
+ log_info('making countgraph')
ct = khmer_args.create_countgraph(args)
K = ct.ksize()
- CUTOFF = args.cutoff
- NORMALIZE_LIMIT = args.normalize_to
-
tempdir = tempfile.mkdtemp('khmer', 'tmp', args.tempdir)
- print('created temporary directory %s; '
- 'use -T to change location' % tempdir, file=sys.stderr)
+ log_info('created temporary directory {temp};\n'
+ 'use -T to change location', temp=tempdir)
+
+ trimmer = Trimmer(ct, not args.variable_coverage, args.cutoff,
+ args.trim_at_coverage)
+ if args.diginorm:
+ trimmer.set_diginorm(args.diginorm_coverage)
# ### FIRST PASS ###
save_pass2_total = 0
- n_bp = 0
- n_reads = 0
written_bp = 0
written_reads = 0
- trimmed_reads = 0
+
+ # only create the file writer once if outfp is specified; otherwise,
+ # create it for each file.
+ if args.output:
+ trimfp = get_file_writer(args.output, args.gzip, args.bzip)
pass2list = []
for filename in args.input_filenames:
+ # figure out temporary filename for 2nd pass
pass2filename = os.path.basename(filename) + '.pass2'
pass2filename = os.path.join(tempdir, pass2filename)
- if args.output is None:
- trimfp = get_file_writer(open(os.path.basename(filename) +
- '.abundtrim', 'wb'),
- args.gzip, args.bzip)
- else:
- trimfp = get_file_writer(args.output, args.gzip, args.bzip)
-
- pass2list.append((filename, pass2filename, trimfp))
-
- screed_iter = screed.open(filename)
pass2fp = open(pass2filename, 'w')
- save_pass2 = 0
- n = 0
+ # construct output filenames
+ if args.output is None:
+ # note: this will be saved in trimfp.
+ outfp = open(os.path.basename(filename) + '.abundtrim', 'wb')
- paired_iter = broken_paired_reader(screed_iter, min_length=K,
- force_single=args.ignore_pairs)
- for n, is_pair, read1, read2 in paired_iter:
- if n % 10000 == 0:
- print('...', n, filename, save_pass2, n_reads, n_bp,
- written_reads, written_bp, file=sys.stderr)
-
- # we want to track paired reads here, to make sure that pairs
- # are not split between first pass and second pass.
-
- if is_pair:
- n_reads += 2
- n_bp += len(read1.sequence) + len(read2.sequence)
-
- seq1 = read1.sequence.replace('N', 'A')
- seq2 = read2.sequence.replace('N', 'A')
-
- med1, _, _ = ct.get_median_count(seq1)
- med2, _, _ = ct.get_median_count(seq2)
-
- if med1 < NORMALIZE_LIMIT or med2 < NORMALIZE_LIMIT:
- ct.consume(seq1)
- ct.consume(seq2)
- write_record_pair(read1, read2, pass2fp)
- save_pass2 += 2
- else:
- _, trim_at1 = ct.trim_on_abundance(seq1, CUTOFF)
- _, trim_at2 = ct.trim_on_abundance(seq2, CUTOFF)
-
- if trim_at1 >= K:
- read1 = trim_record(read1, trim_at1)
-
- if trim_at2 >= K:
- read2 = trim_record(read2, trim_at2)
-
- if trim_at1 != len(seq1):
- trimmed_reads += 1
- if trim_at2 != len(seq2):
- trimmed_reads += 1
-
- write_record_pair(read1, read2, trimfp)
- written_reads += 2
- written_bp += trim_at1 + trim_at2
- else:
- n_reads += 1
- n_bp += len(read1.sequence)
+ # get file handle w/gzip, bzip
+ trimfp = get_file_writer(outfp, args.gzip, args.bzip)
- seq = read1.sequence.replace('N', 'A')
+ # record all this info
+ pass2list.append((filename, pass2filename, trimfp))
- med, _, _ = ct.get_median_count(seq)
+ # input file stuff: get a broken_paired reader.
+ paired_iter = broken_paired_reader(ReadParser(filename), min_length=K,
+ force_single=args.ignore_pairs)
- # has this portion of the graph saturated? if not,
- # consume & save => pass2.
- if med < NORMALIZE_LIMIT:
- ct.consume(seq)
- write_record(read1, pass2fp)
- save_pass2 += 1
- else: # trim!!
- _, trim_at = ct.trim_on_abundance(seq, CUTOFF)
- if trim_at >= K:
- new_read = trim_record(read1, trim_at)
- write_record(new_read, trimfp)
+ # main loop through the file.
+ n_start = trimmer.n_reads
+ save_start = trimmer.n_saved
+
+ watermark = REPORT_EVERY_N_READS
+ for read in trimmer.pass1(paired_iter, pass2fp):
+ if (trimmer.n_reads - n_start) > watermark:
+ log_info("... {filename} {n_saved} {n_reads} {n_bp} "
+ "{w_reads} {w_bp}", filename=filename,
+ n_saved=trimmer.n_saved, n_reads=trimmer.n_reads,
+ n_bp=trimmer.n_bp, w_reads=written_reads,
+ w_bp=written_bp)
+ watermark += REPORT_EVERY_N_READS
+
+ # write out the trimmed/etc sequences that AREN'T going to be
+ # revisited in a 2nd pass.
+ write_record(read, trimfp)
+ written_bp += len(read)
+ written_reads += 1
+ pass2fp.close()
- written_reads += 1
- written_bp += trim_at
+ log_info("{filename}: kept aside {kept} of {total} from first pass",
+ filename=filename, kept=trimmer.n_saved - save_start,
+ total=trimmer.n_reads - n_start)
- if trim_at != len(read1.sequence):
- trimmed_reads += 1
+ # first pass goes across all the data, so record relevant stats...
+ n_reads = trimmer.n_reads
+ n_bp = trimmer.n_bp
+ n_skipped = trimmer.n_skipped
+ bp_skipped = trimmer.bp_skipped
+ save_pass2_total = trimmer.n_saved
- pass2fp.close()
+ # ### SECOND PASS. ###
- print('%s: kept aside %d of %d from first pass, in %s' %
- (filename, save_pass2, n, filename),
- file=sys.stderr)
- save_pass2_total += save_pass2
+ # nothing should have been skipped yet!
+ assert trimmer.n_skipped == 0
+ assert trimmer.bp_skipped == 0
- # ### SECOND PASS. ###
+ if args.single_pass:
+ pass2list = []
- skipped_n = 0
- skipped_bp = 0
+ # go back through all the files again.
for _, pass2filename, trimfp in pass2list:
- print('second pass: looking at sequences kept aside in %s' %
- pass2filename,
- file=sys.stderr)
+ log_info('second pass: looking at sequences kept aside in {pass2}',
+ pass2=pass2filename)
# note that for this second pass, we don't care about paired
# reads - they will be output in the same order they're read in,
# so pairs will stay together if not orphaned. This is in contrast
- # to the first loop.
-
- for n, read in enumerate(screed.open(pass2filename)):
- if n % 10000 == 0:
- print('... x 2', n, pass2filename,
- written_reads, written_bp, file=sys.stderr)
-
- seq = read.sequence.replace('N', 'A')
- med, _, _ = ct.get_median_count(seq)
-
- # do we retain low-abundance components unchanged?
- if med < NORMALIZE_LIMIT and args.variable_coverage:
- write_record(read, trimfp)
-
- written_reads += 1
- written_bp += len(read.sequence)
- skipped_n += 1
- skipped_bp += len(read.sequence)
-
- # otherwise, examine/trim/truncate.
- else: # med >= NORMALIZE LIMIT or not args.variable_coverage
- _, trim_at = ct.trim_on_abundance(seq, CUTOFF)
- if trim_at >= K:
- new_read = trim_record(read, trim_at)
- write_record(new_read, trimfp)
-
- written_reads += 1
- written_bp += trim_at
+ # to the first loop. Hence, force_single=True below.
+
+ read_parser = ReadParser(pass2filename)
+ paired_iter = broken_paired_reader(read_parser,
+ min_length=K,
+ force_single=True)
+
+ watermark = REPORT_EVERY_N_READS
+ for read in trimmer.pass2(paired_iter):
+ if (trimmer.n_reads - n_start) > watermark:
+ log_info('... x 2 {a} {b} {c} {d} {e} {f} {g}',
+ a=trimmer.n_reads - n_start,
+ b=pass2filename, c=trimmer.n_saved,
+ d=trimmer.n_reads, e=trimmer.n_bp,
+ f=written_reads, g=written_bp)
+ watermark += REPORT_EVERY_N_READS
+
+ write_record(read, trimfp)
+ written_reads += 1
+ written_bp += len(read)
+
+ read_parser.close()
+
+ log_info('removing {pass2}', pass2=pass2filename)
+ os.unlink(pass2filename)
- if trim_at != len(read.sequence):
- trimmed_reads += 1
+ # if we created our own trimfps, close 'em.
+ if not args.output:
+ trimfp.close()
- print('removing %s' % pass2filename, file=sys.stderr)
- os.unlink(pass2filename)
+ try:
+ log_info('removing temp directory & contents ({temp})', temp=tempdir)
+ shutil.rmtree(tempdir)
+ except OSError as oe:
+ log_info('WARNING: unable to remove {temp} (probably an NFS issue); '
+ 'please remove manually', temp=tempdir)
- print('removing temp directory & contents (%s)' % tempdir, file=sys.stderr)
- shutil.rmtree(tempdir)
+ trimmed_reads = trimmer.trimmed_reads
n_passes = 1.0 + (float(save_pass2_total) / n_reads)
percent_reads_trimmed = float(trimmed_reads + (n_reads - written_reads)) /\
n_reads * 100.0
- print('read %d reads, %d bp' % (n_reads, n_bp,), file=sys.stderr)
- print('wrote %d reads, %d bp' % (written_reads, written_bp,),
- file=sys.stderr)
- print('looked at %d reads twice (%.2f passes)' % (save_pass2_total,
- n_passes),
- file=sys.stderr)
- print('removed %d reads and trimmed %d reads (%.2f%%)' %
- (n_reads - written_reads, trimmed_reads, percent_reads_trimmed),
- file=sys.stderr)
- print('trimmed or removed %.2f%% of bases (%d total)' %
- ((1 - (written_bp / float(n_bp))) * 100.0, n_bp - written_bp),
- file=sys.stderr)
+ log_info('read {read} reads, {bp} bp', read=n_reads, bp=n_bp)
+ log_info('wrote {wr} reads, {wbp} bp', wr=written_reads, wbp=written_bp)
+ log_info('looked at {st} reads twice ({np:.2f} passes)',
+ st=save_pass2_total, np=n_passes)
+ log_info('removed {r} reads and trimmed {t} reads ({p:.2f}%)',
+ r=n_reads - written_reads, t=trimmed_reads,
+ p=percent_reads_trimmed)
+ log_info('trimmed or removed {p:.2f}%% of bases ({bp} total)',
+ p=(1 - (written_bp / float(n_bp))) * 100.0, bp=n_bp - written_bp)
if args.variable_coverage:
- percent_reads_hicov = 100.0 * float(n_reads - skipped_n) / n_reads
- print('%d reads were high coverage (%.2f%%);' % (n_reads - skipped_n,
- percent_reads_hicov),
- file=sys.stderr)
- print('skipped %d reads/%d bases because of low coverage' %
- (skipped_n, skipped_bp),
- file=sys.stderr)
+ percent_reads_hicov = 100.0 * float(n_reads - n_skipped) / n_reads
+ log_info('{n} reads were high coverage ({p:.2f}%);',
+ n=n_reads - n_skipped, p=percent_reads_hicov)
+ log_info('skipped {r} reads/{bp} bases because of low coverage',
+ r=n_skipped, bp=bp_skipped)
fp_rate = \
khmer.calc_expected_collisions(ct, args.force, max_false_pos=.8)
# for max_false_pos see Zhang et al., http://arxiv.org/abs/1309.2975
- print('fp rate estimated to be {fpr:1.3f}'.format(fpr=fp_rate),
- file=sys.stderr)
+ log_info('fp rate estimated to be {fpr:1.3f}', fpr=fp_rate)
- print('output in *.abundtrim', file=sys.stderr)
+ log_info('output in *.abundtrim')
if args.savegraph:
- print("Saving k-mer countgraph to",
- args.savegraph, file=sys.stderr)
+ log_info("Saving k-mer countgraph to {graph}", graph=args.savegraph)
ct.save(args.savegraph)
diff --git a/scripts/unique-kmers.py b/scripts/unique-kmers.py
index f72b22a..a41a4e4 100755
--- a/scripts/unique-kmers.py
+++ b/scripts/unique-kmers.py
@@ -44,19 +44,14 @@ Use '-h' for parameter help.
"""
from __future__ import print_function
-
import argparse
import os
import sys
import textwrap
import khmer
-from khmer.khmer_args import (DEFAULT_K, info, ComboFormatter,
- _VersionStdErrAction, sanitize_help)
-from khmer.utils import write_record
+from khmer.khmer_args import DEFAULT_K, sanitize_help, KhmerArgumentParser
from khmer.khmer_args import graphsize_args_report
-from khmer import __version__
-import screed
def get_parser():
@@ -98,15 +93,12 @@ def get_parser():
unique-kmers.py -R unique_count -k 30 \\
tests/test-data/test-abund-read-paired.fa""" # noqa
- parser = argparse.ArgumentParser(
+ parser = KhmerArgumentParser(
description=descr, epilog=textwrap.dedent(epilog),
- formatter_class=ComboFormatter)
+ citations=['SeqAn', 'hll'])
env_ksize = os.environ.get('KHMER_KSIZE', DEFAULT_K)
- parser.add_argument('--version', action=_VersionStdErrAction,
- version='khmer {v}'.format(v=__version__))
-
parser.add_argument('-q', '--quiet', dest='quiet', default=False,
action='store_true')
@@ -136,22 +128,20 @@ def get_parser():
def main():
- info('unique-kmers.py', ['SeqAn', 'hll'])
args = sanitize_help(get_parser()).parse_args()
total_hll = khmer.HLLCounter(args.error_rate, args.ksize)
report_fp = args.report
input_filename = None
- for index, input_filename in enumerate(args.input_filenames):
+ for _, input_filename in enumerate(args.input_filenames):
hllcpp = khmer.HLLCounter(args.error_rate, args.ksize)
- hllcpp.consume_fasta(input_filename,
- stream_records=args.stream_records)
+ hllcpp.consume_seqfile(input_filename,
+ stream_records=args.stream_records)
cardinality = hllcpp.estimate_cardinality()
print('Estimated number of unique {0}-mers in {1}: {2}'.format(
- args.ksize, input_filename, cardinality),
- file=sys.stderr)
+ args.ksize, input_filename, cardinality), file=sys.stderr)
if report_fp:
print(cardinality, args.ksize, '(total)', file=report_fp)
@@ -160,8 +150,7 @@ def main():
cardinality = total_hll.estimate_cardinality()
print('Total estimated number of unique {0}-mers: {1}'.format(
- args.ksize, cardinality),
- file=sys.stderr)
+ args.ksize, cardinality), file=sys.stderr)
to_print = graphsize_args_report(cardinality, args.error_rate)
if args.diagnostics:
diff --git a/setup.cfg b/setup.cfg
index a04f6d1..2293a7d 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,9 +1,3 @@
-[nosetests]
-verbosity = 2
-stop = FALSE
-attr = !known_failing,!jenkins,!huge
-#processes = -1 # breaks xunit output
-
[build_ext]
define = SEQAN_HAS_BZIP2,SEQAN_HAS_ZLIB
undef = NO_UNIQUE_RC
@@ -20,3 +14,21 @@ include-dirs = lib:third-party/zlib:third-party/bzip2:third-party/seqan/core/inc
[easy_install]
+[aliases]
+test=pytest
+
+# See the docstring in versioneer.py for instructions. Note that you must
+# re-run 'versioneer.py setup' after changing this section, and commit the
+# resulting files.
+
+[versioneer]
+VCS = git
+style = pep440
+versionfile_source = khmer/_version.py
+versionfile_build = khmer/_version.py
+tag_prefix = v
+parentdir_prefix = .
+
+[pep8]
+exclude = _version.py
+ignore = E309,E226
diff --git a/setup.py b/setup.py
index 14999e5..05f181e 100755
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
# vim: set fileencoding=utf-8
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2013-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -57,11 +57,6 @@ from distutils.errors import DistutilsPlatformError
import versioneer
ez_setup.use_setuptools(version="3.4.1")
-versioneer.VCS = 'git'
-versioneer.versionfile_source = 'khmer/_version.py'
-versioneer.versionfile_build = 'khmer/_version.py'
-versioneer.tag_prefix = 'v' # tags are like v1.2.0
-versioneer.parentdir_prefix = '.'
CMDCLASS = versioneer.get_cmdclass()
# strip out -Wstrict-prototypes; a hack suggested by
@@ -99,8 +94,8 @@ def check_for_openmp():
# Attempt to compile a test script.
# See http://openmp.org/wp/openmp-compilers/
filename = r'test.c'
- file = open(filename, 'wt', 1)
- file.write(
+ source = open(filename, 'wt', 1)
+ source.write(
"""
#include <omp.h>
#include <stdio.h>
@@ -116,7 +111,7 @@ def check_for_openmp():
stdout=fnull, stderr=fnull)
# Clean up
- file.close()
+ source.close()
finally:
os.chdir(curdir)
shutil.rmtree(tmpdir)
@@ -132,15 +127,19 @@ BZIP2DIR = 'third-party/bzip2'
BUILD_DEPENDS = []
BUILD_DEPENDS.extend(path_join("lib", bn + ".hh") for bn in [
- "khmer", "kmer_hash", "hashtable", "counting", "hashbits", "labelhash",
+ "khmer", "kmer_hash", "hashtable", "labelhash", "hashgraph",
"hllcounter", "khmer_exception", "read_aligner", "subset", "read_parsers",
- "traversal"])
+ "kmer_filters", "traversal", "assembler", "alphabets", "storage"])
+BUILD_DEPENDS.extend(path_join("khmer", bn + ".hh") for bn in [
+ "_cpy_counttable", "_cpy_hashgraph", "_cpy_nodetable",
+ "_cpy_smallcounttable", "_cpy_smallcountgraph"])
SOURCES = ["khmer/_khmer.cc"]
SOURCES.extend(path_join("lib", bn + ".cc") for bn in [
- "read_parsers", "kmer_hash", "hashtable",
- "hashbits", "labelhash", "counting", "subset", "read_aligner",
- "hllcounter", "traversal"])
+ "read_parsers", "kmer_hash", "hashtable", "hashgraph",
+ "labelhash", "subset", "read_aligner",
+ "hllcounter", "traversal", "kmer_filters", "assembler", "alphabets",
+ "storage"])
SOURCES.extend(path_join("third-party", "smhasher", bn + ".cc") for bn in [
"MurmurHash3"])
@@ -168,8 +167,7 @@ EXTENSION_MOD_DICT = \
"define_macros": [("VERSION", versioneer.get_version()), ],
}
-EXTENSION_MOD = Extension("khmer._khmer", # pylint: disable=W0142
- ** EXTENSION_MOD_DICT)
+EXTENSION_MOD = Extension("khmer._khmer", ** EXTENSION_MOD_DICT)
SCRIPTS = []
SCRIPTS.extend([path_join("scripts", script)
for script in os_listdir("scripts")
@@ -225,13 +223,15 @@ SETUP_METADATA = \
# "maintainer_email": 'mcrusoe at msu.edu', # so don't include it
# http://docs.python.org/2/distutils/setupscript.html
# additional-meta-data note #3
- "url": 'https://khmer.readthedocs.org/',
+ "url": 'https://khmer.readthedocs.io/',
"packages": ['khmer', 'khmer.tests', 'oxli'],
"package_dir": {'khmer.tests': 'tests'},
"install_requires": ['screed >= 0.9', 'bz2file'],
+ "setup_requires": ["pytest-runner>=2.0,<3dev"],
"extras_require": {':python_version=="2.6"': ['argparse>=1.2.1'],
'docs': ['sphinx', 'sphinxcontrib-autoprogram'],
- 'tests': ['nose >= 1.0']},
+ 'tests': ['pytest>=2.9'],
+ 'read_aligner_training': ['simplesam']},
"scripts": SCRIPTS,
# "entry_points": { # Not ready for distribution yet.
# 'console_scripts': [
@@ -248,7 +248,6 @@ SETUP_METADATA = \
class KhmerBuildExt(_build_ext): # pylint: disable=R0904
-
"""Specialized Python extension builder for khmer project.
Only run the library setup when needed, not on every invocation.
@@ -263,6 +262,9 @@ class KhmerBuildExt(_build_ext): # pylint: disable=R0904
raise DistutilsPlatformError("%s require 64-bit operating system" %
SETUP_METADATA["packages"])
+ if sys.platform == 'darwin' and 'gcov' in self.libraries:
+ self.libraries.remove('gcov')
+
if "z" not in self.libraries:
zcmd = ['bash', '-c', 'cd ' + ZLIBDIR + ' && ( test Makefile -nt'
' configure || bash ./configure --static ) && make -f '
@@ -292,7 +294,7 @@ def reinitialize_command(self, command, reinit_subcommands):
"""Monkeypatch the original version from distutils.
It's supposed to match the behavior of Distribution.get_command_obj()
- This fixes issues with 'pip install -e' and './setup.py nosetests' not
+ This fixes issues with 'pip install -e' and './setup.py test' not
respecting the setup.cfg configuration directives for the build_ext
command.
"""
@@ -305,6 +307,4 @@ def reinitialize_command(self, command, reinit_subcommands):
Distribution.reinitialize_command = reinitialize_command
-# pylint: disable=W0142
-setup(cmdclass=CMDCLASS,
- **SETUP_METADATA)
+setup(cmdclass=CMDCLASS, **SETUP_METADATA)
diff --git a/tests/__init__.py b/tests/__init__.py
index 34ae3f8..d41fee0 100644
--- a/tests/__init__.py
+++ b/tests/__init__.py
@@ -32,3 +32,4 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
+"""Tests for khmer."""
diff --git a/tests/khmer_tst_utils.py b/tests/khmer_tst_utils.py
index 12d3f28..7239ac2 100644
--- a/tests/khmer_tst_utils.py
+++ b/tests/khmer_tst_utils.py
@@ -1,6 +1,7 @@
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2010-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
+# Copyright (C) 2016, Google, Inc
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -32,17 +33,23 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
+# pylint: disable=missing-docstring
+
from __future__ import print_function
import tempfile
import os
import shutil
+import pkg_resources
from pkg_resources import Requirement, resource_filename, ResolutionError
-import nose
import sys
import traceback
import subprocess
-from io import open
+from io import open # pylint: disable=redefined-builtin
+from hashlib import md5
+
+from khmer import reverse_complement as revcomp
+import pytest
try:
from StringIO import StringIO
@@ -50,6 +57,20 @@ except ImportError:
from io import StringIO
+def _equals_rc(query, match):
+ return (query == match) or (revcomp(query) == match)
+
+
+def _contains_rc(match, query):
+ return (query in match) or (revcomp(query) in match)
+
+
+def _calc_md5(fp):
+ m = md5()
+ m.update(fp.read())
+ return m.hexdigest()
+
+
def get_test_data(filename):
filepath = None
try:
@@ -62,28 +83,27 @@ def get_test_data(filename):
filename)
return filepath
-cleanup_list = []
+CLEANUPLIST = []
def get_temp_filename(filename, tempdir=None):
if tempdir is None:
tempdir = tempfile.mkdtemp(prefix='khmertest_')
- cleanup_list.append(tempdir)
+ CLEANUPLIST.append(tempdir)
return os.path.join(tempdir, filename)
def cleanup():
- global cleanup_list
+ global CLEANUPLIST # pylint: disable=global-statement
- for path in cleanup_list:
+ for path in CLEANUPLIST:
shutil.rmtree(path, ignore_errors=True)
- cleanup_list = []
+ CLEANUPLIST = []
def scriptpath(scriptname='interleave-reads.py'):
- "Return the path to the scripts, in both dev and install situations."
-
+ """Return the path to the scripts, in both dev and install situations."""
# note - it doesn't matter what the scriptname is here, as long as
# it's some khmer script present in this version of khmer.
@@ -101,31 +121,30 @@ def scriptpath(scriptname='interleave-reads.py'):
def _runscript(scriptname, sandbox=False):
- """
- Find & run a script with exec (i.e. not via os.system or subprocess).
- """
-
- import pkg_resources
- ns = {"__name__": "__main__"}
- ns['sys'] = globals()['sys']
+ """Find & run a script with exec (i.e. not via os.system or subprocess)."""
+ namespace = {"__name__": "__main__"}
+ namespace['sys'] = globals()['sys']
try:
pkg_resources.get_distribution("khmer").run_script(
- scriptname, ns)
+ scriptname, namespace)
return 0
- except pkg_resources.ResolutionError as err:
- if sandbox:
- path = os.path.join(os.path.dirname(__file__), "../sandbox")
- else:
- path = scriptpath()
+ except pkg_resources.ResolutionError:
+ pass
+
+ if sandbox:
+ path = os.path.join(os.path.dirname(__file__), "../sandbox")
+ else:
+ path = scriptpath()
- scriptfile = os.path.join(path, scriptname)
+ scriptfile = os.path.join(path, scriptname)
+ if os.path.isfile(scriptfile):
if os.path.isfile(scriptfile):
- if os.path.isfile(scriptfile):
- exec(compile(open(scriptfile).read(), scriptfile, 'exec'), ns)
- return 0
- elif sandbox:
- raise nose.SkipTest("sandbox tests are only run in a repository.")
+ exec(compile(open(scriptfile).read(), scriptfile, 'exec'),
+ namespace)
+ return 0
+ elif sandbox:
+ pytest.skip("sandbox tests are only run in a repository.")
return -1
@@ -165,11 +184,9 @@ def runscript(scriptname, args, in_directory=None,
print('arguments', sysargs, file=oldout)
status = _runscript(scriptname, sandbox=sandbox)
- except nose.SkipTest:
- raise
- except SystemExit as e:
- status = e.code
- except:
+ except SystemExit as err:
+ status = err.code
+ except: # pylint: disable=bare-except
traceback.print_exc(file=sys.stderr)
status = -1
finally:
@@ -194,19 +211,19 @@ def run_shell_cmd(cmd, fail_ok=False, in_directory=None):
print('running: ', cmd)
try:
- p = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE,
- stderr=subprocess.PIPE)
- (out, err) = p.communicate()
+ proc = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE)
+ (out, err) = proc.communicate()
out = out.decode('utf-8')
err = err.decode('utf-8')
- if p.returncode != 0 and not fail_ok:
+ if proc.returncode != 0 and not fail_ok:
print('out:', out)
print('err:', err)
- raise AssertionError("exit code is non zero: %d" % p.returncode)
+ raise AssertionError("exit code is non zero: %d" % proc.returncode)
- return (p.returncode, out, err)
+ return (proc.returncode, out, err)
finally:
os.chdir(cwd)
@@ -219,5 +236,14 @@ def longify(listofints):
"""
# For map(long, [list of ints]) cross-version hackery
if sys.version_info.major < 3:
- return map(long, listofints)
+ return map(long, listofints) # pylint: disable=bad-builtin
return listofints
+
+
+def copy_test_data(testfile, newfilename=None):
+ basename = os.path.basename(testfile)
+ if newfilename is not None:
+ basename = newfilename
+ infile = get_temp_filename(basename)
+ shutil.copyfile(get_test_data(testfile), infile)
+ return infile
diff --git a/tests/test-data/README.rst b/tests/test-data/README.rst
new file mode 100644
index 0000000..e193cac
--- /dev/null
+++ b/tests/test-data/README.rst
@@ -0,0 +1,10 @@
+simple-genome-reads.fa
+----------------------
+
+* generated from https://github.com/dib-lab/nullgraph,
+ commit 2146df2017d0dabc22a5a
+
+* commands::
+
+ make-random-genome.py -l 1000 -s 1 > simple-genome.fa
+ make-reads.py -S 1 -e .01 -r 100 -C 100 simple-genome.fa > simple-genome-reads.fa
diff --git a/tests/test-data/paired-mixed-witherror.fa.pe b/tests/test-data/paired-mixed-witherror.fa.pe
new file mode 100644
index 0000000..3b0abc3
--- /dev/null
+++ b/tests/test-data/paired-mixed-witherror.fa.pe
@@ -0,0 +1,12 @@
+>895:1:37:17593:9954/1
+GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG
+>895:1:37:17593:9954/2
+GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG
+>895:1:37:17593:9954/1
+GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG
+>895:1:37:17593:9954/2
+GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG
+>895:1:37:17593:9954/1
+GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG
+>895:1:37:17593:9954/2
+GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGGCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG
diff --git a/tests/test-data/paired.malformat.fq b/tests/test-data/paired.malformat.fq
new file mode 100644
index 0000000..b6df542
--- /dev/null
+++ b/tests/test-data/paired.malformat.fq
@@ -0,0 +1,24 @@
+ at 895:1:37:17593:9954/1
+GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG
++
+##################################################################################################################
+ at 895:1:37:17593:9954/3
+GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG
++
+##################################################################################################################
+ at 895:1:37:17593:9954/1
+GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG
++
+##################################################################################################################
+ at 895:1:37:17593:9954/3
+GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG
++
+##################################################################################################################
+ at 895:1:37:17593:9954/1
+GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG
++
+##################################################################################################################
+ at 895:1:37:17593:9954/3
+GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG
++
+##################################################################################################################
diff --git a/tests/test-data/paired.malformat.fq.2 b/tests/test-data/paired.malformat.fq.2
new file mode 100644
index 0000000..3f7491a
--- /dev/null
+++ b/tests/test-data/paired.malformat.fq.2
@@ -0,0 +1,12 @@
+ at 895:1:37:17593:9954/3
+GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG
++
+##################################################################################################################
+ at 895:1:37:17593:9954/3
+GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG
++
+##################################################################################################################
+ at 895:1:37:17593:9954/3
+GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG
++
+##################################################################################################################
diff --git a/tests/test-data/simple-genome-reads.fa b/tests/test-data/simple-genome-reads.fa
new file mode 100644
index 0000000..4341297
--- /dev/null
+++ b/tests/test-data/simple-genome-reads.fa
@@ -0,0 +1,2000 @@
+>read0f start=121,mutations=2
+ATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTgCGCCTTGCCATACAGACCACCTAAGACCGCAGAtCCTCCTCCTTACCACATGCGA
+>read1f start=485,mutations=1
+GTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAaCTGGAGATCCTC
+>read2f start=309,mutations=0
+GTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTATTG
+>read3r start=272,mutations=1
+AAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTgCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAACGACTTTCCC
+>read4f start=865,mutations=4
+GGCATATGAACACTATTGcGCTTTGTAGACcTTCCTCAcCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCtTGCTAACGTTA
+>read5f start=809,mutations=0
+CATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATG
+>read6f start=868,mutations=0
+ATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTATAT
+>read7r start=30,mutations=0
+GAACTTCATGGATCAGCACCAGCGCGGCACCCAGTTAAGTGTGCACCAATCCATTAAATGACGCTGCGTGTGAATGACCTTCATTGCAGGTTAATCATGG
+>read8r start=804,mutations=1
+ATGAGGAATGTCcACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACCCTGTGAGTAAGCAGAATGTGCTT
+>read9f start=852,mutations=2
+ATcTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAtGGAGAGC
+>read10f start=693,mutations=2
+TTATAAAGGAACTgACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCtAAAA
+>read11r start=506,mutations=1
+TCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGtAACGTCATCTTTCACTTCC
+>read12r start=281,mutations=1
+TCCTAAGTTAAAaACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAAC
+>read13f start=830,mutations=1
+AAGTTCCTGAAGTATTcATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATT
+>read14f start=495,mutations=2
+TATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGaAGATCCTCTCATAGCGaC
+>read15r start=803,mutations=4
+TaAGGAgTGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACgTTACATTAATACTTCAGGAACTTACgCTGTGAGTAAGCAGAATGTGCTTA
+>read16r start=196,mutations=0
+TCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGGTCT
+>read17r start=763,mutations=1
+TCTTTCCACATTACATTAATACTTCAGGAACTTACCtTGTGAGTAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAAAGGTACCAATGAATTTACA
+>read18f start=630,mutations=2
+CCCGGGGACCGGCCCCAACGTGAtATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAAGTTATGTAAGGACTaT
+>read19f start=875,mutations=0
+CACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTATATTCGGTCT
+>read20r start=632,mutations=2
+TAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACTtTCACGAGCACTATAAAGAACGGCAGaCCAGGCATTTCACGTTGGGGCCGGTCCCCG
+>read21r start=816,mutations=0
+GATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACCCTGTGAGTAAG
+>read22r start=550,mutations=1
+CGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGGCGtCATGGTGCTG
+>read23r start=38,mutations=4
+GTCCAGATGAACTaCATGGATCAGCACCAGCGCGGCACCCAGTTAAGTtTGCACtAATCCATTAAATGACGCTGCGTGTGAATGACCTTCATTGCcGGTT
+>read24f start=793,mutations=0
+ATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAG
+>read25f start=506,mutations=1
+GGAAGTGAAAGATGACtTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGA
+>read26f start=60,mutations=1
+CACGCAGCGTCATTTAATGGATTGGTcCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTC
+>read27f start=453,mutations=1
+CGGACAGGCTTgAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAG
+>read28r start=688,mutations=0
+GGCAAAAGGTACCAATGAATTTACACACGTGGACGACTTGACGGACCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACTA
+>read29r start=445,mutations=2
+CCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTAgAAAGGATAaAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTT
+>read30r start=222,mutations=2
+TTTCCCCaTTTACGTAGGAGCTCCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGACACCGcTTCCCACGC
+>read31r start=517,mutations=1
+AATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTGCaGCGGTTCCTCCAACAGCGACGGCCGCAACGTCAT
+>read32f start=893,mutations=5
+ACATTCCTCATCCATtCTGTActAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTgTATTCGaTCTTACCACGGGCTCGATAGT
+>read33f start=767,mutations=0
+AATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGG
+>read34f start=55,mutations=0
+ATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCT
+>read35r start=223,mutations=1
+GTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAACGACTTcCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACG
+>read36f start=509,mutations=2
+AGTaAAAGATGACGTTGCGGCCGTCGCTGTgGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATGC
+>read37r start=579,mutations=1
+CTATAAAGAACGGCAGGCCAGGCATTTCACGTTGGGaCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGAT
+>read38r start=891,mutations=0
+TATCGAGCCCGTGGTAAGACCGAATATAACGTTAGCACGGCTCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCT
+>read39r start=651,mutations=1
+TTGACGGACCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACTATCACGAGCACTATAAAGAACGGCAGGtCAGGCATTTC
+>read40f start=186,mutations=2
+CTAAGACCGCAGACCCTCCTCCTTACCACATGaGATGCGTGGaAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGAAAGTCGTTTG
+>read41f start=692,mutations=3
+GTTATAAAGGAACTcAgATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTgGCCGAAA
+>read42f start=135,mutations=1
+GACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTaCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGG
+>read43r start=679,mutations=0
+TACCAATGAATTTACACACGTGGACGACTTGACGGACCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACTATCACGAGCA
+>read44f start=669,mutations=0
+TTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAA
+>read45f start=894,mutations=2
+CcTTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCtGTGCTAACGTTATATTCGGTCTTACCACGGGCTCGATAGTT
+>read46r start=610,mutations=0
+TGTTAGTTCCTTTATAACACTATCACGAGCACTATAAAGAACGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATAC
+>read47f start=716,mutations=1
+TATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCAaATTCTG
+>read48r start=206,mutations=1
+GGAGCTCCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCaTCCTGTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGG
+>read49f start=127,mutations=1
+TTCATCgGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTG
+>read50r start=15,mutations=0
+GCACCAGCGCGGCACCCAGTTAAGTGTGCACCAATCCATTAAATGACGCTGCGTGTGAATGACCTTCATTGCAGGTTAATCATGGCTCAACCTAGTCACC
+>read51r start=490,mutations=0
+TATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCA
+>read52r start=139,mutations=2
+aACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTTAGGTGcTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACA
+>read53f start=5,mutations=1
+CCCAGCACCGGGTGACTAGGTTGAGCCATGATTAACCTtCAATGAAGGTCATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTGCC
+>read54r start=632,mutations=1
+TAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACTATCACGAGCACTATAAAGAAgGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCG
+>read55f start=721,mutations=1
+AAGGgCTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTAC
+>read56f start=173,mutations=1
+CCAgACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCAG
+>read57r start=884,mutations=0
+CCCGTGGTAAGACCGAATATAACGTTAGCACGGCTCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGC
+>read58f start=90,mutations=1
+ACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCcCCTAA
+>read59f start=519,mutations=1
+GACGTTGCGGCCGTCGCTGTTGGAGGAcCCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAA
+>read60r start=74,mutations=1
+GCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACCAGCGCGGCACCCAGTgAAGTGTGCACCAATCCATTA
+>read61f start=98,mutations=0
+GGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAG
+>read62r start=454,mutations=1
+GCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTTACAAAATCCaAGCTTTGTAGCTTAAGCCTGTCC
+>read63r start=818,mutations=3
+CTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCAaATGCCTGTCTTaCCACATTACATTAATACTTCAGGAACTTACCCTGTGAGgA
+>read64r start=563,mutations=0
+GCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGG
+>read65f start=434,mutations=0
+TCTAACAATCGAAGCAATTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTC
+>read66f start=609,mutations=2
+TGTATATTAAGCACACAAcAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCtGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAAC
+>read67r start=178,mutations=1
+TTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGcGTCTGCGGTCTTAGGTGGTCTG
+>read68r start=385,mutations=1
+AAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGGCtATAAGCGGTGGCAGTTGTTCGG
+>read69f start=737,mutations=0
+GCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCC
+>read70f start=709,mutations=0
+ATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCA
+>read71r start=747,mutations=0
+TAATACTTCAGGAACTTACCCTGTGAGTAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAAAGGTACCAATGAATTTACACACGTGGACGACTTGA
+>read72r start=205,mutations=1
+GAGCTCCACTCTCTTCCGGCAcACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGA
+>read73r start=670,mutations=3
+ATTTACACACGTGaACGACTTGACGGACCACGCaATTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACTATCACGAGCACTAaAAAGA
+>read74r start=519,mutations=0
+TTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTC
+>read75r start=156,mutations=1
+TAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTTAGGTGGaCTGTATGGCAAGGCGGAAATGGAAG
+>read76r start=390,mutations=1
+CTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAcCTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTG
+>read77r start=206,mutations=1
+GGAaCTCCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGG
+>read78f start=325,mutations=1
+CgTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTATTGCCCCGGCAGGCGGTAG
+>read79r start=887,mutations=1
+GAGCCCGTGGTcAGACCGAATATAACGTTAGCACGGCTCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAA
+>read80f start=255,mutations=0
+ACACAGGAAGGCACCCAGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGC
+>read81r start=319,mutations=0
+CCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTT
+>read82f start=765,mutations=2
+TAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACgTTCTGCTTACTCACAGGGcAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACA
+>read83f start=711,mutations=0
+CAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACA
+>read84r start=670,mutations=0
+ATTTACACACGTGGACGACTTGACGGACCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACTATCACGAGCACTATAAAGA
+>read85f start=238,mutations=2
+CAAAGtCGGGTGCCGCTACACAGGAAGGCACCCAGGGAAAGTCGTTTGCCGGAAGAcAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTC
+>read86r start=891,mutations=4
+TATCGAGCCCGTGGTAAGACCGAATATAACcTTAGaACGGCaCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATcCAGCATGGATGAGGAATGTCT
+>read87r start=894,mutations=1
+AACTATCGAGCCCGTGGTAAGACCGAgTATAACGTTAGCACGGCTCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATG
+>read88r start=843,mutations=2
+TACGAAAGGGGCGAATTGTAgATTACTGATAgAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAAT
+>read89r start=696,mutations=2
+AATTTcTCGGCAAtAGGTACCAATGAATTTACACACGTGGACGACTTGACGGACCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTA
+>read90f start=269,mutations=3
+CCAGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGaTTGGATTCCCCgTTGCCGATTCGGCtCTATCAGGATGTA
+>read91f start=251,mutations=0
+CGCTACACAGGAAGGCACCCAGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATT
+>read92r start=351,mutations=0
+TTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAATACATCCTGATAGGGCCG
+>read93r start=569,mutations=1
+CGGCAGGCCAGGCATTTCACGTTGGaGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCG
+>read94r start=387,mutations=2
+ACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAcATCGTGGAAACTACCGCCTGtCGGGGCAATAAGCGGTGGCAGTTGTTC
+>read95r start=487,mutations=3
+GAGAGGATCTCCAGCTCGCACAGGCGCCATGtTGCTGCGGTTCCaCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACtAAGGATAGAGCACTT
+>read96f start=796,mutations=3
+TGAAAGCTAAGCACgTTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAgTGTGGAAAGACAGGCATATGAACACTATTGGGCTTTtTAGACA
+>read97f start=333,mutations=2
+GATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAtCAACTGCCACCGCTTATTGCCCCGGCAGGCGGTcGTTTCCACG
+>read98r start=489,mutations=0
+ATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCAC
+>read99f start=895,mutations=2
+ATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTaCTAACGTTATATTCGGTCTTACCACGGGCTCGATAGaTT
+>read100f start=581,mutations=4
+CCTCTCAcAGCGTCAGcGCACGGGATGCTGTATATTcAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAcTG
+>read101f start=175,mutations=0
+ATACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCAGGG
+>read102f start=435,mutations=2
+CTAACAATCGAAGCAATTCGGACAGGCTTgAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAgGATGACGTTGCGGCCGTCG
+>read103f start=422,mutations=0
+TAGTTTCCACGATCTAACAATCGAAGCAATTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGAC
+>read104r start=142,mutations=0
+TTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGT
+>read105f start=733,mutations=1
+AATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAgATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAG
+>read106f start=870,mutations=0
+ATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTATATTC
+>read107r start=482,mutations=2
+GATCTCCAGCTCcCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCgTACAAAGGATAGAGCACTTACAAA
+>read108r start=151,mutations=0
+GCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCT
+>read109r start=663,mutations=1
+CACGTGGACGACTTGACGGACCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATtACACTATCACGAGCACTATAAAGAACGGCAG
+>read110f start=474,mutations=1
+GCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGgCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGC
+>read111f start=189,mutations=1
+AGACCGCAGACCCTCCTCCaTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGAAAGTCGTTTGCCG
+>read112f start=890,mutations=3
+TAGACcTTCCTCATCCATGCTGTATCAGTAATGTACgATTCGCCCCTTTtGTAAAGGAGAGCCGTGCTAACGTTATATTCGGTCTTACCACGGGCTCGAT
+>read113f start=448,mutations=3
+CAATTCGGACAGGCTTAAaCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATtACGTTGCGGCgGTCGCTGTTGGAGGAAC
+>read114f start=287,mutations=2
+CGGAAGAGAaTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTgGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACC
+>read115f start=738,mutations=0
+CGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCT
+>read116f start=18,mutations=2
+GACTAGGTTGAGCCATGATTAACCTGCAATGAAGGTCATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGgGCCGCGCTGGaGCTGA
+>read117r start=629,mutations=0
+AAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACTATCACGAGCACTATAAAGAACGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGC
+>read118r start=684,mutations=0
+AAAGGTACCAATGAATTTACACACGTGGACGACTTGACGGACCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACTATCAC
+>read119f start=257,mutations=0
+ACAGGAAGGCACCCAGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCC
+>read120r start=668,mutations=2
+TTACACACGTGGACGACTTGACGGACCACGCTATcGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATcACACTATCACGAGCACTATAAAGAAC
+>read121f start=747,mutations=2
+TCAAGTCGTCCACGTGTGgAAATTCtTTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTA
+>read122r start=159,mutations=2
+GTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTgcGGCAAGGCGGAAATGG
+>read123f start=173,mutations=2
+CCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAtCCGGTGTCAAAGACGGaTGCCGCTACACAGGAAGGCACCCAG
+>read124f start=334,mutations=1
+ATTCCCCCTTGCCGATTCaGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTATTGCCCCGGCAGGCGGTAGTTTCCACGA
+>read125r start=375,mutations=0
+CTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAA
+>read126r start=431,mutations=3
+GGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGcGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCCcGTCCGAATcGCTTCGATTGTTAGATCG
+>read127r start=57,mutations=0
+GGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACCAGCGCGGCACCCAGTTAAGTGTGCACCAATCCATTAAATGACGCTGCGTGTGA
+>read128f start=70,mutations=0
+CATTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCC
+>read129r start=736,mutations=1
+GAACTTACCgTGTGAGTAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAAAGGTACCAATGAATTTACACACGTGGACGACTTGACGGACCACGCT
+>read130f start=389,mutations=1
+ACAACTGCCACCGCTTATTGCCCCGGCAGGCGGTAGTTTCCACtATCTAACAATCGAAGCAATTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAA
+>read131r start=470,mutations=1
+GCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACaGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTTACAAAATCCGAGCTTTG
+>read132r start=386,mutations=3
+CAAAATCCGAGCTcTGTAGCTTAAGCCTGTCCGcATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGGaAATAAGCGGTGGCAGTTGTTCG
+>read133r start=416,mutations=3
+TTTCACTTCCgACAAAGGATAGAGCtCTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGtTTCGATTGTTAGATCGTGGAAACTACCGCCT
+>read134r start=158,mutations=0
+TGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGA
+>read135r start=367,mutations=3
+CTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGtCTGCCGGGGCtATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAcATA
+>read136f start=583,mutations=0
+TCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCT
+>read137f start=522,mutations=1
+GTaGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCA
+>read138f start=306,mutations=0
+TACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTA
+>read139f start=77,mutations=0
+TGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCAT
+>read140f start=448,mutations=0
+CAATTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAAC
+>read141r start=75,mutations=0
+GGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACCAGCGCGGCACCCAGTTAAGTGTGCACCAATCCATT
+>read142f start=798,mutations=1
+AAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGtCATATGAACACTATTGGGCTTTGTAGACATT
+>read143r start=572,mutations=1
+GAACGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCaCTGACGCTATGAGAGGATCTCCAGC
+>read144r start=513,mutations=0
+TACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTT
+>read145f start=49,mutations=2
+AAGGTCATTCACACGCAGCGTCgTTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGtTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCG
+>read146r start=12,mutations=0
+CCAGCGCGGCACCCAGTTAAGTGTGCACCAATCCATTAAATGACGCTGCGTGTGAATGACCTTCATTGCAGGTTAATCATGGCTCAACCTAGTCACCCGG
+>read147f start=895,mutations=0
+ATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTATATTCGGTCTTACCACGGGCTCGATAGTTT
+>read148f start=349,mutations=1
+TTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTATTGCCCCGGCAGGCGGTAGcTTCCACGATCTAACAATCGAAGC
+>read149f start=280,mutations=3
+CGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCtCCCTTGCCGATTCGGCCCTgTCAGGATGTATTTAACTTAGG
+>read150r start=610,mutations=1
+TGTTAGTTCCTTTATAAgACTATCACGAGCACTATAAAGAACGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATAC
+>read151f start=823,mutations=0
+ACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATG
+>read152f start=465,mutations=0
+AGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCC
+>read153f start=534,mutations=2
+GCgGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCaTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCG
+>read154f start=854,mutations=2
+GTGGAAAGACAGGCATATGAACACTATTGGGCaTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGgAAAGGAGAGCCG
+>read155r start=396,mutations=1
+AGAGCACTTACAAAATCCGAGCTcTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGG
+>read156f start=84,mutations=3
+GTGCACACTTAACTcGGTGCCGCGCTGGTGCTGATCCATGAAGTTtATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTtCCATACAGACC
+>read157r start=692,mutations=0
+TTTCGGCAAAAGGTACCAATGAATTTACACACGTGGACGACTTGACGGACCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAAC
+>read158f start=285,mutations=2
+GCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCaCCCTTGCgGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAA
+>read159f start=25,mutations=1
+TTGAGCCATGATTAACCTGCAATGAAGGTCATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTtATCCATGA
+>read160f start=283,mutations=0
+TTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGA
+>read161f start=56,mutations=1
+TTCACACGCAGCGTCATTTAATGGATTGaTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTC
+>read162r start=727,mutations=0
+CTGTGAGTAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAAAGGTACCAATGAATTTACACACGTGGACGACTTGACGGACCACGCTATTGTAAAA
+>read163r start=97,mutations=0
+TGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACCAGCGCGGCACCCA
+>read164r start=861,mutations=0
+GTTAGCACGGCTCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTC
+>read165r start=853,mutations=0
+GGCTCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACA
+>read166f start=324,mutations=1
+ACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGtAGAAACCGAACAACTGCCACCGCTTATTGCCCCGGCAGGCGGTA
+>read167f start=300,mutations=1
+AGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCaTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCAC
+>read168r start=414,mutations=3
+TCACTTtCTACAAAGGATAGAGCACTTACAAAAgCCGAGCTTTGTAGCTTAAGCCaGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGC
+>read169r start=452,mutations=3
+TGCGtTTCCTCCAACAGCGAtGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTaACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGA
+>read170r start=86,mutations=0
+GTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACCAGCGCGGCACCCAGTTAAGTGTGC
+>read171r start=213,mutations=1
+TTACGTAGGAGtTCCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGT
+>read172r start=281,mutations=3
+TCgTAAGTTAAtTACATCCTGATAGGGCCGAtTCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAAC
+>read173r start=222,mutations=1
+TTTCCCCGTTTACGaAGGAGCTCCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGC
+>read174r start=895,mutations=1
+AAACTATCGAGCCCGTGGTAAGACCGAATATAACGTTAGCACGGCTCTCCTTTACGAAAGaGGCGAATTGTACATTACTGATACAGCATGGATGAGGAAT
+>read175r start=897,mutations=0
+GCAAACTATCGAGCCCGTGGTAAGACCGAATATAACGTTAGCACGGCTCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGA
+>read176f start=455,mutations=3
+GACAGGCTcAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTAcCCTTTGTAGGAAGTGAtAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCA
+>read177f start=314,mutations=1
+CGGGGAAACCACTTGTTTGGATTCCCCCaTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTATTGCCCCG
+>read178f start=498,mutations=0
+CCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGA
+>read179r start=601,mutations=3
+CTTTATAACgCTATCACGAGCACTATAAAGAACGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTcTTGTGTGCTTAATATACAGCATCCCt
+>read180r start=237,mutations=1
+AATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGtTCCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGA
+>read181f start=717,mutations=2
+ATGTAAaGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCcGC
+>read182f start=538,mutations=0
+TTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGA
+>read183f start=669,mutations=1
+TTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAAGgTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAA
+>read184r start=488,mutations=2
+TGAGAGGATCTCCAGCTCGCACAGGCGCCATGGgGCTGCcGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACT
+>read185f start=98,mutations=1
+GGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCgCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAG
+>read186f start=463,mutations=2
+TAAcCTACAAAGCgCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCG
+>read187r start=573,mutations=1
+AGAACGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATaTCCAG
+>read188r start=359,mutations=2
+TGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCcGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAtTACATCCTGA
+>read189r start=824,mutations=0
+ACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACCCTG
+>read190f start=188,mutations=1
+AAGACCGCAGACCCTCCTCCTgACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGAAAGTCGTTTGCC
+>read191f start=136,mutations=2
+ACTTGTACGTGCGACAGCTCCTTCCATTaCCGCCTTGtCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGGT
+>read192r start=205,mutations=5
+GAGCTCCgCTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTgCTGTGTAGCGGCACCCGTCTgTGgCACCGGTTCCCACaCATCGCATGTGGTAAGGA
+>read193r start=607,mutations=2
+TAGTTCCTTTATAACACTATCACGAGCACTAgAAAGAACGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCcTAATATACAGC
+>read194f start=59,mutations=1
+ACACGCAGCGTCATTTAATGGATTGGcGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTT
+>read195r start=613,mutations=0
+TGATGTTAGTTCCTTTATAACACTATCACGAGCACTATAAAGAACGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATA
+>read196r start=835,mutations=1
+GGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTgTCCACATTACATTAATACTTCAGG
+>read197f start=259,mutations=0
+AGGAAGGCACCCAGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTA
+>read198r start=272,mutations=0
+AAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAACGACTTTCCC
+>read199r start=211,mutations=1
+ACGTAGGAGCTCCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCCTaTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGG
+>read200r start=373,mutations=2
+TTGTAGCTTAAGCCTGTCCGAATTGCTTCGAcTGTTAGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGgTGTTCGGTTTCTCCTAAGT
+>read201f start=731,mutations=1
+ACAATAGCGTGGTCCGTCAAGTCGTCgACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTA
+>read202f start=326,mutations=1
+TTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTcCCACCGCTTATTGCCCCGGCAGGCGGTAGT
+>read203r start=798,mutations=1
+AATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTcTCCACATTACATTAATACTTCAGGAACTTACCCTGTGAGTAAGCAGAATGTGCTTAGCTTT
+>read204r start=453,mutations=0
+CTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCG
+>read205r start=862,mutations=2
+CGTTAGCACGGCTgTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCtCAATAGTGTTCATATGCCTGT
+>read206f start=30,mutations=3
+CCATGATTAACCTGCAATGAAGGTCATaCACACGCAGCtTCATcTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTC
+>read207r start=698,mutations=2
+CAAATTTTTCGGCAAAAGGTACCAATGAATTTACACACGTGGACGACTTcACGGACCACGCTATTGTAAAAGTCCTTAtATAACTTGATGTTAGTTCCTT
+>read208f start=240,mutations=1
+AAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACtACTTGTTTGGATTCCC
+>read209f start=13,mutations=2
+CGGGTGACTAGGTTGAGCCATGATcAACCTGCAATGAAGGTCAgTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGT
+>read210r start=163,mutations=2
+TCCTGgGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGGTgTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAA
+>read211r start=348,mutations=3
+CTTCGATTGTTAGtTCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAAcACATCCTGATgGGGCCGAAT
+>read212f start=458,mutations=2
+tGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAAtCGCAGCACCA
+>read213r start=775,mutations=0
+TTCATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACCCTGTGAGTAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAAAGGTACC
+>read214f start=747,mutations=0
+TCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTA
+>read215r start=548,mutations=2
+TTGGGGCCGGTCCCCGaGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAcAGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCG
+>read216f start=135,mutations=3
+GACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATAtAGACCACCTAAGACCGaAGACCCTCCTCCTTACCACATGCGATGCGTGcGAACCGG
+>read217f start=593,mutations=1
+TCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTgGTGATAGTG
+>read218r start=123,mutations=0
+CATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTC
+>read219r start=687,mutations=0
+GCAAAAGGTACCAATGAATTTACACACGTGGACGACTTGACGGACCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACTAT
+>read220f start=659,mutations=1
+TGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAAGTTATGTAAGGACTTTTACAATAGCGcGGTCCGTCAAGTCGTCCA
+>read221r start=89,mutations=0
+TAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACCAGCGCGGCACCCAGTTAAGTG
+>read222r start=826,mutations=1
+GTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGaCTTTCCACATTACATTAATACTTCAGGAACTTACCC
+>read223f start=796,mutations=2
+TGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATcTGAACACTATTGGGCTTTGcAGACA
+>read224f start=897,mutations=1
+TCCTCATCCATGCTGTATCAGTAtTGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTATATTCGGTCTTACCACGGGCTCGATAGTTTGC
+>read225r start=367,mutations=1
+CTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAtTTAAATA
+>read226f start=369,mutations=1
+TTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTATTGCCCCGGCAGGCGGTAGTTTCCACGATCTAACAATCGAAGCcATTCGGACAGGCTTAAGCT
+>read227r start=2,mutations=0
+ACCCAGTTAAGTGTGCACCAATCCATTAAATGACGCTGCGTGTGAATGACCTTCATTGCAGGTTAATCATGGCTCAACCTAGTCACCCGGTGCTGGGCGG
+>read228r start=286,mutations=2
+GTgTCTCCTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCgTCCGG
+>read229r start=306,mutations=0
+TAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTA
+>read230f start=718,mutations=2
+TGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTcTAAATTCAgTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCT
+>read231r start=649,mutations=0
+GACGGACCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACTATCACGAGCACTATAAAGAACGGCAGGCCAGGCATTTCAC
+>read232r start=271,mutations=2
+AATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCtCTCTCTTCCGGCAAACGACTTTCCaT
+>read233r start=334,mutations=1
+TCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGcTGGCAGTTGTTCGGTTTCTCCTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAAT
+>read234r start=22,mutations=2
+TGGATCAGCACCAGCGCGGCACaCAGTTAAGTGTGtACCAATCCATTAAATGACGCTGCGTGTGAATGACCTTCATTGCAGGTTAATCATGGCTCAACCT
+>read235r start=483,mutations=0
+GGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTTACAA
+>read236r start=878,mutations=0
+GTAAGACCGAATATAACGTTAGCACGGCTCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATA
+>read237f start=662,mutations=1
+CCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACgAACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGT
+>read238f start=110,mutations=1
+GGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTgCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTT
+>read239r start=340,mutations=1
+GTTAGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTgAATACATCCTGATAGGGCCGAATCGGCAAGG
+>read240r start=667,mutations=0
+TACACACGTGGACGACTTGACGGACCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACTATCACGAGCACTATAAAGAACG
+>read241r start=260,mutations=0
+ATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCC
+>read242r start=596,mutations=0
+TAACACTATCACGAGCACTATAAAGAACGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTC
+>read243r start=899,mutations=2
+GGGCAAACTATCGAGCCCGTGGTAAGACCGAATATAACtTTAcCACGGCTCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAG
+>read244r start=245,mutations=1
+CAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAgACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCC
+>read245f start=514,mutations=1
+AAGATGACGTTGCGGCCGTgGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTAT
+>read246f start=436,mutations=1
+TAACAATCGAAGCAATTCGGACAcGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGC
+>read247r start=384,mutations=1
+AAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCgGGGGCAATAAGCGGTGGCAGTTGTTCGGT
+>read248f start=53,mutations=1
+TCATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAt
+>read249r start=236,mutations=0
+ATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGAC
+>read250f start=190,mutations=3
+GACCGCAGACCCTCCTCCTTACCACATGCaATGCGTcGGAACCGGTGTCAAAGACGGGTGCCGCTACAtAGGAAGGCACCCAGGGAAAGTCGTTTGCCGG
+>read251f start=69,mutations=1
+TCATTTAATGGATTGGTGCACACTTAtCTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGC
+>read252r start=717,mutations=0
+GCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAAAGGTACCAATGAATTTACACACGTGGACGACTTGACGGACCACGCTATTGTAAAAGTCCTTACAT
+>read253r start=99,mutations=1
+TCgGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACCAGCGCGGCACC
+>read254f start=278,mutations=1
+GTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGAaGTATTTAACTTA
+>read255f start=749,mutations=0
+AAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAAT
+>read256r start=4,mutations=1
+GCACCCAGTTAAGTGTGCACCAATCCATTAAATGACGCTGCGTGTGAATGACCTTCATTGCAGGTgAATCATGGCTCAACCTAGTCACCCGGTGCTGGGC
+>read257r start=883,mutations=1
+CCGTGGTAAGACCGAATATAACGTTAGCACGGCTCTCCgTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCC
+>read258f start=405,mutations=1
+ATTGCCCCGGCAGtCGGTAGTTTCCACGATCTAACAATCGAAGCAATTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGT
+>read259r start=178,mutations=1
+TTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAcGAGGGTCTGCGGTCTTAGGTGGTCTG
+>read260r start=849,mutations=1
+CTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACAaTAC
+>read261f start=839,mutations=0
+AAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTT
+>read262f start=700,mutations=1
+GGAACTAACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCAtGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAA
+>read263r start=861,mutations=1
+GTTAGCACGGCTCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCtAATAGTGTTCATATGCCTGTC
+>read264r start=113,mutations=0
+GGTAAGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGC
+>read265r start=647,mutations=3
+CGGACCACGCcATTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACTATCACGAGCACTAaAAAGgACGGCAGGCCAGGCATTTCACGT
+>read266f start=135,mutations=3
+GACaTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTACgACATGCGAcGCGTGGGAACCGG
+>read267r start=347,mutations=1
+TTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTcAAATACATCCTGATAGGGCCGAATC
+>read268f start=617,mutations=2
+AAGCACACAgTAcCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAAGTT
+>read269f start=872,mutations=1
+GAACACTgTTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTATATTCGG
+>read270r start=194,mutations=0
+TCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGGTCTGC
+>read271r start=293,mutations=0
+TTGTTCGGTTTCTCCTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCT
+>read272f start=440,mutations=4
+AATCGAAGCAATTCGcACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATaCTTTGTAGGAAaTGAAAGATGACGTTGCGGCCGTCGCTGTa
+>read273r start=144,mutations=3
+TCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGtCgAGGCGGAtATGGAAGGAGCTGTCGCAC
+>read274r start=615,mutations=0
+CTTGATGTTAGTTCCTTTATAACACTATCACGAGCACTATAAAGAACGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAA
+>read275r start=669,mutations=1
+TTTACACACGTGGACGACTTGACGGACCACGCTATTGTAAAAGTCCTTACATAACTTtATGTTAGTTCCTTTATAACACTATCACGAGCACTATAAAGAA
+>read276r start=105,mutations=1
+GGAGGGTCTGCGaTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACCAGCGC
+>read277r start=668,mutations=1
+TTACACACGTGGACGACTTGACGGACCACGCTATTGTAAAAGTCCTTACATAACcTGATGTTAGTTCCTTTATAACACTATCACGAGCACTATAAAGAAC
+>read278f start=700,mutations=0
+GGAACTAACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAA
+>read279f start=300,mutations=2
+AGCTCCTAgGTAAACGGGGAAACaACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCAC
+>read280r start=851,mutations=1
+CTCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAtTGTTCATATGCCTGTCTTTCCACATT
+>read281r start=303,mutations=0
+GCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGA
+>read282r start=734,mutations=1
+ACTTACCCTGTGAGTAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAAAGGTACaAATGAATTTACACACGTGGACGACTTGACGGACCACGCTAT
+>read283r start=21,mutations=1
+GGATCAGCtCCAGCGCGGCACCCAGTTAAGTGTGCACCAATCCATTAAATGACGCTGCGTGTGAATGACCTTCATTGCAGGTTAATCATGGCTCAACCTA
+>read284r start=316,mutations=3
+GCCaGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTgCTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAAGGtGGAATCCAAACAAGTGGTTTCCC
+>read285f start=451,mutations=0
+TTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGC
+>read286r start=562,mutations=1
+CCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATgTCCAGCTCGCACAGGC
+>read287f start=233,mutations=1
+GGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGAAAGTCGTTTcCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTG
+>read288f start=873,mutations=0
+AACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTATATTCGGT
+>read289f start=214,mutations=3
+CcTGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCgGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAA
+>read290f start=648,mutations=1
+CGTGAAATGCCTGGCCTGCCGTTaTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGT
+>read291r start=390,mutations=0
+CTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTG
+>read292r start=404,mutations=3
+CAAAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATaGCTaCGATTGTTAGATCGTGGtAACTACCGCCTGCCGGGGCAATA
+>read293f start=304,mutations=1
+CCTACGTAAACtGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCT
+>read294f start=511,mutations=2
+TGAAcGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCtGAGCACGGGATGCTG
+>read295r start=460,mutations=0
+CATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGC
+>read296f start=474,mutations=1
+GCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCgCCATGGCGCCTGTGCGAGC
+>read297r start=18,mutations=1
+TCAGCACCAGCGCGGCACCCAGTTAAGTGTGCACCAATCCATTAAATGACGCTGCGTGTGAATGACCTTCATTGCAGGTTAATCATGGCTCAACCTAGcC
+>read298r start=95,mutations=1
+CGcTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACCAGCGCGGCACCCAGT
+>read299f start=155,mutations=0
+CCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCT
+>read300f start=437,mutations=0
+AACAATCGAAGCAATTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCT
+>read301f start=770,mutations=0
+TCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCAT
+>read302r start=659,mutations=1
+TGGACGACTTGACGGACCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACTgTCACGAGCACTATAAAGAACGGCAGGCCA
+>read303f start=287,mutations=2
+CGGAAGAGAGTGGAGCTCCTACtTAAACGGaGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACC
+>read304r start=490,mutations=1
+TATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGAgGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCA
+>read305r start=762,mutations=2
+CTTTCCACATTACATTAATACTTCAGGAACTTACCCTGTGAGTAAcCAGAATGTGCTTAGCTTTCAAATTTgTCGGCAAAAGGTACCAATGAATTTACAC
+>read306r start=854,mutations=0
+CGGCTCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCAC
+>read307f start=879,mutations=1
+ATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTgATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTATATTCGGTCTTACC
+>read308r start=521,mutations=4
+GCTcAATATACAGCATCCCGTGCTCTGACtCTATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTtCTGCGGTTCCTCCAACAGCGAaGGCCGCAACG
+>read309r start=504,mutations=2
+CCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTaTCACcTCCTA
+>read310r start=879,mutations=0
+GGTAAGACCGAATATAACGTTAGCACGGCTCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAAT
+>read311r start=156,mutations=1
+TAGCGGCACCaGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAG
+>read312r start=723,mutations=1
+GAGTAAGCAGAATGTGCTTAGCTTTCtAATTTTTCGGCAAAAGGTACCAATGAATTTACACACGTGGACGACTTGACGGACCACGCTATTGTAAAAGTCC
+>read313r start=248,mutations=2
+CGGtAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTgCGTAGGAGCTCCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGCA
+>read314f start=281,mutations=1
+GTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACcTAGGA
+>read315f start=239,mutations=0
+AAAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCC
+>read316f start=104,mutations=4
+CGaGCTGGTGCTGATCCATGAcGTTaATCTGGACTTGTACGTGCGACAGtTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTC
+>read317f start=379,mutations=1
+GAGAAACCGAACAACTGCCACCGCTTATTGCCCCGGCAGGCGGTAGTTTCCACGATCTAACAATCGAAcCAATTCGGACAGGCTTAAGCTACAAAGCTCG
+>read318f start=451,mutations=1
+TTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTcCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGC
+>read319f start=149,mutations=0
+ACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGT
+>read320r start=272,mutations=1
+AAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGaCAAACGACTTTCCC
+>read321r start=797,mutations=2
+ATGgCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACCtTGTGAGTAAGCAGAATGTGCTTAGCTTTC
+>read322r start=581,mutations=1
+CACTATAAAGAACGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATaCCGTGCTCTGACGCTATGAGAGG
+>read323f start=760,mutations=0
+GTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAA
+>read324r start=483,mutations=1
+GGATCTCCAGCTCGCACAGGCGCCATGGTGCcGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTTACAA
+>read325r start=311,mutations=0
+GGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTT
+>read326f start=219,mutations=0
+GATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGG
+>read327r start=485,mutations=0
+GAGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTTAC
+>read328f start=759,mutations=2
+CGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGaTAAGTaCCTGAAGTATTAATGTAATGTGGA
+>read329r start=841,mutations=0
+CGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATAC
+>read330f start=204,mutations=1
+CTCCTTcCCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCT
+>read331r start=270,mutations=1
+ATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTaCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAACGACTTTCCCTG
+>read332r start=240,mutations=1
+GGGAcTCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTT
+>read333f start=309,mutations=2
+GTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGtCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCAtCGCTTATTG
+>read334r start=282,mutations=2
+CTCCTAAGTTAAATACATCCgGATAGGGCCGAATCGGCAAGGGGGAAgCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAA
+>read335r start=825,mutations=1
+TACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACAaTAATACTTCAGGAACTTACCCT
+>read336f start=275,mutations=1
+AAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCtATTCGGCCCTATCAGGATGTATTTAAC
+>read337f start=613,mutations=2
+TATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGcAACTAACATCc
+>read338f start=281,mutations=1
+GTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGaGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGA
+>read339f start=820,mutations=0
+CTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTA
+>read340f start=215,mutations=0
+ATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAAC
+>read341f start=468,mutations=2
+TACAAAGCTCGGATTTTGcAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGaACCATGGCGCCTGT
+>read342f start=672,mutations=0
+TTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTC
+>read343f start=835,mutations=1
+CCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAtTAATGTACAATTCGCCC
+>read344r start=20,mutations=2
+GATCAGCACCAGCGCGGCACCCtGTTAAGTGTGCACCAATCCATTAAATGACGCTGCGTGTGAATGACCTTCATTGCAGGTTAATgATGGCTCAACCTAG
+>read345f start=446,mutations=2
+AGCAATgCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTaTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGA
+>read346r start=235,mutations=3
+TtCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAACGACTTTCCCTcGGTtCCTTCCTGTGTAGCGGCACCCGTCTTTGACA
+>read347r start=337,mutations=2
+AGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGtAGTTGTTCGGTTTCTCCTAAGTTAAATACATCCTGAcAGGGCCGAATCGGCAAGGGGG
+>read348r start=807,mutations=2
+TGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATcACtTTAATACTTCAGGAACTTACCCTGTGAGTAAGCAGAATGTG
+>read349r start=524,mutations=0
+TGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCA
+>read350f start=785,mutations=0
+GCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGG
+>read351f start=30,mutations=2
+CCATGATTAACCTGCAATGAAGGTCATTCACACGCAGCGTCATTTAATGGtTTGGTGCACACTTAACcGGGTGCCGCGCTGGTGCTGATCCATGAAGTTC
+>read352f start=850,mutations=1
+TAATGTGGAAAGACAGGCATATGtACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGA
+>read353f start=564,mutations=2
+CTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTaTATATTAAGCACACAATAGCCCGGaGACCGGCCCCAACGTGAAATGCCTGGCC
+>read354f start=493,mutations=2
+TCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGtCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTaCGAGCTGGAGATCCTCTCATAGCG
+>read355r start=461,mutations=0
+CCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAG
+>read356f start=90,mutations=0
+ACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAA
+>read357f start=283,mutations=4
+TTGCCGGAAGAGAcTGGAGCTCCTACGTAAAaGGGGAAACCACTTcTTgGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGA
+>read358f start=721,mutations=0
+AAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTAC
+>read359r start=875,mutations=1
+AGACCGAATATAACGTTAGCACGGCTCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAtGAATGTCTACAAAGCCCAATAGTG
+>read360f start=84,mutations=0
+GTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACC
+>read361r start=899,mutations=6
+GGGCAAACgATaGAGCCCGTcGTAAGACCGAATATAACGTTAGCACGGtTCTCCgTTACGtAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAG
+>read362r start=110,mutations=0
+AAGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACC
+>read363f start=882,mutations=0
+GGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTATATTCGGTCTTACCACG
+>read364f start=895,mutations=1
+ATTCCTCATCCATGCcGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTATATTCGGTCTTACCACGGGCTCGATAGTTT
+>read365f start=300,mutations=1
+AGCTCCTACGTAAACGGGGAAACCACTTGTTgGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCAC
+>read366r start=842,mutations=1
+ACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCaACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATA
+>read367r start=230,mutations=2
+ACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCgAACGtCTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGACACCGGT
+>read368f start=65,mutations=1
+AGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTGtCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTT
+>read369f start=40,mutations=3
+CCTaCAATGcAGGTCATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGAaCCATGAAGTTCATCTGGACTT
+>read370r start=507,mutations=2
+ATCCCGTGCcCTGACGCTATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCgCCAACAGCGACGGCCGCAACGTCATCTTTCACTTC
+>read371r start=210,mutations=1
+CGTAGGAGCTCCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTgCCTGTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGT
+>read372f start=459,mutations=0
+GGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCAT
+>read373f start=753,mutations=2
+CGTCtACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCtCATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAA
+>read374r start=389,mutations=1
+TTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGtGGCAATAAGCGGTGGCAGTTGT
+>read375f start=893,mutations=0
+ACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTATATTCGGTCTTACCACGGGCTCGATAGT
+>read376r start=566,mutations=1
+CAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATtTCCAGCTCGCAC
+>read377f start=435,mutations=0
+CTAACAATCGAAGCAATTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCG
+>read378r start=459,mutations=2
+ATGGTGCTcCGGTTCCTCCAACAGtGACGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCC
+>read379r start=411,mutations=3
+CTTCgTACAAAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATcGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCaGG
+>read380f start=432,mutations=1
+GATCTAACAATCGAAGCAATTCGGACAGGCTTAAcCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCG
+>read381r start=569,mutations=1
+aGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCG
+>read382r start=697,mutations=3
+AAATTTTTCGGCAAAAGGTACCAATGAAgTTcCACACGTGGACGACTTGACGGACCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTAcTTCCTTT
+>read383r start=163,mutations=0
+TCCTGTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAA
+>read384f start=645,mutations=1
+CAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAAGTTgTGTAAGGACTTTTACAATAGCGTGGTC
+>read385f start=899,mutations=1
+CTCATCCATcCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTATATTCGGTCTTACCACGGGCTCGATAGTTTGCCC
+>read386f start=576,mutations=1
+GAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACAtAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTA
+>read387r start=583,mutations=1
+AGCACTATAAAGAACGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATAaACAGCATCCCGTGCTCTGACGCTATGAGA
+>read388f start=133,mutations=2
+TGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTAaCACATGCGAaGCGTGGGAACC
+>read389f start=737,mutations=1
+GCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGcGTAAGTTCC
+>read390f start=182,mutations=0
+CCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGAAAGTCG
+>read391f start=796,mutations=0
+TGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACA
+>read392r start=783,mutations=0
+CAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACCCTGTGAGTAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAA
+>read393f start=692,mutations=3
+GTTATAAAGGAACTAACATCAAGTTATGTAAGGACTTTTACAATAcCGTGGTCCGTCAAGTCGTCCACGTGaGTAAAaTCATTGGTACCTTTTGCCGAAA
+>read394f start=450,mutations=1
+ATTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGaTGTTGGAGGAACCG
+>read395f start=584,mutations=2
+CTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCAaACAATtGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTC
+>read396f start=217,mutations=0
+GCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGG
+>read397r start=513,mutations=0
+TACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTT
+>read398r start=324,mutations=0
+TACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGT
+>read399r start=279,mutations=0
+CTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAACGA
+>read400f start=550,mutations=0
+CAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACG
+>read401f start=897,mutations=0
+TCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTATATTCGGTCTTACCACGGGCTCGATAGTTTGC
+>read402r start=203,mutations=1
+GCTCCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACgCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGG
+>read403f start=540,mutations=1
+GGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGgACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACC
+>read404f start=449,mutations=1
+AATTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTtGCTGTTGGAGGAACC
+>read405r start=337,mutations=1
+AGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAATACATCCTGATcGGGCCGAATCGGCAAGGGGG
+>read406r start=470,mutations=1
+GCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCAtTTCCTACAAAGGATAGAGCACTTACAAAATCCGAGCTTTG
+>read407r start=404,mutations=1
+CAAAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGtCTGCCGGGGCAATA
+>read408f start=70,mutations=0
+CATTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCC
+>read409f start=885,mutations=1
+CTTTGTAGACATTCCTCATCCATGCTGTATCAGTAAgGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTATATTCGGTCTTACCACGGGC
+>read410f start=349,mutations=1
+TcCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTATTGCCCCGGCAGGCGGTAGTTTCCACGATCTAACAATCGAAGC
+>read411r start=40,mutations=1
+AAGTCCAGATGAACTTCATGGATCAGCACCAGCGCGGCACCCAGTTAAGTGTGCACCAATCCATTAAATcACGCTGCGTGTGAATGACCTTCATTGCAGG
+>read412r start=582,mutations=1
+GCACTATAAAGAACGGCAGGCCAGGCATTTaACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAG
+>read413f start=625,mutations=0
+AATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAAGTTATGTAAGG
+>read414r start=428,mutations=0
+CGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGG
+>read415f start=307,mutations=1
+ACGTAAACGGGGAAACCACTTGTTTGGATTCCtCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTAT
+>read416r start=720,mutations=2
+TAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAtAGGTACCAATGAATTTACACACGTGGACGACTTGACGGAaCACGCTATTGTAAAAGTCCTTA
+>read417f start=848,mutations=0
+TGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGA
+>read418r start=90,mutations=2
+TTAGGTGaTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATtAGCACCAGCGCGGCACCCAGTTAAGT
+>read419r start=848,mutations=1
+TCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCcACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACA
+>read420r start=561,mutations=1
+CAGGCAaTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGGCG
+>read421f start=106,mutations=0
+CGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCT
+>read422r start=236,mutations=0
+ATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGAC
+>read423r start=390,mutations=0
+CTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTG
+>read424r start=403,mutations=1
+AAAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGAaCGTGGAAACTACCGCCTGCCGGGGCAATAA
+>read425f start=18,mutations=4
+GACTAGGTTGAGCCATGATTAgCCTGCtATGAAGGTCATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTcgCGCGCTGGTGCTGA
+>read426r start=110,mutations=1
+AAGGAGGAGGGTCTGCGGTCTTcGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACC
+>read427f start=569,mutations=0
+CGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCG
+>read428r start=473,mutations=1
+CTCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACcTACAAAATCCGAGCT
+>read429r start=184,mutations=1
+AACGACcTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTTAGGT
+>read430r start=148,mutations=0
+CCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTC
+>read431r start=775,mutations=2
+TTCATATcCCTGTCTTTCCACATTACATTAATACTTCAaGAACTTACCCTGTGAGTAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAAAGGTACC
+>read432f start=56,mutations=1
+TTCACACGCAGCGTtATTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTC
+>read433f start=412,mutations=3
+CGGCAGGCGGTAGTTTCCACGATCTAACAATCGAAGCAATTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAaTGCTCTATCCTgTGTAGGtAGT
+>read434f start=315,mutations=0
+GGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTATTGCCCCGG
+>read435r start=815,mutations=0
+ATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACCCTGTGAGTAAGC
+>read436f start=165,mutations=1
+CCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTtGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAG
+>read437r start=353,mutations=1
+AATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTcAAATACATCCTGATAGGGC
+>read438f start=246,mutations=1
+GGTGCCGCTACACAGGAcGGCACCCAGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGC
+>read439r start=697,mutations=2
+AAATTTTTCGGCAAAAGGTACCAATGAATTTACACACaTGGACGACTTGACGGACCACGCTATgGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTT
+>read440f start=448,mutations=1
+CAATTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTgGCGGCCGTCGCTGTTGGAGGAAC
+>read441r start=268,mutations=1
+ACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAACGACaTTCCCTGGG
+>read442f start=768,mutations=1
+ATTCATTGcTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGC
+>read443r start=720,mutations=2
+TAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAAAGGTACCAATGAATTTACACACGTGGACGAgTTGACGGACCgCGCTATTGTAAAAGTCCTTA
+>read444r start=677,mutations=1
+CCAATGAATTTACACACGTGGACGACTTGACGGACCACGCTcTTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACTATCACGAGCACT
+>read445f start=568,mutations=0
+GCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCC
+>read446f start=145,mutations=1
+TGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTgCCACATGCGATGCGTGGGAACCGGTGTCAAAGAC
+>read447r start=200,mutations=0
+CCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGG
+>read448r start=299,mutations=1
+TGGCAGTTGTTCGGTTTCTCCTAAGTTAAATACATCCTGATAGGtCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTC
+>read449f start=293,mutations=0
+AGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAA
+>read450f start=477,mutations=3
+CGGATTTTGTAcGTGCcCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAcCTGG
+>read451f start=100,mutations=1
+GTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAgGACCGCAGAC
+>read452f start=590,mutations=1
+GCGTCAGAGCACGGGAcGCTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATA
+>read453f start=648,mutations=0
+CGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGT
+>read454f start=826,mutations=0
+GGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTAC
+>read455r start=472,mutations=1
+TCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAtGGATAGAGCACTTACAAAATCCGAGCTT
+>read456f start=524,mutations=3
+TGCGGCCGTCGCTGTTGGAGGAACCGCAGCACaATGGCGCtTGTGCGAGCTGGAGATCCTCTCATAGCtTCAGAGCACGGGATGCTGTATATTAAGCACA
+>read457r start=452,mutations=0
+TGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGA
+>read458r start=729,mutations=2
+CCCTGTGAGTAAGCAGAATGTGCTTAGCTTTCAAgTTTTTCGGCAAAAGGTACCAATGAATTTACACACGTGGACGACTTGACGGtCCACGCTATTGTAA
+>read459r start=850,mutations=0
+TCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTA
+>read460r start=853,mutations=0
+GGCTCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACA
+>read461f start=250,mutations=2
+CCGCTACACAGGAAGGCACCCAGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACcTAAACGGGGAAACCACTTGTTTtGATTCCCCCTTGCCGAT
+>read462f start=17,mutations=2
+TGACTAGGTTGAGCCATGATTAACCTGCAAaGAAGGTCATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGgTGGTGCTG
+>read463r start=822,mutations=0
+ATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACCCTGTG
+>read464f start=828,mutations=1
+GTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAg
+>read465f start=292,mutations=0
+GAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACA
+>read466f start=894,mutations=0
+CATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTATATTCGGTCTTACCACGGGCTCGATAGTT
+>read467r start=92,mutations=1
+TCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTaCAGATGAACTTCATGGATCAGCACCAGCGCGGCACCCAGTTAA
+>read468f start=855,mutations=2
+TGGAAAtACAGGCATATGAgCACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGT
+>read469r start=291,mutations=1
+GTTCGGTTTCTCCTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAcTCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCT
+>read470f start=436,mutations=4
+TAACAATCGAAGCAATTgcGACAGGCTTAAGCTACAAAGCcCGGAaTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGC
+>read471r start=171,mutations=1
+GGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGgATGGCA
+>read472f start=563,mutations=0
+CCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGC
+>read473f start=615,mutations=1
+TTAAGgACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAAG
+>read474r start=811,mutations=1
+AGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATACcTCAGGAACTTACCCTGTGAGTAAGCAGAA
+>read475f start=35,mutations=0
+ATTAACCTGCAATGAAGGTCATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTG
+>read476r start=421,mutations=2
+TCATCTTTCACTTCCTACAAAGGATAGAGCACTTAgAAAATCCGtGCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTAC
+>read477r start=27,mutations=0
+CTTCATGGATCAGCACCAGCGCGGCACCCAGTTAAGTGTGCACCAATCCATTAAATGACGCTGCGTGTGAATGACCTTCATTGCAGGTTAATCATGGCTC
+>read478r start=388,mutations=0
+TACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTT
+>read479r start=353,mutations=0
+AATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAATACATCCTGATAGGGC
+>read480r start=332,mutations=2
+GTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTcCTCCTAAGTTAAATACATCCTGATAGGGCCGAATCGGaAAGGGGGAATCC
+>read481f start=107,mutations=0
+GCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTC
+>read482f start=168,mutations=4
+CCTTGCCATACAGACCACCTAcGACCGCAGACCtTCCTCCTTACCACATGCGATGCtTGGGAACtGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCA
+>read483f start=830,mutations=1
+AAGTTCCTGAAGcATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATT
+>read484f start=506,mutations=0
+GGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGA
+>read485f start=312,mutations=1
+AACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATcCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTATTGCCC
+>read486f start=494,mutations=0
+CTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGT
+>read487f start=177,mutations=0
+ACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGAA
+>read488f start=847,mutations=2
+ATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATaAGTAATGTACAATTCGCCCCTTTCGTgAAGG
+>read489f start=545,mutations=1
+AACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCtGGGACCGGCCC
+>read490f start=154,mutations=0
+TCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGC
+>read491f start=481,mutations=0
+TTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGAT
+>read492r start=868,mutations=1
+ATATAACGTTAGCACGGCTCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACtAAGCCCAATAGTGTTCATAT
+>read493f start=450,mutations=2
+ATTCGGACAGGCTTAAGCTAaAAAGCTCGGATTTTGTgAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCG
+>read494r start=340,mutations=1
+GTTAGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAcGG
+>read495f start=2,mutations=1
+CCGCCCAGCAaCGGGTGACTAGGTTGAGCCATGATTAACCTGCAATGAAGGTCATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGT
+>read496f start=533,mutations=0
+CGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCC
+>read497f start=880,mutations=0
+TTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTATATTCGGTCTTACCA
+>read498r start=891,mutations=0
+TATCGAGCCCGTGGTAAGACCGAATATAACGTTAGCACGGCTCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCT
+>read499f start=863,mutations=2
+CAaGCATATGAACACTAaTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGT
+>read500r start=181,mutations=3
+GACTTTCCCTGGGTGCCTTCCTtTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCAaCGCATGTGGTAAGGAGGAGGGTCTGCcGTCTTAGGTGGT
+>read501f start=690,mutations=1
+GgGTTATAAAGGAACTAACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGA
+>read502r start=540,mutations=3
+GGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCcGACGCTATaAGAGcATCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCC
+>read503f start=150,mutations=0
+CAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTG
+>read504f start=759,mutations=0
+CGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGA
+>read505r start=412,mutations=2
+ACTTaCTACAAAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTaCGATTGTTAGATCGTGGAAACTACCGCCTGCCG
+>read506f start=675,mutations=0
+ATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATT
+>read507f start=154,mutations=2
+TCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGcGAACCGGTGTCAAAtACGGGTGCCGC
+>read508f start=848,mutations=0
+TGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGA
+>read509f start=500,mutations=0
+TTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGC
+>read510f start=181,mutations=2
+ACaACCTAAGACCGCAGACCCTgCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGAAAGTC
+>read511r start=556,mutations=0
+ATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGGCGCCATG
+>read512f start=713,mutations=0
+AGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATT
+>read513r start=818,mutations=1
+CTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACCCTcTGAGTA
+>read514f start=481,mutations=0
+TTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGAT
+>read515f start=549,mutations=1
+GCAGCACCATGGCGCCTGTGCGAGCcGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAAC
+>read516f start=622,mutations=2
+CACAATAGCCCGGGGACCGGCCCCAAtGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGAcAGTGTTATAAAGGAACTAACATCAAGTTATGTA
+>read517r start=28,mutations=0
+ACTTCATGGATCAGCACCAGCGCGGCACCCAGTTAAGTGTGCACCAATCCATTAAATGACGCTGCGTGTGAATGACCTTCATTGCAGGTTAATCATGGCT
+>read518r start=349,mutations=0
+GCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAATACATCCTGATAGGGCCGAA
+>read519r start=663,mutations=0
+CACGTGGACGACTTGACGGACCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACTATCACGAGCACTATAAAGAACGGCAG
+>read520f start=626,mutations=3
+ATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTaGCCTGCCGTTCTTTATAGTGCTCGTGAcAGTGTTATAtAGGAACTAACATCAAGTTATGTAAGGA
+>read521f start=484,mutations=2
+TGTAAGTGCTCTATCCTTTGTAGGAAGTtAAAGATGAtGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCT
+>read522f start=666,mutations=2
+CCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAAGTTATGTAAGGACTTTTAaAATAGCGTGGTgCGTCAAGTCGTCCACGTGTGT
+>read523r start=71,mutations=0
+AGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACCAGCGCGGCACCCAGTTAAGTGTGCACCAATCCATTAAAT
+>read524r start=109,mutations=0
+AGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACCA
+>read525f start=590,mutations=0
+GCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATA
+>read526r start=795,mutations=1
+GTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACCCTGTGAGTAAGCAGAATGTGCTTAGCTcTCAA
+>read527f start=82,mutations=1
+TGGTGCACAtTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGA
+>read528r start=12,mutations=1
+CCAGCGCGGCACCCAGTTAAGTGTGCACCAATCCATTAAATGACGCTGCGTGTGAATGACCTTCATTGCAGcTTAATCATGGCTCAACCTAGTCACCCGG
+>read529f start=496,mutations=0
+ATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCA
+>read530r start=329,mutations=2
+GAAACTACCGCtTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAcATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAA
+>read531f start=801,mutations=0
+GCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCT
+>read532f start=881,mutations=1
+TGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATtTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTATATTCGGTCTTACCAC
+>read533f start=835,mutations=1
+CCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACcTTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCC
+>read534f start=141,mutations=3
+TACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCtTCCTCCTTAtCACATGCGATGCGTGtGAACCGGTGTCAA
+>read535r start=74,mutations=0
+GCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACCAGCGCGGCACCCAGTTAAGTGTGCACCAATCCATTA
+>read536f start=2,mutations=2
+CCGCCCAGCACCtGGTGACTAGGTTGAGCCATGATTAACCTGCAATGAAGGTCATTCACACGCAGCaTCATTTAATGGATTGGTGCACACTTAACTGGGT
+>read537r start=424,mutations=0
+ACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAAC
+>read538r start=563,mutations=0
+GCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGG
+>read539f start=282,mutations=2
+TTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGcGGAAACCACTTGTTTGGATTCCCCCTTaCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAG
+>read540f start=734,mutations=0
+ATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGT
+>read541f start=597,mutations=0
+AGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTAT
+>read542f start=569,mutations=2
+CGAGCTGGAGAgCCTCTCATcGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCG
+>read543r start=22,mutations=1
+TGGATCAGCACCAGCGCGGCACCCAGTTAAGTGTGCACCAATCCATTAAATGACGCTGCGTGTGAATGACCTTCATTGCAGGTTAAgCATGGCTCAACCT
+>read544f start=512,mutations=2
+GAAAcATGACaTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGT
+>read545r start=780,mutations=2
+TAGcGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACCCTcTGAGTAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAAAG
+>read546f start=69,mutations=1
+TCATTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAcCTCCTTCCATTTCCGC
+>read547f start=841,mutations=1
+tTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCG
+>read548f start=492,mutations=1
+CTCTATCCaTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGC
+>read549f start=135,mutations=1
+GACTTGTACGTGCGACAtCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGG
+>read550f start=656,mutations=0
+GCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGT
+>read551f start=255,mutations=1
+ACACAGGAAGGCACCCAGGGAAAGTCGTTTGCCGGtAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGC
+>read552r start=286,mutations=1
+GTTTCTCCTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTgCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGG
+>read553f start=372,mutations=1
+AACTTAGGAGAAACtGAACAACTGCCACCGCTTATTGCCCCGGCAGGCGGTAGTTTCCACGATCTAACAATCGAAGCAATTCGGACAGGCTTAAGCTACA
+>read554f start=187,mutations=2
+TAAGACCGaAtACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGAAAGTCGTTTGC
+>read555f start=315,mutations=2
+GGGGAAACCACTTGTTTGGATTCaCCCTTGCCGATTCGGCCCTATCAcGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTATTGCCCCGG
+>read556f start=557,mutations=1
+ATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACCaGCCCCAACGTGAAATG
+>read557f start=594,mutations=1
+CAGAGtACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGT
+>read558r start=158,mutations=1
+TGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTgAGGTGGTCTGTATGGCAAGGCGGAAATGGA
+>read559f start=24,mutations=1
+GTTGAGCCATGATTAACCTGCAATGAAGGTCATTCACACGCAGCGTCATTTAATGGATTGGTGaACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATG
+>read560f start=369,mutations=2
+TTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTATTGCCCCGGCAGGCGGTAGTTTCCACGgTCTAACAATCGAAGCAATTCGaACAGGCTTAAGCT
+>read561f start=28,mutations=1
+AGCCATGATTAACCTGCAATGAAGGTCcTTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGT
+>read562f start=655,mutations=0
+TGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCG
+>read563f start=342,mutations=3
+TTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACcGCCACCGCTTATTGCCggGGCAGGCGGTAGTTTCCACGATCTAACAA
+>read564r start=187,mutations=1
+GCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTaGTAAGGAGGAGGGTCTGCGGTCTTA
+>read565r start=573,mutations=0
+AGAACGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAG
+>read566r start=375,mutations=1
+CTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACtGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAA
+>read567r start=779,mutations=0
+AGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACCCTGTGAGTAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAAAGG
+>read568f start=811,mutations=2
+TTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGaGCTTTGTAGACATTCCTtATCCATGCT
+>read569r start=49,mutations=3
+CGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACCAGCGCGGCACCCAGTTAAGTGTGCACCAATCCAgTAAATGACGCTGaGTGTGAATGACCTa
+>read570f start=5,mutations=2
+CCCAGCACCGGGTGACTAGGTTGAGCCATGATTAACCTGgAATGAAGGTCATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGcGTGCC
+>read571f start=83,mutations=2
+GGTGCACACTTAACTGGaTGCCGCGCTGGTGCTGATCCATGAAGTTgATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGAC
+>read572r start=843,mutations=0
+TACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAAT
+>read573f start=45,mutations=3
+AATGAAaGTCATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTGgCGCGCTGGTGCTGATCCATGAAGTTCATCTtGACTTGTACG
+>read574f start=611,mutations=3
+TATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCaTaCCGTTCTTTATAGTGCTCGTGgTAGTGTTATAAAGGAACTAACAT
+>read575f start=648,mutations=0
+CGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGT
+>read576r start=188,mutations=2
+GGCAAACGACTTTCCCTGGGTGCCTTCCaGTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACaCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTT
+>read577r start=593,mutations=1
+CACTATCACGAGCACTATAAAGAACGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATaCCGTGCTCTGA
+>read578f start=714,mutations=0
+GTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTC
+>read579f start=498,mutations=1
+CCTTTGTAGGAAGTGAAAGAcGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGA
+>read580f start=567,mutations=1
+TaCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGC
+>read581f start=739,mutations=2
+GTGGTCCGTCAAGTCGTCCACGTGTGTAAAgTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGtGTAAGTTCCTG
+>read582f start=126,mutations=1
+GTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTgCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGT
+>read583r start=291,mutations=1
+GTTCGGTTTCTCCTAAGTTAAATACATCCTGATAtGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCT
+>read584f start=65,mutations=2
+cGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTaCTTCCATTT
+>read585r start=627,mutations=3
+GTCCTTACATAACTTGATGTTAGTTCCaTTATAACACTATCAaGtGCACTATAAAGAACGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTA
+>read586r start=549,mutations=0
+GTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGC
+>read587r start=131,mutations=1
+TTCCCACGCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTaTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGA
+>read588f start=819,mutations=3
+ACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGtAgAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCcTGCTGTATCAGT
+>read589f start=572,mutations=1
+GCTtGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTC
+>read590r start=892,mutations=0
+CTATCGAGCCCGTGGTAAGACCGAATATAACGTTAGCACGGCTCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTC
+>read591r start=532,mutations=2
+GGCTATTGTGTGCTTAATATACAGCATCCCGTGCTtTGACGCTATGAGAGGATCTCCAGCTCtCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGA
+>read592f start=559,mutations=0
+GGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCC
+>read593r start=642,mutations=1
+CACGCTATTGTAAAAGTCCTcACATAACTTGATGTTAGTTCCTTTATAACACTATCACGAGCACTATAAAGAACGGCAGGCCAGGCATTTCACGTTGGGG
+>read594f start=674,mutations=1
+TATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAAaTCAT
+>read595r start=458,mutations=0
+TGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCCT
+>read596f start=103,mutations=0
+CCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCT
+>read597r start=55,mutations=3
+AGCTaTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACCAGCGCGGCACCCAGTTAAGTGTGCtCCAATCCATTAAATaACGCTGCGTGTGAAT
+>read598f start=457,mutations=1
+CAtGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACC
+>read599f start=301,mutations=2
+GCTCCTAgGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCgACC
+>read600r start=251,mutations=0
+AATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGCG
+>read601r start=705,mutations=0
+TAGCTTTCAAATTTTTCGGCAAAAGGTACCAATGAATTTACACACGTGGACGACTTGACGGACCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTA
+>read602f start=613,mutations=1
+TATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGcGTTATAAAGGAACTAACATCA
+>read603r start=757,mutations=0
+CACATTACATTAATACTTCAGGAACTTACCCTGTGAGTAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAAAGGTACCAATGAATTTACACACGTG
+>read604f start=254,mutations=0
+TACACAGGAAGGCACCCAGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGG
+>read605f start=77,mutations=0
+TGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCAT
+>read606r start=409,mutations=1
+TCCTACAAAGGATAGAGaACTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGG
+>read607r start=846,mutations=2
+CTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTAtAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATaACATT
+>read608f start=92,mutations=2
+TTAACTGGGTGCCGCGCTGGTtCTGATCCATGAAGgTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGA
+>read609r start=397,mutations=1
+TAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGtGGCAATAAGCGGTG
+>read610f start=308,mutations=0
+CGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTATT
+>read611r start=51,mutations=2
+GTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACCAGCGCGGCACCCAGTTAtGTGTGCACCAATCCAcTAAATGACGCTGCGTGTGAATGACC
+>read612f start=777,mutations=1
+TACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGcAGTATTAATGTAATGTGGAAAGACAGGCATATGAACA
+>read613r start=148,mutations=0
+CCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTC
+>read614f start=331,mutations=1
+TGGATTCCCCCTTGCCGATcCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTATTGCCCCGGCAGGCGGTAGTTTCCA
+>read615r start=329,mutations=0
+GAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAA
+>read616f start=760,mutations=1
+GTGTGTAAATTCATTGGTAgCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAA
+>read617f start=703,mutations=1
+ACTAACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAgGC
+>read618r start=8,mutations=1
+CGCGGCACCCAGTTAAGTGTGCACCAATCCATTAAATGACtCTGCGTGTGAATGACCTTCATTGCAGGTTAATCATGGCTCAACCTAGTCACCCGGTGCT
+>read619r start=100,mutations=0
+GTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACCAGCGCGGCAC
+>read620r start=360,mutations=0
+CTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAATACATCCTG
+>read621f start=737,mutations=0
+GCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCC
+>read622f start=63,mutations=2
+GCAGCGTCATTTAATGGATTGGTGCACgCTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTaCGACAGCTCCTTCCAT
+>read623r start=343,mutations=1
+ATTGTTAGATCGTGGAAACTACCGCCTcCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAATACATCCTGATAGGGCCGAATCGGCA
+>read624f start=487,mutations=0
+AAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTC
+>read625f start=682,mutations=1
+TCGTGATAGTGTTATAAAGGAACTAACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAcGTCGTCCACGTGTGTAAATTCATTGGTACCT
+>read626r start=590,mutations=1
+TATCACGAGCACTATAAAGAACGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTAcTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGC
+>read627f start=41,mutations=1
+CTGCAATGAAGGTCATTCACACGCAGCGTCATTTAATGGATTGGTGCAgACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTG
+>read628f start=95,mutations=0
+ACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCG
+>read629f start=776,mutations=0
+GTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAAC
+>read630f start=271,mutations=1
+AGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGaCCTATCAGGATGTATT
+>read631f start=772,mutations=0
+ATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATAT
+>read632r start=36,mutations=0
+CCAGATGAACTTCATGGATCAGCACCAGCGCGGCACCCAGTTAAGTGTGCACCAATCCATTAAATGACGCTGCGTGTGAATGACCTTCATTGCAGGTTAA
+>read633f start=327,mutations=0
+TGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTATTGCCCCGGCAGGCGGTAGTT
+>read634f start=255,mutations=0
+ACACAGGAAGGCACCCAGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGC
+>read635f start=558,mutations=0
+TGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGC
+>read636f start=169,mutations=1
+CTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACaGGTGCCGCTACACAGGAAGGCAC
+>read637f start=278,mutations=0
+GTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTA
+>read638r start=455,mutations=2
+TGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAAtGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAtGCCTGTC
+>read639f start=347,mutations=0
+GATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTATTGCCCCGGCAGGCGGTAGTTTCCACGATCTAACAATCGAA
+>read640r start=736,mutations=1
+GAACTTACCCTGTGAGTAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAAAGGTACtAATGAATTTACACACGTGGACGACTTGACGGACCACGCT
+>read641f start=473,mutations=0
+AGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAG
+>read642f start=708,mutations=1
+CATCAAGTTATGTAAcGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGC
+>read643f start=190,mutations=3
+GACCGCAGAaCCTCCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGgtAGTCGTTTGCCGG
+>read644f start=498,mutations=0
+CCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGA
+>read645f start=791,mutations=1
+AAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAAaGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGT
+>read646r start=60,mutations=1
+GAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACCAGCGCGGCACCCAGTTAAGTGTGCACCAATCCATTAAATGACGCTtCGTG
+>read647r start=457,mutations=3
+GGTGCTGCGGTTCCTCCAACtGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTTACAAAcTCCGAGCaTTGTAGCTTAAGCCTG
+>read648r start=607,mutations=2
+TAGTTCCTTTATAACACTATCACGAGCACTATAAAGAACGGCAGtaCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGC
+>read649f start=785,mutations=1
+GCCGAAAtATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGG
+>read650f start=106,mutations=1
+CGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACtCTCCT
+>read651f start=608,mutations=1
+CTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGtAACTAA
+>read652r start=109,mutations=0
+AGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACCA
+>read653r start=534,mutations=0
+CGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGC
+>read654f start=846,mutations=0
+AATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAG
+>read655f start=46,mutations=1
+ATGAAGGTCATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGaGCTGATCCATGAAGTTCATCTGGACTTGTACGT
+>read656f start=217,mutations=3
+GtGATGCGTGGGAACCGGTGTCAAAGACGGGcGCCGCTACACAGGAAGGCACCCAGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGG
+>read657f start=129,mutations=3
+CATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCcTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTgACCACATGCGATGCGgGGG
+>read658f start=393,mutations=0
+CTGCCACCGCTTATTGCCCCGGCAGGCGGTAGTTTCCACGATCTAACAATCGAAGCAATTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGC
+>read659f start=226,mutations=1
+GGGAACCGGTGTCAAAGACGGGTGCaGCTACACAGGAAGGCACCCAGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCAC
+>read660f start=790,mutations=1
+AAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTaGGCTTTG
+>read661f start=784,mutations=2
+TGCCGAAAAATTTGAAAGCTAAGCACgTTCTGCTTACTCACAGGGTAAGTTCCTtAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGG
+>read662r start=757,mutations=0
+CACATTACATTAATACTTCAGGAACTTACCCTGTGAGTAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAAAGGTACCAATGAATTTACACACGTG
+>read663f start=708,mutations=1
+CATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGcTACCTTTTGCCGAAAAATTTGAAAGCTAAGC
+>read664f start=369,mutations=1
+TTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTATTGCCCCGGCAGGCGGTAGTTTCCAaGATCTAACAATCGAAGCAATTCGGACAGGCTTAAGCT
+>read665r start=267,mutations=2
+CATCCTaATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTtCGGCAAACGACTTTCCCTGGGT
+>read666f start=855,mutations=0
+TGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGT
+>read667r start=425,mutations=0
+AACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAA
+>read668r start=112,mutations=2
+GTAAGGAGGAcGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGaCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCA
+>read669r start=129,mutations=0
+CCCACGCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATG
+>read670f start=425,mutations=3
+TcTCCACGATCTAACAATCGAAGCAATTCGGACAGGCTTAAGCTACAAAGCTCaGATTTTGTAAGaGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTT
+>read671r start=605,mutations=1
+GTTCCTTTATAACACTATCACGAGCACTATAAAGAACGGCAGGCCAGGCATTTCACGTTGcGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCAT
+>read672r start=630,mutations=0
+AAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACTATCACGAGCACTATAAAGAACGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGG
+>read673r start=459,mutations=2
+ATGGTGCTGCGGTTCCTgCAACAGCGACGGCCGCAACGTCATCaTTCACTTCCTACAAAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCC
+>read674r start=320,mutations=0
+GCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTT
+>read675r start=565,mutations=2
+AGGCCAGGCATaTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTaAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACA
+>read676r start=413,mutations=3
+CACTTCCTACAAAGGATAGAGCtCTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGtTTGTTAGATCGTGGAAcCTACCGCCTGCC
+>read677r start=368,mutations=1
+GCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGcCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAAT
+>read678f start=312,mutations=2
+AACGGGGAAACCACTTGTTTGGATTCCCCCTTGCaGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACaGCTTATTGCCC
+>read679r start=856,mutations=3
+CACGGCTCTCCTTTACGcAAGGGGCGAtTTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAtGCCCAATAGTGTTCATATGCCTGTCTTTCC
+>read680r start=376,mutations=0
+GCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTA
+>read681f start=19,mutations=2
+ACTAGGTTGAGCCATGATTAACCTGCAATGAAGGTCATTCACACGCAGCGTCATTTAtTGGATTGcTGCACACTTAACTGGGTGCCGCGCTGGTGCTGAT
+>read682f start=574,mutations=1
+TGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTtAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTT
+>read683r start=476,mutations=3
+CAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCtAACAGCGACGGCCGCAgCGTCATCTTTCACTTCCTACAAAGGATAGAaCACTTACAAAATCCGA
+>read684r start=31,mutations=1
+TGAACTTCATGGATtAGCACCAGCGCGGCACCCAGTTAAGTGTGCACCAATCCATTAAATGACGCTGCGTGTGAATGACCTTCATTGCAGGTTAATCATG
+>read685r start=246,mutations=0
+GCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACC
+>read686f start=260,mutations=3
+GGAAGGCACCCAGGGAAAGTCGTTTaCCGGAAGAGAGTGGAGCTCCTACGTAAtCGGGGAAcCCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTAT
+>read687r start=243,mutations=1
+AGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTcCCGGCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGT
+>read688f start=449,mutations=0
+AATTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACC
+>read689f start=393,mutations=0
+CTGCCACCGCTTATTGCCCCGGCAGGCGGTAGTTTCCACGATCTAACAATCGAAGCAATTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGC
+>read690f start=81,mutations=3
+TTGGTGCACACgTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATtTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATAaAG
+>read691f start=788,mutations=1
+GAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTcAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTT
+>read692r start=813,mutations=1
+ACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACcTACCCTGTGAGTAAGCAG
+>read693f start=410,mutations=0
+CCCGGCAGGCGGTAGTTTCCACGATCTAACAATCGAAGCAATTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAA
+>read694f start=776,mutations=0
+GTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAAC
+>read695f start=861,mutations=2
+GACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCaCTTTCGTgAAGGAGAGCCGTGCTAAC
+>read696r start=289,mutations=1
+TCGGTTTCTCCTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGgTTCCCCGTTTACGTAGGAGCTCCACTCTCTTC
+>read697f start=880,mutations=1
+TTGGGCTTTGaAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTATATTCGGTCTTACCA
+>read698r start=581,mutations=2
+CACTATAAAGAACGGCAGGCCAGGCATTTCACtTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAAcATACAGCATCCCGTGCTCTGACGCTATGAGAGG
+>read699f start=868,mutations=1
+ATATGAACACTATTGGGCTTTGTAGACATTCCTCATCtATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTATAT
+>read700f start=97,mutations=0
+TGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCA
+>read701r start=810,mutations=2
+GCATGGATGAGGAcTGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCcGGAACTTACCCTGTGAGTAAGCAGAAT
+>read702r start=659,mutations=0
+TGGACGACTTGACGGACCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACTATCACGAGCACTATAAAGAACGGCAGGCCA
+>read703r start=421,mutations=1
+TCATCTTTCACTTCCTACAAAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGAaTGTTAGATCGTGGAAACTAC
+>read704r start=585,mutations=0
+CGAGCACTATAAAGAACGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGA
+>read705r start=250,mutations=0
+ATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGG
+>read706f start=580,mutations=0
+TCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGT
+>read707f start=631,mutations=0
+CCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAAGTTATGTAAGGACTTTT
+>read708f start=572,mutations=0
+GCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTC
+>read709f start=100,mutations=1
+GTGCCGCGCTGGTGCTGATCCATGAAGTTCATgTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGAC
+>read710r start=80,mutations=1
+TGTATGGCAAGGCGGAAATGGAgGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACCAGCGCGGCACCCAGTTAAGTGTGCACCAAT
+>read711f start=260,mutations=0
+GGAAGGCACCCAGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTAT
+>read712f start=156,mutations=0
+CTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCTA
+>read713f start=700,mutations=1
+GGAACTAACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGcA
+>read714f start=311,mutations=2
+AAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTtGGAGAAACCGAAaAACTGCCACCGCTTATTGCC
+>read715r start=43,mutations=2
+TACAAGTCCAGATGAACTTCATGGATCAGCACCAGCGCGGCACCCAGTTAAGTGTGCACCAATCCATTAAATGACtCTGCGTGTGAATGACCTaCATTGC
+>read716f start=300,mutations=0
+AGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCAC
+>read717r start=806,mutations=1
+GGATGAGGAATGTCTACAAAGCCCAATAGTGTTCAaATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACCCTGTGAGTAAGCAGAATGTGC
+>read718f start=794,mutations=0
+TTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGA
+>read719r start=828,mutations=0
+TTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTAC
+>read720r start=604,mutations=1
+TTCCTTTATAACACTATCACGAGCACTATAAAGAACGGCAGGCCAGGCATTTCACGTTGGGGCCGGTgCCCGGGCTATTGTGTGCTTAATATACAGCATC
+>read721f start=788,mutations=0
+GAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTT
+>read722f start=304,mutations=0
+CCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCT
+>read723f start=836,mutations=0
+CTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCC
+>read724f start=75,mutations=2
+AATGGATTGGTGCACACTTAACTGaGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCAcTTCCGCCTTGCC
+>read725r start=281,mutations=0
+TCCTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAAC
+>read726r start=302,mutations=0
+CGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAG
+>read727r start=405,mutations=1
+ACAAAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCCTaTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGGCAAT
+>read728r start=72,mutations=3
+AAGGCGGAgATGGAAGGAGCTGTCGCACGTACAAGTCCAGcTGAgCTTCATGGATCAGCACCAGCGCGGCACCCAGTTAAGTGTGCACCAATCCATTAAA
+>read729f start=384,mutations=0
+ACCGAACAACTGCCACCGCTTATTGCCCCGGCAGGCGGTAGTTTCCACGATCTAACAATCGAAGCAATTCGGACAGGCTTAAGCTACAAAGCTCGGATTT
+>read730r start=825,mutations=0
+TACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACCCT
+>read731r start=859,mutations=1
+TAGCACGGCTCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAtTGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTT
+>read732r start=779,mutations=0
+AGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACCCTGTGAGTAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAAAGG
+>read733r start=465,mutations=3
+GGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAtCGTCATCTTTCACTTCCTACAAAGcATAGAGCACTTACAAAATCCGAGCTTaGTAGCT
+>read734r start=281,mutations=1
+TCCTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGgGCTCCACTCTCTTCCGGCAAAC
+>read735r start=811,mutations=2
+AGCATaGATGAGGAATGTCTACAAAGaCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACCCTGTGAGTAAGCAGAA
+>read736f start=647,mutations=3
+tCGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAcTGTTATAAAGGAACTAACATCAAGTTATGTAAGGACTTTaACAATAGCGTGGTCCG
+>read737r start=532,mutations=0
+GGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGA
+>read738f start=617,mutations=0
+AAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAAGTT
+>read739f start=94,mutations=0
+AACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACC
+>read740r start=596,mutations=1
+TAACACTATCACGAGCACTATAAAGAACGGCAGGCCAGGCATTTtACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTC
+>read741f start=567,mutations=0
+TGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGC
+>read742r start=323,mutations=0
+ACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTG
+>read743r start=279,mutations=0
+CTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAACGA
+>read744r start=509,mutations=0
+GCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACT
+>read745r start=545,mutations=0
+GGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTT
+>read746r start=813,mutations=0
+ACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACCCTGTGAGTAAGCAG
+>read747f start=60,mutations=2
+CACGCAcCGTCtTTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTC
+>read748r start=88,mutations=1
+AGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGcTGAACTTCATGGATCAGCACCAGCGCGGCACCCAGTTAAGTGT
+>read749r start=244,mutations=3
+AAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCgTCCGGCAAACGACTTTCCtTGGGTGCCTTCCTGTGTAGCcGCACCCG
+>read750r start=147,mutations=1
+CCGTCTTTGACACCGGTTCCCACGCATCGCATtTGGTAAGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCG
+>read751f start=817,mutations=2
+TTACTCACAGGGTAAGTTCCTGAAGTATTAtTGTAtTGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCA
+>read752r start=769,mutations=2
+TGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACCCTGcGAGTAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAAAGGTACCAATGAt
+>read753r start=755,mutations=1
+CATTACATTAATACTTCAGGAACTTACCgTGTGAGTAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAAAGGTACCAATGAATTTACACACGTGGA
+>read754f start=132,mutations=0
+CTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAAC
+>read755f start=47,mutations=0
+TGAAGGTCATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTG
+>read756f start=300,mutations=0
+AGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCAC
+>read757f start=584,mutations=2
+CTCATAGCGTCAGAGCACGGGATGCTGTAcATTAAGCACACAATAGaCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTC
+>read758r start=111,mutations=0
+TAAGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCAC
+>read759r start=494,mutations=0
+ACGCTATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAG
+>read760r start=441,mutations=3
+CAAtAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATcGCTTCGgT
+>read761r start=196,mutations=0
+TCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGGTCT
+>read762r start=432,mutations=0
+CGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATC
+>read763r start=548,mutations=1
+TTGtGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCG
+>read764f start=184,mutations=1
+ACCTAAGACCGCAGACCCTCCTCCTTACCACcTGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGAAAGTCGTT
+>read765r start=673,mutations=0
+TGAATTTACACACGTGGACGACTTGACGGACCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACTATCACGAGCACTATAA
+>read766f start=489,mutations=4
+GTGCTCTATtCTTTGTAGGAAGTGAAAGAgGACGTTGCGGCCcTCGtTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCAT
+>read767r start=315,mutations=1
+CCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAATgCATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCC
+>read768r start=475,mutations=1
+AGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGcCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTTACAAAATCCGAG
+>read769f start=400,mutations=1
+CGCTcATTGCCCCGGCAGGCGGTAGTTTCCACGATCTAACAATCGAAGCAATTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCC
+>read770r start=617,mutations=2
+AACTTGATGTTAGTTCCTTTATAACACTATCACGAGCACTATtAAGAACGGCAGGCCAGGCATTTCAtGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTT
+>read771r start=146,mutations=1
+CGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGcAAGGAGCTGTCGC
+>read772f start=420,mutations=1
+GGTAGTTTCCACGATCTAACAATCGAAGCAATTCGGACAGGgTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATG
+>read773f start=554,mutations=0
+ACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAA
+>read774r start=9,mutations=0
+GCGCGGCACCCAGTTAAGTGTGCACCAATCCATTAAATGACGCTGCGTGTGAATGACCTTCATTGCAGGTTAATCATGGCTCAACCTAGTCACCCGGTGC
+>read775f start=453,mutations=1
+CGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAAgCGCAG
+>read776r start=452,mutations=1
+TGCGGTTCCTCCAACAGCGACGGCCGCAACGTCAcCTTTCACTTCCTACAAAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGA
+>read777f start=705,mutations=2
+TAACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTgCACGTGTGTAAATTgATTGGTACCTTTTGCCGAAAAATTTGAAAGCTA
+>read778r start=413,mutations=2
+CACTTCCTACAAAGGATAGAGCACTTACAAtATCCGAGCTcTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCC
+>read779r start=825,mutations=1
+TACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGaTCATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACCCT
+>read780f start=297,mutations=1
+TGGAGCTCCTACGTAAACGGGGAAACCACTcGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGC
+>read781r start=0,mutations=1
+CCAGTTAAGTGTGCACCAATCCATTAAATGACGCTGCGTGTGAATGACCTTCATTGCAGGTTAATCATGGCTCAACCTAGTCACCgGGTGCTGGGCGGCA
+>read782r start=699,mutations=1
+TCAAATTTTTCGGCAAAcGGTACCAATGAATTTACACACGTGGACGACTTGACGGACCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCT
+>read783f start=89,mutations=0
+CACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTA
+>read784r start=511,mutations=1
+CAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCcCCAACAGCGACGGCCGCAACGTCATCTTTCA
+>read785f start=321,mutations=3
+ACCACTTGTTTGGATTCCCCCTTGCCGATTCtGCCCTATCAGGATGTATTTAACTTAGGAGAAACgGAACAACTGCCACCGCTTATTGCCCCtGCAGGCG
+>read786f start=23,mutations=0
+GGTTGAGCCATGATTAACCTGCAATGAAGGTCATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCAT
+>read787f start=81,mutations=1
+TTGGTGCACtCTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAG
+>read788r start=500,mutations=1
+GCTCTGACGCTATGAGAGGATCTCCAGCTCGCcCAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAA
+>read789f start=181,mutations=0
+ACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGAAAGTC
+>read790r start=900,mutations=3
+GGGGCAAACTATCGAGCCCGTGGTgAGACCGAATATAACGTTAGCACGGgTCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATAaAGCATGGATGA
+>read791r start=724,mutations=0
+TGAGTAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAAAGGTACCAATGAATTTACACACGTGGACGACTTGACGGACCACGCTATTGTAAAAGTC
+>read792f start=51,mutations=3
+GGTCATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTcCCGCGCTGGTGCTGATCCATGAAGTTCATCaGGACTTGTACGgGCGAC
+>read793f start=879,mutations=4
+tTTGGGCTTTGcAGACATTCCTCATCCtTGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGaCGTGCTAACGTTATATTCGGTCTTACC
+>read794r start=772,mutations=1
+ATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACCCTGTGAGTAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAAAGGTACCAtT
+>read795r start=599,mutations=2
+TTATAgCACTATCACGAGCACTATAAAGAACGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCgGGGCTATTGTGTGCTTAATATACAGCATCCCGTG
+>read796f start=597,mutations=0
+AGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTAT
+>read797r start=265,mutations=1
+TCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGaAAACGACTTTCCCTGGGTGC
+>read798f start=258,mutations=2
+CAGGAAGGCACCCAGGGAAAGTCcTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCtATTCGGCCCT
+>read799f start=703,mutations=2
+ACTAACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGcCGTCCACGgGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGC
+>read800r start=110,mutations=2
+AAGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGgAATGGAAGGAGCTGTCGCACGTACAAGTCCAtATGAACTTCATGGATCAGCACC
+>read801r start=263,mutations=1
+CTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGaAGGAGCTCCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCT
+>read802f start=651,mutations=0
+GAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAA
+>read803r start=804,mutations=0
+ATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACCCTGTGAGTAAGCAGAATGTGCTT
+>read804r start=817,mutations=2
+TGATACAGCATGGATGAGGAcTGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACCCTGTGAGTgA
+>read805f start=807,mutations=0
+CACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCA
+>read806f start=532,mutations=0
+TCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCC
+>read807r start=843,mutations=2
+TACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCgGTCTTTCCACATTACATTAAg
+>read808f start=189,mutations=0
+AGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGAAAGTCGTTTGCCG
+>read809f start=898,mutations=1
+CCTCATCCATGCTGTATCAGTAATGTAgAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTATATTCGGTCTTACCACGGGCTCGATAGTTTGCC
+>read810r start=12,mutations=1
+CCAGCGCGGaACCCAGTTAAGTGTGCACCAATCCATTAAATGACGCTGCGTGTGAATGACCTTCATTGCAGGTTAATCATGGCTCAACCTAGTCACCCGG
+>read811r start=511,mutations=4
+CAGCATCCCGTGCTCTGACGCTAgGAGAGGATaTtCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCaGCAACGTCATCTTTCA
+>read812f start=450,mutations=1
+ATTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGcTGACGTTGCGGCCGTCGCTGTTGGAGGAACCG
+>read813r start=557,mutations=1
+CAgTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGGCGCCAT
+>read814f start=679,mutations=0
+TGCTCGTGATAGTGTTATAAAGGAACTAACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTA
+>read815r start=416,mutations=2
+TTTCACTTCCTACAgAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTaCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCT
+>read816f start=615,mutations=3
+TTAAGCACACAAcAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTttCATCAAG
+>read817f start=653,mutations=1
+AATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAtCATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGT
+>read818r start=252,mutations=0
+GAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGC
+>read819f start=79,mutations=0
+GATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATAC
+>read820f start=524,mutations=1
+TGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATcCTGTATATTAAGCACA
+>read821f start=508,mutations=0
+AAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATG
+>read822f start=502,mutations=0
+TGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCAC
+>read823f start=628,mutations=1
+AGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAAGTTATGTAAGGAaT
+>read824f start=482,mutations=0
+TTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATC
+>read825f start=779,mutations=1
+CCTTTTGCCGAAAAATTTGAAAGCTAgGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACT
+>read826r start=836,mutations=0
+GGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCAG
+>read827r start=547,mutations=2
+TGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGcGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGGaGCCATGGTGCTGCGG
+>read828f start=838,mutations=1
+GAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTAgTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTT
+>read829f start=13,mutations=0
+CGGGTGACTAGGTTGAGCCATGATTAACCTGCAATGAAGGTCATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGT
+>read830r start=564,mutations=1
+GGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAtCTCGCACAG
+>read831f start=5,mutations=0
+CCCAGCACCGGGTGACTAGGTTGAGCCATGATTAACCTGCAATGAAGGTCATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTGCC
+>read832f start=786,mutations=0
+CCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGC
+>read833f start=676,mutations=3
+TAGTGCTCGTGATAGTGTTATAAgGGAACTAACATCAAGTTATGTAAGGtCTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGcAAATTCATTG
+>read834r start=570,mutations=0
+ACGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTC
+>read835r start=458,mutations=0
+TGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCCT
+>read836r start=669,mutations=2
+TTTACACACGTGGACGACTTGACGGACCACGCgATTGTAAAAGTCCTTACAcAACTTGATGTTAGTTCCTTTATAACACTATCACGAGCACTATAAAGAA
+>read837r start=682,mutations=0
+AGGTACCAATGAATTTACACACGTGGACGACTTGACGGACCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACTATCACGA
+>read838f start=396,mutations=0
+CCACCGCTTATTGCCCCGGCAGGCGGTAGTTTCCACGATCTAACAATCGAAGCAATTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCT
+>read839r start=310,mutations=0
+GCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTA
+>read840f start=537,mutations=1
+GTTGGAGGAACCGCgGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGG
+>read841r start=109,mutations=0
+AGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACCA
+>read842f start=254,mutations=1
+TACACAGGAAGGCACCCAGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAcCGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGG
+>read843f start=318,mutations=0
+GAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTATTGCCCCGGCAG
+>read844f start=587,mutations=0
+ATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTG
+>read845f start=190,mutations=0
+GACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGAAAGTCGTTTGCCGG
+>read846r start=155,mutations=1
+AGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAgGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGG
+>read847f start=563,mutations=1
+CCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGa
+>read848f start=741,mutations=2
+GGgCCGTCAAGTCGTCCACGTGTGTAAAaTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAA
+>read849r start=94,mutations=1
+GGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCAtCAGCGCGGCACCCAGTT
+>read850r start=329,mutations=1
+GAAACTACCGCCTGCCGGGGCAATAAaCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAA
+>read851f start=864,mutations=1
+AGGCATATGAACACTATTGGGCTTTGTAGACATTCaTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTT
+>read852r start=385,mutations=0
+AAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGG
+>read853r start=378,mutations=0
+GAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCC
+>read854r start=844,mutations=1
+TTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTgTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAA
+>read855r start=332,mutations=1
+GTGGAAACTACCGCCTGCCGGGGCAATAAGCtGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCC
+>read856f start=201,mutations=2
+CTCCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCgcCACAGGAAGGCACCCAGGGAAAGTCGTTTGCCGGAAGAGAGTGGA
+>read857f start=471,mutations=0
+AAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCG
+>read858r start=183,mutations=2
+cCGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACaCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTTAGGTG
+>read859r start=654,mutations=0
+GACTTGACGGACCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACTATCACGAGCACTATAAAGAACGGCAGGCCAGGCAT
+>read860f start=84,mutations=0
+GTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACC
+>read861f start=576,mutations=1
+GAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGaGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTA
+>read862r start=130,mutations=1
+TCCCACGCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCtAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGAT
+>read863f start=240,mutations=0
+AAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCC
+>read864f start=863,mutations=0
+CAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGT
+>read865r start=452,mutations=0
+TGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGA
+>read866f start=184,mutations=4
+ACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCaTGaGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACaCAaGGAAAGTCGTT
+>read867f start=483,mutations=0
+TTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCC
+>read868f start=155,mutations=0
+CCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCT
+>read869r start=794,mutations=0
+TCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACCCTGTGAGTAAGCAGAATGTGCTTAGCTTTCAAA
+>read870f start=478,mutations=1
+GGATTTTGTAAGTGCTtTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGA
+>read871r start=238,mutations=1
+GAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAACGACTTTCCCaGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTG
+>read872r start=539,mutations=2
+GTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAcAGGATCTCCAGCTCGCACAGGCGCCATGGTcCTGCGGTTCCTCCA
+>read873r start=21,mutations=0
+GGATCAGCACCAGCGCGGCACCCAGTTAAGTGTGCACCAATCCATTAAATGACGCTGCGTGTGAATGACCTTCATTGCAGGTTAATCATGGCTCAACCTA
+>read874r start=144,mutations=1
+TCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGcAAGGAGCTGTCGCAC
+>read875r start=129,mutations=1
+CCCACGCATCGCATGTGGTAAGGAGGAGGGTgTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATG
+>read876r start=538,mutations=1
+TCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCcCAGGCGCCATGGTGCTGCGGTTCCTCCAA
+>read877f start=839,mutations=0
+AAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTT
+>read878r start=598,mutations=0
+TATAACACTATCACGAGCACTATAAAGAACGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGC
+>read879f start=576,mutations=1
+GAGATCCTCTCATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACcCAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTA
+>read880f start=115,mutations=2
+TGATCCATGAAGTTaATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCcCCTTACCAC
+>read881r start=875,mutations=1
+AGACCGAATATAACGTTAGCACGGCTCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTcCAAAGCCCAATAGTG
+>read882f start=865,mutations=0
+GGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTA
+>read883r start=557,mutations=0
+CATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGGCGCCAT
+>read884f start=268,mutations=2
+CCCAGtGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATcT
+>read885r start=182,mutations=2
+CGACTTTCCCTGGGTGCCTTCCTGaGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAtGGTCTGCGGTCTTAGGTGG
+>read886f start=4,mutations=0
+GCCCAGCACCGGGTGACTAGGTTGAGCCATGATTAACCTGCAATGAAGGTCATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTGC
+>read887f start=815,mutations=2
+GCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGgAATGTGGAAAGACtGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTAT
+>read888r start=440,mutations=2
+AACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAgGGATAGAGCtCTTACAAAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATT
+>read889r start=897,mutations=0
+GCAAACTATCGAGCCCGTGGTAAGACCGAATATAACGTTAGCACGGCTCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGA
+>read890r start=264,mutations=1
+CCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACtAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCC
+>read891f start=141,mutations=0
+TACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAA
+>read892f start=732,mutations=0
+CAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAA
+>read893f start=76,mutations=3
+ATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGcGCGACAGCTCCTTgCATTTCCcCCTTGCCA
+>read894f start=15,mutations=0
+GGTGACTAGGTTGAGCCATGATTAACCTGCAATGAAGGTCATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGC
+>read895f start=780,mutations=0
+CTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTA
+>read896r start=564,mutations=2
+GGCCAGGCATTTCACGTTGGGGCCGGTCCaCGcGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAG
+>read897f start=893,mutations=1
+ACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTATATTCGGTCgTACCACGGGCTCGATAGT
+>read898r start=681,mutations=0
+GGTACCAATGAATTTACACACGTGGACGACTTGACGGACCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACTATCACGAG
+>read899r start=553,mutations=1
+TCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGAgGCTATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTG
+>read900f start=454,mutations=0
+GGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGC
+>read901r start=611,mutations=1
+ATGTTAGTTCCTTTATAACACTATCACGAGCACTATAAAGAACGGCAGGCCAGGCATTTCAtGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATA
+>read902f start=344,mutations=2
+GCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTATTGCCCCGGCAGGCGGTAGTTaCCACcATCTAACAATC
+>read903f start=530,mutations=1
+CGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGgCAGAGCACGGGATGCTGTATATTAAGCACACAATAG
+>read904f start=226,mutations=1
+GGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTgCTACGTAAACGGGGAAACCAC
+>read905r start=747,mutations=1
+TAATACTTCAGGAACTTACCCcGTGAGTAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAAAGGTACCAATGAATTTACACACGTGGACGACTTGA
+>read906r start=249,mutations=1
+TCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGgTCCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGC
+>read907f start=807,mutations=1
+CACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGaGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCA
+>read908f start=853,mutations=0
+TGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCC
+>read909r start=868,mutations=0
+ATATAACGTTAGCACGGCTCTCCTTTACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATAT
+>read910r start=518,mutations=1
+TAATATACAGCATCCCGTGCTCTGACtCTATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCA
+>read911r start=566,mutations=0
+CAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCAC
+>read912r start=767,mutations=1
+CCTGTCTTTCCcCATTACATTAATACTTCAGGAACTTACCCTGTGAGTAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAAAGGTACCAATGAATT
+>read913f start=417,mutations=1
+GGCGGTAGTTTCCACGATCTAACAATCGAAGgAATTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAG
+>read914f start=650,mutations=1
+TGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAAGTTATGTAAGGACTcTTACAATAGCGTGGTCCGTCA
+>read915f start=459,mutations=1
+GGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGgAGCACCAT
+>read916r start=643,mutations=1
+CCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACgATCACGAGCACTATAAAGAACGGCAGGCCAGGCATTTCACGTTGGG
+>read917f start=793,mutations=0
+ATTTGAAAGCTAAGCACATTCTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAG
+>read918f start=424,mutations=0
+GTTTCCACGATCTAACAATCGAAGCAATTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGT
+>read919r start=384,mutations=0
+AAATCCGAGCTTTGTAGCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGT
+>read920f start=336,mutations=3
+TCaCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAtAAACCGAACAACTGCCACCGCTTATTGCCCgGGCAGGCGGTAGTTTCCACGATC
+>read921r start=155,mutations=1
+AGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAcATGGAAGG
+>read922f start=337,mutations=0
+CCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTATTGCCCCGGCAGGCGGTAGTTTCCACGATCT
+>read923f start=164,mutations=2
+TCCGCCTTGCCATACAGACCACCTAAGACCGCgGACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCaACACAGGAA
+>read924r start=470,mutations=2
+GCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGgCGGCCGCAACGTCATCTTTCACTTCCTACAAAGtATAGAGCACTTACAAAATCCGAGCTTTG
+>read925r start=1,mutations=1
+CCCAGTTcAGTGTGCACCAATCCATTAAATGACGCTGCGTGTGAATGACCTTCATTGCAGGTTAATCATGGCTCAACCTAGTCACCCGGTGCTGGGCGGC
+>read926f start=651,mutations=0
+GAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAA
+>read927f start=810,mutations=2
+ATTCTGCTTACTCACAGGaTAAGTTgCTGAAGTATTAATGTAATGTGGAAAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGC
+>read928f start=330,mutations=1
+TTGGATTCCCCCcTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTATTGCCCCGGCAGGCGGTAGTTTCC
+>read929r start=12,mutations=0
+CCAGCGCGGCACCCAGTTAAGTGTGCACCAATCCATTAAATGACGCTGCGTGTGAATGACCTTCATTGCAGGTTAATCATGGCTCAACCTAGTCACCCGG
+>read930f start=690,mutations=0
+GTGTTATAAAGGAACTAACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGA
+>read931r start=200,mutations=1
+CCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGACACCGGTTCCaACGCATCGCATGTGGTAAGGAGGAGG
+>read932r start=462,mutations=0
+GCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTTACAAAATCCGAGCTTTGTAGCTTAA
+>read933r start=212,mutations=0
+TACGTAGGAGCTCCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTG
+>read934r start=516,mutations=0
+ATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATC
+>read935f start=35,mutations=0
+ATTAACCTGCAATGAAGGTCATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTG
+>read936r start=62,mutations=2
+TGGAAGGAGaTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACCAGCGCGGCACCCAaTTAAGTGTGCACCAATCCATTAAATGACGCTGCG
+>read937f start=646,mutations=1
+AACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAACATCAtGTTATGTAAGGACTTTTACAATAGCGTGGTCC
+>read938r start=155,mutations=0
+AGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGG
+>read939f start=125,mutations=1
+AGTTCATCTGGACTTGTACGTGCtACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCG
+>read940r start=567,mutations=1
+GCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCaCA
+>read941f start=402,mutations=1
+CTTATTGCCCCGGCAGGCGtTAGTTTCCACGATCTAACAATCGAAGCAATTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTT
+>read942f start=176,mutations=0
+TACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGA
+>read943f start=856,mutations=2
+GGAAAGACAGGCATATGAACcCTATTGGGCTTTGTAGACATTCgTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTG
+>read944f start=222,mutations=5
+GCGTGGGAACCGGgGTCAAAGACGGGTGCCGCTACACAGGAAaGCACCCcGGGAAAGTCGTTTGCCtGAgGAGAGTGGAGCTCCTACGTAAACGGGGAAA
+>read945r start=836,mutations=1
+GGGaCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCAG
+>read946r start=536,mutations=0
+CCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACA
+>read947r start=373,mutations=1
+TTGTAcCTTAAGCCTGTCCGAATTGCTTCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGT
+>read948r start=893,mutations=2
+ACTATCGAGCCCGTGGTAAGACCGAATATAACGTTAGCACGGCTCTCCTTTACGAAAGGGGCGAtTTGTACATTACTGATACAGCATGGAgGAGGAATGT
+>read949r start=231,mutations=0
+AACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAACGACTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGACACCGG
+>read950r start=665,mutations=1
+CACACGTGGACGACTTGACGGACCACGCaATTGTAAAAGTCCTTACATAACTTGATGTTAGTTCCTTTATAACACTATCACGAGCACTATAAAGAACGGC
+>read951r start=754,mutations=2
+AcTACATTAATACTTCgGGAACTTACCCTGTGAGTAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAAAGGTACCAATGAATTTACACACGTGGAC
+>read952f start=176,mutations=4
+TACAGACCACCTAAGACCGCAGACCCTCCTaCTTACCACATGCGtTGCGTGGGAACCGGTGTCAAAGACGGGTaCCGCTACACAGGAAGGCACCCAtGGA
+>read953f start=723,mutations=2
+GGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAAcTCATTGGTACCTTTTGCCGAAAAATTTGcAAGCTAAGCACATTCTGCTTACTC
+>read954r start=827,mutations=0
+TGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTCAGGAACTTACC
+>read955f start=626,mutations=2
+gTAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAcGAACTAACATCAAGTTATGTAAGGA
+>read956f start=877,mutations=2
+CTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTAcCAGTAATGTACAATTCGCCCCTTTCGTAgAGGAGAGCCGTGCTAACGTTATATTCGGTCTTA
+>read957r start=660,mutations=2
+GTGcACGACTTGACGGACCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTAaTTCCTTTATAACACTATCACGAGCACTATAAAGAACGGCAGGCC
+>read958f start=859,mutations=0
+AAGACAGGCATATGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTA
+>read959r start=704,mutations=1
+AGCTTTCtAATTTTTCGGCAAAAGGTACCAATGAATTTACACACGTGGACGACTTGACGGACCACGCTATTGTAAAAGTCCTTACATAACTTGATGTTAG
+>read960f start=818,mutations=1
+TACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGGAAAGACAGGCATtTGAACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAG
+>read961r start=842,mutations=0
+ACGAAAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATA
+>read962f start=874,mutations=0
+ACACTATTGGGCTTTGTAGACATTCCTCATCCATGCTGTATCAGTAATGTACAATTCGCCCCTTTCGTAAAGGAGAGCCGTGCTAACGTTATATTCGGTC
+>read963r start=93,mutations=1
+GTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACCAGCGCGGCACCCAGTTc
+>read964r start=565,mutations=2
+AGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATgGTGTGCTTAATATACAGCATCCCGTGCTCTGACGCTATGAGAGGATCTCCgGCTCGCACA
+>read965f start=608,mutations=0
+CTGTATATTAAGCACACAATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGATAGTGTTATAAAGGAACTAA
+>read966f start=626,mutations=1
+ATAGCCCGGGGACCGGCCCCAACGTGAAATGCCTGGCCTGCCGTTCTTTATAGTGCTCGTGAcAGTGTTATAAAGGAACTAACATCAAGTTATGTAAGGA
+>read967f start=18,mutations=2
+GACTAGGTTGAGCCATGATTAACCTGCAATGAAGGTCATTCACACGCAGCGTCATTTAATGcATTGGTGCACACTTAACTGGGTGCCGCGCaGGTGCTGA
+>read968f start=758,mutations=2
+ACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAgTTTGAAAGCTAAGCACATTtTGCTTACTCACAGGGTAAGTTCCTGAAGTATTAATGTAATGTGG
+>read969r start=838,mutations=0
+AAGGGGCGAATTGTACATTACTGATACAGCATGGATGAGGAATGTCTACAAAGCCCAATAGTGTTCATATGCCTGTCTTTCCACATTACATTAATACTTC
+>read970f start=7,mutations=0
+CAGCACCGGGTGACTAGGTTGAGCCATGATTAACCTGCAATGAAGGTCATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTGCCGC
+>read971r start=103,mutations=1
+AGGGTCTGCGGTaTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACAAGTCCAGATGAACTTCATGGATCAGCACCAGCGCGG
+>read972f start=188,mutations=1
+AAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGAgAGTCGTTTGCC
+>read973r start=180,mutations=2
+ACTTTCCCTGGGTGCCTTCCTGaGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGcTCTGCGGTCTTAGGTGGTC
+>read974f start=536,mutations=2
+TGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATgCTCTaATAGCGTCAGAGCACGGGATGCTGTATATTAAGCACACAATAGCCCGGG
+>read975f start=707,mutations=1
+ACATCAAGTTATGTAAGGACTTTTACAATAGCGTGaTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAG
+>read976f start=15,mutations=2
+GGTGACTAGGTgGAGCCATGATTAACCTGCAATGAAGGTCATTCACACGCAGCGTCATTTAATGGATgGGTGCACACTTAACTGGGTGCCGCGCTGGTGC
+>read977f start=110,mutations=0
+GGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTT
+>read978r start=139,mutations=1
+GACACCGGTTCCCACGCATCGCATGTGGTAAGGAtGAGGGTCTGCGGTCTTAGGTGGTCTGTATGGCAAGGCGGAAATGGAAGGAGCTGTCGCACGTACA
+>read979f start=504,mutations=0
+TAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTCTCATAGCGTCAGAGCACGG
+>read980f start=295,mutations=0
+AGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACT
+>read981r start=179,mutations=2
+CTTTCCCTGGGTGCCTTCCTGTGTAGCGGCACCCGTCTTTGACACCGGTTCCCACGCATCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTaAGGgGGTCT
+>read982f start=543,mutations=2
+GGAACCGCAGCACCATGGCGCCTGTGCGAGCTGGAGATCCTaTCATAGCGTCAGAGCACGGGATGCTGTATcTTAAGCACACAATAGCCCGGGGACCGGC
+>read983r start=272,mutations=0
+AAATACATCCTGATAGGGCCGAATCGGCAAGGGGGAATCCAAACAAGTGGTTTCCCCGTTTACGTAGGAGCTCCACTCTCTTCCGGCAAACGACTTTCCC
+>read984f start=733,mutations=2
+AATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGCTAAGCACATTCcGCTTACTCACAcGGTAAG
+>read985r start=357,mutations=2
+TCCGAAaTGCTaCGATTGTTAGATCGTGGAAACTACCGCCTGCCGGGGCAATAAGCGGTGGCAGTTGTTCGGTTTCTCCTAAGTTAAATACATCCTGATA
+>read986f start=52,mutations=1
+GcCATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACA
+>read987r start=480,mutations=1
+TCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTTACAAAAg
+>read988r start=121,mutations=4
+TCGCATGTGGTAAGGAGGAGGGTCTGCGGTCTTAGGTGGTCcGTATGGCAAGGCGGAAATGGAAGaAGCTGTCGCACGTACAtGTCCcGATGAACTTCAT
+>read989f start=68,mutations=1
+GTCATTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCAcTTCCG
+>read990r start=780,mutations=1
+TAGTGTTCATATGCCTGTtTTTCCACATTACATTAATACTTCAGGAACTTACCCTGTGAGTAAGCAGAATGTGCTTAGCTTTCAAATTTTTCGGCAAAAG
+>read991f start=117,mutations=0
+ATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACAT
+>read992f start=312,mutations=1
+AACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAtGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTATTGCCC
+>read993f start=703,mutations=0
+ACTAACATCAAGTTATGTAAGGACTTTTACAATAGCGTGGTCCGTCAAGTCGTCCACGTGTGTAAATTCATTGGTACCTTTTGCCGAAAAATTTGAAAGC
+>read994r start=598,mutations=0
+TATAACACTATCACGAGCACTATAAAGAACGGCAGGCCAGGCATTTCACGTTGGGGCCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGC
+>read995f start=330,mutations=0
+TTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTATTGCCCCGGCAGGCGGTAGTTTCC
+>read996f start=463,mutations=1
+TAAGCTACAAAGCTCGGATTTTGTAAGTGCTCTATCCTTTGTAGGAAGTGAAAGATGACGTTGCGGCCGTCGCTGTTGGAGGAAaCGCAGCACCATGGCG
+>read997r start=567,mutations=3
+GCAGGCCAGGCATTTCACGTTGGtGaCGGTCCCCGGGCTATTGTGTGCTTAATATACAGCATCCCGTGCTtTGACGCTATGAGAGGATCTCCAGCTCGCA
+>read998f start=164,mutations=0
+TCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAA
+>read999r start=484,mutations=1
+AGGATCTCCAGCTCGCACAGGCGCCATGGTGCTGCGGTTCCTCCAACAGCGACGGCCGCAACGTCATCTTTCACTTCCTACAAAGGATAGAGCACTgACA
diff --git a/tests/test-data/simple-genome.fa b/tests/test-data/simple-genome.fa
new file mode 100644
index 0000000..b949490
--- /dev/null
+++ b/tests/test-data/simple-genome.fa
@@ -0,0 +1,2 @@
+>genome
+TGCCGCCCAGCACCGGGTGACTAGGTTGAGCCATGATTAACCTGCAATGAAGGTCATTCACACGCAGCGTCATTTAATGGATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTTCATCTGGACTTGTACGTGCGACAGCTCCTTCCATTTCCGCCTTGCCATACAGACCACCTAAGACCGCAGACCCTCCTCCTTACCACATGCGATGCGTGGGAACCGGTGTCAAAGACGGGTGCCGCTACACAGGAAGGCACCCAGGGAAAGTCGTTTGCCGGAAGAGAGTGGAGCTCCTACGTAAACGGGGAAACCACTTGTTTGGATTCCCCCTTGCCGATTCGGCCCTATCAGGATGTATTTAACTTAGGAGAAACCGAACAACTGCCACCGCTTATTGCCCCGGCAGGCGGTAGTTTCCACGATCTAACAATCGAAGCAATTCGGACAGGCTTAAGCTACAAAGCTCGGATTTTGTAAGTG [...]
diff --git a/tests/test-data/single-read.fa b/tests/test-data/single-read.fa
new file mode 100644
index 0000000..a20016c
--- /dev/null
+++ b/tests/test-data/single-read.fa
@@ -0,0 +1,2 @@
+>895:1:1:1246:14654 1:N:0:NNNNN
+CAGGCGCCCACCACCGTGCCCTCCAACCTGATGGT
diff --git a/tests/test-data/unclean-reads.fastq b/tests/test-data/unclean-reads.fastq
new file mode 100644
index 0000000..c675658
--- /dev/null
+++ b/tests/test-data/unclean-reads.fastq
@@ -0,0 +1,8 @@
+ at read1
+GGTTGACGGGGNNNAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGG
++
+####################################################################################################
+ at read2
+GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGANNNCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGG
++
+####################################################################################################
diff --git a/tests/test_assembly.py b/tests/test_assembly.py
new file mode 100644
index 0000000..d3ba0a4
--- /dev/null
+++ b/tests/test_assembly.py
@@ -0,0 +1,886 @@
+# -*- coding: UTF-8 -*-
+#
+# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# Copyright (C) 2010-2015, Michigan State University.
+# Copyright (C) 2015-2016, The Regents of the University of California.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+#
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# * Redistributions in binary form must reproduce the above
+# copyright notice, this list of conditions and the following
+# disclaimer in the documentation and/or other materials provided
+# with the distribution.
+#
+# * Neither the name of the Michigan State University nor the names
+# of its contributors may be used to endorse or promote products
+# derived from this software without specific prior written
+# permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Contact: khmer-project at idyll.org
+# pylint: disable=missing-docstring,protected-access,no-member,invalid-name
+
+from __future__ import print_function
+from __future__ import absolute_import
+
+import itertools
+import random
+
+import khmer
+from khmer.khmer_args import estimate_optimal_with_K_and_f as optimal_fp
+from khmer import ReadParser
+from khmer import reverse_complement as revcomp
+from . import khmer_tst_utils as utils
+
+import pytest
+import screed
+
+
+def teardown():
+ utils.cleanup()
+
+# We just define this globally rather than in a module-level fixture,
+# as we need it during parameterization and whatnot.
+K = 21
+
+
+class Kmer(str):
+
+ def __init__(self, value, pos=0):
+ self.pos = pos
+
+ def __new__(cls, value, pos=0):
+ if not len(value) == K:
+ raise ValueError('bad k-mer length')
+ return str.__new__(cls, value)
+
+
+def mutate_base(base):
+ if base in 'AT':
+ return random.choice('GC')
+ elif base in 'GC':
+ return random.choice('AT')
+ else:
+ assert False, 'bad base'
+
+
+def mutate_sequence(sequence, N=1):
+ sequence = list(sequence)
+ positions = random.sample(range(len(sequence)), N)
+
+ for i in positions:
+ sequence[i] = mutate_base(sequence[i])
+
+ return ''.join(sequence)
+
+
+def mutate_position(sequence, pos):
+ sequence = list(sequence)
+ sequence[pos] = mutate_base(sequence[pos])
+ return ''.join(sequence)
+
+
+def get_random_sequence(length, exclude=None):
+ '''Generate a random (non-looping) nucleotide sequence.
+
+ To be non-overlapping, the sequence should not include any repeated
+ length K-1 k-mers.
+
+ Args:
+ exclude (str): If not None, add the k-mers from this sequence to the
+ seen set.
+
+ Returns:
+ str: A random non-looping sequence.
+ '''
+
+ seen = set()
+
+ def add_seen(kmer):
+ seen.add(kmer)
+ seen.add(revcomp(kmer))
+
+ if exclude is not None:
+ for pos in range(0, len(exclude) - K):
+ add_seen(exclude[pos:pos + K - 1])
+
+ seq = [random.choice('ACGT') for _ in range(K - 1)] # do first K-1 bases
+ add_seen(''.join(seq))
+
+ while(len(seq) < length):
+ next_base = random.choice('ACGT')
+ next_kmer = ''.join(seq[-K + 2:] + [next_base])
+ assert len(next_kmer) == K - 1
+ if (next_kmer) not in seen:
+ seq.append(next_base)
+ add_seen(next_kmer)
+ else:
+ continue
+ return ''.join(seq)
+
+
+def reads(sequence, L=100, N=100):
+ positions = list(range(len(sequence) - L))
+ for i in range(N):
+ start = random.choice(positions)
+ yield sequence[start:start + L]
+
+
+def kmers(sequence):
+ for i in range(len(sequence) - K + 1):
+ yield sequence[i:i + K]
+
+
+def test_mutate_sequence():
+ for _ in range(100):
+ assert 'A' not in mutate_sequence('A' * 10, 10)
+ assert 'T' not in mutate_sequence('T' * 10, 10)
+ assert 'C' not in mutate_sequence('C' * 10, 10)
+ assert 'G' not in mutate_sequence('G' * 10, 10)
+
+
+def test_mutate_position():
+ assert mutate_position('AAAA', 2) in ['AACA', 'AAGA']
+ assert mutate_position('TTTT', 2) in ['TTCT', 'TTGT']
+ assert mutate_position('CCCC', 2) in ['CCAC', 'CCTC']
+ assert mutate_position('GGGG', 2) in ['GGAG', 'GGTG']
+
+
+def test_reads():
+ contigfile = utils.get_test_data('simple-genome.fa')
+ contig = list(screed.open(contigfile))[0].sequence
+
+ for read in reads(contig):
+ assert read in contig
+
+ for read in reads(contig):
+ assert mutate_sequence(read) not in contig
+
+
+'''
+# GRAPH STRUCTURE FIXTURES
+
+These fixtures emit various graph structures with their corresponding
+sequences and important nodes. They take a random sequence fixture and
+a graph fixture, then consume sequence and generate k-mers accordingly.
+
+We're using a bespoke but simple language to describe graph structures in the
+docstrings of these tests. It is as follows:
+
+ o: Node
+ [x:y]: Node at position in sequence
+ [x:y]+S: Node at position in sequence with extra base (where S in ACGT)
+ (Name), ([x:y] Name): Named node, named node at position
+ → : Edge
+ ~~: Tandem →o→ repeats
+'''
+
+
+ at pytest.fixture(params=['simple-genome.fa'])
+def known_sequence(request):
+ fn = utils.get_test_data(request.param)
+ return list(screed.open(fn))[0].sequence
+
+
+ at pytest.fixture(params=list(range(500, 1600, 500)),
+ ids=lambda val: '(L={0})'.format(val))
+def random_sequence(request):
+
+ def get(exclude=None):
+ return get_random_sequence(request.param, exclude=exclude)
+
+ return get
+
+
+ at pytest.fixture(params=[khmer.Nodegraph, khmer.Countgraph],
+ ids=['(Type=Nodegraph)', '(Type=Countgraph)'])
+def graph(request):
+
+ num_kmers = 50000
+ des_fp = 0.00001
+ args = optimal_fp(num_kmers, des_fp)
+ print('Graph Params:', args)
+
+ return request.param(K, args.htable_size, args.num_htables)
+
+
+def hdn_counts(sequence, graph):
+ '''Get the degree distribution of nodes with degree more than 2.
+ '''
+
+ hdns = {}
+ for kmer in kmers(sequence):
+ d = graph.kmer_degree(kmer)
+ if d > 2:
+ hdns[d] = hdns.get(d, 0) + 1
+
+ return hdns
+
+
+ at pytest.fixture
+def linear_structure(request, graph, random_sequence):
+ '''Sets up a simple linear path graph structure.
+
+ sequence
+ [0]→o→o~~o→o→[-1]
+ '''
+ sequence = random_sequence()
+ graph.consume(sequence)
+
+ # Check for false positive neighbors in our graph
+ # Mark as an expected failure if any are found
+ if hdn_counts(sequence, graph):
+ request.applymarker(pytest.mark.xfail)
+
+ return graph, sequence
+
+
+ at pytest.fixture(params=[K * 2, -K * 2],
+ ids=['(Where={0})'.format(i) for i in ['Start', 'End']])
+def right_tip_structure(request, graph, random_sequence):
+ '''
+ Sets up a graph structure like so:
+ ([S+1:S+K]+B tip)
+ sequence ↗
+ [0]→o→o~~o→(L)→([S:S+K] HDN)→(R)→o→o→o~~o→[-1]
+
+ Where S is the start position of the high degreen node (HDN).
+ That is, it has a single branch at the Sth K-mer.
+ '''
+ sequence = random_sequence()
+ S = request.param
+ if S < 0:
+ S = len(sequence) + S
+ # the HDN
+ HDN = Kmer(sequence[S:S + K], pos=S)
+ # left of the HDN
+ L = Kmer(sequence[S - 1:S - 1 + K], pos=S - 1)
+ # right of the HDN
+ R = Kmer(sequence[S + 1:S + 1 + K], pos=S + 1)
+ # the branch kmer
+ tip = Kmer(mutate_position(R, -1),
+ pos=R.pos)
+
+ graph.consume(sequence)
+ graph.count(tip)
+
+ # Check for false positive neighbors and mark as expected failure if found
+ if hdn_counts(sequence, graph) != {3: 1}:
+ request.applymarker(pytest.mark.xfail)
+
+ return graph, sequence, L, HDN, R, tip
+
+
+ at pytest.fixture(params=[K * 2, -K * 2],
+ ids=['(Where={0})'.format(i) for i in ['Start', 'End']])
+def right_double_fork_structure(request, linear_structure, random_sequence):
+ '''
+ Sets up a graph structure like so:
+ branch
+ ([S+1:S+K]+B)→o~~o→o
+ core_sequence ↗
+ [0]→o→o~~o→(L)→([S:S+K] HDN)→(R)→o→o→o~~o→[-1]
+
+ Where S is the start position of the high degreen node (HDN)
+ and B is the mutated base starting the branch.
+ '''
+
+ graph, core_sequence = linear_structure
+ print('\nCore Len:', len(core_sequence))
+ branch_sequence = random_sequence(exclude=core_sequence)
+ print('Branch len:', len(branch_sequence))
+
+ # start position of the HDN
+ S = request.param
+ if S < 0:
+ S = len(core_sequence) + S
+ # the HDN
+ HDN = Kmer(core_sequence[S:S + K], pos=S)
+ # left of the HDN
+ L = Kmer(core_sequence[S - 1:S - 1 + K], pos=S - 1)
+ # right of the HDN
+ R = Kmer(core_sequence[S + 1:S + 1 + K], pos=S + 1)
+ # the branch sequence, mutated at position S+1
+ branch_start = core_sequence[:R.pos] + mutate_position(R, -1)
+ branch_sequence = branch_start + branch_sequence
+
+ graph.consume(core_sequence)
+ graph.consume(branch_sequence)
+
+ # Check for false positive neighbors and mark as expected failure if found
+ core_hdns = hdn_counts(core_sequence, graph)
+ branch_hdns = hdn_counts(branch_sequence, graph)
+
+ # the core and branch sequences should each have exactly
+ # ONE node of degree 3 (HDN)
+ if core_hdns != {3: 1} or branch_hdns != {3: 1}:
+ print(core_hdns, branch_hdns)
+ request.applymarker(pytest.mark.xfail)
+
+ return graph, core_sequence, L, HDN, R, branch_sequence
+
+
+ at pytest.fixture
+def right_triple_fork_structure(request, right_double_fork_structure,
+ random_sequence):
+ '''
+ Sets up a graph structure like so:
+
+ top_branch
+ ([:S+1]+B)→o~~o→o
+ core_sequence ↗
+ [0]→o→o~~o→(L)→([S:S+K] HDN)→(R)→o→o→o~~o→[-1]
+ ↘
+ ([:S+1]+B)→o~~o→o
+ bottom_branch
+
+ Where S is the start position of the high degreen node (HDN).
+ '''
+
+ graph, core_sequence, L, HDN, R, top_sequence = right_double_fork_structure
+ bottom_branch = random_sequence(exclude=core_sequence + top_sequence)
+ print(len(core_sequence), len(top_sequence), len(bottom_branch))
+
+ # the branch sequence, mutated at position S+1
+ # choose a base not already represented at that position
+ bases = {'A', 'C', 'G', 'T'}
+ mutated = random.choice(list(bases - {R[-1], top_sequence[R.pos + K - 1]}))
+
+ bottom_sequence = core_sequence[:HDN.pos + K] + mutated + bottom_branch
+
+ graph.consume(bottom_sequence)
+
+ # Check for false positive neighbors and mark as expected failure if found
+ core_hdns = hdn_counts(core_sequence, graph)
+ top_hdns = hdn_counts(top_sequence, graph)
+ bottom_hdns = hdn_counts(bottom_sequence, graph)
+
+ # the core, top, and bottom sequences should each have exactly
+ # ONE node of degree 4 (HDN)
+ if not (core_hdns == top_hdns == bottom_hdns == {4: 1}):
+ print(core_hdns, top_hdns, bottom_hdns)
+ request.applymarker(pytest.mark.xfail)
+
+ return graph, core_sequence, L, HDN, R, top_sequence, bottom_sequence
+
+
+ at pytest.fixture(params=[K * 2, -K * 2],
+ ids=['(Where={0})'.format(i) for i in ['Start', 'End']])
+def left_tip_structure(request, graph, random_sequence):
+ '''
+ Sets up a graph structure like so:
+
+ branch
+ (B+[S:S+K-1] tip)
+ ↘ sequence
+ [0]→o~~o→(L)→([S:S+K] HDN)→(R)→o→o~~o→[-1]
+
+ Where S is the start position of the HDN.
+ '''
+ sequence = random_sequence()
+ S = request.param
+ if S < 0:
+ S = len(sequence) + S
+ tip = Kmer(mutate_position(sequence[S - 1:S - 1 + K], 0),
+ pos=S - 1 + K)
+ HDN = Kmer(sequence[S:S + K], pos=S)
+ L = Kmer(sequence[S - 1:S - 1 + K], pos=S - 1)
+ R = Kmer(sequence[S + 1:S + 1 + K], pos=S + 1)
+
+ graph.consume(sequence)
+ graph.count(tip)
+
+ # Check for false positive neighbors and mark as expected failure if found
+ if hdn_counts(sequence, graph) != {3: 1}:
+ request.applymarker(pytest.mark.xfail)
+
+ return graph, sequence, L, HDN, R, tip
+
+
+ at pytest.fixture(params=[K * 2, -K * 2],
+ ids=['(Where={0})'.format(i) for i in ['Start', 'End']])
+def left_double_fork_structure(request, linear_structure, random_sequence):
+ '''
+ Sets up a graph structure like so:
+
+ o→o~~o→(B+[S:S+K-1])
+ ↘ core_sequence
+ [0]→o→o~~o→(L)→([S:S+K] HDN)→(R)→o→o→o~~o→[-1]
+
+ Where S is the start position of the high degreen node (HDN).
+ '''
+
+ graph, core_sequence = linear_structure
+ branch_sequence = random_sequence(exclude=core_sequence)
+
+ # start position of the HDN
+ S = request.param
+ if S < 0:
+ S = len(core_sequence) + S
+ # the HDN
+ HDN = Kmer(core_sequence[S:S + K], pos=S)
+ # left of the HDN
+ L = Kmer(core_sequence[S - 1:S - 1 + K], pos=S - 1)
+ # right of the HDN
+ R = Kmer(core_sequence[S + 1:S + 1 + K], pos=S + 1)
+ # the branch sequence, mutated at position 0 in L,
+ # whih is equivalent to the K-1 prefix of HDN prepended with a new base
+ branch_start = mutate_position(L, 0)
+ branch_sequence = branch_sequence + \
+ branch_start + core_sequence[L.pos + K:]
+
+ graph.consume(core_sequence)
+ graph.consume(branch_sequence)
+
+ # Check for false positive neighbors and mark as expected failure if found
+ core_hdns = hdn_counts(core_sequence, graph)
+ branch_hdns = hdn_counts(branch_sequence, graph)
+
+ # the core and branch sequences should each have exactly
+ # ONE node of degree 3 (HDN)
+ if not (core_hdns == branch_hdns == {3: 1}):
+ request.applymarker(pytest.mark.xfail)
+
+ return graph, core_sequence, L, HDN, R, branch_sequence
+
+
+ at pytest.fixture(params=[K * 2, (-K * 2) - 2],
+ ids=['(Where={0})'.format(i) for i in ['Start', 'End']])
+def snp_bubble_structure(request, linear_structure):
+ '''
+ Sets up a graph structure resulting from a SNP (Single Nucleotide
+ Polymorphism).
+
+ (HDN_L[1:]+SNP)→o~~o→(SNP+)
+ ↗ ↘
+ o~~([S:S+K] HDN_L) ([S+K+1:S+2K+1] HDN_R)~~o
+ ↘ ↗
+ (HDN_L[1:]+W)→o~~o~~o→(W+)
+
+ Where S is the start position of HDN directly left of the SNP (HDN_L),
+ SNP is the mutated base, and W is the wildtype (original) base.
+ Of course, W and SNP could be interchanged here, we don't actually
+ know which is which ;)
+
+ Note our parameterization: we need a bit more room from the ends,
+ so we bring the rightmost SNP a tad left.
+ '''
+
+ graph, wildtype_sequence = linear_structure
+ S = request.param
+ if S < 0:
+ S = len(wildtype_sequence) + S
+ snp_sequence = mutate_position(wildtype_sequence, S + K)
+ HDN_L = Kmer(wildtype_sequence[S:S + K], pos=S)
+ HDN_R = Kmer(wildtype_sequence[S + K + 1:S + 2 * K + 1], pos=S + K + 1)
+
+ graph.consume(wildtype_sequence)
+ graph.consume(snp_sequence)
+
+ # Check for false positive neighbors and mark as expected failure if found
+ w_hdns = hdn_counts(wildtype_sequence, graph)
+ snp_hdns = hdn_counts(snp_sequence, graph)
+ if not (w_hdns == snp_hdns == {3: 2}):
+ print(w_hdns, snp_hdns)
+ print(HDN_L, HDN_R)
+ print(wildtype_sequence[HDN_L.pos + K + 1])
+ print(snp_sequence[HDN_L.pos + K + 1])
+ request.applymarker(pytest.mark.xfail)
+
+ return graph, wildtype_sequence, snp_sequence, HDN_L, HDN_R
+
+
+ at pytest.fixture(params=[2, 3, 4, 5, 6, 7, 8])
+def tandem_repeat_structure(request, linear_structure):
+
+ graph, sequence = linear_structure
+
+ tandem_repeats = sequence * request.param
+ graph.consume(tandem_repeats)
+
+ if hdn_counts(tandem_repeats, graph):
+ request.applymarker(pytest.mark.xfail)
+
+ return graph, sequence, tandem_repeats
+
+
+class TestNonBranching:
+
+ def test_all_start_positions(self, linear_structure):
+ # assemble entire contig, starting from wherever
+ graph, contig = linear_structure
+ asm = khmer.LinearAssembler(graph)
+
+ for start in range(0, len(contig), 150):
+ path = asm.assemble(contig[start:start + K])
+ assert utils._equals_rc(path, contig), start
+
+ def test_all_left_to_beginning(self, linear_structure):
+ # assemble directed left
+ graph, contig = linear_structure
+ asm = khmer.LinearAssembler(graph)
+
+ for start in range(0, len(contig), 150):
+ path = asm.assemble(contig[start:start + K], direction='L')
+ print(path, ', ', contig[:start])
+ assert utils._equals_rc(path, contig[:start + K]), start
+
+ def test_all_right_to_end(self, linear_structure):
+ # assemble directed right
+ graph, contig = linear_structure
+ asm = khmer.LinearAssembler(graph)
+
+ for start in range(0, len(contig), 150):
+ path = asm.assemble(contig[start:start + K], direction='R')
+ print(path, ', ', contig[:start])
+ assert utils._equals_rc(path, contig[start:]), start
+
+
+class TestLinearAssembler_RightBranching:
+
+ def test_branch_point(self, right_tip_structure):
+ graph, contig, L, HDN, R, tip = right_tip_structure
+
+ assert graph.kmer_degree(HDN) == 3
+
+ def test_beginning_to_branch(self, right_tip_structure):
+ # assemble from beginning of contig, up until branch point
+ graph, contig, L, HDN, R, tip = right_tip_structure
+ asm = khmer.LinearAssembler(graph)
+ path = asm.assemble(contig[0:K])
+
+ assert len(path) == HDN.pos + K
+ assert utils._equals_rc(path, contig[:len(path)])
+
+ def test_beginning_to_branch_revcomp(self, right_tip_structure):
+ # assemble from beginning of contig, up until branch point
+ # starting from rev comp
+ graph, contig, L, HDN, R, tip = right_tip_structure
+ asm = khmer.LinearAssembler(graph)
+ path = asm.assemble(revcomp(contig[0:K]))
+
+ assert len(path) == HDN.pos + K
+ assert utils._equals_rc(path, contig[:len(path)])
+
+ def test_left_of_branch_to_beginning(self, right_tip_structure):
+ # start from HDN (left of branch)
+ graph, contig, L, HDN, R, tip = right_tip_structure
+ asm = khmer.LinearAssembler(graph)
+ path = asm.assemble(L)
+
+ assert len(path) == HDN.pos + K
+ assert utils._equals_rc(path, contig[:len(path)])
+
+ def test_left_of_branch_to_beginning_revcomp(self, right_tip_structure):
+ # start from revcomp of HDN (left of branch)
+ graph, contig, L, HDN, R, tip = right_tip_structure
+ asm = khmer.LinearAssembler(graph)
+ path = asm.assemble(revcomp(L))
+
+ assert len(path) == HDN.pos + K
+ assert utils._equals_rc(path, contig[:len(path)])
+
+ def test_right_of_branch_outwards_to_ends(self, right_tip_structure):
+ # assemble from right of branch point (at R)
+ # Should get the *entire* original contig, as the assembler
+ # will move left relative to the branch, and not consider it
+ # as a high degree node
+ graph, contig, L, HDN, R, tip = right_tip_structure
+ asm = khmer.LinearAssembler(graph)
+ path = asm.assemble(R)
+
+ assert len(path) == len(contig)
+ assert utils._equals_rc(path, contig)
+
+ def test_end_to_beginning(self, right_tip_structure):
+ # should have exact same behavior as right_of_branch_outwards
+ graph, contig, L, HDN, R, tip = right_tip_structure
+ asm = khmer.LinearAssembler(graph)
+ path = asm.assemble(contig[-K:])
+
+ assert len(path) == len(contig)
+ assert utils._equals_rc(path, contig)
+
+
+class TestLinearAssembler_LeftBranching:
+
+ def test_branch_point(self, left_tip_structure):
+ graph, contig, L, HDN, R, tip = left_tip_structure
+
+ assert graph.kmer_degree(HDN) == 3
+
+ def test_end_to_branch(self, left_tip_structure):
+ # assemble from end until branch point
+ # should include HDN
+ graph, contig, L, HDN, R, tip = left_tip_structure
+ asm = khmer.LinearAssembler(graph)
+ path = asm.assemble(contig[-K:])
+
+ assert len(path) == len(contig) - HDN.pos
+ assert utils._equals_rc(path, contig[HDN.pos:])
+
+ def test_branch_to_end(self, left_tip_structure):
+ # assemble from branch point until end
+ graph, contig, L, HDN, R, tip = left_tip_structure
+ asm = khmer.LinearAssembler(graph)
+ path = asm.assemble(HDN)
+
+ assert len(path) == len(contig) - HDN.pos
+ assert utils._equals_rc(path, contig[HDN.pos:])
+
+ def test_from_branch_to_ends_with_stopbf(self, left_tip_structure):
+ # block the tip with the stop_bf. should return a full length contig.
+ graph, contig, L, HDN, R, tip = left_tip_structure
+ asm = khmer.LinearAssembler(graph)
+
+ stop_bf = khmer.Nodegraph(K, 1e5, 4)
+ stop_bf.count(tip)
+
+ path = asm.assemble(HDN, stop_bf)
+
+ assert len(path) == len(contig)
+ assert utils._equals_rc(path, contig)
+
+ def test_from_branch_to_ends_with_stopbf_revcomp(self, left_tip_structure):
+ # block the tip with the stop_bf. should return a full length contig.
+ graph, contig, L, HDN, R, tip = left_tip_structure
+ asm = khmer.LinearAssembler(graph)
+ stop_bf = khmer.Nodegraph(K, 1e5, 4)
+ stop_bf.count(tip)
+
+ path = asm.assemble(revcomp(HDN), stop_bf)
+
+ assert len(path) == len(contig)
+ assert utils._equals_rc(path, contig)
+
+ def test_end_thru_tip_with_stopbf(self, left_tip_structure):
+ # assemble up to branch point, and include introduced branch b/c
+ # of stop bf
+ graph, contig, L, HDN, R, tip = left_tip_structure
+ asm = khmer.LinearAssembler(graph)
+
+ stop_bf = khmer.Nodegraph(K, 1e5, 4)
+ stop_bf.count(L) # ...and block original path
+ path = asm.assemble(contig[-K:], stop_bf)
+ assert len(path) == len(contig) - HDN.pos + 1
+
+ # should be the tip k-kmer, plus the last base of the HDN thru
+ # the end of the contig
+ assert utils._equals_rc(path, tip + contig[HDN.pos + K - 1:])
+
+ def test_single_node_flanked_by_hdns(self, left_tip_structure):
+ # assemble single node flanked by high-degree nodes
+ # we'll copy the main nodegraph before mutating it
+ graph, contig, L, HDN, R, tip = left_tip_structure
+ asm = khmer.LinearAssembler(graph)
+
+ graph.consume(mutate_position(contig, HDN.pos + K))
+
+ path = asm.assemble(HDN)
+
+ assert len(path) == K
+ assert utils._equals_rc(path, HDN)
+
+
+class TestLabeledAssembler:
+
+ def test_beginning_to_end_across_tip(self, right_tip_structure):
+ # assemble entire contig, ignoring branch point b/c of labels
+ graph, contig, L, HDN, R, tip = right_tip_structure
+ lh = khmer._GraphLabels(graph)
+ asm = khmer.SimpleLabeledAssembler(lh)
+ hdn = graph.find_high_degree_nodes(contig)
+ # L, HDN, and R will be labeled with 1
+ lh.label_across_high_degree_nodes(contig, hdn, 1)
+
+ path = asm.assemble(contig[:K])
+
+ assert len(path) == 1, "there should only be one path"
+ path = path[0] # @CTB
+
+ assert len(path) == len(contig)
+ assert utils._equals_rc(path, contig)
+
+ def test_assemble_right_double_fork(self, right_double_fork_structure):
+ # assemble two contigs from a double forked structure
+ graph, contig, L, HDN, R, branch = right_double_fork_structure
+ lh = khmer._GraphLabels(graph)
+ asm = khmer.SimpleLabeledAssembler(lh)
+
+ hdn = graph.find_high_degree_nodes(contig)
+ hdn += graph.find_high_degree_nodes(branch)
+ print(list(hdn))
+ lh.label_across_high_degree_nodes(contig, hdn, 1)
+ lh.label_across_high_degree_nodes(branch, hdn, 2)
+ print(lh.get_tag_labels(list(hdn)[0]))
+
+ paths = asm.assemble(contig[:K])
+ print('Path lengths', [len(x) for x in paths])
+
+ assert len(paths) == 2
+
+ assert any(utils._equals_rc(path, contig) for path in paths)
+ assert any(utils._equals_rc(path, branch) for path in paths)
+
+ def test_assemble_right_triple_fork(self, right_triple_fork_structure):
+ # assemble three contigs from a trip fork
+ (graph, contig, L, HDN, R,
+ top_sequence, bottom_sequence) = right_triple_fork_structure
+ lh = khmer._GraphLabels(graph)
+ asm = khmer.SimpleLabeledAssembler(lh)
+
+ hdn = graph.find_high_degree_nodes(contig)
+ hdn += graph.find_high_degree_nodes(top_sequence)
+ hdn += graph.find_high_degree_nodes(bottom_sequence)
+ print(list(hdn))
+ lh.label_across_high_degree_nodes(contig, hdn, 1)
+ lh.label_across_high_degree_nodes(top_sequence, hdn, 2)
+ lh.label_across_high_degree_nodes(bottom_sequence, hdn, 3)
+ print(lh.get_tag_labels(list(hdn)[0]))
+
+ paths = asm.assemble(contig[:K])
+ print([len(x) for x in paths])
+
+ assert len(paths) == 3
+
+ assert any(utils._equals_rc(path, contig) for path in paths)
+ assert any(utils._equals_rc(path, top_sequence) for path in paths)
+ assert any(utils._equals_rc(path, bottom_sequence) for path in paths)
+
+ def test_assemble_left_double_fork(self, left_double_fork_structure):
+ # assemble entire contig + branch points b/c of labels; start from end
+ graph, contig, L, HDN, R, branch = left_double_fork_structure
+ lh = khmer._GraphLabels(graph)
+ asm = khmer.SimpleLabeledAssembler(lh)
+
+ # first try without the labels
+ paths = asm.assemble(contig[-K:])
+
+ assert len(paths) == 1
+ # without labels, should get the beginning of the HDN thru the end
+ assert paths[0] == contig[HDN.pos:]
+
+ # now add labels and check that we get two full length paths
+ hdn = graph.find_high_degree_nodes(contig)
+ hdn += graph.find_high_degree_nodes(branch)
+ print(list(hdn))
+ lh.label_across_high_degree_nodes(contig, hdn, 1)
+ lh.label_across_high_degree_nodes(branch, hdn, 2)
+ print(lh.get_tag_labels(list(hdn)[0]))
+
+ paths = asm.assemble(contig[-K:])
+
+ assert len(paths) == 2
+
+ assert any(utils._equals_rc(path, contig) for path in paths)
+ assert any(utils._equals_rc(path, branch) for path in paths)
+
+ def test_assemble_snp_bubble_single(self, snp_bubble_structure):
+ # assemble entire contig + one of two paths through a bubble
+ graph, wildtype, mutant, HDN_L, HDN_R = snp_bubble_structure
+ lh = khmer._GraphLabels(graph)
+ asm = khmer.SimpleLabeledAssembler(lh)
+
+ hdn = graph.find_high_degree_nodes(wildtype)
+ assert len(hdn) == 2
+ lh.label_across_high_degree_nodes(wildtype, hdn, 1)
+
+ paths = asm.assemble(wildtype[:K])
+
+ assert len(paths) == 1
+ assert utils._equals_rc(paths[0], wildtype)
+
+ def test_assemble_snp_bubble_both(self, snp_bubble_structure):
+ # assemble entire contig + both paths
+ graph, wildtype, mutant, HDN_L, HDN_R = snp_bubble_structure
+ lh = khmer._GraphLabels(graph)
+ asm = khmer.SimpleLabeledAssembler(lh)
+
+ hdn = graph.find_high_degree_nodes(wildtype)
+ hdn += graph.find_high_degree_nodes(mutant)
+ assert len(hdn) == 2
+ lh.label_across_high_degree_nodes(wildtype, hdn, 1)
+ lh.label_across_high_degree_nodes(mutant, hdn, 2)
+
+ paths = asm.assemble(wildtype[:K])
+
+ assert len(paths) == 2
+
+ assert any(utils._contains_rc(wildtype, path) for path in paths)
+ assert any(utils._contains_rc(mutant, path) for path in paths)
+ # assert all(path[:HDN_L.pos+K][-K:] == HDN_L for path in paths)
+ # assert all(path[HDN_R.pos:][:K] == HDN_R for path in paths)
+ # assert paths[0][:HDN_L.pos+K] == paths[1][:HDN_L.pos+K]
+ # assert paths[0][HDN_R.pos:] == paths[1][HDN_R.pos:]
+
+ def test_assemble_snp_bubble_stopbf(self, snp_bubble_structure):
+ # assemble one side of bubble, blocked with stop_bf,
+ # when labels on both branches
+ # stop_bf should trip a filter failure, negating the label spanning
+ graph, wildtype, mutant, HDN_L, HDN_R = snp_bubble_structure
+ stop_bf = khmer.Nodegraph(K, 1e5, 4)
+ lh = khmer._GraphLabels(graph)
+ asm = khmer.SimpleLabeledAssembler(lh)
+
+ hdn = graph.find_high_degree_nodes(wildtype)
+ hdn += graph.find_high_degree_nodes(mutant)
+ assert len(hdn) == 2
+ lh.label_across_high_degree_nodes(wildtype, hdn, 1)
+ lh.label_across_high_degree_nodes(mutant, hdn, 2)
+
+ # do the labeling, but block the mutant with stop_bf
+ stop_bf.count(mutant[HDN_L.pos + 1:HDN_L.pos + K + 1])
+ paths = asm.assemble(wildtype[:K], stop_bf)
+
+ assert len(paths) == 1
+ assert any(utils._equals_rc(path, wildtype) for path in paths)
+
+ # @pytest.mark.skip(reason='destroys your computer and then the world')
+ def test_assemble_tandem_repeats(self, tandem_repeat_structure):
+ # assemble one copy of a tandem repeat
+ graph, repeat, tandem_repeats = tandem_repeat_structure
+ lh = khmer._GraphLabels(graph)
+ asm = khmer.SimpleLabeledAssembler(lh)
+ paths = asm.assemble(repeat[:K])
+
+ assert len(paths) == 1
+ # There are K-1 k-mers spanning the junction between
+ # the beginning and end of the repeat
+ assert len(paths[0]) == len(repeat) + K - 1
+
+
+class TestJunctionCountAssembler:
+
+ def test_beginning_to_end_across_tip(self, right_tip_structure):
+ # assemble entire contig, ignoring branch point b/c of labels
+ graph, contig, L, HDN, R, tip = right_tip_structure
+ asm = khmer.JunctionCountAssembler(graph)
+ asm.consume(contig)
+ asm.consume(contig)
+ asm.consume(contig)
+
+ path = asm.assemble(contig[:K])
+ print('P:', path[0])
+ print('T:', tip)
+ print('C:', contig)
+ assert len(path) == 1, "there should only be one path"
+ path = path[0] # @CTB
+
+ assert len(path) == len(contig)
+ assert utils._equals_rc(path, contig)
diff --git a/tests/test_countgraph.py b/tests/test_countgraph.py
index ceaca36..0e3763d 100644
--- a/tests/test_countgraph.py
+++ b/tests/test_countgraph.py
@@ -1,6 +1,7 @@
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2010-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
+# Copyright (C) 2016, Google, Inc
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -32,23 +33,20 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
-# pylint: disable=missing-docstring,protected-access
+# pylint: disable=missing-docstring,protected-access,no-member,invalid-name
from __future__ import print_function
from __future__ import absolute_import, unicode_literals
+
import gzip
import os
-import shutil
import khmer
from . import khmer_tst_utils as utils
from khmer import ReadParser
import screed
-import nose
-from nose.plugins.attrib import attr
-from nose.tools import assert_raises
-
+import pytest
MAX_COUNT = 255
MAX_BIGCOUNT = 65535
@@ -68,6 +66,54 @@ def teardown():
utils.cleanup()
+def test_count_1():
+ hi = khmer._Countgraph(12, PRIMES_1m)
+
+ kmer = 'G' * 12
+ hashval = hi.hash('G' * 12)
+
+ assert hi.get(kmer) == 0
+ assert hi.get(hashval) == 0
+
+ hi.count(kmer)
+ assert hi.get(kmer) == 1
+ assert hi.get(hashval) == 1
+
+ hi.count(kmer)
+ assert hi.get(kmer) == 2
+ assert hi.get(hashval) == 2
+
+ kmer = 'G' * 11
+
+ with pytest.raises(ValueError):
+ hi.hash(kmer)
+
+
+def test_count_2():
+ hi = khmer._Countgraph(12, PRIMES_1m)
+ kmer = 'G' * 12
+ hashval = hi.hash('G' * 12)
+
+ assert hi.get(kmer) == 0
+ assert hi.get(hashval) == 0
+
+ hi.count(kmer)
+ assert hi.get(kmer) == 1
+ assert hi.get(hashval) == 1
+
+ hi.count(hashval) # count hashes same as strings
+ assert hi.get(kmer) == 2
+ assert hi.get(hashval) == 2
+
+
+def test_revhash_1():
+ hi = khmer._Countgraph(12, [1])
+ kmer = 'C' * 12
+ hashval = hi.hash('C' * 12)
+
+ assert hi.reverse_hash(hashval) == kmer
+
+
class Test_Countgraph(object):
def setup(self):
@@ -160,6 +206,17 @@ def test_get_raw_tables():
assert size == len(table)
+def test_get_raw_tables_smallcountgraph():
+ # for the same number of entries a SmallCountgraph uses ~half the memory
+ # of a normal Countgraph
+ ht = khmer.SmallCountgraph(20, 1e5, 4)
+ tables = ht.get_raw_tables()
+
+ for size, table in zip(ht.hashsizes(), tables):
+ assert isinstance(table, memoryview)
+ assert size // 2 + 1 == len(table)
+
+
def test_get_raw_tables_view():
ht = khmer.Countgraph(20, 1e5, 4)
tables = ht.get_raw_tables()
@@ -170,10 +227,22 @@ def test_get_raw_tables_view():
assert sum(tab.tolist()) == 1
- at attr('huge')
+def test_get_raw_tables_view_smallcountgraph():
+ ht = khmer.SmallCountgraph(4, 1e5, 4)
+ tables = ht.get_raw_tables()
+ for tab in tables:
+ assert sum(tab.tolist()) == 0
+ ht.consume('AAAA')
+ # the actual count is 1 but stored in the first 4bits of a Byte
+ # and so becomes 16
+ for tab in tables:
+ assert sum(tab.tolist()) == int('00010000', 2)
+
+
+ at pytest.mark.huge
def test_toobig():
try:
- ct = khmer.Countgraph(30, 1e13, 1)
+ khmer.Countgraph(30, 1e13, 1)
assert 0, "this should fail"
except MemoryError as err:
print(str(err))
@@ -390,7 +459,7 @@ def test_median_at_least_exception():
try:
ht.median_at_least('ATGGCTGATCGAT', 1)
assert 0, "should have thrown ValueError"
- except ValueError as e:
+ except ValueError:
pass
@@ -492,6 +561,43 @@ def test_get_kmer_hashes():
assert hi.get(hashes[1]) == 3
+def test_get_kmer_hashes_as_hashset():
+ hi = khmer.Countgraph(6, 1e6, 2)
+
+ def get_counts(hs):
+ return list(sorted([hi.get(h) for h in hs]))
+
+ hi.consume("AAAAAA")
+ hashes = hi.get_kmer_hashes_as_hashset("AAAAAA")
+ print(hashes)
+ assert len(hashes) == 1
+ assert [1] == get_counts(hashes)
+
+ hi.consume("AAAAAA")
+ hashes = hi.get_kmer_hashes_as_hashset("AAAAAA")
+ print(hashes)
+ assert len(hashes) == 1
+ assert [2] == get_counts(hashes)
+
+ hi.consume("AAAAAT")
+ hashes = hi.get_kmer_hashes_as_hashset("AAAAAAT")
+ print(hashes)
+ assert len(hashes) == 2
+ assert [1, 2] == get_counts(hashes)
+
+ hi.consume("AAAAAT")
+ hashes = hi.get_kmer_hashes_as_hashset("AAAAAAT")
+ print(hashes)
+ assert len(hashes) == 2
+ assert [2, 2] == get_counts(hashes)
+
+ hi.consume("AAAAAT")
+ hashes = hi.get_kmer_hashes_as_hashset("AAAAAAT")
+ print(hashes)
+ assert len(hashes) == 2
+ assert [2, 3] == get_counts(hashes)
+
+
def test_get_kmers():
hi = khmer.Countgraph(6, 1e6, 2)
@@ -501,49 +607,64 @@ def test_get_kmers():
kmers = hi.get_kmers("AAAAAAT")
assert kmers == ["AAAAAA", "AAAAAT"]
+ kmers = hi.get_kmers("AGCTTTTC")
+ assert kmers == ['AGCTTT', 'GCTTTT', 'CTTTTC']
- at attr("huge")
-def test_save_load_large():
- def do_test(ctfile):
- inpath = utils.get_test_data('random-20-a.fa')
- savepath = utils.get_temp_filename(ctfile)
- sizes = khmer.get_n_primes_near_x(1, 2 ** 31 + 1000)
+ at pytest.mark.huge
+ at pytest.mark.parametrize("ctfile", ['temp.ct', 'temp.ct.gz'])
+def test_save_load_large(ctfile):
+ inpath = utils.get_test_data('random-20-a.fa')
+ savepath = utils.get_temp_filename(ctfile)
+
+ sizes = khmer.get_n_primes_near_x(1, 2 ** 31 + 1000)
+
+ orig = khmer._Countgraph(12, sizes)
+ orig.consume_seqfile(inpath)
+ orig.save(savepath)
- orig = khmer._Countgraph(12, sizes)
- orig.consume_fasta(inpath)
- orig.save(savepath)
+ loaded = khmer.load_countgraph(savepath)
- loaded = khmer.load_countgraph(savepath)
+ orig_count = orig.n_occupied()
+ loaded_count = loaded.n_occupied()
+ assert orig_count == 3966, orig_count
+ assert loaded_count == orig_count, loaded_count
- orig_count = orig.n_occupied()
- loaded_count = loaded.n_occupied()
- assert orig_count == 3966, orig_count
- assert loaded_count == orig_count, loaded_count
- for ctfile in ['temp.ct.gz', 'temp.ct']:
- do_test(ctfile)
+ at pytest.mark.parametrize("ctfile", ['temp.ct', 'temp.ct.gz'])
+def test_save_load_occupied(ctfile):
+ print('working with', ctfile)
+ inpath = utils.get_test_data('random-20-a.fa')
+ savepath = utils.get_temp_filename(ctfile)
+
+ orig = khmer.Countgraph(12, 1e5, 4)
+ orig.consume_seqfile(inpath)
+ orig.save(savepath)
+ loaded = khmer.load_countgraph(savepath)
-def test_save_load_occupied():
- def do_test(ctfile):
- print('working with', ctfile)
- inpath = utils.get_test_data('random-20-a.fa')
- savepath = utils.get_temp_filename(ctfile)
+ orig_count = orig.n_occupied()
+ loaded_count = loaded.n_occupied()
+ assert orig_count == 3886, orig_count
+ assert loaded_count == orig_count, loaded_count
- orig = khmer.Countgraph(12, 1e5, 4)
- orig.consume_fasta(inpath)
- orig.save(savepath)
- loaded = khmer.load_countgraph(savepath)
+ at pytest.mark.parametrize("ctfile", ['temp.ct', 'temp.ct.gz'])
+def test_save_load_occupied_small(ctfile):
+ print('working with', ctfile)
+ inpath = utils.get_test_data('random-20-a.fa')
+ savepath = utils.get_temp_filename(ctfile)
- orig_count = orig.n_occupied()
- loaded_count = loaded.n_occupied()
- assert orig_count == 3886, orig_count
- assert loaded_count == orig_count, loaded_count
+ orig = khmer.SmallCountgraph(12, 1e5, 4)
+ orig.consume_seqfile(inpath)
+ orig.save(savepath)
- for ctfile in ['temp.ct', 'temp.ct.gz']:
- do_test(ctfile)
+ loaded = khmer.load_countgraph(savepath, small=True)
+
+ orig_count = orig.n_occupied()
+ loaded_count = loaded.n_occupied()
+ assert orig_count == 3886, orig_count
+ assert loaded_count == orig_count, loaded_count
def test_save_load():
@@ -554,12 +675,11 @@ def test_save_load():
sizes.append(1000005)
hi = khmer._Countgraph(12, sizes)
- hi.consume_fasta(inpath)
+ hi.consume_seqfile(inpath)
hi.save(savepath)
- ht = khmer._Countgraph(12, sizes)
try:
- ht.load(savepath)
+ ht = khmer.load_countgraph(savepath)
except OSError as err:
assert 0, 'Should not produce an OSError: ' + str(err)
@@ -581,7 +701,7 @@ def test_load_truncated():
sizes = khmer.get_n_primes_near_x(3, 200)
hi = khmer._Countgraph(12, sizes)
- hi.consume_fasta(inpath)
+ hi.consume_seqfile(inpath)
hi.save(savepath)
data = open(savepath, 'rb').read()
@@ -591,7 +711,7 @@ def test_load_truncated():
fp.close()
try:
- ht = khmer.load_countgraph(truncpath)
+ khmer.load_countgraph(truncpath)
assert 0, "this should not be reached!"
except OSError as err:
print(str(err))
@@ -608,7 +728,7 @@ def test_load_gz():
# save uncompressed hashtable.
hi = khmer._Countgraph(12, sizes)
- hi.consume_fasta(inpath)
+ hi.consume_seqfile(inpath)
hi.save(savepath)
# compress.
@@ -619,9 +739,8 @@ def test_load_gz():
in_file.close()
# load compressed hashtable.
- ht = khmer._Countgraph(12, sizes)
try:
- ht.load(loadpath)
+ ht = khmer.load_countgraph(loadpath)
except OSError as err:
assert 0, "Should not produce an OSError: " + str(err)
@@ -643,12 +762,11 @@ def test_save_load_gz():
sizes.append(1000005)
hi = khmer._Countgraph(12, sizes)
- hi.consume_fasta(inpath)
+ hi.consume_seqfile(inpath)
hi.save(savepath)
- ht = khmer._Countgraph(12, sizes)
try:
- ht.load(savepath)
+ ht = khmer.load_countgraph(savepath)
except OSError as err:
assert 0, 'Should not produce an OSError: ' + str(err)
@@ -662,15 +780,12 @@ def test_save_load_gz():
assert x == y, (x, y)
-def test_load_empty_files():
- def do_load_ct(fname):
- with assert_raises(OSError):
- ct = khmer.load_countgraph(fname)
-
+ at pytest.mark.parametrize("ext", ['', '.gz'])
+def test_load_empty_files(ext):
# Check empty files, compressed or not
- for ext in ['', '.gz']:
- fn = utils.get_test_data('empty-file' + ext)
- do_load_ct(fn)
+ fname = utils.get_test_data('empty-file' + ext)
+ with pytest.raises(OSError):
+ khmer.load_countgraph(fname)
def test_trim_full():
@@ -679,7 +794,7 @@ def test_trim_full():
hi.consume(DNA)
hi.consume(DNA)
- seq, pos = hi.trim_on_abundance(DNA, 2)
+ seq, _ = hi.trim_on_abundance(DNA, 2)
assert DNA == seq, seq
@@ -769,13 +884,13 @@ def test_find_spectral_error_positions_err():
hi = khmer.Countgraph(8, 1e6, 2)
try:
- posns = hi.find_spectral_error_positions(DNA[:6], 1)
+ hi.find_spectral_error_positions(DNA[:6], 1)
assert 0, "should raise ValueError; too short"
except ValueError:
pass
try:
- posns = hi.find_spectral_error_positions("ACGTACGN", 1)
+ hi.find_spectral_error_positions("ACGTACGN", 1)
assert 0, "should raise ValueError; contains N"
except ValueError:
pass
@@ -787,7 +902,7 @@ def test_maxcount():
kh.set_use_bigcount(False)
last_count = None
- for i in range(0, 1000):
+ for _ in range(0, 1000):
kh.count('AAAA')
c = kh.get('AAAA')
@@ -805,7 +920,7 @@ def test_maxcount_with_bigcount():
kh.set_use_bigcount(True)
last_count = None
- for i in range(0, 1000):
+ for _ in range(0, 1000):
kh.count('AAAA')
c = kh.get('AAAA')
@@ -822,16 +937,15 @@ def test_maxcount_with_bigcount_save():
kh = khmer.Countgraph(4, 4 ** 4, 4)
kh.set_use_bigcount(True)
- for i in range(0, 1000):
+ for _ in range(0, 1000):
kh.count('AAAA')
c = kh.get('AAAA')
savepath = utils.get_temp_filename('tempcountingsave.ht')
kh.save(savepath)
- kh = khmer.Countgraph(1, 1, 1)
try:
- kh.load(savepath)
+ kh = khmer.load_countgraph(savepath)
except OSError as err:
assert 0, "Should not produce an OSError: " + str(err)
@@ -848,9 +962,8 @@ def test_bigcount_save():
savepath = utils.get_temp_filename('tempcountingsave.ht')
kh.save(savepath)
- kh = khmer.Countgraph(1, 1, 1)
try:
- kh.load(savepath)
+ kh = khmer.load_countgraph(savepath)
except OSError as err:
assert 0, "Should not produce an OSError: " + str(err)
@@ -858,7 +971,7 @@ def test_bigcount_save():
assert kh.get('AAAA') == 0
- for i in range(0, 1000):
+ for _ in range(0, 1000):
kh.count('AAAA')
kh.get('AAAA')
@@ -872,9 +985,8 @@ def test_nobigcount_save():
savepath = utils.get_temp_filename('tempcountingsave.ht')
kh.save(savepath)
- kh = khmer.Countgraph(1, 1, 1)
try:
- kh.load(savepath)
+ kh = khmer.load_countgraph(savepath)
except OSError as err:
assert 0, 'Should not produce an OSError: ' + str(err)
@@ -882,7 +994,7 @@ def test_nobigcount_save():
assert kh.get('AAAA') == 0
- for i in range(0, 1000):
+ for _ in range(0, 1000):
kh.count('AAAA')
kh.get('AAAA')
@@ -896,7 +1008,7 @@ def test_bigcount_abund_dist():
seqpath = utils.get_test_data('test-abund-read-2.fa')
- kh.consume_fasta(seqpath)
+ kh.consume_seqfile(seqpath)
dist = kh.abundance_distribution(seqpath, tracking)
print(kh.get('GGTTGACGGGGCTCAGGG'))
@@ -912,7 +1024,7 @@ def test_bigcount_abund_dist_2():
seqpath = utils.get_test_data('test-abund-read.fa')
- kh.consume_fasta(seqpath)
+ kh.consume_seqfile(seqpath)
for i in range(1000):
kh.count('GGTTGACGGGGCTCAGGG')
@@ -927,7 +1039,7 @@ def test_bigcount_overflow():
kh = khmer.Countgraph(18, 1e7, 4)
kh.set_use_bigcount(True)
- for i in range(0, 70000):
+ for _ in range(0, 70000):
kh.count('GGTTGACGGGGCTCAGGG')
assert kh.get('GGTTGACGGGGCTCAGGG') == MAX_BIGCOUNT
@@ -946,19 +1058,11 @@ def test_get_hashsizes():
assert kh.hashsizes() == expected, kh.hashsizes()
-# def test_collect_high_abundance_kmers():
-# seqpath = utils.get_test_data('test-abund-read-2.fa')
-#
-# kh = khmer.Countgraph(18, 1e6, 4)
-# hb = kh.collect_high_abundance_kmers(seqpath, 2, 4)
-
-
def test_load_notexist_should_fail():
savepath = utils.get_temp_filename('tempcountingsave0.ht')
- hi = khmer.Countgraph(12, 1000, 2)
try:
- hi.load(savepath)
+ hi = khmer.load_countgraph(savepath)
assert 0, "load should fail"
except OSError as e:
print(str(e))
@@ -969,7 +1073,7 @@ def test_load_truncated_should_fail():
savepath = utils.get_temp_filename('tempcountingsave0.ht')
hi = khmer.Countgraph(12, 1000, 2)
- hi.consume_fasta(inpath)
+ hi.consume_seqfile(inpath)
hi.save(savepath)
fp = open(savepath, 'rb')
@@ -980,9 +1084,8 @@ def test_load_truncated_should_fail():
fp.write(data[:1000])
fp.close()
- hi = khmer._Countgraph(12, [1])
try:
- hi.load(savepath)
+ hi = khmer.load_countgraph(savepath)
assert 0, "load should fail"
except OSError as e:
print(str(e))
@@ -991,9 +1094,8 @@ def test_load_truncated_should_fail():
def test_load_gz_notexist_should_fail():
savepath = utils.get_temp_filename('tempcountingsave0.ht.gz')
- hi = khmer.Countgraph(12, 1000, 2)
try:
- hi.load(savepath)
+ hi = khmer.load_countgraph(savepath)
assert 0, "load should fail"
except OSError as e:
print(str(e))
@@ -1004,7 +1106,7 @@ def test_load_gz_truncated_should_fail():
savepath = utils.get_temp_filename('tempcountingsave0.ht.gz')
hi = khmer.Countgraph(12, 1000, 2)
- hi.consume_fasta(inpath)
+ hi.consume_seqfile(inpath)
hi.save(savepath)
fp = open(savepath, 'rb')
@@ -1015,9 +1117,8 @@ def test_load_gz_truncated_should_fail():
fp.write(data[:1000])
fp.close()
- hi = khmer._Countgraph(12, [1])
try:
- hi.load(savepath)
+ hi = khmer.load_countgraph(savepath)
assert 0, "load should fail"
except OSError as e:
print(str(e))
@@ -1036,12 +1137,11 @@ def test_counting_file_version_check():
def test_counting_gz_file_version_check():
- ht = khmer.Countgraph(12, 1, 1)
inpath = utils.get_test_data('badversion-k12.ct.gz')
try:
- ht.load(inpath)
+ ht = khmer.load_countgraph(inpath)
assert 0, "this should fail"
except OSError as e:
print(str(e))
@@ -1050,24 +1150,18 @@ def test_counting_gz_file_version_check():
def test_counting_file_type_check():
inpath = utils.get_test_data('goodversion-k12.ht')
- kh = khmer.Countgraph(12, 1, 1)
-
try:
- kh.load(inpath)
+ kh = khmer.load_countgraph(inpath)
assert 0, "this should fail"
except OSError as e:
print(str(e))
def test_counting_gz_file_type_check():
- ht = khmer.Nodegraph(12, 1, 1)
-
inpath = utils.get_test_data('goodversion-k12.ht.gz')
- kh = khmer.Countgraph(12, 1, 1)
-
try:
- kh.load(inpath)
+ kh = khmer.load_countgraph(inpath)
assert 0, "this should fail"
except OSError as e:
print(str(e))
@@ -1075,7 +1169,7 @@ def test_counting_gz_file_type_check():
def test_counting_bad_primes_list():
try:
- ht = khmer._Countgraph(12, ["a", "b", "c"], 1)
+ khmer._Countgraph(12, ["a", "b", "c"], 1)
assert 0, "bad list of primes should fail"
except TypeError as e:
print(str(e))
@@ -1095,7 +1189,7 @@ def test_bad_use_bigcount():
def test_consume_absentfasta():
countgraph = khmer.Countgraph(4, 4 ** 4, 4)
try:
- countgraph.consume_fasta("absent_file.fa")
+ countgraph.consume_seqfile("absent_file.fa")
assert 0, "This should fail"
except OSError as err:
print(str(err))
@@ -1104,13 +1198,13 @@ def test_consume_absentfasta():
def test_consume_absentfasta_with_reads_parser():
countgraph = khmer.Countgraph(4, 4 ** 4, 4)
try:
- countgraph.consume_fasta_with_reads_parser()
+ countgraph.consume_seqfile_with_reads_parser()
assert 0, "this should fail"
except TypeError as err:
print(str(err))
try:
readparser = ReadParser(utils.get_test_data('empty-file'))
- countgraph.consume_fasta_with_reads_parser(readparser)
+ countgraph.consume_seqfile_with_reads_parser(readparser)
assert 0, "this should fail"
except OSError as err:
print(str(err))
@@ -1211,30 +1305,10 @@ def test_badtrim():
countgraph.trim_on_abundance("AAAAAA", 1)
-def test_badfasta_count_kmers_by_position():
- countgraph = khmer.Countgraph(4, 4 ** 4, 4)
- try:
- countgraph.fasta_count_kmers_by_position()
- except TypeError as err:
- print(str(err))
-
- filename = utils.get_test_data("test-short.fa")
- try:
- countgraph.fasta_count_kmers_by_position(filename, -1, 0)
- assert 0, "this should fail"
- except ValueError as err:
- print(str(err))
- try:
- countgraph.fasta_count_kmers_by_position(filename, 0, -1)
- assert 0, "this should fail"
- except ValueError as err:
- print(str(err))
-
-
def test_badload():
- countgraph = khmer.Countgraph(4, 4 ** 4, 4)
+
try:
- countgraph.load()
+ countgraph = khmer.load_countgraph()
assert 0, "this should fail"
except TypeError as err:
print(str(err))
@@ -1276,14 +1350,14 @@ def test_badconsume_and_tag():
print(str(err))
-def test_consume_fasta_and_tag():
+def test_consume_seqfile_and_tag():
countgraph = khmer.Countgraph(4, 4 ** 4, 4)
try:
- countgraph.consume_fasta_and_tag()
+ countgraph.consume_seqfile_and_tag()
assert 0, "this should fail"
except TypeError as err:
print(str(err))
- countgraph.consume_fasta_and_tag(utils.get_test_data("test-graph2.fa"))
+ countgraph.consume_seqfile_and_tag(utils.get_test_data("test-graph2.fa"))
def test_consume_and_retrieve_tags_1():
@@ -1299,7 +1373,7 @@ def test_consume_and_retrieve_tags_1():
ss = set()
tt = set()
for record in screed.open(utils.get_test_data('test-graph2.fa')):
- for p, tag in ct.get_tags_and_positions(record.sequence):
+ for _, tag in ct.get_tags_and_positions(record.sequence):
ss.add(tag)
for start in range(len(record.sequence) - 3):
@@ -1322,7 +1396,7 @@ def test_consume_and_retrieve_tags_empty():
ss = set()
tt = set()
for record in screed.open(utils.get_test_data('test-graph2.fa')):
- for p, tag in ct.get_tags_and_positions(record.sequence):
+ for _, tag in ct.get_tags_and_positions(record.sequence):
ss.add(tag)
for start in range(len(record.sequence) - 3):
@@ -1354,8 +1428,7 @@ def test_find_all_tags_list_error():
def test_abund_dist_gz_bigcount():
- infile = utils.get_temp_filename('test.fa')
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
+ infile = utils.copy_test_data('test-abund-read-2.fa')
script = 'load-into-counting.py'
htfile = utils.get_temp_filename('test_ct')
args = ['-x', str(1e7), '-N', str(2), '-k', str(2), htfile, infile]
@@ -1391,8 +1464,7 @@ def test_abund_dist_gz_bigcount():
def test_abund_dist_gz_bigcount_compressed_first():
- infile = utils.get_temp_filename('test.fa')
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
+ infile = utils.copy_test_data('test-abund-read-2.fa')
script = 'load-into-counting.py'
htfile = utils.get_temp_filename('test_ct.gz')
args = ['-x', str(1e7), '-N', str(2), '-k', str(2), htfile, infile]
@@ -1434,3 +1506,10 @@ def test_counting_load_bigcount():
print(i, count_table.count('ATATATATAT'))
count = count_table.get('ATATATATAT')
assert count == 500
+
+
+def test_bad_create():
+ try:
+ countgraph = khmer._Countgraph(5, [])
+ except ValueError as err:
+ assert 'tablesizes needs to be one or more numbers' in str(err)
diff --git a/tests/test_counting_single.py b/tests/test_counting_single.py
index 71cf5af..0d6845c 100644
--- a/tests/test_counting_single.py
+++ b/tests/test_counting_single.py
@@ -1,6 +1,6 @@
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2010-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -32,21 +32,24 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
-# pylint: disable=C0111,C0103
+# pylint: disable=C0111,C0103,missing-docstring,no-member,protected-access
+
from __future__ import print_function
from __future__ import absolute_import
import khmer
+
+import pytest
from . import khmer_tst_utils as utils
-from nose.plugins.attrib import attr
+
MAX_COUNT = 255
- at attr('huge')
+ at pytest.mark.huge
def test_toobig():
try:
- ct = khmer.Countgraph(4, 1000000000000, 1)
+ khmer.Countgraph(4, 1000000000000, 1)
assert 0, "this should fail"
except MemoryError as err:
print(str(err))
@@ -101,7 +104,7 @@ def test_complete_no_collision():
assert n_rc_filled == n_entries, n_rc_filled
assert n_palindromes == 16, n_palindromes
assert n_fwd_filled == n_entries // 2 + n_palindromes // 2, \
- n_fwd_filled
+ (n_fwd_filled, n_entries // 2 + n_palindromes // 2)
def test_complete_2_collision():
@@ -316,12 +319,12 @@ def test_64bitshift_2():
def test_very_short_read():
short_filename = utils.get_test_data('test-short.fa')
kh = khmer.Countgraph(9, 4, 1)
- n_reads, n_kmers = kh.consume_fasta(short_filename)
+ n_reads, n_kmers = kh.consume_seqfile(short_filename)
assert n_reads == 1, n_reads
assert n_kmers == 0, n_kmers
kh = khmer.Countgraph(8, 4, 1)
- n_reads, n_kmers = kh.consume_fasta(short_filename)
+ n_reads, n_kmers = kh.consume_seqfile(short_filename)
assert n_reads == 1, n_reads
assert n_kmers == 1, n_kmers
@@ -343,45 +346,6 @@ class Test_ConsumeString(object):
except TypeError as err:
print(str(err))
- def test_abundance_by_pos(self):
- kh = self.kh
-
- for _ in range(0, 300):
- kh.count('ATCG')
-
- for _ in range(0, 10):
- kh.count('ATGG')
-
- short_filename = utils.get_test_data('test-short.fa')
- dist = kh.fasta_count_kmers_by_position(short_filename, 6, 10)
- assert dist[4] == 1
- assert sum(dist) == 1
-
- dist = kh.fasta_count_kmers_by_position(short_filename, 6, MAX_COUNT)
- assert dist[0] == 1, dist[0]
- assert dist[2] == 1
- assert sum(dist) == 2
-
- def test_abundance_by_pos_bigcount(self):
- kh = self.kh
- kh.set_use_bigcount(True) # count past MAX_COUNT
-
- for _ in range(0, 300):
- kh.count('ATCG')
-
- for _ in range(0, 10):
- kh.count('ATGG')
-
- short_filename = utils.get_test_data('test-short.fa')
- dist = kh.fasta_count_kmers_by_position(short_filename, 6, 10)
- assert dist[4] == 1
- assert sum(dist) == 1
-
- dist = kh.fasta_count_kmers_by_position(short_filename, 6, 300)
- assert dist[0] == 1, dist[0]
- assert dist[2] == 1
- assert sum(dist) == 2
-
def test_simple(self):
n = self.kh.consume('AAAA')
assert n == 1
@@ -415,7 +379,7 @@ class Test_AbundanceDistribution(object):
def setup(self):
self.kh = khmer._Countgraph(4, [5])
A_filename = utils.get_test_data('all-A.fa')
- self.kh.consume_fasta(A_filename)
+ self.kh.consume_seqfile(A_filename)
def test_count_A(self):
A_filename = utils.get_test_data('all-A.fa')
diff --git a/sandbox/hi-lo-abundance-by-position.py b/tests/test_counttable.py
old mode 100755
new mode 100644
similarity index 62%
rename from sandbox/hi-lo-abundance-by-position.py
rename to tests/test_counttable.py
index c651387..bbba9bc
--- a/sandbox/hi-lo-abundance-by-position.py
+++ b/tests/test_counttable.py
@@ -1,7 +1,5 @@
-#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) 2010-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -15,7 +13,7 @@
# disclaimer in the documentation and/or other materials provided
# with the distribution.
#
-# * Neither the name of the Michigan State University nor the names
+# * Neither the name of the University of California nor the names
# of its contributors may be used to endorse or promote products
# derived from this software without specific prior written
# permission.
@@ -33,33 +31,33 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
-from __future__ import print_function
-import sys
-import os
-import khmer
-
+# pylint: disable=C0111,C0103,missing-docstring,no-member,protected-access
-def write_dist(dist, fp):
- for n, i in enumerate(dist):
- fp.write('%d %d\n' % (n, i))
+from __future__ import print_function
+from __future__ import absolute_import
+import khmer
-def main():
- hashfile = sys.argv[1]
- filename = sys.argv[2]
- outfile = os.path.basename(filename)
+import pytest
+from . import khmer_tst_utils as utils
- print('loading kh file', hashfile)
- ht = khmer.load_countgraph(hashfile)
- x = ht.fasta_count_kmers_by_position(filename, 100, 1)
- write_dist(x, open(outfile + '.pos.abund=1', 'w'))
- print('wrote', outfile + '.pos.abund=1')
+def test_get_kmer_hashes():
+ s = "ATGGATATGGAGGACAAGTATATGGAGGACAAGTATATGGAGGACAAGTAT"
+ a = khmer.Counttable(33, 1e6, 3)
+ assert a.get_kmer_hashes(s[:33]) == [4743239192574154715]
+ assert a.get_kmer_hashes(s[:34]) == [4743239192574154715,
+ 2122462908541313313]
- y = ht.fasta_count_kmers_by_position(filename, 100, 255)
- write_dist(y, open(outfile + '.pos.abund=255', 'w'))
- print('wrote', outfile + '.pos.abund=255')
+ assert a.get_kmer_hashes(s[0:33]) == [4743239192574154715]
+ assert a.get_kmer_hashes(s[1:34]) == [2122462908541313313]
-if __name__ == '__main__':
- main()
+ at pytest.mark.parametrize('kmer', [
+ ('GATTACA' * 3),
+ ('ATG' * 7),
+ ('AGGACAAGTATATGGAGGACA'),
+])
+def test_kmer_revcom_hash(kmer):
+ a = khmer.Counttable(21, 1e4, 3)
+ assert a.hash(kmer) == a.hash(khmer.reverse_complement(kmer))
diff --git a/sandbox/fasta-to-abundance-hist.py b/tests/test_cpython_hierarchy.py
old mode 100755
new mode 100644
similarity index 57%
rename from sandbox/fasta-to-abundance-hist.py
rename to tests/test_cpython_hierarchy.py
index 639561a..951f365
--- a/sandbox/fasta-to-abundance-hist.py
+++ b/tests/test_cpython_hierarchy.py
@@ -1,7 +1,5 @@
-#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) 2010-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -15,7 +13,7 @@
# disclaimer in the documentation and/or other materials provided
# with the distribution.
#
-# * Neither the name of the Michigan State University nor the names
+# * Neither the name of the University of California nor the names
# of its contributors may be used to endorse or promote products
# derived from this software without specific prior written
# permission.
@@ -33,25 +31,52 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
+# pylint: disable=C0111,C0103,missing-docstring,no-member,protected-access
+
from __future__ import print_function
-import sys
+from __future__ import absolute_import
+
import khmer
+import pytest
+from . import khmer_tst_utils as utils
+
+
+def test_countgraph_vs_table():
+ x = khmer.Counttable(4, 21, 3)
+ y = khmer.Countgraph(4, 21, 3)
+
+ assert hasattr(x, 'add')
+ assert hasattr(y, 'add')
+
+ assert not hasattr(x, 'consume_and_tag')
+ assert hasattr(y, 'consume_and_tag')
+
+
+def test_nodegraph_vs_table():
+ x = khmer.Nodetable(4, 21, 3)
+ y = khmer.Nodegraph(4, 21, 3)
+
+ assert hasattr(x, 'add')
+ assert hasattr(y, 'add')
+
+ assert not hasattr(x, 'consume_and_tag')
+ assert hasattr(y, 'consume_and_tag')
+
-def main():
- files = sys.argv[2:]
+def test_counttable_no_unhash():
+ x = khmer.Counttable(4, 21, 3)
- total_reads = len(files) * [0]
- n_consumed = len(files) * [0]
- n_seq_kept = len(files) * [0]
+ with pytest.raises(ValueError):
+ x.reverse_hash(1)
- print('loading ht')
- ht = khmer.load_countgraph(sys.argv[1])
- for i, infile in enumerate(files):
- print('outputting', infile + '.freq')
- ht.output_fasta_kmer_pos_freq(infile, infile + ".freq")
+def test_smallcountgraph_vs_table():
+ x = khmer.SmallCounttable(4, 21, 3)
+ y = khmer.SmallCountgraph(4, 21, 3)
+ assert hasattr(x, 'add')
+ assert hasattr(y, 'add')
-if __name__ == '__main__':
- main()
+ assert not hasattr(x, 'consume_and_tag')
+ assert hasattr(y, 'consume_and_tag')
diff --git a/tests/test_filter.py b/tests/test_filter.py
deleted file mode 100644
index b33c860..0000000
--- a/tests/test_filter.py
+++ /dev/null
@@ -1,91 +0,0 @@
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) 2010-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are
-# met:
-#
-# * Redistributions of source code must retain the above copyright
-# notice, this list of conditions and the following disclaimer.
-#
-# * Redistributions in binary form must reproduce the above
-# copyright notice, this list of conditions and the following
-# disclaimer in the documentation and/or other materials provided
-# with the distribution.
-#
-# * Neither the name of the Michigan State University nor the names
-# of its contributors may be used to endorse or promote products
-# derived from this software without specific prior written
-# permission.
-#
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
-# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
-# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-#
-# Contact: khmer-project at idyll.org
-from __future__ import print_function
-from __future__ import absolute_import
-import khmer
-from screed.fasta import fasta_iter
-from nose.plugins.attrib import attr
-
-from . import khmer_tst_utils as utils
-
-
-def teardown():
- utils.cleanup()
-
-
-def load_fa_seq_names(filename):
- fp = open(filename)
- records = list(fasta_iter(fp))
- names = [r['name'] for r in records]
- return names
-
-
-class Test_Filter(object):
-
- def test_abund(self):
- ht = khmer.Countgraph(10, 4 ** 10, 1)
-
- filename = utils.get_test_data('test-abund-read.fa')
- outname = utils.get_temp_filename('test_abund.out')
-
- ht.consume_fasta(filename)
- try:
- ht.consume_fasta()
- assert 0, "should fail"
- except TypeError as err:
- print(str(err))
- try:
- ht.consume_fasta("nonexistent")
- assert 0, "should fail"
- except OSError as err:
- print(str(err))
- ht.output_fasta_kmer_pos_freq(filename, outname)
- try:
- ht.output_fasta_kmer_pos_freq()
- assert 0, "should fail"
- except TypeError as err:
- print(str(err))
-
- fd = open(outname, "r")
-
- output = fd.readlines()
- assert len(output) == 1
-
- output = output[0]
- output = output.strip().split()
-
- assert ['1'] * (114 - 10 + 1) == output
-
- fd.close()
diff --git a/tests/test_filter_abund.py b/tests/test_filter_abund.py
new file mode 100644
index 0000000..99e2970
--- /dev/null
+++ b/tests/test_filter_abund.py
@@ -0,0 +1,432 @@
+# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# Copyright (C) 2016, The Regents of the University of California.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+#
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# * Redistributions in binary form must reproduce the above
+# copyright notice, this list of conditions and the following
+# disclaimer in the documentation and/or other materials provided
+# with the distribution.
+#
+# * Neither the name of the Michigan State University nor the names
+# of its contributors may be used to endorse or promote products
+# derived from this software without specific prior written
+# permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Contact: khmer-project at idyll.org
+# pylint: disable=missing-docstring
+import os
+import khmer
+import screed
+from . import khmer_tst_utils as utils
+from .test_scripts import _make_counting
+
+
+def test_filter_abund_1():
+ script = 'filter-abund.py'
+
+ infile = utils.copy_test_data('test-abund-read-2.fa')
+ n_infile = utils.copy_test_data('test-fastq-n-reads.fq')
+
+ in_dir = os.path.dirname(infile)
+ n_in_dir = os.path.dirname(n_infile)
+
+ counting_ht = _make_counting(infile, K=17)
+ n_counting_ht = _make_counting(n_infile, K=17)
+
+ args = [counting_ht, infile]
+ utils.runscript(script, args, in_dir)
+
+ outfile = infile + '.abundfilt'
+ n_outfile = n_infile + '.abundfilt'
+ n_outfile2 = n_infile + '2.abundfilt'
+
+ assert os.path.exists(outfile), outfile
+
+ seqs = set([r.sequence for r in screed.open(outfile)])
+
+ assert len(seqs) == 1, seqs
+ assert 'GGTTGACGGGGCTCAGGG' in seqs
+
+ args = [n_counting_ht, n_infile]
+ utils.runscript(script, args, n_in_dir)
+
+ seqs = set([r.sequence for r in screed.open(n_infile)])
+ assert os.path.exists(n_outfile), n_outfile
+
+ args = [n_counting_ht, n_infile, '-o', n_outfile2]
+ utils.runscript(script, args, in_dir)
+ assert os.path.exists(n_outfile2), n_outfile2
+
+
+def test_filter_abund_2():
+ infile = utils.copy_test_data('test-abund-read-2.fa')
+ in_dir = os.path.dirname(infile)
+
+ counting_ht = _make_counting(infile, K=17)
+
+ script = 'filter-abund.py'
+ args = ['-C', '1', counting_ht, infile, infile]
+ utils.runscript(script, args, in_dir)
+
+ outfile = infile + '.abundfilt'
+ assert os.path.exists(outfile), outfile
+
+ seqs = set([r.sequence for r in screed.open(outfile)])
+ assert len(seqs) == 2, seqs
+ assert 'GGTTGACGGGGCTCAGGG' in seqs
+
+
+def test_filter_abund_2_stdin():
+ infile = utils.copy_test_data('test-abund-read-2.fa')
+ in_dir = os.path.dirname(infile)
+
+ counting_ht = _make_counting(infile, K=17)
+
+ script = 'filter-abund.py'
+ args = ['-C', '1', counting_ht, '-']
+ (status, out, err) = utils.runscript(script, args, in_dir, fail_ok=True)
+ assert status == 1
+ assert "Accepting input from stdin; output filename must be provided" \
+ in str(err)
+
+
+def test_filter_abund_2_stdin_gzip_out():
+ infile = utils.copy_test_data('test-abund-read-2.fa')
+ in_dir = os.path.dirname(infile)
+ outfile = utils.get_temp_filename('out.fa.gz')
+
+ counting_ht = _make_counting(infile, K=17)
+
+ script = 'filter-abund.py'
+ args = ['-C', '1', counting_ht, infile, '-o', outfile, '--gzip']
+ (status, out, err) = utils.runscript(script, args, in_dir, fail_ok=True)
+ print(out)
+ print(err)
+ assert status == 0
+
+# make sure that FASTQ records are retained.
+
+
+def test_filter_abund_3_fq_retained():
+ infile = utils.copy_test_data('test-abund-read-2.fq')
+ in_dir = os.path.dirname(infile)
+
+ counting_ht = _make_counting(infile, K=17)
+
+ script = 'filter-abund.py'
+ args = ['-C', '1', counting_ht, infile, infile]
+ utils.runscript(script, args, in_dir)
+
+ outfile = infile + '.abundfilt'
+ assert os.path.exists(outfile), outfile
+
+ seqs = set([r.sequence for r in screed.open(outfile)])
+ assert len(seqs) == 2, seqs
+ assert 'GGTTGACGGGGCTCAGGG' in seqs
+
+ # check for 'quality' string.
+ quals = set([r.quality for r in screed.open(outfile)])
+ assert len(quals) == 2, quals
+ assert '##################' in quals
+
+
+# make sure that FASTQ names are properly parsed, both formats.
+
+
+def test_filter_abund_4_fq_casava_18():
+ infile = utils.copy_test_data('test-abund-read-2.paired2.fq')
+ in_dir = os.path.dirname(infile)
+
+ counting_ht = _make_counting(infile, K=17)
+
+ script = 'filter-abund.py'
+ args = [counting_ht, infile, infile]
+ utils.runscript(script, args, in_dir)
+
+ outfile = infile + '.abundfilt'
+ assert os.path.exists(outfile), outfile
+
+ seqs = set([r.name for r in screed.open(outfile)])
+ assert 'pair:foo 1::N' in seqs, seqs
+
+
+def test_filter_abund_1_singlefile():
+ infile = utils.copy_test_data('test-abund-read-2.fa')
+ in_dir = os.path.dirname(infile)
+
+ script = 'filter-abund-single.py'
+ args = ['-x', '1e7', '-N', '2', '-k', '17', infile]
+ (status, out, err) = utils.runscript(script, args, in_dir)
+
+ assert 'Total number of unique k-mers: 98' in err, err
+
+ outfile = infile + '.abundfilt'
+ assert os.path.exists(outfile), outfile
+
+ seqs = set([r.sequence for r in screed.open(outfile)])
+ assert len(seqs) == 1, seqs
+ assert 'GGTTGACGGGGCTCAGGG' in seqs
+
+
+def test_filter_abund_2_singlefile():
+ infile = utils.copy_test_data('test-abund-read-2.fa')
+ in_dir = os.path.dirname(infile)
+ tabfile = utils.get_temp_filename('test-savegraph.ct')
+
+ script = 'filter-abund-single.py'
+ args = ['-x', '1e7', '-N', '2', '-k', '17', '--savegraph',
+ tabfile, infile]
+ (status, out, err) = utils.runscript(script, args, in_dir)
+
+ assert 'Total number of unique k-mers: 98' in err, err
+
+ outfile = infile + '.abundfilt'
+ assert os.path.exists(outfile), outfile
+
+ seqs = set([r.sequence for r in screed.open(outfile)])
+ assert len(seqs) == 1, seqs
+ assert 'GGTTGACGGGGCTCAGGG' in seqs
+
+
+def test_filter_abund_2_singlefile_fq_casava_18():
+ infile = utils.copy_test_data('test-abund-read-2.paired2.fq')
+ in_dir = os.path.dirname(infile)
+
+ script = 'filter-abund-single.py'
+ args = ['-x', '1e7', '-N', '2', '-k', '17', infile]
+ (status, out, err) = utils.runscript(script, args, in_dir)
+
+ outfile = infile + '.abundfilt'
+ assert os.path.exists(outfile), outfile
+
+ seqs = set([r.name for r in screed.open(outfile)])
+ assert 'pair:foo 1::N' in seqs, seqs
+
+
+def test_filter_abund_4_retain_low_abund():
+ # test that the -V option does not trim sequences that are low abundance
+ infile = utils.copy_test_data('test-abund-read-2.fa')
+ in_dir = os.path.dirname(infile)
+
+ counting_ht = _make_counting(infile, K=17)
+
+ script, args = ('filter-abund.py', ['-V', counting_ht, infile])
+ utils.runscript(script, args, in_dir)
+
+ outfile = infile + '.abundfilt'
+ assert os.path.exists(outfile), outfile
+
+ seqs = set([r.sequence for r in screed.open(outfile)])
+ assert len(seqs) == 2, seqs
+ assert 'GGTTGACGGGGCTCAGGG' in seqs
+
+
+def test_filter_abund_single_4_retain_low_abund():
+ # test that the -V option does not trim sequences that are low abundance
+ infile = utils.copy_test_data('test-abund-read-2.fa')
+ in_dir = os.path.dirname(infile)
+
+ counting_ht = _make_counting(infile, K=17)
+
+ script, args = ('filter-abund-single.py', ['-k', '17', '-V', infile])
+ utils.runscript(script, args, in_dir)
+
+ outfile = infile + '.abundfilt'
+ assert os.path.exists(outfile), outfile
+
+ seqs = set([r.sequence for r in screed.open(outfile)])
+ assert len(seqs) == 2, seqs
+ assert 'GGTTGACGGGGCTCAGGG' in seqs
+
+
+def test_filter_abund_5_trim_high_abund():
+ # test that the -V option *does* trim sequences that are high abundance
+ infile = utils.copy_test_data('test-abund-read-3.fa')
+ in_dir = os.path.dirname(infile)
+
+ counting_ht = _make_counting(infile, K=17)
+
+ script, args = ('filter-abund.py', ['-V', counting_ht, infile])
+ utils.runscript(script, args, in_dir)
+
+ outfile = infile + '.abundfilt'
+ assert os.path.exists(outfile), outfile
+
+ seqs = set([r.sequence for r in screed.open(outfile)])
+ assert len(seqs) == 2, seqs
+
+ # trimmed sequence @ error
+ assert 'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGC' in seqs
+
+
+def test_filter_abund_single_trim_high_abund():
+ # test that the -V option *does* trim sequences that are high abundance
+ infile = utils.copy_test_data('test-abund-read-3.fa')
+ in_dir = os.path.dirname(infile)
+
+ script, args = ('filter-abund-single.py', ['-k', '17', '-V', infile])
+ utils.runscript(script, args, in_dir)
+
+ outfile = infile + '.abundfilt'
+ assert os.path.exists(outfile), outfile
+
+ seqs = set([r.sequence for r in screed.open(outfile)])
+ assert len(seqs) == 2, seqs
+
+ # trimmed sequence @ error
+ assert 'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGC' in seqs
+
+
+def test_filter_abund_6_trim_high_abund_Z():
+ # test that -V/-Z settings interact properly -
+ # trimming should not happen if -Z is set high enough.
+
+ infile = utils.copy_test_data('test-abund-read-3.fa')
+ in_dir = os.path.dirname(infile)
+
+ counting_ht = _make_counting(infile, K=17)
+
+ for script, args in (('filter-abund.py',
+ ['-V', '-Z', '25', counting_ht, infile]),
+ ('filter-abund-single.py',
+ ['-k', '17', '-V', '-Z', '25', infile])):
+ utils.runscript(script, args, in_dir)
+
+ outfile = infile + '.abundfilt'
+ assert os.path.exists(outfile), outfile
+
+ seqs = set([r.sequence for r in screed.open(outfile)])
+ assert len(seqs) == 2, seqs
+
+ # untrimmed seq.
+ badseq = 'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCgtgCCGCAGCTG' \
+ 'TCGTCAGGGGATTTCCGGGCGG'
+ assert badseq in seqs # should be there, untrimmed
+
+
+def test_filter_abund_7_retain_Ns():
+ # check that filter-abund retains sequences with Ns, and treats them as As.
+
+ infile = utils.copy_test_data('test-filter-abund-Ns.fq')
+ in_dir = os.path.dirname(infile)
+
+ # copy test file over to test.fq & load into countgraph
+ counting_ht = _make_counting(infile, K=17)
+
+ script = 'filter-abund.py'
+ args = ['-C', '3', counting_ht, infile]
+ utils.runscript(script, args, in_dir)
+
+ outfile = infile + '.abundfilt'
+ assert os.path.exists(outfile), outfile
+
+ # test for a sequence with an 'N' in it --
+ names = set([r.name for r in screed.open(outfile)])
+ assert '895:1:37:17593:9954 1::FOO_withN' in names, names
+
+ # check to see if that 'N' was properly changed to an 'A'
+ seqs = set([r.sequence for r in screed.open(outfile)])
+ assert 'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAG' not in seqs, seqs
+
+ # ...and that an 'N' remains in the output sequences
+ found_N = False
+ for s in seqs:
+ if 'N' in s:
+ found_N = True
+ assert found_N, seqs
+
+
+def test_filter_abund_single_8_retain_Ns():
+ # check that filter-abund-single retains
+ # sequences with Ns, and treats them as As.
+
+ infile = utils.copy_test_data('test-filter-abund-Ns.fq')
+ in_dir = os.path.dirname(infile)
+
+ script = 'filter-abund-single.py'
+ args = ['-k', '17', '-x', '1e7', '-N', '2', '-C', '3', infile]
+ utils.runscript(script, args, in_dir)
+
+ outfile = infile + '.abundfilt'
+ assert os.path.exists(outfile), outfile
+
+ # test for a sequence with an 'N' in it --
+ names = set([r.name for r in screed.open(outfile)])
+ assert '895:1:37:17593:9954 1::FOO_withN' in names, names
+
+ # check to see if that 'N' was properly changed to an 'A'
+ seqs = set([r.sequence for r in screed.open(outfile)])
+ assert 'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAG' not in seqs, seqs
+
+ # ...and that an 'N' remains in the output sequences
+ found_N = False
+ for s in seqs:
+ if 'N' in s:
+ found_N = True
+ assert found_N, seqs
+
+
+def test_outfile():
+ infile = utils.get_test_data('paired-mixed-witherror.fa.pe')
+ outfile = utils.get_temp_filename('paired-mixed-witherror.fa.pe.abundfilt')
+ script = 'filter-abund-single.py'
+ args = ['-o', outfile, infile]
+ (status, out, err) = utils.runscript(script, args)
+ md5hash = utils._calc_md5(open(outfile, 'rb'))
+ assert md5hash == 'f17122f4c0c3dc0bcc4eeb375de93040', md5hash
+
+
+def test_filter_abund_1_quiet():
+ script = 'filter-abund.py'
+
+ infile = utils.copy_test_data('test-abund-read-2.fa')
+ n_infile = utils.copy_test_data('test-fastq-n-reads.fq')
+
+ in_dir = os.path.dirname(infile)
+ n_in_dir = os.path.dirname(n_infile)
+
+ counting_ht = _make_counting(infile, K=17)
+ n_counting_ht = _make_counting(n_infile, K=17)
+
+ args = ['-q', counting_ht, infile]
+ status, out, err = utils.runscript(script, args, in_dir)
+
+ assert len(err) == 0
+
+ outfile = infile + '.abundfilt'
+ n_outfile = n_infile + '.abundfilt'
+ n_outfile2 = n_infile + '2.abundfilt'
+
+ assert os.path.exists(outfile), outfile
+
+
+def test_filter_abund_1_singlefile_quiet():
+ infile = utils.copy_test_data('test-abund-read-2.fa')
+ in_dir = os.path.dirname(infile)
+
+ script = 'filter-abund-single.py'
+ args = ['-q', '-x', '1e7', '-N', '2', '-k', '17', infile]
+ (status, out, err) = utils.runscript(script, args, in_dir)
+
+ assert len(err) == 0
+
+ outfile = infile + '.abundfilt'
+ assert os.path.exists(outfile), outfile
diff --git a/tests/test_functions.py b/tests/test_functions.py
index dd0c7ba..483b0e1 100644
--- a/tests/test_functions.py
+++ b/tests/test_functions.py
@@ -1,6 +1,6 @@
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2010-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -32,15 +32,18 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
+# pylint: disable=missing-docstring,invalid-name,no-member
from __future__ import print_function
from __future__ import absolute_import
+
+import screed
import khmer
import os
import sys
-import collections
+import pytest
from . import khmer_tst_utils as utils
from khmer.utils import (check_is_pair, broken_paired_reader, check_is_left,
- check_is_right)
+ check_is_right, clean_input_reads)
from khmer.kfile import check_input_files, get_file_writer
try:
from StringIO import StringIO
@@ -54,6 +57,9 @@ def test_forward_hash():
assert khmer.forward_hash('CCCC', 4) == 170
assert khmer.forward_hash('GGGG', 4) == 170
+ h = 13607885392109549066
+ assert khmer.forward_hash('GGTTGACGGGGCTCAGGGGGCGGCTGACTCCG', 32) == h
+
def test_get_file_writer_fail():
somefile = utils.get_temp_filename("potato")
@@ -62,7 +68,7 @@ def test_get_file_writer_fail():
try:
get_file_writer(somefile, True, True)
stopped = False
- except Exception as err:
+ except ValueError as err:
assert "Cannot specify both bzip and gzip" in str(err), str(err)
assert stopped, "Expected exception"
@@ -96,11 +102,60 @@ def test_reverse_hash():
assert s == "GGGG"
+def test_reverse_complement():
+ s = 'AATTCCGG'
+ assert khmer.reverse_complement(s) == 'CCGGAATT'
+
+ s = 'A'
+ assert khmer.reverse_complement(s) == 'T'
+ s = 'T'
+ assert khmer.reverse_complement(s) == 'A'
+ s = 'C'
+ assert khmer.reverse_complement(s) == 'G'
+ s = 'G'
+ assert khmer.reverse_complement(s) == 'C'
+
+
+def test_reverse_complement_exception():
+ # deal with DNA, ignore rest
+ assert khmer.reverse_complement('FGF') == 'FCF'
+
+
+def test_reverse_hash_longs():
+ # test explicitly with long integers, only needed for python2
+ # the builtin `long` exists in the global scope only
+ global long # pylint: disable=global-variable-undefined
+ if sys.version_info > (3,):
+ long = int
+
+ s = khmer.reverse_hash(long(0), 4)
+ assert s == "AAAA"
+
+ s = khmer.reverse_hash(long(85), 4)
+ assert s == "TTTT"
+
+ s = khmer.reverse_hash(long(170), 4)
+ assert s == "CCCC"
+
+ s = khmer.reverse_hash(long(255), 4)
+ assert s == "GGGG"
+
+
+def test_reverse_hash_raises():
+ with pytest.raises(TypeError) as excinfo:
+ khmer.reverse_hash('2345', 4)
+
+ assert 'int' in str(excinfo.value)
+
+
def test_hash_murmur3():
assert khmer.hash_murmur3('AAAA') == 526240128537019279
assert khmer.hash_murmur3('TTTT') == 526240128537019279
assert khmer.hash_murmur3('CCCC') == 14391997331386449225
assert khmer.hash_murmur3('GGGG') == 14391997331386449225
+ assert khmer.hash_murmur3('TATATATATATATATATATA') != 0
+ assert khmer.hash_murmur3('TTTTGCAAAA') != 0
+ assert khmer.hash_murmur3('GAAAATTTTC') != 0
def test_hash_no_rc_murmur3():
@@ -122,10 +177,15 @@ def test_get_primes():
assert primes == [19, 17, 13, 11, 7, 5, 3]
+ primes_not_float = khmer.get_n_primes_near_x(7, 20.)
+
+ assert primes_not_float == [19, 17, 13, 11, 7, 5, 3]
+ assert all(isinstance(p, int) for p in primes_not_float)
+
def test_get_primes_fal():
try:
- primes = khmer.get_n_primes_near_x(5, 5)
+ khmer.get_n_primes_near_x(5, 5)
assert 0, "previous statement should fail"
except RuntimeError as err:
assert "unable to find 5 prime numbers < 5" in str(err)
@@ -149,9 +209,8 @@ def test_extract_countgraph_info():
try:
info = khmer.extract_countgraph_info(fn)
except ValueError as err:
- raise
assert 0, 'Should not throw a ValueErorr: ' + str(err)
- ksize, table_size, n_tables, _, _, _, _ = info
+ ksize, n_tables, table_size, _, _, _, _ = info
print(ksize, table_size, n_tables)
assert(ksize) == 25
@@ -196,7 +255,6 @@ def test_extract_nodegraph_info():
def test_check_file_status_kfile():
fn = utils.get_temp_filename('thisfiledoesnotexist')
- check_file_status_exited = False
old_stderr = sys.stderr
sys.stderr = capture = StringIO()
@@ -225,55 +283,51 @@ def test_check_file_status_kfile_force():
assert "does not exist" in capture.getvalue(), capture.getvalue()
-FakeFQRead = collections.namedtuple('Read', ['name', 'quality', 'sequence'])
-FakeFastaRead = collections.namedtuple('Read', ['name', 'sequence'])
-
-
def test_check_is_pair_1():
- read1 = FakeFQRead(name='seq', quality='###', sequence='AAA')
- read2 = FakeFQRead(name='seq2', quality='###', sequence='AAA')
+ read1 = screed.Record(name='seq', quality='###', sequence='AAA')
+ read2 = screed.Record(name='seq2', quality='###', sequence='AAA')
assert not check_is_pair(read1, read2)
def test_check_is_pair_2():
- read1 = FakeFQRead(name='seq/1', quality='###', sequence='AAA')
- read2 = FakeFQRead(name='seq/2', quality='###', sequence='AAA')
+ read1 = screed.Record(name='seq/1', quality='###', sequence='AAA')
+ read2 = screed.Record(name='seq/2', quality='###', sequence='AAA')
assert check_is_pair(read1, read2)
def test_check_is_pair_3_fq():
- read1 = FakeFQRead(name='seq 1::', quality='###', sequence='AAA')
- read2 = FakeFQRead(name='seq 2::', quality='###', sequence='AAA')
+ read1 = screed.Record(name='seq 1::', quality='###', sequence='AAA')
+ read2 = screed.Record(name='seq 2::', quality='###', sequence='AAA')
assert check_is_pair(read1, read2)
def test_check_is_pair_3_broken_fq_1():
- read1 = FakeFQRead(name='seq', quality='###', sequence='AAA')
- read2 = FakeFQRead(name='seq 2::', quality='###', sequence='AAA')
+ read1 = screed.Record(name='seq', quality='###', sequence='AAA')
+ read2 = screed.Record(name='seq 2::', quality='###', sequence='AAA')
assert not check_is_pair(read1, read2)
def test_check_is_pair_3_broken_fq_2():
- read1 = FakeFQRead(name='seq 1::', quality='###', sequence='AAA')
- read2 = FakeFQRead(name='seq', quality='###', sequence='AAA')
+ read1 = screed.Record(name='seq 1::', quality='###', sequence='AAA')
+ read2 = screed.Record(name='seq', quality='###', sequence='AAA')
assert not check_is_pair(read1, read2)
def test_check_is_pair_3_fa():
- read1 = FakeFastaRead(name='seq 1::', sequence='AAA')
- read2 = FakeFastaRead(name='seq 2::', sequence='AAA')
+ read1 = screed.Record(name='seq 1::', sequence='AAA')
+ read2 = screed.Record(name='seq 2::', sequence='AAA')
assert check_is_pair(read1, read2)
def test_check_is_pair_4():
- read1 = FakeFQRead(name='seq/1', quality='###', sequence='AAA')
- read2 = FakeFastaRead(name='seq/2', sequence='AAA')
+ read1 = screed.Record(name='seq/1', quality='###', sequence='AAA')
+ read2 = screed.Record(name='seq/2', sequence='AAA')
try:
check_is_pair(read1, read2)
@@ -283,8 +337,8 @@ def test_check_is_pair_4():
def test_check_is_pair_4b():
- read1 = FakeFastaRead(name='seq/1', sequence='AAA')
- read2 = FakeFQRead(name='seq/2', quality='###', sequence='AAA')
+ read1 = screed.Record(name='seq/1', sequence='AAA')
+ read2 = screed.Record(name='seq/2', quality='###', sequence='AAA')
try:
check_is_pair(read1, read2)
@@ -294,22 +348,22 @@ def test_check_is_pair_4b():
def test_check_is_pair_5():
- read1 = FakeFastaRead(name='seq/1', sequence='AAA')
- read2 = FakeFastaRead(name='seq/2', sequence='AAA')
+ read1 = screed.Record(name='seq/1', sequence='AAA')
+ read2 = screed.Record(name='seq/2', sequence='AAA')
assert check_is_pair(read1, read2)
def test_check_is_pair_6():
- read1 = FakeFastaRead(name='seq1', sequence='AAA')
- read2 = FakeFastaRead(name='seq2', sequence='AAA')
+ read1 = screed.Record(name='seq1', sequence='AAA')
+ read2 = screed.Record(name='seq2', sequence='AAA')
assert not check_is_pair(read1, read2)
def test_check_is_pair_7():
- read1 = FakeFastaRead(name='seq/2', sequence='AAA')
- read2 = FakeFastaRead(name='seq/1', sequence='AAA')
+ read1 = screed.Record(name='seq/2', sequence='AAA')
+ read2 = screed.Record(name='seq/1', sequence='AAA')
assert not check_is_pair(read1, read2)
@@ -337,29 +391,31 @@ def test_check_is_left():
'@HWI-ST412:261:d15khacxx:8:1101:3149:2157 1:N:0:ATCACG')
+def gather(stream, **kw):
+ itr = broken_paired_reader(stream, **kw)
+
+ x = []
+ m = 0
+ num = 0
+ for num, is_pair, read1, read2 in itr:
+ if is_pair:
+ x.append((read1.name, read2.name))
+ else:
+ x.append((read1.name, None))
+ m += 1
+
+ return x, num, m
+
+
class Test_BrokenPairedReader(object):
- stream = [FakeFastaRead(name='seq1/1', sequence='A' * 5),
- FakeFastaRead(name='seq1/2', sequence='A' * 4),
- FakeFastaRead(name='seq2/1', sequence='A' * 5),
- FakeFastaRead(name='seq3/1', sequence='A' * 3),
- FakeFastaRead(name='seq3/2', sequence='A' * 5)]
-
- def gather(self, **kw):
- iter = broken_paired_reader(self.stream, **kw)
-
- x = []
- m = 0
- for n, is_pair, read1, read2 in iter:
- if is_pair:
- x.append((read1.name, read2.name))
- else:
- x.append((read1.name, None))
- m += 1
-
- return x, n, m
+ stream = [screed.Record(name='seq1/1', sequence='A' * 5),
+ screed.Record(name='seq1/2', sequence='A' * 4),
+ screed.Record(name='seq2/1', sequence='A' * 5),
+ screed.Record(name='seq3/1', sequence='A' * 3),
+ screed.Record(name='seq3/2', sequence='A' * 5)]
def testDefault(self):
- x, n, m = self.gather(min_length=1)
+ x, n, m = gather(self.stream, min_length=1)
expected = [('seq1/1', 'seq1/2'),
('seq2/1', None),
@@ -369,7 +425,7 @@ class Test_BrokenPairedReader(object):
assert n == 3, n
def testMinLength(self):
- x, n, m = self.gather(min_length=3)
+ x, n, m = gather(self.stream, min_length=3)
expected = [('seq1/1', 'seq1/2'),
('seq2/1', None),
@@ -379,7 +435,7 @@ class Test_BrokenPairedReader(object):
assert n == 3, n
def testMinLength_2(self):
- x, n, m = self.gather(min_length=4)
+ x, n, m = gather(self.stream, min_length=4)
expected = [('seq1/1', 'seq1/2'),
('seq2/1', None),
@@ -389,7 +445,7 @@ class Test_BrokenPairedReader(object):
assert n == 3, n
def testForceSingle(self):
- x, n, m = self.gather(force_single=True)
+ x, n, m = gather(self.stream, force_single=True)
expected = [('seq1/1', None),
('seq1/2', None),
@@ -401,7 +457,7 @@ class Test_BrokenPairedReader(object):
assert n == 4, n
def testForceSingleAndMinLength(self):
- x, n, m = self.gather(min_length=5, force_single=True)
+ x, n, m = gather(self.stream, min_length=5, force_single=True)
expected = [('seq1/1', None),
('seq2/1', None),
@@ -409,3 +465,111 @@ class Test_BrokenPairedReader(object):
assert x == expected, x
assert m == 3, m
assert n == 2, n
+
+
+def test_BrokenPairedReader_OnPairs():
+ stream = [screed.Record(name='seq1/1', sequence='A' * 5),
+ screed.Record(name='seq1/2', sequence='A' * 4),
+ screed.Record(name='seq3/1', sequence='A' * 3),
+ screed.Record(name='seq3/2', sequence='A' * 5)]
+
+ x, n, m = gather(stream, min_length=4, require_paired=True)
+
+ expected = [('seq1/1', 'seq1/2')]
+ assert x == expected, x
+ assert m == 1
+ assert n == 0, n
+
+
+def test_BrokenPairedReader_OnPairs_2():
+ stream = [screed.Record(name='seq1/1', sequence='A' * 5),
+ screed.Record(name='seq1/2', sequence='A' * 4),
+ screed.Record(name='seq3/1', sequence='A' * 5), # switched
+ screed.Record(name='seq3/2', sequence='A' * 3)] # wrt previous
+
+ x, n, m = gather(stream, min_length=4, require_paired=True)
+
+ expected = [('seq1/1', 'seq1/2')]
+ assert x == expected, x
+ assert m == 1
+ assert n == 0, n
+
+
+def test_BrokenPairedReader_OnPairs_3():
+ stream = [screed.Record(name='seq1/1', sequence='A' * 5),
+ screed.Record(name='seq1/2', sequence='A' * 4),
+ screed.Record(name='seq3/1', sequence='A' * 3), # both short
+ screed.Record(name='seq3/2', sequence='A' * 3)]
+
+ x, n, m = gather(stream, min_length=4, require_paired=True)
+
+ expected = [('seq1/1', 'seq1/2')]
+ assert x == expected, x
+ assert m == 1
+ assert n == 0, n
+
+
+def test_BrokenPairedReader_OnPairs_4():
+ stream = [screed.Record(name='seq1/1', sequence='A' * 3), # too short
+ screed.Record(name='seq1/2', sequence='A' * 4),
+ screed.Record(name='seq3/1', sequence='A' * 4),
+ screed.Record(name='seq3/2', sequence='A' * 5)]
+
+ x, n, m = gather(stream, min_length=4, require_paired=True)
+
+ expected = [('seq3/1', 'seq3/2')]
+ assert x == expected, x
+ assert m == 1
+ assert n == 0, n
+
+
+def test_BrokenPairedReader_lowercase():
+ stream = [screed.Record(name='seq1/1', sequence='acgtn'),
+ screed.Record(name='seq1/2', sequence='AcGtN'),
+ screed.Record(name='seq1/2', sequence='aCgTn')]
+ stream = clean_input_reads(stream)
+
+ results = []
+ for num, is_pair, read1, read2 in broken_paired_reader(stream):
+ results.append((read1, read2))
+
+ a, b = results[0]
+ assert a.sequence == 'acgtn'
+ assert a.cleaned_seq == 'ACGTA'
+ assert b.sequence == 'AcGtN'
+ assert b.cleaned_seq == 'ACGTA'
+
+ c, d = results[1]
+ assert c.sequence == 'aCgTn'
+ assert c.cleaned_seq == 'ACGTA'
+ assert d is None
+
+
+def test_BrokenPairedReader_lowercase_khmer_Read():
+ # use khmer.Read objects which should automatically have a `cleaned_seq`
+ # attribute
+ stream = [khmer.Read(name='seq1/1', sequence='acgtn'),
+ khmer.Read(name='seq1/2', sequence='AcGtN'),
+ khmer.Read(name='seq1/2', sequence='aCgTn')]
+
+ results = []
+ for num, is_pair, read1, read2 in broken_paired_reader(stream):
+ results.append((read1, read2))
+
+ a, b = results[0]
+ assert a.sequence == 'acgtn'
+ assert a.cleaned_seq == 'ACGTA'
+ assert b.sequence == 'AcGtN'
+ assert b.cleaned_seq == 'ACGTA'
+
+ c, d = results[1]
+ assert c.sequence == 'aCgTn'
+ assert c.cleaned_seq == 'ACGTA'
+ assert d is None
+
+
+def test_clean_input_reads():
+ # all Read attributes are read only
+ stream = [khmer.Read(name='seq1/1', sequence='ACGT')]
+ with pytest.raises(AttributeError):
+ next(clean_input_reads(stream))
diff --git a/tests/test_graph.py b/tests/test_graph.py
index 40a195e..dfe038f 100644
--- a/tests/test_graph.py
+++ b/tests/test_graph.py
@@ -32,15 +32,16 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
+# pylint: disable=missing-docstring,no-member,invalid-name,no-self-use
+# pylint: disable=protected-access
from __future__ import print_function
from __future__ import absolute_import
+
import khmer
import screed
from . import khmer_tst_utils as utils
-from nose.plugins.attrib import attr
-
def teardown():
utils.cleanup()
@@ -53,7 +54,7 @@ class Test_ExactGraphFu(object):
def test_counts(self):
ht = self.ht
- ht.consume_fasta(utils.get_test_data('test-graph.fa'))
+ ht.consume_seqfile(utils.get_test_data('test-graph.fa'))
kmer = "TTAGGACTGCAC"
x = ht.calc_connected_graph_size(kmer)
@@ -223,12 +224,11 @@ class Test_InexactGraphFu(object):
class Test_Partitioning(object):
def test_output_unassigned(self):
- import screed
filename = utils.get_test_data('random-20-a.fa')
ht = khmer._Nodegraph(21, [5, 7, 11, 13])
- ht.consume_fasta_and_tag(filename)
+ ht.consume_seqfile_and_tag(filename)
output_file = utils.get_temp_filename('part0test')
ht.output_partitions(filename, output_file, True)
@@ -240,12 +240,11 @@ class Test_Partitioning(object):
assert len1 == len2, (len1, len2)
def test_not_output_unassigned(self):
- import screed
filename = utils.get_test_data('random-20-a.fa')
ht = khmer._Nodegraph(21, [5, 7, 11, 13])
- ht.consume_fasta_and_tag(filename)
+ ht.consume_seqfile_and_tag(filename)
output_file = utils.get_temp_filename('parttest')
ht.output_partitions(filename, output_file, False)
@@ -260,7 +259,7 @@ class Test_Partitioning(object):
filename = utils.get_test_data('random-20-a.fq')
ht = khmer.Nodegraph(20, 1e4, 4)
- ht.consume_fasta_and_tag(filename)
+ ht.consume_seqfile_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
ht.merge_subset(subset)
@@ -276,7 +275,7 @@ class Test_Partitioning(object):
filename = utils.get_test_data('random-20-a.fa')
ht = khmer.Nodegraph(21, 1e5, 4)
- ht.consume_fasta_and_tag(filename)
+ ht.consume_seqfile_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
x = ht.subset_count_partitions(subset)
@@ -286,7 +285,7 @@ class Test_Partitioning(object):
filename = utils.get_test_data('random-20-a.fa')
ht = khmer.Nodegraph(20, 1e4, 4)
- ht.consume_fasta_and_tag(filename)
+ ht.consume_seqfile_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
x = ht.subset_count_partitions(subset)
@@ -296,7 +295,7 @@ class Test_Partitioning(object):
filename = utils.get_test_data('random-20-b.fa')
ht = khmer.Nodegraph(21, 1e4, 4)
- ht.consume_fasta_and_tag(filename)
+ ht.consume_seqfile_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
x = ht.subset_count_partitions(subset)
@@ -306,7 +305,7 @@ class Test_Partitioning(object):
filename = utils.get_test_data('random-20-b.fa')
ht = khmer.Nodegraph(20, 1e4, 4)
- ht.consume_fasta_and_tag(filename)
+ ht.consume_seqfile_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
x = ht.subset_count_partitions(subset)
@@ -316,7 +315,7 @@ class Test_Partitioning(object):
filename = utils.get_test_data('random-31-c.fa')
ht = khmer.Nodegraph(32, 1e6, 4)
- ht.consume_fasta_and_tag(filename)
+ ht.consume_seqfile_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
x = ht.subset_count_partitions(subset)
@@ -326,7 +325,7 @@ class Test_Partitioning(object):
filename = utils.get_test_data('random-31-c.fa')
ht = khmer.Nodegraph(31, 1e5, 4)
- ht.consume_fasta_and_tag(filename)
+ ht.consume_seqfile_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
x = ht.subset_count_partitions(subset)
@@ -341,18 +340,17 @@ class Test_PythonAPI(object):
ht = khmer.Nodegraph(20, 4 ** 4 + 1, 2)
a = "ATTGGGACTCTGGGAGCACTTATCATGGAGAT"
- b = "GAGCACTTTAACCCTGCAGAGTGGCCAAGGCT"
c = "GGAGCACTTATCATGGAGATATATCCCGTGCTTAAACATCGCACTTTAACCCTGCAGAGT"
print(ht.consume(a))
try:
- ppi = ht.find_all_tags(c[:19])
+ ht.find_all_tags(c[:19])
assert False, "should raise a ValueError for wrong k-mer size"
except ValueError:
pass
try:
- ppi = ht.find_all_tags(c[:21])
+ ht.find_all_tags(c[:21])
assert False, "should raise a ValueError for wrong k-mer size"
except ValueError:
pass
diff --git a/tests/test_hashset.py b/tests/test_hashset.py
new file mode 100644
index 0000000..e68934c
--- /dev/null
+++ b/tests/test_hashset.py
@@ -0,0 +1,169 @@
+# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# Copyright (C) 2010-2015, Michigan State University.
+# Copyright (C) 2015-2016, The Regents of the University of California.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+#
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# * Redistributions in binary form must reproduce the above
+# copyright notice, this list of conditions and the following
+# disclaimer in the documentation and/or other materials provided
+# with the distribution.
+#
+# * Neither the name of the Michigan State University nor the names
+# of its contributors may be used to endorse or promote products
+# derived from this software without specific prior written
+# permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Contact: khmer-project at idyll.org
+# pylint: disable=C0111,C0103
+"""
+Test code for HashSet objects.
+"""
+from __future__ import print_function
+from __future__ import absolute_import
+
+import khmer
+from . import khmer_tst_utils as utils
+
+
+def test_bad_construct():
+ try:
+ hs = khmer.HashSet()
+ assert 0, "HashSet constructor should fail w/o argument"
+ except TypeError:
+ pass
+
+ try:
+ hs = khmer.HashSet(5, [{}])
+ assert 0, "HashSet constructor should fail w/o list of k-mers"
+ except ValueError:
+ pass
+
+
+def test_iter_single():
+ hs = khmer.HashSet(5, [6])
+ for k in hs:
+ assert k == 6
+ print(k)
+
+
+def test_iter_double():
+ x = [6, 9, 20]
+ hs = khmer.HashSet(5, x)
+ for i, k in enumerate(hs):
+ assert k == x[i], (k, x[i])
+
+
+def test_iter_single():
+ hs = khmer.HashSet(5, [6])
+ k = iter(hs)
+ k2 = iter(k)
+ assert k == k2
+
+
+def test_add():
+ hs = khmer.HashSet(5)
+ hs.add(7)
+ hs.add(4)
+
+ assert list(sorted(hs)) == [4, 7]
+
+
+def test_update():
+ hs = khmer.HashSet(5)
+ x = [5, 10, 15, 2**35]
+ hs.update(x)
+
+ assert list(sorted(hs)) == [5, 10, 15, 2**35]
+
+
+def test_update_bad():
+ hs = khmer.HashSet(5)
+ x = [5, 10, 15, 2**35, {}]
+ try:
+ hs.update(x)
+ assert 0, "cannot add dict to a HashSet"
+ except ValueError:
+ pass
+
+
+def test_remove():
+ hs = khmer.HashSet(5, [8, 10])
+ assert len(hs) == 2
+ hs.remove(8)
+ assert len(hs) == 1
+ assert list(hs) == [10]
+
+
+def test_remove_2():
+ hs = khmer.HashSet(5, [8, 10])
+ assert len(hs) == 2
+ try:
+ hs.remove(15)
+ assert 0, "hs.remove should raise an Exception"
+ except ValueError:
+ pass
+ assert len(hs) == 2
+ assert list(sorted(hs)) == [8, 10]
+
+
+def test_contains_1():
+ hs = khmer.HashSet(5, [8, 10])
+ assert 8 in hs
+ assert 10 in hs
+ assert 2**35 not in hs
+
+
+def test_concat_1():
+ hs = khmer.HashSet(5, [10, 12])
+ hs2 = khmer.HashSet(5, [10, 13])
+
+ hs3 = hs + hs2
+ assert list(sorted(hs3)) == [10, 12, 13]
+
+
+def test_concat_2():
+ hs = khmer.HashSet(5, [10, 12])
+ hs2 = khmer.HashSet(5, [10, 13])
+
+ hs += hs2
+ assert list(sorted(hs)) == [10, 12, 13]
+
+
+def test_concat_1_fail():
+ hs = khmer.HashSet(5, [10, 12])
+ hs2 = khmer.HashSet(4, [10, 13])
+
+ try:
+ hs3 = hs + hs2
+ assert 0, "concat should fail - different ksize"
+ except ValueError:
+ pass
+
+
+def test_concat_2_fail():
+ hs = khmer.HashSet(5, [10, 12])
+ hs2 = khmer.HashSet(4, [10, 13])
+
+ try:
+ hs += hs2
+ assert 0, "inplace concat should fail - different ksize"
+ except ValueError:
+ pass
diff --git a/tests/test_hll.py b/tests/test_hll.py
index 623c481..5770b0f 100644
--- a/tests/test_hll.py
+++ b/tests/test_hll.py
@@ -1,6 +1,6 @@
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2014-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -32,18 +32,16 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
-# pylint: disable=missing-docstring,protected-access
+# pylint: disable=missing-docstring,protected-access,no-member,invalid-name
from __future__ import division, print_function, unicode_literals
from __future__ import absolute_import
-import math
-
import khmer
from screed.fasta import fasta_iter
from . import khmer_tst_utils as utils
-from nose.tools import assert_raises
+import pytest
K = 20 # size of kmer
@@ -90,7 +88,7 @@ def test_hll_consume_string():
filename = utils.get_test_data('random-20-a.fa')
hllcpp = khmer.HLLCounter(ERR_RATE, K)
- n_consumed = 0
+ n_consumed = n = 0
for n, record in enumerate(fasta_iter(open(filename)), 1):
n_consumed += hllcpp.consume_string(record['sequence'])
@@ -102,29 +100,29 @@ def test_hll_consume_string():
def test_hll_empty_fasta():
filename = utils.get_test_data('test-empty.fa')
hll = khmer.HLLCounter(ERR_RATE, K)
- with assert_raises(OSError):
- hll.consume_fasta(filename)
+ with pytest.raises(OSError):
+ hll.consume_seqfile(filename)
-def test_hll_consume_fasta():
+def test_hll_consume_seqfile():
# test c++ code to count unique kmers using HyperLogLog
filename = utils.get_test_data('random-20-a.fa')
hllcpp = khmer.HLLCounter(ERR_RATE, K)
- n, n_consumed = hllcpp.consume_fasta(filename)
+ n, n_consumed = hllcpp.consume_seqfile(filename)
assert n == 99
assert n_consumed == 3960
assert abs(1 - float(hllcpp.estimate_cardinality()) / N_UNIQUE) < ERR_RATE
-def test_hll_consume_fasta_ep():
+def test_hll_consume_seqfile_ep():
# During estimation trigger the _Ep() method,
# we need all internal counters values to be different than zero for this.
filename = utils.get_test_data('paired-mixed.fa')
hll = khmer.HLLCounter(0.36, 32)
- n, n_consumed = hll.consume_fasta(filename)
+ n, n_consumed = hll.consume_seqfile(filename)
assert all(c != 0 for c in hll.counters)
assert len(hll) == 236
@@ -132,7 +130,7 @@ def test_hll_consume_fasta_ep():
assert n_consumed == 575
-def test_hll_consume_fasta_estimate_bias():
+def test_hll_consume_seqfile_estimate_bias():
# During estimation trigger the estimate_bias method,
# we need all internal counters values to be different than zero for this,
# and also the cardinality should be small (if it is large we fall on the
@@ -140,7 +138,7 @@ def test_hll_consume_fasta_estimate_bias():
filename = utils.get_test_data("test-abund-read-3.fa")
hll = khmer.HLLCounter(0.36, K)
- n, n_consumed = hll.consume_fasta(filename)
+ n, n_consumed = hll.consume_seqfile(filename)
assert all(c != 0 for c in hll.counters)
assert len(hll) == 79
@@ -151,7 +149,7 @@ def test_hll_consume_fasta_estimate_bias():
def test_hll_len():
filename = utils.get_test_data('random-20-a.fa')
hllcpp = khmer.HLLCounter(ERR_RATE, K)
- n, n_consumed = hllcpp.consume_fasta(filename)
+ n, n_consumed = hllcpp.consume_seqfile(filename)
assert n == 99
assert n_consumed == 3960
@@ -166,7 +164,7 @@ def test_hll_empty():
def test_hll_readonly_alpha():
hllcpp = khmer.HLLCounter(ERR_RATE, K)
- with assert_raises(AttributeError):
+ with pytest.raises(AttributeError):
hllcpp.alpha = 5
@@ -188,26 +186,25 @@ def test_hll_cover_calc_alpha():
def test_hll_invalid_base():
- # this test should raise a ValueError,
- # since there are invalid bases in read.
-
hllcpp = khmer.HLLCounter(ERR_RATE, 5)
- with assert_raises(ValueError):
- hllcpp.consume_string("ACGTTTCGNAATNNNNN")
+
+ # this should succeed; invalid bases need to be removed before
+ # hashing.
+ hllcpp.consume_string("ACGTTTCGNAATNNNNN")
def test_hll_invalid_error_rate():
# test if error_rate is a valid value
- with assert_raises(ValueError):
- hllcpp = khmer.HLLCounter(-0.01, K)
+ with pytest.raises(ValueError):
+ khmer.HLLCounter(-0.01, K)
def test_hll_invalid_error_rate_max():
# test if error_rate is a valid value
- with assert_raises(ValueError):
- hllcpp = khmer.HLLCounter(0.367696, K)
+ with pytest.raises(ValueError):
+ khmer.HLLCounter(0.367696, K)
def test_hll_error_rate_max():
@@ -220,8 +217,8 @@ def test_hll_error_rate_max():
def test_hll_invalid_error_rate_min():
# test if error_rate is a valid value
- with assert_raises(ValueError):
- hllcpp = khmer.HLLCounter(0.0040624, K)
+ with pytest.raises(ValueError):
+ khmer.HLLCounter(0.0040624, K)
def test_hll_error_rate_min():
@@ -240,21 +237,21 @@ def test_hll_change_error_rate():
hllcpp.error_rate = 0.01
assert hllcpp.error_rate == 0.008125
- with assert_raises(TypeError):
+ with pytest.raises(TypeError):
del hllcpp.error_rate
- with assert_raises(TypeError):
+ with pytest.raises(TypeError):
hllcpp.error_rate = 5
- with assert_raises(ValueError):
+ with pytest.raises(ValueError):
hllcpp.error_rate = 2.5
- with assert_raises(ValueError):
+ with pytest.raises(ValueError):
hllcpp.error_rate = -10.
# error rate can only be changed prior to first counting,
hllcpp.consume_string('AAACCACTTGTGCATGTCAGTGCAGTCAGT')
- with assert_raises(AttributeError):
+ with pytest.raises(AttributeError):
hllcpp.error_rate = 0.3
@@ -268,18 +265,18 @@ def test_hll_change_ksize():
hllcpp.ksize = 12
assert hllcpp.ksize == 12
- with assert_raises(ValueError):
+ with pytest.raises(ValueError):
hllcpp.ksize = -20
- with assert_raises(TypeError):
+ with pytest.raises(TypeError):
del hllcpp.ksize
- with assert_raises(TypeError):
+ with pytest.raises(TypeError):
hllcpp.ksize = 33.4
# error rate can only be changed prior to first counting,
hllcpp.consume_string('AAACCACTTGTGCATGTCAGTGCAGTCAGT')
- with assert_raises(AttributeError):
+ with pytest.raises(AttributeError):
hllcpp.ksize = 30
@@ -318,10 +315,10 @@ def test_hll_merge_3():
filename = utils.get_test_data('paired-mixed.fa')
hll = khmer.HLLCounter(0.36, 32)
- hll.consume_fasta(filename)
+ hll.consume_seqfile(filename)
hll2 = khmer.HLLCounter(0.36, 32)
- hll2.consume_fasta(filename)
+ hll2.consume_seqfile(filename)
assert len(hll) == 236
assert len(hll2) == 236
diff --git a/tests/test_labelhash.py b/tests/test_labelhash.py
index 644ab85..feb8e2d 100644
--- a/tests/test_labelhash.py
+++ b/tests/test_labelhash.py
@@ -1,6 +1,6 @@
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2013-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -32,17 +32,18 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
-# pylint: disable=missing-docstring,protected-access
+# pylint: disable=missing-docstring,protected-access,no-member,invalid-name
from __future__ import print_function
from __future__ import absolute_import
+
import os
import khmer
from khmer import GraphLabels, CountingGraphLabels
-from screed.fasta import fasta_iter
import screed
+import pytest
+
from . import khmer_tst_utils as utils
-from nose.plugins.attrib import attr
def teardown():
@@ -53,10 +54,10 @@ def teardown():
# * thread-safety
- at attr('huge')
+ at pytest.mark.huge
def test_toobig():
try:
- lh = GraphLabels(20, 1e13, 1)
+ GraphLabels(20, 1e13, 1)
assert 0, "This should fail."
except MemoryError as err:
print(str(err))
@@ -65,7 +66,7 @@ def test_toobig():
def test_error_create():
from khmer import _GraphLabels
try:
- lh = _GraphLabels(None)
+ _GraphLabels(None)
assert 0, "This should fail."
except ValueError as err:
print(str(err))
@@ -74,18 +75,18 @@ def test_error_create():
def test_n_labels():
lh = GraphLabels(20, 1e7, 4)
filename = utils.get_test_data('test-labels.fa')
- lh.consume_fasta_and_tag_with_labels(filename)
+ lh.consume_seqfile_and_tag_with_labels(filename)
print(lh.n_labels())
assert lh.n_labels() == 4
-def test_get_label_dict():
+def test_get_all_labels():
lb = GraphLabels(20, 1e7, 4)
filename = utils.get_test_data('test-labels.fa')
- lb.consume_fasta_and_tag_with_labels(filename)
+ lb.consume_seqfile_and_tag_with_labels(filename)
- labels = lb.get_label_dict()
+ labels = lb.get_all_labels()
expected = [0, 1, 2, 3]
for e_label in expected:
assert e_label in labels
@@ -93,10 +94,10 @@ def test_get_label_dict():
assert a_label in expected
-def test_get_label_dict_save_load():
+def test_get_labels_save_load():
lb_pre = GraphLabels(20, 1e7, 4)
filename = utils.get_test_data('test-labels.fa')
- lb_pre.consume_fasta_and_tag_with_labels(filename)
+ lb_pre.consume_seqfile_and_tag_with_labels(filename)
# save labels to a file
savepath = utils.get_temp_filename('saved.labels')
@@ -109,7 +110,7 @@ def test_get_label_dict_save_load():
lb = GraphLabels(20, 1e7, 4)
lb.load_labels_and_tags(savepath)
- labels = lb.get_label_dict()
+ labels = lb.get_all_labels()
expected = [0, 1, 2, 3]
for e_label in expected:
assert e_label in labels
@@ -117,10 +118,10 @@ def test_get_label_dict_save_load():
assert a_label in expected
-def test_get_label_dict_save_load_wrong_ksize():
+def test_get_labels_save_load_wrong_ksize():
lb_pre = GraphLabels(19, 1e7, 4)
filename = utils.get_test_data('test-labels.fa')
- lb_pre.consume_fasta_and_tag_with_labels(filename)
+ lb_pre.consume_seqfile_and_tag_with_labels(filename)
# save labels to a file
savepath = utils.get_temp_filename('saved.labels')
@@ -142,7 +143,7 @@ def test_get_label_dict_save_load_wrong_ksize():
def test_save_load_corrupted():
lb_pre = GraphLabels(20, 1e7, 4)
filename = utils.get_test_data('test-labels.fa')
- lb_pre.consume_fasta_and_tag_with_labels(filename)
+ lb_pre.consume_seqfile_and_tag_with_labels(filename)
# save labels to a file
savepath = utils.get_temp_filename('saved.labels')
@@ -168,10 +169,12 @@ def test_save_load_corrupted():
print('expected failure for', i, ': ', str(err))
+# note: if run as root, will fail b/c root can write to anything
+ at pytest.mark.noroot
def test_save_fail_readonly():
lb_pre = GraphLabels(20, 1e7, 4)
filename = utils.get_test_data('test-labels.fa')
- lb_pre.consume_fasta_and_tag_with_labels(filename)
+ lb_pre.consume_seqfile_and_tag_with_labels(filename)
# save labels to a file
savepath = utils.get_temp_filename('saved.labels')
@@ -190,7 +193,7 @@ def test_save_fail_readonly():
def test_get_tag_labels():
lb = GraphLabels(20, 1e7, 4)
filename = utils.get_test_data('single-read.fq')
- lb.consume_fasta_and_tag_with_labels(filename)
+ lb.consume_seqfile_and_tag_with_labels(filename)
tag = 173473779682
labels = lb.get_tag_labels(tag)
@@ -198,19 +201,19 @@ def test_get_tag_labels():
assert labels.pop() == 0
-def test_consume_fasta_and_tag_with_labels():
+def test_consume_seqfile_and_tag_with_labels():
lb = GraphLabels(20, 1e7, 4)
read_1 = 'ACGTAACCGGTTAAACCCGGGTTTAAAACCCCGGGGTTTT'
filename = utils.get_test_data('test-transcript.fa')
- total_reads, n_consumed = lb.consume_fasta_and_tag_with_labels(filename)
+ total_reads, _ = lb.consume_seqfile_and_tag_with_labels(filename)
print("doing get")
assert lb.graph.get(read_1[:20])
assert total_reads == 3
print("doing n_labels")
print(lb.n_labels())
- print("doing label dict")
- print(lb.get_label_dict())
+ print("doing all labels")
+ print(lb.get_all_labels())
print("get tagset")
for tag in lb.graph.get_tagset():
print("forward hash")
@@ -227,7 +230,7 @@ def test_consume_partitioned_fasta_and_tag_with_labels():
lb = GraphLabels(20, 1e7, 4)
filename = utils.get_test_data('real-partition-small.fa')
- total_reads, n_consumed = lb.consume_partitioned_fasta_and_tag_with_labels(
+ lb.consume_partitioned_fasta_and_tag_with_labels(
filename)
labels = set()
for record in screed.open(filename):
@@ -245,7 +248,7 @@ def test_consume_sequence_and_tag_with_labels():
label = 0
sequence = 'ATGCATCGATCGATCGATCGATCGATCGATCGATCGATCG'
- n_consumed = lb.consume_sequence_and_tag_with_labels(sequence, label)
+ lb.consume_sequence_and_tag_with_labels(sequence, label)
labels = set()
labels.update(lb.sweep_label_neighborhood(sequence))
@@ -256,35 +259,34 @@ def test_consume_sequence_and_tag_with_labels():
def test_sweep_tag_neighborhood():
lb = GraphLabels(20, 1e7, 4)
filename = utils.get_test_data('single-read.fq')
- lb.graph.consume_fasta_and_tag(filename)
+ lb.graph.consume_seqfile_and_tag(filename)
tags = lb.sweep_tag_neighborhood('CAGGCGCCCACCACCGTGCCCTCCAACCTGATGGT')
assert len(tags) == 1
- assert tags.pop() == 173473779682
+ assert list(tags) == [173473779682]
def test_sweep_label_neighborhood():
lb = GraphLabels(20, 1e7, 4)
filename = utils.get_test_data('single-read.fq')
- lb.consume_fasta_and_tag_with_labels(filename)
+ lb.consume_seqfile_and_tag_with_labels(filename)
labels = lb.sweep_label_neighborhood('CAGGCGCCCACCACCGTGCCCTCCAACCTGATGGT')
assert len(labels) == 1
assert labels.pop() == 0
-'''
-* The test data set as four reads: A, B, C, and D
-* Overlaps are A <-> B <-> C, with D on its own
-* Thus, traversing from A should find labels from A and B,
- traversing from B should find labels from A, B, and C,
- and traversing from C should find labels from B and C
-'''
+#
+# * The test data set as four reads: A, B, C, and D
+# * Overlaps are A <-> B <-> C, with D on its own
+# * Thus, traversing from A should find labels from A and B,
+# traversing from B should find labels from A, B, and C,
+# and traversing from C should find labels from B and C
def test_label_tag_correctness():
lb = GraphLabels(20, 1e7, 4)
filename = utils.get_test_data('test-labels.fa')
- lb.consume_fasta_and_tag_with_labels(filename)
+ lb.consume_seqfile_and_tag_with_labels(filename)
# read A
labels = lb.sweep_label_neighborhood(
@@ -330,7 +332,7 @@ def test_label_tag_correctness():
def test_counting_label_tag_correctness():
lb = CountingGraphLabels(20, 1e7, 4)
filename = utils.get_test_data('test-labels.fa')
- lb.consume_fasta_and_tag_with_labels(filename)
+ lb.consume_seqfile_and_tag_with_labels(filename)
# read A
labels = lb.sweep_label_neighborhood(
@@ -376,7 +378,7 @@ def test_counting_label_tag_correctness():
def test_label_tag_correctness_save_load():
lb_pre = GraphLabels(20, 1e7, 4)
filename = utils.get_test_data('test-labels.fa')
- lb_pre.consume_fasta_and_tag_with_labels(filename)
+ lb_pre.consume_seqfile_and_tag_with_labels(filename)
# save labels to a file
savepath = utils.get_temp_filename('saved.labels')
diff --git a/tests/test_lump.py b/tests/test_lump.py
index c4adfce..70b4786 100644
--- a/tests/test_lump.py
+++ b/tests/test_lump.py
@@ -32,13 +32,12 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
-# pylint: disable=missing-docstring
+# pylint: disable=missing-docstring,no-member,protected-access,invalid-name
from __future__ import absolute_import
+
import khmer
-import screed
from . import khmer_tst_utils as utils
-from nose.plugins.attrib import attr
# Below, 'fakelump.fa' is an artificial data set of 3x1 kb sequences in
# which the last 79 bases are common between the 3 sequences.
@@ -48,12 +47,12 @@ def test_fakelump_together():
fakelump_fa = utils.get_test_data('fakelump.fa')
ht = khmer.Nodegraph(32, 1e5, 4)
- ht.consume_fasta_and_tag(fakelump_fa)
+ ht.consume_seqfile_and_tag(fakelump_fa)
subset = ht.do_subset_partition(0, 0)
ht.merge_subset(subset)
- (n_partitions, n_singletons) = ht.count_partitions()
+ (n_partitions, _) = ht.count_partitions()
assert n_partitions == 1, n_partitions
# try loading stop tags from previously saved
@@ -64,7 +63,7 @@ def test_fakelump_stop():
fakelump_stoptags_txt = utils.get_test_data('fakelump.fa.stoptags.txt')
ht = khmer.Nodegraph(32, 1e5, 4)
- ht.consume_fasta_and_tag(fakelump_fa)
+ ht.consume_seqfile_and_tag(fakelump_fa)
for line in open(fakelump_stoptags_txt):
ht.add_stop_tag(line.strip())
@@ -72,7 +71,7 @@ def test_fakelump_stop():
subset = ht.do_subset_partition(0, 0, True)
ht.merge_subset(subset)
- (n_partitions, n_singletons) = ht.count_partitions()
+ (n_partitions, _) = ht.count_partitions()
assert n_partitions == 3, n_partitions
# check specific insertion of stop tag
@@ -82,14 +81,14 @@ def test_fakelump_stop2():
fakelump_fa = utils.get_test_data('fakelump.fa')
ht = khmer.Nodegraph(32, 1e5, 4)
- ht.consume_fasta_and_tag(fakelump_fa)
+ ht.consume_seqfile_and_tag(fakelump_fa)
ht.add_stop_tag('GGGGAGGGGTGCAGTTGTGACTTGCTCGAGAG')
subset = ht.do_subset_partition(0, 0, True)
ht.merge_subset(subset)
- (n_partitions, n_singletons) = ht.count_partitions()
+ (n_partitions, _) = ht.count_partitions()
assert n_partitions == 3, n_partitions
# try repartitioning
@@ -100,12 +99,12 @@ def test_fakelump_repartitioning():
fakelump_fa_foo = utils.get_temp_filename('fakelump.fa.stopfoo')
ht = khmer.Nodegraph(32, 1e5, 4)
- ht.consume_fasta_and_tag(fakelump_fa)
+ ht.consume_seqfile_and_tag(fakelump_fa)
subset = ht.do_subset_partition(0, 0)
ht.merge_subset(subset)
- (n_partitions, n_singletons) = ht.count_partitions()
+ (n_partitions, _) = ht.count_partitions()
assert n_partitions == 1, n_partitions
# now, break partitions on any k-mer that you see more than once
@@ -128,13 +127,13 @@ def test_fakelump_repartitioning():
# ok, now re-do everything with these stop tags, specifically.
ht = khmer.Nodegraph(32, 1e5, 4)
- ht.consume_fasta_and_tag(fakelump_fa)
+ ht.consume_seqfile_and_tag(fakelump_fa)
ht.load_stop_tags(fakelump_fa_foo)
subset = ht.do_subset_partition(0, 0, True)
ht.merge_subset(subset)
- (n_partitions, n_singletons) = ht.count_partitions()
+ (n_partitions, _) = ht.count_partitions()
assert n_partitions == 6, n_partitions
@@ -143,12 +142,12 @@ def test_fakelump_load_stop_tags_trunc():
fakelump_fa_foo = utils.get_temp_filename('fakelump.fa.stopfoo')
ht = khmer.Nodegraph(32, 1e5, 4)
- ht.consume_fasta_and_tag(fakelump_fa)
+ ht.consume_seqfile_and_tag(fakelump_fa)
subset = ht.do_subset_partition(0, 0)
ht.merge_subset(subset)
- (n_partitions, n_singletons) = ht.count_partitions()
+ (n_partitions, _) = ht.count_partitions()
assert n_partitions == 1, n_partitions
# now, break partitions on any k-mer that you see more than once
@@ -175,7 +174,7 @@ def test_fakelump_load_stop_tags_trunc():
# ok, now try loading these stop tags; should fail.
ht = khmer._Nodegraph(32, [5, 7, 11, 13])
- ht.consume_fasta_and_tag(fakelump_fa)
+ ht.consume_seqfile_and_tag(fakelump_fa)
try:
ht.load_stop_tags(fakelump_fa_foo)
diff --git a/tests/test_nibblestorage.py b/tests/test_nibblestorage.py
new file mode 100644
index 0000000..99c6971
--- /dev/null
+++ b/tests/test_nibblestorage.py
@@ -0,0 +1,129 @@
+# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# Copyright (C) 2016, The Regents of the University of California.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+#
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# * Redistributions in binary form must reproduce the above
+# copyright notice, this list of conditions and the following
+# disclaimer in the documentation and/or other materials provided
+# with the distribution.
+#
+# * Neither the name of the Michigan State University nor the names
+# of its contributors may be used to endorse or promote products
+# derived from this software without specific prior written
+# permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Contact: khmer-project at idyll.org
+
+from __future__ import print_function
+from __future__ import absolute_import
+
+import random
+
+from khmer import SmallCounttable
+
+from . import khmer_tst_utils as utils
+
+
+# This mostly tests the underlying NibbleStorage class
+
+def test_single_add():
+ sct = SmallCounttable(4, 1e6, 4)
+ sct.add("AAAA")
+ assert sct.get("AAAA") == 1
+
+
+def test_split_byte():
+ # check the byte is correctly split
+ sct = SmallCounttable(4, 4, 1)
+
+ a = "AAAA"
+ b = "AAAT"
+
+ assert sct.get_kmer_hashes(a) == [0]
+ assert sct.get_kmer_hashes(b) == [1]
+
+ sct.add(a)
+
+ assert sct.get(a) == 1
+ assert sct.get(b) == 0
+
+
+def test_overflow():
+ # check that we do not overflow into other part of the byte
+ sct = SmallCounttable(4, 1e6, 4)
+ a = "AAAA"
+ b = "AAAT"
+
+ # try to overflow our 4bit counter
+ for n in range(17):
+ sct.add(a)
+
+ assert sct.get(a) == 15
+ assert sct.get(b) == 0
+
+ # repeat with the other kmer that hashes to the other half of the byte
+ sct = SmallCounttable(4, 1e6, 4)
+ a = "AAAA"
+ b = "AAAT"
+
+ # try to overflow our 4bit counter
+ for n in range(17):
+ sct.add(b)
+
+ assert sct.get(b) == 15
+ assert sct.get(a) == 0
+
+
+def test_random_kmers():
+ # check for out-of-bounds errors and similar with random kmers
+ rng = random.Random(1)
+
+ sct = SmallCounttable(20, 1e2, 4)
+
+ kmers = ["".join(rng.choice("ACGT") for _ in range(20))
+ for n in range(400)]
+ for kmer in kmers:
+ sct.add(kmer)
+
+ for kmer in kmers:
+ sct.get(kmer)
+
+
+def test_read_write():
+ rng = random.Random(1)
+
+ sct = SmallCounttable(20, 1e2, 4)
+
+ kmers = ["".join(rng.choice("ACGT") for _ in range(20))
+ for n in range(400)]
+ for kmer in kmers:
+ sct.add(kmer)
+
+ fname = utils.get_temp_filename('zzz')
+
+ sct.save(fname)
+
+ # on purpose choose parameters that are different from sct
+ sct2 = SmallCounttable(3, 1e4, 2)
+ sct2.load(fname)
+ assert sct.ksize() == sct2.ksize()
+ for kmer in kmers:
+ assert sct.get(kmer) == sct2.get(kmer)
diff --git a/tests/test_nodegraph.py b/tests/test_nodegraph.py
index b87ffd4..9aff656 100644
--- a/tests/test_nodegraph.py
+++ b/tests/test_nodegraph.py
@@ -1,6 +1,6 @@
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2010-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -32,36 +32,44 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
-# pylint: disable=missing-docstring,protected-access,no-member,
+# pylint: disable=missing-docstring,protected-access,no-member,invalid-name
from __future__ import print_function
from __future__ import absolute_import
import khmer
from khmer import ReadParser
+from khmer import reverse_complement as revcomp
import screed
+import pytest
+
from . import khmer_tst_utils as utils
-from nose.plugins.attrib import attr
def teardown():
utils.cleanup()
- at attr('huge')
+ at pytest.mark.huge
def test_toobig():
try:
- pt = khmer.Nodegraph(32, 1e13, 1)
+ khmer.Nodegraph(32, 1e13, 1)
assert 0, "This should fail"
except MemoryError as err:
print(str(err))
+def test_bad_create():
+ try:
+ nodegraph = khmer._Nodegraph(5, [])
+ except ValueError as err:
+ assert 'tablesizes needs to be one or more numbers' in str(err)
+
+
def test__get_set_tag_density():
nodegraph = khmer._Nodegraph(32, [1])
-
orig = nodegraph._get_tag_density()
assert orig != 2
nodegraph._set_tag_density(2)
@@ -74,29 +82,52 @@ def test_update_from():
assert nodegraph.get('AAAAA') == 0
assert nodegraph.get('GCGCG') == 0
+ assert nodegraph.n_occupied() == 0
assert other_nodegraph.get('AAAAA') == 0
assert other_nodegraph.get('GCGCG') == 0
+ assert other_nodegraph.n_occupied() == 0
other_nodegraph.count('AAAAA')
assert nodegraph.get('AAAAA') == 0
assert nodegraph.get('GCGCG') == 0
+ assert nodegraph.n_occupied() == 0
assert other_nodegraph.get('AAAAA') == 1
assert other_nodegraph.get('GCGCG') == 0
+ assert other_nodegraph.n_occupied() == 1
nodegraph.count('GCGCG')
assert nodegraph.get('AAAAA') == 0
assert nodegraph.get('GCGCG') == 1
+ assert nodegraph.n_occupied() == 1
assert other_nodegraph.get('AAAAA') == 1
assert other_nodegraph.get('GCGCG') == 0
+ assert other_nodegraph.n_occupied() == 1
nodegraph.update(other_nodegraph)
assert nodegraph.get('AAAAA') == 1
assert nodegraph.get('GCGCG') == 1
+ assert nodegraph.n_occupied() == 2
assert other_nodegraph.get('AAAAA') == 1
assert other_nodegraph.get('GCGCG') == 0
+ assert other_nodegraph.n_occupied() == 1
+
+
+def test_update_from_2():
+
+ ng1 = khmer.Nodegraph(20, 1000, 4)
+ ng2 = khmer.Nodegraph(20, 1000, 4)
+
+ filename = utils.get_test_data('random-20-a.fa')
+ ng1.consume_seqfile(filename)
+ ng2.consume_seqfile(filename)
+
+ assert ng1.n_occupied() == ng2.n_occupied()
+ ng1.update(ng2)
+
+ assert ng1.n_occupied() == ng2.n_occupied()
def test_update_from_diff_ksize_2():
@@ -169,8 +200,8 @@ def test_bloom_python_1():
for _, record in enumerate(screed.open(filename)):
sequence = record.sequence
seq_len = len(sequence)
- for n in range(0, seq_len + 1 - ksize):
- kmer = sequence[n:n + ksize]
+ for num in range(0, seq_len + 1 - ksize):
+ kmer = sequence[num:num + ksize]
if not nodegraph.get(kmer):
n_unique += 1
nodegraph.count(kmer)
@@ -202,8 +233,6 @@ def test_bloom_c_1():
def test_n_occupied_2(): # simple one
ksize = 4
- htable_size = 10 # use 11
- num_nodegraphs = 1
nodegraph = khmer._Nodegraph(ksize, [11])
nodegraph.count('AAAA') # 00 00 00 00 = 0
@@ -219,6 +248,23 @@ def test_n_occupied_2(): # simple one
assert nodegraph.n_occupied() == 2, nodegraph.n_occupied()
+def test_n_occupied_2_add_is_count(): # 'add' synonym for 'count'
+ ksize = 4
+
+ nodegraph = khmer._Nodegraph(ksize, [11])
+ nodegraph.add('AAAA') # 00 00 00 00 = 0
+ assert nodegraph.n_occupied() == 1
+
+ nodegraph.add('ACTG') # 00 10 01 11 =
+ assert nodegraph.n_occupied() == 2
+
+ nodegraph.add('AACG') # 00 00 10 11 = 11 # collision 1
+
+ assert nodegraph.n_occupied() == 2
+ nodegraph.add('AGAC') # 00 11 00 10 # collision 2
+ assert nodegraph.n_occupied() == 2, nodegraph.n_occupied()
+
+
def test_bloom_c_2(): # simple one
ksize = 4
@@ -248,21 +294,6 @@ def test_bloom_c_2(): # simple one
assert other_nodegraph.n_unique_kmers() == 3
-def test_filter_if_present():
- nodegraph = khmer._Nodegraph(32, [3, 5])
-
- maskfile = utils.get_test_data('filter-test-A.fa')
- inputfile = utils.get_test_data('filter-test-B.fa')
- outfile = utils.get_temp_filename('filter')
-
- nodegraph.consume_fasta(maskfile)
- nodegraph.filter_if_present(inputfile, outfile)
-
- records = list(screed.open(outfile))
- assert len(records) == 1
- assert records[0]['name'] == '3'
-
-
def test_combine_pe():
inpfile = utils.get_test_data('combine_parts_1.fa')
nodegraph = khmer._Nodegraph(32, [1])
@@ -309,7 +340,7 @@ def test_count_within_radius_simple():
inpfile = utils.get_test_data('all-A.fa')
nodegraph = khmer._Nodegraph(4, [3, 5])
- print(nodegraph.consume_fasta(inpfile))
+ print(nodegraph.consume_seqfile(inpfile))
n = nodegraph.count_kmers_within_radius('AAAA', 1)
assert n == 1
@@ -321,12 +352,12 @@ def test_count_within_radius_big():
inpfile = utils.get_test_data('random-20-a.fa')
nodegraph = khmer.Nodegraph(20, 1e5, 4)
- nodegraph.consume_fasta(inpfile)
+ nodegraph.consume_seqfile(inpfile)
n = nodegraph.count_kmers_within_radius('CGCAGGCTGGATTCTAGAGG', int(1e6))
assert n == 3961, n
nodegraph = khmer.Nodegraph(21, 1e5, 4)
- nodegraph.consume_fasta(inpfile)
+ nodegraph.consume_seqfile(inpfile)
n = nodegraph.count_kmers_within_radius('CGCAGGCTGGATTCTAGAGGC', int(1e6))
assert n == 39
@@ -334,7 +365,7 @@ def test_count_within_radius_big():
def test_count_kmer_degree():
inpfile = utils.get_test_data('all-A.fa')
nodegraph = khmer._Nodegraph(4, [3, 5])
- nodegraph.consume_fasta(inpfile)
+ nodegraph.consume_seqfile(inpfile)
assert nodegraph.kmer_degree('AAAA') == 2
assert nodegraph.kmer_degree('AAAT') == 1
@@ -342,6 +373,53 @@ def test_count_kmer_degree():
assert nodegraph.kmer_degree('TAAA') == 1
+def test_kmer_neighbors():
+ inpfile = utils.get_test_data('all-A.fa')
+ nodegraph = khmer._Nodegraph(4, [3, 5])
+ nodegraph.consume_seqfile(inpfile)
+
+ h = khmer.forward_hash('AAAA', 4)
+ print(type('AAAA'))
+ assert nodegraph.neighbors(h) == [0, 0] # AAAA on both sides
+ assert nodegraph.neighbors('AAAA') == [0, 0] # AAAA on both sides
+
+ h = khmer.forward_hash('AAAT', 4)
+ assert nodegraph.neighbors(h) == [0] # AAAA on one side
+ assert nodegraph.neighbors('AAAT') == [0] # AAAA on one side
+
+ h = khmer.forward_hash('AATA', 4)
+ assert nodegraph.neighbors(h) == [] # no neighbors
+ assert nodegraph.neighbors('AATA') == [] # AAAA on one side
+
+ h = khmer.forward_hash('TAAA', 4)
+ assert nodegraph.neighbors(h) == [0] # AAAA on both sides
+ assert nodegraph.neighbors('TAAA') == [0] # AAAA on both sides
+
+
+def test_kmer_neighbors_wrong_ksize():
+ inpfile = utils.get_test_data('all-A.fa')
+ nodegraph = khmer._Nodegraph(4, [3, 5])
+ nodegraph.consume_seqfile(inpfile)
+
+ try:
+ nodegraph.neighbors('AAAAA')
+ assert 0, "neighbors() should fail with too long string"
+ except ValueError:
+ pass
+
+ try:
+ nodegraph.neighbors(b'AAAAA')
+ assert 0, "neighbors() should fail with too long string"
+ except ValueError:
+ pass
+
+ try:
+ nodegraph.neighbors({})
+ assert 0, "neighbors() should fail with non hash/str arg"
+ except ValueError:
+ pass
+
+
def test_save_load_tagset():
nodegraph = khmer._Nodegraph(32, [1])
@@ -400,7 +478,7 @@ def test_stop_traverse():
nodegraph.add_stop_tag('TTGCATACGTTGAGCCAGCG')
# DO NOT join reads across stoptags
- nodegraph.consume_fasta_and_tag(filename)
+ nodegraph.consume_seqfile_and_tag(filename)
subset = nodegraph.do_subset_partition(0, 0, True)
nodegraph.merge_subset(subset)
@@ -408,73 +486,6 @@ def test_stop_traverse():
assert n == 2, n
-def test_tag_across_stoptraverse():
- filename = utils.get_test_data('random-20-a.fa')
-
- ksize = 20 # size of kmer
- htable_size = 1e4 # size of hashtable
- num_nodegraphs = 3 # number of hashtables
-
- nodegraph = khmer.Nodegraph(ksize, htable_size, num_nodegraphs)
-
- # without tagging/joining across consume, this breaks into two partition;
- # with, it is one partition.
- nodegraph.add_stop_tag('CCGAATATATAACAGCGACG')
-
- # DO join reads across
- nodegraph.consume_fasta_and_tag_with_stoptags(filename)
- subset = nodegraph.do_subset_partition(0, 0)
- n, _ = nodegraph.count_partitions()
- assert n == 99 # reads only connected by traversal...
-
- n, _ = nodegraph.subset_count_partitions(subset)
- assert n == 2 # but need main to cross stoptags.
-
- nodegraph.merge_subset(subset)
-
- n, _ = nodegraph.count_partitions() # ta-da!
- assert n == 1, n
-
-
-def test_notag_across_stoptraverse():
- filename = utils.get_test_data('random-20-a.fa')
-
- ksize = 20 # size of kmer
- htable_size = 1e4 # size of hashtable
- num_nodegraphs = 3 # number of hashtables
-
- nodegraph = khmer.Nodegraph(ksize, htable_size, num_nodegraphs)
-
- # connecting k-mer at the beginning/end of a read: breaks up into two.
- nodegraph.add_stop_tag('TTGCATACGTTGAGCCAGCG')
-
- nodegraph.consume_fasta_and_tag_with_stoptags(filename)
-
- subset = nodegraph.do_subset_partition(0, 0)
- nodegraph.merge_subset(subset)
-
- n, _ = nodegraph.count_partitions()
- assert n == 2, n
-
-
-def test_find_stoptags():
- nodegraph = khmer._Nodegraph(5, [1])
- nodegraph.add_stop_tag("AAAAA")
-
- assert nodegraph.identify_stoptags_by_position("AAAAA") == [0]
- assert nodegraph.identify_stoptags_by_position("AAAAAA") == [0, 1]
- assert nodegraph.identify_stoptags_by_position("TTTTT") == [0]
- assert nodegraph.identify_stoptags_by_position("TTTTTT") == [0, 1]
-
-
-def test_find_stoptagsecond_seq():
- nodegraph = khmer._Nodegraph(4, [1])
- nodegraph.add_stop_tag("ATGC")
-
- x = nodegraph.identify_stoptags_by_position("ATGCATGCGCAT")
- assert x == [0, 2, 4, 8], x
-
-
def test_get_ksize():
kh = khmer._Nodegraph(22, [1])
assert kh.ksize() == 22
@@ -541,70 +552,16 @@ def test_extract_unique_paths_4():
assert x == ['TGGAGAGACACAGATAGACAGG', 'TAGACAGGAGTGGCGAT']
-def test_find_unpart():
- filename = utils.get_test_data('random-20-a.odd.fa')
- filename2 = utils.get_test_data('random-20-a.even.fa')
-
- ksize = 20 # size of kmer
- htable_size = 1e4 # size of hashtable
- num_nodegraphs = 3 # number of hashtables
-
- nodegraph = khmer.Nodegraph(ksize, htable_size, num_nodegraphs)
- nodegraph.consume_fasta_and_tag(filename)
-
- subset = nodegraph.do_subset_partition(0, 0)
- nodegraph.merge_subset(subset)
-
- n, _ = nodegraph.count_partitions()
- assert n == 49
-
- nodegraph.find_unpart(filename2, True, False)
- n, _ = nodegraph.count_partitions()
- assert n == 1, n # all sequences connect
-
-
-def test_find_unpart_notraverse():
- filename = utils.get_test_data('random-20-a.odd.fa')
- filename2 = utils.get_test_data('random-20-a.even.fa')
-
- ksize = 20 # size of kmer
- htable_size = 1e4 # size of hashtable
- num_nodegraphs = 3 # number of hashtables
-
- nodegraph = khmer.Nodegraph(ksize, htable_size, num_nodegraphs)
- nodegraph.consume_fasta_and_tag(filename)
-
- subset = nodegraph.do_subset_partition(0, 0)
- nodegraph.merge_subset(subset)
-
- n, _ = nodegraph.count_partitions()
- assert n == 49
-
- nodegraph.find_unpart(filename2, False, False) # <-- don't traverse
- n, _ = nodegraph.count_partitions()
- assert n == 99, n # all sequences disconnected
-
-
-def test_find_unpart_fail():
- filename = utils.get_test_data('random-20-a.odd.fa')
- filename2 = utils.get_test_data('random-20-a.odd.fa') # <- switch to odd
-
- ksize = 20 # size of kmer
- htable_size = 1e4 # size of hashtable
- num_nodegraphs = 3 # number of hashtables
-
- nodegraph = khmer.Nodegraph(ksize, htable_size, num_nodegraphs)
- nodegraph.consume_fasta_and_tag(filename)
-
- subset = nodegraph.do_subset_partition(0, 0)
- nodegraph.merge_subset(subset)
-
- n, _ = nodegraph.count_partitions()
- assert n == 49
+def test_get_raw_tables():
+ kh = khmer.Nodegraph(10, 1e6, 4)
+ kh.consume('ATGGAGAGAC')
+ kh.consume('AGTGGCGATG')
+ kh.consume('ATAGACAGGA')
+ tables = kh.get_raw_tables()
- nodegraph.find_unpart(filename2, True, False)
- n, _ = nodegraph.count_partitions()
- assert n == 49, n # only 49 sequences worth of tags
+ for size, table in zip(kh.hashsizes(), tables):
+ assert isinstance(table, memoryview)
+ assert size == len(table)
def test_simple_median():
@@ -654,9 +611,8 @@ def test_badget():
def test_load_notexist_should_fail():
savepath = utils.get_temp_filename('tempnodegraphsave0.htable')
- hi = khmer._Countgraph(12, [1])
try:
- hi.load(savepath)
+ hi = khmer.load_countgraph(savepath)
assert 0, "load should fail"
except OSError:
pass
@@ -668,7 +624,7 @@ def test_load_truncated_should_fail():
hi = khmer.Countgraph(12, 1000, 2)
- hi.consume_fasta(inpath)
+ hi.consume_seqfile(inpath)
hi.save(savepath)
fp = open(savepath, 'rb')
@@ -679,9 +635,8 @@ def test_load_truncated_should_fail():
fp.write(data[:1000])
fp.close()
- hi = khmer._Countgraph(12, [1])
try:
- hi.load(savepath)
+ hi = khmer.load_countgraph(savepath)
assert 0, "load should fail"
except OSError as e:
print(str(e))
@@ -740,8 +695,8 @@ def _build_testfiles():
# nodegraph file
inpath = utils.get_test_data('random-20-a.fa')
- hi = khmer.Nodegraph(12, 2)
- hi.consume_fasta(inpath)
+ hi = khmer._Nodegraph(12, 2)
+ hi.consume_seqfile(inpath)
hi.save('/tmp/goodversion-k12.htable')
# tagset file
@@ -757,7 +712,7 @@ def _build_testfiles():
fakelump_fa = utils.get_test_data('fakelump.fa')
nodegraph = khmer.Nodegraph(32, 4, 4)
- nodegraph.consume_fasta_and_tag(fakelump_fa)
+ nodegraph.consume_seqfile_and_tag(fakelump_fa)
subset = nodegraph.do_subset_partition(0, 0)
nodegraph.merge_subset(subset)
@@ -776,12 +731,11 @@ def _build_testfiles():
def test_hashbits_file_version_check():
- nodegraph = khmer._Nodegraph(12, [1])
inpath = utils.get_test_data('badversion-k12.htable')
try:
- nodegraph.load(inpath)
+ nodegraph = khmer.load_nodegraph(inpath)
assert 0, "this should fail"
except OSError as e:
print(str(e))
@@ -792,10 +746,8 @@ def test_nodegraph_file_type_check():
savepath = utils.get_temp_filename('tempcountingsave0.ct')
kh.save(savepath)
- nodegraph = khmer._Nodegraph(12, [1])
-
try:
- nodegraph.load(savepath)
+ nodegraph = khmer.load_nodegraph(savepath)
assert 0, "this should fail"
except OSError as e:
print(str(e))
@@ -890,7 +842,7 @@ def test_tagset_filetype_check():
def test_bad_primes_list():
try:
- coutingtable = khmer._Nodegraph(31, ["a", "b", "c"], 1)
+ khmer._Nodegraph(31, ["a", "b", "c"], 1)
assert 0, "Bad primes list should fail"
except TypeError as e:
print(str(e))
@@ -899,13 +851,13 @@ def test_bad_primes_list():
def test_consume_absentfasta_with_reads_parser():
nodegraph = khmer._Nodegraph(31, [1])
try:
- nodegraph.consume_fasta_with_reads_parser()
+ nodegraph.consume_seqfile_with_reads_parser()
assert 0, "this should fail"
except TypeError as err:
print(str(err))
try:
readparser = ReadParser(utils.get_test_data('empty-file'))
- nodegraph.consume_fasta_with_reads_parser(readparser)
+ nodegraph.consume_seqfile_with_reads_parser(readparser)
assert 0, "this should fail"
except OSError as err:
print(str(err))
@@ -915,18 +867,18 @@ def test_consume_absentfasta_with_reads_parser():
def test_bad_primes():
try:
- countgraph = khmer._Nodegraph.__new__(
+ khmer._Nodegraph.__new__(
khmer._Nodegraph, 6, ["a", "b", "c"])
assert 0, "this should fail"
except TypeError as e:
print(str(e))
-def test_consume_fasta_and_tag_with_badreads_parser():
+def test_consume_seqfile_and_tag_with_badreads_parser():
nodegraph = khmer.Nodegraph(6, 1e6, 2)
try:
readsparser = khmer.ReadParser(utils.get_test_data("test-empty.fa"))
- nodegraph.consume_fasta_and_tag_with_reads_parser(readsparser)
+ nodegraph.consume_seqfile_and_tag_with_reads_parser(readsparser)
assert 0, "this should fail"
except OSError as e:
print(str(e))
@@ -965,7 +917,7 @@ def test_n_occupied_vs_countgraph():
assert nodegraph.n_unique_kmers() == 0, nodegraph.n_unique_kmers()
assert countgraph.n_unique_kmers() == 0, countgraph.n_unique_kmers()
- for n, record in enumerate(screed.open(filename)):
+ for _, record in enumerate(screed.open(filename)):
nodegraph.consume(record.sequence)
countgraph.consume(record.sequence)
@@ -991,7 +943,7 @@ def test_n_occupied_vs_countgraph_another_size():
assert nodegraph.n_unique_kmers() == 0, nodegraph.n_unique_kmers()
assert countgraph.n_unique_kmers() == 0, countgraph.n_unique_kmers()
- for n, record in enumerate(screed.open(filename)):
+ for _, record in enumerate(screed.open(filename)):
nodegraph.consume(record.sequence)
countgraph.consume(record.sequence)
@@ -1003,3 +955,151 @@ def test_n_occupied_vs_countgraph_another_size():
assert nodegraph.n_unique_kmers() == 3916, nodegraph.n_unique_kmers()
assert countgraph.n_unique_kmers() == 3916, countgraph.n_unique_kmers()
+
+
+def test_traverse_linear_path():
+ contigfile = utils.get_test_data('simple-genome.fa')
+ contig = list(screed.open(contigfile))[0].sequence
+
+ K = 21
+
+ nodegraph = khmer.Nodegraph(K, 1e5, 4)
+ stopgraph = khmer.Nodegraph(K, 1e5, 4)
+
+ nodegraph.consume(contig)
+
+ degree_nodes = khmer.HashSet(K)
+ size, conns, visited = nodegraph.traverse_linear_path(contig[:K],
+ degree_nodes,
+ stopgraph)
+ assert size == 980
+ assert len(conns) == 0
+ assert len(visited) == 980
+
+
+def test_find_high_degree_nodes():
+ contigfile = utils.get_test_data('simple-genome.fa')
+ contig = list(screed.open(contigfile))[0].sequence
+
+ K = 21
+
+ nodegraph = khmer.Nodegraph(K, 1e5, 4)
+ stopgraph = khmer.Nodegraph(K, 1e5, 4)
+
+ nodegraph.consume(contig)
+
+ degree_nodes = nodegraph.find_high_degree_nodes(contig)
+ assert len(degree_nodes) == 0
+
+
+def test_find_high_degree_nodes_2():
+ contigfile = utils.get_test_data('simple-genome.fa')
+ contig = list(screed.open(contigfile))[0].sequence
+
+ K = 21
+
+ nodegraph = khmer.Nodegraph(K, 1e5, 4)
+
+ nodegraph.consume(contig)
+ nodegraph.count(contig[2:22] + 'G') # will add another neighbor to 1:22
+ print(nodegraph.neighbors(contig[1:22]))
+
+ degree_nodes = nodegraph.find_high_degree_nodes(contig)
+ assert len(degree_nodes) == 1
+ assert nodegraph.hash(contig[1:22]) in degree_nodes
+
+
+def test_traverse_linear_path_2():
+ contigfile = utils.get_test_data('simple-genome.fa')
+ contig = list(screed.open(contigfile))[0].sequence
+ print('contig len', len(contig))
+
+ K = 21
+
+ nodegraph = khmer.Nodegraph(K, 1e5, 4)
+ stopgraph = khmer.Nodegraph(K, 1e5, 4)
+
+ nodegraph.consume(contig)
+ nodegraph.count(contig[101:121] + 'G') # will add another neighbor
+ print(nodegraph.neighbors(contig[101:122]))
+
+ degree_nodes = nodegraph.find_high_degree_nodes(contig)
+
+ assert len(degree_nodes) == 1
+ assert nodegraph.hash(contig[100:121]) in degree_nodes
+
+ # traverse from start, should end at node 100:121
+ size, conns, visited = nodegraph.traverse_linear_path(contig[0:21],
+ degree_nodes,
+ stopgraph)
+
+ print(size, list(conns), list(visited))
+ assert size == 100
+ assert len(visited) == 100
+ assert nodegraph.hash(contig[100:121]) in conns
+ assert len(conns) == 1
+
+ # traverse from immediately after 100:121, should end at the end
+ size, conns, visited = nodegraph.traverse_linear_path(contig[101:122],
+ degree_nodes,
+ stopgraph)
+
+ print(size, list(conns), list(visited))
+ assert size == 879
+ assert len(visited) == 879
+ assert nodegraph.hash(contig[100:121]) in conns
+ assert len(conns) == 1
+
+ # traverse from end, should end at 100:121
+ size, conns, visited = nodegraph.traverse_linear_path(contig[-21:],
+ degree_nodes,
+ stopgraph)
+
+ print(size, list(conns), len(visited))
+ assert size == 879
+ assert len(visited) == 879
+ assert nodegraph.hash(contig[100:121]) in conns
+ assert len(conns) == 1
+
+
+def test_traverse_linear_path_3_stopgraph():
+ contigfile = utils.get_test_data('simple-genome.fa')
+ contig = list(screed.open(contigfile))[0].sequence
+ print('contig len', len(contig))
+
+ K = 21
+
+ nodegraph = khmer.Nodegraph(K, 1e5, 4)
+ stopgraph = khmer.Nodegraph(K, 1e5, 4)
+
+ nodegraph.consume(contig)
+ nodegraph.count(contig[101:121] + 'G') # will add another neighbor
+ print(nodegraph.neighbors(contig[101:122]))
+
+ degree_nodes = nodegraph.find_high_degree_nodes(contig)
+
+ assert len(degree_nodes) == 1
+ assert nodegraph.hash(contig[100:121]) in degree_nodes
+
+ stopgraph.count(contig[101:122]) # stop traversal - only adj to start
+
+ size, conns, visited = nodegraph.traverse_linear_path(contig[101:122],
+ degree_nodes,
+ stopgraph)
+
+ print(size, list(conns), len(visited))
+ assert size == 0
+ assert len(visited) == 0
+ assert len(conns) == 0
+
+
+def test_assemble_linear_path_bad_seed():
+ # assemble single node.
+ contigfile = utils.get_test_data('simple-genome.fa')
+ contig = list(screed.open(contigfile))[0].sequence
+
+ nodegraph = khmer.Nodegraph(21, 1e5, 4)
+ nodegraph.consume(contig)
+
+ path = nodegraph.assemble_linear_path('GATTACA' * 3)
+ assert path == ''
diff --git a/tests/test_normalize_by_median.py b/tests/test_normalize_by_median.py
index 6e78fb2..3b4b25a 100644
--- a/tests/test_normalize_by_median.py
+++ b/tests/test_normalize_by_median.py
@@ -1,5 +1,5 @@
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -31,20 +31,18 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
-# pylint: disable=missing-docstring,invalid-name,unused-variable
-from __future__ import print_function
-from __future__ import absolute_import
-from __future__ import unicode_literals
+# pylint: disable=missing-docstring,invalid-name
+from __future__ import print_function, absolute_import, unicode_literals
+
import os
-import shutil
import threading
import io
-
+import shutil
import screed
import khmer
+import pytest
from . import khmer_tst_utils as utils
-from nose.plugins.attrib import attr
from .test_scripts import _make_counting
@@ -66,22 +64,21 @@ def test_normalize_by_median_loadgraph_with_args():
script = "load-into-counting.py"
args = [tablefile, infile]
- (status, out, err) = utils.runscript(script, args)
+ (_, _, err) = utils.runscript(script, args)
script = "normalize-by-median.py"
args = ["--ksize", "7", "--loadgraph", tablefile, infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
+ (_, _, err) = utils.runscript(script, args, in_dir)
assert 'WARNING: You are loading a saved k-mer countgraph from' in err, err
def test_normalize_by_median_empty_file():
- infile = utils.get_temp_filename('empty')
- shutil.copyfile(utils.get_test_data('empty-file'), infile)
+ infile = utils.copy_test_data('empty-file')
script = 'normalize-by-median.py'
in_dir = os.path.dirname(infile)
args = [infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
+ (_, _, err) = utils.runscript(script, args, in_dir)
assert 'WARNING:' in err, err
assert 'is empty' in err, err
@@ -91,14 +88,12 @@ def test_normalize_by_median_empty_file():
def test_normalize_by_median():
CUTOFF = '1'
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-2.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
-
script = 'normalize-by-median.py'
args = ['-C', CUTOFF, '-k', '17', infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
+ (_, _, err) = utils.runscript(script, args, in_dir)
assert 'Total number of unique k-mers: 98' in err, err
@@ -114,14 +109,12 @@ def test_normalize_by_median():
def test_normalize_by_median_quiet():
CUTOFF = '1'
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-2.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
-
script = 'normalize-by-median.py'
args = ['-C', CUTOFF, '-k', '17', '--quiet', '-M', '2e6', infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
+ (_, out, err) = utils.runscript(script, args, in_dir)
assert len(out) == 0, out
assert len(err) < 460, len(err)
@@ -138,72 +131,62 @@ def test_normalize_by_median_quiet():
def test_normalize_by_median_unpaired_final_read():
CUTOFF = '1'
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('single-read.fq')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('single-read.fq'), infile)
-
script = 'normalize-by-median.py'
args = ['-C', CUTOFF, '-k', '17', '-p', infile]
- (status, out, err) = utils.runscript(script, args, in_dir, fail_ok=True)
+ (status, _, err) = utils.runscript(script, args, in_dir, fail_ok=True)
assert status != 0
assert "ERROR: Unpaired reads when require_paired" in err, err
def test_normalize_by_median_sanity_check_0():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('single-read.fq')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('single-read.fq'), infile)
-
script = 'normalize-by-median.py'
args = ['-U', '1024', '--max-mem', '60', infile]
- (status, out, err) = utils.runscript(script, args, in_dir, fail_ok=True)
+ (status, _, err) = utils.runscript(script, args, in_dir, fail_ok=True)
assert status != 0, status
assert "recommended false positive ceiling of 0.1!" in err, err
def test_normalize_by_median_sanity_check_1():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-filter-abund-Ns.fq')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-filter-abund-Ns.fq'), infile)
-
script = 'normalize-by-median.py'
args = ['-U', '83', '--max-tablesize', '17', infile]
- (status, out, err) = utils.runscript(script, args, in_dir, fail_ok=True)
+ (status, _, err) = utils.runscript(script, args, in_dir, fail_ok=True)
assert status != 0
assert "Warning: The given tablesize is too small!" in err, err
def test_normalize_by_median_sanity_check_2():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-filter-abund-Ns.fq')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-filter-abund-Ns.fq'), infile)
-
script = 'normalize-by-median.py'
args = ['-U', '83', infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
+ (_, _, err) = utils.runscript(script, args, in_dir)
assert "*** INFO: set memory ceiling automatically." in err, err
assert "*** Ceiling is: 1e+06 bytes" in err, err
def test_normalize_by_median_sanity_check_3():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-filter-abund-Ns.fq')
in_dir = os.path.dirname(infile)
tablefile = utils.get_temp_filename('table', in_dir)
- shutil.copyfile(utils.get_test_data('test-filter-abund-Ns.fq'), infile)
-
script = 'normalize-by-median.py'
args = ['-s', tablefile, '-U', '83', '--fp-rate', '0.7', infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
+ (_, _, err) = utils.runscript(script, args, in_dir)
assert "Overriding default fp 0.1 with new fp: 0.7" in err, err
args = ['--loadgraph', tablefile, '-U', '83', infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
+ (_, _, err) = utils.runscript(script, args, in_dir)
assert "WARNING: You have asked that the graph size be auto" in err, err
assert "NOT be set automatically" in err, err
@@ -218,7 +201,7 @@ def test_normalize_by_median_unforced_badfile():
in_dir = os.path.dirname(infile)
script = 'normalize-by-median.py'
args = ['-C', CUTOFF, '-k', '17', infile]
- (status, out, err) = utils.runscript(script, args, in_dir, fail_ok=True)
+ (status, _, err) = utils.runscript(script, args, in_dir, fail_ok=True)
assert status != 0
assert "ERROR: [Errno 2] No such file or directory:" in err, err
@@ -227,16 +210,14 @@ def test_normalize_by_median_unforced_badfile():
def test_normalize_by_median_contradictory_args():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-large.fa')
in_dir = os.path.dirname(infile)
outfile = utils.get_temp_filename('report.out')
- shutil.copyfile(utils.get_test_data('test-large.fa'), infile)
-
script = 'normalize-by-median.py'
args = ['-C', '1', '-k', '17', '--force_single', '-p', '-R',
outfile, infile]
- (status, out, err) = utils.runscript(script, args, in_dir, fail_ok=True)
+ (status, _, err) = utils.runscript(script, args, in_dir, fail_ok=True)
assert status != 0
assert "cannot both be set" in err, err
@@ -244,59 +225,50 @@ def test_normalize_by_median_contradictory_args():
def test_normalize_by_median_stdout_3():
CUTOFF = '1'
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-2.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
-
script = 'normalize-by-median.py'
args = ['-C', CUTOFF, '-k', '17', infile, '--out', '-']
- (status, out, err) = utils.runscript(script, args, in_dir)
+ (_, _, err) = utils.runscript(script, args, in_dir)
assert 'Total number of unique k-mers: 98' in err, err
assert 'in block device' in err, err
assert "I/O Errors" not in err
- at attr('known_failing')
+ at pytest.mark.known_failing
def test_normalize_by_median_known_good():
CUTOFF = '2'
- infile = utils.get_temp_filename('test.fa.gz')
+ infile = utils.copy_test_data('100k-filtered.fa.gz')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('100k-filtered.fa.gz'), infile)
script = 'normalize-by-median.py'
args = ['-C', CUTOFF, '-k', '20', '-x', '4e6', infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
+ utils.runscript(script, args, in_dir)
outfile = infile + '.keep'
assert os.path.exists(outfile), outfile
iter_known = screed.open(utils.get_test_data('100k-filtered.fa.keep.gz'))
iter_out = screed.open(outfile)
- try:
- for rknown, rout in zip(iter_known, iter_out):
- assert rknown.name == rout.name
- except Exception as e:
- print(e)
- assert False
+ for rknown, rout in zip(iter_known, iter_out):
+ assert rknown.name == rout.name
def test_normalize_by_median_report_fp():
# this tests basic reporting of diginorm stats => report.out, including
# a test of aggregate stats for two input files.
- infile = utils.get_temp_filename('test.fa')
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
- infile2 = utils.get_temp_filename('test2.fa')
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile2)
+ infile = utils.copy_test_data("test-abund-read-2.fa")
+ infile2 = utils.copy_test_data("test-abund-read-2.fa", "copyDataTwo")
in_dir = os.path.dirname(infile)
outfile = utils.get_temp_filename('report.out')
script = 'normalize-by-median.py'
args = ['-C', '1', '-k', '17', '-R', outfile, infile, infile2]
- (status, out, err) = utils.runscript(script, args, in_dir)
+ utils.runscript(script, args, in_dir)
assert os.path.exists(outfile)
report = open(outfile, 'r')
@@ -312,8 +284,7 @@ def test_normalize_by_median_report_fp_hifreq():
# this tests high-frequency reporting of diginorm stats for a single
# file => report.out.
- infile = utils.get_temp_filename('test.fa')
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
+ infile = utils.copy_test_data('test-abund-read-2.fa')
in_dir = os.path.dirname(infile)
outfile = utils.get_temp_filename('report.out')
@@ -321,7 +292,7 @@ def test_normalize_by_median_report_fp_hifreq():
script = 'normalize-by-median.py'
args = ['-C', '1', '-k', '17', '-R', outfile, infile,
'--report-frequency', '100']
- (status, out, err) = utils.runscript(script, args, in_dir)
+ utils.runscript(script, args, in_dir)
assert os.path.exists(outfile)
report = open(outfile, 'r')
@@ -333,20 +304,18 @@ def test_normalize_by_median_report_fp_hifreq():
assert line == '200,1,0.005', line
- at attr('huge')
+ at pytest.mark.huge
def test_normalize_by_median_report_fp_huge():
# this tests reporting of diginorm stats => report.out for a large
# file, with the default reporting interval of once every 100k.
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-large.fa')
in_dir = os.path.dirname(infile)
outfile = utils.get_temp_filename('report.out')
- shutil.copyfile(utils.get_test_data('test-large.fa'), infile)
-
script = 'normalize-by-median.py'
args = ['-C', '1', '-k', '17', '-R', outfile, infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
+ (_, _, err) = utils.runscript(script, args, in_dir)
assert "fp rate estimated to be 0.623" in err, err
report = open(outfile, 'r')
@@ -358,17 +327,14 @@ def test_normalize_by_median_report_fp_huge():
def test_normalize_by_median_unpaired_and_paired():
CUTOFF = '1'
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-paired.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-paired.fa'), infile)
-
- unpairedfile = utils.get_temp_filename('test1.fa', tempdir=in_dir)
- shutil.copyfile(utils.get_test_data('random-20-a.fa'), unpairedfile)
+ unpairedfile = utils.copy_test_data('random-20-a.fa')
script = 'normalize-by-median.py'
args = ['-C', CUTOFF, '-k', '17', '-u', unpairedfile, '-p', infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
+ (_, _, err) = utils.runscript(script, args, in_dir)
assert 'Total number of unique k-mers: 4061' in err, err
@@ -378,35 +344,32 @@ def test_normalize_by_median_unpaired_and_paired():
def test_normalize_by_median_count_kmers_PE():
CUTOFF = '1'
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('paired_one.base.dif.fa')
in_dir = os.path.dirname(infile)
# The test file has one pair of identical read except for the last base
# The 2nd read should be discarded in the unpaired mode
# but kept in the paired end mode adding only one more unique kmer
- shutil.copyfile(utils.get_test_data('paired_one.base.dif.fa'), infile)
script = 'normalize-by-median.py'
args = ['-C', CUTOFF, '-k', '17', '--force_single', infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
+ (_, _, err) = utils.runscript(script, args, in_dir)
assert 'Total number of unique k-mers: 98' in err, err
assert 'kept 1 of 2 or 50.0%' in err, err
args = ['-C', CUTOFF, '-k', '17', '-p', infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
+ (_, _, err) = utils.runscript(script, args, in_dir)
assert 'Total number of unique k-mers: 99' in err, err
assert 'kept 2 of 2 or 100.0%' in err, err
def test_normalize_by_median_double_file_name():
- infile = utils.get_temp_filename('test-abund-read-2.fa')
+ infile = utils.copy_test_data('test-abund-read-2.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
-
script = 'normalize-by-median.py'
args = [utils.get_test_data('test-abund-read-2.fa'), infile]
- (status, out, err) = utils.runscript(script, args, in_dir, fail_ok=True)
+ (status, _, err) = utils.runscript(script, args, in_dir, fail_ok=True)
assert status != 0
assert "Duplicate filename--Cannot handle this!" in err, err
@@ -418,23 +381,21 @@ def test_normalize_by_median_stdin_no_out():
script = 'normalize-by-median.py'
args = ["-"]
- (status, out, err) = utils.runscript(script, args, in_dir, fail_ok=True)
+ (status, _, err) = utils.runscript(script, args, in_dir, fail_ok=True)
assert status != 0
assert "Accepting input from stdin; output filename" in err, err
def test_normalize_by_median_overwrite():
- outfile = utils.get_temp_filename('test.fa.keep')
- shutil.copyfile(utils.get_test_data('test-abund-read.fa'), outfile)
+ outfile = utils.copy_test_data('test-abund-read.fa')
in_dir = os.path.dirname(outfile)
CUTOFF = '1'
- infile = utils.get_temp_filename('test.fa', in_dir)
- shutil.copyfile(utils.get_test_data('test-abund-read-3.fa'), infile)
+ infile = utils.copy_test_data('test-abund-read-3.fa')
script = 'normalize-by-median.py'
args = ['-C', CUTOFF, '-k', '17', '-o', outfile, infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
+ utils.runscript(script, args, in_dir)
assert os.path.exists(outfile), outfile
seqs = [r.sequence for r in screed.open(outfile)]
assert len(seqs) == 1, seqs
@@ -444,7 +405,7 @@ def test_normalize_by_median_overwrite():
def test_normalize_by_median_version():
script = 'normalize-by-median.py'
args = ['--version']
- status, out, err = utils.runscript(script, args)
+ _, _, err = utils.runscript(script, args)
errlines = err.splitlines()
for err in errlines:
@@ -462,11 +423,9 @@ def test_normalize_by_median_version():
def test_normalize_by_median_2():
CUTOFF = '2'
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-2.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
-
script = 'normalize-by-median.py'
args = ['-C', CUTOFF, '-k', '17', infile]
utils.runscript(script, args, in_dir)
@@ -483,11 +442,9 @@ def test_normalize_by_median_2():
def test_normalize_by_median_paired():
CUTOFF = '1'
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-paired.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-paired.fa'), infile)
-
script = 'normalize-by-median.py'
args = ['-C', CUTOFF, '-p', '-k', '17', infile]
utils.runscript(script, args, in_dir)
@@ -504,11 +461,9 @@ def test_normalize_by_median_paired():
def test_normalize_by_median_paired_fq():
CUTOFF = '20'
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-paired.fq')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-paired.fq'), infile)
-
script = 'normalize-by-median.py'
args = ['-C', CUTOFF, '-p', '-k', '17', infile]
_, out, err = utils.runscript(script, args, in_dir)
@@ -532,70 +487,54 @@ def test_normalize_by_median_paired_fq():
def test_normalize_by_median_impaired():
CUTOFF = '1'
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-impaired.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-impaired.fa'), infile)
-
script = 'normalize-by-median.py'
args = ['-C', CUTOFF, '-p', '-k', '17', infile]
- status, out, err = utils.runscript(script, args, in_dir, fail_ok=True)
- status != 0
+ status, _, err = utils.runscript(script, args, in_dir, fail_ok=True)
+ assert status != 0
assert 'ERROR: Unpaired reads ' in err, err
def test_normalize_by_median_force():
CUTOFF = '1'
- corrupt_infile = utils.get_temp_filename('test-corrupt.fq')
- good_infile = utils.get_temp_filename('test-good.fq',
- tempdir=os.path.dirname(
- corrupt_infile))
+ corrupt_infile = utils.copy_test_data('test-error-reads.fq')
+ good_infile = utils.copy_test_data('test-fastq-reads.fq')
in_dir = os.path.dirname(good_infile)
- shutil.copyfile(utils.get_test_data('test-error-reads.fq'), corrupt_infile)
- shutil.copyfile(utils.get_test_data('test-fastq-reads.fq'), good_infile)
-
script = 'normalize-by-median.py'
args = ['-f', '-C', CUTOFF, '-k', '17', corrupt_infile, good_infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
+ _, _, err = utils.runscript(script, args, in_dir)
assert '*** Skipping' in err
assert '** I/O Errors' in err
def test_normalize_by_median_no_bigcount():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data("test-abund-read-2.fa")
hashfile = utils.get_temp_filename('test-out.ct')
- outfile = infile + '.keep'
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
- counting_ht = _make_counting(infile, K=8)
-
script = 'normalize-by-median.py'
- args = ['-C', '1000', '-k 8', '--savegraph', hashfile, infile]
+ # 256 is outside the range of valid values for C
+ args = ['-C', '256', '-k 8', '--savegraph', hashfile, infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
- assert status == 0, (out, err)
+ (status, out, err) = utils.runscript(script, args, in_dir, fail_ok=True)
+ assert status == 1, (out, err)
+ assert "ERROR: khmer only supports 0 <= cutoff < 256" in err
print((out, err))
- assert os.path.exists(hashfile), hashfile
- kh = khmer.load_countgraph(hashfile)
-
- assert kh.get('GGTTGACG') == 255
-
def test_normalize_by_median_empty():
CUTOFF = '1'
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-empty.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-empty.fa'), infile)
-
script = 'normalize-by-median.py'
args = ['-C', CUTOFF, '-k', '17', infile]
utils.runscript(script, args, in_dir)
@@ -607,11 +546,9 @@ def test_normalize_by_median_empty():
def test_normalize_by_median_emptycountgraph():
CUTOFF = '1'
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-empty.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-empty.fa'), infile)
-
script = 'normalize-by-median.py'
args = ['-C', CUTOFF, '--loadgraph', infile, infile]
(status, out, err) = utils.runscript(script, args, in_dir, fail_ok=True)
@@ -622,14 +559,13 @@ def test_normalize_by_median_emptycountgraph():
def test_normalize_by_median_fpr():
MAX_TABLESIZE_PARAM = 12
- infile = utils.get_temp_filename('test-fpr.fq')
+ infile = utils.copy_test_data('test-fastq-reads.fq')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-fastq-reads.fq'), infile)
script = 'normalize-by-median.py'
args = ['-f', '-k 17', '-x ' + str(MAX_TABLESIZE_PARAM), infile]
- (status, out, err) = utils.runscript(script, args, in_dir, fail_ok=True)
+ (status, _, err) = utils.runscript(script, args, in_dir, fail_ok=True)
assert status != 0
assert os.path.exists(infile + '.keep'), infile
assert '** ERROR: the graph structure is too small' in err, err
@@ -662,7 +598,7 @@ def test_normalize_by_median_streaming_0():
# Execute diginorm
script = 'normalize-by-median.py'
args = ['-C', CUTOFF, '-k', '17', '-o', fifo, infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
+ utils.runscript(script, args, in_dir)
# Merge the thread
thread.join()
@@ -689,7 +625,7 @@ def test_normalize_by_median_streaming_1():
# Execute diginorm
script = 'normalize-by-median.py'
args = ['-C', CUTOFF, '-k', '17', '-o', outfile, fifo]
- (status, out, err) = utils.runscript(script, args, in_dir)
+ (_, _, err) = utils.runscript(script, args, in_dir)
# Merge the thread
thread.join()
@@ -705,12 +641,9 @@ def test_diginorm_basic_functionality_1():
CUTOFF = ['-C', '1']
PAIRING = ['-p']
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('dn-test-all-paired-all-keep.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('dn-test-all-paired-all-keep.fa'),
- infile)
-
script = 'normalize-by-median.py'
args = list(CUTOFF) + list(PAIRING) + ['-k', '15', infile]
_, out, err = utils.runscript(script, args, in_dir)
@@ -736,12 +669,9 @@ def test_diginorm_basic_functionality_2():
CUTOFF = ['-C', '1']
PAIRING = ['--force_single']
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('dn-test-all-paired-all-keep.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('dn-test-all-paired-all-keep.fa'),
- infile)
-
script = 'normalize-by-median.py'
args = list(CUTOFF) + list(PAIRING) + ['-k', '15', infile]
_, out, err = utils.runscript(script, args, in_dir)
@@ -767,12 +697,9 @@ def test_diginorm_basic_functionality_3():
CUTOFF = ['-C', '1']
PAIRING = []
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('dn-test-none-paired.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('dn-test-none-paired.fa'),
- infile)
-
script = 'normalize-by-median.py'
args = list(CUTOFF) + list(PAIRING) + ['-k', '15', infile]
_, out, err = utils.runscript(script, args, in_dir)
@@ -796,12 +723,9 @@ def test_diginorm_basic_functionality_4():
CUTOFF = ['-C', '1']
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('dn-test-some-paired-all-keep.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('dn-test-some-paired-all-keep.fa'),
- infile)
-
script = 'normalize-by-median.py'
args = list(CUTOFF) + ['-k', '15', infile]
@@ -826,12 +750,9 @@ def test_diginorm_basic_functionality_5():
CUTOFF = ['-C', '1']
PAIRING = ['-p']
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('dn-test-all-paired-all-keep.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('dn-test-all-paired-all-keep.fa'),
- infile)
-
script = 'normalize-by-median.py'
args = list(CUTOFF) + list(PAIRING) + ['-k', '15', infile]
_, out, err = utils.runscript(script, args, in_dir)
@@ -847,3 +768,14 @@ def test_diginorm_basic_functionality_5():
'b/1', 'b/2',
'c/1', 'c/2',
'd/1', 'd/2']), seqs
+
+
+def test_normalize_by_median_outfile_closed_err():
+ infile1 = utils.get_test_data('paired-mixed.fa.pe')
+ infile2 = utils.get_test_data("test-abund-read-2.fa")
+ outfile = utils.get_temp_filename('outfile_xxx')
+ script = 'normalize-by-median.py'
+ args = ['-o', outfile, infile1, infile2]
+ (status, out, err) = utils.runscript(script, args)
+ assert status == 0, (out, err)
+ assert os.path.exists(outfile)
diff --git a/tests/test_oxli_functions.py b/tests/test_oxli_functions.py
index d5b865b..bf1dcef 100644
--- a/tests/test_oxli_functions.py
+++ b/tests/test_oxli_functions.py
@@ -31,13 +31,10 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
-# pylint: disable=C0111,C0103,E1103,W0612
-from __future__ import print_function
-from __future__ import absolute_import
-from __future__ import unicode_literals
+# pylint: disable=missing-docstring,invalid-name,no-member
+from __future__ import print_function, absolute_import, unicode_literals
from . import khmer_tst_utils as utils
-import khmer
# Technically not from 'oxli' but it's what they are
from khmer.khmer_args import (estimate_optimal_with_K_and_M,
@@ -115,4 +112,4 @@ def test_optimal_size_function():
def test_output_gen():
- res = graphsize_args_report(99, 0.00701925498897)
+ graphsize_args_report(99, 0.00701925498897)
diff --git a/tests/test_read_aligner.py b/tests/test_read_aligner.py
index b676323..b4f3dbc 100644
--- a/tests/test_read_aligner.py
+++ b/tests/test_read_aligner.py
@@ -1,6 +1,6 @@
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2013-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -32,11 +32,12 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
+# pylint: disable=missing-docstring,no-member,invalid-name,unused-variable
from __future__ import print_function
from __future__ import absolute_import
+
import khmer
from . import khmer_tst_utils as utils
-# from nose.tools import assert_almost_equals
def pretty_compare(a, b):
@@ -84,7 +85,7 @@ def test_align_nothing():
read = "ACCAAGGCTCGAGATTTACC"
aligner = khmer.ReadAligner(ch, 0, 0)
- for i in range(20):
+ for _ in range(20):
ch.consume("AGAGGGAAAGCTAGGTTCGACAAGTCCTTGACAGAT")
score, graphAlign, readAlign, trunc = aligner.align(read)
@@ -99,10 +100,10 @@ def test_alignnocov():
ch = khmer.Countgraph(10, 1048576, 1)
read = "ACCTAGGTTCGACATGTACC"
aligner = khmer.ReadAligner(ch, 0, 0)
- for i in range(20):
+ for _ in range(20):
ch.consume("AGAGGGAAAGCTAGGTTCGACAAGTCCTTGACAGAT")
ch.consume("ACCTAGGTTCGACATGTACC")
- score, graphAlign, readAlign, trunc = aligner.align(read)
+ _, graphAlign, readAlign, trunc = aligner.align(read)
# should be the same
eq_(readAlign, 'ACCTAGGTTCGACATGTACC')
@@ -114,10 +115,10 @@ def test_align_middle():
ch = khmer.Countgraph(10, 1048576, 1)
read = "TCGACAAGTCCTTGACAGAT"
aligner = khmer.ReadAligner(ch, 0, 0)
- for i in range(20):
+ for _ in range(20):
ch.consume("AGAGGGAAAGCTAGGTTCGACAAGTCCTTGACAGAT")
ch.consume(read)
- score, graphAlign, readAlign, trunc = aligner.align(read)
+ _, graphAlign, readAlign, trunc = aligner.align(read)
# should be the same
eq_(readAlign, read)
@@ -131,12 +132,12 @@ def test_align_middle_trunc():
ch = khmer.Countgraph(10, 1048576, 1)
read = "TCGACAAGTCCTTGACAGATGGGGGG"
aligner = khmer.ReadAligner(ch, 0, 0)
- for i in range(20):
+ for _ in range(20):
ch.consume("AGAGGGAAAGCTAGGTTCGACAAGTCCTTGACAGAT")
# omit suffix from graph
ch.consume(read[:-5])
- score, graphAlign, readAlign, trunc = aligner.align(read)
+ _, graphAlign, readAlign, trunc = aligner.align(read)
# should not be the same...
neq_(readAlign, read)
@@ -155,12 +156,12 @@ def test_align_middle_trunc_2():
ch = khmer.Countgraph(10, 1048576, 1)
read = "GGGGGGGGGGGGTCGACAAGTCCTTGACAGAT"
aligner = khmer.ReadAligner(ch, 0, 0)
- for i in range(20):
+ for _ in range(20):
ch.consume("AAAAAAAAAAAATCGACAAGTCCTTGACAGAT")
# omit prefix from graph
ch.consume(read[12:])
- score, graphAlign, readAlign, trunc = aligner.align(read)
+ _, graphAlign, readAlign, trunc = aligner.align(read)
# here, the alignment must start not at the beginning
print(readAlign)
@@ -178,7 +179,7 @@ def test_align_fwd_nothing():
read = "ACCAAGGCTCGAGATTTACC"
aligner = khmer.ReadAligner(ch, 0, 0)
- for i in range(20):
+ for _ in range(20):
ch.consume("AGAGGGAAAGCTAGGTTCGACAAGTCCTTGACAGAT")
score, graphAlign, readAlign, trunc, _ = aligner.align_forward(read)
@@ -193,10 +194,10 @@ def test_align_fwd_nocov():
ch = khmer.Countgraph(10, 1048576, 1)
read = "ACCTAGGTTCGACATGTACC"
aligner = khmer.ReadAligner(ch, 0, 0)
- for i in range(20):
+ for _ in range(20):
ch.consume("AGAGGGAAAGCTAGGTTCGACAAGTCCTTGACAGAT")
ch.consume("ACCTAGGTTCGACATGTACC")
- score, graphAlign, readAlign, trunc, _ = aligner.align_forward(read)
+ _, graphAlign, readAlign, trunc, _ = aligner.align_forward(read)
# should be the same
eq_(readAlign, 'ACCTAGGTTCGACATGTACC')
@@ -208,7 +209,7 @@ def test_align_fwd_middle():
ch = khmer.Countgraph(10, 1048576, 1)
read = "TCGACAAGTCCTTGACAGAT"
aligner = khmer.ReadAligner(ch, 0, 0)
- for i in range(20):
+ for _ in range(20):
ch.consume("AGAGGGAAAGCTAGGTTCGACAAGTCCTTGACAGAT")
ch.consume(read)
score, graphAlign, readAlign, trunc, _ = aligner.align_forward(read)
@@ -246,12 +247,12 @@ def test_align_fwd_middle_trunc_2():
ch = khmer.Countgraph(10, 1048576, 1)
read = "GGGGGGGGGGGGTCGACAAGTCCTTGACAGAT"
aligner = khmer.ReadAligner(ch, 0, 0)
- for i in range(20):
+ for _ in range(20):
ch.consume("AAAAAAAAAAAATCGACAAGTCCTTGACAGAT")
# omit prefix from graph
ch.consume(read[12:])
- score, graphAlign, readAlign, trunc, _ = aligner.align_forward(read)
+ _, graphAlign, readAlign, trunc, _ = aligner.align_forward(read)
# this will fail, because align_forward chooses the first kmer as the
# seed.
@@ -414,7 +415,7 @@ def test_readalign():
ch.consume("GCTTTTAAAAAGGTTCGACAAAGGCCCGGG")
- score, graphAlign, readAlign, trunc = aligner.align(read)
+ score, graphAlign, readAlign, _ = aligner.align(read)
eq_(readAlign, 'ACCTAGGTTCGACATGTACC')
eq_(graphAlign, 'AGCTAGGTTCGACAAGTCCT')
@@ -436,54 +437,54 @@ ht_seqs = ["TTAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGATTATCAATTTTGCCGCTTTAACTGG"
queries = [
{
"seq": "TTAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGATTATCAATTTTGCCGCTTTAA"
- "CTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCCTGTGTTGCAATCTTAACAA"
- "CCTCTTTAC",
+ "CTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCCTGTGTTGCAATC"
+ "TTAACAACCTCTTTAC",
"score": 274.76338282696173,
"graph_aln": "TTAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGATTATCAATTTTGCCG"
- "CTTTAACTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCCTGTGTTGCAATCT"
- "TAACAACCTCTTTAC",
+ "CTTTAACTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCC"
+ "TGTGTTGCAATCTTAACAACCTCTTTAC",
"read_aln": "TTAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGATTATCAATTTTGCCGC"
- "TTTAACTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCCTGTGTTGCAATCTT"
- "AACAACCTCTTTAC",
+ "TTTAACTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCCTG"
+ "TGTTGCAATCTTAACAACCTCTTTAC",
"truncated": False
},
{
"seq": "TTAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGATTATCAATTTTGCCGCTTTAA"
- "CTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCCTGTATTGCAATCTTAACAA"
- "CCTCTTTAC",
+ "CTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCCTGTATTGCAATC"
+ "TAACAACCTCTTTAC",
"score": 274.76338282696173,
"graph_aln": "TTAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGATTATCAATTTTGCCG"
- "CTTTAACTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCCTGTATTGCAATCT"
- "TAACAACCTCTTTAC",
+ "CTTTAACTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCC"
+ "TGTATTGCAATCTTAACAACCTCTTTAC",
"read_aln": "TTAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGATTATCAATTTTGCCGC"
- "TTTAACTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCCTGTATTGCAATCTT"
- "AACAACCTCTTTAC",
+ "TTTAACTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCCTG"
+ "TATTGCAATCTTAACAACCTCTTTAC",
"truncated": False
},
{
"seq": "TAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGATTATCAATTTTGCCGCTTTAAC"
- "TGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCCTGTGTTGCAATCTTAACAAC"
- "CTCTTTAC",
+ "TGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCCTGTGTTGCAATCT"
+ "TAACAACCTCTTTAC",
"score": 272.841515695261,
"graph_aln": "TAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGATTATCAATTTTGCCGC"
- "TTTAACTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCCTGTGTTGCAATCTT"
- "AACAACCTCTTTAC",
+ "TTTAACTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCCT"
+ "GTGTTGCAATCTTAACAACCTCTTTAC",
"read_aln": "TAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGATTATCAATTTTGCCGCT"
- "TTAACTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCCTGTGTTGCAATCTTA"
- "ACAACCTCTTTAC",
+ "TTAACTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCCTGT"
+ "GTTGCAATCTTAACAACCTCTTTAC",
"truncated": False
},
{
"seq": "TAAATGCGCAATTTTTCCCTCTTTTCTTCTATATGTTTGATTATCAATTTTGCCGCTTTAAC"
- "TGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCCTGTGTTGCAATCTTAACAAC"
- "CTCTTTAC",
+ "TGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCCTGTGTTGCAATCT"
+ "TAACAACCTCTTTAC",
"score": 268.2640868672253,
"graph_aln": "TAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGATTATCAATTTTGCCGC"
- "TTTAACTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCCTGTGTTGCAATCTT"
- "AACAACCTCTTTAC",
+ "TTTAACTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCCT"
+ "GTGTTGCAATCTTAACAACCTCTTTAC",
"read_aln": "TAAATGCGCAATTTTTCCCTCTTTTCTTCTATATGTTTGATTATCAATTTTGCCGCT"
- "TTAACTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCCTGTGTTGCAATCTTA"
- "ACAACCTCTTTAC",
+ "TTAACTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCCTGT"
+ "GTTGCAATCTTAACAACCTCTTTAC",
"truncated": False
},
{
@@ -530,40 +531,38 @@ queries = [
},
{
"seq": "TTAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGATTATAATTTTGCCGCTTTAAC"
- "TGGGTCTAGTTTCTACTGCAAACTTTCCACCAACTAGTTTTTCTGCATCCTTTGTTGCAATCTTAACAA"
- "CCTCTTTAC",
+ "TGGGTCTAGTTTCTACTGCAAACTTTCCACCAACTAGTTTTTCTGCATCCTTTGTTGCAATC"
+ "TTAACAACCTCTTTAC",
"score": 237.81111469018322,
- "graph_aln": "TTAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGATTATcAATTTTGCC"
- "GCTTTAACTGGGTCT-GTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATCCTGTGTTGCAAT"
- "CTTAACAACCTCTTTAC",
- "read_aln": "TTAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGATTAT-AATTTTGCCG"
- "CTTTAACTGGGTCTaGTTTCTACTGCAAACTTTCCACCAACTAGTTTTTCTGCATCCTTTGTTGCAATC"
- "TTAACAACCTCTTTAC",
+ "graph_aln": "TTAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGATTATcAATTTTGCCG"
+ "CTTTAACTGGGTCT-GTTTCTACTGCAAACTTTCCACCAACAAGTTTTTCTGCATC"
+ "CTGTGTTGCAATCTTAACAACCTCTTTAC",
+ "read_aln": "TTAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGATTAT-AATTTTGCCGC"
+ "TTTAACTGGGTCTaGTTTCTACTGCAAACTTTCCACCAACTAGTTTTTCTGCATCCT"
+ "TTGTTGCAATCTTAACAACCTCTTTAC",
"truncated": False
},
{
"seq": "TTAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGAAAATAATTAAAAAAAAAAAAA"
- "AAAAAAAAAAAAAAAAAAAAAAAAAA",
+ "AAAAAAAAAAAAAAAAAAAAAAAAAA",
"score": 5.331560863368736,
- "graph_aln":
- "TTAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGATTATCAATTTTGCCGCTTTAACTGGGTC"
- "TGTTTCTACTGCAAACTTT",
- "read_aln":
- "TTAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGAAAATAATTAAAAAAAAAAAAAAAAAAAA"
- "AAAAAAAAAAAAAAAAAAA",
+ "graph_aln": "TTAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGATTATCAATTTTGCCG"
+ "CTTTAACTGGGTCTGTTTCTACTGCAAACTTT",
+ "read_aln": "TTAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGAAAATAATTAAAAAAAA"
+ "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"truncated": False
},
{
"seq": "TTAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGATTATCAATTTTGCCGCTTTAA"
- "CTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGAAAAATGTCATCCTGTATTGCAATCTTAACAA"
- "CCTCTTTAC",
+ "CTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGAAAAATGTCATCCTGTATTGCAATC"
+ "TTAACAACCTCTTTAC",
"score": 274.76338282696173,
"graph_aln": "TTAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGATTATCAATTTTGCCG"
- "CTTTAACTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGAAAAATGTCATCCTGTATTGCAATC"
- "TTAACAACCTCTTTAC",
+ "CTTTAACTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGAAAAATGTCATCC"
+ "TGTATTGCAATCTTAACAACCTCTTTAC",
"read_aln": "TTAAATGCCCAATTTTTCCCTCTTTTCTTCTATATGTTTGATTATCAATTTTGCCGC"
- "TTTAACTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGAAAAATGTCATCCTGTATTGCAATCT"
- "TAACAACCTCTTTAC",
+ "TTTAACTGGGTCTGTTTCTACTGCAAACTTTCCACCAACAAGAAAAATGTCATCCTG"
+ "TATTGCAATCTTAACAACCTCTTTAC",
"truncated": False
},
{ # the motif of 32 bases are identical match to HT seqs, the rest are
@@ -635,7 +634,7 @@ def check_query(aligner, query):
(readAlign, query["read_aln"])
eq_(trunc, query["truncated"])
if query["score"] > 0:
- assert_almost_equals(score, query["score"])
+ assert round(score - query["score"], 7) == 0
def test_readalign_new():
diff --git a/tests/test_read_handling.py b/tests/test_read_handling.py
new file mode 100644
index 0000000..81f32c9
--- /dev/null
+++ b/tests/test_read_handling.py
@@ -0,0 +1,789 @@
+# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# Copyright (C) 2014-2015, Michigan State University.
+# Copyright (C) 2015-2016, The Regents of the University of California.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+#
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# * Redistributions in binary form must reproduce the above
+# copyright notice, this list of conditions and the following
+# disclaimer in the documentation and/or other materials provided
+# with the distribution.
+#
+# * Neither the name of the Michigan State University nor the names
+# of its contributors may be used to endorse or promote products
+# derived from this software without specific prior written
+# permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Contact: khmer-project at idyll.org
+# pylint: disable=C0111,C0103,E1103,W0612
+
+from __future__ import print_function
+from __future__ import absolute_import
+from __future__ import unicode_literals
+
+import gzip
+import os
+import pytest
+
+from . import khmer_tst_utils as utils
+import khmer
+import khmer.kfile
+import khmer.utils
+import screed
+
+
+def test_interleave_read_stdout():
+ # create input files
+ infile1 = utils.get_test_data('paired-slash1.fq.1')
+ infile2 = utils.get_test_data('paired-slash1.fq.2')
+
+ # correct output
+ ex_outfile = utils.get_test_data('paired-slash1.fq')
+
+ # actual output file
+ outfile = utils.get_temp_filename('out.fq')
+
+ script = 'interleave-reads.py'
+ args = [infile1, infile2]
+
+ (stats, out, err) = utils.runscript(script, args)
+
+ with open(outfile, 'w') as ofile:
+ ofile.write(out)
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile), screed.open(outfile)):
+ n += 1
+ assert r.name == q.name
+ assert r.sequence == q.sequence
+ assert n > 0
+
+
+def test_interleave_read_seq1_fq():
+ # create input files
+ infile1 = utils.get_test_data('paired-slash1.fq.1')
+ infile2 = utils.get_test_data('paired-slash1.fq.2')
+
+ # correct output
+ ex_outfile = utils.get_test_data('paired-slash1.fq')
+
+ # actual output file
+ outfile = utils.get_temp_filename('out.fq')
+
+ script = 'interleave-reads.py'
+ args = [infile1, infile2, '-o', outfile]
+
+ utils.runscript(script, args)
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile), screed.open(outfile)):
+ n += 1
+ assert r.name == q.name
+ assert r.sequence == q.sequence
+ assert n > 0
+
+
+def test_interleave_read_badleft_badright():
+ # create input files
+ infile1 = utils.get_test_data('paired-broken.fq.badleft')
+ infile2 = utils.get_test_data('paired-broken.fq.badright')
+
+ # correct output
+ ex_outfile = utils.get_test_data('paired-broken.fq.paired_bad')
+
+ # actual output file
+ outfile = utils.get_temp_filename('out.fq')
+
+ script = 'interleave-reads.py'
+ args = [infile1, infile2, '-o', outfile]
+
+ utils.runscript(script, args)
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile), screed.open(outfile)):
+ n += 1
+ assert r.name == q.name
+ assert r.sequence == q.sequence
+ assert n > 0
+
+
+def test_interleave_reads_1_fq():
+ # test input files
+ infile1 = utils.get_test_data('paired.fq.1')
+ infile2 = utils.get_test_data('paired.fq.2')
+
+ # correct output
+ ex_outfile = utils.get_test_data('paired.fq')
+
+ # actual output file
+ outfile = utils.get_temp_filename('out.fq')
+
+ script = 'interleave-reads.py'
+ args = [infile1, infile2, '-o', outfile]
+
+ utils.runscript(script, args)
+
+ r = open(ex_outfile).read()
+ q = open(outfile).read()
+
+ assert r == q, (r, q)
+
+
+def test_interleave_reads_no_reformat():
+ infile1 = utils.get_test_data('paired.fq.1')
+ infile2 = utils.get_test_data('paired.malformat.fq.2')
+
+ ex_outfile = utils.get_test_data('paired.malformat.fq')
+ outfile = utils.get_temp_filename('out.fq')
+
+ script = 'interleave-reads.py'
+ args = [infile1, infile2, '--no-reformat', '-o', outfile]
+
+ utils.runscript(script, args)
+
+ r = open(ex_outfile).read()
+ q = open(outfile).read()
+
+ assert r == q, (r, q)
+
+
+def test_interleave_reads_broken_fq():
+ # test input files
+ infile1 = utils.get_test_data('paired-broken.fq.1')
+ infile2 = utils.get_test_data('paired-broken.fq.2')
+
+ # actual output file
+ outfile = utils.get_temp_filename('out.fq')
+
+ script = 'interleave-reads.py'
+ args = [infile1, infile2, '-o', outfile]
+
+ status, out, err = utils.runscript(script, args, fail_ok=True)
+ assert status == 1
+ assert 'ERROR: Input files contain different number of records.' in err
+
+
+def test_interleave_reads_broken_fq_2():
+ # test input files
+ infile1 = utils.get_test_data('paired-broken2.fq.1')
+ infile2 = utils.get_test_data('paired-broken2.fq.2')
+
+ # actual output file
+ outfile = utils.get_temp_filename('out.fq')
+
+ script = 'interleave-reads.py'
+ args = [infile1, infile2, '-o', outfile]
+
+ status, out, err = utils.runscript(script, args, fail_ok=True)
+ assert status == 1
+ assert "ERROR: This doesn't look like paired data!" in err
+
+
+def test_interleave_reads_broken_fq_3():
+ # test input files
+ infile1 = utils.get_test_data('paired-broken3.fq.1')
+ infile2 = utils.get_test_data('paired-broken3.fq.2')
+
+ # actual output file
+ outfile = utils.get_temp_filename('out.fq')
+
+ script = 'interleave-reads.py'
+ args = [infile1, infile2, '-o', outfile]
+
+ status, out, err = utils.runscript(script, args, fail_ok=True)
+ assert status == 1
+ assert "ERROR: This doesn't look like paired data!" in err
+
+
+def test_interleave_reads_broken_fq_5():
+ # test input files
+ infile1 = utils.get_test_data('paired-broken4.fq.1')
+ infile2 = utils.get_test_data('paired-broken4.fq.2')
+
+ # actual output file
+ outfile = utils.get_temp_filename('out.fq')
+
+ script = 'interleave-reads.py'
+ args = [infile1, infile2, '-o', outfile]
+
+ status, out, err = utils.runscript(script, args, fail_ok=True)
+ assert status == 1
+ assert "ERROR: This doesn't look like paired data!" in err
+
+
+def test_interleave_reads_2_fa():
+ # test input files
+ infile1 = utils.get_test_data('paired.fa.1')
+ infile2 = utils.get_test_data('paired.fa.2')
+
+ # correct output
+ ex_outfile = utils.get_test_data('paired.fa')
+
+ # actual output file
+ outfile = utils.get_temp_filename('out.fa')
+
+ script = 'interleave-reads.py'
+ args = [infile1, infile2, '-o', outfile]
+
+ utils.runscript(script, args)
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile), screed.open(outfile)):
+ n += 1
+ assert r.name == q.name
+ assert r.sequence == q.sequence
+ assert n > 0
+
+
+def test_split_paired_reads_1_fa():
+ # test input file
+ infile = utils.get_test_data('paired.fa')
+
+ ex_outfile1 = utils.get_test_data('paired.fa.1')
+ ex_outfile2 = utils.get_test_data('paired.fa.2')
+
+ # actual output files...
+ outfile1 = utils.get_temp_filename('paired.fa.1')
+ in_dir = os.path.dirname(outfile1)
+ outfile2 = utils.get_temp_filename('paired.fa.2', in_dir)
+
+ script = 'split-paired-reads.py'
+ args = [infile]
+
+ utils.runscript(script, args, in_dir)
+
+ assert os.path.exists(outfile1), outfile1
+ assert os.path.exists(outfile2), outfile2
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
+ n += 1
+ assert r.name == q.name
+ assert r.sequence == q.sequence
+ assert n > 0
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
+ n += 1
+ assert r.name == q.name
+ assert r.sequence == q.sequence
+ assert n > 0
+
+
+def test_split_paired_reads_2_fq():
+ # test input file
+ infile = utils.get_test_data('paired.fq')
+
+ ex_outfile1 = utils.get_test_data('paired.fq.1')
+ ex_outfile2 = utils.get_test_data('paired.fq.2')
+
+ # actual output files...
+ outfile1 = utils.get_temp_filename('paired.fq.1')
+ in_dir = os.path.dirname(outfile1)
+ outfile2 = utils.get_temp_filename('paired.fq.2', in_dir)
+
+ script = 'split-paired-reads.py'
+ args = [infile]
+
+ utils.runscript(script, args, in_dir)
+
+ assert os.path.exists(outfile1), outfile1
+ assert os.path.exists(outfile2), outfile2
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
+ n += 1
+ assert r.name == q.name
+ assert r.sequence == q.sequence
+ assert r.quality == q.quality
+ assert n > 0
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
+ n += 1
+ assert r.name == q.name
+ assert r.sequence == q.sequence
+ assert r.quality == q.quality
+ assert n > 0
+
+
+def test_split_paired_reads_2_mixed_fq_require_pair():
+ # test input file
+ infile = utils.copy_test_data('paired-mixed.fq')
+ in_dir = os.path.dirname(infile)
+
+ script = 'split-paired-reads.py'
+ args = [infile]
+
+ status, out, err = utils.runscript(script, args, in_dir, fail_ok=True)
+ assert status == 1, status
+ assert "Unpaired reads found" in err
+
+
+def test_split_paired_reads_2_stdin_no_out():
+ script = 'split-paired-reads.py'
+ args = ['-']
+
+ status, out, err = utils.runscript(script, args, fail_ok=True)
+ assert status == 1
+ assert "Accepting input from stdin; output filenames must " in err
+
+
+def test_split_paired_reads_2_mixed_fq():
+ # test input file
+ infile = utils.copy_test_data('paired-mixed-2.fq')
+ in_dir = os.path.dirname(infile)
+
+ script = 'split-paired-reads.py'
+ args = ['-0', '/dev/null', infile]
+
+ status, out, err = utils.runscript(script, args, in_dir)
+ assert status == 0
+ assert "split 6 sequences (3 left, 3 right, 5 orphans)" in err, err
+
+
+def test_split_paired_reads_2_mixed_fq_orphans_to_file():
+ # test input file
+ infile = utils.copy_test_data('paired-mixed-2.fq')
+ in_dir = os.path.dirname(infile)
+ outfile = utils.get_temp_filename('out.fq')
+
+ script = 'split-paired-reads.py'
+ args = ['-0', outfile, infile]
+
+ status, out, err = utils.runscript(script, args, in_dir)
+ assert status == 0
+ assert "split 6 sequences (3 left, 3 right, 5 orphans)" in err, err
+
+ n_orphans = len([1 for record in screed.open(outfile)])
+ assert n_orphans == 5
+ n_left = len([1 for record in screed.open(infile + '.1')])
+ assert n_left == 3
+ n_right = len([1 for record in screed.open(infile + '.2')])
+ assert n_right == 3
+ for filename in [outfile, infile + '.1', infile + '.2']:
+ fp = gzip.open(filename)
+ try:
+ fp.read()
+ except IOError as e:
+ assert "Not a gzipped file" in str(e), str(e)
+ fp.close()
+
+
+def test_split_paired_reads_2_mixed_fq_gzfile():
+ # test input file
+ infile = utils.copy_test_data('paired-mixed-2.fq')
+ in_dir = os.path.dirname(infile)
+ outfile = utils.get_temp_filename('out.fq')
+
+ script = 'split-paired-reads.py'
+ args = ['-0', outfile, '--gzip', infile]
+
+ status, out, err = utils.runscript(script, args, in_dir)
+ assert status == 0
+ assert "split 6 sequences (3 left, 3 right, 5 orphans)" in err, err
+
+ n_orphans = len([1 for record in screed.open(outfile)])
+ assert n_orphans == 5
+ n_left = len([1 for record in screed.open(infile + '.1')])
+ assert n_left == 3
+ n_right = len([1 for record in screed.open(infile + '.2')])
+ assert n_right == 3
+
+ for filename in [outfile, infile + '.1', infile + '.2']:
+ fp = gzip.open(filename)
+ fp.read() # this will fail if not gzip file.
+ fp.close()
+
+
+def test_split_paired_reads_2_mixed_fq_broken_pairing_format():
+ # test input file
+ infile = utils.copy_test_data('paired-mixed-broken.fq')
+ in_dir = os.path.dirname(infile)
+
+ script = 'split-paired-reads.py'
+ args = [infile]
+
+ status, out, err = utils.runscript(script, args, in_dir, fail_ok=True)
+ assert status == 1
+ assert "Unpaired reads found starting at 895:1:37:17593:9954" in err, err
+
+
+def test_split_paired_reads_3_output_dir():
+ # test input file
+ infile = utils.get_test_data('paired.fq')
+
+ ex_outfile1 = utils.get_test_data('paired.fq.1')
+ ex_outfile2 = utils.get_test_data('paired.fq.2')
+
+ # actual output files...
+ testdir = utils.get_temp_filename('test')
+ output_dir = os.path.join(os.path.dirname(testdir), "out")
+ outfile1 = utils.get_temp_filename('paired.fq.1', output_dir)
+ outfile2 = utils.get_temp_filename('paired.fq.2', output_dir)
+
+ script = 'split-paired-reads.py'
+ args = ['--output-dir', output_dir, infile]
+
+ utils.runscript(script, args)
+
+ assert os.path.exists(outfile1), outfile1
+ assert os.path.exists(outfile2), outfile2
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
+ n += 1
+ assert r.name == q.name
+ assert r.sequence == q.sequence
+ assert r.quality == q.quality
+ assert n > 0
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
+ n += 1
+ assert r.name == q.name
+ assert r.sequence == q.sequence
+ assert r.quality == q.quality
+ assert n > 0
+
+
+def test_split_paired_reads_3_output_files():
+ # test input file
+ infile = utils.get_test_data('paired.fq')
+
+ ex_outfile1 = utils.get_test_data('paired.fq.1')
+ ex_outfile2 = utils.get_test_data('paired.fq.2')
+
+ # actual output files...
+ outfile1 = utils.get_temp_filename('xxx')
+ output_dir = os.path.dirname(outfile1)
+ outfile2 = utils.get_temp_filename('yyy', output_dir)
+
+ script = 'split-paired-reads.py'
+ args = ['-1', outfile1, '-2', outfile2, infile]
+
+ utils.runscript(script, args)
+
+ assert os.path.exists(outfile1), outfile1
+ assert os.path.exists(outfile2), outfile2
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
+ n += 1
+ assert r.name == q.name
+ assert r.sequence == q.sequence
+ assert r.quality == q.quality
+ assert n > 0
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
+ n += 1
+ assert r.name == q.name
+ assert r.sequence == q.sequence
+ assert r.quality == q.quality
+ assert n > 0
+
+
+def test_split_paired_reads_3_output_files_left():
+ # test input file
+ infile = utils.get_test_data('paired.fq')
+
+ ex_outfile1 = utils.get_test_data('paired.fq.1')
+ ex_outfile2 = utils.get_test_data('paired.fq.2')
+
+ # actual output files...
+ outfile1 = utils.get_temp_filename('xxx')
+ output_dir = os.path.dirname(outfile1)
+ outfile2 = utils.get_temp_filename('paired.fq.2', output_dir)
+
+ script = 'split-paired-reads.py'
+ args = ['-d', output_dir, '-1', outfile1, infile]
+
+ utils.runscript(script, args)
+
+ assert os.path.exists(outfile1), outfile1
+ assert os.path.exists(outfile2), outfile2
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
+ n += 1
+ assert r.name == q.name
+ assert r.sequence == q.sequence
+ assert r.quality == q.quality
+ assert n > 0
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
+ n += 1
+ assert r.name == q.name
+ assert r.sequence == q.sequence
+ assert r.quality == q.quality
+ assert n > 0
+
+
+def test_split_paired_reads_3_output_files_right():
+ # test input file
+ infile = utils.get_test_data('paired.fq')
+
+ ex_outfile1 = utils.get_test_data('paired.fq.1')
+ ex_outfile2 = utils.get_test_data('paired.fq.2')
+
+ # actual output files...
+ outfile1 = utils.get_temp_filename('paired.fq.1')
+ output_dir = os.path.dirname(outfile1)
+ outfile2 = utils.get_temp_filename('yyy', output_dir)
+
+ script = 'split-paired-reads.py'
+ args = ['-2', outfile2, '-d', output_dir, infile]
+
+ utils.runscript(script, args)
+
+ assert os.path.exists(outfile1), outfile1
+ assert os.path.exists(outfile2), outfile2
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
+ n += 1
+ assert r.name == q.name
+ assert r.sequence == q.sequence
+ assert r.quality == q.quality
+ assert n > 0
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
+ n += 1
+ assert r.name == q.name
+ assert r.sequence == q.sequence
+ assert r.quality == q.quality
+ assert n > 0
+
+
+def test_extract_paired_reads_unpaired():
+ # test input file
+ infile = utils.get_test_data('random-20-a.fa')
+
+ # actual output files...
+ outfile1 = utils.get_temp_filename('unpaired.pe.fa')
+ in_dir = os.path.dirname(outfile1)
+ outfile2 = utils.get_temp_filename('unpaired.se.fa', in_dir)
+
+ script = 'extract-paired-reads.py'
+ args = [infile]
+
+ (_, _, err) = utils.runscript(script, args, in_dir, fail_ok=True)
+ assert 'no paired reads!? check file formats...' in err, err
+
+
+def test_extract_paired_reads_1_fa():
+ # test input file
+ infile = utils.get_test_data('paired-mixed.fa')
+
+ ex_outfile1 = utils.get_test_data('paired-mixed.fa.pe')
+ ex_outfile2 = utils.get_test_data('paired-mixed.fa.se')
+
+ # actual output files...
+ outfile1 = utils.get_temp_filename('paired-mixed.fa.pe')
+ in_dir = os.path.dirname(outfile1)
+ outfile2 = utils.get_temp_filename('paired-mixed.fa.se', in_dir)
+
+ script = 'extract-paired-reads.py'
+ args = [infile]
+
+ utils.runscript(script, args, in_dir)
+
+ assert os.path.exists(outfile1), outfile1
+ assert os.path.exists(outfile2), outfile2
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
+ n += 1
+ assert r.name == q.name
+ assert r.sequence == q.sequence
+ assert n > 0
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
+ n += 1
+ assert r.name == q.name
+ assert r.sequence == q.sequence
+ assert n > 0
+
+
+def test_extract_paired_reads_2_fq():
+ # test input file
+ infile = utils.get_test_data('paired-mixed.fq')
+
+ ex_outfile1 = utils.get_test_data('paired-mixed.fq.pe')
+ ex_outfile2 = utils.get_test_data('paired-mixed.fq.se')
+
+ # actual output files...
+ outfile1 = utils.get_temp_filename('paired-mixed.fq.pe')
+ in_dir = os.path.dirname(outfile1)
+ outfile2 = utils.get_temp_filename('paired-mixed.fq.se', in_dir)
+
+ script = 'extract-paired-reads.py'
+ args = [infile]
+
+ utils.runscript(script, args, in_dir)
+
+ assert os.path.exists(outfile1), outfile1
+ assert os.path.exists(outfile2), outfile2
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile1),
+ screed.open(outfile1)):
+ n += 1
+ assert r.name == q.name, (r.name, q.name, n)
+ assert r.sequence == q.sequence
+ assert r.quality == q.quality
+ assert n > 0
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile2),
+ screed.open(outfile2)):
+ n += 1
+ assert r.name == q.name
+ assert r.sequence == q.sequence
+ assert r.quality == q.quality
+ assert n > 0
+
+
+def test_extract_paired_reads_3_output_dir():
+ # test input file
+ infile = utils.get_test_data('paired-mixed.fa')
+
+ ex_outfile1 = utils.get_test_data('paired-mixed.fa.pe')
+ ex_outfile2 = utils.get_test_data('paired-mixed.fa.se')
+
+ # output directory
+ out_dir = utils.get_temp_filename('output')
+
+ script = 'extract-paired-reads.py'
+ args = [infile, '-d', out_dir]
+
+ utils.runscript(script, args)
+
+ outfile1 = os.path.join(out_dir, 'paired-mixed.fa.pe')
+ outfile2 = os.path.join(out_dir, 'paired-mixed.fa.se')
+ assert os.path.exists(outfile1), outfile1
+ assert os.path.exists(outfile2), outfile2
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
+ n += 1
+ assert r.name == q.name
+ assert r.sequence == q.sequence
+ assert n > 0
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
+ n += 1
+ assert r.name == q.name
+ assert r.sequence == q.sequence
+ assert n > 0
+
+
+def test_extract_paired_reads_4_output_files():
+ # test input file
+ infile = utils.get_test_data('paired-mixed.fa')
+
+ ex_outfile1 = utils.get_test_data('paired-mixed.fa.pe')
+ ex_outfile2 = utils.get_test_data('paired-mixed.fa.se')
+
+ # actual output files...
+ outfile1 = utils.get_temp_filename('out_pe')
+ outfile2 = utils.get_temp_filename('out_se')
+
+ script = 'extract-paired-reads.py'
+ args = [infile, '-p', outfile1, '-s', outfile2]
+
+ utils.runscript(script, args)
+
+ assert os.path.exists(outfile1), outfile1
+ assert os.path.exists(outfile2), outfile2
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
+ n += 1
+ assert r.name == q.name
+ assert r.sequence == q.sequence
+ assert n > 0
+
+ n = 0
+ for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
+ n += 1
+ assert r.name == q.name
+ assert r.sequence == q.sequence
+ assert n > 0
+
+
+def test_extract_paired_reads_5_stdin_error():
+ script = 'extract-paired-reads.py'
+ args = ['-f', '/dev/stdin']
+
+ status, out, err = utils.runscript(script, args, fail_ok=True)
+ assert status == 1
+ assert "output filenames must be provided." in err
+
+
+def test_read_bundler():
+ infile = utils.get_test_data('unclean-reads.fastq')
+ records = [r for r in khmer.ReadParser(infile)]
+ bundle = khmer.utils.ReadBundle(*records)
+
+ raw_seqs = (
+ 'GGTTGACGGGGNNNAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCG'
+ 'GGGCGGAGGCCGCAGACGCGAGTGGTGGAGG',
+ 'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGANNNCCG'
+ 'GGGCGGAGGCCGCAGACGCGAGTGGTGGAGG',
+ )
+
+ cleaned_seqs = (
+ 'GGTTGACGGGGAAAAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCG'
+ 'GGGCGGAGGCCGCAGACGCGAGTGGTGGAGG',
+ 'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGAAAACCG'
+ 'GGGCGGAGGCCGCAGACGCGAGTGGTGGAGG',
+ )
+
+ assert bundle.num_reads == 2
+ assert bundle.total_length == 200
+
+ for read, raw_seq, clean_seq in zip(bundle.reads, raw_seqs, cleaned_seqs):
+ assert read.sequence == raw_seq
+ assert read.cleaned_seq == clean_seq
+
+
+def test_read_bundler_single_read():
+ infile = utils.get_test_data('single-read.fq')
+ records = [r for r in khmer.ReadParser(infile)]
+ bundle = khmer.utils.ReadBundle(*records)
+ assert bundle.num_reads == 1
+ assert bundle.reads[0].sequence == bundle.reads[0].cleaned_seq
+
+
+def test_read_bundler_empty_file():
+ infile = utils.get_test_data('empty-file')
+ with pytest.raises(OSError):
+ records = [r for r in khmer.ReadParser(infile)]
+
+
+def test_read_bundler_empty_list():
+ bundle = khmer.utils.ReadBundle(*[])
+ assert bundle.num_reads == 0
diff --git a/tests/test_read_parsers.py b/tests/test_read_parsers.py
index 8d2bbce..22cdf32 100644
--- a/tests/test_read_parsers.py
+++ b/tests/test_read_parsers.py
@@ -1,6 +1,6 @@
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2013-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -32,15 +32,55 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
+# pylint: disable=missing-docstring,invalid-name
# Tests for the ReadParser and Read classes.
from __future__ import print_function
from __future__ import absolute_import
-import khmer
+from khmer import Read
from khmer import ReadParser
+from screed import Record
from . import khmer_tst_utils as utils
-from nose.plugins.attrib import attr
-from functools import reduce
+import pytest
+from functools import reduce # pylint: disable=redefined-builtin
+
+
+def test_read_type_basic():
+ # test that basic properties of khmer.Read behave like screed.Record
+ # Constructing without mandatory arguments should raise an exception
+ with pytest.raises(TypeError):
+ Read()
+
+ name = "895:1:1:1246:14654 1:N:0:NNNNN"
+ sequence = "ACGT"
+ r = Read(name, sequence)
+ s = Record(dict(name=name, sequence=sequence))
+
+ for x in (r, s):
+ assert x.name == name
+ assert x.sequence == sequence
+ assert not hasattr(x, 'quality'), x
+ assert not hasattr(x, 'description'), x
+
+
+def test_read_quality_none():
+ r = Read(name="test", sequence="ACGT", quality=None)
+ assert not hasattr(r, 'quality')
+
+
+def test_read_type_attributes():
+ r = Read(sequence='ACGT', quality='good', name='1234', description='desc')
+ assert r.sequence == 'ACGT'
+ assert r.cleaned_seq == 'ACGT'
+ assert r.quality == 'good'
+ assert r.name == '1234'
+ assert r.description == 'desc'
+
+
+def test_read_type_cleaned_seq():
+ r = Read(sequence='acgtnN', name='1234')
+ assert r.sequence == 'acgtnN'
+ assert r.cleaned_seq == 'ACGTAA'
def test_read_properties():
@@ -52,10 +92,25 @@ def test_read_properties():
for read in rparser:
assert read.name == "895:1:1:1246:14654 1:N:0:NNNNN"
assert read.sequence == "CAGGCGCCCACCACCGTGCCCTCCAACCTGATGGT"
- assert read.annotations == ""
+ # if an attribute is empty it shouldn't exist
+ assert not hasattr(read, 'annotations')
assert read.quality == """][aaX__aa[`ZUZ[NONNFNNNNNO_____^RQ_"""
+def test_read_properties_fa():
+
+ # Note: Using a data file with only one read.
+ rparser = ReadParser(utils.get_test_data("single-read.fa"))
+
+ # Check the properties of all one reads in data set.
+ for read in rparser:
+ print(read.name)
+ assert read.name == "895:1:1:1246:14654 1:N:0:NNNNN"
+ assert read.sequence == "CAGGCGCCCACCACCGTGCCCTCCAACCTGATGGT"
+ # if an attribute is empty it shouldn't exist
+ assert not hasattr(read, 'quality')
+
+
def test_with_default_arguments():
read_names = []
@@ -84,7 +139,7 @@ def test_num_reads():
assert rparser.num_reads == 100
- at attr('multithread')
+ at pytest.mark.multithread
def test_num_reads_threads():
"""Test threadsaftey of ReadParser's read counting"""
import threading
@@ -111,7 +166,7 @@ def test_num_reads_truncated():
n_reads = 0
rparser = ReadParser(utils.get_test_data("truncated.fq"))
try:
- for read in rparser:
+ for _ in rparser:
n_reads += 1
except ValueError as err:
assert "Sequence is empty" in str(err), str(err)
@@ -122,7 +177,7 @@ def test_num_reads_truncated():
def test_gzip_decompression():
reads_count = 0
rparser = ReadParser(utils.get_test_data("100-reads.fq.gz"))
- for read in rparser:
+ for _ in rparser:
reads_count += 1
assert 100 == reads_count
@@ -132,7 +187,7 @@ def test_gzip_decompression_truncated():
rparser = ReadParser(utils.get_test_data("100-reads.fq.truncated.gz"))
try:
- for read in rparser:
+ for _ in rparser:
pass
assert 0, "this should fail"
except OSError as err:
@@ -143,7 +198,7 @@ def test_gzip_decompression_truncated_pairiter():
rparser = ReadParser(utils.get_test_data("100-reads.fq.truncated.gz"))
try:
- for read in rparser.iter_read_pairs():
+ for _ in rparser.iter_read_pairs():
pass
assert 0, "this should fail"
except OSError as err:
@@ -156,7 +211,7 @@ def test_bzip2_decompression():
reads_count = 0
rparser = ReadParser(utils.get_test_data("100-reads.fq.bz2"))
- for read in rparser:
+ for _ in rparser:
reads_count += 1
assert 100 == reads_count
@@ -166,7 +221,7 @@ def test_bzip2_decompression_truncated():
rparser = ReadParser(utils.get_test_data("100-reads.fq.truncated.bz2"))
try:
- for read in rparser:
+ for _ in rparser:
pass
assert 0, "this should fail"
except OSError as err:
@@ -179,7 +234,7 @@ def test_bzip2_decompression_truncated_pairiter():
rparser = ReadParser(utils.get_test_data("100-reads.fq.truncated.bz2"))
try:
- for read in rparser.iter_read_pairs():
+ for _ in rparser.iter_read_pairs():
pass
assert 0, "this should fail"
except OSError as err:
@@ -191,7 +246,7 @@ def test_bzip2_decompression_truncated_pairiter():
def test_badbzip2():
try:
rparser = ReadParser(utils.get_test_data("test-empty.fa.bz2"))
- for read in rparser:
+ for _ in rparser:
pass
assert 0, "this should fail"
except OSError as err:
@@ -200,7 +255,7 @@ def test_badbzip2():
print(str(err))
- at attr('multithread')
+ at pytest.mark.multithread
def test_with_multiple_threads(testfile="test-reads.fq.bz2"):
import operator
@@ -208,7 +263,7 @@ def test_with_multiple_threads(testfile="test-reads.fq.bz2"):
reads_count_1thr = 0
rparser = ReadParser(utils.get_test_data(testfile))
- for read in rparser:
+ for _ in rparser:
reads_count_1thr += 1
def count_reads(rparser, counters, tnum):
@@ -233,12 +288,12 @@ def test_with_multiple_threads(testfile="test-reads.fq.bz2"):
reads_counts_per_thread
- at attr('multithread')
+ at pytest.mark.multithread
def test_with_multiple_threads_big():
test_with_multiple_threads(testfile="test-large.fa")
- at attr('multithread')
+ at pytest.mark.multithread
def test_old_illumina_pair_mating():
import threading
@@ -246,11 +301,11 @@ def test_old_illumina_pair_mating():
rparser = ReadParser(utils.get_test_data("test-reads.fa"))
def thread_1_runtime(rparser):
- for read in rparser:
+ for _ in rparser:
pass
def thread_2_runtime(rparser):
- for readnum, read in enumerate(rparser):
+ for readnum, _ in enumerate(rparser):
if 0 == readnum:
pass
@@ -264,7 +319,7 @@ def test_old_illumina_pair_mating():
t2.join()
- at attr('multithread')
+ at pytest.mark.multithread
def test_casava_1_8_pair_mating():
import threading
@@ -275,11 +330,11 @@ def test_casava_1_8_pair_mating():
rparser = ReadParser(utils.get_test_data("test-reads.fq.bz2"))
def thread_1_runtime(rparser):
- for read in rparser:
+ for _ in rparser:
pass
def thread_2_runtime(rparser):
- for readnum, read in enumerate(rparser):
+ for readnum, _ in enumerate(rparser):
if 0 == readnum:
pass
# assert "895:1:1:1761:13189 2:N:0:NNNNN" == read.name, read.name
@@ -298,7 +353,7 @@ def test_read_truncated():
rparser = ReadParser(utils.get_test_data("truncated.fq"))
try:
- for read in rparser:
+ for _ in rparser:
pass
assert 0, "No exception raised on a truncated file"
except ValueError as err:
@@ -313,7 +368,7 @@ def test_iterator_identities():
assert rparser is rparser.iter_reads()
- at attr('known_failing')
+ at pytest.mark.known_failing
def test_read_pair_iterator_in_error_mode():
assert 0
@@ -341,15 +396,12 @@ def test_read_pair_iterator_in_error_mode():
for read_1, read_2 \
in rparser.iter_read_pairs(ReadParser.PAIR_MODE_ERROR_ON_UNPAIRED):
read_pairs_2.append([read_1, read_2])
- matches = \
- list(map(
- lambda rp1, rp2: rp1[0].name == rp2[0].name,
- read_pairs_1, read_pairs_2
- ))
+ matches = [(rp1, rp2) for rp1, rp2 in zip(read_pairs_1, read_pairs_2)
+ if rp1[0].name == rp2[0].name]
assert all(matches) # Assert ALL the matches. :-]
- at attr('linux')
+ at pytest.mark.linux
def test_read_pair_iterator_in_error_mode_xfail():
rparser = \
@@ -357,7 +409,7 @@ def test_read_pair_iterator_in_error_mode_xfail():
failed = True
try:
- for rpair in rparser.iter_read_pairs():
+ for _ in rparser.iter_read_pairs():
pass
failed = False
except ValueError as exc:
@@ -372,15 +424,15 @@ def test_read_pair_iterator_in_error_mode_xfail_osxsafe():
failed = True
try:
- for rpair in rparser.iter_read_pairs():
+ for _ in rparser.iter_read_pairs():
pass
failed = False
- except ValueError as exc:
+ except ValueError:
pass
assert failed
- at attr('known_failing')
+ at pytest.mark.known_failing
def test_read_pair_iterator_in_ignore_mode():
assert 0
@@ -399,13 +451,13 @@ def test_constructor():
# Note: Using a data file with only one read.
try:
- rparser = ReadParser(utils.get_test_data("single-read.fq"), "a")
+ ReadParser(utils.get_test_data("single-read.fq"), "a")
assert 0, ("ReadParser's constructor shouldn't accept a character for "
"the number of threads")
except TypeError as err:
print(str(err))
try:
- rparser = ReadParser("non-existent-file-name")
+ ReadParser("non-existent-file-name")
assert 0, "ReadParser shouldn't accept a non-existant file name"
except ValueError as err:
print(str(err))
@@ -424,4 +476,12 @@ def test_iternext():
print(str(err))
except ValueError as err:
print(str(err))
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
+
+
+def test_clean_seq():
+ for read in ReadParser(utils.get_test_data("test-abund-read-3.fa")):
+ clean = read.sequence.upper().replace("N", "A")
+ assert clean == read.cleaned_seq
+
+# vim: set filetype=python tabstop=4 softtabstop=4 shiftwidth=4 expandtab:
+# vim: set textwidth=79:
diff --git a/tests/test_sandbox_scripts.py b/tests/test_sandbox_scripts.py
index f8c5022..69b5885 100644
--- a/tests/test_sandbox_scripts.py
+++ b/tests/test_sandbox_scripts.py
@@ -1,6 +1,6 @@
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2014-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -42,16 +42,14 @@ from __future__ import unicode_literals
import sys
import os
import os.path
-import shutil
from io import StringIO
import traceback
-import nose
-from nose.plugins.attrib import attr
import glob
import imp
+import pytest
+
from . import khmer_tst_utils as utils
-import khmer
import screed
from .test_scripts import _make_counting
@@ -64,37 +62,26 @@ def teardown():
utils.cleanup()
-def test_import_all():
+def _sandbox_scripts():
sandbox_path = os.path.join(os.path.dirname(__file__), "../sandbox")
if not os.path.exists(sandbox_path):
- raise nose.SkipTest("sandbox scripts are only tested in a repository")
+ pytest.skip("sandbox scripts are only tested in a repository")
path = os.path.join(sandbox_path, "*.py")
- scripts = glob.glob(path)
- for s in scripts:
- s = os.path.normpath(s)
- yield _checkImportSucceeds('test_sandbox_scripts.py', s)
-
+ return [os.path.normpath(s) for s in glob.glob(path)]
-class _checkImportSucceeds(object):
- def __init__(self, tag, filename):
- self.tag = tag
- self.filename = filename
- self.description = '%s: test import %s' % (self.tag,
- os.path.split(filename)[-1])
-
- def __call__(self):
- try:
- mod = imp.load_source('__zzz', self.filename)
- except:
- print(traceback.format_exc())
- raise AssertionError("%s cannot be imported" % (self.filename,))
-
- #
+ at pytest.mark.parametrize("filename", _sandbox_scripts())
+def test_import_succeeds(filename, tmpdir):
+ try:
+ mod = imp.load_source('__zzz', filename)
+ except:
+ print(traceback.format_exc())
+ raise AssertionError("%s cannot be imported" % (filename,))
+ with tmpdir.as_cwd():
oldargs = sys.argv
- sys.argv = [self.filename]
+ sys.argv = [filename]
oldout, olderr = sys.stdout, sys.stderr
sys.stdout = StringIO()
@@ -103,14 +90,14 @@ class _checkImportSucceeds(object):
try:
try:
global_dict = {'__name__': '__main__'}
- exec(
- compile(open(self.filename).read(), self.filename, 'exec'),
+ exec( # pylint: disable=exec-used
+ compile(open(filename).read(), filename, 'exec'),
global_dict)
except (ImportError, SyntaxError) as err:
print("{0}".format(err))
- raise AssertionError("%s cannot be exec'd" % (self.filename),
+ raise AssertionError("%s cannot be exec'd" % (filename),
"{0}".format(traceback))
- except:
+ except: # pylint: disable=bare-except
pass # other failures are expected :)
finally:
sys.argv = oldargs
@@ -119,13 +106,10 @@ class _checkImportSucceeds(object):
def test_sweep_reads():
- readfile = utils.get_temp_filename('reads.fa')
- contigfile = utils.get_temp_filename('contigs.fp')
+ readfile = utils.copy_test_data('test-sweep-reads.fa')
+ contigfile = utils.copy_test_data('test-sweep-contigs.fp')
in_dir = os.path.dirname(contigfile)
- shutil.copyfile(utils.get_test_data('test-sweep-reads.fa'), readfile)
- shutil.copyfile(utils.get_test_data('test-sweep-contigs.fp'), contigfile)
-
script = scriptpath('sweep-reads.py')
args = ['-k', '25', '--prefix', 'test', '--label-by-pid',
contigfile, readfile, 'junkfile.fa']
@@ -165,13 +149,10 @@ def test_sweep_reads():
def test_sweep_reads_fq():
- readfile = utils.get_temp_filename('reads.fa')
- contigfile = utils.get_temp_filename('contigs.fp')
+ readfile = utils.copy_test_data('test-sweep-reads.fq')
+ contigfile = utils.copy_test_data('test-sweep-contigs.fp')
in_dir = os.path.dirname(contigfile)
- shutil.copyfile(utils.get_test_data('test-sweep-reads.fq'), readfile)
- shutil.copyfile(utils.get_test_data('test-sweep-contigs.fp'), contigfile)
-
script = scriptpath('sweep-reads.py')
args = ['-k', '25', '--prefix', 'test', '--label-by-pid',
contigfile, readfile, 'junkfile.fa']
@@ -219,10 +200,9 @@ def test_sweep_reads_fq():
def test_sweep_reads_2():
- infile = utils.get_temp_filename('seqs.fa')
- inref = utils.get_temp_filename('ref.fa')
- shutil.copyfile(utils.get_test_data('random-20-X2.fa'), infile)
- shutil.copyfile(utils.get_test_data('random-20-a.fa'), inref)
+ infile = utils.copy_test_data('random-20-X2.fa')
+ inref = utils.copy_test_data('random-20-a.fa')
+
wdir = os.path.dirname(inref)
script = scriptpath('sweep-reads.py')
args = ['-m', '50', '-k', '20', '-l', '9', '-b', '60', '--prefix',
@@ -241,8 +221,7 @@ def test_sweep_reads_2():
def test_sweep_reads_3():
- infile = utils.get_temp_filename('seqs.fa')
- shutil.copyfile(utils.get_test_data('random-20-a.fa'), infile)
+ infile = utils.copy_test_data('random-20-a.fa')
wdir = os.path.dirname(infile)
script = scriptpath('sweep-reads.py')
args = ['-m', '75', '-k', '20', '-l', '1', '--prefix',
@@ -289,8 +268,7 @@ def test_saturate_by_median():
def test_count_kmers_1():
- infile = utils.get_temp_filename('input.fa')
- shutil.copyfile(utils.get_test_data('random-20-a.fa'), infile)
+ infile = utils.copy_test_data('random-20-a.fa')
ctfile = _make_counting(infile)
script = scriptpath('count-kmers.py')
@@ -304,8 +282,7 @@ def test_count_kmers_1():
def test_count_kmers_2_single():
- infile = utils.get_temp_filename('input.fa')
- shutil.copyfile(utils.get_test_data('random-20-a.fa'), infile)
+ infile = utils.copy_test_data('random-20-a.fa')
script = scriptpath('count-kmers-single.py')
args = ['-x', '1e7', '-k', '20', '-N', '2', infile]
@@ -318,12 +295,23 @@ def test_count_kmers_2_single():
def test_multirename_fasta():
- infile1 = utils.get_temp_filename('test-multi.fa')
+ infile1 = utils.copy_test_data('test-multi.fa')
multioutfile = utils.get_temp_filename('out.fa')
- infile2 = utils.get_temp_filename('out.fa')
- shutil.copyfile(utils.get_test_data('test-multi.fa'), infile1)
- shutil.copyfile(utils.get_test_data('multi-output.fa'), infile2)
+ infile2 = utils.copy_test_data('multi-output.fa')
args = ['assembly', infile1]
_, out, err = utils.runscript('multi-rename.py', args, sandbox=True)
r = open(infile2).read()
assert r in out
+
+
+def test_extract_compact_dbg_1():
+ infile = utils.get_test_data('simple-genome.fa')
+ outfile = utils.get_temp_filename('out.gml')
+ args = ['-x', '1e4', '-o', outfile, infile]
+ _, out, err = utils.runscript('extract-compact-dbg.py', args, sandbox=True)
+
+ print(out)
+ print(err)
+ assert os.path.exists(outfile)
+
+ assert '174 segments, containing 2803 nodes' in out
diff --git a/tests/test_script_arguments.py b/tests/test_script_arguments.py
index ee10672..991f309 100644
--- a/tests/test_script_arguments.py
+++ b/tests/test_script_arguments.py
@@ -1,6 +1,6 @@
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2014-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -32,6 +32,7 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
+# pylint: disable=missing-docstring,invalid-name,no-member
"""
Tests for various argument-handling code.
"""
@@ -42,8 +43,8 @@ import sys
import io
import collections
from . import khmer_tst_utils as utils
+import pytest
-import argparse
import khmer.kfile
from khmer import khmer_args
try:
@@ -51,12 +52,10 @@ try:
except ImportError:
from io import StringIO
-import sys
-
# For map(long, [list of ints]) cross-version hackery
if sys.version_info.major > 2:
- long = int
+ long = int # pylint: disable=redefined-builtin
def test_check_space():
@@ -73,22 +72,54 @@ def test_check_space():
sys.stderr = save_stderr
-def test_check_tablespace():
- outfile = utils.get_test_data('truncated.fq')
- save_stderr, sys.stderr = sys.stderr, io.StringIO()
+ at pytest.mark.parametrize('graph_type,buckets_per_byte', [
+ ('countgraph', 1),
+ ('smallcountgraph', 2),
+ ('nodegraph', 8),
+])
+def test_check_tablespace(graph_type, buckets_per_byte):
+ oldstderr = sys.stderr
+ sys.stderr = StringIO()
+ outfile = utils.get_test_data('truncated.fq')
parser = khmer_args.build_counting_args()
- args = parser.parse_args(['-M', '1e9'])
-
- try:
- tablesize = khmer_args.calculate_graphsize(args, 'countgraph')
- khmer.kfile.check_space_for_graph(outfile, tablesize,
- False, _testhook_free_space=0)
- assert 0, "this should fail"
- except SystemExit as e:
- print(str(e))
- finally:
- sys.stderr = save_stderr
+ args = parser.parse_args(['-M', '16G'])
+
+ buckets_per_table = khmer_args.calculate_graphsize(args, graph_type)
+ total_buckets = buckets_per_table * args.n_tables
+ space_needed = total_buckets / buckets_per_byte
+
+ # First, try with insufficient space
+ with pytest.raises(SystemExit) as se:
+ khmer.kfile.check_space_for_graph(outfile, space_needed, force=False,
+ _testhook_free_space=10e9)
+ assert 'ERROR: Not enough free space' in str(se)
+
+ # Now, try with insufficient space, but in force mode
+ khmer.kfile.check_space_for_graph(outfile, space_needed, force=True,
+ _testhook_free_space=10e9)
+ assert 'WARNING: Not enough free space' in sys.stderr.getvalue()
+
+ # Finally, try with sufficient space
+ sys.stderr = StringIO()
+ khmer.kfile.check_space_for_graph(outfile, space_needed, force=False,
+ _testhook_free_space=20e9)
+ assert sys.stderr.getvalue() == ''
+ sys.stderr = oldstderr
+
+
+ at pytest.mark.parametrize('graph_type,exp_buckets', [
+ ('countgraph', '3.0 million buckets'),
+ ('smallcountgraph', '6.0 million buckets'),
+ ('nodegraph', '24.0 million buckets'),
+])
+def test_check_tablespace_nodegraph(graph_type, exp_buckets):
+ parser = khmer_args.build_counting_args()
+ args = parser.parse_args(['-M', '3G'])
+ buckets_per_table = khmer_args.calculate_graphsize(args, graph_type)
+ total_buckets = buckets_per_table * args.n_tables
+ sizestr = '{:.1f} million buckets'.format(float(total_buckets) / 1e9)
+ assert sizestr == exp_buckets
def test_check_space_force():
@@ -152,7 +183,9 @@ FakeArgparseObject = collections.namedtuple('FakeArgs',
['ksize', 'n_tables',
'max_tablesize',
'max_memory_usage',
- 'unique_kmers'])
+ 'unique_kmers',
+ 'small_count',
+ 'force'])
def test_create_countgraph_1():
@@ -161,7 +194,8 @@ def test_create_countgraph_1():
max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
max_mem = 1e7
- args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0)
+ args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0,
+ False, 0)
countgraph = khmer_args.create_countgraph(args)
expected_hashsz = utils.longify([2499997, 2499989, 2499983, 2499967])
@@ -177,7 +211,8 @@ def test_create_countgraph_2():
max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
max_mem = 1e7
- args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0)
+ args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0,
+ False, 0)
countgraph = khmer_args.create_countgraph(args, ksize=15)
assert countgraph.ksize() == 15
@@ -191,13 +226,14 @@ def test_create_countgraph_3():
max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
max_mem = 1e7
- args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0)
+ args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0,
+ False, 0)
old_stderr = sys.stderr
sys.stderr = capture = StringIO()
try:
- countgraph = khmer_args.create_countgraph(args, ksize=35)
+ khmer_args.create_countgraph(args, ksize=35)
assert 0, "should not reach this"
except SystemExit:
err = capture.getvalue()
@@ -206,13 +242,63 @@ def test_create_countgraph_3():
sys.stderr = old_stderr
+def test_create_countgraph_4():
+ # tests too-big n_tables WITHOUT force
+
+ ksize = khmer_args.DEFAULT_K
+ n_tables = 21 # some number larger than 20
+ max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
+ max_mem = 1e7
+
+ args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0,
+ False, 0)
+
+ old_stderr = sys.stderr
+ sys.stderr = capture = StringIO()
+
+ try:
+ khmer_args.create_countgraph(args, ksize=None)
+ assert 0, "should not reach this"
+ except SystemExit:
+ err = capture.getvalue()
+ assert 'khmer only supports number of tables <= 20.' in err, err
+ finally:
+ sys.stderr = old_stderr
+
+
+def test_create_countgraph_5():
+ # tests too-big n_tables WITH force
+
+ ksize = khmer_args.DEFAULT_K
+ n_tables = 21 # some number larger than 20
+ max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
+ max_mem = 1e7
+
+ args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0,
+ False, 1)
+
+ old_stderr = sys.stderr
+ sys.stderr = capture = StringIO()
+
+ try:
+ khmer_args.create_countgraph(args, ksize=None)
+ message = "Warning: Maximum recommended number of tables is 20, " + \
+ "discarded by force nonetheless!"
+ assert message in capture.getvalue()
+ except SystemExit as e:
+ print(str(e))
+ finally:
+ sys.stderr = old_stderr
+
+
def test_create_countgraph_4_multiplier():
ksize = khmer_args.DEFAULT_K
n_tables = khmer_args.DEFAULT_N_TABLES
max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
max_mem = 1e7
- args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0)
+ args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0,
+ False, 0)
countgraph = khmer_args.create_countgraph(args, multiplier=2.0)
assert sum(countgraph.hashsizes()) < max_mem / 2.0, \
@@ -225,7 +311,8 @@ def test_create_nodegraph_1():
max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
max_mem = 1e7
- args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0)
+ args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0,
+ False, 0)
nodegraph = khmer_args.create_nodegraph(args)
expected_hashsz = utils.longify([19999999, 19999981, 19999963, 19999927])
@@ -243,7 +330,8 @@ def test_create_nodegraph_2():
max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
max_mem = 1e7
- args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0)
+ args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0,
+ False, 0)
nodegraph = khmer_args.create_nodegraph(args, ksize=15)
assert nodegraph.ksize() == 15
@@ -257,26 +345,70 @@ def test_create_nodegraph_3():
max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
max_mem = 1e7
- args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0)
+ args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0,
+ False, 0)
- old_stderr = sys.stderr
sys.stderr = capture = StringIO()
try:
- nodegraph = khmer_args.create_nodegraph(args, ksize=35)
+ khmer_args.create_nodegraph(args, ksize=35)
assert 0, "should not reach this"
except SystemExit:
err = capture.getvalue()
assert 'khmer only supports k-mer sizes <= 32.' in err, err
+def test_create_nodegraph_4():
+ # tests too-big number of tables WITHOUT force
+
+ ksize = khmer_args.DEFAULT_K
+ n_tables = 21 # some number larger than 20
+ max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
+ max_mem = 1e7
+
+ args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0,
+ False, 0)
+
+ sys.stderr = capture = StringIO()
+
+ try:
+ khmer_args.create_nodegraph(args, ksize=None)
+ assert 0, "should not reach this"
+ except SystemExit:
+ err = capture.getvalue()
+ assert 'khmer only supports number of tables <= 20.' in err, err
+
+
+def test_create_nodegraph_5():
+ # tests too-big number of tables WITH force
+
+ ksize = khmer_args.DEFAULT_K
+ n_tables = 21 # some number larger than 20
+ max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
+ max_mem = 1e7
+
+ args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0,
+ False, 1)
+
+ sys.stderr = capture = StringIO()
+
+ try:
+ khmer_args.create_nodegraph(args, ksize=None)
+ message = "Warning: Maximum recommended number of tables is 20, " + \
+ "discarded by force nonetheless!"
+ assert message in capture.getvalue()
+ except SystemExit as e:
+ print(str(e))
+
+
def test_create_nodegraph_4_multiplier():
ksize = khmer_args.DEFAULT_K
n_tables = khmer_args.DEFAULT_N_TABLES
max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
max_mem = 1e7
- args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0)
+ args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0,
+ False, 0)
nodegraph = khmer_args.create_nodegraph(args, multiplier=2.0)
assert sum(nodegraph.hashsizes()) / 8.0 < max_mem / 2.0, \
@@ -289,7 +421,8 @@ def test_report_on_config_bad_graphtype():
max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
max_mem = 1e7
- args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0)
+ args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0,
+ False, 0)
try:
khmer_args.report_on_config(args, 'foograph')
@@ -306,10 +439,44 @@ def test_fail_calculate_foograph_size():
max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
max_mem = 1e7
- args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0)
+ args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0,
+ False, 0)
try:
- nodegraph = khmer_args.calculate_graphsize(args, 'foograph')
+ khmer_args.calculate_graphsize(args, 'foograph')
assert 0, "previous statement should fail"
except ValueError as err:
assert "unknown graph type: foograph" in str(err), str(err)
+
+
+def test_memory_setting():
+ assert khmer_args.memory_setting('1') == 1.0
+ assert khmer_args.memory_setting('42') == 42.0
+ assert khmer_args.memory_setting('10000') == 1e4
+ assert khmer_args.memory_setting('2.3e5') == 230000.0
+ assert khmer_args.memory_setting('1e9') == 1e9
+ assert khmer_args.memory_setting('1K') == 1e3
+ assert khmer_args.memory_setting('3.14m') == 3.14e6
+ assert khmer_args.memory_setting('8G') == 8e9
+ assert khmer_args.memory_setting('8g') == 8e9
+ assert khmer_args.memory_setting('16T') == 16e12
+ try:
+ _ = khmer_args.memory_setting('16Tb')
+ assert False, 'previous command should have failed'
+ except ValueError as err:
+ assert 'cannot parse memory setting' in str(err)
+ try:
+ _ = khmer_args.memory_setting('16E')
+ assert False, 'previous command should have failed'
+ except ValueError as err:
+ assert 'cannot parse memory setting' in str(err)
+ try:
+ _ = khmer_args.memory_setting('16Ki')
+ assert False, 'previous command should have failed'
+ except ValueError as err:
+ assert 'cannot parse memory setting' in str(err)
+ try:
+ _ = khmer_args.memory_setting('b0gu$G')
+ assert False, 'previous command should have failed'
+ except ValueError as err:
+ assert 'cannot parse memory setting' in str(err)
diff --git a/tests/test_script_output.py b/tests/test_script_output.py
new file mode 100644
index 0000000..f1caf3d
--- /dev/null
+++ b/tests/test_script_output.py
@@ -0,0 +1,184 @@
+# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# Copyright (C) 2010-2015, Michigan State University.
+# Copyright (C) 2015, The Regents of the University of California.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+#
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# * Redistributions in binary form must reproduce the above
+# copyright notice, this list of conditions and the following
+# disclaimer in the documentation and/or other materials provided
+# with the distribution.
+#
+# * Neither the name of the Michigan State University nor the names
+# of its contributors may be used to endorse or promote products
+# derived from this software without specific prior written
+# permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Contact: khmer-project at idyll.org
+# pylint: disable=C0111,C0103
+"""
+Test code that verifies current script output md5 hashes against recorded
+hashes, to ensure that script function isn't changing.
+"""
+from __future__ import print_function
+from __future__ import absolute_import
+
+import khmer
+from . import khmer_tst_utils as utils
+
+#
+# hashes recorded as of git commit 799039ffcf15d2a3ac6902ae62ae2da81030e8d2
+# (for trim-low-abund without --diginorm behavior) and
+# b939a34b565ce973224abdd0eeb53d6b52833c01 (for trim-low-abund updates).
+#
+
+
+def test_normalize_by_median_k21_C20_M1e7():
+ infile = utils.get_test_data('simple-genome-reads.fa')
+ outfile = utils.get_temp_filename('out')
+ utils.runscript('normalize-by-median.py', ['-C', '20', '-k', '21',
+ '-M', '1e7', '-o', outfile,
+ infile])
+
+ hash = utils._calc_md5(open(outfile, 'rb'))
+ assert hash == '942e9024c25a8d85033d755d86aba4a3', hash
+
+
+def test_normalize_by_median_k21_C15_M1e7():
+ infile = utils.get_test_data('simple-genome-reads.fa')
+ outfile = utils.get_temp_filename('out')
+ utils.runscript('normalize-by-median.py', ['-C', '15', '-k', '21',
+ '-M', '1e7', '-o', outfile,
+ infile])
+
+ hash = utils._calc_md5(open(outfile, 'rb'))
+ assert hash == '0d1b4b9d4c76cb8cdeee5a98f6e70163', hash
+
+
+def test_trim_low_abund_k21_C0_M1e7_diginorm():
+ # should be same as normalize-by-median -C 20 -k 21 -M 1e7
+ infile = utils.get_test_data('simple-genome-reads.fa')
+ outfile = utils.get_temp_filename('out')
+ utils.runscript('trim-low-abund.py', ['-C', '0', '-k', '21',
+ '--diginorm',
+ '--diginorm-coverage', '20',
+ '-M', '1e7', '-o', outfile,
+ infile])
+
+ hash = utils._calc_md5(open(outfile, 'rb'))
+ assert hash == '942e9024c25a8d85033d755d86aba4a3', hash
+
+
+def test_trim_low_abund_k21_C0_M1e7_diginorm_dn15():
+ # should be same as normalize-by-median -C 15 -k 21 -M 1e7
+ infile = utils.get_test_data('simple-genome-reads.fa')
+ outfile = utils.get_temp_filename('out')
+ utils.runscript('trim-low-abund.py', ['-C', '0', '-k', '21',
+ '--diginorm',
+ '--diginorm-coverage', '15',
+ '-M', '1e7', '-o', outfile,
+ infile])
+
+ hash = utils._calc_md5(open(outfile, 'rb'))
+ assert hash == '0d1b4b9d4c76cb8cdeee5a98f6e70163', hash
+
+
+def test_trim_low_abund_k21_C2_M1e7_diginorm_dn15():
+ # should be same as normalize-by-median -C 15 -k 21 -M 1e7
+ infile = utils.get_test_data('simple-genome-reads.fa')
+ outfile = utils.get_temp_filename('out')
+ utils.runscript('trim-low-abund.py', ['-C', '2', '-k', '21',
+ '--diginorm',
+ '--diginorm-coverage', '15',
+ '-M', '1e7', '-o', outfile,
+ infile])
+
+ hash = utils._calc_md5(open(outfile, 'rb'))
+ assert hash == 'fa09d094a9e623639a34f772b04d766c', hash
+
+
+def test_trim_low_abund_k21_M1e7_C2():
+ infile = utils.get_test_data('simple-genome-reads.fa')
+ outfile = utils.get_temp_filename('out')
+ utils.runscript('trim-low-abund.py', ['-C', '2', '-k', '21',
+ '-M', '1e7', '-o', outfile,
+ infile])
+
+ hash = utils._calc_md5(open(outfile, 'rb'))
+ assert hash == '9495801b282ff6b08961b685d12a954c', hash
+
+
+def test_trim_low_abund_k21_M1e7_C3():
+ infile = utils.get_test_data('simple-genome-reads.fa')
+ outfile = utils.get_temp_filename('out')
+ utils.runscript('trim-low-abund.py', ['-C', '3', '-k', '21',
+ '-M', '1e7', '-o', outfile,
+ infile])
+
+ hash = utils._calc_md5(open(outfile, 'rb'))
+ assert hash == 'da36ec64e7d001470c04dc19af5b8635', hash
+
+
+def test_trim_low_abund_k21_M1e7_C4():
+ infile = utils.get_test_data('simple-genome-reads.fa')
+ outfile = utils.get_temp_filename('out')
+ utils.runscript('trim-low-abund.py', ['-C', '4', '-k', '21',
+ '-M', '1e7', '-o', outfile,
+ infile])
+
+ hash = utils._calc_md5(open(outfile, 'rb'))
+ assert hash == '65596253b87ed8d5aeb14dc8cf5a7406', hash
+
+
+def test_trim_low_abund_k21_M1e7_C4_variable():
+ infile = utils.get_test_data('simple-genome-reads.fa')
+ outfile = utils.get_temp_filename('out')
+ utils.runscript('trim-low-abund.py', ['-C', '4', '-k', '21',
+ '-V',
+ '-M', '1e7', '-o', outfile,
+ infile])
+
+ hash = utils._calc_md5(open(outfile, 'rb'))
+ assert hash == '324871db807839f8bddd43548abcbeda', hash
+
+
+def test_trim_low_abund_k21_M1e7_C4_variable_Z25():
+ infile = utils.get_test_data('simple-genome-reads.fa')
+ outfile = utils.get_temp_filename('out')
+ utils.runscript('trim-low-abund.py', ['-C', '4', '-k', '21',
+ '-V', '-Z', '25',
+ '-M', '1e7', '-o', outfile,
+ infile])
+
+ hash = utils._calc_md5(open(outfile, 'rb'))
+ assert hash == '6ec4f9874262f3eaf98cab4910c428f5', hash
+
+
+def test_trim_low_abund_k21_M1e7_C4_variable_Z15():
+ infile = utils.get_test_data('simple-genome-reads.fa')
+ outfile = utils.get_temp_filename('out')
+ utils.runscript('trim-low-abund.py', ['-C', '4', '-k', '21',
+ '-V', '-Z', '15',
+ '-M', '1e7', '-o', outfile,
+ infile])
+
+ with open(outfile, 'rb') as output:
+ hashval = utils._calc_md5(output)
+ assert hashval == '393805ac92e8bed31a374de9ee89ead8', hash
diff --git a/tests/test_scripts.py b/tests/test_scripts.py
index 7df2153..431b0c9 100644
--- a/tests/test_scripts.py
+++ b/tests/test_scripts.py
@@ -1,6 +1,6 @@
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2014-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -32,25 +32,23 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
-# pylint: disable=C0111,C0103,E1103,W0612
+# pylint: disable=C0111,C0103,E1103,unused-variable,protected-access
from __future__ import print_function
from __future__ import absolute_import
from __future__ import unicode_literals
+
import json
import sys
import os
-import stat
import shutil
-from io import StringIO
-import traceback
-from nose.plugins.attrib import attr
+import stat
import threading
-import bz2
import gzip
import io
import re
+import pytest
from . import khmer_tst_utils as utils
import khmer
import khmer.kfile
@@ -82,6 +80,21 @@ def test_load_into_counting():
assert os.path.exists(outfile)
+def test_load_into_counting_quiet():
+ script = 'load-into-counting.py'
+ args = ['-q', '-x', '1e3', '-N', '2', '-k', '20']
+
+ outfile = utils.get_temp_filename('out.ct')
+ infile = utils.get_test_data('test-abund-read-2.fa')
+
+ args.extend([outfile, infile])
+
+ (status, out, err) = utils.runscript(script, args)
+ assert len(out) == 0
+ assert len(err) == 0
+ assert os.path.exists(outfile)
+
+
def test_load_into_counting_autoargs_0():
script = 'load-into-counting.py'
@@ -202,6 +215,8 @@ def test_load_into_counting_abundance_dist_squashing():
assert lines[2].strip() == "1,83,83,1.0", lines[2]
+# note: if run as root, will fail b/c root can write to anything
+ at pytest.mark.noroot
def test_load_into_counting_nonwritable():
script = 'load-into-counting.py'
args = ['-x', '1e3', '-N', '2', '-k', '20']
@@ -220,7 +235,7 @@ def test_load_into_counting_nonwritable():
assert status == 1, status
- at attr('huge')
+ at pytest.mark.huge
def test_load_into_counting_toobig():
script = 'load-into-counting.py'
args = ['-x', '1e12', '-N', '2', '-k', '20', '--force']
@@ -333,6 +348,29 @@ def test_load_into_counting_bad_summary_fmt():
assert "invalid choice: 'badfmt'" in err, err
+def test_load_into_counting_info_version():
+ script = 'load-into-counting.py'
+ args = ['-x', '1e5', '-N', '2', '-k', '20'] # use small HT
+
+ outfile = utils.get_temp_filename('out')
+ infile = utils.get_test_data('random-20-a.fa')
+
+ args.extend([outfile, infile])
+
+ (status, out, err) = utils.runscript(script, args)
+
+ ht_file = outfile
+ assert os.path.exists(ht_file), ht_file
+
+ info_file = outfile + '.info'
+ assert os.path.exists(info_file), info_file
+ with open(info_file) as info_fp:
+ versionline = info_fp.readline()
+ version = versionline.split(':')[1].strip()
+ assert versionline.startswith('khmer version:'), versionline
+ assert version == khmer.__version__, version
+
+
def _make_counting(infilename, SIZE=1e7, N=2, K=20, BIGCOUNT=True):
script = 'load-into-counting.py'
args = ['-x', str(SIZE), '-N', str(N), '-k', str(K)]
@@ -350,330 +388,12 @@ def _make_counting(infilename, SIZE=1e7, N=2, K=20, BIGCOUNT=True):
return outfile
-def test_filter_abund_1():
- script = 'filter-abund.py'
-
- infile = utils.get_temp_filename('test.fa')
- n_infile = utils.get_temp_filename('test-fastq-n-reads.fq')
-
- in_dir = os.path.dirname(infile)
- n_in_dir = os.path.dirname(n_infile)
-
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
- shutil.copyfile(utils.get_test_data('test-fastq-n-reads.fq'), n_infile)
-
- counting_ht = _make_counting(infile, K=17)
- n_counting_ht = _make_counting(n_infile, K=17)
-
- args = [counting_ht, infile]
- utils.runscript(script, args, in_dir)
-
- outfile = infile + '.abundfilt'
- n_outfile = n_infile + '.abundfilt'
- n_outfile2 = n_infile + '2.abundfilt'
-
- assert os.path.exists(outfile), outfile
-
- seqs = set([r.sequence for r in screed.open(outfile)])
-
- assert len(seqs) == 1, seqs
- assert 'GGTTGACGGGGCTCAGGG' in seqs
-
- args = [n_counting_ht, n_infile]
- utils.runscript(script, args, n_in_dir)
-
- seqs = set([r.sequence for r in screed.open(n_infile)])
- assert os.path.exists(n_outfile), n_outfile
-
- args = [n_counting_ht, n_infile, '-o', n_outfile2]
- utils.runscript(script, args, in_dir)
- assert os.path.exists(n_outfile2), n_outfile2
-
-
-def test_filter_abund_2():
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
- counting_ht = _make_counting(infile, K=17)
-
- script = 'filter-abund.py'
- args = ['-C', '1', counting_ht, infile, infile]
- utils.runscript(script, args, in_dir)
-
- outfile = infile + '.abundfilt'
- assert os.path.exists(outfile), outfile
-
- seqs = set([r.sequence for r in screed.open(outfile)])
- assert len(seqs) == 2, seqs
- assert 'GGTTGACGGGGCTCAGGG' in seqs
-
-
-def test_filter_abund_2_stdin():
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
- counting_ht = _make_counting(infile, K=17)
-
- script = 'filter-abund.py'
- args = ['-C', '1', counting_ht, '-']
- (status, out, err) = utils.runscript(script, args, in_dir, fail_ok=True)
- assert status == 1
- assert "Accepting input from stdin; output filename must be provided" \
- in str(err)
-
-# make sure that FASTQ records are retained.
-
-
-def test_filter_abund_3_fq_retained():
- infile = utils.get_temp_filename('test.fq')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fq'), infile)
- counting_ht = _make_counting(infile, K=17)
-
- script = 'filter-abund.py'
- args = ['-C', '1', counting_ht, infile, infile]
- utils.runscript(script, args, in_dir)
-
- outfile = infile + '.abundfilt'
- assert os.path.exists(outfile), outfile
-
- seqs = set([r.sequence for r in screed.open(outfile)])
- assert len(seqs) == 2, seqs
- assert 'GGTTGACGGGGCTCAGGG' in seqs
-
- # check for 'quality' string.
- quals = set([r.quality for r in screed.open(outfile)])
- assert len(quals) == 2, quals
- assert '##################' in quals
-
-
-# make sure that FASTQ names are properly parsed, both formats.
-
-
-def test_filter_abund_4_fq_casava_18():
- infile = utils.get_temp_filename('test.fq')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('test-abund-read-2.paired2.fq'),
- infile)
- counting_ht = _make_counting(infile, K=17)
-
- script = 'filter-abund.py'
- args = [counting_ht, infile, infile]
- utils.runscript(script, args, in_dir)
-
- outfile = infile + '.abundfilt'
- assert os.path.exists(outfile), outfile
-
- seqs = set([r.name for r in screed.open(outfile)])
- assert 'pair:foo 1::N' in seqs, seqs
-
-
-def test_filter_abund_1_singlefile():
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
-
- script = 'filter-abund-single.py'
- args = ['-x', '1e7', '-N', '2', '-k', '17', infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
-
- assert 'Total number of unique k-mers: 98' in err, err
-
- outfile = infile + '.abundfilt'
- assert os.path.exists(outfile), outfile
-
- seqs = set([r.sequence for r in screed.open(outfile)])
- assert len(seqs) == 1, seqs
- assert 'GGTTGACGGGGCTCAGGG' in seqs
-
-
-def test_filter_abund_2_singlefile():
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
- tabfile = utils.get_temp_filename('test-savegraph.ct')
-
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
-
- script = 'filter-abund-single.py'
- args = ['-x', '1e7', '-N', '2', '-k', '17', '--savegraph',
- tabfile, infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
-
- assert 'Total number of unique k-mers: 98' in err, err
-
- outfile = infile + '.abundfilt'
- assert os.path.exists(outfile), outfile
-
- seqs = set([r.sequence for r in screed.open(outfile)])
- assert len(seqs) == 1, seqs
- assert 'GGTTGACGGGGCTCAGGG' in seqs
-
-
-def test_filter_abund_2_singlefile_fq_casava_18():
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('test-abund-read-2.paired2.fq'),
- infile)
-
- script = 'filter-abund-single.py'
- args = ['-x', '1e7', '-N', '2', '-k', '17', infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
-
- outfile = infile + '.abundfilt'
- assert os.path.exists(outfile), outfile
-
- seqs = set([r.name for r in screed.open(outfile)])
- assert 'pair:foo 1::N' in seqs, seqs
-
-
-def test_filter_abund_4_retain_low_abund():
- # test that the -V option does not trim sequences that are low abundance
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
- counting_ht = _make_counting(infile, K=17)
-
- script = 'filter-abund.py'
- args = ['-V', counting_ht, infile]
- utils.runscript(script, args, in_dir)
-
- outfile = infile + '.abundfilt'
- assert os.path.exists(outfile), outfile
-
- seqs = set([r.sequence for r in screed.open(outfile)])
- assert len(seqs) == 2, seqs
- assert 'GGTTGACGGGGCTCAGGG' in seqs
-
-
-def test_filter_abund_5_trim_high_abund():
- # test that the -V option *does* trim sequences that are high abundance
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('test-abund-read-3.fa'), infile)
- counting_ht = _make_counting(infile, K=17)
-
- script = 'filter-abund.py'
- args = ['-V', counting_ht, infile]
- utils.runscript(script, args, in_dir)
-
- outfile = infile + '.abundfilt'
- assert os.path.exists(outfile), outfile
-
- seqs = set([r.sequence for r in screed.open(outfile)])
- assert len(seqs) == 2, seqs
-
- # trimmed sequence @ error
- assert 'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGC' in seqs
-
-
-def test_filter_abund_6_trim_high_abund_Z():
- # test that -V/-Z settings interact properly -
- # trimming should not happen if -Z is set high enough.
-
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('test-abund-read-3.fa'), infile)
- counting_ht = _make_counting(infile, K=17)
-
- script = 'filter-abund.py'
- args = ['-V', '-Z', '25', counting_ht, infile]
- utils.runscript(script, args, in_dir)
-
- outfile = infile + '.abundfilt'
- assert os.path.exists(outfile), outfile
-
- seqs = set([r.sequence for r in screed.open(outfile)])
- assert len(seqs) == 2, seqs
-
- # untrimmed seq.
- badseq = 'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCgtgCCGCAGCTGTCGTCAGGG' \
- 'GATTTCCGGGCGG'
- assert badseq in seqs # should be there, untrimmed
-
-
-def test_filter_abund_7_retain_Ns():
- # check that filter-abund retains sequences with Ns, and treats them as As.
-
- infile = utils.get_temp_filename('test.fq')
- in_dir = os.path.dirname(infile)
-
- # copy test file over to test.fq & load into countgraph
- shutil.copyfile(utils.get_test_data('test-filter-abund-Ns.fq'), infile)
- counting_ht = _make_counting(infile, K=17)
-
- script = 'filter-abund.py'
- args = ['-C', '3', counting_ht, infile]
- utils.runscript(script, args, in_dir)
-
- outfile = infile + '.abundfilt'
- assert os.path.exists(outfile), outfile
-
- # test for a sequence with an 'N' in it --
- names = set([r.name for r in screed.open(outfile)])
- assert '895:1:37:17593:9954 1::FOO_withN' in names, names
-
- # check to see if that 'N' was properly changed to an 'A'
- seqs = set([r.sequence for r in screed.open(outfile)])
- assert 'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAG' not in seqs, seqs
-
- # ...and that an 'N' remains in the output sequences
- found_N = False
- for s in seqs:
- if 'N' in s:
- found_N = True
- assert found_N, seqs
-
-
-def test_filter_abund_single_8_retain_Ns():
- # check that filter-abund-single retains
- # sequences with Ns, and treats them as As.
-
- infile = utils.get_temp_filename('test.fq')
- in_dir = os.path.dirname(infile)
-
- # copy test file over to test.fq & load into countgraph
- shutil.copyfile(utils.get_test_data('test-filter-abund-Ns.fq'), infile)
-
- script = 'filter-abund-single.py'
- args = ['-k', '17', '-x', '1e7', '-N', '2', '-C', '3', infile]
- utils.runscript(script, args, in_dir)
-
- outfile = infile + '.abundfilt'
- assert os.path.exists(outfile), outfile
-
- # test for a sequence with an 'N' in it --
- names = set([r.name for r in screed.open(outfile)])
- assert '895:1:37:17593:9954 1::FOO_withN' in names, names
-
- # check to see if that 'N' was properly changed to an 'A'
- seqs = set([r.sequence for r in screed.open(outfile)])
- assert 'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAG' not in seqs, seqs
-
- # ...and that an 'N' remains in the output sequences
- found_N = False
- for s in seqs:
- if 'N' in s:
- found_N = True
- assert found_N, seqs
-
-
def test_filter_stoptags():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-2.fa')
in_dir = os.path.dirname(infile)
stopfile = utils.get_temp_filename('stoptags', in_dir)
# first, copy test-abund-read-2.fa to 'test.fa' in the temp dir.
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
-
# now, create a file with some stop tags in it --
K = 18
kh = khmer._Nodegraph(K, [1])
@@ -698,12 +418,11 @@ def test_filter_stoptags():
def test_filter_stoptags_fq():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-2.fq')
in_dir = os.path.dirname(infile)
stopfile = utils.get_temp_filename('stoptags', in_dir)
# first, copy test-abund-read-2.fa to 'test.fa' in the temp dir.
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fq'), infile)
# now, create a file with some stop tags in it --
K = 18
@@ -734,10 +453,9 @@ def test_filter_stoptags_fq():
def test_count_median():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-2.fa')
outfile = infile + '.counts'
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
counting_ht = _make_counting(infile, K=8)
script = 'count-median.py'
@@ -754,10 +472,9 @@ def test_count_median():
def test_count_median_fq_csv():
- infile = utils.get_temp_filename('test.fq')
+ infile = utils.copy_test_data('test-abund-read-2.fq')
outfile = infile + '.counts'
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fq'), infile)
counting_ht = _make_counting(infile, K=8)
script = 'count-median.py'
@@ -778,10 +495,9 @@ def test_count_median_fq_csv():
def test_count_median_fq_csv_stdout():
- infile = utils.get_temp_filename('test.fq')
+ infile = utils.copy_test_data('test-abund-read-2.fq')
outfile = '-'
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fq'), infile)
counting_ht = _make_counting(infile, K=8)
script = 'count-median.py'
@@ -825,7 +541,7 @@ def test_load_graph():
assert x == (1, 0), x
- at attr('known_failing')
+ at pytest.mark.known_failing
def test_oxli_build_graph():
script = 'oxli'
args = ['build-graph', '-x', '1e7', '-N', '2', '-k', '20']
@@ -856,7 +572,7 @@ def test_oxli_build_graph():
assert x == (1, 0), x
- at attr('known_failing')
+ at pytest.mark.known_failing
def test_oxli_build_graph_unique_kmers_arg():
script = 'oxli'
args = ['build-graph', '-x', '1e7', '-N', '2', '-k', '20', '-U', '3960']
@@ -889,7 +605,7 @@ def test_oxli_build_graph_unique_kmers_arg():
assert x == (1, 0), x
- at attr('known_failing')
+ at pytest.mark.known_failing
def test_oxli_nocommand():
script = 'oxli'
@@ -920,7 +636,7 @@ def test_load_graph_no_tags():
# loading the ht file...
- at attr('known_failing')
+ at pytest.mark.known_failing
def test_oxli_build_graph_no_tags():
script = 'oxli'
args = ['build-graph', '-x', '1e7', '-N', '2', '-k', '20', '-n']
@@ -958,7 +674,7 @@ def test_load_graph_fail():
assert "** ERROR: the graph structure is too small" in err
- at attr('known_failing')
+ at pytest.mark.known_failing
def test_oxli_build_graph_fail():
script = 'oxli'
args = ['build-graph', '-x', '1e3', '-N', '2', '-k', '20'] # use small HT
@@ -973,6 +689,21 @@ def test_oxli_build_graph_fail():
assert "** ERROR: the graph structure is too small" in err
+ at pytest.mark.known_failing
+def test_oxli_build_graph_yuge():
+ script = 'oxli'
+ args = ['build-graph', '-M', '800T', '-k', '20']
+
+ outfile = utils.get_temp_filename('out')
+ infile = utils.get_test_data('random-20-a.fa')
+
+ args.extend([outfile, infile])
+
+ (status, out, err) = utils.runscript(script, args, fail_ok=True)
+ assert status != 0, status
+ assert 'ERROR: Not enough free space on disk' in err
+
+
def test_load_graph_write_fp():
script = 'load-graph.py'
args = ['-x', '1e5', '-N', '2', '-k', '20'] # use small HT
@@ -995,7 +726,7 @@ def test_load_graph_write_fp():
assert 'false positive rate estimated to be 0.002' in data
- at attr('known_failing')
+ at pytest.mark.known_failing
def test_oxli_build_graph_write_fp():
script = 'oxli'
# use small HT
@@ -1030,7 +761,7 @@ def test_load_graph_multithread():
(status, out, err) = utils.runscript(script, args)
- at attr('known_failing')
+ at pytest.mark.known_failing
def test_oxli_build_graph_multithread():
script = 'oxli'
@@ -1154,6 +885,21 @@ def test_partition_graph_nojoin_k21():
assert x == (99, 0), x # should be 99 partitions at K=21
+def test_partition_load_empty_pmap():
+ graphbase = _make_graph(utils.get_test_data('random-20-a.fa'), ksize=24)
+
+ script = 'partition-graph.py'
+ args = [graphbase, '-s', '10']
+
+ utils.runscript(script, args)
+
+ script = 'merge-partitions.py'
+ args = [graphbase, '-k', '24']
+ status, out, err = utils.runscript(script, args, fail_ok=True)
+ assert status == -1
+ assert 'only a header and no partition IDs' in err
+
+
def test_partition_graph_nojoin_stoptags():
# test with stoptags
graphbase = _make_graph(utils.get_test_data('random-20-a.fa'))
@@ -1344,6 +1090,34 @@ def test_extract_partitions():
assert len(parts) == 1, len(parts)
+def test_extract_paired_inconsistent_formats():
+ fa_seqfile = utils.get_test_data('random-20-a.fa')
+ fq_seqfile = utils.get_test_data('random-20-a.fq')
+ graphbase = _make_graph(
+ fa_seqfile, do_partition=True, annotate_partitions=True)
+ fa_in_dir = os.path.dirname(graphbase)
+ graphbase = _make_graph(
+ fq_seqfile, do_partition=True, annotate_partitions=True)
+ fq_in_dir = os.path.dirname(graphbase)
+ # XXX
+ # get the final part file
+ fa_partfile = os.path.join(fa_in_dir, 'random-20-a.fa.part')
+ fq_partfile = os.path.join(fq_in_dir, 'random-20-a.fq.part')
+
+ # ok, now run extract-partitions.
+ script = 'extract-partitions.py'
+ args = ['extracted', fa_partfile, fq_partfile]
+
+ failed = True
+ try:
+ utils.runscript(script, args, fa_in_dir)
+ failed = False
+ except AssertionError as err:
+ assert "Input files must have consistent format." in str(err), err
+
+ assert failed, "Expected to fail"
+
+
def test_extract_partitions_header_whitespace():
seqfile = utils.get_test_data('test-overlap2.fa')
graphbase = _make_graph(
@@ -1468,9 +1242,7 @@ def test_extract_partitions_no_output_groups():
def test_extract_partitions_pid_0():
- basefile = utils.get_test_data('random-20-a.fa.part')
- partfile = utils.get_temp_filename('random-20-a.fa.part')
- shutil.copyfile(basefile, partfile)
+ partfile = utils.copy_test_data('random-20-a.fa.part')
in_dir = os.path.dirname(partfile)
# ok, now run extract-partitions.
@@ -1492,9 +1264,7 @@ def test_extract_partitions_pid_0():
def test_extract_partitions_multi_groups():
- basefile = utils.get_test_data('random-20-a.fa.part')
- partfile = utils.get_temp_filename('random-20-a.fa.part')
- shutil.copyfile(basefile, partfile)
+ partfile = utils.copy_test_data('random-20-a.fa.part')
in_dir = os.path.dirname(partfile)
@@ -1514,10 +1284,7 @@ def test_extract_partitions_multi_groups():
def test_extract_partitions_no_groups():
- empty_file = utils.get_temp_filename('empty-file')
- basefile = utils.get_test_data('empty-file')
-
- shutil.copyfile(basefile, empty_file)
+ empty_file = utils.copy_test_data('empty-file')
in_dir = os.path.dirname(empty_file)
# ok, now run extract-partitions.
@@ -1534,12 +1301,10 @@ def test_extract_partitions_no_groups():
def test_abundance_dist():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-2.fa')
outfile = utils.get_temp_filename('test.dist')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
-
htfile = _make_counting(infile, K=17)
script = 'abundance-dist.py'
@@ -1555,28 +1320,46 @@ def test_abundance_dist():
assert line == '1001,2,98,1.0', line
-def test_abundance_dist_stdout():
- infile = utils.get_temp_filename('test.fa')
+def test_abundance_dist_quiet():
+ infile = utils.copy_test_data('test-abund-read-2.fa')
+ outfile = utils.get_temp_filename('test.dist')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
-
htfile = _make_counting(infile, K=17)
script = 'abundance-dist.py'
- args = ['-z', htfile, infile, "-"]
- (status, out, err) = utils.runscript(script, args, in_dir)
-
- assert '1,96,96,0.98' in out, out
- assert '1001,2,98,1.0' in out, out
+ args = ['-z', '-q', htfile, infile, outfile]
+ status, out, err = utils.runscript(script, args, in_dir)
+ assert len(err) == 0
-def test_abundance_dist_nobigcount():
- infile = utils.get_temp_filename('test.fa')
- outfile = utils.get_temp_filename('test.dist')
+ with open(outfile) as fp:
+ line = fp.readline().strip()
+ assert (line == 'abundance,count,cumulative,cumulative_fraction'), line
+ line = fp.readline().strip()
+ assert line == '1,96,96,0.98', line
+ line = fp.readline().strip()
+ assert line == '1001,2,98,1.0', line
+
+
+def test_abundance_dist_stdout():
+ infile = utils.copy_test_data('test-abund-read-2.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
+ htfile = _make_counting(infile, K=17)
+
+ script = 'abundance-dist.py'
+ args = ['-z', htfile, infile, "-"]
+ (status, out, err) = utils.runscript(script, args, in_dir)
+
+ assert '1,96,96,0.98' in out, out
+ assert '1001,2,98,1.0' in out, out
+
+
+def test_abundance_dist_nobigcount():
+ infile = utils.copy_test_data('test-abund-read-2.fa')
+ outfile = utils.get_temp_filename('test.dist')
+ in_dir = os.path.dirname(infile)
htfile = _make_counting(infile, K=17)
@@ -1593,12 +1376,10 @@ def test_abundance_dist_nobigcount():
def test_abundance_dist_threaded():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-2.fa')
outfile = utils.get_temp_filename('test.dist')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
-
script = 'abundance-dist-single.py'
args = ['-x', '1e7', '-N', '2', '-k', '17', '-z', '--threads', '18',
infile, outfile]
@@ -1615,12 +1396,10 @@ def test_abundance_dist_threaded():
def test_abundance_dist_single_csv():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-2.fa')
outfile = utils.get_temp_filename('test.dist')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
-
script = 'abundance-dist-single.py'
args = ['-x', '1e7', '-N', '2', '-k', '17', '-z', infile,
outfile]
@@ -1636,12 +1415,10 @@ def test_abundance_dist_single_csv():
def test_abundance_dist_single_nobigcount():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-2.fa')
outfile = utils.get_temp_filename('test.dist')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
-
script = 'abundance-dist-single.py'
args = ['-x', '1e7', '-N', '2', '-k', '17', '-z', '-b', infile, outfile]
utils.runscript(script, args, in_dir)
@@ -1655,12 +1432,10 @@ def test_abundance_dist_single_nobigcount():
def test_abundance_dist_single_nosquash():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-2.fa')
outfile = utils.get_temp_filename('test-abund-read-2.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
-
script = 'abundance-dist-single.py'
args = ['-x', '1e7', '-N', '2', '-k', '17', '-z', infile, outfile]
utils.runscript(script, args, in_dir)
@@ -1673,14 +1448,31 @@ def test_abundance_dist_single_nosquash():
assert line == '1001,2,98,1.0', line
+def test_abundance_dist_single_quiet():
+ infile = utils.copy_test_data('test-abund-read-2.fa')
+ outfile = utils.get_temp_filename('test-abund-read-2.fa')
+ in_dir = os.path.dirname(infile)
+
+ script = 'abundance-dist-single.py'
+ args = ['-q', '-x', '1e7', '-N', '2', '-k', '17', '-z', infile, outfile]
+ status, out, err = utils.runscript(script, args, in_dir)
+
+ assert len(err) == 0
+
+ with open(outfile) as fp:
+ line = fp.readline().strip() # skip header
+ line = fp.readline().strip()
+ assert line == '1,96,96,0.98', line
+ line = fp.readline().strip()
+ assert line == '1001,2,98,1.0', line
+
+
def test_abundance_dist_single_savegraph():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-2.fa')
outfile = utils.get_temp_filename('test.dist')
tabfile = utils.get_temp_filename('test-savegraph.ct')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
-
script = 'abundance-dist-single.py'
args = ['-x', '1e7', '-N', '2', '-k', '17', '-z', '--savegraph',
tabfile, infile, outfile]
@@ -1769,198 +1561,12 @@ def test_do_partition_2_fq():
assert '46 1::FIZ' in names
-def test_interleave_read_stdout():
- # create input files
- infile1 = utils.get_test_data('paired-slash1.fq.1')
- infile2 = utils.get_test_data('paired-slash1.fq.2')
-
- # correct output
- ex_outfile = utils.get_test_data('paired-slash1.fq')
-
- # actual output file
- outfile = utils.get_temp_filename('out.fq')
-
- script = 'interleave-reads.py'
- args = [infile1, infile2]
-
- (stats, out, err) = utils.runscript(script, args)
-
- with open(outfile, 'w') as ofile:
- ofile.write(out)
-
- n = 0
- for r, q in zip(screed.open(ex_outfile), screed.open(outfile)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert n > 0
-
-
-def test_interleave_read_seq1_fq():
- # create input files
- infile1 = utils.get_test_data('paired-slash1.fq.1')
- infile2 = utils.get_test_data('paired-slash1.fq.2')
-
- # correct output
- ex_outfile = utils.get_test_data('paired-slash1.fq')
-
- # actual output file
- outfile = utils.get_temp_filename('out.fq')
-
- script = 'interleave-reads.py'
- args = [infile1, infile2, '-o', outfile]
-
- utils.runscript(script, args)
-
- n = 0
- for r, q in zip(screed.open(ex_outfile), screed.open(outfile)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert n > 0
-
-
-def test_interleave_read_badleft_badright():
- # create input files
- infile1 = utils.get_test_data('paired-broken.fq.badleft')
- infile2 = utils.get_test_data('paired-broken.fq.badright')
-
- # correct output
- ex_outfile = utils.get_test_data('paired-broken.fq.paired_bad')
-
- # actual output file
- outfile = utils.get_temp_filename('out.fq')
-
- script = 'interleave-reads.py'
- args = [infile1, infile2, '-o', outfile]
-
- utils.runscript(script, args)
-
- n = 0
- for r, q in zip(screed.open(ex_outfile), screed.open(outfile)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert n > 0
-
-
-def test_interleave_reads_1_fq():
- # test input files
- infile1 = utils.get_test_data('paired.fq.1')
- infile2 = utils.get_test_data('paired.fq.2')
-
- # correct output
- ex_outfile = utils.get_test_data('paired.fq')
-
- # actual output file
- outfile = utils.get_temp_filename('out.fq')
-
- script = 'interleave-reads.py'
- args = [infile1, infile2, '-o', outfile]
-
- utils.runscript(script, args)
-
- r = open(ex_outfile).read()
- q = open(outfile).read()
-
- assert r == q, (r, q)
-
-
-def test_interleave_reads_broken_fq():
- # test input files
- infile1 = utils.get_test_data('paired-broken.fq.1')
- infile2 = utils.get_test_data('paired-broken.fq.2')
-
- # actual output file
- outfile = utils.get_temp_filename('out.fq')
-
- script = 'interleave-reads.py'
- args = [infile1, infile2, '-o', outfile]
-
- status, out, err = utils.runscript(script, args, fail_ok=True)
- assert status == 1
- assert 'ERROR: Input files contain different number of records.' in err
-
-
-def test_interleave_reads_broken_fq_2():
- # test input files
- infile1 = utils.get_test_data('paired-broken2.fq.1')
- infile2 = utils.get_test_data('paired-broken2.fq.2')
-
- # actual output file
- outfile = utils.get_temp_filename('out.fq')
-
- script = 'interleave-reads.py'
- args = [infile1, infile2, '-o', outfile]
-
- status, out, err = utils.runscript(script, args, fail_ok=True)
- assert status == 1
- assert "ERROR: This doesn't look like paired data!" in err
-
-
-def test_interleave_reads_broken_fq_3():
- # test input files
- infile1 = utils.get_test_data('paired-broken3.fq.1')
- infile2 = utils.get_test_data('paired-broken3.fq.2')
-
- # actual output file
- outfile = utils.get_temp_filename('out.fq')
-
- script = 'interleave-reads.py'
- args = [infile1, infile2, '-o', outfile]
-
- status, out, err = utils.runscript(script, args, fail_ok=True)
- assert status == 1
- assert "ERROR: This doesn't look like paired data!" in err
-
-
-def test_interleave_reads_broken_fq_5():
- # test input files
- infile1 = utils.get_test_data('paired-broken4.fq.1')
- infile2 = utils.get_test_data('paired-broken4.fq.2')
-
- # actual output file
- outfile = utils.get_temp_filename('out.fq')
-
- script = 'interleave-reads.py'
- args = [infile1, infile2, '-o', outfile]
-
- status, out, err = utils.runscript(script, args, fail_ok=True)
- assert status == 1
- assert "ERROR: This doesn't look like paired data!" in err
-
-
-def test_interleave_reads_2_fa():
- # test input files
- infile1 = utils.get_test_data('paired.fa.1')
- infile2 = utils.get_test_data('paired.fa.2')
-
- # correct output
- ex_outfile = utils.get_test_data('paired.fa')
-
- # actual output file
- outfile = utils.get_temp_filename('out.fa')
-
- script = 'interleave-reads.py'
- args = [infile1, infile2, '-o', outfile]
-
- utils.runscript(script, args)
-
- n = 0
- for r, q in zip(screed.open(ex_outfile), screed.open(outfile)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert n > 0
-
-
def test_make_initial_stoptags():
# gen input files using load-graph.py -t
# should keep test_data directory size down
# or something like that
# this assumes (obv.) load-graph.py works properly
- bzinfile = utils.get_temp_filename('test-reads.fq.bz2')
- shutil.copyfile(utils.get_test_data('test-reads.fq.bz2'), bzinfile)
+ bzinfile = utils.copy_test_data('test-reads.fq.bz2')
in_dir = os.path.dirname(bzinfile)
genscript = 'load-graph.py'
@@ -1991,8 +1597,7 @@ def test_make_initial_stoptags_load_stoptags():
# should keep test_data directory size down
# or something like that
# this assumes (obv.) load-graph.py works properly
- bzinfile = utils.get_temp_filename('test-reads.fq.bz2')
- shutil.copyfile(utils.get_test_data('test-reads.fq.bz2'), bzinfile)
+ bzinfile = utils.copy_test_data('test-reads.fq.bz2')
in_dir = os.path.dirname(bzinfile)
genscript = 'load-graph.py'
@@ -2020,569 +1625,10 @@ def test_make_initial_stoptags_load_stoptags():
assert os.path.exists(outfile1), outfile1
-def test_extract_paired_reads_unpaired():
- # test input file
- infile = utils.get_test_data('random-20-a.fa')
-
- # actual output files...
- outfile1 = utils.get_temp_filename('unpaired.pe.fa')
- in_dir = os.path.dirname(outfile1)
- outfile2 = utils.get_temp_filename('unpaired.se.fa', in_dir)
-
- script = 'extract-paired-reads.py'
- args = [infile]
-
- (_, _, err) = utils.runscript(script, args, in_dir, fail_ok=True)
- assert 'no paired reads!? check file formats...' in err, err
-
-
-def test_extract_paired_reads_1_fa():
- # test input file
- infile = utils.get_test_data('paired-mixed.fa')
-
- ex_outfile1 = utils.get_test_data('paired-mixed.fa.pe')
- ex_outfile2 = utils.get_test_data('paired-mixed.fa.se')
-
- # actual output files...
- outfile1 = utils.get_temp_filename('paired-mixed.fa.pe')
- in_dir = os.path.dirname(outfile1)
- outfile2 = utils.get_temp_filename('paired-mixed.fa.se', in_dir)
-
- script = 'extract-paired-reads.py'
- args = [infile]
-
- utils.runscript(script, args, in_dir)
-
- assert os.path.exists(outfile1), outfile1
- assert os.path.exists(outfile2), outfile2
-
- n = 0
- for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert n > 0
-
- n = 0
- for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert n > 0
-
-
-def test_extract_paired_reads_2_fq():
- # test input file
- infile = utils.get_test_data('paired-mixed.fq')
-
- ex_outfile1 = utils.get_test_data('paired-mixed.fq.pe')
- ex_outfile2 = utils.get_test_data('paired-mixed.fq.se')
-
- # actual output files...
- outfile1 = utils.get_temp_filename('paired-mixed.fq.pe')
- in_dir = os.path.dirname(outfile1)
- outfile2 = utils.get_temp_filename('paired-mixed.fq.se', in_dir)
-
- script = 'extract-paired-reads.py'
- args = [infile]
-
- utils.runscript(script, args, in_dir)
-
- assert os.path.exists(outfile1), outfile1
- assert os.path.exists(outfile2), outfile2
-
- n = 0
- for r, q in zip(screed.open(ex_outfile1),
- screed.open(outfile1)):
- n += 1
- assert r.name == q.name, (r.name, q.name, n)
- assert r.sequence == q.sequence
- assert r.quality == q.quality
- assert n > 0
-
- n = 0
- for r, q in zip(screed.open(ex_outfile2),
- screed.open(outfile2)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert r.quality == q.quality
- assert n > 0
-
-
-def test_extract_paired_reads_3_output_dir():
- # test input file
- infile = utils.get_test_data('paired-mixed.fa')
-
- ex_outfile1 = utils.get_test_data('paired-mixed.fa.pe')
- ex_outfile2 = utils.get_test_data('paired-mixed.fa.se')
-
- # output directory
- out_dir = utils.get_temp_filename('output')
-
- script = 'extract-paired-reads.py'
- args = [infile, '-d', out_dir]
-
- utils.runscript(script, args)
-
- outfile1 = os.path.join(out_dir, 'paired-mixed.fa.pe')
- outfile2 = os.path.join(out_dir, 'paired-mixed.fa.se')
- assert os.path.exists(outfile1), outfile1
- assert os.path.exists(outfile2), outfile2
-
- n = 0
- for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert n > 0
-
- n = 0
- for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert n > 0
-
-
-def test_extract_paired_reads_4_output_files():
- # test input file
- infile = utils.get_test_data('paired-mixed.fa')
-
- ex_outfile1 = utils.get_test_data('paired-mixed.fa.pe')
- ex_outfile2 = utils.get_test_data('paired-mixed.fa.se')
-
- # actual output files...
- outfile1 = utils.get_temp_filename('out_pe')
- outfile2 = utils.get_temp_filename('out_se')
-
- script = 'extract-paired-reads.py'
- args = [infile, '-p', outfile1, '-s', outfile2]
-
- utils.runscript(script, args)
-
- assert os.path.exists(outfile1), outfile1
- assert os.path.exists(outfile2), outfile2
-
- n = 0
- for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert n > 0
-
- n = 0
- for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert n > 0
-
-
-def test_extract_paired_reads_5_stdin_error():
- script = 'extract-paired-reads.py'
- args = ['-f', '/dev/stdin']
-
- status, out, err = utils.runscript(script, args, fail_ok=True)
- assert status == 1
- assert "output filenames must be provided." in err
-
-
-def execute_extract_paired_streaming(ifilename):
- fifo = utils.get_temp_filename('fifo')
- in_dir = os.path.dirname(fifo)
- outfile1 = utils.get_temp_filename('paired.pe')
- outfile2 = utils.get_temp_filename('paired.se')
- script = 'extract-paired-reads.py'
- args = [fifo, '-p', outfile1, '-s', outfile2]
-
- # make a fifo to simulate streaming
- os.mkfifo(fifo)
-
- thread = threading.Thread(target=utils.runscript,
- args=(script, args, in_dir))
- thread.start()
- ifile = open(ifilename, 'r')
- fifofile = open(fifo, 'w')
- chunk = ifile.read(4)
- while len(chunk) > 0:
- fifofile.write(chunk)
- chunk = ifile.read(4)
- fifofile.close()
- thread.join()
- assert os.path.exists(outfile1), outfile1
- assert os.path.exists(outfile2), outfile2
-
-
-def test_extract_paired_streaming():
- testinput = utils.get_test_data('paired-mixed.fa')
- o = execute_extract_paired_streaming(testinput)
-
-
-def execute_split_paired_streaming(ifilename):
- fifo = utils.get_temp_filename('fifo')
- in_dir = os.path.dirname(fifo)
- outfile1 = utils.get_temp_filename('paired-1.fa')
- outfile2 = utils.get_temp_filename('paired-2.fa')
- script = 'split-paired-reads.py'
- args = [fifo, '-1', outfile1, '-2', outfile2]
-
- # make a fifo to simulate streaming
- os.mkfifo(fifo)
-
- thread = threading.Thread(target=utils.runscript,
- args=(script, args, in_dir))
- thread.start()
- ifile = open(ifilename, 'r')
- fifofile = open(fifo, 'w')
- chunk = ifile.read(4)
- while len(chunk) > 0:
- fifofile.write(chunk)
- chunk = ifile.read(4)
- fifofile.close()
- thread.join()
- assert os.path.exists(outfile1), outfile1
- assert os.path.exists(outfile2), outfile2
-
-
-def test_split_paired_streaming():
- o = execute_split_paired_streaming(utils.get_test_data('paired.fa'))
-
-
-def test_split_paired_reads_1_fa():
- # test input file
- infile = utils.get_test_data('paired.fa')
-
- ex_outfile1 = utils.get_test_data('paired.fa.1')
- ex_outfile2 = utils.get_test_data('paired.fa.2')
-
- # actual output files...
- outfile1 = utils.get_temp_filename('paired.fa.1')
- in_dir = os.path.dirname(outfile1)
- outfile2 = utils.get_temp_filename('paired.fa.2', in_dir)
-
- script = 'split-paired-reads.py'
- args = [infile]
-
- utils.runscript(script, args, in_dir)
-
- assert os.path.exists(outfile1), outfile1
- assert os.path.exists(outfile2), outfile2
-
- n = 0
- for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert n > 0
-
- n = 0
- for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert n > 0
-
-
-def test_split_paired_reads_2_fq():
- # test input file
- infile = utils.get_test_data('paired.fq')
-
- ex_outfile1 = utils.get_test_data('paired.fq.1')
- ex_outfile2 = utils.get_test_data('paired.fq.2')
-
- # actual output files...
- outfile1 = utils.get_temp_filename('paired.fq.1')
- in_dir = os.path.dirname(outfile1)
- outfile2 = utils.get_temp_filename('paired.fq.2', in_dir)
-
- script = 'split-paired-reads.py'
- args = [infile]
-
- utils.runscript(script, args, in_dir)
-
- assert os.path.exists(outfile1), outfile1
- assert os.path.exists(outfile2), outfile2
-
- n = 0
- for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert r.quality == q.quality
- assert n > 0
-
- n = 0
- for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert r.quality == q.quality
- assert n > 0
-
-
-def test_split_paired_reads_2_mixed_fq_require_pair():
- # test input file
- infile = utils.get_temp_filename('test.fq')
- shutil.copyfile(utils.get_test_data('paired-mixed.fq'), infile)
- in_dir = os.path.dirname(infile)
-
- script = 'split-paired-reads.py'
- args = [infile]
-
- status, out, err = utils.runscript(script, args, in_dir, fail_ok=True)
- assert status == 1, status
- assert "Unpaired reads found" in err
-
-
-def test_split_paired_reads_2_stdin_no_out():
- script = 'split-paired-reads.py'
- args = ['-']
-
- status, out, err = utils.runscript(script, args, fail_ok=True)
- assert status == 1
- assert "Accepting input from stdin; output filenames must " in err
-
-
-def test_split_paired_reads_2_mixed_fq():
- # test input file
- infile = utils.get_temp_filename('test.fq')
- shutil.copyfile(utils.get_test_data('paired-mixed-2.fq'), infile)
- in_dir = os.path.dirname(infile)
-
- script = 'split-paired-reads.py'
- args = ['-0', '/dev/null', infile]
-
- status, out, err = utils.runscript(script, args, in_dir)
- assert status == 0
- assert "split 6 sequences (3 left, 3 right, 5 orphans)" in err, err
-
-
-def test_split_paired_reads_2_mixed_fq_orphans_to_file():
- # test input file
- infile = utils.get_temp_filename('test.fq')
- shutil.copyfile(utils.get_test_data('paired-mixed-2.fq'), infile)
- in_dir = os.path.dirname(infile)
- outfile = utils.get_temp_filename('out.fq')
-
- script = 'split-paired-reads.py'
- args = ['-0', outfile, infile]
-
- status, out, err = utils.runscript(script, args, in_dir)
- assert status == 0
- assert "split 6 sequences (3 left, 3 right, 5 orphans)" in err, err
-
- n_orphans = len([1 for record in screed.open(outfile)])
- assert n_orphans == 5
- n_left = len([1 for record in screed.open(infile + '.1')])
- assert n_left == 3
- n_right = len([1 for record in screed.open(infile + '.2')])
- assert n_right == 3
- for filename in [outfile, infile + '.1', infile + '.2']:
- fp = gzip.open(filename)
- try:
- fp.read()
- except IOError as e:
- assert "Not a gzipped file" in str(e), str(e)
- fp.close()
-
-
-def test_split_paired_reads_2_mixed_fq_gzfile():
- # test input file
- infile = utils.get_temp_filename('test.fq')
- shutil.copyfile(utils.get_test_data('paired-mixed-2.fq'), infile)
- in_dir = os.path.dirname(infile)
- outfile = utils.get_temp_filename('out.fq')
-
- script = 'split-paired-reads.py'
- args = ['-0', outfile, '--gzip', infile]
-
- status, out, err = utils.runscript(script, args, in_dir)
- assert status == 0
- assert "split 6 sequences (3 left, 3 right, 5 orphans)" in err, err
-
- n_orphans = len([1 for record in screed.open(outfile)])
- assert n_orphans == 5
- n_left = len([1 for record in screed.open(infile + '.1')])
- assert n_left == 3
- n_right = len([1 for record in screed.open(infile + '.2')])
- assert n_right == 3
-
- for filename in [outfile, infile + '.1', infile + '.2']:
- fp = gzip.open(filename)
- fp.read() # this will fail if not gzip file.
- fp.close()
-
-
-def test_split_paired_reads_2_mixed_fq_broken_pairing_format():
- # test input file
- infile = utils.get_temp_filename('test.fq')
- shutil.copyfile(utils.get_test_data('paired-mixed-broken.fq'), infile)
- in_dir = os.path.dirname(infile)
-
- script = 'split-paired-reads.py'
- args = [infile]
-
- status, out, err = utils.runscript(script, args, in_dir, fail_ok=True)
- assert status == 1
- assert "Unpaired reads found starting at 895:1:37:17593:9954" in err, err
-
-
-def test_split_paired_reads_3_output_dir():
- # test input file
- infile = utils.get_test_data('paired.fq')
-
- ex_outfile1 = utils.get_test_data('paired.fq.1')
- ex_outfile2 = utils.get_test_data('paired.fq.2')
-
- # actual output files...
- testdir = utils.get_temp_filename('test')
- output_dir = os.path.join(os.path.dirname(testdir), "out")
- outfile1 = utils.get_temp_filename('paired.fq.1', output_dir)
- outfile2 = utils.get_temp_filename('paired.fq.2', output_dir)
-
- script = 'split-paired-reads.py'
- args = ['--output-dir', output_dir, infile]
-
- utils.runscript(script, args)
-
- assert os.path.exists(outfile1), outfile1
- assert os.path.exists(outfile2), outfile2
-
- n = 0
- for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert r.quality == q.quality
- assert n > 0
-
- n = 0
- for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert r.quality == q.quality
- assert n > 0
-
-
-def test_split_paired_reads_3_output_files():
- # test input file
- infile = utils.get_test_data('paired.fq')
-
- ex_outfile1 = utils.get_test_data('paired.fq.1')
- ex_outfile2 = utils.get_test_data('paired.fq.2')
-
- # actual output files...
- outfile1 = utils.get_temp_filename('xxx')
- output_dir = os.path.dirname(outfile1)
- outfile2 = utils.get_temp_filename('yyy', output_dir)
-
- script = 'split-paired-reads.py'
- args = ['-1', outfile1, '-2', outfile2, infile]
-
- utils.runscript(script, args)
-
- assert os.path.exists(outfile1), outfile1
- assert os.path.exists(outfile2), outfile2
-
- n = 0
- for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert r.quality == q.quality
- assert n > 0
-
- n = 0
- for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert r.quality == q.quality
- assert n > 0
-
-
-def test_split_paired_reads_3_output_files_left():
- # test input file
- infile = utils.get_test_data('paired.fq')
-
- ex_outfile1 = utils.get_test_data('paired.fq.1')
- ex_outfile2 = utils.get_test_data('paired.fq.2')
-
- # actual output files...
- outfile1 = utils.get_temp_filename('xxx')
- output_dir = os.path.dirname(outfile1)
- outfile2 = utils.get_temp_filename('paired.fq.2', output_dir)
-
- script = 'split-paired-reads.py'
- args = ['-d', output_dir, '-1', outfile1, infile]
-
- utils.runscript(script, args)
-
- assert os.path.exists(outfile1), outfile1
- assert os.path.exists(outfile2), outfile2
-
- n = 0
- for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert r.quality == q.quality
- assert n > 0
-
- n = 0
- for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert r.quality == q.quality
- assert n > 0
-
-
-def test_split_paired_reads_3_output_files_right():
- # test input file
- infile = utils.get_test_data('paired.fq')
-
- ex_outfile1 = utils.get_test_data('paired.fq.1')
- ex_outfile2 = utils.get_test_data('paired.fq.2')
-
- # actual output files...
- outfile1 = utils.get_temp_filename('paired.fq.1')
- output_dir = os.path.dirname(outfile1)
- outfile2 = utils.get_temp_filename('yyy', output_dir)
-
- script = 'split-paired-reads.py'
- args = ['-2', outfile2, '-d', output_dir, infile]
-
- utils.runscript(script, args)
-
- assert os.path.exists(outfile1), outfile1
- assert os.path.exists(outfile2), outfile2
-
- n = 0
- for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert r.quality == q.quality
- assert n > 0
-
- n = 0
- for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert r.quality == q.quality
- assert n > 0
-
-
def test_sample_reads_randomly():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-reads.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-reads.fa'), infile)
-
script = 'sample-reads-randomly.py'
# fix random number seed for reproducibility
args = ['-N', '10', '-M', '12000', '-R', '1']
@@ -2622,11 +1668,9 @@ def test_sample_reads_randomly():
def test_sample_reads_randomly_force_single():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-reads.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-reads.fa'), infile)
-
script = 'sample-reads-randomly.py'
# fix random number seed for reproducibility
args = ['-N', '10', '-M', '12000', '-R', '1', '--force_single']
@@ -2666,11 +1710,9 @@ def test_sample_reads_randomly_force_single():
def test_sample_reads_randomly_force_single_outfile():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-reads.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-reads.fa'), infile)
-
script = 'sample-reads-randomly.py'
# fix random number seed for reproducibility
args = ['-N', '10', '-M', '12000', '-R', '1', '--force_single', '-o',
@@ -2712,11 +1754,9 @@ def test_sample_reads_randomly_force_single_outfile():
def test_sample_reads_randomly_fq():
- infile = utils.get_temp_filename('test.fq.gz')
+ infile = utils.copy_test_data('test-reads.fq.gz')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-reads.fq.gz'), infile)
-
script = 'sample-reads-randomly.py'
# fix random number seed for reproducibility
args = ['-N', '10', '-M', '12000', '-R', '1']
@@ -2766,11 +1806,8 @@ def test_sample_reads_randomly_stdin_no_out():
def test_fastq_to_fasta():
script = 'fastq-to-fasta.py'
- clean_infile = utils.get_temp_filename('test-clean.fq')
- n_infile = utils.get_temp_filename('test-n.fq')
-
- shutil.copyfile(utils.get_test_data('test-fastq-reads.fq'), clean_infile)
- shutil.copyfile(utils.get_test_data('test-fastq-n-reads.fq'), n_infile)
+ clean_infile = utils.copy_test_data('test-fastq-reads.fq')
+ n_infile = utils.copy_test_data('test-fastq-n-reads.fq')
clean_outfile = clean_infile + '.keep.fa'
n_outfile = n_infile + '.keep.fa'
@@ -2825,11 +1862,10 @@ def test_fastq_to_fasta():
def test_fastq_to_fasta_streaming_compressed_gzip():
script = 'fastq-to-fasta.py'
- infile = utils.get_temp_filename('test-clean.fq')
+ infile = utils.copy_test_data('test-reads.fq.gz')
in_dir = os.path.dirname(infile)
fifo = utils.get_temp_filename('fifo')
copyfilepath = utils.get_temp_filename('copied.fa.gz', in_dir)
- shutil.copyfile(utils.get_test_data('test-reads.fq.gz'), infile)
# make a fifo to simulate streaming
os.mkfifo(fifo)
@@ -2871,11 +1907,10 @@ def test_fastq_to_fasta_streaming_compressed_gzip():
def test_fastq_to_fasta_streaming_compressed_bzip():
script = 'fastq-to-fasta.py'
- infile = utils.get_temp_filename('test-clean.fq')
+ infile = utils.copy_test_data('test-reads.fq.gz')
in_dir = os.path.dirname(infile)
fifo = utils.get_temp_filename('fifo')
copyfilepath = utils.get_temp_filename('copied.fa.bz', in_dir)
- shutil.copyfile(utils.get_test_data('test-reads.fq.gz'), infile)
# make a fifo to simulate streaming
os.mkfifo(fifo)
@@ -2917,9 +1952,7 @@ def test_fastq_to_fasta_streaming_compressed_bzip():
def test_extract_long_sequences_fa():
script = 'extract-long-sequences.py'
- fa_infile = utils.get_temp_filename('test.fa')
-
- shutil.copyfile(utils.get_test_data('paired-mixed.fa'), fa_infile)
+ fa_infile = utils.copy_test_data('paired-mixed.fa')
fa_outfile = fa_infile + '.keep.fa'
@@ -2939,9 +1972,7 @@ def test_extract_long_sequences_fa():
def test_extract_long_sequences_fq():
script = 'extract-long-sequences.py'
- fq_infile = utils.get_temp_filename('test.fq')
-
- shutil.copyfile(utils.get_test_data('paired-mixed.fq'), fq_infile)
+ fq_infile = utils.copy_test_data('paired-mixed.fq')
fq_outfile = fq_infile + '.keep.fq'
@@ -2959,11 +1990,9 @@ def test_extract_long_sequences_fq():
def test_sample_reads_randomly_S():
- infile = utils.get_temp_filename('test.fq')
+ infile = utils.copy_test_data('test-fastq-reads.fq')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-fastq-reads.fq'), infile)
-
script = 'sample-reads-randomly.py'
# fix random number seed for reproducibility
@@ -3084,9 +2113,8 @@ def _execute_load_graph_streaming(filename):
'''
scripts = utils.scriptpath()
- infile = utils.get_temp_filename('temp')
+ infile = utils.copy_test_data(filename)
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data(filename), infile)
args = '-x 1e7 -N 2 -k 20 out -'
@@ -3155,7 +2183,7 @@ def test_screed_streaming_bzipfa():
assert seqs[0].startswith('GGTTGACGGGGCTCAGGGGG')
- at attr('known_failing')
+ at pytest.mark.known_failing
def test_screed_streaming_gzipfq():
# gzip compressed fq
o = execute_streaming_diginorm(utils.get_test_data('100-reads.fq.gz'))
@@ -3164,7 +2192,7 @@ def test_screed_streaming_gzipfq():
assert seqs[0].startswith('CAGGCGCCCACCACCGTGCCCTCCAACCTG')
- at attr('known_failing')
+ at pytest.mark.known_failing
def test_screed_streaming_gzipfa():
o = execute_streaming_diginorm(
utils.get_test_data('test-abund-read-2.fa.gz'))
@@ -3183,7 +2211,7 @@ def test_read_parser_streaming_ufq():
_execute_load_graph_streaming(utils.get_test_data('random-20-a.fq'))
- at attr('known_failing')
+ at pytest.mark.known_failing
def test_read_parser_streaming_bzfq():
# bzip compressed FASTQ
_execute_load_graph_streaming(utils.get_test_data('random-20-a.fq.bz2'))
@@ -3194,7 +2222,7 @@ def test_read_parser_streaming_gzfq():
_execute_load_graph_streaming(utils.get_test_data('random-20-a.fq.gz'))
- at attr('known_failing')
+ at pytest.mark.known_failing
def test_read_parser_streaming_bzfa():
# bzip compressed FASTA
_execute_load_graph_streaming(utils.get_test_data('random-20-a.fa.bz2'))
@@ -3265,11 +2293,9 @@ def test_readstats_empty():
def test_trim_low_abund_1():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-2.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
-
args = ["-k", "17", "-x", "1e7", "-N", "2", infile]
utils.runscript('trim-low-abund.py', args, in_dir)
@@ -3282,11 +2308,9 @@ def test_trim_low_abund_1():
def test_trim_low_abund_1_duplicate_filename_err():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-2.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
-
args = ["-k", "17", "-x", "1e7", "-N", "2", '-C', '1', infile, infile]
(status, out, err) = utils.runscript('trim-low-abund.py', args, in_dir,
fail_ok=True)
@@ -3305,13 +2329,10 @@ def test_trim_low_abund_1_stdin_err():
def test_trim_low_abund_2():
- infile = utils.get_temp_filename('test.fa')
- infile2 = utils.get_temp_filename('test2.fa')
+ infile = utils.copy_test_data('test-abund-read-2.fa')
+ infile2 = utils.copy_test_data('test-abund-read-2.fa', 'copyDataTwo')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile2)
-
args = ["-k", "17", "-x", "1e7", "-N", "2", '-C', '1', infile, infile2]
utils.runscript('trim-low-abund.py', args, in_dir)
@@ -3322,17 +2343,30 @@ def test_trim_low_abund_2():
assert len(seqs) == 2, seqs
assert 'GGTTGACGGGGCTCAGGG' in seqs
+
+def test_trim_low_abund_2_o_gzip():
+ infile = utils.copy_test_data('test-abund-read-2.fa')
+ infile2 = utils.copy_test_data('test-abund-read-2.fa', 'copyDataTwo')
+ outfile = utils.get_temp_filename('out.gz')
+ in_dir = os.path.dirname(infile)
+
+ args = ["-k", "17", "-x", "1e7", "-N", "2", '-C', '1',
+ "-o", outfile, "--gzip",
+ infile, infile2]
+ utils.runscript('trim-low-abund.py', args, in_dir)
+
+ assert os.path.exists(outfile), outfile
+ x = list(screed.open(outfile))
+ assert len(x)
+
# make sure that FASTQ records are retained.
def test_trim_low_abund_3_fq_retained():
- infile = utils.get_temp_filename('test.fq')
- infile2 = utils.get_temp_filename('test2.fq')
+ infile = utils.copy_test_data('test-abund-read-2.fq')
+ infile2 = utils.copy_test_data('test-abund-read-2.fq', 'copyDataTwo')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fq'), infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fq'), infile2)
-
args = ["-k", "17", "-x", "1e7", "-N", "2", '-C', '1', infile, infile2]
utils.runscript('trim-low-abund.py', args, in_dir)
@@ -3353,11 +2387,9 @@ def test_trim_low_abund_3_fq_retained():
def test_trim_low_abund_4_retain_low_abund():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-2.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
-
args = ["-k", "17", "-x", "1e7", "-N", "2", '-V', infile]
utils.runscript('trim-low-abund.py', args, in_dir)
@@ -3372,11 +2404,9 @@ def test_trim_low_abund_4_retain_low_abund():
def test_trim_low_abund_5_trim_high_abund():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-3.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-3.fa'), infile)
-
args = ["-k", "17", "-x", "1e7", "-N", "2", '-V', infile]
utils.runscript('trim-low-abund.py', args, in_dir)
@@ -3393,11 +2423,9 @@ def test_trim_low_abund_5_trim_high_abund():
def test_trim_low_abund_6_trim_high_abund_Z():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-3.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-3.fa'), infile)
-
args = ["-k", "17", "-x", "1e7", "-N", "2", '-V', '-Z', '25', infile]
utils.runscript('trim-low-abund.py', args, in_dir)
@@ -3414,11 +2442,9 @@ def test_trim_low_abund_6_trim_high_abund_Z():
def test_trim_low_abund_keep_paired():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-2.paired.fq')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.paired.fq'), infile)
-
args = ["-k", "17", "-x", "1e7", "-N", "2", "-V", infile]
utils.runscript('trim-low-abund.py', args, in_dir)
@@ -3430,12 +2456,9 @@ def test_trim_low_abund_keep_paired():
def test_trim_low_abund_keep_paired_casava18():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-2.paired2.fq')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.paired2.fq'),
- infile)
-
args = ["-k", "17", "-x", "1e7", "-N", "2", "-V", infile]
utils.runscript('trim-low-abund.py', args, in_dir)
@@ -3447,11 +2470,9 @@ def test_trim_low_abund_keep_paired_casava18():
def test_trim_low_abund_highfpr():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-2.paired.fq')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.paired.fq'), infile)
-
args = ["-k", "17", "-x", "1", "-N", "1", "-V", infile]
code, out, err = utils.runscript('trim-low-abund.py', args, in_dir,
fail_ok=True)
@@ -3461,11 +2482,9 @@ def test_trim_low_abund_highfpr():
def test_trim_low_abund_trimtest():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-2.paired.fq')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.paired.fq'), infile)
-
args = ["-k", "17", "-x", "1e7", "-N", "2", "-Z", "2", "-C", "1",
"-V", infile]
utils.runscript('trim-low-abund.py', args, in_dir)
@@ -3489,13 +2508,11 @@ def test_trim_low_abund_trimtest():
def test_trim_low_abund_trimtest_after_load():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-2.paired.fq')
in_dir = os.path.dirname(infile)
saved_table = utils.get_temp_filename('save.ct')
- shutil.copyfile(utils.get_test_data('test-abund-read-2.paired.fq'), infile)
-
args = ["-k", "17", "-x", "1e7", "-N", "2", saved_table, infile]
utils.runscript('load-into-counting.py', args, in_dir)
@@ -3521,13 +2538,11 @@ def test_trim_low_abund_trimtest_after_load():
def test_trim_low_abund_trimtest_savegraph():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-2.paired.fq')
in_dir = os.path.dirname(infile)
saved_table = utils.get_temp_filename('save.ct')
- shutil.copyfile(utils.get_test_data('test-abund-read-2.paired.fq'), infile)
-
args = ["-k", "17", "-x", "1e7", "-N", "2",
"-Z", "2", "-C", "2", "-V", '--savegraph', saved_table, infile]
utils.runscript('trim-low-abund.py', args, in_dir)
@@ -3554,26 +2569,95 @@ def test_trim_low_abund_trimtest_savegraph():
def test_trim_low_abund_stdout():
- infile = utils.get_temp_filename('test.fa')
+ infile = utils.copy_test_data('test-abund-read-2.fa')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
-
args = ["-k", "17", "-x", "1e7", "-N", "2", infile, "-o", "-"]
_, out, err = utils.runscript('trim-low-abund.py', args, in_dir)
assert 'GGTTGACGGGGCTCAGGG' in out
+def test_trim_low_abund_diginorm_coverage_err():
+ infile = utils.copy_test_data('test-abund-read-2.fa')
+ in_dir = os.path.dirname(infile)
+
+ args = ["-M", "1e7", infile, "--diginorm-coverage", "21"]
+ status, out, err = utils.runscript('trim-low-abund.py', args, in_dir,
+ fail_ok=True)
+
+ print(out, err)
+ assert status == 1
+ assert 'Error: --diginorm-coverage given, but --diginorm not specified.' \
+ in err, err
+
+
+def test_trim_low_abund_diginorm_single_pass():
+ infile = utils.copy_test_data('test-abund-read-2.fa')
+ in_dir = os.path.dirname(infile)
+
+ args = ["-M", "1e7", infile, "--diginorm", "--single-pass"]
+ status, out, err = utils.runscript('trim-low-abund.py', args, in_dir,
+ fail_ok=True)
+
+ assert status == 1
+ assert "Error: --diginorm and --single-pass are incompatible!" \
+ in err, err
+
+
+def test_trim_low_abund_varcov_err():
+ infile = utils.copy_test_data('test-abund-read-2.fa')
+ in_dir = os.path.dirname(infile)
+
+ args = ["-M", "1e7", infile, "-Z", "21"]
+ status, out, err = utils.runscript('trim-low-abund.py', args, in_dir,
+ fail_ok=True)
+
+ print(out, err)
+ assert status == 1
+ assert 'Error: --trim-at-coverage/-Z given' in err, err
+
+
+def test_trim_low_abund_single_pass():
+ infile = utils.copy_test_data('test-abund-read-2.fa')
+ in_dir = os.path.dirname(infile)
+
+ args = ["-M", "1e7", infile, "-V", '--single-pass']
+ status, out, err = utils.runscript('trim-low-abund.py', args, in_dir)
+
+ assert status == 0
+
+
+def test_trim_low_abund_quiet():
+ infile = utils.copy_test_data('test-reads.fa')
+ in_dir = os.path.dirname(infile)
+
+ args = ["-q", "-M", "1e7", infile, "-V", '-Z', '5', '-C', '1']
+ status, out, err = utils.runscript('trim-low-abund.py', args, in_dir)
+
+ assert status == 0
+ assert len(out) == 0
+ assert len(err) == 0
+
+
+def test_trim_low_abund_reporting():
+ infile = utils.copy_test_data('test-reads.fa')
+ in_dir = os.path.dirname(infile)
+
+ args = ["-M", "1e7", infile, "-V", '-Z', '5', '-C', '1']
+ status, out, err = utils.runscript('trim-low-abund.py', args, in_dir)
+
+ assert status == 0
+ assert '11157 11161 848236 2 152' in err
+
+
def test_roundtrip_casava_format_1():
# check to make sure that extract-paired-reads produces a file identical
# to the input file when only paired data is given.
- infile = utils.get_temp_filename('test.fq')
+ infile = utils.copy_test_data('casava_18-pe.fq')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('casava_18-pe.fq'), infile)
-
_, out, err = utils.runscript('extract-paired-reads.py', [infile], in_dir)
r = open(infile).read()
@@ -3587,12 +2671,10 @@ def test_roundtrip_casava_format_2():
# check that split-paired-reads -> interleave-reads produces a file
# identical to input, when only paired reads are given.
- infile = utils.get_temp_filename('test.fq')
+ infile = utils.copy_test_data('casava_18-pe.fq')
outfile = utils.get_temp_filename('test2.fq')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('casava_18-pe.fq'), infile)
-
_, out, err = utils.runscript('split-paired-reads.py', [infile], in_dir)
utils.runscript('interleave-reads.py', [infile + '.1',
@@ -3604,7 +2686,7 @@ def test_roundtrip_casava_format_2():
assert r == r2, (r, r2)
-def test_existance_failure():
+def test_existence_failure():
expected_output = 'ERROR: Input file'
args = [utils.get_temp_filename('thisfiledoesnotexistatall')]
@@ -3622,13 +2704,10 @@ def test_roundtrip_commented_format():
This should produce a file identical to the input when only paired
reads are given.
"""
- infile = utils.get_temp_filename('test.fq')
+ infile = utils.copy_test_data('old-style-format-w-comments.fq')
outfile = utils.get_temp_filename('test2.fq')
in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('old-style-format-w-comments.fq'),
- infile)
-
_, out, err = utils.runscript('split-paired-reads.py', [infile], in_dir)
utils.runscript('interleave-reads.py', [infile + '.1',
@@ -3641,8 +2720,7 @@ def test_roundtrip_commented_format():
def test_unique_kmers_defaults():
- infile = utils.get_temp_filename('random-20-a.fa')
- shutil.copyfile(utils.get_test_data('random-20-a.fa'), infile)
+ infile = utils.copy_test_data('random-20-a.fa')
args = ['-k', '20', '-e', '0.01', infile]
@@ -3656,8 +2734,7 @@ def test_unique_kmers_defaults():
def test_unique_kmers_report_fp():
- infile = utils.get_temp_filename('random-20-a.fa')
- shutil.copyfile(utils.get_test_data('random-20-a.fa'), infile)
+ infile = utils.copy_test_data('random-20-a.fa')
outfile = utils.get_temp_filename('report.unique')
args = ['-k', '20', '-e', '0.01', '-R', outfile, infile]
@@ -3677,8 +2754,7 @@ def test_unique_kmers_report_fp():
def test_unique_kmers_diagnostics():
- infile = utils.get_temp_filename('random-20-a.fa')
- shutil.copyfile(utils.get_test_data('random-20-a.fa'), infile)
+ infile = utils.copy_test_data('random-20-a.fa')
args = ['-k', '20', '-e', '0.01', '--diagnostics', infile]
@@ -3693,8 +2769,7 @@ def test_unique_kmers_diagnostics():
def test_unique_kmers_multiple_inputs():
infiles = []
for fname in ('random-20-a.fa', 'paired-mixed.fa'):
- infile = utils.get_temp_filename(fname)
- shutil.copyfile(utils.get_test_data(fname), infile)
+ infile = utils.copy_test_data(fname)
infiles.append(infile)
args = ['-k', '20', '-e', '0.01']
@@ -3711,20 +2786,30 @@ def test_unique_kmers_multiple_inputs():
assert 'Total estimated number of unique 20-mers: 4170' in err
-def check_version_and_basic_citation(scriptname):
- version = re.compile("^khmer .*$", re.MULTILINE)
- status, out, err = utils.runscript(scriptname, ["--version"])
- assert status == 0, status
- assert "publication" in err, err
- assert version.search(err) is not None, err
-
-
-def test_version():
- for entry in os.listdir(utils.scriptpath()):
- if entry.endswith(".py"):
- with open(os.path.join(utils.scriptpath(), entry)) as script:
- line = script.readline()
- line = script.readline()
- if 'khmer' in line: # simple check of copyright line.
- yield check_version_and_basic_citation, entry
- # emit test for each script
+ at pytest.mark.parametrize("scriptname",
+ [entry for entry in os.listdir(utils.scriptpath())
+ if entry.endswith('.py')])
+def test_version_and_basic_citation(scriptname):
+ with open(os.path.join(utils.scriptpath(), scriptname)) as script:
+ line = script.readline()
+ line = script.readline()
+ if 'khmer' in line:
+ # check citation information appears when using --info
+ status, out, err = utils.runscript(scriptname, ["--info"])
+ assert status == 0, status
+ print(out)
+ print(err)
+ assert "publication" in err, err
+ assert "usage:" not in err, err
+
+ # check citation information appears in --version
+ status, out, err = utils.runscript(scriptname, ["--version"])
+ assert status == 0, status
+ assert "publication" in err, err
+ assert "usage:" not in err, err
+
+ # check citation information appears in --help
+ status, out, err = utils.runscript(scriptname, ["--help"])
+ assert status == 0, status
+ assert "publication" in err, err
+ assert "usage:" in out, out
diff --git a/tests/test_streaming_io.py b/tests/test_streaming_io.py
index 00cb7d3..86ed37f 100644
--- a/tests/test_streaming_io.py
+++ b/tests/test_streaming_io.py
@@ -1,5 +1,5 @@
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -31,6 +31,7 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
+# pylint: disable=missing-docstring,invalid-name
# important note -- these tests do not contribute to code coverage, because
# of the use of subprocess to execute. Most script tests should go into
@@ -102,7 +103,7 @@ def test_interleave_split_2_fail():
in1=in1, in2=in2,
out1=out1, out2=out2)
- (status, out, err) = run_shell_cmd(cmd, fail_ok=True)
+ (status, _, err) = run_shell_cmd(cmd, fail_ok=True)
assert status != 0
assert "Accepting input from stdin; output filenames must be provided." \
in err, err
@@ -209,19 +210,36 @@ def test_extract_paired_se():
assert files_are_equal(out1, out_test), diff_files(out1, out_test)
-def test_extract_paired_se_fail():
+def test_extract_paired_stdin_equivalence():
+ # Use '/dev/stdin' instead of '-' to check it is treated the same way
in1 = utils.get_test_data('paired-mixed.fq')
out_test = utils.get_test_data('paired-mixed.fq.se')
out1 = utils.get_temp_filename('a.fq')
cmd = """
cat {in1} |
+ {scripts}/extract-paired-reads.py /dev/stdin -p /dev/null -s - > {out1}
+ """
+
+ cmd = cmd.format(scripts=scriptpath(), in1=in1, out1=out1)
+
+ run_shell_cmd(cmd)
+
+ assert files_are_equal(out1, out_test), diff_files(out1, out_test)
+
+
+def test_extract_paired_se_fail():
+ in1 = utils.get_test_data('paired-mixed.fq')
+ out1 = utils.get_temp_filename('a.fq')
+
+ cmd = """
+ cat {in1} |
{scripts}/extract-paired-reads.py -p /dev/null - > {out1}
"""
cmd = cmd.format(scripts=scriptpath(), in1=in1, out1=out1)
- (status, out, err) = run_shell_cmd(cmd, fail_ok=True)
+ (status, _, err) = run_shell_cmd(cmd, fail_ok=True)
assert status != 0
assert "Accepting input from stdin; output filenames must be provided." \
in err, err
@@ -247,7 +265,6 @@ def test_norm_by_median_1():
def test_norm_by_median_2_fail():
in1 = utils.get_test_data('paired-mixed.fq')
- out_test = utils.get_test_data('paired-mixed.fq.pe')
out1 = utils.get_temp_filename('a.fq')
cmd = """
@@ -258,7 +275,7 @@ def test_norm_by_median_2_fail():
cmd = cmd.format(scripts=scriptpath(), in1=in1, out1=out1)
- (status, out, err) = run_shell_cmd(cmd, fail_ok=True)
+ (status, _, err) = run_shell_cmd(cmd, fail_ok=True)
assert status != 0
assert "Accepting input from stdin; output filename must be provided with"\
in err, err
@@ -291,7 +308,7 @@ def test_sample_reads_randomly_2_fail():
cmd = cmd.format(scripts=scriptpath(), in1=in1, out1=out1)
- (status, out, err) = run_shell_cmd(cmd, fail_ok=True)
+ (status, _, err) = run_shell_cmd(cmd, fail_ok=True)
assert status != 0
assert "Accepting input from stdin; output filename must be provided with"\
in err, err
@@ -343,7 +360,7 @@ def test_load_into_counting_1():
cmd = cmd.format(scripts=scriptpath(), in1=in1, out1=out1)
print(cmd)
- (status, out, err) = run_shell_cmd(cmd)
+ run_shell_cmd(cmd)
assert os.path.exists(out1)
khmer.load_countgraph(out1)
@@ -361,7 +378,7 @@ def test_load_graph_1():
cmd = cmd.format(scripts=scriptpath(), in1=in1, out1=out1)
print(cmd)
- (status, out, err) = run_shell_cmd(cmd)
+ run_shell_cmd(cmd)
assert os.path.exists(out1)
khmer.load_nodegraph(out1)
@@ -403,7 +420,7 @@ def test_filter_abund_2_fail():
cmd = cmd.format(scripts=scriptpath(), in1=in1, out1=out1,
countgraph=countgraph)
- (status, out, err) = run_shell_cmd(cmd, fail_ok=True)
+ status, _, err = run_shell_cmd(cmd, fail_ok=True)
assert status != 0
assert "Accepting input from stdin; output filename must be provided with"\
in err, err
@@ -427,11 +444,11 @@ def test_abundance_dist_1():
run_shell_cmd(cmd)
assert os.path.exists(out1)
- with open(out1) as fp:
- line = fp.readline().strip()
- line = fp.readline().strip()
+ with open(out1) as fpout1:
+ line = fpout1.readline().strip()
+ line = fpout1.readline().strip()
assert line == '1,96,96,0.98', line
- line = fp.readline().strip()
+ line = fpout1.readline().strip()
assert line == '1001,2,98,1.0', line
@@ -455,6 +472,47 @@ def test_trim_low_abund_1():
assert 'GGTTGACGGGGCTCAGGG' in seqs
+def test_trim_low_abund_smallcount():
+ in1 = utils.get_test_data('test-abund-read-2.fa')
+ out1 = utils.get_temp_filename('out.abundtrim')
+
+ cmd = """
+ cat {in1} |
+ {scripts}/trim-low-abund.py --small-count \
+ -k 17 -x 1e7 -N 2 - -o - > {out1}
+ """
+
+ cmd = cmd.format(scripts=scriptpath(), in1=in1, out1=out1)
+
+ run_shell_cmd(cmd)
+
+ assert os.path.exists(out1)
+ seqs = set([r.sequence for r in screed.open(out1)])
+
+ assert len(seqs) == 1, seqs
+ assert 'GGTTGACGGGGCTCAGGG' in seqs
+
+
+def test_trim_low_abund_1_gzip_o():
+ in1 = utils.get_test_data('test-abund-read-2.fa')
+ out1 = utils.get_temp_filename('out.abundtrim.gz')
+
+ cmd = """
+ cat {in1} |
+ {scripts}/trim-low-abund.py -k 17 -x 1e7 -N 2 - -o - --gzip > {out1}
+ """
+
+ cmd = cmd.format(scripts=scriptpath(), in1=in1, out1=out1)
+
+ run_shell_cmd(cmd)
+
+ assert os.path.exists(out1)
+ seqs = set([r.sequence for r in screed.open(out1)])
+
+ assert len(seqs) == 1, seqs
+ assert 'GGTTGACGGGGCTCAGGG' in seqs
+
+
def test_trim_low_abund_2_fail():
in1 = utils.get_test_data('test-abund-read-2.fa')
out1 = utils.get_temp_filename('out.abundtrim')
@@ -466,7 +524,7 @@ def test_trim_low_abund_2_fail():
cmd = cmd.format(scripts=scriptpath(), in1=in1, out1=out1)
- (status, out, err) = run_shell_cmd(cmd, fail_ok=True)
+ (status, _, err) = run_shell_cmd(cmd, fail_ok=True)
assert status != 0
assert "Accepting input from stdin; output filename must be provided with"\
in err, err
@@ -516,7 +574,7 @@ def test_unique_kmers_stream_out_fasta():
cmd = "{scripts}/unique-kmers.py -k 20 -e 0.01 --stream-records {infile}"
cmd = cmd.format(scripts=scriptpath(), infile=infile)
- (status, out, err) = run_shell_cmd(cmd)
+ (_, out, err) = run_shell_cmd(cmd)
expected = ('Estimated number of unique 20-mers in {infile}: 3950'
.format(infile=infile))
@@ -533,7 +591,7 @@ def test_unique_kmers_stream_out_fastq_with_N():
cmd = "{scripts}/unique-kmers.py -k 20 -e 0.01 --stream-records {infile}"
cmd = cmd.format(scripts=scriptpath(), infile=infile)
- (status, out, err) = run_shell_cmd(cmd)
+ (_, out, err) = run_shell_cmd(cmd)
expected = ('Estimated number of unique 20-mers in {infile}: 94'
.format(infile=infile))
diff --git a/tests/test_subset_graph.py b/tests/test_subset_graph.py
index 0a33d0e..bab7b62 100644
--- a/tests/test_subset_graph.py
+++ b/tests/test_subset_graph.py
@@ -1,6 +1,6 @@
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2010-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -32,9 +32,10 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
-# pylint: disable=missing-docstring,invalid-name,unused-variable,no-member
-from __future__ import print_function
-from __future__ import absolute_import
+# pylint: disable=missing-docstring,invalid-name,no-member,no-self-use
+# pylint: disable=protected-access
+from __future__ import print_function, absolute_import
+
import khmer
import screed
@@ -53,12 +54,12 @@ class Test_RandomData(object):
filename = utils.get_test_data('test-graph2.fa')
- (total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
+ (total_reads, _) = ht.consume_seqfile_and_tag(filename)
assert total_reads == 3, total_reads
divvy = ht.divide_tags_into_subsets(1)
assert len(divvy) is 3
- (a, b, c) = divvy
+ (a, b, _) = divvy
x = ht.do_subset_partition(a, a)
ht.merge_subset(x)
@@ -74,7 +75,7 @@ class Test_RandomData(object):
ht = khmer.Nodegraph(20, 4 ** 4 + 1, 2)
filename = utils.get_test_data('test-graph2.fa')
- (total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
+ (total_reads, _) = ht.consume_seqfile_and_tag(filename)
assert total_reads == 3, total_reads
divvy = ht.divide_tags_into_subsets(1)
@@ -95,10 +96,11 @@ class Test_RandomData(object):
ht = khmer.Nodegraph(20, 4 ** 4 + 1, 2)
filename = utils.get_test_data('test-graph5.fa')
- (total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
+ (total_reads, _) = ht.consume_seqfile_and_tag(filename)
assert total_reads == 6, total_reads
divvy = ht.divide_tags_into_subsets(1)
+ divvy = list(divvy)
x = ht.do_subset_partition(divvy[0], divvy[4])
ht.merge_subset(x)
@@ -115,10 +117,11 @@ class Test_RandomData(object):
filename = utils.get_test_data('random-20-a.fa')
outfile = utils.get_temp_filename('out')
- total_reads, _ = ht.consume_fasta_and_tag(filename)
+ total_reads, _ = ht.consume_seqfile_and_tag(filename)
subset_size = total_reads // 2 + total_reads % 2
divvy = ht.divide_tags_into_subsets(subset_size)
+ divvy = list(divvy)
assert len(divvy) == 4
x = ht.do_subset_partition(divvy[0], divvy[2])
@@ -134,10 +137,11 @@ class Test_RandomData(object):
filename = utils.get_test_data('random-20-a.fa')
outfile = utils.get_temp_filename('out')
- total_reads, _ = ht.consume_fasta_and_tag(filename)
+ total_reads, _ = ht.consume_seqfile_and_tag(filename)
subset_size = total_reads // 2 + total_reads % 2
divvy = ht.divide_tags_into_subsets(subset_size)
+ divvy = list(divvy)
assert len(divvy) == 4
x = ht.do_subset_partition(divvy[0], divvy[2])
@@ -153,10 +157,11 @@ class Test_RandomData(object):
filename = utils.get_test_data('random-20-a.fa')
outfile = utils.get_temp_filename('out')
- total_reads, _ = ht.consume_fasta_and_tag(filename)
+ total_reads, _ = ht.consume_seqfile_and_tag(filename)
subset_size = total_reads // 2 + total_reads % 2
divvy = ht.divide_tags_into_subsets(subset_size)
+ divvy = list(divvy)
assert len(divvy) == 4, len(divvy)
x = ht.do_subset_partition(divvy[0], divvy[2])
@@ -176,10 +181,11 @@ class Test_RandomData(object):
filename = utils.get_test_data('random-20-a.fa')
outfile = utils.get_temp_filename('out')
- total_reads, _ = ht.consume_fasta_and_tag(filename)
+ ht.consume_seqfile_and_tag(filename)
subsets = []
divvy = ht.divide_tags_into_subsets(1)
+ divvy = list(divvy)
divvy.append(0)
for i in range(len(divvy) - 1):
x = ht.do_subset_partition(divvy[i], divvy[i + 1])
@@ -199,7 +205,7 @@ class Test_RandomData(object):
savefile_tags = utils.get_temp_filename('tags')
outfile = filename + utils.get_temp_filename('out')
- total_reads, _ = ht.consume_fasta_and_tag(filename)
+ ht.consume_seqfile_and_tag(filename)
ht.save(savefile_ht)
ht.save_tagset(savefile_tags)
@@ -211,6 +217,7 @@ class Test_RandomData(object):
ht.load_tagset(savefile_tags)
divvy = ht.divide_tags_into_subsets(1)
+ divvy = list(divvy)
divvy.append(0)
subsets = []
@@ -231,13 +238,12 @@ class Test_SaveLoadPmap(object):
ht = khmer.Nodegraph(20, 4 ** 4 + 1, 2)
filename = utils.get_test_data('test-graph2.fa')
- (total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
+ (total_reads, _) = ht.consume_seqfile_and_tag(filename)
assert total_reads == 3, total_reads
divvy = ht.divide_tags_into_subsets(1)
- print(divvy)
assert len(divvy) == 3
- (a, b, c) = divvy
+ (a, b, _) = divvy
outfile1 = utils.get_temp_filename('x.pmap')
outfile2 = utils.get_temp_filename('y.pmap')
@@ -264,13 +270,13 @@ class Test_SaveLoadPmap(object):
ht = khmer.Nodegraph(20, 4 ** 4 + 1, 2)
filename = utils.get_test_data('test-graph2.fa')
- (total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
+ (total_reads, _) = ht.consume_seqfile_and_tag(filename)
assert total_reads == 3, total_reads
divvy = ht.divide_tags_into_subsets(1)
print(divvy)
assert len(divvy) is 3
- (a, b, c) = divvy
+ (a, b, _) = divvy
outfile1 = utils.get_temp_filename('x.pmap')
outfile2 = utils.get_temp_filename('y.pmap')
@@ -301,10 +307,11 @@ class Test_SaveLoadPmap(object):
ht = khmer.Nodegraph(20, 4 ** 8 + 1, 2)
filename = utils.get_test_data('random-20-a.fa')
- (total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
+ (total_reads, _) = ht.consume_seqfile_and_tag(filename)
subset_size = total_reads // 2 + total_reads % 2
divvy = ht.divide_tags_into_subsets(subset_size)
+ divvy = list(divvy)
outfile1 = utils.get_temp_filename('x.pmap')
outfile2 = utils.get_temp_filename('y.pmap')
@@ -332,7 +339,7 @@ class Test_SaveLoadPmap(object):
def test_save_load_merge_nexist(self):
ht = khmer._Nodegraph(20, [1])
try:
- a = ht.load_subset_partitionmap('this does not exist')
+ ht.load_subset_partitionmap('this does not exist')
assert 0, "this should not succeed"
except OSError as e:
print(str(e))
@@ -341,12 +348,12 @@ class Test_SaveLoadPmap(object):
ht = khmer.Nodegraph(20, 4 ** 4 + 1, 2)
filename = utils.get_test_data('test-graph2.fa')
- (total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
+ (total_reads, _) = ht.consume_seqfile_and_tag(filename)
assert total_reads == 3, total_reads
divvy = ht.divide_tags_into_subsets(1)
print(divvy)
- (a, b, c) = divvy
+ (a, b, _) = divvy
outfile1 = utils.get_temp_filename('x.pmap')
outfile2 = utils.get_temp_filename('y.pmap')
@@ -370,10 +377,11 @@ class Test_SaveLoadPmap(object):
ht = khmer.Nodegraph(20, 4 ** 7 + 1, 2)
filename = utils.get_test_data('random-20-a.fa')
- (total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
+ (total_reads, _) = ht.consume_seqfile_and_tag(filename)
subset_size = total_reads // 2 + total_reads % 2
divvy = ht.divide_tags_into_subsets(subset_size)
+ divvy = list(divvy)
outfile1 = utils.get_temp_filename('x.pmap')
outfile2 = utils.get_temp_filename('y.pmap')
@@ -399,13 +407,9 @@ class Test_SaveLoadPmap(object):
ht = khmer.Nodegraph(20, 4 ** 4 + 1, 2)
filename = utils.get_test_data('test-graph2.fa')
- (total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
+ (total_reads, _) = ht.consume_seqfile_and_tag(filename)
assert total_reads == 3, total_reads
- divvy = ht.divide_tags_into_subsets(1)
- print(divvy)
- (a, b, c) = divvy
-
outfile1 = utils.get_temp_filename('x.pmap')
# fail to create file... => failure expected
@@ -440,12 +444,12 @@ class Test_SaveLoadPmap(object):
ht = khmer.Nodegraph(20, 4 ** 4 + 1, 2)
filename = utils.get_test_data('test-graph2.fa')
- (total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
+ (total_reads, _) = ht.consume_seqfile_and_tag(filename)
assert total_reads == 3, total_reads
divvy = ht.divide_tags_into_subsets(1)
print(divvy)
- (a, b, c) = divvy
+ (a, b, _) = divvy
outfile1 = utils.get_temp_filename('x.pmap')
x = ht.do_subset_partition(a, b)
@@ -464,13 +468,13 @@ def test_save_load_merge_on_graph():
ht = khmer.Nodegraph(20, 4 ** 4 + 1, 2)
filename = utils.get_test_data('test-graph2.fa')
- (total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
+ (total_reads, _) = ht.consume_seqfile_and_tag(filename)
assert total_reads == 3, total_reads
divvy = ht.divide_tags_into_subsets(1)
print(divvy)
assert len(divvy) is 3
- (a, b, c) = divvy
+ (a, b, _) = divvy
outfile1 = utils.get_temp_filename('x.pmap')
outfile2 = utils.get_temp_filename('y.pmap')
@@ -497,13 +501,13 @@ def test_save_load_on_graph_truncate():
ht = khmer.Nodegraph(20, 4 ** 4 + 1, 2)
filename = utils.get_test_data('test-graph2.fa')
- (total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
+ (total_reads, _) = ht.consume_seqfile_and_tag(filename)
assert total_reads == 3, total_reads
divvy = ht.divide_tags_into_subsets(1)
print(divvy)
assert len(divvy) is 3
- (a, b, c) = divvy
+ (a, b, _) = divvy
outfile1 = utils.get_temp_filename('x.pmap')
outfile2 = utils.get_temp_filename('y.pmap')
@@ -560,7 +564,7 @@ def test_tiny_real_partitions():
filename = utils.get_test_data('real-partition-tiny.fa')
ht = khmer.Nodegraph(32, 8e2, 4)
- ht.consume_fasta_and_tag(filename)
+ ht.consume_seqfile_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
ht.merge_subset(subset)
@@ -587,7 +591,7 @@ def test_small_real_partitions():
filename = utils.get_test_data('real-partition-small.fa')
ht = khmer.Nodegraph(32, 2e3, 4)
- ht.consume_fasta_and_tag(filename)
+ ht.consume_seqfile_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
ht.merge_subset(subset)
@@ -608,7 +612,7 @@ def test_small_real_partitions():
test_small_real_partitions.runme = True
-a = """\
+first = """\
CAGACTTGGAAGCTGAGAGTCCGACGTCACTGCCTCAACTCGCGCAAATGTTCCCGCCAA\
ATTGTATCCTAGGGATCTTCCATAAGCTTATATACGGGGGTTTCCAAGGCCCTGATGCCA\
GTGCCTAATCTTTTGGAGTCCTCTCAGGGCCACTAGATGCCATGCTACGCGTCCCAGGTT\
@@ -616,7 +620,7 @@ GGCCTGAGGGTCTACACGGAGTGGGAAGCATGGGTACCTTAGCGAACATTCATACTGGCC\
TGTTTATGCTTATCAGACTTCAGCTTCGCTTAGCGCGTCACCGTTTGTAACTTGTTATCT\
"""
-b = """\
+second = """\
TGTTTATGCTTATCAGACTTCAGCTTCGCTTAGCGCGTCACCGTTTGTAACTTGTTATCT\
GACTGTAGACTTGAACCTCGATGGAATGCAGGTCCCATTCTCTGGCCTGACTCATGGAAC\
CGAGGCCAAAAAAGCATGGCACGAAGACGCTATGCGAGGGTGCTCGCCCATGTCGTCGCC\
@@ -626,14 +630,12 @@ CCTCGGGCCTTTCCGTTCCGTTGCCGCCCAAGCTCTCTAGCATCGAATCGGTCAAGCGGT\
def test_partition_on_abundance_1():
- print((a,))
- print((b,))
kh = khmer.Countgraph(20, 1e3, 4)
- for i in range(10):
- print(kh.consume_and_tag(a))
+ for _ in range(10):
+ print(kh.consume_and_tag(first))
- for i in range(10):
- print(kh.consume_and_tag(b))
+ for _ in range(10):
+ print(kh.consume_and_tag(second))
# all paths in 'a' and 'b'
p = kh.do_subset_partition_with_abundance(10, 50)
@@ -643,11 +645,11 @@ def test_partition_on_abundance_1():
def test_partition_on_abundance_2():
kh = khmer.Countgraph(20, 1e3, 4)
- for i in range(10):
- print(kh.consume_and_tag(a))
+ for _ in range(10):
+ print(kh.consume_and_tag(first))
- for i in range(5):
- print(kh.consume_and_tag(b))
+ for _ in range(5):
+ print(kh.consume_and_tag(second))
# all paths in 'a'
p = kh.do_subset_partition_with_abundance(10, 50)
@@ -657,11 +659,11 @@ def test_partition_on_abundance_2():
def test_partition_on_abundance_3():
kh = khmer.Countgraph(20, 1e4, 4)
- for i in range(10):
- print(kh.consume_and_tag(a))
+ for _ in range(10):
+ print(kh.consume_and_tag(first))
- for i in range(5):
- print(kh.consume_and_tag(b))
+ for _ in range(5):
+ print(kh.consume_and_tag(second))
# this will get paths only in 'a'
p = kh.do_subset_partition_with_abundance(10, 50)
@@ -674,34 +676,13 @@ def test_partition_on_abundance_3():
assert x == (2, 2) # two partitions, two ignored tags
-def test_partition_overlap_1():
- kh = khmer.Countgraph(20, 1e3, 4)
- for i in range(10):
- kh.consume_and_tag(a)
-
- for i in range(10):
- kh.consume_and_tag(b)
-
- # this will get paths only in 'a'
- p1 = kh.do_subset_partition_with_abundance(10, 50)
-
- # this will get paths only in 'a', again -- should be the same!
- p2 = kh.do_subset_partition_with_abundance(10, 50)
-
- # p1.report_on_partitions()
- # p2.report_on_partitions()
-
- x = p1.compare_partitions(3, p2, 3)
- assert x == (0, 0, 14), x
-
-
def test_partition_overlap_2():
kh = khmer.Countgraph(20, 1e4, 4)
- for i in range(10):
- kh.consume_and_tag(a)
+ for _ in range(10):
+ kh.consume_and_tag(first)
- for i in range(5):
- kh.consume_and_tag(b)
+ for _ in range(5):
+ kh.consume_and_tag(second)
# this will get paths only in 'a'
p1 = kh.do_subset_partition_with_abundance(10, 50)
@@ -712,17 +693,11 @@ def test_partition_overlap_2():
# p1.report_on_partitions()
# p2.report_on_partitions()
- x = p1.compare_partitions(3, p2, 3)
- assert x == (8, 6, 0), x
-
- x = p1.compare_partitions(3, p2, 5)
- assert x == (2, 0, 6), x
-
x = p1.partition_sizes()
assert x == ([(3, 8)], 0), x
x = p2.partition_sizes()
- assert x == ([(3, 6), (5, 6)], 2), x
+ assert x == ([(3, 6), (5, 6)], 0), x
x = p1.partition_average_coverages(kh)
assert x == [(3, 11)]
diff --git a/tests/test_tabletype.py b/tests/test_tabletype.py
new file mode 100644
index 0000000..6d5293b
--- /dev/null
+++ b/tests/test_tabletype.py
@@ -0,0 +1,446 @@
+"""
+Tests for common features of *all* tables, including 1-bit presence/absence
+tables.
+
+This tests:
+
+* method implementations in common between all "table types", including
+ error handling code;
+* basic API compatibility between all "table types", for methods with
+ their own implementations.
+
+Error handling & other class-specific code (e.g. in methods like
+'load' and 'save' that are implemented differently for each type) will
+be tested separately. We can use code coverage to identify that
+code...
+"""
+
+import sys
+import pytest
+
+
+from . import khmer_tst_utils as utils
+import khmer
+from khmer import _Countgraph, _Counttable, _SmallCountgraph, _SmallCounttable
+from khmer import _Nodegraph, _Nodetable
+from khmer import ReadParser
+import screed
+
+
+PRIMES_1m = [1000003, 1009837]
+
+
+# all the table types!
+ at pytest.fixture(params=[_Countgraph, _Counttable, _SmallCountgraph,
+ _SmallCounttable, _Nodegraph, _Nodetable])
+def tabletype(request):
+ return request.param
+
+# For map(long, [list of ints]) cross-version hackery
+if sys.version_info.major > 2:
+ long = int # pylint: disable=redefined-builtin
+ unicode = str
+
+
+def test_presence(tabletype):
+ # basic get/add test
+ tt = tabletype(12, PRIMES_1m)
+
+ kmer = 'G' * 12
+ hashval = tt.hash('G' * 12)
+
+ assert tt.get(kmer) == 0
+ assert tt.get(hashval) == 0
+
+ tt.add(kmer)
+ assert tt.get(kmer) == 1
+ assert tt.get(hashval) == 1
+
+
+def test_bad_create(tabletype):
+ # creation should fail w/bad parameters
+ try:
+ tt = tabletype(5, [])
+ except ValueError as err:
+ assert 'tablesizes needs to be one or more numbers' in str(err)
+
+
+def test_get_ksize(tabletype):
+ # ksize() function.
+ kh = tabletype(22, PRIMES_1m)
+ assert kh.ksize() == 22
+
+
+def test_hash(tabletype):
+ # hashing of strings -> numbers.
+ kh = tabletype(5, PRIMES_1m)
+ x = kh.hash("ATGGC")
+ assert type(x) == long
+
+
+def test_hash_bad_dna(tabletype):
+ # hashing of bad dna -> succeeds w/o complaint
+ kh = tabletype(5, PRIMES_1m)
+
+ x = kh.hash("ATGYC")
+
+
+def test_hash_bad_length(tabletype):
+ # hashing of bad dna length -> error
+ kh = tabletype(5, PRIMES_1m)
+
+ with pytest.raises(ValueError):
+ x = kh.hash("ATGGGC")
+
+ with pytest.raises(ValueError):
+ x = kh.hash("ATGG")
+
+
+def test_reverse_hash(tabletype):
+ # hashing of strings -> numbers.
+ kh = tabletype(5, PRIMES_1m)
+
+ try:
+ x = kh.reverse_hash(15)
+ except ValueError:
+ pytest.skip("reverse_hash not implemented on this table type")
+
+ assert isinstance(x, (unicode, str))
+
+
+def test_hashsizes(tabletype):
+ # hashsizes method.
+ kh = tabletype(5, PRIMES_1m)
+ assert kh.hashsizes() == PRIMES_1m
+
+
+def test_add_hashval(tabletype):
+ # test add(hashval)
+ kh = tabletype(5, PRIMES_1m)
+ x = kh.hash("ATGGC")
+ y = kh.add(x)
+ assert y
+
+ z = kh.get(x)
+ assert z == 1
+
+
+def test_add_dna_kmer(tabletype):
+ # test add(dna)
+ kh = tabletype(5, PRIMES_1m)
+ x = kh.add("ATGGC")
+ assert x
+
+ z = kh.get("ATGGC")
+ assert z == 1
+
+
+def test_add_bad_dna_kmer(tabletype):
+ # even with 'bad' dna, should succeed.
+ kh = tabletype(5, PRIMES_1m)
+
+ x = kh.add("ATYGC")
+
+
+def test_get_hashval(tabletype):
+ # test get(hashval)
+ kh = tabletype(5, PRIMES_1m)
+ hashval = kh.hash("ATGGC")
+ kh.add(hashval)
+
+ z = kh.get(hashval)
+ assert z == 1
+
+
+def test_get_hashval_rc(tabletype):
+ # test get(hashval)
+ kh = tabletype(4, PRIMES_1m)
+ hashval = kh.hash("ATGC")
+ rc = kh.hash("GCAT")
+
+ assert hashval == rc
+
+
+def test_get_dna_kmer(tabletype):
+ # test get(dna)
+ kh = tabletype(5, PRIMES_1m)
+ hashval = kh.hash("ATGGC")
+ kh.add(hashval)
+
+ z = kh.get("ATGGC")
+ assert z == 1
+
+
+def test_get_bad_dna_kmer(tabletype):
+ # test get(dna) with bad dna; should be fine.
+ kh = tabletype(5, PRIMES_1m)
+
+ kh.hash("ATYGC")
+
+
+def test_consume_and_count(tabletype):
+ tt = tabletype(6, PRIMES_1m)
+
+ x = "ATGCCGATGCA"
+ num_kmers = tt.consume(x)
+ assert num_kmers == len(x) - tt.ksize() + 1 # num k-mers consumed
+
+ for start in range(len(x) - 6 + 1):
+ assert tt.get(x[start:start + 6]) == 1
+
+
+def test_consume_and_count_bad_dna(tabletype):
+ # while we don't specifically handle bad DNA, we should at least be
+ # consistent...
+ tt = tabletype(6, PRIMES_1m)
+
+ x = "ATGCCGNTGCA"
+ num_kmers = tt.consume(x)
+
+ for start in range(len(x) - 6 + 1):
+ assert tt.get(x[start:start + 6]) == 1
+
+
+def test_consume_short(tabletype):
+ # raise error on too short when consume is run
+ tt = tabletype(6, PRIMES_1m)
+
+ x = "ATGCA"
+ with pytest.raises(ValueError):
+ tt.consume(x)
+
+
+def test_get_kmer_counts(tabletype):
+ hi = tabletype(6, PRIMES_1m)
+
+ hi.consume("AAAAAA")
+ counts = hi.get_kmer_counts("AAAAAA")
+ print(counts)
+ assert len(counts) == 1
+ assert counts[0] == 1
+
+ hi.consume("AAAAAA")
+ counts = hi.get_kmer_counts("AAAAAA")
+ print(counts)
+ assert len(counts) == 1
+ assert counts[0] >= 1
+
+ hi.consume("AAAAAT")
+ counts = hi.get_kmer_counts("AAAAAAT")
+ print(counts)
+ assert len(counts) == 2
+ assert counts[0] >= 1
+ assert counts[1] == 1
+
+
+def test_get_kmer_hashes(tabletype):
+ hi = tabletype(6, PRIMES_1m)
+
+ hashes = hi.get_kmer_hashes("ACGTGCGT")
+ print(hashes)
+ assert len(hashes) == 3
+ assert hashes[0] == hi.hash("ACGTGC")
+ assert hashes[1] == hi.hash("CGTGCG")
+ assert hashes[2] == hi.hash("GTGCGT")
+
+
+def test_get_min_count(tabletype):
+ hi = tabletype(6, PRIMES_1m)
+
+ # master string, 3 k-mers
+ x = "ACGTGCGT"
+
+ hi.add("ACGTGC") # 3
+ hi.add("ACGTGC")
+ hi.add("ACGTGC")
+
+ hi.add("CGTGCG") # 1
+
+ hi.add("GTGCGT") # 2
+ hi.add("GTGCGT")
+
+ counts = hi.get_kmer_counts(x)
+ assert hi.get_min_count(x) == min(counts)
+ assert hi.get_max_count(x) == max(counts)
+ med, _, _ = hi.get_median_count(x)
+ assert med == list(sorted(counts))[len(counts) // 2]
+
+
+def test_get_kmers(tabletype):
+ hi = tabletype(6, PRIMES_1m)
+
+ kmers = hi.get_kmers("AAAAAA")
+ assert kmers == ["AAAAAA"]
+
+ kmers = hi.get_kmers("AAAAAAT")
+ assert kmers == ["AAAAAA", "AAAAAT"]
+
+ kmers = hi.get_kmers("AGCTTTTC")
+ assert kmers == ['AGCTTT', 'GCTTTT', 'CTTTTC']
+
+
+def test_trim_on_abundance(tabletype):
+ hi = tabletype(6, PRIMES_1m)
+
+ x = "ATGGCAGTAGCAGTGAGC"
+ hi.consume(x[:10])
+
+ (y, pos) = hi.trim_on_abundance(x, 1)
+ assert pos == 10
+ assert x[:pos] == y
+
+
+def test_trim_below_abundance(tabletype):
+ hi = tabletype(6, PRIMES_1m)
+
+ x = "ATGGCAGTAGCAGTGAGC"
+ x_rc = screed.rc(x)
+ hi.consume(x_rc[:10])
+
+ print(len(x))
+
+ (y, pos) = hi.trim_below_abundance(x, 0)
+ assert pos == len(x) - hi.ksize() + 1
+ assert x[:pos] == y
+
+
+DNA = "AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC"
+
+
+def test_find_spectral_error_positions(tabletype):
+ kh = tabletype(8, PRIMES_1m)
+
+ kh.consume(DNA[:30])
+
+ for n in range(len(DNA) - 8 + 1):
+ print(n, kh.get(DNA[n:n + 8]))
+
+ posns = kh.find_spectral_error_positions(DNA, 0)
+ assert posns == [30], posns
+
+
+def test_find_spectral_error_positions_6(tabletype):
+ kh = tabletype(8, PRIMES_1m)
+
+ kh.consume(DNA[1:])
+
+ for n in range(len(DNA) - 8 + 1):
+ print(n, kh.get(DNA[n:n + 8]))
+
+ posns = kh.find_spectral_error_positions(DNA, 0)
+ assert posns == [0], posns
+
+
+def test_find_spectral_error_positions_5(tabletype):
+ kh = tabletype(8, PRIMES_1m)
+
+ kh.consume(DNA[:10])
+ kh.consume(DNA[11:])
+
+ posns = kh.find_spectral_error_positions(DNA, 0)
+ assert posns == [10], posns
+
+
+def test_consume_seqfile_reads_parser(tabletype):
+ kh = tabletype(5, PRIMES_1m)
+ rparser = ReadParser(utils.get_test_data('test-fastq-reads.fq'))
+
+ kh.consume_seqfile_with_reads_parser(rparser)
+
+ kh2 = tabletype(5, PRIMES_1m)
+ for record in screed.open(utils.get_test_data('test-fastq-reads.fq')):
+ kh2.consume(record.sequence)
+
+ assert kh.get('CCGGC') == kh2.get('CCGGC')
+
+
+def test_consume_seqfile(tabletype):
+ kh = tabletype(5, PRIMES_1m)
+ kh.consume_seqfile(utils.get_test_data('test-fastq-reads.fq'))
+
+ kh2 = tabletype(5, PRIMES_1m)
+ for record in screed.open(utils.get_test_data('test-fastq-reads.fq')):
+ kh2.consume(record.sequence)
+
+ assert kh.get('CCGGC') == kh2.get('CCGGC')
+
+
+def test_save_load(tabletype):
+ kh = tabletype(5, PRIMES_1m)
+ savefile = utils.get_temp_filename('tablesave.out')
+
+ # test add(dna)
+ x = kh.add("ATGGC")
+ z = kh.get("ATGGC")
+ assert z == 1
+
+ kh.save(savefile)
+
+ # should we provide a single load function here? yes, probably. @CTB
+ if tabletype == _Countgraph:
+ loaded = khmer.load_countgraph(savefile)
+ elif tabletype == _Counttable:
+ loaded = khmer.load_counttable(savefile)
+ elif tabletype == _SmallCountgraph:
+ loaded = khmer.load_countgraph(savefile, small=True)
+ elif tabletype == _SmallCounttable:
+ loaded = khmer.load_counttable(savefile, small=True)
+ elif tabletype in (_Nodegraph, _Nodetable):
+ loaded = khmer.load_nodegraph(savefile)
+ else:
+ raise Exception("unknown tabletype")
+
+ z = loaded.get('ATGGC')
+ assert z == 1
+
+
+def test_get_bigcount(tabletype):
+ # get_bigcount should return false by default
+ tt = tabletype(12, PRIMES_1m)
+
+ assert not tt.get_use_bigcount()
+
+
+def test_set_bigcount(tabletype):
+ supports_bigcount = [_Countgraph, _Counttable]
+ tt = tabletype(12, PRIMES_1m)
+
+ if tabletype in supports_bigcount:
+ tt.set_use_bigcount(True)
+
+ for i in range(300):
+ tt.add('G'*12)
+ assert tt.get('G'*12) == 300
+
+ else:
+ with pytest.raises(ValueError):
+ tt.set_use_bigcount(True)
+
+
+def test_abund_dist_A(tabletype):
+ A_filename = utils.get_test_data('all-A.fa')
+
+ kh = tabletype(4, PRIMES_1m)
+ tracking = khmer._Nodegraph(4, PRIMES_1m)
+
+ kh.consume_seqfile(A_filename)
+ dist = kh.abundance_distribution(A_filename, tracking)
+
+ print(dist[:10])
+ assert sum(dist) == 1
+ assert dist[0] == 0
+
+
+def test_abund_dist_A_readparser(tabletype):
+ A_filename = utils.get_test_data('all-A.fa')
+ rparser = ReadParser(A_filename)
+
+ kh = tabletype(4, PRIMES_1m)
+ tracking = khmer._Nodetable(4, PRIMES_1m)
+
+ kh.consume_seqfile(A_filename)
+ dist = kh.abundance_distribution(A_filename, tracking)
+
+ print(dist[:10])
+ assert sum(dist) == 1
+ assert dist[0] == 0
diff --git a/tests/test_threaded_sequence_processor.py b/tests/test_threaded_sequence_processor.py
index eebd233..aaa7b37 100644
--- a/tests/test_threaded_sequence_processor.py
+++ b/tests/test_threaded_sequence_processor.py
@@ -32,13 +32,12 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
+# pylint: disable=missing-docstring,invalid-name
-import sys
from khmer.thread_utils import ThreadedSequenceProcessor, SequenceGroup
from io import StringIO
from screed.fasta import fasta_iter
from screed.fastq import fastq_iter
-from nose.plugins.attrib import attr
import screed
# stdlib queue module was renamed on Python 3
@@ -73,7 +72,7 @@ odd_counter = 0
def every_other(record):
- global odd_counter
+ global odd_counter # pylint: disable=global-statement
odd_counter += 1
if odd_counter % 2 == 1:
return None, None
@@ -86,11 +85,11 @@ def every_other(record):
def test_basic():
tsp = ThreadedSequenceProcessor(idem, 1, 1, verbose=False)
- input = [screed.Record(name='a', sequence='AAA'),
- screed.Record(name='b', sequence='TTT'), ]
+ inseqs = [screed.Record(name='a', sequence='AAA'),
+ screed.Record(name='b', sequence='TTT'), ]
outfp = StringIO()
- tsp.start(input, outfp)
+ tsp.start(inseqs, outfp)
x = load_records_d(outfp)
assert len(x) == 2, x
@@ -101,11 +100,11 @@ def test_basic():
def test_basic_fastq_like():
tsp = ThreadedSequenceProcessor(idem, 1, 1, verbose=False)
- input = [screed.Record(name='a', sequence='AAA', quality='###'),
- screed.Record(name='b', sequence='TTT', quality='###'), ]
+ inseqs = [screed.Record(name='a', sequence='AAA', quality='###'),
+ screed.Record(name='b', sequence='TTT', quality='###'), ]
outfp = StringIO()
- tsp.start(input, outfp)
+ tsp.start(inseqs, outfp)
x = load_records_fastq(outfp)
for i in x:
@@ -115,11 +114,11 @@ def test_basic_fastq_like():
def test_odd():
tsp = ThreadedSequenceProcessor(every_other, 1, 1, verbose=False)
- input = [screed.Record(name='a', sequence='AAA'),
- screed.Record(name='b', sequence='TTT'), ]
+ inseqs = [screed.Record(name='a', sequence='AAA'),
+ screed.Record(name='b', sequence='TTT'), ]
outfp = StringIO()
- tsp.start(input, outfp)
+ tsp.start(inseqs, outfp)
x = load_records_d(outfp)
assert len(x) == 1, x
@@ -129,11 +128,11 @@ def test_odd():
def test_basic_2thread():
tsp = ThreadedSequenceProcessor(idem, 2, 1, verbose=False)
- input = [screed.Record(name='a', sequence='AAA'),
- screed.Record(name='b', sequence='TTT'), ]
+ inseqs = [screed.Record(name='a', sequence='AAA'),
+ screed.Record(name='b', sequence='TTT'), ]
outfp = StringIO()
- tsp.start(input, outfp)
+ tsp.start(inseqs, outfp)
x = load_records_d(outfp)
assert len(x) == 2, x
@@ -147,7 +146,6 @@ def test_paired_2thread():
def do_process(self):
inq = self.inqueue
- outq = self.outqueue
while not self.done or not inq.empty():
try:
@@ -178,11 +176,11 @@ def test_paired_2thread():
tsp = TSP_TestPairedProcess(idem, 1, 1, verbose=False)
- input = [screed.Record(name='a/1', sequence='AAA'),
- screed.Record(name='a/2', sequence='TTT'), ]
+ inseqs = [screed.Record(name='a/1', sequence='AAA'),
+ screed.Record(name='a/2', sequence='TTT'), ]
outfp = StringIO()
- tsp.start(input, outfp)
+ tsp.start(inseqs, outfp)
x = load_records_d(outfp)
assert len(x) == 2, x
@@ -196,7 +194,6 @@ def test_paired_2thread_more_seq():
def do_process(self):
inq = self.inqueue
- outq = self.outqueue
while not self.done or not inq.empty():
try:
@@ -227,13 +224,13 @@ def test_paired_2thread_more_seq():
tsp = TSP_TestPairedProcess(idem, 1, 1, verbose=False)
- input = [screed.Record(name='b/1', sequence='AAA'),
- screed.Record(name='a/1', sequence='AAA'),
- screed.Record(name='a/2', sequence='TTT'),
- screed.Record(name='c/2', sequence='AAA'), ]
+ inseqs = [screed.Record(name='b/1', sequence='AAA'),
+ screed.Record(name='a/1', sequence='AAA'),
+ screed.Record(name='a/2', sequence='TTT'),
+ screed.Record(name='c/2', sequence='AAA'), ]
outfp = StringIO()
- tsp.start(input, outfp)
+ tsp.start(inseqs, outfp)
x = load_records_d(outfp)
assert len(x) == 4, x
diff --git a/tests/test_version.py b/tests/test_version.py
index e435b87..d436669 100644
--- a/tests/test_version.py
+++ b/tests/test_version.py
@@ -1,6 +1,6 @@
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2011-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
@@ -32,15 +32,16 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project at idyll.org
+# pylint: disable=missing-docstring
from __future__ import print_function, unicode_literals
+
import khmer
-from nose.plugins.attrib import attr
+import pytest
- at attr('jenkins')
+ at pytest.mark.jenkins
def test_python_and_c_match():
- # checks c++ compiler option version against versioneer version
- # (respectively)
+ """checks c++ compiler option version against versioneer version"""
print('c++ version {0}:'.format(khmer.__version_cpp__()))
print('versioneer (python) version: {0}'.format(khmer.__version__))
assert khmer.__version_cpp__() == khmer.__version__
diff --git a/third-party/bzip2/.gitignore b/third-party/bzip2/.gitignore
new file mode 100644
index 0000000..0dadbab
--- /dev/null
+++ b/third-party/bzip2/.gitignore
@@ -0,0 +1,2 @@
+bzip2-shared
+libbz2.so.*
diff --git a/third-party/bzip2/CHANGES b/third-party/bzip2/CHANGES
new file mode 100644
index 0000000..81e97ca
--- /dev/null
+++ b/third-party/bzip2/CHANGES
@@ -0,0 +1,327 @@
+ ------------------------------------------------------------------
+ This file is part of bzip2/libbzip2, a program and library for
+ lossless, block-sorting data compression.
+
+ bzip2/libbzip2 version 1.0.6 of 6 September 2010
+ Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
+
+ Please read the WARNING, DISCLAIMER and PATENTS sections in the
+ README file.
+
+ This program is released under the terms of the license contained
+ in the file LICENSE.
+ ------------------------------------------------------------------
+
+
+0.9.0
+~~~~~
+First version.
+
+
+0.9.0a
+~~~~~~
+Removed 'ranlib' from Makefile, since most modern Unix-es
+don't need it, or even know about it.
+
+
+0.9.0b
+~~~~~~
+Fixed a problem with error reporting in bzip2.c. This does not effect
+the library in any way. Problem is: versions 0.9.0 and 0.9.0a (of the
+program proper) compress and decompress correctly, but give misleading
+error messages (internal panics) when an I/O error occurs, instead of
+reporting the problem correctly. This shouldn't give any data loss
+(as far as I can see), but is confusing.
+
+Made the inline declarations disappear for non-GCC compilers.
+
+
+0.9.0c
+~~~~~~
+Fixed some problems in the library pertaining to some boundary cases.
+This makes the library behave more correctly in those situations. The
+fixes apply only to features (calls and parameters) not used by
+bzip2.c, so the non-fixedness of them in previous versions has no
+effect on reliability of bzip2.c.
+
+In bzlib.c:
+ * made zero-length BZ_FLUSH work correctly in bzCompress().
+ * fixed bzWrite/bzRead to ignore zero-length requests.
+ * fixed bzread to correctly handle read requests after EOF.
+ * wrong parameter order in call to bzDecompressInit in
+ bzBuffToBuffDecompress. Fixed.
+
+In compress.c:
+ * changed setting of nGroups in sendMTFValues() so as to
+ do a bit better on small files. This _does_ effect
+ bzip2.c.
+
+
+0.9.5a
+~~~~~~
+Major change: add a fallback sorting algorithm (blocksort.c)
+to give reasonable behaviour even for very repetitive inputs.
+Nuked --repetitive-best and --repetitive-fast since they are
+no longer useful.
+
+Minor changes: mostly a whole bunch of small changes/
+bugfixes in the driver (bzip2.c). Changes pertaining to the
+user interface are:
+
+ allow decompression of symlink'd files to stdout
+ decompress/test files even without .bz2 extension
+ give more accurate error messages for I/O errors
+ when compressing/decompressing to stdout, don't catch control-C
+ read flags from BZIP2 and BZIP environment variables
+ decline to break hard links to a file unless forced with -f
+ allow -c flag even with no filenames
+ preserve file ownerships as far as possible
+ make -s -1 give the expected block size (100k)
+ add a flag -q --quiet to suppress nonessential warnings
+ stop decoding flags after --, so files beginning in - can be handled
+ resolved inconsistent naming: bzcat or bz2cat ?
+ bzip2 --help now returns 0
+
+Programming-level changes are:
+
+ fixed syntax error in GET_LL4 for Borland C++ 5.02
+ let bzBuffToBuffDecompress return BZ_DATA_ERROR{_MAGIC}
+ fix overshoot of mode-string end in bzopen_or_bzdopen
+ wrapped bzlib.h in #ifdef __cplusplus ... extern "C" { ... }
+ close file handles under all error conditions
+ added minor mods so it compiles with DJGPP out of the box
+ fixed Makefile so it doesn't give problems with BSD make
+ fix uninitialised memory reads in dlltest.c
+
+0.9.5b
+~~~~~~
+Open stdin/stdout in binary mode for DJGPP.
+
+0.9.5c
+~~~~~~
+Changed BZ_N_OVERSHOOT to be ... + 2 instead of ... + 1. The + 1
+version could cause the sorted order to be wrong in some extremely
+obscure cases. Also changed setting of quadrant in blocksort.c.
+
+0.9.5d
+~~~~~~
+The only functional change is to make bzlibVersion() in the library
+return the correct string. This has no effect whatsoever on the
+functioning of the bzip2 program or library. Added a couple of casts
+so the library compiles without warnings at level 3 in MS Visual
+Studio 6.0. Included a Y2K statement in the file Y2K_INFO. All other
+changes are minor documentation changes.
+
+1.0
+~~~
+Several minor bugfixes and enhancements:
+
+* Large file support. The library uses 64-bit counters to
+ count the volume of data passing through it. bzip2.c
+ is now compiled with -D_FILE_OFFSET_BITS=64 to get large
+ file support from the C library. -v correctly prints out
+ file sizes greater than 4 gigabytes. All these changes have
+ been made without assuming a 64-bit platform or a C compiler
+ which supports 64-bit ints, so, except for the C library
+ aspect, they are fully portable.
+
+* Decompression robustness. The library/program should be
+ robust to any corruption of compressed data, detecting and
+ handling _all_ corruption, instead of merely relying on
+ the CRCs. What this means is that the program should
+ never crash, given corrupted data, and the library should
+ always return BZ_DATA_ERROR.
+
+* Fixed an obscure race-condition bug only ever observed on
+ Solaris, in which, if you were very unlucky and issued
+ control-C at exactly the wrong time, both input and output
+ files would be deleted.
+
+* Don't run out of file handles on test/decompression when
+ large numbers of files have invalid magic numbers.
+
+* Avoid library namespace pollution. Prefix all exported
+ symbols with BZ2_.
+
+* Minor sorting enhancements from my DCC2000 paper.
+
+* Advance the version number to 1.0, so as to counteract the
+ (false-in-this-case) impression some people have that programs
+ with version numbers less than 1.0 are in some way, experimental,
+ pre-release versions.
+
+* Create an initial Makefile-libbz2_so to build a shared library.
+ Yes, I know I should really use libtool et al ...
+
+* Make the program exit with 2 instead of 0 when decompression
+ fails due to a bad magic number (ie, an invalid bzip2 header).
+ Also exit with 1 (as the manual claims :-) whenever a diagnostic
+ message would have been printed AND the corresponding operation
+ is aborted, for example
+ bzip2: Output file xx already exists.
+ When a diagnostic message is printed but the operation is not
+ aborted, for example
+ bzip2: Can't guess original name for wurble -- using wurble.out
+ then the exit value 0 is returned, unless some other problem is
+ also detected.
+
+ I think it corresponds more closely to what the manual claims now.
+
+
+1.0.1
+~~~~~
+* Modified dlltest.c so it uses the new BZ2_ naming scheme.
+* Modified makefile-msc to fix minor build probs on Win2k.
+* Updated README.COMPILATION.PROBLEMS.
+
+There are no functionality changes or bug fixes relative to version
+1.0.0. This is just a documentation update + a fix for minor Win32
+build problems. For almost everyone, upgrading from 1.0.0 to 1.0.1 is
+utterly pointless. Don't bother.
+
+
+1.0.2
+~~~~~
+A bug fix release, addressing various minor issues which have appeared
+in the 18 or so months since 1.0.1 was released. Most of the fixes
+are to do with file-handling or documentation bugs. To the best of my
+knowledge, there have been no data-loss-causing bugs reported in the
+compression/decompression engine of 1.0.0 or 1.0.1.
+
+Note that this release does not improve the rather crude build system
+for Unix platforms. The general plan here is to autoconfiscate/
+libtoolise 1.0.2 soon after release, and release the result as 1.1.0
+or perhaps 1.2.0. That, however, is still just a plan at this point.
+
+Here are the changes in 1.0.2. Bug-reporters and/or patch-senders in
+parentheses.
+
+* Fix an infinite segfault loop in 1.0.1 when a directory is
+ encountered in -f (force) mode.
+ (Trond Eivind Glomsrod, Nicholas Nethercote, Volker Schmidt)
+
+* Avoid double fclose() of output file on certain I/O error paths.
+ (Solar Designer)
+
+* Don't fail with internal error 1007 when fed a long stream (> 48MB)
+ of byte 251. Also print useful message suggesting that 1007s may be
+ caused by bad memory.
+ (noticed by Juan Pedro Vallejo, fixed by me)
+
+* Fix uninitialised variable silly bug in demo prog dlltest.c.
+ (Jorj Bauer)
+
+* Remove 512-MB limitation on recovered file size for bzip2recover
+ on selected platforms which support 64-bit ints. At the moment
+ all GCC supported platforms, and Win32.
+ (me, Alson van der Meulen)
+
+* Hard-code header byte values, to give correct operation on platforms
+ using EBCDIC as their native character set (IBM's OS/390).
+ (Leland Lucius)
+
+* Copy file access times correctly.
+ (Marty Leisner)
+
+* Add distclean and check targets to Makefile.
+ (Michael Carmack)
+
+* Parameterise use of ar and ranlib in Makefile. Also add $(LDFLAGS).
+ (Rich Ireland, Bo Thorsen)
+
+* Pass -p (create parent dirs as needed) to mkdir during make install.
+ (Jeremy Fusco)
+
+* Dereference symlinks when copying file permissions in -f mode.
+ (Volker Schmidt)
+
+* Majorly simplify implementation of uInt64_qrm10.
+ (Bo Lindbergh)
+
+* Check the input file still exists before deleting the output one,
+ when aborting in cleanUpAndFail().
+ (Joerg Prante, Robert Linden, Matthias Krings)
+
+Also a bunch of patches courtesy of Philippe Troin, the Debian maintainer
+of bzip2:
+
+* Wrapper scripts (with manpages): bzdiff, bzgrep, bzmore.
+
+* Spelling changes and minor enhancements in bzip2.1.
+
+* Avoid race condition between creating the output file and setting its
+ interim permissions safely, by using fopen_output_safely().
+ No changes to bzip2recover since there is no issue with file
+ permissions there.
+
+* do not print senseless report with -v when compressing an empty
+ file.
+
+* bzcat -f works on non-bzip2 files.
+
+* do not try to escape shell meta-characters on unix (the shell takes
+ care of these).
+
+* added --fast and --best aliases for -1 -9 for gzip compatibility.
+
+
+1.0.3 (15 Feb 05)
+~~~~~~~~~~~~~~~~~
+Fixes some minor bugs since the last version, 1.0.2.
+
+* Further robustification against corrupted compressed data.
+ There are currently no known bitstreams which can cause the
+ decompressor to crash, loop or access memory which does not
+ belong to it. If you are using bzip2 or the library to
+ decompress bitstreams from untrusted sources, an upgrade
+ to 1.0.3 is recommended. This fixes CAN-2005-1260.
+
+* The documentation has been converted to XML, from which html
+ and pdf can be derived.
+
+* Various minor bugs in the documentation have been fixed.
+
+* Fixes for various compilation warnings with newer versions of
+ gcc, and on 64-bit platforms.
+
+* The BZ_NO_STDIO cpp symbol was not properly observed in 1.0.2.
+ This has been fixed.
+
+
+1.0.4 (20 Dec 06)
+~~~~~~~~~~~~~~~~~
+Fixes some minor bugs since the last version, 1.0.3.
+
+* Fix file permissions race problem (CAN-2005-0953).
+
+* Avoid possible segfault in BZ2_bzclose. From Coverity's NetBSD
+ scan.
+
+* 'const'/prototype cleanups in the C code.
+
+* Change default install location to /usr/local, and handle multiple
+ 'make install's without error.
+
+* Sanitise file names more carefully in bzgrep. Fixes CAN-2005-0758
+ to the extent that applies to bzgrep.
+
+* Use 'mktemp' rather than 'tempfile' in bzdiff.
+
+* Tighten up a couple of assertions in blocksort.c following automated
+ analysis.
+
+* Fix minor doc/comment bugs.
+
+
+1.0.5 (10 Dec 07)
+~~~~~~~~~~~~~~~~~
+Security fix only. Fixes CERT-FI 20469 as it applies to bzip2.
+
+
+1.0.6 (6 Sept 10)
+~~~~~~~~~~~~~~~~~
+
+* Security fix for CVE-2010-0405. This was reported by Mikolaj
+ Izdebski.
+
+* Make the documentation build on Ubuntu 10.04
diff --git a/third-party/bzip2/LICENSE b/third-party/bzip2/LICENSE
new file mode 100644
index 0000000..cc61417
--- /dev/null
+++ b/third-party/bzip2/LICENSE
@@ -0,0 +1,42 @@
+
+--------------------------------------------------------------------------
+
+This program, "bzip2", the associated library "libbzip2", and all
+documentation, are copyright (C) 1996-2010 Julian R Seward. All
+rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions
+are met:
+
+1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+2. The origin of this software must not be misrepresented; you must
+ not claim that you wrote the original software. If you use this
+ software in a product, an acknowledgment in the product
+ documentation would be appreciated but is not required.
+
+3. Altered source versions must be plainly marked as such, and must
+ not be misrepresented as being the original software.
+
+4. The name of the author may not be used to endorse or promote
+ products derived from this software without specific prior written
+ permission.
+
+THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS
+OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
+DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Julian Seward, jseward at bzip.org
+bzip2/libbzip2 version 1.0.6 of 6 September 2010
+
+--------------------------------------------------------------------------
diff --git a/third-party/bzip2/Makefile b/third-party/bzip2/Makefile
new file mode 100644
index 0000000..9754ddf
--- /dev/null
+++ b/third-party/bzip2/Makefile
@@ -0,0 +1,217 @@
+# ------------------------------------------------------------------
+# This file is part of bzip2/libbzip2, a program and library for
+# lossless, block-sorting data compression.
+#
+# bzip2/libbzip2 version 1.0.6 of 6 September 2010
+# Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
+#
+# Please read the WARNING, DISCLAIMER and PATENTS sections in the
+# README file.
+#
+# This program is released under the terms of the license contained
+# in the file LICENSE.
+# ------------------------------------------------------------------
+
+SHELL=/bin/sh
+
+# To assist in cross-compiling
+CC=gcc
+AR=ar
+RANLIB=ranlib
+LDFLAGS=
+
+BIGFILES=-D_FILE_OFFSET_BITS=64
+CFLAGS=-Wall -Winline -O2 -g $(BIGFILES)
+
+# Where you want it installed when you do 'make install'
+PREFIX=/usr/local
+
+
+OBJS= blocksort.o \
+ huffman.o \
+ crctable.o \
+ randtable.o \
+ compress.o \
+ decompress.o \
+ bzlib.o
+
+all: libbz2.a bzip2 bzip2recover test
+
+bzip2: libbz2.a bzip2.o
+ $(CC) $(CFLAGS) $(LDFLAGS) -o bzip2 bzip2.o -L. -lbz2
+
+bzip2recover: bzip2recover.o
+ $(CC) $(CFLAGS) $(LDFLAGS) -o bzip2recover bzip2recover.o
+
+libbz2.a: $(OBJS)
+ rm -f libbz2.a
+ $(AR) cq libbz2.a $(OBJS)
+ @if ( test -f $(RANLIB) -o -f /usr/bin/ranlib -o \
+ -f /bin/ranlib -o -f /usr/ccs/bin/ranlib ) ; then \
+ echo $(RANLIB) libbz2.a ; \
+ $(RANLIB) libbz2.a ; \
+ fi
+
+check: test
+test: bzip2
+ @cat words1
+ ./bzip2 -1 < sample1.ref > sample1.rb2
+ ./bzip2 -2 < sample2.ref > sample2.rb2
+ ./bzip2 -3 < sample3.ref > sample3.rb2
+ ./bzip2 -d < sample1.bz2 > sample1.tst
+ ./bzip2 -d < sample2.bz2 > sample2.tst
+ ./bzip2 -ds < sample3.bz2 > sample3.tst
+ cmp sample1.bz2 sample1.rb2
+ cmp sample2.bz2 sample2.rb2
+ cmp sample3.bz2 sample3.rb2
+ cmp sample1.tst sample1.ref
+ cmp sample2.tst sample2.ref
+ cmp sample3.tst sample3.ref
+ @cat words3
+
+install: bzip2 bzip2recover
+ if ( test ! -d $(PREFIX)/bin ) ; then mkdir -p $(PREFIX)/bin ; fi
+ if ( test ! -d $(PREFIX)/lib ) ; then mkdir -p $(PREFIX)/lib ; fi
+ if ( test ! -d $(PREFIX)/man ) ; then mkdir -p $(PREFIX)/man ; fi
+ if ( test ! -d $(PREFIX)/man/man1 ) ; then mkdir -p $(PREFIX)/man/man1 ; fi
+ if ( test ! -d $(PREFIX)/include ) ; then mkdir -p $(PREFIX)/include ; fi
+ cp -f bzip2 $(PREFIX)/bin/bzip2
+ cp -f bzip2 $(PREFIX)/bin/bunzip2
+ cp -f bzip2 $(PREFIX)/bin/bzcat
+ cp -f bzip2recover $(PREFIX)/bin/bzip2recover
+ chmod a+x $(PREFIX)/bin/bzip2
+ chmod a+x $(PREFIX)/bin/bunzip2
+ chmod a+x $(PREFIX)/bin/bzcat
+ chmod a+x $(PREFIX)/bin/bzip2recover
+ cp -f bzip2.1 $(PREFIX)/man/man1
+ chmod a+r $(PREFIX)/man/man1/bzip2.1
+ cp -f bzlib.h $(PREFIX)/include
+ chmod a+r $(PREFIX)/include/bzlib.h
+ cp -f libbz2.a $(PREFIX)/lib
+ chmod a+r $(PREFIX)/lib/libbz2.a
+ cp -f bzgrep $(PREFIX)/bin/bzgrep
+ ln -s -f $(PREFIX)/bin/bzgrep $(PREFIX)/bin/bzegrep
+ ln -s -f $(PREFIX)/bin/bzgrep $(PREFIX)/bin/bzfgrep
+ chmod a+x $(PREFIX)/bin/bzgrep
+ cp -f bzmore $(PREFIX)/bin/bzmore
+ ln -s -f $(PREFIX)/bin/bzmore $(PREFIX)/bin/bzless
+ chmod a+x $(PREFIX)/bin/bzmore
+ cp -f bzdiff $(PREFIX)/bin/bzdiff
+ ln -s -f $(PREFIX)/bin/bzdiff $(PREFIX)/bin/bzcmp
+ chmod a+x $(PREFIX)/bin/bzdiff
+ cp -f bzgrep.1 bzmore.1 bzdiff.1 $(PREFIX)/man/man1
+ chmod a+r $(PREFIX)/man/man1/bzgrep.1
+ chmod a+r $(PREFIX)/man/man1/bzmore.1
+ chmod a+r $(PREFIX)/man/man1/bzdiff.1
+ echo ".so man1/bzgrep.1" > $(PREFIX)/man/man1/bzegrep.1
+ echo ".so man1/bzgrep.1" > $(PREFIX)/man/man1/bzfgrep.1
+ echo ".so man1/bzmore.1" > $(PREFIX)/man/man1/bzless.1
+ echo ".so man1/bzdiff.1" > $(PREFIX)/man/man1/bzcmp.1
+
+clean:
+ rm -f *.o libbz2.a bzip2 bzip2recover \
+ sample1.rb2 sample2.rb2 sample3.rb2 \
+ sample1.tst sample2.tst sample3.tst
+
+blocksort.o: blocksort.c
+ @cat words0
+ $(CC) $(CFLAGS) -c blocksort.c
+huffman.o: huffman.c
+ $(CC) $(CFLAGS) -c huffman.c
+crctable.o: crctable.c
+ $(CC) $(CFLAGS) -c crctable.c
+randtable.o: randtable.c
+ $(CC) $(CFLAGS) -c randtable.c
+compress.o: compress.c
+ $(CC) $(CFLAGS) -c compress.c
+decompress.o: decompress.c
+ $(CC) $(CFLAGS) -c decompress.c
+bzlib.o: bzlib.c
+ $(CC) $(CFLAGS) -c bzlib.c
+bzip2.o: bzip2.c
+ $(CC) $(CFLAGS) -c bzip2.c
+bzip2recover.o: bzip2recover.c
+ $(CC) $(CFLAGS) -c bzip2recover.c
+
+
+distclean: clean
+ rm -f manual.ps manual.html manual.pdf
+
+DISTNAME=bzip2-1.0.6
+dist: check manual
+ rm -f $(DISTNAME)
+ ln -s -f . $(DISTNAME)
+ tar cvf $(DISTNAME).tar \
+ $(DISTNAME)/blocksort.c \
+ $(DISTNAME)/huffman.c \
+ $(DISTNAME)/crctable.c \
+ $(DISTNAME)/randtable.c \
+ $(DISTNAME)/compress.c \
+ $(DISTNAME)/decompress.c \
+ $(DISTNAME)/bzlib.c \
+ $(DISTNAME)/bzip2.c \
+ $(DISTNAME)/bzip2recover.c \
+ $(DISTNAME)/bzlib.h \
+ $(DISTNAME)/bzlib_private.h \
+ $(DISTNAME)/Makefile \
+ $(DISTNAME)/LICENSE \
+ $(DISTNAME)/bzip2.1 \
+ $(DISTNAME)/bzip2.1.preformatted \
+ $(DISTNAME)/bzip2.txt \
+ $(DISTNAME)/words0 \
+ $(DISTNAME)/words1 \
+ $(DISTNAME)/words2 \
+ $(DISTNAME)/words3 \
+ $(DISTNAME)/sample1.ref \
+ $(DISTNAME)/sample2.ref \
+ $(DISTNAME)/sample3.ref \
+ $(DISTNAME)/sample1.bz2 \
+ $(DISTNAME)/sample2.bz2 \
+ $(DISTNAME)/sample3.bz2 \
+ $(DISTNAME)/dlltest.c \
+ $(DISTNAME)/manual.html \
+ $(DISTNAME)/manual.pdf \
+ $(DISTNAME)/manual.ps \
+ $(DISTNAME)/README \
+ $(DISTNAME)/README.COMPILATION.PROBLEMS \
+ $(DISTNAME)/README.XML.STUFF \
+ $(DISTNAME)/CHANGES \
+ $(DISTNAME)/libbz2.def \
+ $(DISTNAME)/libbz2.dsp \
+ $(DISTNAME)/dlltest.dsp \
+ $(DISTNAME)/makefile.msc \
+ $(DISTNAME)/unzcrash.c \
+ $(DISTNAME)/spewG.c \
+ $(DISTNAME)/mk251.c \
+ $(DISTNAME)/bzdiff \
+ $(DISTNAME)/bzdiff.1 \
+ $(DISTNAME)/bzmore \
+ $(DISTNAME)/bzmore.1 \
+ $(DISTNAME)/bzgrep \
+ $(DISTNAME)/bzgrep.1 \
+ $(DISTNAME)/Makefile-libbz2_so \
+ $(DISTNAME)/bz-common.xsl \
+ $(DISTNAME)/bz-fo.xsl \
+ $(DISTNAME)/bz-html.xsl \
+ $(DISTNAME)/bzip.css \
+ $(DISTNAME)/entities.xml \
+ $(DISTNAME)/manual.xml \
+ $(DISTNAME)/format.pl \
+ $(DISTNAME)/xmlproc.sh
+ gzip -v $(DISTNAME).tar
+
+# For rebuilding the manual from sources on my SuSE 9.1 box
+
+MANUAL_SRCS= bz-common.xsl bz-fo.xsl bz-html.xsl bzip.css \
+ entities.xml manual.xml
+
+manual: manual.html manual.ps manual.pdf
+
+manual.ps: $(MANUAL_SRCS)
+ ./xmlproc.sh -ps manual.xml
+
+manual.pdf: $(MANUAL_SRCS)
+ ./xmlproc.sh -pdf manual.xml
+
+manual.html: $(MANUAL_SRCS)
+ ./xmlproc.sh -html manual.xml
diff --git a/third-party/bzip2/Makefile-libbz2_so b/third-party/bzip2/Makefile-libbz2_so
new file mode 100644
index 0000000..e1a09f5
--- /dev/null
+++ b/third-party/bzip2/Makefile-libbz2_so
@@ -0,0 +1,59 @@
+
+# This Makefile builds a shared version of the library,
+# libbz2.so.1.0.6, with soname libbz2.so.1.0,
+# at least on x86-Linux (RedHat 7.2),
+# with gcc-2.96 20000731 (Red Hat Linux 7.1 2.96-98).
+# Please see the README file for some important info
+# about building the library like this.
+
+# ------------------------------------------------------------------
+# This file is part of bzip2/libbzip2, a program and library for
+# lossless, block-sorting data compression.
+#
+# bzip2/libbzip2 version 1.0.6 of 6 September 2010
+# Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
+#
+# Please read the WARNING, DISCLAIMER and PATENTS sections in the
+# README file.
+#
+# This program is released under the terms of the license contained
+# in the file LICENSE.
+# ------------------------------------------------------------------
+
+
+SHELL=/bin/sh
+CC=gcc
+BIGFILES=-D_FILE_OFFSET_BITS=64
+CFLAGS=-fpic -fPIC -Wall -Winline -O2 -g $(BIGFILES)
+
+OBJS= blocksort.o \
+ huffman.o \
+ crctable.o \
+ randtable.o \
+ compress.o \
+ decompress.o \
+ bzlib.o
+
+all: $(OBJS)
+ #$(CC) -shared -Wl,-soname -Wl,libbz2.so.1.0 -o libbz2.so.1.0.6 $(OBJS)
+ #$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.so.1.0.6
+ #rm -f libbz2.so.1.0
+ #ln -s libbz2.so.1.0.6 libbz2.so.1.0
+
+clean:
+ rm -f $(OBJS) bzip2.o libbz2.so.1.0.6 libbz2.so.1.0 bzip2-shared
+
+blocksort.o: blocksort.c
+ $(CC) $(CFLAGS) -c blocksort.c
+huffman.o: huffman.c
+ $(CC) $(CFLAGS) -c huffman.c
+crctable.o: crctable.c
+ $(CC) $(CFLAGS) -c crctable.c
+randtable.o: randtable.c
+ $(CC) $(CFLAGS) -c randtable.c
+compress.o: compress.c
+ $(CC) $(CFLAGS) -c compress.c
+decompress.o: decompress.c
+ $(CC) $(CFLAGS) -c decompress.c
+bzlib.o: bzlib.c
+ $(CC) $(CFLAGS) -c bzlib.c
diff --git a/third-party/bzip2/README b/third-party/bzip2/README
new file mode 100644
index 0000000..9fb0f63
--- /dev/null
+++ b/third-party/bzip2/README
@@ -0,0 +1,215 @@
+
+This is the README for bzip2/libzip2.
+This version is fully compatible with the previous public releases.
+
+------------------------------------------------------------------
+This file is part of bzip2/libbzip2, a program and library for
+lossless, block-sorting data compression.
+
+bzip2/libbzip2 version 1.0.6 of 6 September 2010
+Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
+
+Please read the WARNING, DISCLAIMER and PATENTS sections in this file.
+
+This program is released under the terms of the license contained
+in the file LICENSE.
+------------------------------------------------------------------
+
+Complete documentation is available in Postscript form (manual.ps),
+PDF (manual.pdf) or html (manual.html). A plain-text version of the
+manual page is available as bzip2.txt.
+
+
+HOW TO BUILD -- UNIX
+
+Type 'make'. This builds the library libbz2.a and then the programs
+bzip2 and bzip2recover. Six self-tests are run. If the self-tests
+complete ok, carry on to installation:
+
+To install in /usr/local/bin, /usr/local/lib, /usr/local/man and
+/usr/local/include, type
+
+ make install
+
+To install somewhere else, eg, /xxx/yyy/{bin,lib,man,include}, type
+
+ make install PREFIX=/xxx/yyy
+
+If you are (justifiably) paranoid and want to see what 'make install'
+is going to do, you can first do
+
+ make -n install or
+ make -n install PREFIX=/xxx/yyy respectively.
+
+The -n instructs make to show the commands it would execute, but not
+actually execute them.
+
+
+HOW TO BUILD -- UNIX, shared library libbz2.so.
+
+Do 'make -f Makefile-libbz2_so'. This Makefile seems to work for
+Linux-ELF (RedHat 7.2 on an x86 box), with gcc. I make no claims
+that it works for any other platform, though I suspect it probably
+will work for most platforms employing both ELF and gcc.
+
+bzip2-shared, a client of the shared library, is also built, but not
+self-tested. So I suggest you also build using the normal Makefile,
+since that conducts a self-test. A second reason to prefer the
+version statically linked to the library is that, on x86 platforms,
+building shared objects makes a valuable register (%ebx) unavailable
+to gcc, resulting in a slowdown of 10%-20%, at least for bzip2.
+
+Important note for people upgrading .so's from 0.9.0/0.9.5 to version
+1.0.X. All the functions in the library have been renamed, from (eg)
+bzCompress to BZ2_bzCompress, to avoid namespace pollution.
+Unfortunately this means that the libbz2.so created by
+Makefile-libbz2_so will not work with any program which used an older
+version of the library. I do encourage library clients to make the
+effort to upgrade to use version 1.0, since it is both faster and more
+robust than previous versions.
+
+
+HOW TO BUILD -- Windows 95, NT, DOS, Mac, etc.
+
+It's difficult for me to support compilation on all these platforms.
+My approach is to collect binaries for these platforms, and put them
+on the master web site (http://www.bzip.org). Look there. However
+(FWIW), bzip2-1.0.X is very standard ANSI C and should compile
+unmodified with MS Visual C. If you have difficulties building, you
+might want to read README.COMPILATION.PROBLEMS.
+
+At least using MS Visual C++ 6, you can build from the unmodified
+sources by issuing, in a command shell:
+
+ nmake -f makefile.msc
+
+(you may need to first run the MSVC-provided script VCVARS32.BAT
+ so as to set up paths to the MSVC tools correctly).
+
+
+VALIDATION
+
+Correct operation, in the sense that a compressed file can always be
+decompressed to reproduce the original, is obviously of paramount
+importance. To validate bzip2, I used a modified version of Mark
+Nelson's churn program. Churn is an automated test driver which
+recursively traverses a directory structure, using bzip2 to compress
+and then decompress each file it encounters, and checking that the
+decompressed data is the same as the original.
+
+
+
+Please read and be aware of the following:
+
+WARNING:
+
+ This program and library (attempts to) compress data by
+ performing several non-trivial transformations on it.
+ Unless you are 100% familiar with *all* the algorithms
+ contained herein, and with the consequences of modifying them,
+ you should NOT meddle with the compression or decompression
+ machinery. Incorrect changes can and very likely *will*
+ lead to disastrous loss of data.
+
+
+DISCLAIMER:
+
+ I TAKE NO RESPONSIBILITY FOR ANY LOSS OF DATA ARISING FROM THE
+ USE OF THIS PROGRAM/LIBRARY, HOWSOEVER CAUSED.
+
+ Every compression of a file implies an assumption that the
+ compressed file can be decompressed to reproduce the original.
+ Great efforts in design, coding and testing have been made to
+ ensure that this program works correctly. However, the complexity
+ of the algorithms, and, in particular, the presence of various
+ special cases in the code which occur with very low but non-zero
+ probability make it impossible to rule out the possibility of bugs
+ remaining in the program. DO NOT COMPRESS ANY DATA WITH THIS
+ PROGRAM UNLESS YOU ARE PREPARED TO ACCEPT THE POSSIBILITY, HOWEVER
+ SMALL, THAT THE DATA WILL NOT BE RECOVERABLE.
+
+ That is not to say this program is inherently unreliable.
+ Indeed, I very much hope the opposite is true. bzip2/libbzip2
+ has been carefully constructed and extensively tested.
+
+
+PATENTS:
+
+ To the best of my knowledge, bzip2/libbzip2 does not use any
+ patented algorithms. However, I do not have the resources
+ to carry out a patent search. Therefore I cannot give any
+ guarantee of the above statement.
+
+
+
+WHAT'S NEW IN 0.9.0 (as compared to 0.1pl2) ?
+
+ * Approx 10% faster compression, 30% faster decompression
+ * -t (test mode) is a lot quicker
+ * Can decompress concatenated compressed files
+ * Programming interface, so programs can directly read/write .bz2 files
+ * Less restrictive (BSD-style) licensing
+ * Flag handling more compatible with GNU gzip
+ * Much more documentation, i.e., a proper user manual
+ * Hopefully, improved portability (at least of the library)
+
+WHAT'S NEW IN 0.9.5 ?
+
+ * Compression speed is much less sensitive to the input
+ data than in previous versions. Specifically, the very
+ slow performance caused by repetitive data is fixed.
+ * Many small improvements in file and flag handling.
+ * A Y2K statement.
+
+WHAT'S NEW IN 1.0.0 ?
+
+ See the CHANGES file.
+
+WHAT'S NEW IN 1.0.2 ?
+
+ See the CHANGES file.
+
+WHAT'S NEW IN 1.0.3 ?
+
+ See the CHANGES file.
+
+WHAT'S NEW IN 1.0.4 ?
+
+ See the CHANGES file.
+
+WHAT'S NEW IN 1.0.5 ?
+
+ See the CHANGES file.
+
+WHAT'S NEW IN 1.0.6 ?
+
+ See the CHANGES file.
+
+
+I hope you find bzip2 useful. Feel free to contact me at
+ jseward at bzip.org
+if you have any suggestions or queries. Many people mailed me with
+comments, suggestions and patches after the releases of bzip-0.15,
+bzip-0.21, and bzip2 versions 0.1pl2, 0.9.0, 0.9.5, 1.0.0, 1.0.1,
+1.0.2 and 1.0.3, and the changes in bzip2 are largely a result of this
+feedback. I thank you for your comments.
+
+bzip2's "home" is http://www.bzip.org/
+
+Julian Seward
+jseward at bzip.org
+Cambridge, UK.
+
+18 July 1996 (version 0.15)
+25 August 1996 (version 0.21)
+ 7 August 1997 (bzip2, version 0.1)
+29 August 1997 (bzip2, version 0.1pl2)
+23 August 1998 (bzip2, version 0.9.0)
+ 8 June 1999 (bzip2, version 0.9.5)
+ 4 Sept 1999 (bzip2, version 0.9.5d)
+ 5 May 2000 (bzip2, version 1.0pre8)
+30 December 2001 (bzip2, version 1.0.2pre1)
+15 February 2005 (bzip2, version 1.0.3)
+20 December 2006 (bzip2, version 1.0.4)
+10 December 2007 (bzip2, version 1.0.5)
+ 6 Sept 2010 (bzip2, version 1.0.6)
diff --git a/third-party/bzip2/README.COMPILATION.PROBLEMS b/third-party/bzip2/README.COMPILATION.PROBLEMS
new file mode 100644
index 0000000..667d0d6
--- /dev/null
+++ b/third-party/bzip2/README.COMPILATION.PROBLEMS
@@ -0,0 +1,58 @@
+------------------------------------------------------------------
+This file is part of bzip2/libbzip2, a program and library for
+lossless, block-sorting data compression.
+
+bzip2/libbzip2 version 1.0.6 of 6 September 2010
+Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
+
+Please read the WARNING, DISCLAIMER and PATENTS sections in the
+README file.
+
+This program is released under the terms of the license contained
+in the file LICENSE.
+------------------------------------------------------------------
+
+bzip2-1.0.6 should compile without problems on the vast majority of
+platforms. Using the supplied Makefile, I've built and tested it
+myself for x86-linux and amd64-linux. With makefile.msc, Visual C++
+6.0 and nmake, you can build a native Win32 version too. Large file
+support seems to work correctly on at least on amd64-linux.
+
+When I say "large file" I mean a file of size 2,147,483,648 (2^31)
+bytes or above. Many older OSs can't handle files above this size,
+but many newer ones can. Large files are pretty huge -- most files
+you'll encounter are not Large Files.
+
+Early versions of bzip2 (0.1, 0.9.0, 0.9.5) compiled on a wide variety
+of platforms without difficulty, and I hope this version will continue
+in that tradition. However, in order to support large files, I've had
+to include the define -D_FILE_OFFSET_BITS=64 in the Makefile. This
+can cause problems.
+
+The technique of adding -D_FILE_OFFSET_BITS=64 to get large file
+support is, as far as I know, the Recommended Way to get correct large
+file support. For more details, see the Large File Support
+Specification, published by the Large File Summit, at
+
+ http://ftp.sas.com/standards/large.file
+
+As a general comment, if you get compilation errors which you think
+are related to large file support, try removing the above define from
+the Makefile, ie, delete the line
+
+ BIGFILES=-D_FILE_OFFSET_BITS=64
+
+from the Makefile, and do 'make clean ; make'. This will give you a
+version of bzip2 without large file support, which, for most
+applications, is probably not a problem.
+
+Alternatively, try some of the platform-specific hints listed below.
+
+You can use the spewG.c program to generate huge files to test bzip2's
+large file support, if you are feeling paranoid. Be aware though that
+any compilation problems which affect bzip2 will also affect spewG.c,
+alas.
+
+AIX: I have reports that for large file support, you need to specify
+-D_LARGE_FILES rather than -D_FILE_OFFSET_BITS=64. I have not tested
+this myself.
diff --git a/third-party/bzip2/README.XML.STUFF b/third-party/bzip2/README.XML.STUFF
new file mode 100644
index 0000000..3a57f3f
--- /dev/null
+++ b/third-party/bzip2/README.XML.STUFF
@@ -0,0 +1,45 @@
+ ----------------------------------------------------------------
+ This file is part of bzip2/libbzip2, a program and library for
+ lossless, block-sorting data compression.
+
+ bzip2/libbzip2 version 1.0.6 of 6 September 2010
+ Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
+
+ Please read the WARNING, DISCLAIMER and PATENTS sections in the
+ README file.
+
+ This program is released under the terms of the license contained
+ in the file LICENSE.
+ ----------------------------------------------------------------
+
+The script xmlproc.sh takes an xml file as input,
+and processes it to create .pdf, .html or .ps output.
+It uses format.pl, a perl script to format <pre> blocks nicely,
+ and add CDATA tags so writers do not have to use eg. <
+
+The file "entities.xml" must be edited to reflect current
+version, year, etc.
+
+
+Usage:
+
+ ./xmlproc.sh -v manual.xml
+ Validates an xml file to ensure no dtd-compliance errors
+
+ ./xmlproc.sh -html manual.xml
+ Output: manual.html
+
+ ./xmlproc.sh -pdf manual.xml
+ Output: manual.pdf
+
+ ./xmlproc.sh -ps manual.xml
+ Output: manual.ps
+
+
+Notum bene:
+- pdfxmltex barfs if given a filename with an underscore in it
+
+- xmltex won't work yet - there's a bug in passivetex
+ which we are all waiting for Sebastian to fix.
+ So we are going the xml -> pdf -> ps route for the time being,
+ using pdfxmltex.
diff --git a/third-party/bzip2/blocksort.c b/third-party/bzip2/blocksort.c
new file mode 100644
index 0000000..d0d662c
--- /dev/null
+++ b/third-party/bzip2/blocksort.c
@@ -0,0 +1,1094 @@
+
+/*-------------------------------------------------------------*/
+/*--- Block sorting machinery ---*/
+/*--- blocksort.c ---*/
+/*-------------------------------------------------------------*/
+
+/* ------------------------------------------------------------------
+ This file is part of bzip2/libbzip2, a program and library for
+ lossless, block-sorting data compression.
+
+ bzip2/libbzip2 version 1.0.6 of 6 September 2010
+ Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
+
+ Please read the WARNING, DISCLAIMER and PATENTS sections in the
+ README file.
+
+ This program is released under the terms of the license contained
+ in the file LICENSE.
+ ------------------------------------------------------------------ */
+
+
+#include "bzlib_private.h"
+
+/*---------------------------------------------*/
+/*--- Fallback O(N log(N)^2) sorting ---*/
+/*--- algorithm, for repetitive blocks ---*/
+/*---------------------------------------------*/
+
+/*---------------------------------------------*/
+static
+__inline__
+void fallbackSimpleSort ( UInt32* fmap,
+ UInt32* eclass,
+ Int32 lo,
+ Int32 hi )
+{
+ Int32 i, j, tmp;
+ UInt32 ec_tmp;
+
+ if (lo == hi) return;
+
+ if (hi - lo > 3) {
+ for ( i = hi-4; i >= lo; i-- ) {
+ tmp = fmap[i];
+ ec_tmp = eclass[tmp];
+ for ( j = i+4; j <= hi && ec_tmp > eclass[fmap[j]]; j += 4 )
+ fmap[j-4] = fmap[j];
+ fmap[j-4] = tmp;
+ }
+ }
+
+ for ( i = hi-1; i >= lo; i-- ) {
+ tmp = fmap[i];
+ ec_tmp = eclass[tmp];
+ for ( j = i+1; j <= hi && ec_tmp > eclass[fmap[j]]; j++ )
+ fmap[j-1] = fmap[j];
+ fmap[j-1] = tmp;
+ }
+}
+
+
+/*---------------------------------------------*/
+#define fswap(zz1, zz2) \
+ { Int32 zztmp = zz1; zz1 = zz2; zz2 = zztmp; }
+
+#define fvswap(zzp1, zzp2, zzn) \
+{ \
+ Int32 yyp1 = (zzp1); \
+ Int32 yyp2 = (zzp2); \
+ Int32 yyn = (zzn); \
+ while (yyn > 0) { \
+ fswap(fmap[yyp1], fmap[yyp2]); \
+ yyp1++; yyp2++; yyn--; \
+ } \
+}
+
+
+#define fmin(a,b) ((a) < (b)) ? (a) : (b)
+
+#define fpush(lz,hz) { stackLo[sp] = lz; \
+ stackHi[sp] = hz; \
+ sp++; }
+
+#define fpop(lz,hz) { sp--; \
+ lz = stackLo[sp]; \
+ hz = stackHi[sp]; }
+
+#define FALLBACK_QSORT_SMALL_THRESH 10
+#define FALLBACK_QSORT_STACK_SIZE 100
+
+
+static
+void fallbackQSort3 ( UInt32* fmap,
+ UInt32* eclass,
+ Int32 loSt,
+ Int32 hiSt )
+{
+ Int32 unLo, unHi, ltLo, gtHi, n, m;
+ Int32 sp, lo, hi;
+ UInt32 med, r, r3;
+ Int32 stackLo[FALLBACK_QSORT_STACK_SIZE];
+ Int32 stackHi[FALLBACK_QSORT_STACK_SIZE];
+
+ r = 0;
+
+ sp = 0;
+ fpush ( loSt, hiSt );
+
+ while (sp > 0) {
+
+ AssertH ( sp < FALLBACK_QSORT_STACK_SIZE - 1, 1004 );
+
+ fpop ( lo, hi );
+ if (hi - lo < FALLBACK_QSORT_SMALL_THRESH) {
+ fallbackSimpleSort ( fmap, eclass, lo, hi );
+ continue;
+ }
+
+ /* Random partitioning. Median of 3 sometimes fails to
+ avoid bad cases. Median of 9 seems to help but
+ looks rather expensive. This too seems to work but
+ is cheaper. Guidance for the magic constants
+ 7621 and 32768 is taken from Sedgewick's algorithms
+ book, chapter 35.
+ */
+ r = ((r * 7621) + 1) % 32768;
+ r3 = r % 3;
+ if (r3 == 0) med = eclass[fmap[lo]]; else
+ if (r3 == 1) med = eclass[fmap[(lo+hi)>>1]]; else
+ med = eclass[fmap[hi]];
+
+ unLo = ltLo = lo;
+ unHi = gtHi = hi;
+
+ while (1) {
+ while (1) {
+ if (unLo > unHi) break;
+ n = (Int32)eclass[fmap[unLo]] - (Int32)med;
+ if (n == 0) {
+ fswap(fmap[unLo], fmap[ltLo]);
+ ltLo++; unLo++;
+ continue;
+ };
+ if (n > 0) break;
+ unLo++;
+ }
+ while (1) {
+ if (unLo > unHi) break;
+ n = (Int32)eclass[fmap[unHi]] - (Int32)med;
+ if (n == 0) {
+ fswap(fmap[unHi], fmap[gtHi]);
+ gtHi--; unHi--;
+ continue;
+ };
+ if (n < 0) break;
+ unHi--;
+ }
+ if (unLo > unHi) break;
+ fswap(fmap[unLo], fmap[unHi]); unLo++; unHi--;
+ }
+
+ AssertD ( unHi == unLo-1, "fallbackQSort3(2)" );
+
+ if (gtHi < ltLo) continue;
+
+ n = fmin(ltLo-lo, unLo-ltLo); fvswap(lo, unLo-n, n);
+ m = fmin(hi-gtHi, gtHi-unHi); fvswap(unLo, hi-m+1, m);
+
+ n = lo + unLo - ltLo - 1;
+ m = hi - (gtHi - unHi) + 1;
+
+ if (n - lo > hi - m) {
+ fpush ( lo, n );
+ fpush ( m, hi );
+ } else {
+ fpush ( m, hi );
+ fpush ( lo, n );
+ }
+ }
+}
+
+#undef fmin
+#undef fpush
+#undef fpop
+#undef fswap
+#undef fvswap
+#undef FALLBACK_QSORT_SMALL_THRESH
+#undef FALLBACK_QSORT_STACK_SIZE
+
+
+/*---------------------------------------------*/
+/* Pre:
+ nblock > 0
+ eclass exists for [0 .. nblock-1]
+ ((UChar*)eclass) [0 .. nblock-1] holds block
+ ptr exists for [0 .. nblock-1]
+
+ Post:
+ ((UChar*)eclass) [0 .. nblock-1] holds block
+ All other areas of eclass destroyed
+ fmap [0 .. nblock-1] holds sorted order
+ bhtab [ 0 .. 2+(nblock/32) ] destroyed
+*/
+
+#define SET_BH(zz) bhtab[(zz) >> 5] |= (1 << ((zz) & 31))
+#define CLEAR_BH(zz) bhtab[(zz) >> 5] &= ~(1 << ((zz) & 31))
+#define ISSET_BH(zz) (bhtab[(zz) >> 5] & (1 << ((zz) & 31)))
+#define WORD_BH(zz) bhtab[(zz) >> 5]
+#define UNALIGNED_BH(zz) ((zz) & 0x01f)
+
+static
+void fallbackSort ( UInt32* fmap,
+ UInt32* eclass,
+ UInt32* bhtab,
+ Int32 nblock,
+ Int32 verb )
+{
+ Int32 ftab[257];
+ Int32 ftabCopy[256];
+ Int32 H, i, j, k, l, r, cc, cc1;
+ Int32 nNotDone;
+ Int32 nBhtab;
+ UChar* eclass8 = (UChar*)eclass;
+
+ /*--
+ Initial 1-char radix sort to generate
+ initial fmap and initial BH bits.
+ --*/
+ if (verb >= 4)
+ VPrintf0 ( " bucket sorting ...\n" );
+ for (i = 0; i < 257; i++) ftab[i] = 0;
+ for (i = 0; i < nblock; i++) ftab[eclass8[i]]++;
+ for (i = 0; i < 256; i++) ftabCopy[i] = ftab[i];
+ for (i = 1; i < 257; i++) ftab[i] += ftab[i-1];
+
+ for (i = 0; i < nblock; i++) {
+ j = eclass8[i];
+ k = ftab[j] - 1;
+ ftab[j] = k;
+ fmap[k] = i;
+ }
+
+ nBhtab = 2 + (nblock / 32);
+ for (i = 0; i < nBhtab; i++) bhtab[i] = 0;
+ for (i = 0; i < 256; i++) SET_BH(ftab[i]);
+
+ /*--
+ Inductively refine the buckets. Kind-of an
+ "exponential radix sort" (!), inspired by the
+ Manber-Myers suffix array construction algorithm.
+ --*/
+
+ /*-- set sentinel bits for block-end detection --*/
+ for (i = 0; i < 32; i++) {
+ SET_BH(nblock + 2*i);
+ CLEAR_BH(nblock + 2*i + 1);
+ }
+
+ /*-- the log(N) loop --*/
+ H = 1;
+ while (1) {
+
+ if (verb >= 4)
+ VPrintf1 ( " depth %6d has ", H );
+
+ j = 0;
+ for (i = 0; i < nblock; i++) {
+ if (ISSET_BH(i)) j = i;
+ k = fmap[i] - H; if (k < 0) k += nblock;
+ eclass[k] = j;
+ }
+
+ nNotDone = 0;
+ r = -1;
+ while (1) {
+
+ /*-- find the next non-singleton bucket --*/
+ k = r + 1;
+ while (ISSET_BH(k) && UNALIGNED_BH(k)) k++;
+ if (ISSET_BH(k)) {
+ while (WORD_BH(k) == 0xffffffff) k += 32;
+ while (ISSET_BH(k)) k++;
+ }
+ l = k - 1;
+ if (l >= nblock) break;
+ while (!ISSET_BH(k) && UNALIGNED_BH(k)) k++;
+ if (!ISSET_BH(k)) {
+ while (WORD_BH(k) == 0x00000000) k += 32;
+ while (!ISSET_BH(k)) k++;
+ }
+ r = k - 1;
+ if (r >= nblock) break;
+
+ /*-- now [l, r] bracket current bucket --*/
+ if (r > l) {
+ nNotDone += (r - l + 1);
+ fallbackQSort3 ( fmap, eclass, l, r );
+
+ /*-- scan bucket and generate header bits-- */
+ cc = -1;
+ for (i = l; i <= r; i++) {
+ cc1 = eclass[fmap[i]];
+ if (cc != cc1) { SET_BH(i); cc = cc1; };
+ }
+ }
+ }
+
+ if (verb >= 4)
+ VPrintf1 ( "%6d unresolved strings\n", nNotDone );
+
+ H *= 2;
+ if (H > nblock || nNotDone == 0) break;
+ }
+
+ /*--
+ Reconstruct the original block in
+ eclass8 [0 .. nblock-1], since the
+ previous phase destroyed it.
+ --*/
+ if (verb >= 4)
+ VPrintf0 ( " reconstructing block ...\n" );
+ j = 0;
+ for (i = 0; i < nblock; i++) {
+ while (ftabCopy[j] == 0) j++;
+ ftabCopy[j]--;
+ eclass8[fmap[i]] = (UChar)j;
+ }
+ AssertH ( j < 256, 1005 );
+}
+
+#undef SET_BH
+#undef CLEAR_BH
+#undef ISSET_BH
+#undef WORD_BH
+#undef UNALIGNED_BH
+
+
+/*---------------------------------------------*/
+/*--- The main, O(N^2 log(N)) sorting ---*/
+/*--- algorithm. Faster for "normal" ---*/
+/*--- non-repetitive blocks. ---*/
+/*---------------------------------------------*/
+
+/*---------------------------------------------*/
+static
+__inline__
+Bool mainGtU ( UInt32 i1,
+ UInt32 i2,
+ UChar* block,
+ UInt16* quadrant,
+ UInt32 nblock,
+ Int32* budget )
+{
+ Int32 k;
+ UChar c1, c2;
+ UInt16 s1, s2;
+
+ AssertD ( i1 != i2, "mainGtU" );
+ /* 1 */
+ c1 = block[i1]; c2 = block[i2];
+ if (c1 != c2) return (c1 > c2);
+ i1++; i2++;
+ /* 2 */
+ c1 = block[i1]; c2 = block[i2];
+ if (c1 != c2) return (c1 > c2);
+ i1++; i2++;
+ /* 3 */
+ c1 = block[i1]; c2 = block[i2];
+ if (c1 != c2) return (c1 > c2);
+ i1++; i2++;
+ /* 4 */
+ c1 = block[i1]; c2 = block[i2];
+ if (c1 != c2) return (c1 > c2);
+ i1++; i2++;
+ /* 5 */
+ c1 = block[i1]; c2 = block[i2];
+ if (c1 != c2) return (c1 > c2);
+ i1++; i2++;
+ /* 6 */
+ c1 = block[i1]; c2 = block[i2];
+ if (c1 != c2) return (c1 > c2);
+ i1++; i2++;
+ /* 7 */
+ c1 = block[i1]; c2 = block[i2];
+ if (c1 != c2) return (c1 > c2);
+ i1++; i2++;
+ /* 8 */
+ c1 = block[i1]; c2 = block[i2];
+ if (c1 != c2) return (c1 > c2);
+ i1++; i2++;
+ /* 9 */
+ c1 = block[i1]; c2 = block[i2];
+ if (c1 != c2) return (c1 > c2);
+ i1++; i2++;
+ /* 10 */
+ c1 = block[i1]; c2 = block[i2];
+ if (c1 != c2) return (c1 > c2);
+ i1++; i2++;
+ /* 11 */
+ c1 = block[i1]; c2 = block[i2];
+ if (c1 != c2) return (c1 > c2);
+ i1++; i2++;
+ /* 12 */
+ c1 = block[i1]; c2 = block[i2];
+ if (c1 != c2) return (c1 > c2);
+ i1++; i2++;
+
+ k = nblock + 8;
+
+ do {
+ /* 1 */
+ c1 = block[i1]; c2 = block[i2];
+ if (c1 != c2) return (c1 > c2);
+ s1 = quadrant[i1]; s2 = quadrant[i2];
+ if (s1 != s2) return (s1 > s2);
+ i1++; i2++;
+ /* 2 */
+ c1 = block[i1]; c2 = block[i2];
+ if (c1 != c2) return (c1 > c2);
+ s1 = quadrant[i1]; s2 = quadrant[i2];
+ if (s1 != s2) return (s1 > s2);
+ i1++; i2++;
+ /* 3 */
+ c1 = block[i1]; c2 = block[i2];
+ if (c1 != c2) return (c1 > c2);
+ s1 = quadrant[i1]; s2 = quadrant[i2];
+ if (s1 != s2) return (s1 > s2);
+ i1++; i2++;
+ /* 4 */
+ c1 = block[i1]; c2 = block[i2];
+ if (c1 != c2) return (c1 > c2);
+ s1 = quadrant[i1]; s2 = quadrant[i2];
+ if (s1 != s2) return (s1 > s2);
+ i1++; i2++;
+ /* 5 */
+ c1 = block[i1]; c2 = block[i2];
+ if (c1 != c2) return (c1 > c2);
+ s1 = quadrant[i1]; s2 = quadrant[i2];
+ if (s1 != s2) return (s1 > s2);
+ i1++; i2++;
+ /* 6 */
+ c1 = block[i1]; c2 = block[i2];
+ if (c1 != c2) return (c1 > c2);
+ s1 = quadrant[i1]; s2 = quadrant[i2];
+ if (s1 != s2) return (s1 > s2);
+ i1++; i2++;
+ /* 7 */
+ c1 = block[i1]; c2 = block[i2];
+ if (c1 != c2) return (c1 > c2);
+ s1 = quadrant[i1]; s2 = quadrant[i2];
+ if (s1 != s2) return (s1 > s2);
+ i1++; i2++;
+ /* 8 */
+ c1 = block[i1]; c2 = block[i2];
+ if (c1 != c2) return (c1 > c2);
+ s1 = quadrant[i1]; s2 = quadrant[i2];
+ if (s1 != s2) return (s1 > s2);
+ i1++; i2++;
+
+ if (i1 >= nblock) i1 -= nblock;
+ if (i2 >= nblock) i2 -= nblock;
+
+ k -= 8;
+ (*budget)--;
+ }
+ while (k >= 0);
+
+ return False;
+}
+
+
+/*---------------------------------------------*/
+/*--
+ Knuth's increments seem to work better
+ than Incerpi-Sedgewick here. Possibly
+ because the number of elems to sort is
+ usually small, typically <= 20.
+--*/
+static
+Int32 incs[14] = { 1, 4, 13, 40, 121, 364, 1093, 3280,
+ 9841, 29524, 88573, 265720,
+ 797161, 2391484 };
+
+static
+void mainSimpleSort ( UInt32* ptr,
+ UChar* block,
+ UInt16* quadrant,
+ Int32 nblock,
+ Int32 lo,
+ Int32 hi,
+ Int32 d,
+ Int32* budget )
+{
+ Int32 i, j, h, bigN, hp;
+ UInt32 v;
+
+ bigN = hi - lo + 1;
+ if (bigN < 2) return;
+
+ hp = 0;
+ while (incs[hp] < bigN) hp++;
+ hp--;
+
+ for (; hp >= 0; hp--) {
+ h = incs[hp];
+
+ i = lo + h;
+ while (True) {
+
+ /*-- copy 1 --*/
+ if (i > hi) break;
+ v = ptr[i];
+ j = i;
+ while ( mainGtU (
+ ptr[j-h]+d, v+d, block, quadrant, nblock, budget
+ ) ) {
+ ptr[j] = ptr[j-h];
+ j = j - h;
+ if (j <= (lo + h - 1)) break;
+ }
+ ptr[j] = v;
+ i++;
+
+ /*-- copy 2 --*/
+ if (i > hi) break;
+ v = ptr[i];
+ j = i;
+ while ( mainGtU (
+ ptr[j-h]+d, v+d, block, quadrant, nblock, budget
+ ) ) {
+ ptr[j] = ptr[j-h];
+ j = j - h;
+ if (j <= (lo + h - 1)) break;
+ }
+ ptr[j] = v;
+ i++;
+
+ /*-- copy 3 --*/
+ if (i > hi) break;
+ v = ptr[i];
+ j = i;
+ while ( mainGtU (
+ ptr[j-h]+d, v+d, block, quadrant, nblock, budget
+ ) ) {
+ ptr[j] = ptr[j-h];
+ j = j - h;
+ if (j <= (lo + h - 1)) break;
+ }
+ ptr[j] = v;
+ i++;
+
+ if (*budget < 0) return;
+ }
+ }
+}
+
+
+/*---------------------------------------------*/
+/*--
+ The following is an implementation of
+ an elegant 3-way quicksort for strings,
+ described in a paper "Fast Algorithms for
+ Sorting and Searching Strings", by Robert
+ Sedgewick and Jon L. Bentley.
+--*/
+
+#define mswap(zz1, zz2) \
+ { Int32 zztmp = zz1; zz1 = zz2; zz2 = zztmp; }
+
+#define mvswap(zzp1, zzp2, zzn) \
+{ \
+ Int32 yyp1 = (zzp1); \
+ Int32 yyp2 = (zzp2); \
+ Int32 yyn = (zzn); \
+ while (yyn > 0) { \
+ mswap(ptr[yyp1], ptr[yyp2]); \
+ yyp1++; yyp2++; yyn--; \
+ } \
+}
+
+static
+__inline__
+UChar mmed3 ( UChar a, UChar b, UChar c )
+{
+ UChar t;
+ if (a > b) { t = a; a = b; b = t; };
+ if (b > c) {
+ b = c;
+ if (a > b) b = a;
+ }
+ return b;
+}
+
+#define mmin(a,b) ((a) < (b)) ? (a) : (b)
+
+#define mpush(lz,hz,dz) { stackLo[sp] = lz; \
+ stackHi[sp] = hz; \
+ stackD [sp] = dz; \
+ sp++; }
+
+#define mpop(lz,hz,dz) { sp--; \
+ lz = stackLo[sp]; \
+ hz = stackHi[sp]; \
+ dz = stackD [sp]; }
+
+
+#define mnextsize(az) (nextHi[az]-nextLo[az])
+
+#define mnextswap(az,bz) \
+ { Int32 tz; \
+ tz = nextLo[az]; nextLo[az] = nextLo[bz]; nextLo[bz] = tz; \
+ tz = nextHi[az]; nextHi[az] = nextHi[bz]; nextHi[bz] = tz; \
+ tz = nextD [az]; nextD [az] = nextD [bz]; nextD [bz] = tz; }
+
+
+#define MAIN_QSORT_SMALL_THRESH 20
+#define MAIN_QSORT_DEPTH_THRESH (BZ_N_RADIX + BZ_N_QSORT)
+#define MAIN_QSORT_STACK_SIZE 100
+
+static
+void mainQSort3 ( UInt32* ptr,
+ UChar* block,
+ UInt16* quadrant,
+ Int32 nblock,
+ Int32 loSt,
+ Int32 hiSt,
+ Int32 dSt,
+ Int32* budget )
+{
+ Int32 unLo, unHi, ltLo, gtHi, n, m, med;
+ Int32 sp, lo, hi, d;
+
+ Int32 stackLo[MAIN_QSORT_STACK_SIZE];
+ Int32 stackHi[MAIN_QSORT_STACK_SIZE];
+ Int32 stackD [MAIN_QSORT_STACK_SIZE];
+
+ Int32 nextLo[3];
+ Int32 nextHi[3];
+ Int32 nextD [3];
+
+ sp = 0;
+ mpush ( loSt, hiSt, dSt );
+
+ while (sp > 0) {
+
+ AssertH ( sp < MAIN_QSORT_STACK_SIZE - 2, 1001 );
+
+ mpop ( lo, hi, d );
+ if (hi - lo < MAIN_QSORT_SMALL_THRESH ||
+ d > MAIN_QSORT_DEPTH_THRESH) {
+ mainSimpleSort ( ptr, block, quadrant, nblock, lo, hi, d, budget );
+ if (*budget < 0) return;
+ continue;
+ }
+
+ med = (Int32)
+ mmed3 ( block[ptr[ lo ]+d],
+ block[ptr[ hi ]+d],
+ block[ptr[ (lo+hi)>>1 ]+d] );
+
+ unLo = ltLo = lo;
+ unHi = gtHi = hi;
+
+ while (True) {
+ while (True) {
+ if (unLo > unHi) break;
+ n = ((Int32)block[ptr[unLo]+d]) - med;
+ if (n == 0) {
+ mswap(ptr[unLo], ptr[ltLo]);
+ ltLo++; unLo++; continue;
+ };
+ if (n > 0) break;
+ unLo++;
+ }
+ while (True) {
+ if (unLo > unHi) break;
+ n = ((Int32)block[ptr[unHi]+d]) - med;
+ if (n == 0) {
+ mswap(ptr[unHi], ptr[gtHi]);
+ gtHi--; unHi--; continue;
+ };
+ if (n < 0) break;
+ unHi--;
+ }
+ if (unLo > unHi) break;
+ mswap(ptr[unLo], ptr[unHi]); unLo++; unHi--;
+ }
+
+ AssertD ( unHi == unLo-1, "mainQSort3(2)" );
+
+ if (gtHi < ltLo) {
+ mpush(lo, hi, d+1 );
+ continue;
+ }
+
+ n = mmin(ltLo-lo, unLo-ltLo); mvswap(lo, unLo-n, n);
+ m = mmin(hi-gtHi, gtHi-unHi); mvswap(unLo, hi-m+1, m);
+
+ n = lo + unLo - ltLo - 1;
+ m = hi - (gtHi - unHi) + 1;
+
+ nextLo[0] = lo; nextHi[0] = n; nextD[0] = d;
+ nextLo[1] = m; nextHi[1] = hi; nextD[1] = d;
+ nextLo[2] = n+1; nextHi[2] = m-1; nextD[2] = d+1;
+
+ if (mnextsize(0) < mnextsize(1)) mnextswap(0,1);
+ if (mnextsize(1) < mnextsize(2)) mnextswap(1,2);
+ if (mnextsize(0) < mnextsize(1)) mnextswap(0,1);
+
+ AssertD (mnextsize(0) >= mnextsize(1), "mainQSort3(8)" );
+ AssertD (mnextsize(1) >= mnextsize(2), "mainQSort3(9)" );
+
+ mpush (nextLo[0], nextHi[0], nextD[0]);
+ mpush (nextLo[1], nextHi[1], nextD[1]);
+ mpush (nextLo[2], nextHi[2], nextD[2]);
+ }
+}
+
+#undef mswap
+#undef mvswap
+#undef mpush
+#undef mpop
+#undef mmin
+#undef mnextsize
+#undef mnextswap
+#undef MAIN_QSORT_SMALL_THRESH
+#undef MAIN_QSORT_DEPTH_THRESH
+#undef MAIN_QSORT_STACK_SIZE
+
+
+/*---------------------------------------------*/
+/* Pre:
+ nblock > N_OVERSHOOT
+ block32 exists for [0 .. nblock-1 +N_OVERSHOOT]
+ ((UChar*)block32) [0 .. nblock-1] holds block
+ ptr exists for [0 .. nblock-1]
+
+ Post:
+ ((UChar*)block32) [0 .. nblock-1] holds block
+ All other areas of block32 destroyed
+ ftab [0 .. 65536 ] destroyed
+ ptr [0 .. nblock-1] holds sorted order
+ if (*budget < 0), sorting was abandoned
+*/
+
+#define BIGFREQ(b) (ftab[((b)+1) << 8] - ftab[(b) << 8])
+#define SETMASK (1 << 21)
+#define CLEARMASK (~(SETMASK))
+
+static
+void mainSort ( UInt32* ptr,
+ UChar* block,
+ UInt16* quadrant,
+ UInt32* ftab,
+ Int32 nblock,
+ Int32 verb,
+ Int32* budget )
+{
+ Int32 i, j, k, ss, sb;
+ Int32 runningOrder[256];
+ Bool bigDone[256];
+ Int32 copyStart[256];
+ Int32 copyEnd [256];
+ UChar c1;
+ Int32 numQSorted;
+ UInt16 s;
+ if (verb >= 4) VPrintf0 ( " main sort initialise ...\n" );
+
+ /*-- set up the 2-byte frequency table --*/
+ for (i = 65536; i >= 0; i--) ftab[i] = 0;
+
+ j = block[0] << 8;
+ i = nblock-1;
+ for (; i >= 3; i -= 4) {
+ quadrant[i] = 0;
+ j = (j >> 8) | ( ((UInt16)block[i]) << 8);
+ ftab[j]++;
+ quadrant[i-1] = 0;
+ j = (j >> 8) | ( ((UInt16)block[i-1]) << 8);
+ ftab[j]++;
+ quadrant[i-2] = 0;
+ j = (j >> 8) | ( ((UInt16)block[i-2]) << 8);
+ ftab[j]++;
+ quadrant[i-3] = 0;
+ j = (j >> 8) | ( ((UInt16)block[i-3]) << 8);
+ ftab[j]++;
+ }
+ for (; i >= 0; i--) {
+ quadrant[i] = 0;
+ j = (j >> 8) | ( ((UInt16)block[i]) << 8);
+ ftab[j]++;
+ }
+
+ /*-- (emphasises close relationship of block & quadrant) --*/
+ for (i = 0; i < BZ_N_OVERSHOOT; i++) {
+ block [nblock+i] = block[i];
+ quadrant[nblock+i] = 0;
+ }
+
+ if (verb >= 4) VPrintf0 ( " bucket sorting ...\n" );
+
+ /*-- Complete the initial radix sort --*/
+ for (i = 1; i <= 65536; i++) ftab[i] += ftab[i-1];
+
+ s = block[0] << 8;
+ i = nblock-1;
+ for (; i >= 3; i -= 4) {
+ s = (s >> 8) | (block[i] << 8);
+ j = ftab[s] -1;
+ ftab[s] = j;
+ ptr[j] = i;
+ s = (s >> 8) | (block[i-1] << 8);
+ j = ftab[s] -1;
+ ftab[s] = j;
+ ptr[j] = i-1;
+ s = (s >> 8) | (block[i-2] << 8);
+ j = ftab[s] -1;
+ ftab[s] = j;
+ ptr[j] = i-2;
+ s = (s >> 8) | (block[i-3] << 8);
+ j = ftab[s] -1;
+ ftab[s] = j;
+ ptr[j] = i-3;
+ }
+ for (; i >= 0; i--) {
+ s = (s >> 8) | (block[i] << 8);
+ j = ftab[s] -1;
+ ftab[s] = j;
+ ptr[j] = i;
+ }
+
+ /*--
+ Now ftab contains the first loc of every small bucket.
+ Calculate the running order, from smallest to largest
+ big bucket.
+ --*/
+ for (i = 0; i <= 255; i++) {
+ bigDone [i] = False;
+ runningOrder[i] = i;
+ }
+
+ {
+ Int32 vv;
+ Int32 h = 1;
+ do h = 3 * h + 1; while (h <= 256);
+ do {
+ h = h / 3;
+ for (i = h; i <= 255; i++) {
+ vv = runningOrder[i];
+ j = i;
+ while ( BIGFREQ(runningOrder[j-h]) > BIGFREQ(vv) ) {
+ runningOrder[j] = runningOrder[j-h];
+ j = j - h;
+ if (j <= (h - 1)) goto zero;
+ }
+ zero:
+ runningOrder[j] = vv;
+ }
+ } while (h != 1);
+ }
+
+ /*--
+ The main sorting loop.
+ --*/
+
+ numQSorted = 0;
+
+ for (i = 0; i <= 255; i++) {
+
+ /*--
+ Process big buckets, starting with the least full.
+ Basically this is a 3-step process in which we call
+ mainQSort3 to sort the small buckets [ss, j], but
+ also make a big effort to avoid the calls if we can.
+ --*/
+ ss = runningOrder[i];
+
+ /*--
+ Step 1:
+ Complete the big bucket [ss] by quicksorting
+ any unsorted small buckets [ss, j], for j != ss.
+ Hopefully previous pointer-scanning phases have already
+ completed many of the small buckets [ss, j], so
+ we don't have to sort them at all.
+ --*/
+ for (j = 0; j <= 255; j++) {
+ if (j != ss) {
+ sb = (ss << 8) + j;
+ if ( ! (ftab[sb] & SETMASK) ) {
+ Int32 lo = ftab[sb] & CLEARMASK;
+ Int32 hi = (ftab[sb+1] & CLEARMASK) - 1;
+ if (hi > lo) {
+ if (verb >= 4)
+ VPrintf4 ( " qsort [0x%x, 0x%x] "
+ "done %d this %d\n",
+ ss, j, numQSorted, hi - lo + 1 );
+ mainQSort3 (
+ ptr, block, quadrant, nblock,
+ lo, hi, BZ_N_RADIX, budget
+ );
+ numQSorted += (hi - lo + 1);
+ if (*budget < 0) return;
+ }
+ }
+ ftab[sb] |= SETMASK;
+ }
+ }
+
+ AssertH ( !bigDone[ss], 1006 );
+
+ /*--
+ Step 2:
+ Now scan this big bucket [ss] so as to synthesise the
+ sorted order for small buckets [t, ss] for all t,
+ including, magically, the bucket [ss,ss] too.
+ This will avoid doing Real Work in subsequent Step 1's.
+ --*/
+ {
+ for (j = 0; j <= 255; j++) {
+ copyStart[j] = ftab[(j << 8) + ss] & CLEARMASK;
+ copyEnd [j] = (ftab[(j << 8) + ss + 1] & CLEARMASK) - 1;
+ }
+ for (j = ftab[ss << 8] & CLEARMASK; j < copyStart[ss]; j++) {
+ k = ptr[j]-1; if (k < 0) k += nblock;
+ c1 = block[k];
+ if (!bigDone[c1])
+ ptr[ copyStart[c1]++ ] = k;
+ }
+ for (j = (ftab[(ss+1) << 8] & CLEARMASK) - 1; j > copyEnd[ss]; j--) {
+ k = ptr[j]-1; if (k < 0) k += nblock;
+ c1 = block[k];
+ if (!bigDone[c1])
+ ptr[ copyEnd[c1]-- ] = k;
+ }
+ }
+
+ AssertH ( (copyStart[ss]-1 == copyEnd[ss])
+ ||
+ /* Extremely rare case missing in bzip2-1.0.0 and 1.0.1.
+ Necessity for this case is demonstrated by compressing
+ a sequence of approximately 48.5 million of character
+ 251; 1.0.0/1.0.1 will then die here. */
+ (copyStart[ss] == 0 && copyEnd[ss] == nblock-1),
+ 1007 )
+
+ for (j = 0; j <= 255; j++) ftab[(j << 8) + ss] |= SETMASK;
+
+ /*--
+ Step 3:
+ The [ss] big bucket is now done. Record this fact,
+ and update the quadrant descriptors. Remember to
+ update quadrants in the overshoot area too, if
+ necessary. The "if (i < 255)" test merely skips
+ this updating for the last bucket processed, since
+ updating for the last bucket is pointless.
+
+ The quadrant array provides a way to incrementally
+ cache sort orderings, as they appear, so as to
+ make subsequent comparisons in fullGtU() complete
+ faster. For repetitive blocks this makes a big
+ difference (but not big enough to be able to avoid
+ the fallback sorting mechanism, exponential radix sort).
+
+ The precise meaning is: at all times:
+
+ for 0 <= i < nblock and 0 <= j <= nblock
+
+ if block[i] != block[j],
+
+ then the relative values of quadrant[i] and
+ quadrant[j] are meaningless.
+
+ else {
+ if quadrant[i] < quadrant[j]
+ then the string starting at i lexicographically
+ precedes the string starting at j
+
+ else if quadrant[i] > quadrant[j]
+ then the string starting at j lexicographically
+ precedes the string starting at i
+
+ else
+ the relative ordering of the strings starting
+ at i and j has not yet been determined.
+ }
+ --*/
+ bigDone[ss] = True;
+
+ if (i < 255) {
+ Int32 bbStart = ftab[ss << 8] & CLEARMASK;
+ Int32 bbSize = (ftab[(ss+1) << 8] & CLEARMASK) - bbStart;
+ Int32 shifts = 0;
+
+ while ((bbSize >> shifts) > 65534) shifts++;
+
+ for (j = bbSize-1; j >= 0; j--) {
+ Int32 a2update = ptr[bbStart + j];
+ UInt16 qVal = (UInt16)(j >> shifts);
+ quadrant[a2update] = qVal;
+ if (a2update < BZ_N_OVERSHOOT)
+ quadrant[a2update + nblock] = qVal;
+ }
+ AssertH ( ((bbSize-1) >> shifts) <= 65535, 1002 );
+ }
+
+ }
+
+ if (verb >= 4)
+ VPrintf3 ( " %d pointers, %d sorted, %d scanned\n",
+ nblock, numQSorted, nblock - numQSorted );
+}
+
+#undef BIGFREQ
+#undef SETMASK
+#undef CLEARMASK
+
+
+/*---------------------------------------------*/
+/* Pre:
+ nblock > 0
+ arr2 exists for [0 .. nblock-1 +N_OVERSHOOT]
+ ((UChar*)arr2) [0 .. nblock-1] holds block
+ arr1 exists for [0 .. nblock-1]
+
+ Post:
+ ((UChar*)arr2) [0 .. nblock-1] holds block
+ All other areas of block destroyed
+ ftab [ 0 .. 65536 ] destroyed
+ arr1 [0 .. nblock-1] holds sorted order
+*/
+void BZ2_blockSort ( EState* s )
+{
+ UInt32* ptr = s->ptr;
+ UChar* block = s->block;
+ UInt32* ftab = s->ftab;
+ Int32 nblock = s->nblock;
+ Int32 verb = s->verbosity;
+ Int32 wfact = s->workFactor;
+ UInt16* quadrant;
+ Int32 budget;
+ Int32 budgetInit;
+ Int32 i;
+
+ if (nblock < 10000) {
+ fallbackSort ( s->arr1, s->arr2, ftab, nblock, verb );
+ } else {
+ /* Calculate the location for quadrant, remembering to get
+ the alignment right. Assumes that &(block[0]) is at least
+ 2-byte aligned -- this should be ok since block is really
+ the first section of arr2.
+ */
+ i = nblock+BZ_N_OVERSHOOT;
+ if (i & 1) i++;
+ quadrant = (UInt16*)(&(block[i]));
+
+ /* (wfact-1) / 3 puts the default-factor-30
+ transition point at very roughly the same place as
+ with v0.1 and v0.9.0.
+ Not that it particularly matters any more, since the
+ resulting compressed stream is now the same regardless
+ of whether or not we use the main sort or fallback sort.
+ */
+ if (wfact < 1 ) wfact = 1;
+ if (wfact > 100) wfact = 100;
+ budgetInit = nblock * ((wfact-1) / 3);
+ budget = budgetInit;
+
+ mainSort ( ptr, block, quadrant, ftab, nblock, verb, &budget );
+ if (verb >= 3)
+ VPrintf3 ( " %d work, %d block, ratio %5.2f\n",
+ budgetInit - budget,
+ nblock,
+ (float)(budgetInit - budget) /
+ (float)(nblock==0 ? 1 : nblock) );
+ if (budget < 0) {
+ if (verb >= 2)
+ VPrintf0 ( " too repetitive; using fallback"
+ " sorting algorithm\n" );
+ fallbackSort ( s->arr1, s->arr2, ftab, nblock, verb );
+ }
+ }
+
+ s->origPtr = -1;
+ for (i = 0; i < s->nblock; i++)
+ if (ptr[i] == 0)
+ { s->origPtr = i; break; };
+
+ AssertH( s->origPtr != -1, 1003 );
+}
+
+
+/*-------------------------------------------------------------*/
+/*--- end blocksort.c ---*/
+/*-------------------------------------------------------------*/
diff --git a/third-party/bzip2/bz-common.xsl b/third-party/bzip2/bz-common.xsl
new file mode 100644
index 0000000..66fcd6f
--- /dev/null
+++ b/third-party/bzip2/bz-common.xsl
@@ -0,0 +1,39 @@
+<?xml version="1.0"?> <!-- -*- sgml -*- -->
+<xsl:stylesheet
+ xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0">
+
+<!-- we like '1.2 Title' -->
+<xsl:param name="section.autolabel" select="'1'"/>
+<xsl:param name="section.label.includes.component.label" select="'1'"/>
+
+<!-- Do not put 'Chapter' at the start of eg 'Chapter 1. Doing This' -->
+<xsl:param name="local.l10n.xml" select="document('')"/>
+<l:i18n xmlns:l="http://docbook.sourceforge.net/xmlns/l10n/1.0">
+ <l:l10n language="en">
+ <l:context name="title-numbered">
+ <l:template name="chapter" text="%n. %t"/>
+ </l:context>
+ </l:l10n>
+</l:i18n>
+
+<!-- don't generate sub-tocs for qanda sets -->
+<xsl:param name="generate.toc">
+set toc,title
+book toc,title,figure,table,example,equation
+chapter toc,title
+section toc
+sect1 toc
+sect2 toc
+sect3 toc
+sect4 nop
+sect5 nop
+qandaset toc
+qandadiv nop
+appendix toc,title
+article/appendix nop
+article toc,title
+preface toc,title
+reference toc,title
+</xsl:param>
+
+</xsl:stylesheet>
diff --git a/third-party/bzip2/bz-fo.xsl b/third-party/bzip2/bz-fo.xsl
new file mode 100644
index 0000000..ba3e301
--- /dev/null
+++ b/third-party/bzip2/bz-fo.xsl
@@ -0,0 +1,276 @@
+<?xml version="1.0" encoding="UTF-8"?> <!-- -*- sgml -*- -->
+<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
+ xmlns:fo="http://www.w3.org/1999/XSL/Format" version="1.0">
+
+<xsl:import href="http://docbook.sourceforge.net/release/xsl/current/fo/docbook.xsl"/>
+<xsl:import href="bz-common.xsl"/>
+
+<!-- set indent = yes while debugging, then change to NO -->
+<xsl:output method="xml" indent="yes"/>
+
+<!-- ensure only passivetex extensions are on -->
+<xsl:param name="stylesheet.result.type" select="'fo'"/>
+<!-- fo extensions: PDF bookmarks and index terms -->
+<xsl:param name="use.extensions" select="'1'"/>
+<xsl:param name="xep.extensions" select="0"/>
+<xsl:param name="fop.extensions" select="0"/>
+<xsl:param name="saxon.extensions" select="0"/>
+<xsl:param name="passivetex.extensions" select="1"/>
+<xsl:param name="tablecolumns.extension" select="'1'"/>
+
+<!-- ensure we are using single sided -->
+<xsl:param name="double.sided" select="'0'"/>
+
+<!-- insert cross references to page numbers -->
+<xsl:param name="insert.xref.page.number" select="1"/>
+
+<!-- <?custom-pagebreak?> inserts a page break at this point -->
+<xsl:template match="processing-instruction('custom-pagebreak')">
+ <fo:block break-before='page'/>
+</xsl:template>
+
+<!-- show links in color -->
+<xsl:attribute-set name="xref.properties">
+ <xsl:attribute name="color">blue</xsl:attribute>
+</xsl:attribute-set>
+
+<!-- make pre listings indented a bit + a bg colour -->
+<xsl:template match="programlisting | screen">
+ <fo:block start-indent="0.25in" wrap-option="no-wrap"
+ white-space-collapse="false" text-align="start"
+ font-family="monospace" background-color="#f2f2f9"
+ linefeed-treatment="preserve"
+ xsl:use-attribute-sets="normal.para.spacing">
+ <xsl:apply-templates/>
+ </fo:block>
+</xsl:template>
+<!-- make verbatim output prettier -->
+<xsl:template match="literallayout">
+ <fo:block start-indent="0.25in" wrap-option="no-wrap"
+ white-space-collapse="false" text-align="start"
+ font-family="monospace" background-color="#edf7f4"
+ linefeed-treatment="preserve"
+ space-before="0em" space-after="0em">
+ <xsl:apply-templates/>
+ </fo:block>
+</xsl:template>
+
+<!-- workaround bug in passivetex fo output for itemizedlist -->
+<xsl:template match="itemizedlist/listitem">
+ <xsl:variable name="id">
+ <xsl:call-template name="object.id"/></xsl:variable>
+ <xsl:variable name="itemsymbol">
+ <xsl:call-template name="list.itemsymbol">
+ <xsl:with-param name="node" select="parent::itemizedlist"/>
+ </xsl:call-template>
+ </xsl:variable>
+ <xsl:variable name="item.contents">
+ <fo:list-item-label end-indent="label-end()">
+ <fo:block>
+ <xsl:choose>
+ <xsl:when test="$itemsymbol='disc'">•</xsl:when>
+ <xsl:when test="$itemsymbol='bullet'">•</xsl:when>
+ <xsl:otherwise>•</xsl:otherwise>
+ </xsl:choose>
+ </fo:block>
+ </fo:list-item-label>
+ <fo:list-item-body start-indent="body-start()">
+ <xsl:apply-templates/> <!-- removed extra block wrapper -->
+ </fo:list-item-body>
+ </xsl:variable>
+ <xsl:choose>
+ <xsl:when test="parent::*/@spacing = 'compact'">
+ <fo:list-item id="{$id}"
+ xsl:use-attribute-sets="compact.list.item.spacing">
+ <xsl:copy-of select="$item.contents"/>
+ </fo:list-item>
+ </xsl:when>
+ <xsl:otherwise>
+ <fo:list-item id="{$id}" xsl:use-attribute-sets="list.item.spacing">
+ <xsl:copy-of select="$item.contents"/>
+ </fo:list-item>
+ </xsl:otherwise>
+ </xsl:choose>
+</xsl:template>
+
+<!-- workaround bug in passivetex fo output for orderedlist -->
+<xsl:template match="orderedlist/listitem">
+ <xsl:variable name="id">
+ <xsl:call-template name="object.id"/></xsl:variable>
+ <xsl:variable name="item.contents">
+ <fo:list-item-label end-indent="label-end()">
+ <fo:block>
+ <xsl:apply-templates select="." mode="item-number"/>
+ </fo:block>
+ </fo:list-item-label>
+ <fo:list-item-body start-indent="body-start()">
+ <xsl:apply-templates/> <!-- removed extra block wrapper -->
+ </fo:list-item-body>
+ </xsl:variable>
+ <xsl:choose>
+ <xsl:when test="parent::*/@spacing = 'compact'">
+ <fo:list-item id="{$id}"
+ xsl:use-attribute-sets="compact.list.item.spacing">
+ <xsl:copy-of select="$item.contents"/>
+ </fo:list-item>
+ </xsl:when>
+ <xsl:otherwise>
+ <fo:list-item id="{$id}" xsl:use-attribute-sets="list.item.spacing">
+ <xsl:copy-of select="$item.contents"/>
+ </fo:list-item>
+ </xsl:otherwise>
+ </xsl:choose>
+</xsl:template>
+
+<!-- workaround bug in passivetex fo output for variablelist -->
+<xsl:param name="variablelist.as.blocks" select="1"/>
+<xsl:template match="varlistentry" mode="vl.as.blocks">
+ <xsl:variable name="id">
+ <xsl:call-template name="object.id"/></xsl:variable>
+ <fo:block id="{$id}" xsl:use-attribute-sets="list.item.spacing"
+ keep-together.within-column="always"
+ keep-with-next.within-column="always">
+ <xsl:apply-templates select="term"/>
+ </fo:block>
+ <fo:block start-indent="0.5in" end-indent="0in"
+ space-after.minimum="0.2em"
+ space-after.optimum="0.4em"
+ space-after.maximum="0.6em">
+ <fo:block>
+ <xsl:apply-templates select="listitem"/>
+ </fo:block>
+ </fo:block>
+</xsl:template>
+
+
+<!-- workaround bug in footers: force right-align w/two 80|30 cols -->
+<xsl:template name="footer.table">
+ <xsl:param name="pageclass" select="''"/>
+ <xsl:param name="sequence" select="''"/>
+ <xsl:param name="gentext-key" select="''"/>
+ <xsl:choose>
+ <xsl:when test="$pageclass = 'index'">
+ <xsl:attribute name="margin-left">0pt</xsl:attribute>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:variable name="candidate">
+ <fo:table table-layout="fixed" width="100%">
+ <fo:table-column column-number="1" column-width="80%"/>
+ <fo:table-column column-number="2" column-width="20%"/>
+ <fo:table-body>
+ <fo:table-row height="14pt">
+ <fo:table-cell text-align="left" display-align="after">
+ <xsl:attribute name="relative-align">baseline</xsl:attribute>
+ <fo:block>
+ <fo:block> </fo:block><!-- empty cell -->
+ </fo:block>
+ </fo:table-cell>
+ <fo:table-cell text-align="center" display-align="after">
+ <xsl:attribute name="relative-align">baseline</xsl:attribute>
+ <fo:block>
+ <xsl:call-template name="footer.content">
+ <xsl:with-param name="pageclass" select="$pageclass"/>
+ <xsl:with-param name="sequence" select="$sequence"/>
+ <xsl:with-param name="position" select="'center'"/>
+ <xsl:with-param name="gentext-key" select="$gentext-key"/>
+ </xsl:call-template>
+ </fo:block>
+ </fo:table-cell>
+ </fo:table-row>
+ </fo:table-body>
+ </fo:table>
+ </xsl:variable>
+ <!-- Really output a footer? -->
+ <xsl:choose>
+ <xsl:when test="$pageclass='titlepage' and $gentext-key='book'
+ and $sequence='first'">
+ <!-- no, book titlepages have no footers at all -->
+ </xsl:when>
+ <xsl:when test="$sequence = 'blank' and $footers.on.blank.pages = 0">
+ <!-- no output -->
+ </xsl:when>
+ <xsl:otherwise>
+ <xsl:copy-of select="$candidate"/>
+ </xsl:otherwise>
+ </xsl:choose>
+</xsl:template>
+
+
+<!-- fix bug in headers: force right-align w/two 40|60 cols -->
+<xsl:template name="header.table">
+ <xsl:param name="pageclass" select="''"/>
+ <xsl:param name="sequence" select="''"/>
+ <xsl:param name="gentext-key" select="''"/>
+ <xsl:choose>
+ <xsl:when test="$pageclass = 'index'">
+ <xsl:attribute name="margin-left">0pt</xsl:attribute>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:variable name="candidate">
+ <fo:table table-layout="fixed" width="100%">
+ <xsl:call-template name="head.sep.rule">
+ <xsl:with-param name="pageclass" select="$pageclass"/>
+ <xsl:with-param name="sequence" select="$sequence"/>
+ <xsl:with-param name="gentext-key" select="$gentext-key"/>
+ </xsl:call-template>
+ <fo:table-column column-number="1" column-width="40%"/>
+ <fo:table-column column-number="2" column-width="60%"/>
+ <fo:table-body>
+ <fo:table-row height="14pt">
+ <fo:table-cell text-align="left" display-align="before">
+ <xsl:attribute name="relative-align">baseline</xsl:attribute>
+ <fo:block>
+ <fo:block> </fo:block><!-- empty cell -->
+ </fo:block>
+ </fo:table-cell>
+ <fo:table-cell text-align="center" display-align="before">
+ <xsl:attribute name="relative-align">baseline</xsl:attribute>
+ <fo:block>
+ <xsl:call-template name="header.content">
+ <xsl:with-param name="pageclass" select="$pageclass"/>
+ <xsl:with-param name="sequence" select="$sequence"/>
+ <xsl:with-param name="position" select="'center'"/>
+ <xsl:with-param name="gentext-key" select="$gentext-key"/>
+ </xsl:call-template>
+ </fo:block>
+ </fo:table-cell>
+ </fo:table-row>
+ </fo:table-body>
+ </fo:table>
+ </xsl:variable>
+ <!-- Really output a header? -->
+ <xsl:choose>
+ <xsl:when test="$pageclass = 'titlepage' and $gentext-key = 'book'
+ and $sequence='first'">
+ <!-- no, book titlepages have no headers at all -->
+ </xsl:when>
+ <xsl:when test="$sequence = 'blank' and $headers.on.blank.pages = 0">
+ <!-- no output -->
+ </xsl:when>
+ <xsl:otherwise>
+ <xsl:copy-of select="$candidate"/>
+ </xsl:otherwise>
+ </xsl:choose>
+</xsl:template>
+
+
+<!-- Bug-fix for Suse 10 PassiveTex version -->
+<!-- Precompute attribute values 'cos PassiveTex is too stupid: -->
+<xsl:attribute-set name="component.title.properties">
+ <xsl:attribute name="keep-with-next.within-column">always</xsl:attribute>
+ <xsl:attribute name="space-before.optimum">
+ <xsl:value-of select="concat($body.font.master, 'pt')"/>
+ </xsl:attribute>
+ <xsl:attribute name="space-before.minimum">
+ <xsl:value-of select="$body.font.master * 0.8"/>
+ <xsl:text>pt</xsl:text>
+ </xsl:attribute>
+ <xsl:attribute name="space-before.maximum">
+ <xsl:value-of select="$body.font.master * 1.2"/>
+ <xsl:text>pt</xsl:text>
+ </xsl:attribute>
+ <xsl:attribute name="hyphenate">false</xsl:attribute>
+</xsl:attribute-set>
+
+
+</xsl:stylesheet>
diff --git a/third-party/bzip2/bz-html.xsl b/third-party/bzip2/bz-html.xsl
new file mode 100644
index 0000000..1785fff
--- /dev/null
+++ b/third-party/bzip2/bz-html.xsl
@@ -0,0 +1,20 @@
+<?xml version="1.0"?> <!-- -*- sgml -*- -->
+<!DOCTYPE xsl:stylesheet [ <!ENTITY bz-css SYSTEM "./bzip.css"> ]>
+
+<xsl:stylesheet
+ xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0">
+
+<xsl:import href="http://docbook.sourceforge.net/release/xsl/current/html/docbook.xsl"/>
+<xsl:import href="bz-common.xsl"/>
+
+<!-- use 8859-1 encoding -->
+<xsl:output method="html" encoding="ISO-8859-1" indent="yes"/>
+
+<!-- we include the css directly when generating one large file -->
+<xsl:template name="user.head.content">
+ <style type="text/css" media="screen">
+ <xsl:text>&bz-css;</xsl:text>
+ </style>
+</xsl:template>
+
+</xsl:stylesheet>
diff --git a/third-party/bzip2/bzdiff b/third-party/bzip2/bzdiff
new file mode 100644
index 0000000..6fc38f9
--- /dev/null
+++ b/third-party/bzip2/bzdiff
@@ -0,0 +1,76 @@
+#!/bin/sh
+# sh is buggy on RS/6000 AIX 3.2. Replace above line with #!/bin/ksh
+
+# Bzcmp/diff wrapped for bzip2,
+# adapted from zdiff by Philippe Troin <phil at fifi.org> for Debian GNU/Linux.
+
+# Bzcmp and bzdiff are used to invoke the cmp or the diff pro-
+# gram on compressed files. All options specified are passed
+# directly to cmp or diff. If only 1 file is specified, then
+# the files compared are file1 and an uncompressed file1.gz.
+# If two files are specified, then they are uncompressed (if
+# necessary) and fed to cmp or diff. The exit status from cmp
+# or diff is preserved.
+
+PATH="/usr/bin:/bin:$PATH"; export PATH
+prog=`echo $0 | sed 's|.*/||'`
+case "$prog" in
+ *cmp) comp=${CMP-cmp} ;;
+ *) comp=${DIFF-diff} ;;
+esac
+
+OPTIONS=
+FILES=
+for ARG
+do
+ case "$ARG" in
+ -*) OPTIONS="$OPTIONS $ARG";;
+ *) if test -f "$ARG"; then
+ FILES="$FILES $ARG"
+ else
+ echo "${prog}: $ARG not found or not a regular file"
+ exit 1
+ fi ;;
+ esac
+done
+if test -z "$FILES"; then
+ echo "Usage: $prog [${comp}_options] file [file]"
+ exit 1
+fi
+tmp=`mktemp ${TMPDIR:-/tmp}/bzdiff.XXXXXXXXXX` || {
+ echo 'cannot create a temporary file' >&2
+ exit 1
+}
+set $FILES
+if test $# -eq 1; then
+ FILE=`echo "$1" | sed 's/.bz2$//'`
+ bzip2 -cd "$FILE.bz2" | $comp $OPTIONS - "$FILE"
+ STAT="$?"
+
+elif test $# -eq 2; then
+ case "$1" in
+ *.bz2)
+ case "$2" in
+ *.bz2)
+ F=`echo "$2" | sed 's|.*/||;s|.bz2$||'`
+ bzip2 -cdfq "$2" > $tmp
+ bzip2 -cdfq "$1" | $comp $OPTIONS - $tmp
+ STAT="$?"
+ /bin/rm -f $tmp;;
+
+ *) bzip2 -cdfq "$1" | $comp $OPTIONS - "$2"
+ STAT="$?";;
+ esac;;
+ *) case "$2" in
+ *.bz2)
+ bzip2 -cdfq "$2" | $comp $OPTIONS "$1" -
+ STAT="$?";;
+ *) $comp $OPTIONS "$1" "$2"
+ STAT="$?";;
+ esac;;
+ esac
+ exit "$STAT"
+else
+ echo "Usage: $prog [${comp}_options] file [file]"
+ exit 1
+fi
diff --git a/third-party/bzip2/bzdiff.1 b/third-party/bzip2/bzdiff.1
new file mode 100644
index 0000000..adb7a8e
--- /dev/null
+++ b/third-party/bzip2/bzdiff.1
@@ -0,0 +1,47 @@
+\"Shamelessly copied from zmore.1 by Philippe Troin <phil at fifi.org>
+\"for Debian GNU/Linux
+.TH BZDIFF 1
+.SH NAME
+bzcmp, bzdiff \- compare bzip2 compressed files
+.SH SYNOPSIS
+.B bzcmp
+[ cmp_options ] file1
+[ file2 ]
+.br
+.B bzdiff
+[ diff_options ] file1
+[ file2 ]
+.SH DESCRIPTION
+.I Bzcmp
+and
+.I bzdiff
+are used to invoke the
+.I cmp
+or the
+.I diff
+program on bzip2 compressed files. All options specified are passed
+directly to
+.I cmp
+or
+.IR diff "."
+If only 1 file is specified, then the files compared are
+.I file1
+and an uncompressed
+.IR file1 ".bz2."
+If two files are specified, then they are uncompressed if necessary and fed to
+.I cmp
+or
+.IR diff "."
+The exit status from
+.I cmp
+or
+.I diff
+is preserved.
+.SH "SEE ALSO"
+cmp(1), diff(1), bzmore(1), bzless(1), bzgrep(1), bzip2(1)
+.SH BUGS
+Messages from the
+.I cmp
+or
+.I diff
+programs refer to temporary filenames instead of those specified.
diff --git a/third-party/bzip2/bzgrep b/third-party/bzip2/bzgrep
new file mode 100644
index 0000000..9a04b83
--- /dev/null
+++ b/third-party/bzip2/bzgrep
@@ -0,0 +1,75 @@
+#!/bin/sh
+
+# Bzgrep wrapped for bzip2,
+# adapted from zgrep by Philippe Troin <phil at fifi.org> for Debian GNU/Linux.
+## zgrep notice:
+## zgrep -- a wrapper around a grep program that decompresses files as needed
+## Adapted from a version sent by Charles Levert <charles at comm.polymtl.ca>
+
+PATH="/usr/bin:$PATH"; export PATH
+
+prog=`echo $0 | sed 's|.*/||'`
+case "$prog" in
+ *egrep) grep=${EGREP-egrep} ;;
+ *fgrep) grep=${FGREP-fgrep} ;;
+ *) grep=${GREP-grep} ;;
+esac
+pat=""
+while test $# -ne 0; do
+ case "$1" in
+ -e | -f) opt="$opt $1"; shift; pat="$1"
+ if test "$grep" = grep; then # grep is buggy with -e on SVR4
+ grep=egrep
+ fi;;
+ -A | -B) opt="$opt $1 $2"; shift;;
+ -*) opt="$opt $1";;
+ *) if test -z "$pat"; then
+ pat="$1"
+ else
+ break;
+ fi;;
+ esac
+ shift
+done
+
+if test -z "$pat"; then
+ echo "grep through bzip2 files"
+ echo "usage: $prog [grep_options] pattern [files]"
+ exit 1
+fi
+
+list=0
+silent=0
+op=`echo "$opt" | sed -e 's/ //g' -e 's/-//g'`
+case "$op" in
+ *l*) list=1
+esac
+case "$op" in
+ *h*) silent=1
+esac
+
+if test $# -eq 0; then
+ bzip2 -cdfq | $grep $opt "$pat"
+ exit $?
+fi
+
+res=0
+for i do
+ if test -f "$i"; then :; else if test -f "$i.bz2"; then i="$i.bz2"; fi; fi
+ if test $list -eq 1; then
+ bzip2 -cdfq "$i" | $grep $opt "$pat" 2>&1 > /dev/null && echo $i
+ r=$?
+ elif test $# -eq 1 -o $silent -eq 1; then
+ bzip2 -cdfq "$i" | $grep $opt "$pat"
+ r=$?
+ else
+ j=${i//\\/\\\\}
+ j=${j//|/\\|}
+ j=${j//&/\\&}
+ j=`printf "%s" "$j" | tr '\n' ' '`
+ bzip2 -cdfq "$i" | $grep $opt "$pat" | sed "s|^|${j}:|"
+ r=$?
+ fi
+ test "$r" -ne 0 && res="$r"
+done
+exit $res
diff --git a/third-party/bzip2/bzgrep.1 b/third-party/bzip2/bzgrep.1
new file mode 100644
index 0000000..930af8c
--- /dev/null
+++ b/third-party/bzip2/bzgrep.1
@@ -0,0 +1,56 @@
+\"Shamelessly copied from zmore.1 by Philippe Troin <phil at fifi.org>
+\"for Debian GNU/Linux
+.TH BZGREP 1
+.SH NAME
+bzgrep, bzfgrep, bzegrep \- search possibly bzip2 compressed files for a regular expression
+.SH SYNOPSIS
+.B bzgrep
+[ grep_options ]
+.BI [\ -e\ ] " pattern"
+.IR filename ".\|.\|."
+.br
+.B bzegrep
+[ egrep_options ]
+.BI [\ -e\ ] " pattern"
+.IR filename ".\|.\|."
+.br
+.B bzfgrep
+[ fgrep_options ]
+.BI [\ -e\ ] " pattern"
+.IR filename ".\|.\|."
+.SH DESCRIPTION
+.IR Bzgrep
+is used to invoke the
+.I grep
+on bzip2-compressed files. All options specified are passed directly to
+.I grep.
+If no file is specified, then the standard input is decompressed
+if necessary and fed to grep.
+Otherwise the given files are uncompressed if necessary and fed to
+.I grep.
+.PP
+If
+.I bzgrep
+is invoked as
+.I bzegrep
+or
+.I bzfgrep
+then
+.I egrep
+or
+.I fgrep
+is used instead of
+.I grep.
+If the GREP environment variable is set,
+.I bzgrep
+uses it as the
+.I grep
+program to be invoked. For example:
+
+ for sh: GREP=fgrep bzgrep string files
+ for csh: (setenv GREP fgrep; bzgrep string files)
+.SH AUTHOR
+Charles Levert (charles at comm.polymtl.ca). Adapted to bzip2 by Philippe
+Troin <phil at fifi.org> for Debian GNU/Linux.
+.SH "SEE ALSO"
+grep(1), egrep(1), fgrep(1), bzdiff(1), bzmore(1), bzless(1), bzip2(1)
diff --git a/third-party/bzip2/bzip.css b/third-party/bzip2/bzip.css
new file mode 100644
index 0000000..43193d8
--- /dev/null
+++ b/third-party/bzip2/bzip.css
@@ -0,0 +1,74 @@
+/* Colours:
+#74240f dark brown h1, h2, h3, h4
+#336699 medium blue links
+#339999 turquoise link hover colour
+#202020 almost black general text
+#761596 purple md5sum text
+#626262 dark gray pre border
+#eeeeee very light gray pre background
+#f2f2f9 very light blue nav table background
+#3366cc medium blue nav table border
+*/
+
+a, a:link, a:visited, a:active { color: #336699; }
+a:hover { color: #339999; }
+
+body { font: 80%/126% sans-serif; }
+h1, h2, h3, h4 { color: #74240f; }
+
+dt { color: #336699; font-weight: bold }
+dd {
+ margin-left: 1.5em;
+ padding-bottom: 0.8em;
+}
+
+/* -- ruler -- */
+div.hr_blue {
+ height: 3px;
+ background:#ffffff url("/images/hr_blue.png") repeat-x; }
+div.hr_blue hr { display:none; }
+
+/* release styles */
+#release p { margin-top: 0.4em; }
+#release .md5sum { color: #761596; }
+
+
+/* ------ styles for docs|manuals|howto ------ */
+/* -- lists -- */
+ul {
+ margin: 0px 4px 16px 16px;
+ padding: 0px;
+ list-style: url("/images/li-blue.png");
+}
+ul li {
+ margin-bottom: 10px;
+}
+ul ul {
+ list-style-type: none;
+ list-style-image: none;
+ margin-left: 0px;
+}
+
+/* header / footer nav tables */
+table.nav {
+ border: solid 1px #3366cc;
+ background: #f2f2f9;
+ background-color: #f2f2f9;
+ margin-bottom: 0.5em;
+}
+/* don't have underlined links in chunked nav menus */
+table.nav a { text-decoration: none; }
+table.nav a:hover { text-decoration: underline; }
+table.nav td { font-size: 85%; }
+
+code, tt, pre { font-size: 120%; }
+code, tt { color: #761596; }
+
+div.literallayout, pre.programlisting, pre.screen {
+ color: #000000;
+ padding: 0.5em;
+ background: #eeeeee;
+ border: 1px solid #626262;
+ background-color: #eeeeee;
+ margin: 4px 0px 4px 0px;
+}
diff --git a/third-party/bzip2/bzip2.1 b/third-party/bzip2/bzip2.1
new file mode 100644
index 0000000..ce3a78e
--- /dev/null
+++ b/third-party/bzip2/bzip2.1
@@ -0,0 +1,454 @@
+.PU
+.TH bzip2 1
+.SH NAME
+bzip2, bunzip2 \- a block-sorting file compressor, v1.0.6
+.br
+bzcat \- decompresses files to stdout
+.br
+bzip2recover \- recovers data from damaged bzip2 files
+
+.SH SYNOPSIS
+.ll +8
+.B bzip2
+.RB [ " \-cdfkqstvzVL123456789 " ]
+[
+.I "filenames \&..."
+]
+.ll -8
+.br
+.B bunzip2
+.RB [ " \-fkvsVL " ]
+[
+.I "filenames \&..."
+]
+.br
+.B bzcat
+.RB [ " \-s " ]
+[
+.I "filenames \&..."
+]
+.br
+.B bzip2recover
+.I "filename"
+
+.SH DESCRIPTION
+.I bzip2
+compresses files using the Burrows-Wheeler block sorting
+text compression algorithm, and Huffman coding. Compression is
+generally considerably better than that achieved by more conventional
+LZ77/LZ78-based compressors, and approaches the performance of the PPM
+family of statistical compressors.
+
+The command-line options are deliberately very similar to
+those of
+.I GNU gzip,
+but they are not identical.
+
+.I bzip2
+expects a list of file names to accompany the
+command-line flags. Each file is replaced by a compressed version of
+itself, with the name "original_name.bz2".
+Each compressed file
+has the same modification date, permissions, and, when possible,
+ownership as the corresponding original, so that these properties can
+be correctly restored at decompression time. File name handling is
+naive in the sense that there is no mechanism for preserving original
+file names, permissions, ownerships or dates in filesystems which lack
+these concepts, or have serious file name length restrictions, such as
+MS-DOS.
+
+.I bzip2
+and
+.I bunzip2
+will by default not overwrite existing
+files. If you want this to happen, specify the \-f flag.
+
+If no file names are specified,
+.I bzip2
+compresses from standard
+input to standard output. In this case,
+.I bzip2
+will decline to
+write compressed output to a terminal, as this would be entirely
+incomprehensible and therefore pointless.
+
+.I bunzip2
+(or
+.I bzip2 \-d)
+decompresses all
+specified files. Files which were not created by
+.I bzip2
+will be detected and ignored, and a warning issued.
+.I bzip2
+attempts to guess the filename for the decompressed file
+from that of the compressed file as follows:
+
+ filename.bz2 becomes filename
+ filename.bz becomes filename
+ filename.tbz2 becomes filename.tar
+ filename.tbz becomes filename.tar
+ anyothername becomes anyothername.out
+
+If the file does not end in one of the recognised endings,
+.I .bz2,
+.I .bz,
+.I .tbz2
+or
+.I .tbz,
+.I bzip2
+complains that it cannot
+guess the name of the original file, and uses the original name
+with
+.I .out
+appended.
+
+As with compression, supplying no
+filenames causes decompression from
+standard input to standard output.
+
+.I bunzip2
+will correctly decompress a file which is the
+concatenation of two or more compressed files. The result is the
+concatenation of the corresponding uncompressed files. Integrity
+testing (\-t)
+of concatenated
+compressed files is also supported.
+
+You can also compress or decompress files to the standard output by
+giving the \-c flag. Multiple files may be compressed and
+decompressed like this. The resulting outputs are fed sequentially to
+stdout. Compression of multiple files
+in this manner generates a stream
+containing multiple compressed file representations. Such a stream
+can be decompressed correctly only by
+.I bzip2
+version 0.9.0 or
+later. Earlier versions of
+.I bzip2
+will stop after decompressing
+the first file in the stream.
+
+.I bzcat
+(or
+.I bzip2 -dc)
+decompresses all specified files to
+the standard output.
+
+.I bzip2
+will read arguments from the environment variables
+.I BZIP2
+and
+.I BZIP,
+in that order, and will process them
+before any arguments read from the command line. This gives a
+convenient way to supply default arguments.
+
+Compression is always performed, even if the compressed
+file is slightly
+larger than the original. Files of less than about one hundred bytes
+tend to get larger, since the compression mechanism has a constant
+overhead in the region of 50 bytes. Random data (including the output
+of most file compressors) is coded at about 8.05 bits per byte, giving
+an expansion of around 0.5%.
+
+As a self-check for your protection,
+.I
+bzip2
+uses 32-bit CRCs to
+make sure that the decompressed version of a file is identical to the
+original. This guards against corruption of the compressed data, and
+against undetected bugs in
+.I bzip2
+(hopefully very unlikely). The
+chances of data corruption going undetected is microscopic, about one
+chance in four billion for each file processed. Be aware, though, that
+the check occurs upon decompression, so it can only tell you that
+something is wrong. It can't help you
+recover the original uncompressed
+data. You can use
+.I bzip2recover
+to try to recover data from
+damaged files.
+
+Return values: 0 for a normal exit, 1 for environmental problems (file
+not found, invalid flags, I/O errors, &c), 2 to indicate a corrupt
+compressed file, 3 for an internal consistency error (eg, bug) which
+caused
+.I bzip2
+to panic.
+
+.SH OPTIONS
+.TP
+.B \-c --stdout
+Compress or decompress to standard output.
+.TP
+.B \-d --decompress
+Force decompression.
+.I bzip2,
+.I bunzip2
+and
+.I bzcat
+are
+really the same program, and the decision about what actions to take is
+done on the basis of which name is used. This flag overrides that
+mechanism, and forces
+.I bzip2
+to decompress.
+.TP
+.B \-z --compress
+The complement to \-d: forces compression, regardless of the
+invocation name.
+.TP
+.B \-t --test
+Check integrity of the specified file(s), but don't decompress them.
+This really performs a trial decompression and throws away the result.
+.TP
+.B \-f --force
+Force overwrite of output files. Normally,
+.I bzip2
+will not overwrite
+existing output files. Also forces
+.I bzip2
+to break hard links
+to files, which it otherwise wouldn't do.
+
+bzip2 normally declines to decompress files which don't have the
+correct magic header bytes. If forced (-f), however, it will pass
+such files through unmodified. This is how GNU gzip behaves.
+.TP
+.B \-k --keep
+Keep (don't delete) input files during compression
+or decompression.
+.TP
+.B \-s --small
+Reduce memory usage, for compression, decompression and testing. Files
+are decompressed and tested using a modified algorithm which only
+requires 2.5 bytes per block byte. This means any file can be
+decompressed in 2300k of memory, albeit at about half the normal speed.
+
+During compression, \-s selects a block size of 200k, which limits
+memory use to around the same figure, at the expense of your compression
+ratio. In short, if your machine is low on memory (8 megabytes or
+less), use \-s for everything. See MEMORY MANAGEMENT below.
+.TP
+.B \-q --quiet
+Suppress non-essential warning messages. Messages pertaining to
+I/O errors and other critical events will not be suppressed.
+.TP
+.B \-v --verbose
+Verbose mode -- show the compression ratio for each file processed.
+Further \-v's increase the verbosity level, spewing out lots of
+information which is primarily of interest for diagnostic purposes.
+.TP
+.B \-L --license -V --version
+Display the software version, license terms and conditions.
+.TP
+.B \-1 (or \-\-fast) to \-9 (or \-\-best)
+Set the block size to 100 k, 200 k .. 900 k when compressing. Has no
+effect when decompressing. See MEMORY MANAGEMENT below.
+The \-\-fast and \-\-best aliases are primarily for GNU gzip
+compatibility. In particular, \-\-fast doesn't make things
+significantly faster.
+And \-\-best merely selects the default behaviour.
+.TP
+.B \--
+Treats all subsequent arguments as file names, even if they start
+with a dash. This is so you can handle files with names beginning
+with a dash, for example: bzip2 \-- \-myfilename.
+.TP
+.B \--repetitive-fast --repetitive-best
+These flags are redundant in versions 0.9.5 and above. They provided
+some coarse control over the behaviour of the sorting algorithm in
+earlier versions, which was sometimes useful. 0.9.5 and above have an
+improved algorithm which renders these flags irrelevant.
+
+.SH MEMORY MANAGEMENT
+.I bzip2
+compresses large files in blocks. The block size affects
+both the compression ratio achieved, and the amount of memory needed for
+compression and decompression. The flags \-1 through \-9
+specify the block size to be 100,000 bytes through 900,000 bytes (the
+default) respectively. At decompression time, the block size used for
+compression is read from the header of the compressed file, and
+.I bunzip2
+then allocates itself just enough memory to decompress
+the file. Since block sizes are stored in compressed files, it follows
+that the flags \-1 to \-9 are irrelevant to and so ignored
+during decompression.
+
+Compression and decompression requirements,
+in bytes, can be estimated as:
+
+ Compression: 400k + ( 8 x block size )
+
+ Decompression: 100k + ( 4 x block size ), or
+ 100k + ( 2.5 x block size )
+
+Larger block sizes give rapidly diminishing marginal returns. Most of
+the compression comes from the first two or three hundred k of block
+size, a fact worth bearing in mind when using
+.I bzip2
+on small machines.
+It is also important to appreciate that the decompression memory
+requirement is set at compression time by the choice of block size.
+
+For files compressed with the default 900k block size,
+.I bunzip2
+will require about 3700 kbytes to decompress. To support decompression
+of any file on a 4 megabyte machine,
+.I bunzip2
+has an option to
+decompress using approximately half this amount of memory, about 2300
+kbytes. Decompression speed is also halved, so you should use this
+option only where necessary. The relevant flag is -s.
+
+In general, try and use the largest block size memory constraints allow,
+since that maximises the compression achieved. Compression and
+decompression speed are virtually unaffected by block size.
+
+Another significant point applies to files which fit in a single block
+-- that means most files you'd encounter using a large block size. The
+amount of real memory touched is proportional to the size of the file,
+since the file is smaller than a block. For example, compressing a file
+20,000 bytes long with the flag -9 will cause the compressor to
+allocate around 7600k of memory, but only touch 400k + 20000 * 8 = 560
+kbytes of it. Similarly, the decompressor will allocate 3700k but only
+touch 100k + 20000 * 4 = 180 kbytes.
+
+Here is a table which summarises the maximum memory usage for different
+block sizes. Also recorded is the total compressed size for 14 files of
+the Calgary Text Compression Corpus totalling 3,141,622 bytes. This
+column gives some feel for how compression varies with block size.
+These figures tend to understate the advantage of larger block sizes for
+larger files, since the Corpus is dominated by smaller files.
+
+ Compress Decompress Decompress Corpus
+ Flag usage usage -s usage Size
+
+ -1 1200k 500k 350k 914704
+ -2 2000k 900k 600k 877703
+ -3 2800k 1300k 850k 860338
+ -4 3600k 1700k 1100k 846899
+ -5 4400k 2100k 1350k 845160
+ -6 5200k 2500k 1600k 838626
+ -7 6100k 2900k 1850k 834096
+ -8 6800k 3300k 2100k 828642
+ -9 7600k 3700k 2350k 828642
+
+.SH RECOVERING DATA FROM DAMAGED FILES
+.I bzip2
+compresses files in blocks, usually 900kbytes long. Each
+block is handled independently. If a media or transmission error causes
+a multi-block .bz2
+file to become damaged, it may be possible to
+recover data from the undamaged blocks in the file.
+
+The compressed representation of each block is delimited by a 48-bit
+pattern, which makes it possible to find the block boundaries with
+reasonable certainty. Each block also carries its own 32-bit CRC, so
+damaged blocks can be distinguished from undamaged ones.
+
+.I bzip2recover
+is a simple program whose purpose is to search for
+blocks in .bz2 files, and write each block out into its own .bz2
+file. You can then use
+.I bzip2
+\-t
+to test the
+integrity of the resulting files, and decompress those which are
+undamaged.
+
+.I bzip2recover
+takes a single argument, the name of the damaged file,
+and writes a number of files "rec00001file.bz2",
+"rec00002file.bz2", etc, containing the extracted blocks.
+The output filenames are designed so that the use of
+wildcards in subsequent processing -- for example,
+"bzip2 -dc rec*file.bz2 > recovered_data" -- processes the files in
+the correct order.
+
+.I bzip2recover
+should be of most use dealing with large .bz2
+files, as these will contain many blocks. It is clearly
+futile to use it on damaged single-block files, since a
+damaged block cannot be recovered. If you wish to minimise
+any potential data loss through media or transmission errors,
+you might consider compressing with a smaller
+block size.
+
+.SH PERFORMANCE NOTES
+The sorting phase of compression gathers together similar strings in the
+file. Because of this, files containing very long runs of repeated
+symbols, like "aabaabaabaab ..." (repeated several hundred times) may
+compress more slowly than normal. Versions 0.9.5 and above fare much
+better than previous versions in this respect. The ratio between
+worst-case and average-case compression time is in the region of 10:1.
+For previous versions, this figure was more like 100:1. You can use the
+\-vvvv option to monitor progress in great detail, if you want.
+
+Decompression speed is unaffected by these phenomena.
+
+.I bzip2
+usually allocates several megabytes of memory to operate
+in, and then charges all over it in a fairly random fashion. This means
+that performance, both for compressing and decompressing, is largely
+determined by the speed at which your machine can service cache misses.
+Because of this, small changes to the code to reduce the miss rate have
+been observed to give disproportionately large performance improvements.
+I imagine
+.I bzip2
+will perform best on machines with very large caches.
+
+.SH CAVEATS
+I/O error messages are not as helpful as they could be.
+.I bzip2
+tries hard to detect I/O errors and exit cleanly, but the details of
+what the problem is sometimes seem rather misleading.
+
+This manual page pertains to version 1.0.6 of
+.I bzip2.
+Compressed data created by this version is entirely forwards and
+backwards compatible with the previous public releases, versions
+0.1pl2, 0.9.0, 0.9.5, 1.0.0, 1.0.1, 1.0.2 and above, but with the following
+exception: 0.9.0 and above can correctly decompress multiple
+concatenated compressed files. 0.1pl2 cannot do this; it will stop
+after decompressing just the first file in the stream.
+
+.I bzip2recover
+versions prior to 1.0.2 used 32-bit integers to represent
+bit positions in compressed files, so they could not handle compressed
+files more than 512 megabytes long. Versions 1.0.2 and above use
+64-bit ints on some platforms which support them (GNU supported
+targets, and Windows). To establish whether or not bzip2recover was
+built with such a limitation, run it without arguments. In any event
+you can build yourself an unlimited version if you can recompile it
+with MaybeUInt64 set to be an unsigned 64-bit integer.
+
+
+
+.SH AUTHOR
+Julian Seward, jsewardbzip.org.
+
+http://www.bzip.org
+
+The ideas embodied in
+.I bzip2
+are due to (at least) the following
+people: Michael Burrows and David Wheeler (for the block sorting
+transformation), David Wheeler (again, for the Huffman coder), Peter
+Fenwick (for the structured coding model in the original
+.I bzip,
+and many refinements), and Alistair Moffat, Radford Neal and Ian Witten
+(for the arithmetic coder in the original
+.I bzip).
+I am much
+indebted for their help, support and advice. See the manual in the
+source distribution for pointers to sources of documentation. Christian
+von Roques encouraged me to look for faster sorting algorithms, so as to
+speed up compression. Bela Lubkin encouraged me to improve the
+worst-case compression performance.
+Donna Robinson XMLised the documentation.
+The bz* scripts are derived from those of GNU gzip.
+Many people sent patches, helped
+with portability problems, lent machines, gave advice and were generally
+helpful.
diff --git a/third-party/bzip2/bzip2.1.preformatted b/third-party/bzip2/bzip2.1.preformatted
new file mode 100644
index 0000000..63c33be
--- /dev/null
+++ b/third-party/bzip2/bzip2.1.preformatted
@@ -0,0 +1,399 @@
+bzip2(1) bzip2(1)
+
+
+
+NNAAMMEE
+ bzip2, bunzip2 − a block‐sorting file compressor, v1.0.6
+ bzcat − decompresses files to stdout
+ bzip2recover − recovers data from damaged bzip2 files
+
+
+SSYYNNOOPPSSIISS
+ bbzziipp22 [ −−ccddffkkqqssttvvzzVVLL112233445566778899 ] [ _f_i_l_e_n_a_m_e_s _._._. ]
+ bbuunnzziipp22 [ −−ffkkvvssVVLL ] [ _f_i_l_e_n_a_m_e_s _._._. ]
+ bbzzccaatt [ −−ss ] [ _f_i_l_e_n_a_m_e_s _._._. ]
+ bbzziipp22rreeccoovveerr _f_i_l_e_n_a_m_e
+
+
+DDEESSCCRRIIPPTTIIOONN
+ _b_z_i_p_2 compresses files using the Burrows‐Wheeler block
+ sorting text compression algorithm, and Huffman coding.
+ Compression is generally considerably better than that
+ achieved by more conventional LZ77/LZ78‐based compressors,
+ and approaches the performance of the PPM family of sta
+ tistical compressors.
+
+ The command‐line options are deliberately very similar to
+ those of _G_N_U _g_z_i_p_, but they are not identical.
+
+ _b_z_i_p_2 expects a list of file names to accompany the com
+ mand‐line flags. Each file is replaced by a compressed
+ version of itself, with the name "original_name.bz2".
+ Each compressed file has the same modification date, per
+ missions, and, when possible, ownership as the correspond
+ ing original, so that these properties can be correctly
+ restored at decompression time. File name handling is
+ naive in the sense that there is no mechanism for preserv
+ ing original file names, permissions, ownerships or dates
+ in filesystems which lack these concepts, or have serious
+ file name length restrictions, such as MS‐DOS.
+
+ _b_z_i_p_2 and _b_u_n_z_i_p_2 will by default not overwrite existing
+ files. If you want this to happen, specify the −f flag.
+
+ If no file names are specified, _b_z_i_p_2 compresses from
+ standard input to standard output. In this case, _b_z_i_p_2
+ will decline to write compressed output to a terminal, as
+ this would be entirely incomprehensible and therefore
+ pointless.
+
+ _b_u_n_z_i_p_2 (or _b_z_i_p_2 _−_d_) decompresses all specified files.
+ Files which were not created by _b_z_i_p_2 will be detected and
+ ignored, and a warning issued. _b_z_i_p_2 attempts to guess
+ the filename for the decompressed file from that of the
+ compressed file as follows:
+
+ filename.bz2 becomes filename
+ filename.bz becomes filename
+ filename.tbz2 becomes filename.tar
+ filename.tbz becomes filename.tar
+ anyothername becomes anyothername.out
+
+ If the file does not end in one of the recognised endings,
+ _._b_z_2_, _._b_z_, _._t_b_z_2 or _._t_b_z_, _b_z_i_p_2 complains that it cannot
+ guess the name of the original file, and uses the original
+ name with _._o_u_t appended.
+
+ As with compression, supplying no filenames causes decom
+ pression from standard input to standard output.
+
+ _b_u_n_z_i_p_2 will correctly decompress a file which is the con
+ catenation of two or more compressed files. The result is
+ the concatenation of the corresponding uncompressed files.
+ Integrity testing (−t) of concatenated compressed files is
+ also supported.
+
+ You can also compress or decompress files to the standard
+ output by giving the −c flag. Multiple files may be com
+ pressed and decompressed like this. The resulting outputs
+ are fed sequentially to stdout. Compression of multiple
+ files in this manner generates a stream containing multi
+ ple compressed file representations. Such a stream can be
+ decompressed correctly only by _b_z_i_p_2 version 0.9.0 or
+ later. Earlier versions of _b_z_i_p_2 will stop after decom
+ pressing the first file in the stream.
+
+ _b_z_c_a_t (or _b_z_i_p_2 _‐_d_c_) decompresses all specified files to
+ the standard output.
+
+ _b_z_i_p_2 will read arguments from the environment variables
+ _B_Z_I_P_2 and _B_Z_I_P_, in that order, and will process them
+ before any arguments read from the command line. This
+ gives a convenient way to supply default arguments.
+
+ Compression is always performed, even if the compressed
+ file is slightly larger than the original. Files of less
+ than about one hundred bytes tend to get larger, since the
+ compression mechanism has a constant overhead in the
+ region of 50 bytes. Random data (including the output of
+ most file compressors) is coded at about 8.05 bits per
+ byte, giving an expansion of around 0.5%.
+
+ As a self‐check for your protection, _b_z_i_p_2 uses 32‐bit
+ CRCs to make sure that the decompressed version of a file
+ is identical to the original. This guards against corrup
+ tion of the compressed data, and against undetected bugs
+ in _b_z_i_p_2 (hopefully very unlikely). The chances of data
+ corruption going undetected is microscopic, about one
+ chance in four billion for each file processed. Be aware,
+ though, that the check occurs upon decompression, so it
+ can only tell you that something is wrong. It can’t help
+ you recover the original uncompressed data. You can use
+ _b_z_i_p_2_r_e_c_o_v_e_r to try to recover data from damaged files.
+
+ Return values: 0 for a normal exit, 1 for environmental
+ problems (file not found, invalid flags, I/O errors, &c),
+ 2 to indicate a corrupt compressed file, 3 for an internal
+ consistency error (eg, bug) which caused _b_z_i_p_2 to panic.
+
+
+OOPPTTIIOONNSS
+ −−cc ‐‐‐‐ssttddoouutt
+ Compress or decompress to standard output.
+
+ −−dd ‐‐‐‐ddeeccoommpprreessss
+ Force decompression. _b_z_i_p_2_, _b_u_n_z_i_p_2 and _b_z_c_a_t are
+ really the same program, and the decision about
+ what actions to take is done on the basis of which
+ name is used. This flag overrides that mechanism,
+ and forces _b_z_i_p_2 to decompress.
+
+ −−zz ‐‐‐‐ccoommpprreessss
+ The complement to −d: forces compression,
+ regardless of the invocation name.
+
+ −−tt ‐‐‐‐tteesstt
+ Check integrity of the specified file(s), but don’t
+ decompress them. This really performs a trial
+ decompression and throws away the result.
+
+ −−ff ‐‐‐‐ffoorrccee
+ Force overwrite of output files. Normally, _b_z_i_p_2
+ will not overwrite existing output files. Also
+ forces _b_z_i_p_2 to break hard links to files, which it
+ otherwise wouldn’t do.
+
+ bzip2 normally declines to decompress files which
+ don’t have the correct magic header bytes. If
+ forced (‐f), however, it will pass such files
+ through unmodified. This is how GNU gzip behaves.
+
+ −−kk ‐‐‐‐kkeeeepp
+ Keep (don’t delete) input files during compression
+ or decompression.
+
+ −−ss ‐‐‐‐ssmmaallll
+ Reduce memory usage, for compression, decompression
+ and testing. Files are decompressed and tested
+ using a modified algorithm which only requires 2.5
+ bytes per block byte. This means any file can be
+ decompressed in 2300k of memory, albeit at about
+ half the normal speed.
+
+ During compression, −s selects a block size of
+ 200k, which limits memory use to around the same
+ figure, at the expense of your compression ratio.
+ In short, if your machine is low on memory (8
+ megabytes or less), use −s for everything. See
+ MEMORY MANAGEMENT below.
+
+ −−qq ‐‐‐‐qquuiieett
+ Suppress non‐essential warning messages. Messages
+ pertaining to I/O errors and other critical events
+ will not be suppressed.
+
+ −−vv ‐‐‐‐vveerrbboossee
+ Verbose mode ‐‐ show the compression ratio for each
+ file processed. Further −v’s increase the ver
+ bosity level, spewing out lots of information which
+ is primarily of interest for diagnostic purposes.
+
+ −−LL ‐‐‐‐lliicceennssee ‐‐VV ‐‐‐‐vveerrssiioonn
+ Display the software version, license terms and
+ conditions.
+
+ −−11 ((oorr −−−−ffaasstt)) ttoo −−99 ((oorr −−−−bbeesstt))
+ Set the block size to 100 k, 200 k .. 900 k when
+ compressing. Has no effect when decompressing.
+ See MEMORY MANAGEMENT below. The −−fast and −−best
+ aliases are primarily for GNU gzip compatibility.
+ In particular, −−fast doesn’t make things signifi
+ cantly faster. And −−best merely selects the
+ default behaviour.
+
+ −−‐‐ Treats all subsequent arguments as file names, even
+ if they start with a dash. This is so you can han
+ dle files with names beginning with a dash, for
+ example: bzip2 −‐ −myfilename.
+
+ −−‐‐rreeppeettiittiivvee‐‐ffaasstt ‐‐‐‐rreeppeettiittiivvee‐‐bbeesstt
+ These flags are redundant in versions 0.9.5 and
+ above. They provided some coarse control over the
+ behaviour of the sorting algorithm in earlier ver
+ sions, which was sometimes useful. 0.9.5 and above
+ have an improved algorithm which renders these
+ flags irrelevant.
+
+
+MMEEMMOORRYY MMAANNAAGGEEMMEENNTT
+ _b_z_i_p_2 compresses large files in blocks. The block size
+ affects both the compression ratio achieved, and the
+ amount of memory needed for compression and decompression.
+ The flags −1 through −9 specify the block size to be
+ 100,000 bytes through 900,000 bytes (the default) respec
+ tively. At decompression time, the block size used for
+ compression is read from the header of the compressed
+ file, and _b_u_n_z_i_p_2 then allocates itself just enough memory
+ to decompress the file. Since block sizes are stored in
+ compressed files, it follows that the flags −1 to −9 are
+ irrelevant to and so ignored during decompression.
+
+ Compression and decompression requirements, in bytes, can
+ be estimated as:
+
+ Compression: 400k + ( 8 x block size )
+
+ Decompression: 100k + ( 4 x block size ), or
+ 100k + ( 2.5 x block size )
+
+ Larger block sizes give rapidly diminishing marginal
+ returns. Most of the compression comes from the first two
+ or three hundred k of block size, a fact worth bearing in
+ mind when using _b_z_i_p_2 on small machines. It is also
+ important to appreciate that the decompression memory
+ requirement is set at compression time by the choice of
+ block size.
+
+ For files compressed with the default 900k block size,
+ _b_u_n_z_i_p_2 will require about 3700 kbytes to decompress. To
+ support decompression of any file on a 4 megabyte machine,
+ _b_u_n_z_i_p_2 has an option to decompress using approximately
+ half this amount of memory, about 2300 kbytes. Decompres
+ sion speed is also halved, so you should use this option
+ only where necessary. The relevant flag is ‐s.
+
+ In general, try and use the largest block size memory con
+ straints allow, since that maximises the compression
+ achieved. Compression and decompression speed are virtu
+ ally unaffected by block size.
+
+ Another significant point applies to files which fit in a
+ single block ‐‐ that means most files you’d encounter
+ using a large block size. The amount of real memory
+ touched is proportional to the size of the file, since the
+ file is smaller than a block. For example, compressing a
+ file 20,000 bytes long with the flag ‐9 will cause the
+ compressor to allocate around 7600k of memory, but only
+ touch 400k + 20000 * 8 = 560 kbytes of it. Similarly, the
+ decompressor will allocate 3700k but only touch 100k +
+ 20000 * 4 = 180 kbytes.
+
+ Here is a table which summarises the maximum memory usage
+ for different block sizes. Also recorded is the total
+ compressed size for 14 files of the Calgary Text Compres
+ sion Corpus totalling 3,141,622 bytes. This column gives
+ some feel for how compression varies with block size.
+ These figures tend to understate the advantage of larger
+ block sizes for larger files, since the Corpus is domi
+ nated by smaller files.
+
+ Compress Decompress Decompress Corpus
+ Flag usage usage ‐s usage Size
+
+ ‐1 1200k 500k 350k 914704
+ ‐2 2000k 900k 600k 877703
+ ‐3 2800k 1300k 850k 860338
+ ‐4 3600k 1700k 1100k 846899
+ ‐5 4400k 2100k 1350k 845160
+ ‐6 5200k 2500k 1600k 838626
+ ‐7 6100k 2900k 1850k 834096
+ ‐8 6800k 3300k 2100k 828642
+ ‐9 7600k 3700k 2350k 828642
+
+
+RREECCOOVVEERRIINNGG DDAATTAA FFRROOMM DDAAMMAAGGEEDD FFIILLEESS
+ _b_z_i_p_2 compresses files in blocks, usually 900kbytes long.
+ Each block is handled independently. If a media or trans
+ mission error causes a multi‐block .bz2 file to become
+ damaged, it may be possible to recover data from the
+ undamaged blocks in the file.
+
+ The compressed representation of each block is delimited
+ by a 48‐bit pattern, which makes it possible to find the
+ block boundaries with reasonable certainty. Each block
+ also carries its own 32‐bit CRC, so damaged blocks can be
+ distinguished from undamaged ones.
+
+ _b_z_i_p_2_r_e_c_o_v_e_r is a simple program whose purpose is to
+ search for blocks in .bz2 files, and write each block out
+ into its own .bz2 file. You can then use _b_z_i_p_2 −t to test
+ the integrity of the resulting files, and decompress those
+ which are undamaged.
+
+ _b_z_i_p_2_r_e_c_o_v_e_r takes a single argument, the name of the dam
+ aged file, and writes a number of files
+ "rec00001file.bz2", "rec00002file.bz2", etc, containing
+ the extracted blocks. The output filenames are
+ designed so that the use of wildcards in subsequent pro
+ cessing ‐‐ for example, "bzip2 ‐dc rec*file.bz2 > recov
+ ered_data" ‐‐ processes the files in the correct order.
+
+ _b_z_i_p_2_r_e_c_o_v_e_r should be of most use dealing with large .bz2
+ files, as these will contain many blocks. It is clearly
+ futile to use it on damaged single‐block files, since a
+ damaged block cannot be recovered. If you wish to min
+ imise any potential data loss through media or transmis
+ sion errors, you might consider compressing with a smaller
+ block size.
+
+
+PPEERRFFOORRMMAANNCCEE NNOOTTEESS
+ The sorting phase of compression gathers together similar
+ strings in the file. Because of this, files containing
+ very long runs of repeated symbols, like "aabaabaabaab
+ ..." (repeated several hundred times) may compress more
+ slowly than normal. Versions 0.9.5 and above fare much
+ better than previous versions in this respect. The ratio
+ between worst‐case and average‐case compression time is in
+ the region of 10:1. For previous versions, this figure
+ was more like 100:1. You can use the −vvvv option to mon
+ itor progress in great detail, if you want.
+
+ Decompression speed is unaffected by these phenomena.
+
+ _b_z_i_p_2 usually allocates several megabytes of memory to
+ operate in, and then charges all over it in a fairly ran
+ dom fashion. This means that performance, both for com
+ pressing and decompressing, is largely determined by the
+ speed at which your machine can service cache misses.
+ Because of this, small changes to the code to reduce the
+ miss rate have been observed to give disproportionately
+ large performance improvements. I imagine _b_z_i_p_2 will per
+ form best on machines with very large caches.
+
+
+CCAAVVEEAATTSS
+ I/O error messages are not as helpful as they could be.
+ _b_z_i_p_2 tries hard to detect I/O errors and exit cleanly,
+ but the details of what the problem is sometimes seem
+ rather misleading.
+
+ This manual page pertains to version 1.0.6 of _b_z_i_p_2_. Com
+ pressed data created by this version is entirely forwards
+ and backwards compatible with the previous public
+ releases, versions 0.1pl2, 0.9.0, 0.9.5, 1.0.0, 1.0.1,
+ 1.0.2 and above, but with the following exception: 0.9.0
+ and above can correctly decompress multiple concatenated
+ compressed files. 0.1pl2 cannot do this; it will stop
+ after decompressing just the first file in the stream.
+
+ _b_z_i_p_2_r_e_c_o_v_e_r versions prior to 1.0.2 used 32‐bit integers
+ to represent bit positions in compressed files, so they
+ could not handle compressed files more than 512 megabytes
+ long. Versions 1.0.2 and above use 64‐bit ints on some
+ platforms which support them (GNU supported targets, and
+ Windows). To establish whether or not bzip2recover was
+ built with such a limitation, run it without arguments.
+ In any event you can build yourself an unlimited version
+ if you can recompile it with MaybeUInt64 set to be an
+ unsigned 64‐bit integer.
+
+
+
+
+AAUUTTHHOORR
+ Julian Seward, jsewardbzip.org.
+
+ http://www.bzip.org
+
+ The ideas embodied in _b_z_i_p_2 are due to (at least) the fol
+ lowing people: Michael Burrows and David Wheeler (for the
+ block sorting transformation), David Wheeler (again, for
+ the Huffman coder), Peter Fenwick (for the structured cod
+ ing model in the original _b_z_i_p_, and many refinements), and
+ Alistair Moffat, Radford Neal and Ian Witten (for the
+ arithmetic coder in the original _b_z_i_p_)_. I am much
+ indebted for their help, support and advice. See the man
+ ual in the source distribution for pointers to sources of
+ documentation. Christian von Roques encouraged me to look
+ for faster sorting algorithms, so as to speed up compres
+ sion. Bela Lubkin encouraged me to improve the worst‐case
+ compression performance. Donna Robinson XMLised the docu
+ mentation. The bz* scripts are derived from those of GNU
+ gzip. Many people sent patches, helped with portability
+ problems, lent machines, gave advice and were generally
+ helpful.
+
+
+
+ bzip2(1)
diff --git a/third-party/bzip2/bzip2.c b/third-party/bzip2/bzip2.c
new file mode 100644
index 0000000..6de9d1d
--- /dev/null
+++ b/third-party/bzip2/bzip2.c
@@ -0,0 +1,2034 @@
+
+/*-----------------------------------------------------------*/
+/*--- A block-sorting, lossless compressor bzip2.c ---*/
+/*-----------------------------------------------------------*/
+
+/* ------------------------------------------------------------------
+ This file is part of bzip2/libbzip2, a program and library for
+ lossless, block-sorting data compression.
+
+ bzip2/libbzip2 version 1.0.6 of 6 September 2010
+ Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
+
+ Please read the WARNING, DISCLAIMER and PATENTS sections in the
+ README file.
+
+ This program is released under the terms of the license contained
+ in the file LICENSE.
+ ------------------------------------------------------------------ */
+
+
+/* Place a 1 beside your platform, and 0 elsewhere.
+ Generic 32-bit Unix.
+ Also works on 64-bit Unix boxes.
+ This is the default.
+*/
+#define BZ_UNIX 1
+
+/*--
+ Win32, as seen by Jacob Navia's excellent
+ port of (Chris Fraser & David Hanson)'s excellent
+ lcc compiler. Or with MS Visual C.
+ This is selected automatically if compiled by a compiler which
+ defines _WIN32, not including the Cygwin GCC.
+--*/
+#define BZ_LCCWIN32 0
+
+#if defined(_WIN32) && !defined(__CYGWIN__)
+#undef BZ_LCCWIN32
+#define BZ_LCCWIN32 1
+#undef BZ_UNIX
+#define BZ_UNIX 0
+#endif
+
+
+/*---------------------------------------------*/
+/*--
+ Some stuff for all platforms.
+--*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <signal.h>
+#include <math.h>
+#include <errno.h>
+#include <ctype.h>
+#include "bzlib.h"
+
+#define ERROR_IF_EOF(i) { if ((i) == EOF) ioError(); }
+#define ERROR_IF_NOT_ZERO(i) { if ((i) != 0) ioError(); }
+#define ERROR_IF_MINUS_ONE(i) { if ((i) == (-1)) ioError(); }
+
+
+/*---------------------------------------------*/
+/*--
+ Platform-specific stuff.
+--*/
+
+#if BZ_UNIX
+# include <fcntl.h>
+# include <sys/types.h>
+# include <utime.h>
+# include <unistd.h>
+# include <sys/stat.h>
+# include <sys/times.h>
+
+# define PATH_SEP '/'
+# define MY_LSTAT lstat
+# define MY_STAT stat
+# define MY_S_ISREG S_ISREG
+# define MY_S_ISDIR S_ISDIR
+
+# define APPEND_FILESPEC(root, name) \
+ root=snocString((root), (name))
+
+# define APPEND_FLAG(root, name) \
+ root=snocString((root), (name))
+
+# define SET_BINARY_MODE(fd) /**/
+
+# ifdef __GNUC__
+# define NORETURN __attribute__ ((noreturn))
+# else
+# define NORETURN /**/
+# endif
+
+# ifdef __DJGPP__
+# include <io.h>
+# include <fcntl.h>
+# undef MY_LSTAT
+# undef MY_STAT
+# define MY_LSTAT stat
+# define MY_STAT stat
+# undef SET_BINARY_MODE
+# define SET_BINARY_MODE(fd) \
+ do { \
+ int retVal = setmode ( fileno ( fd ), \
+ O_BINARY ); \
+ ERROR_IF_MINUS_ONE ( retVal ); \
+ } while ( 0 )
+# endif
+
+# ifdef __CYGWIN__
+# include <io.h>
+# include <fcntl.h>
+# undef SET_BINARY_MODE
+# define SET_BINARY_MODE(fd) \
+ do { \
+ int retVal = setmode ( fileno ( fd ), \
+ O_BINARY ); \
+ ERROR_IF_MINUS_ONE ( retVal ); \
+ } while ( 0 )
+# endif
+#endif /* BZ_UNIX */
+
+
+
+#if BZ_LCCWIN32
+# include <io.h>
+# include <fcntl.h>
+# include <sys\stat.h>
+
+# define NORETURN /**/
+# define PATH_SEP '\\'
+# define MY_LSTAT _stat
+# define MY_STAT _stat
+# define MY_S_ISREG(x) ((x) & _S_IFREG)
+# define MY_S_ISDIR(x) ((x) & _S_IFDIR)
+
+# define APPEND_FLAG(root, name) \
+ root=snocString((root), (name))
+
+# define APPEND_FILESPEC(root, name) \
+ root = snocString ((root), (name))
+
+# define SET_BINARY_MODE(fd) \
+ do { \
+ int retVal = setmode ( fileno ( fd ), \
+ O_BINARY ); \
+ ERROR_IF_MINUS_ONE ( retVal ); \
+ } while ( 0 )
+
+#endif /* BZ_LCCWIN32 */
+
+
+/*---------------------------------------------*/
+/*--
+ Some more stuff for all platforms :-)
+--*/
+
+typedef char Char;
+typedef unsigned char Bool;
+typedef unsigned char UChar;
+typedef int Int32;
+typedef unsigned int UInt32;
+typedef short Int16;
+typedef unsigned short UInt16;
+
+#define True ((Bool)1)
+#define False ((Bool)0)
+
+/*--
+ IntNative is your platform's `native' int size.
+ Only here to avoid probs with 64-bit platforms.
+--*/
+typedef int IntNative;
+
+
+/*---------------------------------------------------*/
+/*--- Misc (file handling) data decls ---*/
+/*---------------------------------------------------*/
+
+Int32 verbosity;
+Bool keepInputFiles, smallMode, deleteOutputOnInterrupt;
+Bool forceOverwrite, testFailsExist, unzFailsExist, noisy;
+Int32 numFileNames, numFilesProcessed, blockSize100k;
+Int32 exitValue;
+
+/*-- source modes; F==file, I==stdin, O==stdout --*/
+#define SM_I2O 1
+#define SM_F2O 2
+#define SM_F2F 3
+
+/*-- operation modes --*/
+#define OM_Z 1
+#define OM_UNZ 2
+#define OM_TEST 3
+
+Int32 opMode;
+Int32 srcMode;
+
+#define FILE_NAME_LEN 1034
+
+Int32 longestFileName;
+Char inName [FILE_NAME_LEN];
+Char outName[FILE_NAME_LEN];
+Char tmpName[FILE_NAME_LEN];
+Char *progName;
+Char progNameReally[FILE_NAME_LEN];
+FILE *outputHandleJustInCase;
+Int32 workFactor;
+
+static void panic ( const Char* ) NORETURN;
+static void ioError ( void ) NORETURN;
+static void outOfMemory ( void ) NORETURN;
+static void configError ( void ) NORETURN;
+static void crcError ( void ) NORETURN;
+static void cleanUpAndFail ( Int32 ) NORETURN;
+static void compressedStreamEOF ( void ) NORETURN;
+
+static void copyFileName ( Char*, Char* );
+static void* myMalloc ( Int32 );
+static void applySavedFileAttrToOutputFile ( IntNative fd );
+
+
+
+/*---------------------------------------------------*/
+/*--- An implementation of 64-bit ints. Sigh. ---*/
+/*--- Roll on widespread deployment of ANSI C9X ! ---*/
+/*---------------------------------------------------*/
+
+typedef
+ struct { UChar b[8]; }
+ UInt64;
+
+
+static
+void uInt64_from_UInt32s ( UInt64* n, UInt32 lo32, UInt32 hi32 )
+{
+ n->b[7] = (UChar)((hi32 >> 24) & 0xFF);
+ n->b[6] = (UChar)((hi32 >> 16) & 0xFF);
+ n->b[5] = (UChar)((hi32 >> 8) & 0xFF);
+ n->b[4] = (UChar) (hi32 & 0xFF);
+ n->b[3] = (UChar)((lo32 >> 24) & 0xFF);
+ n->b[2] = (UChar)((lo32 >> 16) & 0xFF);
+ n->b[1] = (UChar)((lo32 >> 8) & 0xFF);
+ n->b[0] = (UChar) (lo32 & 0xFF);
+}
+
+
+static
+double uInt64_to_double ( UInt64* n )
+{
+ Int32 i;
+ double base = 1.0;
+ double sum = 0.0;
+ for (i = 0; i < 8; i++) {
+ sum += base * (double)(n->b[i]);
+ base *= 256.0;
+ }
+ return sum;
+}
+
+
+static
+Bool uInt64_isZero ( UInt64* n )
+{
+ Int32 i;
+ for (i = 0; i < 8; i++)
+ if (n->b[i] != 0) return 0;
+ return 1;
+}
+
+
+/* Divide *n by 10, and return the remainder. */
+static
+Int32 uInt64_qrm10 ( UInt64* n )
+{
+ UInt32 rem, tmp;
+ Int32 i;
+ rem = 0;
+ for (i = 7; i >= 0; i--) {
+ tmp = rem * 256 + n->b[i];
+ n->b[i] = tmp / 10;
+ rem = tmp % 10;
+ }
+ return rem;
+}
+
+
+/* ... and the Whole Entire Point of all this UInt64 stuff is
+ so that we can supply the following function.
+*/
+static
+void uInt64_toAscii ( char* outbuf, UInt64* n )
+{
+ Int32 i, q;
+ UChar buf[32];
+ Int32 nBuf = 0;
+ UInt64 n_copy = *n;
+ do {
+ q = uInt64_qrm10 ( &n_copy );
+ buf[nBuf] = q + '0';
+ nBuf++;
+ } while (!uInt64_isZero(&n_copy));
+ outbuf[nBuf] = 0;
+ for (i = 0; i < nBuf; i++)
+ outbuf[i] = buf[nBuf-i-1];
+}
+
+
+/*---------------------------------------------------*/
+/*--- Processing of complete files and streams ---*/
+/*---------------------------------------------------*/
+
+/*---------------------------------------------*/
+static
+Bool myfeof ( FILE* f )
+{
+ Int32 c = fgetc ( f );
+ if (c == EOF) return True;
+ ungetc ( c, f );
+ return False;
+}
+
+
+/*---------------------------------------------*/
+static
+void compressStream ( FILE *stream, FILE *zStream )
+{
+ BZFILE* bzf = NULL;
+ UChar ibuf[5000];
+ Int32 nIbuf;
+ UInt32 nbytes_in_lo32, nbytes_in_hi32;
+ UInt32 nbytes_out_lo32, nbytes_out_hi32;
+ Int32 bzerr, bzerr_dummy, ret;
+
+ SET_BINARY_MODE(stream);
+ SET_BINARY_MODE(zStream);
+
+ if (ferror(stream)) goto errhandler_io;
+ if (ferror(zStream)) goto errhandler_io;
+
+ bzf = BZ2_bzWriteOpen ( &bzerr, zStream,
+ blockSize100k, verbosity, workFactor );
+ if (bzerr != BZ_OK) goto errhandler;
+
+ if (verbosity >= 2) fprintf ( stderr, "\n" );
+
+ while (True) {
+
+ if (myfeof(stream)) break;
+ nIbuf = fread ( ibuf, sizeof(UChar), 5000, stream );
+ if (ferror(stream)) goto errhandler_io;
+ if (nIbuf > 0) BZ2_bzWrite ( &bzerr, bzf, (void*)ibuf, nIbuf );
+ if (bzerr != BZ_OK) goto errhandler;
+
+ }
+
+ BZ2_bzWriteClose64 ( &bzerr, bzf, 0,
+ &nbytes_in_lo32, &nbytes_in_hi32,
+ &nbytes_out_lo32, &nbytes_out_hi32 );
+ if (bzerr != BZ_OK) goto errhandler;
+
+ if (ferror(zStream)) goto errhandler_io;
+ ret = fflush ( zStream );
+ if (ret == EOF) goto errhandler_io;
+ if (zStream != stdout) {
+ Int32 fd = fileno ( zStream );
+ if (fd < 0) goto errhandler_io;
+ applySavedFileAttrToOutputFile ( fd );
+ ret = fclose ( zStream );
+ outputHandleJustInCase = NULL;
+ if (ret == EOF) goto errhandler_io;
+ }
+ outputHandleJustInCase = NULL;
+ if (ferror(stream)) goto errhandler_io;
+ ret = fclose ( stream );
+ if (ret == EOF) goto errhandler_io;
+
+ if (verbosity >= 1) {
+ if (nbytes_in_lo32 == 0 && nbytes_in_hi32 == 0) {
+ fprintf ( stderr, " no data compressed.\n");
+ } else {
+ Char buf_nin[32], buf_nout[32];
+ UInt64 nbytes_in, nbytes_out;
+ double nbytes_in_d, nbytes_out_d;
+ uInt64_from_UInt32s ( &nbytes_in,
+ nbytes_in_lo32, nbytes_in_hi32 );
+ uInt64_from_UInt32s ( &nbytes_out,
+ nbytes_out_lo32, nbytes_out_hi32 );
+ nbytes_in_d = uInt64_to_double ( &nbytes_in );
+ nbytes_out_d = uInt64_to_double ( &nbytes_out );
+ uInt64_toAscii ( buf_nin, &nbytes_in );
+ uInt64_toAscii ( buf_nout, &nbytes_out );
+ fprintf ( stderr, "%6.3f:1, %6.3f bits/byte, "
+ "%5.2f%% saved, %s in, %s out.\n",
+ nbytes_in_d / nbytes_out_d,
+ (8.0 * nbytes_out_d) / nbytes_in_d,
+ 100.0 * (1.0 - nbytes_out_d / nbytes_in_d),
+ buf_nin,
+ buf_nout
+ );
+ }
+ }
+
+ return;
+
+ errhandler:
+ BZ2_bzWriteClose64 ( &bzerr_dummy, bzf, 1,
+ &nbytes_in_lo32, &nbytes_in_hi32,
+ &nbytes_out_lo32, &nbytes_out_hi32 );
+ switch (bzerr) {
+ case BZ_CONFIG_ERROR:
+ configError(); break;
+ case BZ_MEM_ERROR:
+ outOfMemory (); break;
+ case BZ_IO_ERROR:
+ errhandler_io:
+ ioError(); break;
+ default:
+ panic ( "compress:unexpected error" );
+ }
+
+ panic ( "compress:end" );
+ /*notreached*/
+}
+
+
+
+/*---------------------------------------------*/
+static
+Bool uncompressStream ( FILE *zStream, FILE *stream )
+{
+ BZFILE* bzf = NULL;
+ Int32 bzerr, bzerr_dummy, ret, nread, streamNo, i;
+ UChar obuf[5000];
+ UChar unused[BZ_MAX_UNUSED];
+ Int32 nUnused;
+ void* unusedTmpV;
+ UChar* unusedTmp;
+
+ nUnused = 0;
+ streamNo = 0;
+
+ SET_BINARY_MODE(stream);
+ SET_BINARY_MODE(zStream);
+
+ if (ferror(stream)) goto errhandler_io;
+ if (ferror(zStream)) goto errhandler_io;
+
+ while (True) {
+
+ bzf = BZ2_bzReadOpen (
+ &bzerr, zStream, verbosity,
+ (int)smallMode, unused, nUnused
+ );
+ if (bzf == NULL || bzerr != BZ_OK) goto errhandler;
+ streamNo++;
+
+ while (bzerr == BZ_OK) {
+ nread = BZ2_bzRead ( &bzerr, bzf, obuf, 5000 );
+ if (bzerr == BZ_DATA_ERROR_MAGIC) goto trycat;
+ if ((bzerr == BZ_OK || bzerr == BZ_STREAM_END) && nread > 0)
+ fwrite ( obuf, sizeof(UChar), nread, stream );
+ if (ferror(stream)) goto errhandler_io;
+ }
+ if (bzerr != BZ_STREAM_END) goto errhandler;
+
+ BZ2_bzReadGetUnused ( &bzerr, bzf, &unusedTmpV, &nUnused );
+ if (bzerr != BZ_OK) panic ( "decompress:bzReadGetUnused" );
+
+ unusedTmp = (UChar*)unusedTmpV;
+ for (i = 0; i < nUnused; i++) unused[i] = unusedTmp[i];
+
+ BZ2_bzReadClose ( &bzerr, bzf );
+ if (bzerr != BZ_OK) panic ( "decompress:bzReadGetUnused" );
+
+ if (nUnused == 0 && myfeof(zStream)) break;
+ }
+
+ closeok:
+ if (ferror(zStream)) goto errhandler_io;
+ if (stream != stdout) {
+ Int32 fd = fileno ( stream );
+ if (fd < 0) goto errhandler_io;
+ applySavedFileAttrToOutputFile ( fd );
+ }
+ ret = fclose ( zStream );
+ if (ret == EOF) goto errhandler_io;
+
+ if (ferror(stream)) goto errhandler_io;
+ ret = fflush ( stream );
+ if (ret != 0) goto errhandler_io;
+ if (stream != stdout) {
+ ret = fclose ( stream );
+ outputHandleJustInCase = NULL;
+ if (ret == EOF) goto errhandler_io;
+ }
+ outputHandleJustInCase = NULL;
+ if (verbosity >= 2) fprintf ( stderr, "\n " );
+ return True;
+
+ trycat:
+ if (forceOverwrite) {
+ rewind(zStream);
+ while (True) {
+ if (myfeof(zStream)) break;
+ nread = fread ( obuf, sizeof(UChar), 5000, zStream );
+ if (ferror(zStream)) goto errhandler_io;
+ if (nread > 0) fwrite ( obuf, sizeof(UChar), nread, stream );
+ if (ferror(stream)) goto errhandler_io;
+ }
+ goto closeok;
+ }
+
+ errhandler:
+ BZ2_bzReadClose ( &bzerr_dummy, bzf );
+ switch (bzerr) {
+ case BZ_CONFIG_ERROR:
+ configError(); break;
+ case BZ_IO_ERROR:
+ errhandler_io:
+ ioError(); break;
+ case BZ_DATA_ERROR:
+ crcError();
+ case BZ_MEM_ERROR:
+ outOfMemory();
+ case BZ_UNEXPECTED_EOF:
+ compressedStreamEOF();
+ case BZ_DATA_ERROR_MAGIC:
+ if (zStream != stdin) fclose(zStream);
+ if (stream != stdout) fclose(stream);
+ if (streamNo == 1) {
+ return False;
+ } else {
+ if (noisy)
+ fprintf ( stderr,
+ "\n%s: %s: trailing garbage after EOF ignored\n",
+ progName, inName );
+ return True;
+ }
+ default:
+ panic ( "decompress:unexpected error" );
+ }
+
+ panic ( "decompress:end" );
+ return True; /*notreached*/
+}
+
+
+/*---------------------------------------------*/
+static
+Bool testStream ( FILE *zStream )
+{
+ BZFILE* bzf = NULL;
+ Int32 bzerr, bzerr_dummy, ret, nread, streamNo, i;
+ UChar obuf[5000];
+ UChar unused[BZ_MAX_UNUSED];
+ Int32 nUnused;
+ void* unusedTmpV;
+ UChar* unusedTmp;
+
+ nUnused = 0;
+ streamNo = 0;
+
+ SET_BINARY_MODE(zStream);
+ if (ferror(zStream)) goto errhandler_io;
+
+ while (True) {
+
+ bzf = BZ2_bzReadOpen (
+ &bzerr, zStream, verbosity,
+ (int)smallMode, unused, nUnused
+ );
+ if (bzf == NULL || bzerr != BZ_OK) goto errhandler;
+ streamNo++;
+
+ while (bzerr == BZ_OK) {
+ nread = BZ2_bzRead ( &bzerr, bzf, obuf, 5000 );
+ if (bzerr == BZ_DATA_ERROR_MAGIC) goto errhandler;
+ }
+ if (bzerr != BZ_STREAM_END) goto errhandler;
+
+ BZ2_bzReadGetUnused ( &bzerr, bzf, &unusedTmpV, &nUnused );
+ if (bzerr != BZ_OK) panic ( "test:bzReadGetUnused" );
+
+ unusedTmp = (UChar*)unusedTmpV;
+ for (i = 0; i < nUnused; i++) unused[i] = unusedTmp[i];
+
+ BZ2_bzReadClose ( &bzerr, bzf );
+ if (bzerr != BZ_OK) panic ( "test:bzReadGetUnused" );
+ if (nUnused == 0 && myfeof(zStream)) break;
+
+ }
+
+ if (ferror(zStream)) goto errhandler_io;
+ ret = fclose ( zStream );
+ if (ret == EOF) goto errhandler_io;
+
+ if (verbosity >= 2) fprintf ( stderr, "\n " );
+ return True;
+
+ errhandler:
+ BZ2_bzReadClose ( &bzerr_dummy, bzf );
+ if (verbosity == 0)
+ fprintf ( stderr, "%s: %s: ", progName, inName );
+ switch (bzerr) {
+ case BZ_CONFIG_ERROR:
+ configError(); break;
+ case BZ_IO_ERROR:
+ errhandler_io:
+ ioError(); break;
+ case BZ_DATA_ERROR:
+ fprintf ( stderr,
+ "data integrity (CRC) error in data\n" );
+ return False;
+ case BZ_MEM_ERROR:
+ outOfMemory();
+ case BZ_UNEXPECTED_EOF:
+ fprintf ( stderr,
+ "file ends unexpectedly\n" );
+ return False;
+ case BZ_DATA_ERROR_MAGIC:
+ if (zStream != stdin) fclose(zStream);
+ if (streamNo == 1) {
+ fprintf ( stderr,
+ "bad magic number (file not created by bzip2)\n" );
+ return False;
+ } else {
+ if (noisy)
+ fprintf ( stderr,
+ "trailing garbage after EOF ignored\n" );
+ return True;
+ }
+ default:
+ panic ( "test:unexpected error" );
+ }
+
+ panic ( "test:end" );
+ return True; /*notreached*/
+}
+
+
+/*---------------------------------------------------*/
+/*--- Error [non-] handling grunge ---*/
+/*---------------------------------------------------*/
+
+/*---------------------------------------------*/
+static
+void setExit ( Int32 v )
+{
+ if (v > exitValue) exitValue = v;
+}
+
+
+/*---------------------------------------------*/
+static
+void cadvise ( void )
+{
+ if (noisy)
+ fprintf (
+ stderr,
+ "\nIt is possible that the compressed file(s) have become corrupted.\n"
+ "You can use the -tvv option to test integrity of such files.\n\n"
+ "You can use the `bzip2recover' program to attempt to recover\n"
+ "data from undamaged sections of corrupted files.\n\n"
+ );
+}
+
+
+/*---------------------------------------------*/
+static
+void showFileNames ( void )
+{
+ if (noisy)
+ fprintf (
+ stderr,
+ "\tInput file = %s, output file = %s\n",
+ inName, outName
+ );
+}
+
+
+/*---------------------------------------------*/
+static
+void cleanUpAndFail ( Int32 ec )
+{
+ IntNative retVal;
+ struct MY_STAT statBuf;
+
+ if ( srcMode == SM_F2F
+ && opMode != OM_TEST
+ && deleteOutputOnInterrupt ) {
+
+ /* Check whether input file still exists. Delete output file
+ only if input exists to avoid loss of data. Joerg Prante, 5
+ January 2002. (JRS 06-Jan-2002: other changes in 1.0.2 mean
+ this is less likely to happen. But to be ultra-paranoid, we
+ do the check anyway.) */
+ retVal = MY_STAT ( inName, &statBuf );
+ if (retVal == 0) {
+ if (noisy)
+ fprintf ( stderr,
+ "%s: Deleting output file %s, if it exists.\n",
+ progName, outName );
+ if (outputHandleJustInCase != NULL)
+ fclose ( outputHandleJustInCase );
+ retVal = remove ( outName );
+ if (retVal != 0)
+ fprintf ( stderr,
+ "%s: WARNING: deletion of output file "
+ "(apparently) failed.\n",
+ progName );
+ } else {
+ fprintf ( stderr,
+ "%s: WARNING: deletion of output file suppressed\n",
+ progName );
+ fprintf ( stderr,
+ "%s: since input file no longer exists. Output file\n",
+ progName );
+ fprintf ( stderr,
+ "%s: `%s' may be incomplete.\n",
+ progName, outName );
+ fprintf ( stderr,
+ "%s: I suggest doing an integrity test (bzip2 -tv)"
+ " of it.\n",
+ progName );
+ }
+ }
+
+ if (noisy && numFileNames > 0 && numFilesProcessed < numFileNames) {
+ fprintf ( stderr,
+ "%s: WARNING: some files have not been processed:\n"
+ "%s: %d specified on command line, %d not processed yet.\n\n",
+ progName, progName,
+ numFileNames, numFileNames - numFilesProcessed );
+ }
+ setExit(ec);
+ exit(exitValue);
+}
+
+
+/*---------------------------------------------*/
+static
+void panic ( const Char* s )
+{
+ fprintf ( stderr,
+ "\n%s: PANIC -- internal consistency error:\n"
+ "\t%s\n"
+ "\tThis is a BUG. Please report it to me at:\n"
+ "\tjseward at bzip.org\n",
+ progName, s );
+ showFileNames();
+ cleanUpAndFail( 3 );
+}
+
+
+/*---------------------------------------------*/
+static
+void crcError ( void )
+{
+ fprintf ( stderr,
+ "\n%s: Data integrity error when decompressing.\n",
+ progName );
+ showFileNames();
+ cadvise();
+ cleanUpAndFail( 2 );
+}
+
+
+/*---------------------------------------------*/
+static
+void compressedStreamEOF ( void )
+{
+ if (noisy) {
+ fprintf ( stderr,
+ "\n%s: Compressed file ends unexpectedly;\n\t"
+ "perhaps it is corrupted? *Possible* reason follows.\n",
+ progName );
+ perror ( progName );
+ showFileNames();
+ cadvise();
+ }
+ cleanUpAndFail( 2 );
+}
+
+
+/*---------------------------------------------*/
+static
+void ioError ( void )
+{
+ fprintf ( stderr,
+ "\n%s: I/O or other error, bailing out. "
+ "Possible reason follows.\n",
+ progName );
+ perror ( progName );
+ showFileNames();
+ cleanUpAndFail( 1 );
+}
+
+
+/*---------------------------------------------*/
+static
+void mySignalCatcher ( IntNative n )
+{
+ fprintf ( stderr,
+ "\n%s: Control-C or similar caught, quitting.\n",
+ progName );
+ cleanUpAndFail(1);
+}
+
+
+/*---------------------------------------------*/
+static
+void mySIGSEGVorSIGBUScatcher ( IntNative n )
+{
+ if (opMode == OM_Z)
+ fprintf (
+ stderr,
+ "\n%s: Caught a SIGSEGV or SIGBUS whilst compressing.\n"
+ "\n"
+ " Possible causes are (most likely first):\n"
+ " (1) This computer has unreliable memory or cache hardware\n"
+ " (a surprisingly common problem; try a different machine.)\n"
+ " (2) A bug in the compiler used to create this executable\n"
+ " (unlikely, if you didn't compile bzip2 yourself.)\n"
+ " (3) A real bug in bzip2 -- I hope this should never be the case.\n"
+ " The user's manual, Section 4.3, has more info on (1) and (2).\n"
+ " \n"
+ " If you suspect this is a bug in bzip2, or are unsure about (1)\n"
+ " or (2), feel free to report it to me at: jseward at bzip.org.\n"
+ " Section 4.3 of the user's manual describes the info a useful\n"
+ " bug report should have. If the manual is available on your\n"
+ " system, please try and read it before mailing me. If you don't\n"
+ " have the manual or can't be bothered to read it, mail me anyway.\n"
+ "\n",
+ progName );
+ else
+ fprintf (
+ stderr,
+ "\n%s: Caught a SIGSEGV or SIGBUS whilst decompressing.\n"
+ "\n"
+ " Possible causes are (most likely first):\n"
+ " (1) The compressed data is corrupted, and bzip2's usual checks\n"
+ " failed to detect this. Try bzip2 -tvv my_file.bz2.\n"
+ " (2) This computer has unreliable memory or cache hardware\n"
+ " (a surprisingly common problem; try a different machine.)\n"
+ " (3) A bug in the compiler used to create this executable\n"
+ " (unlikely, if you didn't compile bzip2 yourself.)\n"
+ " (4) A real bug in bzip2 -- I hope this should never be the case.\n"
+ " The user's manual, Section 4.3, has more info on (2) and (3).\n"
+ " \n"
+ " If you suspect this is a bug in bzip2, or are unsure about (2)\n"
+ " or (3), feel free to report it to me at: jseward at bzip.org.\n"
+ " Section 4.3 of the user's manual describes the info a useful\n"
+ " bug report should have. If the manual is available on your\n"
+ " system, please try and read it before mailing me. If you don't\n"
+ " have the manual or can't be bothered to read it, mail me anyway.\n"
+ "\n",
+ progName );
+
+ showFileNames();
+ if (opMode == OM_Z)
+ cleanUpAndFail( 3 ); else
+ { cadvise(); cleanUpAndFail( 2 ); }
+}
+
+
+/*---------------------------------------------*/
+static
+void outOfMemory ( void )
+{
+ fprintf ( stderr,
+ "\n%s: couldn't allocate enough memory\n",
+ progName );
+ showFileNames();
+ cleanUpAndFail(1);
+}
+
+
+/*---------------------------------------------*/
+static
+void configError ( void )
+{
+ fprintf ( stderr,
+ "bzip2: I'm not configured correctly for this platform!\n"
+ "\tI require Int32, Int16 and Char to have sizes\n"
+ "\tof 4, 2 and 1 bytes to run properly, and they don't.\n"
+ "\tProbably you can fix this by defining them correctly,\n"
+ "\tand recompiling. Bye!\n" );
+ setExit(3);
+ exit(exitValue);
+}
+
+
+/*---------------------------------------------------*/
+/*--- The main driver machinery ---*/
+/*---------------------------------------------------*/
+
+/* All rather crufty. The main problem is that input files
+ are stat()d multiple times before use. This should be
+ cleaned up.
+*/
+
+/*---------------------------------------------*/
+static
+void pad ( Char *s )
+{
+ Int32 i;
+ if ( (Int32)strlen(s) >= longestFileName ) return;
+ for (i = 1; i <= longestFileName - (Int32)strlen(s); i++)
+ fprintf ( stderr, " " );
+}
+
+
+/*---------------------------------------------*/
+static
+void copyFileName ( Char* to, Char* from )
+{
+ if ( strlen(from) > FILE_NAME_LEN-10 ) {
+ fprintf (
+ stderr,
+ "bzip2: file name\n`%s'\n"
+ "is suspiciously (more than %d chars) long.\n"
+ "Try using a reasonable file name instead. Sorry! :-)\n",
+ from, FILE_NAME_LEN-10
+ );
+ setExit(1);
+ exit(exitValue);
+ }
+
+ strncpy(to,from,FILE_NAME_LEN-10);
+ to[FILE_NAME_LEN-10]='\0';
+}
+
+
+/*---------------------------------------------*/
+static
+Bool fileExists ( Char* name )
+{
+ FILE *tmp = fopen ( name, "rb" );
+ Bool exists = (tmp != NULL);
+ if (tmp != NULL) fclose ( tmp );
+ return exists;
+}
+
+
+/*---------------------------------------------*/
+/* Open an output file safely with O_EXCL and good permissions.
+ This avoids a race condition in versions < 1.0.2, in which
+ the file was first opened and then had its interim permissions
+ set safely. We instead use open() to create the file with
+ the interim permissions required. (--- --- rw-).
+
+ For non-Unix platforms, if we are not worrying about
+ security issues, simple this simply behaves like fopen.
+*/
+static
+FILE* fopen_output_safely ( Char* name, const char* mode )
+{
+# if BZ_UNIX
+ FILE* fp;
+ IntNative fh;
+ fh = open(name, O_WRONLY|O_CREAT|O_EXCL, S_IWUSR|S_IRUSR);
+ if (fh == -1) return NULL;
+ fp = fdopen(fh, mode);
+ if (fp == NULL) close(fh);
+ return fp;
+# else
+ return fopen(name, mode);
+# endif
+}
+
+
+/*---------------------------------------------*/
+/*--
+ if in doubt, return True
+--*/
+static
+Bool notAStandardFile ( Char* name )
+{
+ IntNative i;
+ struct MY_STAT statBuf;
+
+ i = MY_LSTAT ( name, &statBuf );
+ if (i != 0) return True;
+ if (MY_S_ISREG(statBuf.st_mode)) return False;
+ return True;
+}
+
+
+/*---------------------------------------------*/
+/*--
+ rac 11/21/98 see if file has hard links to it
+--*/
+static
+Int32 countHardLinks ( Char* name )
+{
+ IntNative i;
+ struct MY_STAT statBuf;
+
+ i = MY_LSTAT ( name, &statBuf );
+ if (i != 0) return 0;
+ return (statBuf.st_nlink - 1);
+}
+
+
+/*---------------------------------------------*/
+/* Copy modification date, access date, permissions and owner from the
+ source to destination file. We have to copy this meta-info off
+ into fileMetaInfo before starting to compress / decompress it,
+ because doing it afterwards means we get the wrong access time.
+
+ To complicate matters, in compress() and decompress() below, the
+ sequence of tests preceding the call to saveInputFileMetaInfo()
+ involves calling fileExists(), which in turn establishes its result
+ by attempting to fopen() the file, and if successful, immediately
+ fclose()ing it again. So we have to assume that the fopen() call
+ does not cause the access time field to be updated.
+
+ Reading of the man page for stat() (man 2 stat) on RedHat 7.2 seems
+ to imply that merely doing open() will not affect the access time.
+ Therefore we merely need to hope that the C library only does
+ open() as a result of fopen(), and not any kind of read()-ahead
+ cleverness.
+
+ It sounds pretty fragile to me. Whether this carries across
+ robustly to arbitrary Unix-like platforms (or even works robustly
+ on this one, RedHat 7.2) is unknown to me. Nevertheless ...
+*/
+#if BZ_UNIX
+static
+struct MY_STAT fileMetaInfo;
+#endif
+
+static
+void saveInputFileMetaInfo ( Char *srcName )
+{
+# if BZ_UNIX
+ IntNative retVal;
+ /* Note use of stat here, not lstat. */
+ retVal = MY_STAT( srcName, &fileMetaInfo );
+ ERROR_IF_NOT_ZERO ( retVal );
+# endif
+}
+
+
+static
+void applySavedTimeInfoToOutputFile ( Char *dstName )
+{
+# if BZ_UNIX
+ IntNative retVal;
+ struct utimbuf uTimBuf;
+
+ uTimBuf.actime = fileMetaInfo.st_atime;
+ uTimBuf.modtime = fileMetaInfo.st_mtime;
+
+ retVal = utime ( dstName, &uTimBuf );
+ ERROR_IF_NOT_ZERO ( retVal );
+# endif
+}
+
+static
+void applySavedFileAttrToOutputFile ( IntNative fd )
+{
+# if BZ_UNIX
+ IntNative retVal;
+
+ retVal = fchmod ( fd, fileMetaInfo.st_mode );
+ ERROR_IF_NOT_ZERO ( retVal );
+
+ (void) fchown ( fd, fileMetaInfo.st_uid, fileMetaInfo.st_gid );
+ /* chown() will in many cases return with EPERM, which can
+ be safely ignored.
+ */
+# endif
+}
+
+
+/*---------------------------------------------*/
+static
+Bool containsDubiousChars ( Char* name )
+{
+# if BZ_UNIX
+ /* On unix, files can contain any characters and the file expansion
+ * is performed by the shell.
+ */
+ return False;
+# else /* ! BZ_UNIX */
+ /* On non-unix (Win* platforms), wildcard characters are not allowed in
+ * filenames.
+ */
+ for (; *name != '\0'; name++)
+ if (*name == '?' || *name == '*') return True;
+ return False;
+# endif /* BZ_UNIX */
+}
+
+
+/*---------------------------------------------*/
+#define BZ_N_SUFFIX_PAIRS 4
+
+const Char* zSuffix[BZ_N_SUFFIX_PAIRS]
+ = { ".bz2", ".bz", ".tbz2", ".tbz" };
+const Char* unzSuffix[BZ_N_SUFFIX_PAIRS]
+ = { "", "", ".tar", ".tar" };
+
+static
+Bool hasSuffix ( Char* s, const Char* suffix )
+{
+ Int32 ns = strlen(s);
+ Int32 nx = strlen(suffix);
+ if (ns < nx) return False;
+ if (strcmp(s + ns - nx, suffix) == 0) return True;
+ return False;
+}
+
+static
+Bool mapSuffix ( Char* name,
+ const Char* oldSuffix,
+ const Char* newSuffix )
+{
+ if (!hasSuffix(name,oldSuffix)) return False;
+ name[strlen(name)-strlen(oldSuffix)] = 0;
+ strcat ( name, newSuffix );
+ return True;
+}
+
+
+/*---------------------------------------------*/
+static
+void compress ( Char *name )
+{
+ FILE *inStr;
+ FILE *outStr;
+ Int32 n, i;
+ struct MY_STAT statBuf;
+
+ deleteOutputOnInterrupt = False;
+
+ if (name == NULL && srcMode != SM_I2O)
+ panic ( "compress: bad modes\n" );
+
+ switch (srcMode) {
+ case SM_I2O:
+ copyFileName ( inName, (Char*)"(stdin)" );
+ copyFileName ( outName, (Char*)"(stdout)" );
+ break;
+ case SM_F2F:
+ copyFileName ( inName, name );
+ copyFileName ( outName, name );
+ strcat ( outName, ".bz2" );
+ break;
+ case SM_F2O:
+ copyFileName ( inName, name );
+ copyFileName ( outName, (Char*)"(stdout)" );
+ break;
+ }
+
+ if ( srcMode != SM_I2O && containsDubiousChars ( inName ) ) {
+ if (noisy)
+ fprintf ( stderr, "%s: There are no files matching `%s'.\n",
+ progName, inName );
+ setExit(1);
+ return;
+ }
+ if ( srcMode != SM_I2O && !fileExists ( inName ) ) {
+ fprintf ( stderr, "%s: Can't open input file %s: %s.\n",
+ progName, inName, strerror(errno) );
+ setExit(1);
+ return;
+ }
+ for (i = 0; i < BZ_N_SUFFIX_PAIRS; i++) {
+ if (hasSuffix(inName, zSuffix[i])) {
+ if (noisy)
+ fprintf ( stderr,
+ "%s: Input file %s already has %s suffix.\n",
+ progName, inName, zSuffix[i] );
+ setExit(1);
+ return;
+ }
+ }
+ if ( srcMode == SM_F2F || srcMode == SM_F2O ) {
+ MY_STAT(inName, &statBuf);
+ if ( MY_S_ISDIR(statBuf.st_mode) ) {
+ fprintf( stderr,
+ "%s: Input file %s is a directory.\n",
+ progName,inName);
+ setExit(1);
+ return;
+ }
+ }
+ if ( srcMode == SM_F2F && !forceOverwrite && notAStandardFile ( inName )) {
+ if (noisy)
+ fprintf ( stderr, "%s: Input file %s is not a normal file.\n",
+ progName, inName );
+ setExit(1);
+ return;
+ }
+ if ( srcMode == SM_F2F && fileExists ( outName ) ) {
+ if (forceOverwrite) {
+ remove(outName);
+ } else {
+ fprintf ( stderr, "%s: Output file %s already exists.\n",
+ progName, outName );
+ setExit(1);
+ return;
+ }
+ }
+ if ( srcMode == SM_F2F && !forceOverwrite &&
+ (n=countHardLinks ( inName )) > 0) {
+ fprintf ( stderr, "%s: Input file %s has %d other link%s.\n",
+ progName, inName, n, n > 1 ? "s" : "" );
+ setExit(1);
+ return;
+ }
+
+ if ( srcMode == SM_F2F ) {
+ /* Save the file's meta-info before we open it. Doing it later
+ means we mess up the access times. */
+ saveInputFileMetaInfo ( inName );
+ }
+
+ switch ( srcMode ) {
+
+ case SM_I2O:
+ inStr = stdin;
+ outStr = stdout;
+ if ( isatty ( fileno ( stdout ) ) ) {
+ fprintf ( stderr,
+ "%s: I won't write compressed data to a terminal.\n",
+ progName );
+ fprintf ( stderr, "%s: For help, type: `%s --help'.\n",
+ progName, progName );
+ setExit(1);
+ return;
+ };
+ break;
+
+ case SM_F2O:
+ inStr = fopen ( inName, "rb" );
+ outStr = stdout;
+ if ( isatty ( fileno ( stdout ) ) ) {
+ fprintf ( stderr,
+ "%s: I won't write compressed data to a terminal.\n",
+ progName );
+ fprintf ( stderr, "%s: For help, type: `%s --help'.\n",
+ progName, progName );
+ if ( inStr != NULL ) fclose ( inStr );
+ setExit(1);
+ return;
+ };
+ if ( inStr == NULL ) {
+ fprintf ( stderr, "%s: Can't open input file %s: %s.\n",
+ progName, inName, strerror(errno) );
+ setExit(1);
+ return;
+ };
+ break;
+
+ case SM_F2F:
+ inStr = fopen ( inName, "rb" );
+ outStr = fopen_output_safely ( outName, "wb" );
+ if ( outStr == NULL) {
+ fprintf ( stderr, "%s: Can't create output file %s: %s.\n",
+ progName, outName, strerror(errno) );
+ if ( inStr != NULL ) fclose ( inStr );
+ setExit(1);
+ return;
+ }
+ if ( inStr == NULL ) {
+ fprintf ( stderr, "%s: Can't open input file %s: %s.\n",
+ progName, inName, strerror(errno) );
+ if ( outStr != NULL ) fclose ( outStr );
+ setExit(1);
+ return;
+ };
+ break;
+
+ default:
+ panic ( "compress: bad srcMode" );
+ break;
+ }
+
+ if (verbosity >= 1) {
+ fprintf ( stderr, " %s: ", inName );
+ pad ( inName );
+ fflush ( stderr );
+ }
+
+ /*--- Now the input and output handles are sane. Do the Biz. ---*/
+ outputHandleJustInCase = outStr;
+ deleteOutputOnInterrupt = True;
+ compressStream ( inStr, outStr );
+ outputHandleJustInCase = NULL;
+
+ /*--- If there was an I/O error, we won't get here. ---*/
+ if ( srcMode == SM_F2F ) {
+ applySavedTimeInfoToOutputFile ( outName );
+ deleteOutputOnInterrupt = False;
+ if ( !keepInputFiles ) {
+ IntNative retVal = remove ( inName );
+ ERROR_IF_NOT_ZERO ( retVal );
+ }
+ }
+
+ deleteOutputOnInterrupt = False;
+}
+
+
+/*---------------------------------------------*/
+static
+void uncompress ( Char *name )
+{
+ FILE *inStr;
+ FILE *outStr;
+ Int32 n, i;
+ Bool magicNumberOK;
+ Bool cantGuess;
+ struct MY_STAT statBuf;
+
+ deleteOutputOnInterrupt = False;
+
+ if (name == NULL && srcMode != SM_I2O)
+ panic ( "uncompress: bad modes\n" );
+
+ cantGuess = False;
+ switch (srcMode) {
+ case SM_I2O:
+ copyFileName ( inName, (Char*)"(stdin)" );
+ copyFileName ( outName, (Char*)"(stdout)" );
+ break;
+ case SM_F2F:
+ copyFileName ( inName, name );
+ copyFileName ( outName, name );
+ for (i = 0; i < BZ_N_SUFFIX_PAIRS; i++)
+ if (mapSuffix(outName,zSuffix[i],unzSuffix[i]))
+ goto zzz;
+ cantGuess = True;
+ strcat ( outName, ".out" );
+ break;
+ case SM_F2O:
+ copyFileName ( inName, name );
+ copyFileName ( outName, (Char*)"(stdout)" );
+ break;
+ }
+
+ zzz:
+ if ( srcMode != SM_I2O && containsDubiousChars ( inName ) ) {
+ if (noisy)
+ fprintf ( stderr, "%s: There are no files matching `%s'.\n",
+ progName, inName );
+ setExit(1);
+ return;
+ }
+ if ( srcMode != SM_I2O && !fileExists ( inName ) ) {
+ fprintf ( stderr, "%s: Can't open input file %s: %s.\n",
+ progName, inName, strerror(errno) );
+ setExit(1);
+ return;
+ }
+ if ( srcMode == SM_F2F || srcMode == SM_F2O ) {
+ MY_STAT(inName, &statBuf);
+ if ( MY_S_ISDIR(statBuf.st_mode) ) {
+ fprintf( stderr,
+ "%s: Input file %s is a directory.\n",
+ progName,inName);
+ setExit(1);
+ return;
+ }
+ }
+ if ( srcMode == SM_F2F && !forceOverwrite && notAStandardFile ( inName )) {
+ if (noisy)
+ fprintf ( stderr, "%s: Input file %s is not a normal file.\n",
+ progName, inName );
+ setExit(1);
+ return;
+ }
+ if ( /* srcMode == SM_F2F implied && */ cantGuess ) {
+ if (noisy)
+ fprintf ( stderr,
+ "%s: Can't guess original name for %s -- using %s\n",
+ progName, inName, outName );
+ /* just a warning, no return */
+ }
+ if ( srcMode == SM_F2F && fileExists ( outName ) ) {
+ if (forceOverwrite) {
+ remove(outName);
+ } else {
+ fprintf ( stderr, "%s: Output file %s already exists.\n",
+ progName, outName );
+ setExit(1);
+ return;
+ }
+ }
+ if ( srcMode == SM_F2F && !forceOverwrite &&
+ (n=countHardLinks ( inName ) ) > 0) {
+ fprintf ( stderr, "%s: Input file %s has %d other link%s.\n",
+ progName, inName, n, n > 1 ? "s" : "" );
+ setExit(1);
+ return;
+ }
+
+ if ( srcMode == SM_F2F ) {
+ /* Save the file's meta-info before we open it. Doing it later
+ means we mess up the access times. */
+ saveInputFileMetaInfo ( inName );
+ }
+
+ switch ( srcMode ) {
+
+ case SM_I2O:
+ inStr = stdin;
+ outStr = stdout;
+ if ( isatty ( fileno ( stdin ) ) ) {
+ fprintf ( stderr,
+ "%s: I won't read compressed data from a terminal.\n",
+ progName );
+ fprintf ( stderr, "%s: For help, type: `%s --help'.\n",
+ progName, progName );
+ setExit(1);
+ return;
+ };
+ break;
+
+ case SM_F2O:
+ inStr = fopen ( inName, "rb" );
+ outStr = stdout;
+ if ( inStr == NULL ) {
+ fprintf ( stderr, "%s: Can't open input file %s:%s.\n",
+ progName, inName, strerror(errno) );
+ if ( inStr != NULL ) fclose ( inStr );
+ setExit(1);
+ return;
+ };
+ break;
+
+ case SM_F2F:
+ inStr = fopen ( inName, "rb" );
+ outStr = fopen_output_safely ( outName, "wb" );
+ if ( outStr == NULL) {
+ fprintf ( stderr, "%s: Can't create output file %s: %s.\n",
+ progName, outName, strerror(errno) );
+ if ( inStr != NULL ) fclose ( inStr );
+ setExit(1);
+ return;
+ }
+ if ( inStr == NULL ) {
+ fprintf ( stderr, "%s: Can't open input file %s: %s.\n",
+ progName, inName, strerror(errno) );
+ if ( outStr != NULL ) fclose ( outStr );
+ setExit(1);
+ return;
+ };
+ break;
+
+ default:
+ panic ( "uncompress: bad srcMode" );
+ break;
+ }
+
+ if (verbosity >= 1) {
+ fprintf ( stderr, " %s: ", inName );
+ pad ( inName );
+ fflush ( stderr );
+ }
+
+ /*--- Now the input and output handles are sane. Do the Biz. ---*/
+ outputHandleJustInCase = outStr;
+ deleteOutputOnInterrupt = True;
+ magicNumberOK = uncompressStream ( inStr, outStr );
+ outputHandleJustInCase = NULL;
+
+ /*--- If there was an I/O error, we won't get here. ---*/
+ if ( magicNumberOK ) {
+ if ( srcMode == SM_F2F ) {
+ applySavedTimeInfoToOutputFile ( outName );
+ deleteOutputOnInterrupt = False;
+ if ( !keepInputFiles ) {
+ IntNative retVal = remove ( inName );
+ ERROR_IF_NOT_ZERO ( retVal );
+ }
+ }
+ } else {
+ unzFailsExist = True;
+ deleteOutputOnInterrupt = False;
+ if ( srcMode == SM_F2F ) {
+ IntNative retVal = remove ( outName );
+ ERROR_IF_NOT_ZERO ( retVal );
+ }
+ }
+ deleteOutputOnInterrupt = False;
+
+ if ( magicNumberOK ) {
+ if (verbosity >= 1)
+ fprintf ( stderr, "done\n" );
+ } else {
+ setExit(2);
+ if (verbosity >= 1)
+ fprintf ( stderr, "not a bzip2 file.\n" ); else
+ fprintf ( stderr,
+ "%s: %s is not a bzip2 file.\n",
+ progName, inName );
+ }
+
+}
+
+
+/*---------------------------------------------*/
+static
+void testf ( Char *name )
+{
+ FILE *inStr;
+ Bool allOK;
+ struct MY_STAT statBuf;
+
+ deleteOutputOnInterrupt = False;
+
+ if (name == NULL && srcMode != SM_I2O)
+ panic ( "testf: bad modes\n" );
+
+ copyFileName ( outName, (Char*)"(none)" );
+ switch (srcMode) {
+ case SM_I2O: copyFileName ( inName, (Char*)"(stdin)" ); break;
+ case SM_F2F: copyFileName ( inName, name ); break;
+ case SM_F2O: copyFileName ( inName, name ); break;
+ }
+
+ if ( srcMode != SM_I2O && containsDubiousChars ( inName ) ) {
+ if (noisy)
+ fprintf ( stderr, "%s: There are no files matching `%s'.\n",
+ progName, inName );
+ setExit(1);
+ return;
+ }
+ if ( srcMode != SM_I2O && !fileExists ( inName ) ) {
+ fprintf ( stderr, "%s: Can't open input %s: %s.\n",
+ progName, inName, strerror(errno) );
+ setExit(1);
+ return;
+ }
+ if ( srcMode != SM_I2O ) {
+ MY_STAT(inName, &statBuf);
+ if ( MY_S_ISDIR(statBuf.st_mode) ) {
+ fprintf( stderr,
+ "%s: Input file %s is a directory.\n",
+ progName,inName);
+ setExit(1);
+ return;
+ }
+ }
+
+ switch ( srcMode ) {
+
+ case SM_I2O:
+ if ( isatty ( fileno ( stdin ) ) ) {
+ fprintf ( stderr,
+ "%s: I won't read compressed data from a terminal.\n",
+ progName );
+ fprintf ( stderr, "%s: For help, type: `%s --help'.\n",
+ progName, progName );
+ setExit(1);
+ return;
+ };
+ inStr = stdin;
+ break;
+
+ case SM_F2O: case SM_F2F:
+ inStr = fopen ( inName, "rb" );
+ if ( inStr == NULL ) {
+ fprintf ( stderr, "%s: Can't open input file %s:%s.\n",
+ progName, inName, strerror(errno) );
+ setExit(1);
+ return;
+ };
+ break;
+
+ default:
+ panic ( "testf: bad srcMode" );
+ break;
+ }
+
+ if (verbosity >= 1) {
+ fprintf ( stderr, " %s: ", inName );
+ pad ( inName );
+ fflush ( stderr );
+ }
+
+ /*--- Now the input handle is sane. Do the Biz. ---*/
+ outputHandleJustInCase = NULL;
+ allOK = testStream ( inStr );
+
+ if (allOK && verbosity >= 1) fprintf ( stderr, "ok\n" );
+ if (!allOK) testFailsExist = True;
+}
+
+
+/*---------------------------------------------*/
+static
+void license ( void )
+{
+ fprintf ( stderr,
+
+ "bzip2, a block-sorting file compressor. "
+ "Version %s.\n"
+ " \n"
+ " Copyright (C) 1996-2010 by Julian Seward.\n"
+ " \n"
+ " This program is free software; you can redistribute it and/or modify\n"
+ " it under the terms set out in the LICENSE file, which is included\n"
+ " in the bzip2-1.0.6 source distribution.\n"
+ " \n"
+ " This program is distributed in the hope that it will be useful,\n"
+ " but WITHOUT ANY WARRANTY; without even the implied warranty of\n"
+ " MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n"
+ " LICENSE file for more details.\n"
+ " \n",
+ BZ2_bzlibVersion()
+ );
+}
+
+
+/*---------------------------------------------*/
+static
+void usage ( Char *fullProgName )
+{
+ fprintf (
+ stderr,
+ "bzip2, a block-sorting file compressor. "
+ "Version %s.\n"
+ "\n usage: %s [flags and input files in any order]\n"
+ "\n"
+ " -h --help print this message\n"
+ " -d --decompress force decompression\n"
+ " -z --compress force compression\n"
+ " -k --keep keep (don't delete) input files\n"
+ " -f --force overwrite existing output files\n"
+ " -t --test test compressed file integrity\n"
+ " -c --stdout output to standard out\n"
+ " -q --quiet suppress noncritical error messages\n"
+ " -v --verbose be verbose (a 2nd -v gives more)\n"
+ " -L --license display software version & license\n"
+ " -V --version display software version & license\n"
+ " -s --small use less memory (at most 2500k)\n"
+ " -1 .. -9 set block size to 100k .. 900k\n"
+ " --fast alias for -1\n"
+ " --best alias for -9\n"
+ "\n"
+ " If invoked as `bzip2', default action is to compress.\n"
+ " as `bunzip2', default action is to decompress.\n"
+ " as `bzcat', default action is to decompress to stdout.\n"
+ "\n"
+ " If no file names are given, bzip2 compresses or decompresses\n"
+ " from standard input to standard output. You can combine\n"
+ " short flags, so `-v -4' means the same as -v4 or -4v, &c.\n"
+# if BZ_UNIX
+ "\n"
+# endif
+ ,
+
+ BZ2_bzlibVersion(),
+ fullProgName
+ );
+}
+
+
+/*---------------------------------------------*/
+static
+void redundant ( Char* flag )
+{
+ fprintf (
+ stderr,
+ "%s: %s is redundant in versions 0.9.5 and above\n",
+ progName, flag );
+}
+
+
+/*---------------------------------------------*/
+/*--
+ All the garbage from here to main() is purely to
+ implement a linked list of command-line arguments,
+ into which main() copies argv[1 .. argc-1].
+
+ The purpose of this exercise is to facilitate
+ the expansion of wildcard characters * and ? in
+ filenames for OSs which don't know how to do it
+ themselves, like MSDOS, Windows 95 and NT.
+
+ The actual Dirty Work is done by the platform-
+ specific macro APPEND_FILESPEC.
+--*/
+
+typedef
+ struct zzzz {
+ Char *name;
+ struct zzzz *link;
+ }
+ Cell;
+
+
+/*---------------------------------------------*/
+static
+void *myMalloc ( Int32 n )
+{
+ void* p;
+
+ p = malloc ( (size_t)n );
+ if (p == NULL) outOfMemory ();
+ return p;
+}
+
+
+/*---------------------------------------------*/
+static
+Cell *mkCell ( void )
+{
+ Cell *c;
+
+ c = (Cell*) myMalloc ( sizeof ( Cell ) );
+ c->name = NULL;
+ c->link = NULL;
+ return c;
+}
+
+
+/*---------------------------------------------*/
+static
+Cell *snocString ( Cell *root, Char *name )
+{
+ if (root == NULL) {
+ Cell *tmp = mkCell();
+ tmp->name = (Char*) myMalloc ( 5 + strlen(name) );
+ strcpy ( tmp->name, name );
+ return tmp;
+ } else {
+ Cell *tmp = root;
+ while (tmp->link != NULL) tmp = tmp->link;
+ tmp->link = snocString ( tmp->link, name );
+ return root;
+ }
+}
+
+
+/*---------------------------------------------*/
+static
+void addFlagsFromEnvVar ( Cell** argList, Char* varName )
+{
+ Int32 i, j, k;
+ Char *envbase, *p;
+
+ envbase = getenv(varName);
+ if (envbase != NULL) {
+ p = envbase;
+ i = 0;
+ while (True) {
+ if (p[i] == 0) break;
+ p += i;
+ i = 0;
+ while (isspace((Int32)(p[0]))) p++;
+ while (p[i] != 0 && !isspace((Int32)(p[i]))) i++;
+ if (i > 0) {
+ k = i; if (k > FILE_NAME_LEN-10) k = FILE_NAME_LEN-10;
+ for (j = 0; j < k; j++) tmpName[j] = p[j];
+ tmpName[k] = 0;
+ APPEND_FLAG(*argList, tmpName);
+ }
+ }
+ }
+}
+
+
+/*---------------------------------------------*/
+#define ISFLAG(s) (strcmp(aa->name, (s))==0)
+
+IntNative main ( IntNative argc, Char *argv[] )
+{
+ Int32 i, j;
+ Char *tmp;
+ Cell *argList;
+ Cell *aa;
+ Bool decode;
+
+ /*-- Be really really really paranoid :-) --*/
+ if (sizeof(Int32) != 4 || sizeof(UInt32) != 4 ||
+ sizeof(Int16) != 2 || sizeof(UInt16) != 2 ||
+ sizeof(Char) != 1 || sizeof(UChar) != 1)
+ configError();
+
+ /*-- Initialise --*/
+ outputHandleJustInCase = NULL;
+ smallMode = False;
+ keepInputFiles = False;
+ forceOverwrite = False;
+ noisy = True;
+ verbosity = 0;
+ blockSize100k = 9;
+ testFailsExist = False;
+ unzFailsExist = False;
+ numFileNames = 0;
+ numFilesProcessed = 0;
+ workFactor = 30;
+ deleteOutputOnInterrupt = False;
+ exitValue = 0;
+ i = j = 0; /* avoid bogus warning from egcs-1.1.X */
+
+ /*-- Set up signal handlers for mem access errors --*/
+ signal (SIGSEGV, mySIGSEGVorSIGBUScatcher);
+# if BZ_UNIX
+# ifndef __DJGPP__
+ signal (SIGBUS, mySIGSEGVorSIGBUScatcher);
+# endif
+# endif
+
+ copyFileName ( inName, (Char*)"(none)" );
+ copyFileName ( outName, (Char*)"(none)" );
+
+ copyFileName ( progNameReally, argv[0] );
+ progName = &progNameReally[0];
+ for (tmp = &progNameReally[0]; *tmp != '\0'; tmp++)
+ if (*tmp == PATH_SEP) progName = tmp + 1;
+
+
+ /*-- Copy flags from env var BZIP2, and
+ expand filename wildcards in arg list.
+ --*/
+ argList = NULL;
+ addFlagsFromEnvVar ( &argList, (Char*)"BZIP2" );
+ addFlagsFromEnvVar ( &argList, (Char*)"BZIP" );
+ for (i = 1; i <= argc-1; i++)
+ APPEND_FILESPEC(argList, argv[i]);
+
+
+ /*-- Find the length of the longest filename --*/
+ longestFileName = 7;
+ numFileNames = 0;
+ decode = True;
+ for (aa = argList; aa != NULL; aa = aa->link) {
+ if (ISFLAG("--")) { decode = False; continue; }
+ if (aa->name[0] == '-' && decode) continue;
+ numFileNames++;
+ if (longestFileName < (Int32)strlen(aa->name) )
+ longestFileName = (Int32)strlen(aa->name);
+ }
+
+
+ /*-- Determine source modes; flag handling may change this too. --*/
+ if (numFileNames == 0)
+ srcMode = SM_I2O; else srcMode = SM_F2F;
+
+
+ /*-- Determine what to do (compress/uncompress/test/cat). --*/
+ /*-- Note that subsequent flag handling may change this. --*/
+ opMode = OM_Z;
+
+ if ( (strstr ( progName, "unzip" ) != 0) ||
+ (strstr ( progName, "UNZIP" ) != 0) )
+ opMode = OM_UNZ;
+
+ if ( (strstr ( progName, "z2cat" ) != 0) ||
+ (strstr ( progName, "Z2CAT" ) != 0) ||
+ (strstr ( progName, "zcat" ) != 0) ||
+ (strstr ( progName, "ZCAT" ) != 0) ) {
+ opMode = OM_UNZ;
+ srcMode = (numFileNames == 0) ? SM_I2O : SM_F2O;
+ }
+
+
+ /*-- Look at the flags. --*/
+ for (aa = argList; aa != NULL; aa = aa->link) {
+ if (ISFLAG("--")) break;
+ if (aa->name[0] == '-' && aa->name[1] != '-') {
+ for (j = 1; aa->name[j] != '\0'; j++) {
+ switch (aa->name[j]) {
+ case 'c': srcMode = SM_F2O; break;
+ case 'd': opMode = OM_UNZ; break;
+ case 'z': opMode = OM_Z; break;
+ case 'f': forceOverwrite = True; break;
+ case 't': opMode = OM_TEST; break;
+ case 'k': keepInputFiles = True; break;
+ case 's': smallMode = True; break;
+ case 'q': noisy = False; break;
+ case '1': blockSize100k = 1; break;
+ case '2': blockSize100k = 2; break;
+ case '3': blockSize100k = 3; break;
+ case '4': blockSize100k = 4; break;
+ case '5': blockSize100k = 5; break;
+ case '6': blockSize100k = 6; break;
+ case '7': blockSize100k = 7; break;
+ case '8': blockSize100k = 8; break;
+ case '9': blockSize100k = 9; break;
+ case 'V':
+ case 'L': license(); break;
+ case 'v': verbosity++; break;
+ case 'h': usage ( progName );
+ exit ( 0 );
+ break;
+ default: fprintf ( stderr, "%s: Bad flag `%s'\n",
+ progName, aa->name );
+ usage ( progName );
+ exit ( 1 );
+ break;
+ }
+ }
+ }
+ }
+
+ /*-- And again ... --*/
+ for (aa = argList; aa != NULL; aa = aa->link) {
+ if (ISFLAG("--")) break;
+ if (ISFLAG("--stdout")) srcMode = SM_F2O; else
+ if (ISFLAG("--decompress")) opMode = OM_UNZ; else
+ if (ISFLAG("--compress")) opMode = OM_Z; else
+ if (ISFLAG("--force")) forceOverwrite = True; else
+ if (ISFLAG("--test")) opMode = OM_TEST; else
+ if (ISFLAG("--keep")) keepInputFiles = True; else
+ if (ISFLAG("--small")) smallMode = True; else
+ if (ISFLAG("--quiet")) noisy = False; else
+ if (ISFLAG("--version")) license(); else
+ if (ISFLAG("--license")) license(); else
+ if (ISFLAG("--exponential")) workFactor = 1; else
+ if (ISFLAG("--repetitive-best")) redundant(aa->name); else
+ if (ISFLAG("--repetitive-fast")) redundant(aa->name); else
+ if (ISFLAG("--fast")) blockSize100k = 1; else
+ if (ISFLAG("--best")) blockSize100k = 9; else
+ if (ISFLAG("--verbose")) verbosity++; else
+ if (ISFLAG("--help")) { usage ( progName ); exit ( 0 ); }
+ else
+ if (strncmp ( aa->name, "--", 2) == 0) {
+ fprintf ( stderr, "%s: Bad flag `%s'\n", progName, aa->name );
+ usage ( progName );
+ exit ( 1 );
+ }
+ }
+
+ if (verbosity > 4) verbosity = 4;
+ if (opMode == OM_Z && smallMode && blockSize100k > 2)
+ blockSize100k = 2;
+
+ if (opMode == OM_TEST && srcMode == SM_F2O) {
+ fprintf ( stderr, "%s: -c and -t cannot be used together.\n",
+ progName );
+ exit ( 1 );
+ }
+
+ if (srcMode == SM_F2O && numFileNames == 0)
+ srcMode = SM_I2O;
+
+ if (opMode != OM_Z) blockSize100k = 0;
+
+ if (srcMode == SM_F2F) {
+ signal (SIGINT, mySignalCatcher);
+ signal (SIGTERM, mySignalCatcher);
+# if BZ_UNIX
+ signal (SIGHUP, mySignalCatcher);
+# endif
+ }
+
+ if (opMode == OM_Z) {
+ if (srcMode == SM_I2O) {
+ compress ( NULL );
+ } else {
+ decode = True;
+ for (aa = argList; aa != NULL; aa = aa->link) {
+ if (ISFLAG("--")) { decode = False; continue; }
+ if (aa->name[0] == '-' && decode) continue;
+ numFilesProcessed++;
+ compress ( aa->name );
+ }
+ }
+ }
+ else
+
+ if (opMode == OM_UNZ) {
+ unzFailsExist = False;
+ if (srcMode == SM_I2O) {
+ uncompress ( NULL );
+ } else {
+ decode = True;
+ for (aa = argList; aa != NULL; aa = aa->link) {
+ if (ISFLAG("--")) { decode = False; continue; }
+ if (aa->name[0] == '-' && decode) continue;
+ numFilesProcessed++;
+ uncompress ( aa->name );
+ }
+ }
+ if (unzFailsExist) {
+ setExit(2);
+ exit(exitValue);
+ }
+ }
+
+ else {
+ testFailsExist = False;
+ if (srcMode == SM_I2O) {
+ testf ( NULL );
+ } else {
+ decode = True;
+ for (aa = argList; aa != NULL; aa = aa->link) {
+ if (ISFLAG("--")) { decode = False; continue; }
+ if (aa->name[0] == '-' && decode) continue;
+ numFilesProcessed++;
+ testf ( aa->name );
+ }
+ }
+ if (testFailsExist && noisy) {
+ fprintf ( stderr,
+ "\n"
+ "You can use the `bzip2recover' program to attempt to recover\n"
+ "data from undamaged sections of corrupted files.\n\n"
+ );
+ setExit(2);
+ exit(exitValue);
+ }
+ }
+
+ /* Free the argument list memory to mollify leak detectors
+ (eg) Purify, Checker. Serves no other useful purpose.
+ */
+ aa = argList;
+ while (aa != NULL) {
+ Cell* aa2 = aa->link;
+ if (aa->name != NULL) free(aa->name);
+ free(aa);
+ aa = aa2;
+ }
+
+ return exitValue;
+}
+
+
+/*-----------------------------------------------------------*/
+/*--- end bzip2.c ---*/
+/*-----------------------------------------------------------*/
diff --git a/third-party/bzip2/bzip2.txt b/third-party/bzip2/bzip2.txt
new file mode 100644
index 0000000..d2deb39
--- /dev/null
+++ b/third-party/bzip2/bzip2.txt
@@ -0,0 +1,391 @@
+
+NAME
+ bzip2, bunzip2 - a block-sorting file compressor, v1.0.6
+ bzcat - decompresses files to stdout
+ bzip2recover - recovers data from damaged bzip2 files
+
+
+SYNOPSIS
+ bzip2 [ -cdfkqstvzVL123456789 ] [ filenames ... ]
+ bunzip2 [ -fkvsVL ] [ filenames ... ]
+ bzcat [ -s ] [ filenames ... ]
+ bzip2recover filename
+
+
+DESCRIPTION
+ bzip2 compresses files using the Burrows-Wheeler block
+ sorting text compression algorithm, and Huffman coding.
+ Compression is generally considerably better than that
+ achieved by more conventional LZ77/LZ78-based compressors,
+ and approaches the performance of the PPM family of sta-
+ tistical compressors.
+
+ The command-line options are deliberately very similar to
+ those of GNU gzip, but they are not identical.
+
+ bzip2 expects a list of file names to accompany the com-
+ mand-line flags. Each file is replaced by a compressed
+ version of itself, with the name "original_name.bz2".
+ Each compressed file has the same modification date, per-
+ missions, and, when possible, ownership as the correspond-
+ ing original, so that these properties can be correctly
+ restored at decompression time. File name handling is
+ naive in the sense that there is no mechanism for preserv-
+ ing original file names, permissions, ownerships or dates
+ in filesystems which lack these concepts, or have serious
+ file name length restrictions, such as MS-DOS.
+
+ bzip2 and bunzip2 will by default not overwrite existing
+ files. If you want this to happen, specify the -f flag.
+
+ If no file names are specified, bzip2 compresses from
+ standard input to standard output. In this case, bzip2
+ will decline to write compressed output to a terminal, as
+ this would be entirely incomprehensible and therefore
+ pointless.
+
+ bunzip2 (or bzip2 -d) decompresses all specified files.
+ Files which were not created by bzip2 will be detected and
+ ignored, and a warning issued. bzip2 attempts to guess
+ the filename for the decompressed file from that of the
+ compressed file as follows:
+
+ filename.bz2 becomes filename
+ filename.bz becomes filename
+ filename.tbz2 becomes filename.tar
+ filename.tbz becomes filename.tar
+ anyothername becomes anyothername.out
+
+ If the file does not end in one of the recognised endings,
+ .bz2, .bz, .tbz2 or .tbz, bzip2 complains that it cannot
+ guess the name of the original file, and uses the original
+ name with .out appended.
+
+ As with compression, supplying no filenames causes decom-
+ pression from standard input to standard output.
+
+ bunzip2 will correctly decompress a file which is the con-
+ catenation of two or more compressed files. The result is
+ the concatenation of the corresponding uncompressed files.
+ Integrity testing (-t) of concatenated compressed files is
+ also supported.
+
+ You can also compress or decompress files to the standard
+ output by giving the -c flag. Multiple files may be com-
+ pressed and decompressed like this. The resulting outputs
+ are fed sequentially to stdout. Compression of multiple
+ files in this manner generates a stream containing multi-
+ ple compressed file representations. Such a stream can be
+ decompressed correctly only by bzip2 version 0.9.0 or
+ later. Earlier versions of bzip2 will stop after decom-
+ pressing the first file in the stream.
+
+ bzcat (or bzip2 -dc) decompresses all specified files to
+ the standard output.
+
+ bzip2 will read arguments from the environment variables
+ BZIP2 and BZIP, in that order, and will process them
+ before any arguments read from the command line. This
+ gives a convenient way to supply default arguments.
+
+ Compression is always performed, even if the compressed
+ file is slightly larger than the original. Files of less
+ than about one hundred bytes tend to get larger, since the
+ compression mechanism has a constant overhead in the
+ region of 50 bytes. Random data (including the output of
+ most file compressors) is coded at about 8.05 bits per
+ byte, giving an expansion of around 0.5%.
+
+ As a self-check for your protection, bzip2 uses 32-bit
+ CRCs to make sure that the decompressed version of a file
+ is identical to the original. This guards against corrup-
+ tion of the compressed data, and against undetected bugs
+ in bzip2 (hopefully very unlikely). The chances of data
+ corruption going undetected is microscopic, about one
+ chance in four billion for each file processed. Be aware,
+ though, that the check occurs upon decompression, so it
+ can only tell you that something is wrong. It can't help
+ you recover the original uncompressed data. You can use
+ bzip2recover to try to recover data from damaged files.
+
+ Return values: 0 for a normal exit, 1 for environmental
+ problems (file not found, invalid flags, I/O errors, &c),
+ 2 to indicate a corrupt compressed file, 3 for an internal
+ consistency error (eg, bug) which caused bzip2 to panic.
+
+
+OPTIONS
+ -c --stdout
+ Compress or decompress to standard output.
+
+ -d --decompress
+ Force decompression. bzip2, bunzip2 and bzcat are
+ really the same program, and the decision about
+ what actions to take is done on the basis of which
+ name is used. This flag overrides that mechanism,
+ and forces bzip2 to decompress.
+
+ -z --compress
+ The complement to -d: forces compression,
+ regardless of the invocation name.
+
+ -t --test
+ Check integrity of the specified file(s), but don't
+ decompress them. This really performs a trial
+ decompression and throws away the result.
+
+ -f --force
+ Force overwrite of output files. Normally, bzip2
+ will not overwrite existing output files. Also
+ forces bzip2 to break hard links to files, which it
+ otherwise wouldn't do.
+
+ bzip2 normally declines to decompress files which
+ don't have the correct magic header bytes. If
+ forced (-f), however, it will pass such files
+ through unmodified. This is how GNU gzip behaves.
+
+ -k --keep
+ Keep (don't delete) input files during compression
+ or decompression.
+
+ -s --small
+ Reduce memory usage, for compression, decompression
+ and testing. Files are decompressed and tested
+ using a modified algorithm which only requires 2.5
+ bytes per block byte. This means any file can be
+ decompressed in 2300k of memory, albeit at about
+ half the normal speed.
+
+ During compression, -s selects a block size of
+ 200k, which limits memory use to around the same
+ figure, at the expense of your compression ratio.
+ In short, if your machine is low on memory (8
+ megabytes or less), use -s for everything. See
+ MEMORY MANAGEMENT below.
+
+ -q --quiet
+ Suppress non-essential warning messages. Messages
+ pertaining to I/O errors and other critical events
+ will not be suppressed.
+
+ -v --verbose
+ Verbose mode -- show the compression ratio for each
+ file processed. Further -v's increase the ver-
+ bosity level, spewing out lots of information which
+ is primarily of interest for diagnostic purposes.
+
+ -L --license -V --version
+ Display the software version, license terms and
+ conditions.
+
+ -1 (or --fast) to -9 (or --best)
+ Set the block size to 100 k, 200 k .. 900 k when
+ compressing. Has no effect when decompressing.
+ See MEMORY MANAGEMENT below. The --fast and --best
+ aliases are primarily for GNU gzip compatibility.
+ In particular, --fast doesn't make things signifi-
+ cantly faster. And --best merely selects the
+ default behaviour.
+
+ -- Treats all subsequent arguments as file names, even
+ if they start with a dash. This is so you can han-
+ dle files with names beginning with a dash, for
+ example: bzip2 -- -myfilename.
+
+ --repetitive-fast --repetitive-best
+ These flags are redundant in versions 0.9.5 and
+ above. They provided some coarse control over the
+ behaviour of the sorting algorithm in earlier ver-
+ sions, which was sometimes useful. 0.9.5 and above
+ have an improved algorithm which renders these
+ flags irrelevant.
+
+
+MEMORY MANAGEMENT
+ bzip2 compresses large files in blocks. The block size
+ affects both the compression ratio achieved, and the
+ amount of memory needed for compression and decompression.
+ The flags -1 through -9 specify the block size to be
+ 100,000 bytes through 900,000 bytes (the default) respec-
+ tively. At decompression time, the block size used for
+ compression is read from the header of the compressed
+ file, and bunzip2 then allocates itself just enough memory
+ to decompress the file. Since block sizes are stored in
+ compressed files, it follows that the flags -1 to -9 are
+ irrelevant to and so ignored during decompression.
+
+ Compression and decompression requirements, in bytes, can
+ be estimated as:
+
+ Compression: 400k + ( 8 x block size )
+
+ Decompression: 100k + ( 4 x block size ), or
+ 100k + ( 2.5 x block size )
+
+ Larger block sizes give rapidly diminishing marginal
+ returns. Most of the compression comes from the first two
+ or three hundred k of block size, a fact worth bearing in
+ mind when using bzip2 on small machines. It is also
+ important to appreciate that the decompression memory
+ requirement is set at compression time by the choice of
+ block size.
+
+ For files compressed with the default 900k block size,
+ bunzip2 will require about 3700 kbytes to decompress. To
+ support decompression of any file on a 4 megabyte machine,
+ bunzip2 has an option to decompress using approximately
+ half this amount of memory, about 2300 kbytes. Decompres-
+ sion speed is also halved, so you should use this option
+ only where necessary. The relevant flag is -s.
+
+ In general, try and use the largest block size memory con-
+ straints allow, since that maximises the compression
+ achieved. Compression and decompression speed are virtu-
+ ally unaffected by block size.
+
+ Another significant point applies to files which fit in a
+ single block -- that means most files you'd encounter
+ using a large block size. The amount of real memory
+ touched is proportional to the size of the file, since the
+ file is smaller than a block. For example, compressing a
+ file 20,000 bytes long with the flag -9 will cause the
+ compressor to allocate around 7600k of memory, but only
+ touch 400k + 20000 * 8 = 560 kbytes of it. Similarly, the
+ decompressor will allocate 3700k but only touch 100k +
+ 20000 * 4 = 180 kbytes.
+
+ Here is a table which summarises the maximum memory usage
+ for different block sizes. Also recorded is the total
+ compressed size for 14 files of the Calgary Text Compres-
+ sion Corpus totalling 3,141,622 bytes. This column gives
+ some feel for how compression varies with block size.
+ These figures tend to understate the advantage of larger
+ block sizes for larger files, since the Corpus is domi-
+ nated by smaller files.
+
+ Compress Decompress Decompress Corpus
+ Flag usage usage -s usage Size
+
+ -1 1200k 500k 350k 914704
+ -2 2000k 900k 600k 877703
+ -3 2800k 1300k 850k 860338
+ -4 3600k 1700k 1100k 846899
+ -5 4400k 2100k 1350k 845160
+ -6 5200k 2500k 1600k 838626
+ -7 6100k 2900k 1850k 834096
+ -8 6800k 3300k 2100k 828642
+ -9 7600k 3700k 2350k 828642
+
+
+RECOVERING DATA FROM DAMAGED FILES
+ bzip2 compresses files in blocks, usually 900kbytes long.
+ Each block is handled independently. If a media or trans-
+ mission error causes a multi-block .bz2 file to become
+ damaged, it may be possible to recover data from the
+ undamaged blocks in the file.
+
+ The compressed representation of each block is delimited
+ by a 48-bit pattern, which makes it possible to find the
+ block boundaries with reasonable certainty. Each block
+ also carries its own 32-bit CRC, so damaged blocks can be
+ distinguished from undamaged ones.
+
+ bzip2recover is a simple program whose purpose is to
+ search for blocks in .bz2 files, and write each block out
+ into its own .bz2 file. You can then use bzip2 -t to test
+ the integrity of the resulting files, and decompress those
+ which are undamaged.
+
+ bzip2recover takes a single argument, the name of the dam-
+ aged file, and writes a number of files
+ "rec00001file.bz2", "rec00002file.bz2", etc, containing
+ the extracted blocks. The output filenames are
+ designed so that the use of wildcards in subsequent pro-
+ cessing -- for example, "bzip2 -dc rec*file.bz2 > recov-
+ ered_data" -- processes the files in the correct order.
+
+ bzip2recover should be of most use dealing with large .bz2
+ files, as these will contain many blocks. It is clearly
+ futile to use it on damaged single-block files, since a
+ damaged block cannot be recovered. If you wish to min-
+ imise any potential data loss through media or transmis-
+ sion errors, you might consider compressing with a smaller
+ block size.
+
+
+PERFORMANCE NOTES
+ The sorting phase of compression gathers together similar
+ strings in the file. Because of this, files containing
+ very long runs of repeated symbols, like "aabaabaabaab
+ ..." (repeated several hundred times) may compress more
+ slowly than normal. Versions 0.9.5 and above fare much
+ better than previous versions in this respect. The ratio
+ between worst-case and average-case compression time is in
+ the region of 10:1. For previous versions, this figure
+ was more like 100:1. You can use the -vvvv option to mon-
+ itor progress in great detail, if you want.
+
+ Decompression speed is unaffected by these phenomena.
+
+ bzip2 usually allocates several megabytes of memory to
+ operate in, and then charges all over it in a fairly ran-
+ dom fashion. This means that performance, both for com-
+ pressing and decompressing, is largely determined by the
+ speed at which your machine can service cache misses.
+ Because of this, small changes to the code to reduce the
+ miss rate have been observed to give disproportionately
+ large performance improvements. I imagine bzip2 will per-
+ form best on machines with very large caches.
+
+
+CAVEATS
+ I/O error messages are not as helpful as they could be.
+ bzip2 tries hard to detect I/O errors and exit cleanly,
+ but the details of what the problem is sometimes seem
+ rather misleading.
+
+ This manual page pertains to version 1.0.6 of bzip2. Com-
+ pressed data created by this version is entirely forwards
+ and backwards compatible with the previous public
+ releases, versions 0.1pl2, 0.9.0, 0.9.5, 1.0.0, 1.0.1,
+ 1.0.2 and above, but with the following exception: 0.9.0
+ and above can correctly decompress multiple concatenated
+ compressed files. 0.1pl2 cannot do this; it will stop
+ after decompressing just the first file in the stream.
+
+ bzip2recover versions prior to 1.0.2 used 32-bit integers
+ to represent bit positions in compressed files, so they
+ could not handle compressed files more than 512 megabytes
+ long. Versions 1.0.2 and above use 64-bit ints on some
+ platforms which support them (GNU supported targets, and
+ Windows). To establish whether or not bzip2recover was
+ built with such a limitation, run it without arguments.
+ In any event you can build yourself an unlimited version
+ if you can recompile it with MaybeUInt64 set to be an
+ unsigned 64-bit integer.
+
+
+AUTHOR
+ Julian Seward, jsewardbzip.org.
+
+ http://www.bzip.org
+
+ The ideas embodied in bzip2 are due to (at least) the fol-
+ lowing people: Michael Burrows and David Wheeler (for the
+ block sorting transformation), David Wheeler (again, for
+ the Huffman coder), Peter Fenwick (for the structured cod-
+ ing model in the original bzip, and many refinements), and
+ Alistair Moffat, Radford Neal and Ian Witten (for the
+ arithmetic coder in the original bzip). I am much
+ indebted for their help, support and advice. See the man-
+ ual in the source distribution for pointers to sources of
+ documentation. Christian von Roques encouraged me to look
+ for faster sorting algorithms, so as to speed up compres-
+ sion. Bela Lubkin encouraged me to improve the worst-case
+ compression performance. Donna Robinson XMLised the docu-
+ mentation. The bz* scripts are derived from those of GNU
+ gzip. Many people sent patches, helped with portability
+ problems, lent machines, gave advice and were generally
+ helpful.
+
diff --git a/third-party/bzip2/bzip2recover.c b/third-party/bzip2/bzip2recover.c
new file mode 100644
index 0000000..f9de049
--- /dev/null
+++ b/third-party/bzip2/bzip2recover.c
@@ -0,0 +1,514 @@
+/*-----------------------------------------------------------*/
+/*--- Block recoverer program for bzip2 ---*/
+/*--- bzip2recover.c ---*/
+/*-----------------------------------------------------------*/
+
+/* ------------------------------------------------------------------
+ This file is part of bzip2/libbzip2, a program and library for
+ lossless, block-sorting data compression.
+
+ bzip2/libbzip2 version 1.0.6 of 6 September 2010
+ Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
+
+ Please read the WARNING, DISCLAIMER and PATENTS sections in the
+ README file.
+
+ This program is released under the terms of the license contained
+ in the file LICENSE.
+ ------------------------------------------------------------------ */
+
+/* This program is a complete hack and should be rewritten properly.
+ It isn't very complicated. */
+
+#include <stdio.h>
+#include <errno.h>
+#include <stdlib.h>
+#include <string.h>
+
+
+/* This program records bit locations in the file to be recovered.
+ That means that if 64-bit ints are not supported, we will not
+ be able to recover .bz2 files over 512MB (2^32 bits) long.
+ On GNU supported platforms, we take advantage of the 64-bit
+ int support to circumvent this problem. Ditto MSVC.
+
+ This change occurred in version 1.0.2; all prior versions have
+ the 512MB limitation.
+*/
+#ifdef __GNUC__
+ typedef unsigned long long int MaybeUInt64;
+# define MaybeUInt64_FMT "%Lu"
+#else
+#ifdef _MSC_VER
+ typedef unsigned __int64 MaybeUInt64;
+# define MaybeUInt64_FMT "%I64u"
+#else
+ typedef unsigned int MaybeUInt64;
+# define MaybeUInt64_FMT "%u"
+#endif
+#endif
+
+typedef unsigned int UInt32;
+typedef int Int32;
+typedef unsigned char UChar;
+typedef char Char;
+typedef unsigned char Bool;
+#define True ((Bool)1)
+#define False ((Bool)0)
+
+
+#define BZ_MAX_FILENAME 2000
+
+Char inFileName[BZ_MAX_FILENAME];
+Char outFileName[BZ_MAX_FILENAME];
+Char progName[BZ_MAX_FILENAME];
+
+MaybeUInt64 bytesOut = 0;
+MaybeUInt64 bytesIn = 0;
+
+
+/*---------------------------------------------------*/
+/*--- Header bytes ---*/
+/*---------------------------------------------------*/
+
+#define BZ_HDR_B 0x42 /* 'B' */
+#define BZ_HDR_Z 0x5a /* 'Z' */
+#define BZ_HDR_h 0x68 /* 'h' */
+#define BZ_HDR_0 0x30 /* '0' */
+
+
+/*---------------------------------------------------*/
+/*--- I/O errors ---*/
+/*---------------------------------------------------*/
+
+/*---------------------------------------------*/
+static void readError ( void )
+{
+ fprintf ( stderr,
+ "%s: I/O error reading `%s', possible reason follows.\n",
+ progName, inFileName );
+ perror ( progName );
+ fprintf ( stderr, "%s: warning: output file(s) may be incomplete.\n",
+ progName );
+ exit ( 1 );
+}
+
+
+/*---------------------------------------------*/
+static void writeError ( void )
+{
+ fprintf ( stderr,
+ "%s: I/O error reading `%s', possible reason follows.\n",
+ progName, inFileName );
+ perror ( progName );
+ fprintf ( stderr, "%s: warning: output file(s) may be incomplete.\n",
+ progName );
+ exit ( 1 );
+}
+
+
+/*---------------------------------------------*/
+static void mallocFail ( Int32 n )
+{
+ fprintf ( stderr,
+ "%s: malloc failed on request for %d bytes.\n",
+ progName, n );
+ fprintf ( stderr, "%s: warning: output file(s) may be incomplete.\n",
+ progName );
+ exit ( 1 );
+}
+
+
+/*---------------------------------------------*/
+static void tooManyBlocks ( Int32 max_handled_blocks )
+{
+ fprintf ( stderr,
+ "%s: `%s' appears to contain more than %d blocks\n",
+ progName, inFileName, max_handled_blocks );
+ fprintf ( stderr,
+ "%s: and cannot be handled. To fix, increase\n",
+ progName );
+ fprintf ( stderr,
+ "%s: BZ_MAX_HANDLED_BLOCKS in bzip2recover.c, and recompile.\n",
+ progName );
+ exit ( 1 );
+}
+
+
+
+/*---------------------------------------------------*/
+/*--- Bit stream I/O ---*/
+/*---------------------------------------------------*/
+
+typedef
+ struct {
+ FILE* handle;
+ Int32 buffer;
+ Int32 buffLive;
+ Char mode;
+ }
+ BitStream;
+
+
+/*---------------------------------------------*/
+static BitStream* bsOpenReadStream ( FILE* stream )
+{
+ BitStream *bs = malloc ( sizeof(BitStream) );
+ if (bs == NULL) mallocFail ( sizeof(BitStream) );
+ bs->handle = stream;
+ bs->buffer = 0;
+ bs->buffLive = 0;
+ bs->mode = 'r';
+ return bs;
+}
+
+
+/*---------------------------------------------*/
+static BitStream* bsOpenWriteStream ( FILE* stream )
+{
+ BitStream *bs = malloc ( sizeof(BitStream) );
+ if (bs == NULL) mallocFail ( sizeof(BitStream) );
+ bs->handle = stream;
+ bs->buffer = 0;
+ bs->buffLive = 0;
+ bs->mode = 'w';
+ return bs;
+}
+
+
+/*---------------------------------------------*/
+static void bsPutBit ( BitStream* bs, Int32 bit )
+{
+ if (bs->buffLive == 8) {
+ Int32 retVal = putc ( (UChar) bs->buffer, bs->handle );
+ if (retVal == EOF) writeError();
+ bytesOut++;
+ bs->buffLive = 1;
+ bs->buffer = bit & 0x1;
+ } else {
+ bs->buffer = ( (bs->buffer << 1) | (bit & 0x1) );
+ bs->buffLive++;
+ };
+}
+
+
+/*---------------------------------------------*/
+/*--
+ Returns 0 or 1, or 2 to indicate EOF.
+--*/
+static Int32 bsGetBit ( BitStream* bs )
+{
+ if (bs->buffLive > 0) {
+ bs->buffLive --;
+ return ( ((bs->buffer) >> (bs->buffLive)) & 0x1 );
+ } else {
+ Int32 retVal = getc ( bs->handle );
+ if ( retVal == EOF ) {
+ if (errno != 0) readError();
+ return 2;
+ }
+ bs->buffLive = 7;
+ bs->buffer = retVal;
+ return ( ((bs->buffer) >> 7) & 0x1 );
+ }
+}
+
+
+/*---------------------------------------------*/
+static void bsClose ( BitStream* bs )
+{
+ Int32 retVal;
+
+ if ( bs->mode == 'w' ) {
+ while ( bs->buffLive < 8 ) {
+ bs->buffLive++;
+ bs->buffer <<= 1;
+ };
+ retVal = putc ( (UChar) (bs->buffer), bs->handle );
+ if (retVal == EOF) writeError();
+ bytesOut++;
+ retVal = fflush ( bs->handle );
+ if (retVal == EOF) writeError();
+ }
+ retVal = fclose ( bs->handle );
+ if (retVal == EOF) {
+ if (bs->mode == 'w') writeError(); else readError();
+ }
+ free ( bs );
+}
+
+
+/*---------------------------------------------*/
+static void bsPutUChar ( BitStream* bs, UChar c )
+{
+ Int32 i;
+ for (i = 7; i >= 0; i--)
+ bsPutBit ( bs, (((UInt32) c) >> i) & 0x1 );
+}
+
+
+/*---------------------------------------------*/
+static void bsPutUInt32 ( BitStream* bs, UInt32 c )
+{
+ Int32 i;
+
+ for (i = 31; i >= 0; i--)
+ bsPutBit ( bs, (c >> i) & 0x1 );
+}
+
+
+/*---------------------------------------------*/
+static Bool endsInBz2 ( Char* name )
+{
+ Int32 n = strlen ( name );
+ if (n <= 4) return False;
+ return
+ (name[n-4] == '.' &&
+ name[n-3] == 'b' &&
+ name[n-2] == 'z' &&
+ name[n-1] == '2');
+}
+
+
+/*---------------------------------------------------*/
+/*--- ---*/
+/*---------------------------------------------------*/
+
+/* This logic isn't really right when it comes to Cygwin. */
+#ifdef _WIN32
+# define BZ_SPLIT_SYM '\\' /* path splitter on Windows platform */
+#else
+# define BZ_SPLIT_SYM '/' /* path splitter on Unix platform */
+#endif
+
+#define BLOCK_HEADER_HI 0x00003141UL
+#define BLOCK_HEADER_LO 0x59265359UL
+
+#define BLOCK_ENDMARK_HI 0x00001772UL
+#define BLOCK_ENDMARK_LO 0x45385090UL
+
+/* Increase if necessary. However, a .bz2 file with > 50000 blocks
+ would have an uncompressed size of at least 40GB, so the chances
+ are low you'll need to up this.
+*/
+#define BZ_MAX_HANDLED_BLOCKS 50000
+
+MaybeUInt64 bStart [BZ_MAX_HANDLED_BLOCKS];
+MaybeUInt64 bEnd [BZ_MAX_HANDLED_BLOCKS];
+MaybeUInt64 rbStart[BZ_MAX_HANDLED_BLOCKS];
+MaybeUInt64 rbEnd [BZ_MAX_HANDLED_BLOCKS];
+
+Int32 main ( Int32 argc, Char** argv )
+{
+ FILE* inFile;
+ FILE* outFile;
+ BitStream* bsIn, *bsWr;
+ Int32 b, wrBlock, currBlock, rbCtr;
+ MaybeUInt64 bitsRead;
+
+ UInt32 buffHi, buffLo, blockCRC;
+ Char* p;
+
+ strcpy ( progName, argv[0] );
+ inFileName[0] = outFileName[0] = 0;
+
+ fprintf ( stderr,
+ "bzip2recover 1.0.6: extracts blocks from damaged .bz2 files.\n" );
+
+ if (argc != 2) {
+ fprintf ( stderr, "%s: usage is `%s damaged_file_name'.\n",
+ progName, progName );
+ switch (sizeof(MaybeUInt64)) {
+ case 8:
+ fprintf(stderr,
+ "\trestrictions on size of recovered file: None\n");
+ break;
+ case 4:
+ fprintf(stderr,
+ "\trestrictions on size of recovered file: 512 MB\n");
+ fprintf(stderr,
+ "\tto circumvent, recompile with MaybeUInt64 as an\n"
+ "\tunsigned 64-bit int.\n");
+ break;
+ default:
+ fprintf(stderr,
+ "\tsizeof(MaybeUInt64) is not 4 or 8 -- "
+ "configuration error.\n");
+ break;
+ }
+ exit(1);
+ }
+
+ if (strlen(argv[1]) >= BZ_MAX_FILENAME-20) {
+ fprintf ( stderr,
+ "%s: supplied filename is suspiciously (>= %d chars) long. Bye!\n",
+ progName, (int)strlen(argv[1]) );
+ exit(1);
+ }
+
+ strcpy ( inFileName, argv[1] );
+
+ inFile = fopen ( inFileName, "rb" );
+ if (inFile == NULL) {
+ fprintf ( stderr, "%s: can't read `%s'\n", progName, inFileName );
+ exit(1);
+ }
+
+ bsIn = bsOpenReadStream ( inFile );
+ fprintf ( stderr, "%s: searching for block boundaries ...\n", progName );
+
+ bitsRead = 0;
+ buffHi = buffLo = 0;
+ currBlock = 0;
+ bStart[currBlock] = 0;
+
+ rbCtr = 0;
+
+ while (True) {
+ b = bsGetBit ( bsIn );
+ bitsRead++;
+ if (b == 2) {
+ if (bitsRead >= bStart[currBlock] &&
+ (bitsRead - bStart[currBlock]) >= 40) {
+ bEnd[currBlock] = bitsRead-1;
+ if (currBlock > 0)
+ fprintf ( stderr, " block %d runs from " MaybeUInt64_FMT
+ " to " MaybeUInt64_FMT " (incomplete)\n",
+ currBlock, bStart[currBlock], bEnd[currBlock] );
+ } else
+ currBlock--;
+ break;
+ }
+ buffHi = (buffHi << 1) | (buffLo >> 31);
+ buffLo = (buffLo << 1) | (b & 1);
+ if ( ( (buffHi & 0x0000ffff) == BLOCK_HEADER_HI
+ && buffLo == BLOCK_HEADER_LO)
+ ||
+ ( (buffHi & 0x0000ffff) == BLOCK_ENDMARK_HI
+ && buffLo == BLOCK_ENDMARK_LO)
+ ) {
+ if (bitsRead > 49) {
+ bEnd[currBlock] = bitsRead-49;
+ } else {
+ bEnd[currBlock] = 0;
+ }
+ if (currBlock > 0 &&
+ (bEnd[currBlock] - bStart[currBlock]) >= 130) {
+ fprintf ( stderr, " block %d runs from " MaybeUInt64_FMT
+ " to " MaybeUInt64_FMT "\n",
+ rbCtr+1, bStart[currBlock], bEnd[currBlock] );
+ rbStart[rbCtr] = bStart[currBlock];
+ rbEnd[rbCtr] = bEnd[currBlock];
+ rbCtr++;
+ }
+ if (currBlock >= BZ_MAX_HANDLED_BLOCKS)
+ tooManyBlocks(BZ_MAX_HANDLED_BLOCKS);
+ currBlock++;
+
+ bStart[currBlock] = bitsRead;
+ }
+ }
+
+ bsClose ( bsIn );
+
+ /*-- identified blocks run from 1 to rbCtr inclusive. --*/
+
+ if (rbCtr < 1) {
+ fprintf ( stderr,
+ "%s: sorry, I couldn't find any block boundaries.\n",
+ progName );
+ exit(1);
+ };
+
+ fprintf ( stderr, "%s: splitting into blocks\n", progName );
+
+ inFile = fopen ( inFileName, "rb" );
+ if (inFile == NULL) {
+ fprintf ( stderr, "%s: can't open `%s'\n", progName, inFileName );
+ exit(1);
+ }
+ bsIn = bsOpenReadStream ( inFile );
+
+ /*-- placate gcc's dataflow analyser --*/
+ blockCRC = 0; bsWr = 0;
+
+ bitsRead = 0;
+ outFile = NULL;
+ wrBlock = 0;
+ while (True) {
+ b = bsGetBit(bsIn);
+ if (b == 2) break;
+ buffHi = (buffHi << 1) | (buffLo >> 31);
+ buffLo = (buffLo << 1) | (b & 1);
+ if (bitsRead == 47+rbStart[wrBlock])
+ blockCRC = (buffHi << 16) | (buffLo >> 16);
+
+ if (outFile != NULL && bitsRead >= rbStart[wrBlock]
+ && bitsRead <= rbEnd[wrBlock]) {
+ bsPutBit ( bsWr, b );
+ }
+
+ bitsRead++;
+
+ if (bitsRead == rbEnd[wrBlock]+1) {
+ if (outFile != NULL) {
+ bsPutUChar ( bsWr, 0x17 ); bsPutUChar ( bsWr, 0x72 );
+ bsPutUChar ( bsWr, 0x45 ); bsPutUChar ( bsWr, 0x38 );
+ bsPutUChar ( bsWr, 0x50 ); bsPutUChar ( bsWr, 0x90 );
+ bsPutUInt32 ( bsWr, blockCRC );
+ bsClose ( bsWr );
+ }
+ if (wrBlock >= rbCtr) break;
+ wrBlock++;
+ } else
+ if (bitsRead == rbStart[wrBlock]) {
+ /* Create the output file name, correctly handling leading paths.
+ (31.10.2001 by Sergey E. Kusikov) */
+ Char* split;
+ Int32 ofs, k;
+ for (k = 0; k < BZ_MAX_FILENAME; k++)
+ outFileName[k] = 0;
+ strcpy (outFileName, inFileName);
+ split = strrchr (outFileName, BZ_SPLIT_SYM);
+ if (split == NULL) {
+ split = outFileName;
+ } else {
+ ++split;
+ }
+ /* Now split points to the start of the basename. */
+ ofs = split - outFileName;
+ sprintf (split, "rec%5d", wrBlock+1);
+ for (p = split; *p != 0; p++) if (*p == ' ') *p = '0';
+ strcat (outFileName, inFileName + ofs);
+
+ if ( !endsInBz2(outFileName)) strcat ( outFileName, ".bz2" );
+
+ fprintf ( stderr, " writing block %d to `%s' ...\n",
+ wrBlock+1, outFileName );
+
+ outFile = fopen ( outFileName, "wb" );
+ if (outFile == NULL) {
+ fprintf ( stderr, "%s: can't write `%s'\n",
+ progName, outFileName );
+ exit(1);
+ }
+ bsWr = bsOpenWriteStream ( outFile );
+ bsPutUChar ( bsWr, BZ_HDR_B );
+ bsPutUChar ( bsWr, BZ_HDR_Z );
+ bsPutUChar ( bsWr, BZ_HDR_h );
+ bsPutUChar ( bsWr, BZ_HDR_0 + 9 );
+ bsPutUChar ( bsWr, 0x31 ); bsPutUChar ( bsWr, 0x41 );
+ bsPutUChar ( bsWr, 0x59 ); bsPutUChar ( bsWr, 0x26 );
+ bsPutUChar ( bsWr, 0x53 ); bsPutUChar ( bsWr, 0x59 );
+ }
+ }
+
+ fprintf ( stderr, "%s: finished\n", progName );
+ return 0;
+}
+
+
+
+/*-----------------------------------------------------------*/
+/*--- end bzip2recover.c ---*/
+/*-----------------------------------------------------------*/
diff --git a/third-party/bzip2/bzlib.c b/third-party/bzip2/bzlib.c
new file mode 100644
index 0000000..bd358a7
--- /dev/null
+++ b/third-party/bzip2/bzlib.c
@@ -0,0 +1,1572 @@
+
+/*-------------------------------------------------------------*/
+/*--- Library top-level functions. ---*/
+/*--- bzlib.c ---*/
+/*-------------------------------------------------------------*/
+
+/* ------------------------------------------------------------------
+ This file is part of bzip2/libbzip2, a program and library for
+ lossless, block-sorting data compression.
+
+ bzip2/libbzip2 version 1.0.6 of 6 September 2010
+ Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
+
+ Please read the WARNING, DISCLAIMER and PATENTS sections in the
+ README file.
+
+ This program is released under the terms of the license contained
+ in the file LICENSE.
+ ------------------------------------------------------------------ */
+
+/* CHANGES
+ 0.9.0 -- original version.
+ 0.9.0a/b -- no changes in this file.
+ 0.9.0c -- made zero-length BZ_FLUSH work correctly in bzCompress().
+ fixed bzWrite/bzRead to ignore zero-length requests.
+ fixed bzread to correctly handle read requests after EOF.
+ wrong parameter order in call to bzDecompressInit in
+ bzBuffToBuffDecompress. Fixed.
+*/
+
+#include "bzlib_private.h"
+
+
+/*---------------------------------------------------*/
+/*--- Compression stuff ---*/
+/*---------------------------------------------------*/
+
+
+/*---------------------------------------------------*/
+#ifndef BZ_NO_STDIO
+void BZ2_bz__AssertH__fail ( int errcode )
+{
+ fprintf(stderr,
+ "\n\nbzip2/libbzip2: internal error number %d.\n"
+ "This is a bug in bzip2/libbzip2, %s.\n"
+ "Please report it to me at: jseward at bzip.org. If this happened\n"
+ "when you were using some program which uses libbzip2 as a\n"
+ "component, you should also report this bug to the author(s)\n"
+ "of that program. Please make an effort to report this bug;\n"
+ "timely and accurate bug reports eventually lead to higher\n"
+ "quality software. Thanks. Julian Seward, 10 December 2007.\n\n",
+ errcode,
+ BZ2_bzlibVersion()
+ );
+
+ if (errcode == 1007) {
+ fprintf(stderr,
+ "\n*** A special note about internal error number 1007 ***\n"
+ "\n"
+ "Experience suggests that a common cause of i.e. 1007\n"
+ "is unreliable memory or other hardware. The 1007 assertion\n"
+ "just happens to cross-check the results of huge numbers of\n"
+ "memory reads/writes, and so acts (unintendedly) as a stress\n"
+ "test of your memory system.\n"
+ "\n"
+ "I suggest the following: try compressing the file again,\n"
+ "possibly monitoring progress in detail with the -vv flag.\n"
+ "\n"
+ "* If the error cannot be reproduced, and/or happens at different\n"
+ " points in compression, you may have a flaky memory system.\n"
+ " Try a memory-test program. I have used Memtest86\n"
+ " (www.memtest86.com). At the time of writing it is free (GPLd).\n"
+ " Memtest86 tests memory much more thorougly than your BIOSs\n"
+ " power-on test, and may find failures that the BIOS doesn't.\n"
+ "\n"
+ "* If the error can be repeatably reproduced, this is a bug in\n"
+ " bzip2, and I would very much like to hear about it. Please\n"
+ " let me know, and, ideally, save a copy of the file causing the\n"
+ " problem -- without which I will be unable to investigate it.\n"
+ "\n"
+ );
+ }
+
+ exit(3);
+}
+#endif
+
+
+/*---------------------------------------------------*/
+static
+int bz_config_ok ( void )
+{
+ if (sizeof(int) != 4) return 0;
+ if (sizeof(short) != 2) return 0;
+ if (sizeof(char) != 1) return 0;
+ return 1;
+}
+
+
+/*---------------------------------------------------*/
+static
+void* default_bzalloc ( void* opaque, Int32 items, Int32 size )
+{
+ void* v = malloc ( items * size );
+ return v;
+}
+
+static
+void default_bzfree ( void* opaque, void* addr )
+{
+ if (addr != NULL) free ( addr );
+}
+
+
+/*---------------------------------------------------*/
+static
+void prepare_new_block ( EState* s )
+{
+ Int32 i;
+ s->nblock = 0;
+ s->numZ = 0;
+ s->state_out_pos = 0;
+ BZ_INITIALISE_CRC ( s->blockCRC );
+ for (i = 0; i < 256; i++) s->inUse[i] = False;
+ s->blockNo++;
+}
+
+
+/*---------------------------------------------------*/
+static
+void init_RL ( EState* s )
+{
+ s->state_in_ch = 256;
+ s->state_in_len = 0;
+}
+
+
+static
+Bool isempty_RL ( EState* s )
+{
+ if (s->state_in_ch < 256 && s->state_in_len > 0)
+ return False; else
+ return True;
+}
+
+
+/*---------------------------------------------------*/
+int BZ_API(BZ2_bzCompressInit)
+ ( bz_stream* strm,
+ int blockSize100k,
+ int verbosity,
+ int workFactor )
+{
+ Int32 n;
+ EState* s;
+
+ if (!bz_config_ok()) return BZ_CONFIG_ERROR;
+
+ if (strm == NULL ||
+ blockSize100k < 1 || blockSize100k > 9 ||
+ workFactor < 0 || workFactor > 250)
+ return BZ_PARAM_ERROR;
+
+ if (workFactor == 0) workFactor = 30;
+ if (strm->bzalloc == NULL) strm->bzalloc = default_bzalloc;
+ if (strm->bzfree == NULL) strm->bzfree = default_bzfree;
+
+ s = BZALLOC( sizeof(EState) );
+ if (s == NULL) return BZ_MEM_ERROR;
+ s->strm = strm;
+
+ s->arr1 = NULL;
+ s->arr2 = NULL;
+ s->ftab = NULL;
+
+ n = 100000 * blockSize100k;
+ s->arr1 = BZALLOC( n * sizeof(UInt32) );
+ s->arr2 = BZALLOC( (n+BZ_N_OVERSHOOT) * sizeof(UInt32) );
+ s->ftab = BZALLOC( 65537 * sizeof(UInt32) );
+
+ if (s->arr1 == NULL || s->arr2 == NULL || s->ftab == NULL) {
+ if (s->arr1 != NULL) BZFREE(s->arr1);
+ if (s->arr2 != NULL) BZFREE(s->arr2);
+ if (s->ftab != NULL) BZFREE(s->ftab);
+ if (s != NULL) BZFREE(s);
+ return BZ_MEM_ERROR;
+ }
+
+ s->blockNo = 0;
+ s->state = BZ_S_INPUT;
+ s->mode = BZ_M_RUNNING;
+ s->combinedCRC = 0;
+ s->blockSize100k = blockSize100k;
+ s->nblockMAX = 100000 * blockSize100k - 19;
+ s->verbosity = verbosity;
+ s->workFactor = workFactor;
+
+ s->block = (UChar*)s->arr2;
+ s->mtfv = (UInt16*)s->arr1;
+ s->zbits = NULL;
+ s->ptr = (UInt32*)s->arr1;
+
+ strm->state = s;
+ strm->total_in_lo32 = 0;
+ strm->total_in_hi32 = 0;
+ strm->total_out_lo32 = 0;
+ strm->total_out_hi32 = 0;
+ init_RL ( s );
+ prepare_new_block ( s );
+ return BZ_OK;
+}
+
+
+/*---------------------------------------------------*/
+static
+void add_pair_to_block ( EState* s )
+{
+ Int32 i;
+ UChar ch = (UChar)(s->state_in_ch);
+ for (i = 0; i < s->state_in_len; i++) {
+ BZ_UPDATE_CRC( s->blockCRC, ch );
+ }
+ s->inUse[s->state_in_ch] = True;
+ switch (s->state_in_len) {
+ case 1:
+ s->block[s->nblock] = (UChar)ch; s->nblock++;
+ break;
+ case 2:
+ s->block[s->nblock] = (UChar)ch; s->nblock++;
+ s->block[s->nblock] = (UChar)ch; s->nblock++;
+ break;
+ case 3:
+ s->block[s->nblock] = (UChar)ch; s->nblock++;
+ s->block[s->nblock] = (UChar)ch; s->nblock++;
+ s->block[s->nblock] = (UChar)ch; s->nblock++;
+ break;
+ default:
+ s->inUse[s->state_in_len-4] = True;
+ s->block[s->nblock] = (UChar)ch; s->nblock++;
+ s->block[s->nblock] = (UChar)ch; s->nblock++;
+ s->block[s->nblock] = (UChar)ch; s->nblock++;
+ s->block[s->nblock] = (UChar)ch; s->nblock++;
+ s->block[s->nblock] = ((UChar)(s->state_in_len-4));
+ s->nblock++;
+ break;
+ }
+}
+
+
+/*---------------------------------------------------*/
+static
+void flush_RL ( EState* s )
+{
+ if (s->state_in_ch < 256) add_pair_to_block ( s );
+ init_RL ( s );
+}
+
+
+/*---------------------------------------------------*/
+#define ADD_CHAR_TO_BLOCK(zs,zchh0) \
+{ \
+ UInt32 zchh = (UInt32)(zchh0); \
+ /*-- fast track the common case --*/ \
+ if (zchh != zs->state_in_ch && \
+ zs->state_in_len == 1) { \
+ UChar ch = (UChar)(zs->state_in_ch); \
+ BZ_UPDATE_CRC( zs->blockCRC, ch ); \
+ zs->inUse[zs->state_in_ch] = True; \
+ zs->block[zs->nblock] = (UChar)ch; \
+ zs->nblock++; \
+ zs->state_in_ch = zchh; \
+ } \
+ else \
+ /*-- general, uncommon cases --*/ \
+ if (zchh != zs->state_in_ch || \
+ zs->state_in_len == 255) { \
+ if (zs->state_in_ch < 256) \
+ add_pair_to_block ( zs ); \
+ zs->state_in_ch = zchh; \
+ zs->state_in_len = 1; \
+ } else { \
+ zs->state_in_len++; \
+ } \
+}
+
+
+/*---------------------------------------------------*/
+static
+Bool copy_input_until_stop ( EState* s )
+{
+ Bool progress_in = False;
+
+ if (s->mode == BZ_M_RUNNING) {
+
+ /*-- fast track the common case --*/
+ while (True) {
+ /*-- block full? --*/
+ if (s->nblock >= s->nblockMAX) break;
+ /*-- no input? --*/
+ if (s->strm->avail_in == 0) break;
+ progress_in = True;
+ ADD_CHAR_TO_BLOCK ( s, (UInt32)(*((UChar*)(s->strm->next_in))) );
+ s->strm->next_in++;
+ s->strm->avail_in--;
+ s->strm->total_in_lo32++;
+ if (s->strm->total_in_lo32 == 0) s->strm->total_in_hi32++;
+ }
+
+ } else {
+
+ /*-- general, uncommon case --*/
+ while (True) {
+ /*-- block full? --*/
+ if (s->nblock >= s->nblockMAX) break;
+ /*-- no input? --*/
+ if (s->strm->avail_in == 0) break;
+ /*-- flush/finish end? --*/
+ if (s->avail_in_expect == 0) break;
+ progress_in = True;
+ ADD_CHAR_TO_BLOCK ( s, (UInt32)(*((UChar*)(s->strm->next_in))) );
+ s->strm->next_in++;
+ s->strm->avail_in--;
+ s->strm->total_in_lo32++;
+ if (s->strm->total_in_lo32 == 0) s->strm->total_in_hi32++;
+ s->avail_in_expect--;
+ }
+ }
+ return progress_in;
+}
+
+
+/*---------------------------------------------------*/
+static
+Bool copy_output_until_stop ( EState* s )
+{
+ Bool progress_out = False;
+
+ while (True) {
+
+ /*-- no output space? --*/
+ if (s->strm->avail_out == 0) break;
+
+ /*-- block done? --*/
+ if (s->state_out_pos >= s->numZ) break;
+
+ progress_out = True;
+ *(s->strm->next_out) = s->zbits[s->state_out_pos];
+ s->state_out_pos++;
+ s->strm->avail_out--;
+ s->strm->next_out++;
+ s->strm->total_out_lo32++;
+ if (s->strm->total_out_lo32 == 0) s->strm->total_out_hi32++;
+ }
+
+ return progress_out;
+}
+
+
+/*---------------------------------------------------*/
+static
+Bool handle_compress ( bz_stream* strm )
+{
+ Bool progress_in = False;
+ Bool progress_out = False;
+ EState* s = strm->state;
+
+ while (True) {
+
+ if (s->state == BZ_S_OUTPUT) {
+ progress_out |= copy_output_until_stop ( s );
+ if (s->state_out_pos < s->numZ) break;
+ if (s->mode == BZ_M_FINISHING &&
+ s->avail_in_expect == 0 &&
+ isempty_RL(s)) break;
+ prepare_new_block ( s );
+ s->state = BZ_S_INPUT;
+ if (s->mode == BZ_M_FLUSHING &&
+ s->avail_in_expect == 0 &&
+ isempty_RL(s)) break;
+ }
+
+ if (s->state == BZ_S_INPUT) {
+ progress_in |= copy_input_until_stop ( s );
+ if (s->mode != BZ_M_RUNNING && s->avail_in_expect == 0) {
+ flush_RL ( s );
+ BZ2_compressBlock ( s, (Bool)(s->mode == BZ_M_FINISHING) );
+ s->state = BZ_S_OUTPUT;
+ }
+ else
+ if (s->nblock >= s->nblockMAX) {
+ BZ2_compressBlock ( s, False );
+ s->state = BZ_S_OUTPUT;
+ }
+ else
+ if (s->strm->avail_in == 0) {
+ break;
+ }
+ }
+
+ }
+
+ return progress_in || progress_out;
+}
+
+
+/*---------------------------------------------------*/
+int BZ_API(BZ2_bzCompress) ( bz_stream *strm, int action )
+{
+ Bool progress;
+ EState* s;
+ if (strm == NULL) return BZ_PARAM_ERROR;
+ s = strm->state;
+ if (s == NULL) return BZ_PARAM_ERROR;
+ if (s->strm != strm) return BZ_PARAM_ERROR;
+
+ preswitch:
+ switch (s->mode) {
+
+ case BZ_M_IDLE:
+ return BZ_SEQUENCE_ERROR;
+
+ case BZ_M_RUNNING:
+ if (action == BZ_RUN) {
+ progress = handle_compress ( strm );
+ return progress ? BZ_RUN_OK : BZ_PARAM_ERROR;
+ }
+ else
+ if (action == BZ_FLUSH) {
+ s->avail_in_expect = strm->avail_in;
+ s->mode = BZ_M_FLUSHING;
+ goto preswitch;
+ }
+ else
+ if (action == BZ_FINISH) {
+ s->avail_in_expect = strm->avail_in;
+ s->mode = BZ_M_FINISHING;
+ goto preswitch;
+ }
+ else
+ return BZ_PARAM_ERROR;
+
+ case BZ_M_FLUSHING:
+ if (action != BZ_FLUSH) return BZ_SEQUENCE_ERROR;
+ if (s->avail_in_expect != s->strm->avail_in)
+ return BZ_SEQUENCE_ERROR;
+ progress = handle_compress ( strm );
+ if (s->avail_in_expect > 0 || !isempty_RL(s) ||
+ s->state_out_pos < s->numZ) return BZ_FLUSH_OK;
+ s->mode = BZ_M_RUNNING;
+ return BZ_RUN_OK;
+
+ case BZ_M_FINISHING:
+ if (action != BZ_FINISH) return BZ_SEQUENCE_ERROR;
+ if (s->avail_in_expect != s->strm->avail_in)
+ return BZ_SEQUENCE_ERROR;
+ progress = handle_compress ( strm );
+ if (!progress) return BZ_SEQUENCE_ERROR;
+ if (s->avail_in_expect > 0 || !isempty_RL(s) ||
+ s->state_out_pos < s->numZ) return BZ_FINISH_OK;
+ s->mode = BZ_M_IDLE;
+ return BZ_STREAM_END;
+ }
+ return BZ_OK; /*--not reached--*/
+}
+
+
+/*---------------------------------------------------*/
+int BZ_API(BZ2_bzCompressEnd) ( bz_stream *strm )
+{
+ EState* s;
+ if (strm == NULL) return BZ_PARAM_ERROR;
+ s = strm->state;
+ if (s == NULL) return BZ_PARAM_ERROR;
+ if (s->strm != strm) return BZ_PARAM_ERROR;
+
+ if (s->arr1 != NULL) BZFREE(s->arr1);
+ if (s->arr2 != NULL) BZFREE(s->arr2);
+ if (s->ftab != NULL) BZFREE(s->ftab);
+ BZFREE(strm->state);
+
+ strm->state = NULL;
+
+ return BZ_OK;
+}
+
+
+/*---------------------------------------------------*/
+/*--- Decompression stuff ---*/
+/*---------------------------------------------------*/
+
+/*---------------------------------------------------*/
+int BZ_API(BZ2_bzDecompressInit)
+ ( bz_stream* strm,
+ int verbosity,
+ int small )
+{
+ DState* s;
+
+ if (!bz_config_ok()) return BZ_CONFIG_ERROR;
+
+ if (strm == NULL) return BZ_PARAM_ERROR;
+ if (small != 0 && small != 1) return BZ_PARAM_ERROR;
+ if (verbosity < 0 || verbosity > 4) return BZ_PARAM_ERROR;
+
+ if (strm->bzalloc == NULL) strm->bzalloc = default_bzalloc;
+ if (strm->bzfree == NULL) strm->bzfree = default_bzfree;
+
+ s = BZALLOC( sizeof(DState) );
+ if (s == NULL) return BZ_MEM_ERROR;
+ s->strm = strm;
+ strm->state = s;
+ s->state = BZ_X_MAGIC_1;
+ s->bsLive = 0;
+ s->bsBuff = 0;
+ s->calculatedCombinedCRC = 0;
+ strm->total_in_lo32 = 0;
+ strm->total_in_hi32 = 0;
+ strm->total_out_lo32 = 0;
+ strm->total_out_hi32 = 0;
+ s->smallDecompress = (Bool)small;
+ s->ll4 = NULL;
+ s->ll16 = NULL;
+ s->tt = NULL;
+ s->currBlockNo = 0;
+ s->verbosity = verbosity;
+
+ return BZ_OK;
+}
+
+
+/*---------------------------------------------------*/
+/* Return True iff data corruption is discovered.
+ Returns False if there is no problem.
+*/
+static
+Bool unRLE_obuf_to_output_FAST ( DState* s )
+{
+ UChar k1;
+
+ if (s->blockRandomised) {
+
+ while (True) {
+ /* try to finish existing run */
+ while (True) {
+ if (s->strm->avail_out == 0) return False;
+ if (s->state_out_len == 0) break;
+ *( (UChar*)(s->strm->next_out) ) = s->state_out_ch;
+ BZ_UPDATE_CRC ( s->calculatedBlockCRC, s->state_out_ch );
+ s->state_out_len--;
+ s->strm->next_out++;
+ s->strm->avail_out--;
+ s->strm->total_out_lo32++;
+ if (s->strm->total_out_lo32 == 0) s->strm->total_out_hi32++;
+ }
+
+ /* can a new run be started? */
+ if (s->nblock_used == s->save_nblock+1) return False;
+
+ /* Only caused by corrupt data stream? */
+ if (s->nblock_used > s->save_nblock+1)
+ return True;
+
+ s->state_out_len = 1;
+ s->state_out_ch = s->k0;
+ BZ_GET_FAST(k1); BZ_RAND_UPD_MASK;
+ k1 ^= BZ_RAND_MASK; s->nblock_used++;
+ if (s->nblock_used == s->save_nblock+1) continue;
+ if (k1 != s->k0) { s->k0 = k1; continue; };
+
+ s->state_out_len = 2;
+ BZ_GET_FAST(k1); BZ_RAND_UPD_MASK;
+ k1 ^= BZ_RAND_MASK; s->nblock_used++;
+ if (s->nblock_used == s->save_nblock+1) continue;
+ if (k1 != s->k0) { s->k0 = k1; continue; };
+
+ s->state_out_len = 3;
+ BZ_GET_FAST(k1); BZ_RAND_UPD_MASK;
+ k1 ^= BZ_RAND_MASK; s->nblock_used++;
+ if (s->nblock_used == s->save_nblock+1) continue;
+ if (k1 != s->k0) { s->k0 = k1; continue; };
+
+ BZ_GET_FAST(k1); BZ_RAND_UPD_MASK;
+ k1 ^= BZ_RAND_MASK; s->nblock_used++;
+ s->state_out_len = ((Int32)k1) + 4;
+ BZ_GET_FAST(s->k0); BZ_RAND_UPD_MASK;
+ s->k0 ^= BZ_RAND_MASK; s->nblock_used++;
+ }
+
+ } else {
+
+ /* restore */
+ UInt32 c_calculatedBlockCRC = s->calculatedBlockCRC;
+ UChar c_state_out_ch = s->state_out_ch;
+ Int32 c_state_out_len = s->state_out_len;
+ Int32 c_nblock_used = s->nblock_used;
+ Int32 c_k0 = s->k0;
+ UInt32* c_tt = s->tt;
+ UInt32 c_tPos = s->tPos;
+ char* cs_next_out = s->strm->next_out;
+ unsigned int cs_avail_out = s->strm->avail_out;
+ Int32 ro_blockSize100k = s->blockSize100k;
+ /* end restore */
+
+ UInt32 avail_out_INIT = cs_avail_out;
+ Int32 s_save_nblockPP = s->save_nblock+1;
+ unsigned int total_out_lo32_old;
+
+ while (True) {
+
+ /* try to finish existing run */
+ if (c_state_out_len > 0) {
+ while (True) {
+ if (cs_avail_out == 0) goto return_notr;
+ if (c_state_out_len == 1) break;
+ *( (UChar*)(cs_next_out) ) = c_state_out_ch;
+ BZ_UPDATE_CRC ( c_calculatedBlockCRC, c_state_out_ch );
+ c_state_out_len--;
+ cs_next_out++;
+ cs_avail_out--;
+ }
+ s_state_out_len_eq_one:
+ {
+ if (cs_avail_out == 0) {
+ c_state_out_len = 1; goto return_notr;
+ };
+ *( (UChar*)(cs_next_out) ) = c_state_out_ch;
+ BZ_UPDATE_CRC ( c_calculatedBlockCRC, c_state_out_ch );
+ cs_next_out++;
+ cs_avail_out--;
+ }
+ }
+ /* Only caused by corrupt data stream? */
+ if (c_nblock_used > s_save_nblockPP)
+ return True;
+
+ /* can a new run be started? */
+ if (c_nblock_used == s_save_nblockPP) {
+ c_state_out_len = 0; goto return_notr;
+ };
+ c_state_out_ch = c_k0;
+ BZ_GET_FAST_C(k1); c_nblock_used++;
+ if (k1 != c_k0) {
+ c_k0 = k1; goto s_state_out_len_eq_one;
+ };
+ if (c_nblock_used == s_save_nblockPP)
+ goto s_state_out_len_eq_one;
+
+ c_state_out_len = 2;
+ BZ_GET_FAST_C(k1); c_nblock_used++;
+ if (c_nblock_used == s_save_nblockPP) continue;
+ if (k1 != c_k0) { c_k0 = k1; continue; };
+
+ c_state_out_len = 3;
+ BZ_GET_FAST_C(k1); c_nblock_used++;
+ if (c_nblock_used == s_save_nblockPP) continue;
+ if (k1 != c_k0) { c_k0 = k1; continue; };
+
+ BZ_GET_FAST_C(k1); c_nblock_used++;
+ c_state_out_len = ((Int32)k1) + 4;
+ BZ_GET_FAST_C(c_k0); c_nblock_used++;
+ }
+
+ return_notr:
+ total_out_lo32_old = s->strm->total_out_lo32;
+ s->strm->total_out_lo32 += (avail_out_INIT - cs_avail_out);
+ if (s->strm->total_out_lo32 < total_out_lo32_old)
+ s->strm->total_out_hi32++;
+
+ /* save */
+ s->calculatedBlockCRC = c_calculatedBlockCRC;
+ s->state_out_ch = c_state_out_ch;
+ s->state_out_len = c_state_out_len;
+ s->nblock_used = c_nblock_used;
+ s->k0 = c_k0;
+ s->tt = c_tt;
+ s->tPos = c_tPos;
+ s->strm->next_out = cs_next_out;
+ s->strm->avail_out = cs_avail_out;
+ /* end save */
+ }
+ return False;
+}
+
+
+
+/*---------------------------------------------------*/
+__inline__ Int32 BZ2_indexIntoF ( Int32 indx, Int32 *cftab )
+{
+ Int32 nb, na, mid;
+ nb = 0;
+ na = 256;
+ do {
+ mid = (nb + na) >> 1;
+ if (indx >= cftab[mid]) nb = mid; else na = mid;
+ }
+ while (na - nb != 1);
+ return nb;
+}
+
+
+/*---------------------------------------------------*/
+/* Return True iff data corruption is discovered.
+ Returns False if there is no problem.
+*/
+static
+Bool unRLE_obuf_to_output_SMALL ( DState* s )
+{
+ UChar k1;
+
+ if (s->blockRandomised) {
+
+ while (True) {
+ /* try to finish existing run */
+ while (True) {
+ if (s->strm->avail_out == 0) return False;
+ if (s->state_out_len == 0) break;
+ *( (UChar*)(s->strm->next_out) ) = s->state_out_ch;
+ BZ_UPDATE_CRC ( s->calculatedBlockCRC, s->state_out_ch );
+ s->state_out_len--;
+ s->strm->next_out++;
+ s->strm->avail_out--;
+ s->strm->total_out_lo32++;
+ if (s->strm->total_out_lo32 == 0) s->strm->total_out_hi32++;
+ }
+
+ /* can a new run be started? */
+ if (s->nblock_used == s->save_nblock+1) return False;
+
+ /* Only caused by corrupt data stream? */
+ if (s->nblock_used > s->save_nblock+1)
+ return True;
+
+ s->state_out_len = 1;
+ s->state_out_ch = s->k0;
+ BZ_GET_SMALL(k1); BZ_RAND_UPD_MASK;
+ k1 ^= BZ_RAND_MASK; s->nblock_used++;
+ if (s->nblock_used == s->save_nblock+1) continue;
+ if (k1 != s->k0) { s->k0 = k1; continue; };
+
+ s->state_out_len = 2;
+ BZ_GET_SMALL(k1); BZ_RAND_UPD_MASK;
+ k1 ^= BZ_RAND_MASK; s->nblock_used++;
+ if (s->nblock_used == s->save_nblock+1) continue;
+ if (k1 != s->k0) { s->k0 = k1; continue; };
+
+ s->state_out_len = 3;
+ BZ_GET_SMALL(k1); BZ_RAND_UPD_MASK;
+ k1 ^= BZ_RAND_MASK; s->nblock_used++;
+ if (s->nblock_used == s->save_nblock+1) continue;
+ if (k1 != s->k0) { s->k0 = k1; continue; };
+
+ BZ_GET_SMALL(k1); BZ_RAND_UPD_MASK;
+ k1 ^= BZ_RAND_MASK; s->nblock_used++;
+ s->state_out_len = ((Int32)k1) + 4;
+ BZ_GET_SMALL(s->k0); BZ_RAND_UPD_MASK;
+ s->k0 ^= BZ_RAND_MASK; s->nblock_used++;
+ }
+
+ } else {
+
+ while (True) {
+ /* try to finish existing run */
+ while (True) {
+ if (s->strm->avail_out == 0) return False;
+ if (s->state_out_len == 0) break;
+ *( (UChar*)(s->strm->next_out) ) = s->state_out_ch;
+ BZ_UPDATE_CRC ( s->calculatedBlockCRC, s->state_out_ch );
+ s->state_out_len--;
+ s->strm->next_out++;
+ s->strm->avail_out--;
+ s->strm->total_out_lo32++;
+ if (s->strm->total_out_lo32 == 0) s->strm->total_out_hi32++;
+ }
+
+ /* can a new run be started? */
+ if (s->nblock_used == s->save_nblock+1) return False;
+
+ /* Only caused by corrupt data stream? */
+ if (s->nblock_used > s->save_nblock+1)
+ return True;
+
+ s->state_out_len = 1;
+ s->state_out_ch = s->k0;
+ BZ_GET_SMALL(k1); s->nblock_used++;
+ if (s->nblock_used == s->save_nblock+1) continue;
+ if (k1 != s->k0) { s->k0 = k1; continue; };
+
+ s->state_out_len = 2;
+ BZ_GET_SMALL(k1); s->nblock_used++;
+ if (s->nblock_used == s->save_nblock+1) continue;
+ if (k1 != s->k0) { s->k0 = k1; continue; };
+
+ s->state_out_len = 3;
+ BZ_GET_SMALL(k1); s->nblock_used++;
+ if (s->nblock_used == s->save_nblock+1) continue;
+ if (k1 != s->k0) { s->k0 = k1; continue; };
+
+ BZ_GET_SMALL(k1); s->nblock_used++;
+ s->state_out_len = ((Int32)k1) + 4;
+ BZ_GET_SMALL(s->k0); s->nblock_used++;
+ }
+
+ }
+}
+
+
+/*---------------------------------------------------*/
+int BZ_API(BZ2_bzDecompress) ( bz_stream *strm )
+{
+ Bool corrupt;
+ DState* s;
+ if (strm == NULL) return BZ_PARAM_ERROR;
+ s = strm->state;
+ if (s == NULL) return BZ_PARAM_ERROR;
+ if (s->strm != strm) return BZ_PARAM_ERROR;
+
+ while (True) {
+ if (s->state == BZ_X_IDLE) return BZ_SEQUENCE_ERROR;
+ if (s->state == BZ_X_OUTPUT) {
+ if (s->smallDecompress)
+ corrupt = unRLE_obuf_to_output_SMALL ( s ); else
+ corrupt = unRLE_obuf_to_output_FAST ( s );
+ if (corrupt) return BZ_DATA_ERROR;
+ if (s->nblock_used == s->save_nblock+1 && s->state_out_len == 0) {
+ BZ_FINALISE_CRC ( s->calculatedBlockCRC );
+ if (s->verbosity >= 3)
+ VPrintf2 ( " {0x%08x, 0x%08x}", s->storedBlockCRC,
+ s->calculatedBlockCRC );
+ if (s->verbosity >= 2) VPrintf0 ( "]" );
+ if (s->calculatedBlockCRC != s->storedBlockCRC)
+ return BZ_DATA_ERROR;
+ s->calculatedCombinedCRC
+ = (s->calculatedCombinedCRC << 1) |
+ (s->calculatedCombinedCRC >> 31);
+ s->calculatedCombinedCRC ^= s->calculatedBlockCRC;
+ s->state = BZ_X_BLKHDR_1;
+ } else {
+ return BZ_OK;
+ }
+ }
+ if (s->state >= BZ_X_MAGIC_1) {
+ Int32 r = BZ2_decompress ( s );
+ if (r == BZ_STREAM_END) {
+ if (s->verbosity >= 3)
+ VPrintf2 ( "\n combined CRCs: stored = 0x%08x, computed = 0x%08x",
+ s->storedCombinedCRC, s->calculatedCombinedCRC );
+ if (s->calculatedCombinedCRC != s->storedCombinedCRC)
+ return BZ_DATA_ERROR;
+ return r;
+ }
+ if (s->state != BZ_X_OUTPUT) return r;
+ }
+ }
+
+ AssertH ( 0, 6001 );
+
+ return 0; /*NOTREACHED*/
+}
+
+
+/*---------------------------------------------------*/
+int BZ_API(BZ2_bzDecompressEnd) ( bz_stream *strm )
+{
+ DState* s;
+ if (strm == NULL) return BZ_PARAM_ERROR;
+ s = strm->state;
+ if (s == NULL) return BZ_PARAM_ERROR;
+ if (s->strm != strm) return BZ_PARAM_ERROR;
+
+ if (s->tt != NULL) BZFREE(s->tt);
+ if (s->ll16 != NULL) BZFREE(s->ll16);
+ if (s->ll4 != NULL) BZFREE(s->ll4);
+
+ BZFREE(strm->state);
+ strm->state = NULL;
+
+ return BZ_OK;
+}
+
+
+#ifndef BZ_NO_STDIO
+/*---------------------------------------------------*/
+/*--- File I/O stuff ---*/
+/*---------------------------------------------------*/
+
+#define BZ_SETERR(eee) \
+{ \
+ if (bzerror != NULL) *bzerror = eee; \
+ if (bzf != NULL) bzf->lastErr = eee; \
+}
+
+typedef
+ struct {
+ FILE* handle;
+ Char buf[BZ_MAX_UNUSED];
+ Int32 bufN;
+ Bool writing;
+ bz_stream strm;
+ Int32 lastErr;
+ Bool initialisedOk;
+ }
+ bzFile;
+
+
+/*---------------------------------------------*/
+static Bool myfeof ( FILE* f )
+{
+ Int32 c = fgetc ( f );
+ if (c == EOF) return True;
+ ungetc ( c, f );
+ return False;
+}
+
+
+/*---------------------------------------------------*/
+BZFILE* BZ_API(BZ2_bzWriteOpen)
+ ( int* bzerror,
+ FILE* f,
+ int blockSize100k,
+ int verbosity,
+ int workFactor )
+{
+ Int32 ret;
+ bzFile* bzf = NULL;
+
+ BZ_SETERR(BZ_OK);
+
+ if (f == NULL ||
+ (blockSize100k < 1 || blockSize100k > 9) ||
+ (workFactor < 0 || workFactor > 250) ||
+ (verbosity < 0 || verbosity > 4))
+ { BZ_SETERR(BZ_PARAM_ERROR); return NULL; };
+
+ if (ferror(f))
+ { BZ_SETERR(BZ_IO_ERROR); return NULL; };
+
+ bzf = malloc ( sizeof(bzFile) );
+ if (bzf == NULL)
+ { BZ_SETERR(BZ_MEM_ERROR); return NULL; };
+
+ BZ_SETERR(BZ_OK);
+ bzf->initialisedOk = False;
+ bzf->bufN = 0;
+ bzf->handle = f;
+ bzf->writing = True;
+ bzf->strm.bzalloc = NULL;
+ bzf->strm.bzfree = NULL;
+ bzf->strm.opaque = NULL;
+
+ if (workFactor == 0) workFactor = 30;
+ ret = BZ2_bzCompressInit ( &(bzf->strm), blockSize100k,
+ verbosity, workFactor );
+ if (ret != BZ_OK)
+ { BZ_SETERR(ret); free(bzf); return NULL; };
+
+ bzf->strm.avail_in = 0;
+ bzf->initialisedOk = True;
+ return bzf;
+}
+
+
+
+/*---------------------------------------------------*/
+void BZ_API(BZ2_bzWrite)
+ ( int* bzerror,
+ BZFILE* b,
+ void* buf,
+ int len )
+{
+ Int32 n, n2, ret;
+ bzFile* bzf = (bzFile*)b;
+
+ BZ_SETERR(BZ_OK);
+ if (bzf == NULL || buf == NULL || len < 0)
+ { BZ_SETERR(BZ_PARAM_ERROR); return; };
+ if (!(bzf->writing))
+ { BZ_SETERR(BZ_SEQUENCE_ERROR); return; };
+ if (ferror(bzf->handle))
+ { BZ_SETERR(BZ_IO_ERROR); return; };
+
+ if (len == 0)
+ { BZ_SETERR(BZ_OK); return; };
+
+ bzf->strm.avail_in = len;
+ bzf->strm.next_in = buf;
+
+ while (True) {
+ bzf->strm.avail_out = BZ_MAX_UNUSED;
+ bzf->strm.next_out = bzf->buf;
+ ret = BZ2_bzCompress ( &(bzf->strm), BZ_RUN );
+ if (ret != BZ_RUN_OK)
+ { BZ_SETERR(ret); return; };
+
+ if (bzf->strm.avail_out < BZ_MAX_UNUSED) {
+ n = BZ_MAX_UNUSED - bzf->strm.avail_out;
+ n2 = fwrite ( (void*)(bzf->buf), sizeof(UChar),
+ n, bzf->handle );
+ if (n != n2 || ferror(bzf->handle))
+ { BZ_SETERR(BZ_IO_ERROR); return; };
+ }
+
+ if (bzf->strm.avail_in == 0)
+ { BZ_SETERR(BZ_OK); return; };
+ }
+}
+
+
+/*---------------------------------------------------*/
+void BZ_API(BZ2_bzWriteClose)
+ ( int* bzerror,
+ BZFILE* b,
+ int abandon,
+ unsigned int* nbytes_in,
+ unsigned int* nbytes_out )
+{
+ BZ2_bzWriteClose64 ( bzerror, b, abandon,
+ nbytes_in, NULL, nbytes_out, NULL );
+}
+
+
+void BZ_API(BZ2_bzWriteClose64)
+ ( int* bzerror,
+ BZFILE* b,
+ int abandon,
+ unsigned int* nbytes_in_lo32,
+ unsigned int* nbytes_in_hi32,
+ unsigned int* nbytes_out_lo32,
+ unsigned int* nbytes_out_hi32 )
+{
+ Int32 n, n2, ret;
+ bzFile* bzf = (bzFile*)b;
+
+ if (bzf == NULL)
+ { BZ_SETERR(BZ_OK); return; };
+ if (!(bzf->writing))
+ { BZ_SETERR(BZ_SEQUENCE_ERROR); return; };
+ if (ferror(bzf->handle))
+ { BZ_SETERR(BZ_IO_ERROR); return; };
+
+ if (nbytes_in_lo32 != NULL) *nbytes_in_lo32 = 0;
+ if (nbytes_in_hi32 != NULL) *nbytes_in_hi32 = 0;
+ if (nbytes_out_lo32 != NULL) *nbytes_out_lo32 = 0;
+ if (nbytes_out_hi32 != NULL) *nbytes_out_hi32 = 0;
+
+ if ((!abandon) && bzf->lastErr == BZ_OK) {
+ while (True) {
+ bzf->strm.avail_out = BZ_MAX_UNUSED;
+ bzf->strm.next_out = bzf->buf;
+ ret = BZ2_bzCompress ( &(bzf->strm), BZ_FINISH );
+ if (ret != BZ_FINISH_OK && ret != BZ_STREAM_END)
+ { BZ_SETERR(ret); return; };
+
+ if (bzf->strm.avail_out < BZ_MAX_UNUSED) {
+ n = BZ_MAX_UNUSED - bzf->strm.avail_out;
+ n2 = fwrite ( (void*)(bzf->buf), sizeof(UChar),
+ n, bzf->handle );
+ if (n != n2 || ferror(bzf->handle))
+ { BZ_SETERR(BZ_IO_ERROR); return; };
+ }
+
+ if (ret == BZ_STREAM_END) break;
+ }
+ }
+
+ if ( !abandon && !ferror ( bzf->handle ) ) {
+ fflush ( bzf->handle );
+ if (ferror(bzf->handle))
+ { BZ_SETERR(BZ_IO_ERROR); return; };
+ }
+
+ if (nbytes_in_lo32 != NULL)
+ *nbytes_in_lo32 = bzf->strm.total_in_lo32;
+ if (nbytes_in_hi32 != NULL)
+ *nbytes_in_hi32 = bzf->strm.total_in_hi32;
+ if (nbytes_out_lo32 != NULL)
+ *nbytes_out_lo32 = bzf->strm.total_out_lo32;
+ if (nbytes_out_hi32 != NULL)
+ *nbytes_out_hi32 = bzf->strm.total_out_hi32;
+
+ BZ_SETERR(BZ_OK);
+ BZ2_bzCompressEnd ( &(bzf->strm) );
+ free ( bzf );
+}
+
+
+/*---------------------------------------------------*/
+BZFILE* BZ_API(BZ2_bzReadOpen)
+ ( int* bzerror,
+ FILE* f,
+ int verbosity,
+ int small,
+ void* unused,
+ int nUnused )
+{
+ bzFile* bzf = NULL;
+ int ret;
+
+ BZ_SETERR(BZ_OK);
+
+ if (f == NULL ||
+ (small != 0 && small != 1) ||
+ (verbosity < 0 || verbosity > 4) ||
+ (unused == NULL && nUnused != 0) ||
+ (unused != NULL && (nUnused < 0 || nUnused > BZ_MAX_UNUSED)))
+ { BZ_SETERR(BZ_PARAM_ERROR); return NULL; };
+
+ if (ferror(f))
+ { BZ_SETERR(BZ_IO_ERROR); return NULL; };
+
+ bzf = malloc ( sizeof(bzFile) );
+ if (bzf == NULL)
+ { BZ_SETERR(BZ_MEM_ERROR); return NULL; };
+
+ BZ_SETERR(BZ_OK);
+
+ bzf->initialisedOk = False;
+ bzf->handle = f;
+ bzf->bufN = 0;
+ bzf->writing = False;
+ bzf->strm.bzalloc = NULL;
+ bzf->strm.bzfree = NULL;
+ bzf->strm.opaque = NULL;
+
+ while (nUnused > 0) {
+ bzf->buf[bzf->bufN] = *((UChar*)(unused)); bzf->bufN++;
+ unused = ((void*)( 1 + ((UChar*)(unused)) ));
+ nUnused--;
+ }
+
+ ret = BZ2_bzDecompressInit ( &(bzf->strm), verbosity, small );
+ if (ret != BZ_OK)
+ { BZ_SETERR(ret); free(bzf); return NULL; };
+
+ bzf->strm.avail_in = bzf->bufN;
+ bzf->strm.next_in = bzf->buf;
+
+ bzf->initialisedOk = True;
+ return bzf;
+}
+
+
+/*---------------------------------------------------*/
+void BZ_API(BZ2_bzReadClose) ( int *bzerror, BZFILE *b )
+{
+ bzFile* bzf = (bzFile*)b;
+
+ BZ_SETERR(BZ_OK);
+ if (bzf == NULL)
+ { BZ_SETERR(BZ_OK); return; };
+
+ if (bzf->writing)
+ { BZ_SETERR(BZ_SEQUENCE_ERROR); return; };
+
+ if (bzf->initialisedOk)
+ (void)BZ2_bzDecompressEnd ( &(bzf->strm) );
+ free ( bzf );
+}
+
+
+/*---------------------------------------------------*/
+int BZ_API(BZ2_bzRead)
+ ( int* bzerror,
+ BZFILE* b,
+ void* buf,
+ int len )
+{
+ Int32 n, ret;
+ bzFile* bzf = (bzFile*)b;
+
+ BZ_SETERR(BZ_OK);
+
+ if (bzf == NULL || buf == NULL || len < 0)
+ { BZ_SETERR(BZ_PARAM_ERROR); return 0; };
+
+ if (bzf->writing)
+ { BZ_SETERR(BZ_SEQUENCE_ERROR); return 0; };
+
+ if (len == 0)
+ { BZ_SETERR(BZ_OK); return 0; };
+
+ bzf->strm.avail_out = len;
+ bzf->strm.next_out = buf;
+
+ while (True) {
+
+ if (ferror(bzf->handle))
+ { BZ_SETERR(BZ_IO_ERROR); return 0; };
+
+ if (bzf->strm.avail_in == 0 && !myfeof(bzf->handle)) {
+ n = fread ( bzf->buf, sizeof(UChar),
+ BZ_MAX_UNUSED, bzf->handle );
+ if (ferror(bzf->handle))
+ { BZ_SETERR(BZ_IO_ERROR); return 0; };
+ bzf->bufN = n;
+ bzf->strm.avail_in = bzf->bufN;
+ bzf->strm.next_in = bzf->buf;
+ }
+
+ ret = BZ2_bzDecompress ( &(bzf->strm) );
+
+ if (ret != BZ_OK && ret != BZ_STREAM_END)
+ { BZ_SETERR(ret); return 0; };
+
+ if (ret == BZ_OK && myfeof(bzf->handle) &&
+ bzf->strm.avail_in == 0 && bzf->strm.avail_out > 0)
+ { BZ_SETERR(BZ_UNEXPECTED_EOF); return 0; };
+
+ if (ret == BZ_STREAM_END)
+ { BZ_SETERR(BZ_STREAM_END);
+ return len - bzf->strm.avail_out; };
+ if (bzf->strm.avail_out == 0)
+ { BZ_SETERR(BZ_OK); return len; };
+
+ }
+
+ return 0; /*not reached*/
+}
+
+
+/*---------------------------------------------------*/
+void BZ_API(BZ2_bzReadGetUnused)
+ ( int* bzerror,
+ BZFILE* b,
+ void** unused,
+ int* nUnused )
+{
+ bzFile* bzf = (bzFile*)b;
+ if (bzf == NULL)
+ { BZ_SETERR(BZ_PARAM_ERROR); return; };
+ if (bzf->lastErr != BZ_STREAM_END)
+ { BZ_SETERR(BZ_SEQUENCE_ERROR); return; };
+ if (unused == NULL || nUnused == NULL)
+ { BZ_SETERR(BZ_PARAM_ERROR); return; };
+
+ BZ_SETERR(BZ_OK);
+ *nUnused = bzf->strm.avail_in;
+ *unused = bzf->strm.next_in;
+}
+#endif
+
+
+/*---------------------------------------------------*/
+/*--- Misc convenience stuff ---*/
+/*---------------------------------------------------*/
+
+/*---------------------------------------------------*/
+int BZ_API(BZ2_bzBuffToBuffCompress)
+ ( char* dest,
+ unsigned int* destLen,
+ char* source,
+ unsigned int sourceLen,
+ int blockSize100k,
+ int verbosity,
+ int workFactor )
+{
+ bz_stream strm;
+ int ret;
+
+ if (dest == NULL || destLen == NULL ||
+ source == NULL ||
+ blockSize100k < 1 || blockSize100k > 9 ||
+ verbosity < 0 || verbosity > 4 ||
+ workFactor < 0 || workFactor > 250)
+ return BZ_PARAM_ERROR;
+
+ if (workFactor == 0) workFactor = 30;
+ strm.bzalloc = NULL;
+ strm.bzfree = NULL;
+ strm.opaque = NULL;
+ ret = BZ2_bzCompressInit ( &strm, blockSize100k,
+ verbosity, workFactor );
+ if (ret != BZ_OK) return ret;
+
+ strm.next_in = source;
+ strm.next_out = dest;
+ strm.avail_in = sourceLen;
+ strm.avail_out = *destLen;
+
+ ret = BZ2_bzCompress ( &strm, BZ_FINISH );
+ if (ret == BZ_FINISH_OK) goto output_overflow;
+ if (ret != BZ_STREAM_END) goto errhandler;
+
+ /* normal termination */
+ *destLen -= strm.avail_out;
+ BZ2_bzCompressEnd ( &strm );
+ return BZ_OK;
+
+ output_overflow:
+ BZ2_bzCompressEnd ( &strm );
+ return BZ_OUTBUFF_FULL;
+
+ errhandler:
+ BZ2_bzCompressEnd ( &strm );
+ return ret;
+}
+
+
+/*---------------------------------------------------*/
+int BZ_API(BZ2_bzBuffToBuffDecompress)
+ ( char* dest,
+ unsigned int* destLen,
+ char* source,
+ unsigned int sourceLen,
+ int small,
+ int verbosity )
+{
+ bz_stream strm;
+ int ret;
+
+ if (dest == NULL || destLen == NULL ||
+ source == NULL ||
+ (small != 0 && small != 1) ||
+ verbosity < 0 || verbosity > 4)
+ return BZ_PARAM_ERROR;
+
+ strm.bzalloc = NULL;
+ strm.bzfree = NULL;
+ strm.opaque = NULL;
+ ret = BZ2_bzDecompressInit ( &strm, verbosity, small );
+ if (ret != BZ_OK) return ret;
+
+ strm.next_in = source;
+ strm.next_out = dest;
+ strm.avail_in = sourceLen;
+ strm.avail_out = *destLen;
+
+ ret = BZ2_bzDecompress ( &strm );
+ if (ret == BZ_OK) goto output_overflow_or_eof;
+ if (ret != BZ_STREAM_END) goto errhandler;
+
+ /* normal termination */
+ *destLen -= strm.avail_out;
+ BZ2_bzDecompressEnd ( &strm );
+ return BZ_OK;
+
+ output_overflow_or_eof:
+ if (strm.avail_out > 0) {
+ BZ2_bzDecompressEnd ( &strm );
+ return BZ_UNEXPECTED_EOF;
+ } else {
+ BZ2_bzDecompressEnd ( &strm );
+ return BZ_OUTBUFF_FULL;
+ };
+
+ errhandler:
+ BZ2_bzDecompressEnd ( &strm );
+ return ret;
+}
+
+
+/*---------------------------------------------------*/
+/*--
+ Code contributed by Yoshioka Tsuneo (tsuneo at rr.iij4u.or.jp)
+ to support better zlib compatibility.
+ This code is not _officially_ part of libbzip2 (yet);
+ I haven't tested it, documented it, or considered the
+ threading-safeness of it.
+ If this code breaks, please contact both Yoshioka and me.
+--*/
+/*---------------------------------------------------*/
+
+/*---------------------------------------------------*/
+/*--
+ return version like "0.9.5d, 4-Sept-1999".
+--*/
+const char * BZ_API(BZ2_bzlibVersion)(void)
+{
+ return BZ_VERSION;
+}
+
+
+#ifndef BZ_NO_STDIO
+/*---------------------------------------------------*/
+
+#if defined(_WIN32) || defined(OS2) || defined(MSDOS)
+# include <fcntl.h>
+# include <io.h>
+# define SET_BINARY_MODE(file) setmode(fileno(file),O_BINARY)
+#else
+# define SET_BINARY_MODE(file)
+#endif
+static
+BZFILE * bzopen_or_bzdopen
+ ( const char *path, /* no use when bzdopen */
+ int fd, /* no use when bzdopen */
+ const char *mode,
+ int open_mode) /* bzopen: 0, bzdopen:1 */
+{
+ int bzerr;
+ char unused[BZ_MAX_UNUSED];
+ int blockSize100k = 9;
+ int writing = 0;
+ char mode2[10] = "";
+ FILE *fp = NULL;
+ BZFILE *bzfp = NULL;
+ int verbosity = 0;
+ int workFactor = 30;
+ int smallMode = 0;
+ int nUnused = 0;
+
+ if (mode == NULL) return NULL;
+ while (*mode) {
+ switch (*mode) {
+ case 'r':
+ writing = 0; break;
+ case 'w':
+ writing = 1; break;
+ case 's':
+ smallMode = 1; break;
+ default:
+ if (isdigit((int)(*mode))) {
+ blockSize100k = *mode-BZ_HDR_0;
+ }
+ }
+ mode++;
+ }
+ strcat(mode2, writing ? "w" : "r" );
+ strcat(mode2,"b"); /* binary mode */
+
+ if (open_mode==0) {
+ if (path==NULL || strcmp(path,"")==0) {
+ fp = (writing ? stdout : stdin);
+ SET_BINARY_MODE(fp);
+ } else {
+ fp = fopen(path,mode2);
+ }
+ } else {
+#ifdef BZ_STRICT_ANSI
+ fp = NULL;
+#else
+ fp = fdopen(fd,mode2);
+#endif
+ }
+ if (fp == NULL) return NULL;
+
+ if (writing) {
+ /* Guard against total chaos and anarchy -- JRS */
+ if (blockSize100k < 1) blockSize100k = 1;
+ if (blockSize100k > 9) blockSize100k = 9;
+ bzfp = BZ2_bzWriteOpen(&bzerr,fp,blockSize100k,
+ verbosity,workFactor);
+ } else {
+ bzfp = BZ2_bzReadOpen(&bzerr,fp,verbosity,smallMode,
+ unused,nUnused);
+ }
+ if (bzfp == NULL) {
+ if (fp != stdin && fp != stdout) fclose(fp);
+ return NULL;
+ }
+ return bzfp;
+}
+
+
+/*---------------------------------------------------*/
+/*--
+ open file for read or write.
+ ex) bzopen("file","w9")
+ case path="" or NULL => use stdin or stdout.
+--*/
+BZFILE * BZ_API(BZ2_bzopen)
+ ( const char *path,
+ const char *mode )
+{
+ return bzopen_or_bzdopen(path,-1,mode,/*bzopen*/0);
+}
+
+
+/*---------------------------------------------------*/
+BZFILE * BZ_API(BZ2_bzdopen)
+ ( int fd,
+ const char *mode )
+{
+ return bzopen_or_bzdopen(NULL,fd,mode,/*bzdopen*/1);
+}
+
+
+/*---------------------------------------------------*/
+int BZ_API(BZ2_bzread) (BZFILE* b, void* buf, int len )
+{
+ int bzerr, nread;
+ if (((bzFile*)b)->lastErr == BZ_STREAM_END) return 0;
+ nread = BZ2_bzRead(&bzerr,b,buf,len);
+ if (bzerr == BZ_OK || bzerr == BZ_STREAM_END) {
+ return nread;
+ } else {
+ return -1;
+ }
+}
+
+
+/*---------------------------------------------------*/
+int BZ_API(BZ2_bzwrite) (BZFILE* b, void* buf, int len )
+{
+ int bzerr;
+
+ BZ2_bzWrite(&bzerr,b,buf,len);
+ if(bzerr == BZ_OK){
+ return len;
+ }else{
+ return -1;
+ }
+}
+
+
+/*---------------------------------------------------*/
+int BZ_API(BZ2_bzflush) (BZFILE *b)
+{
+ /* do nothing now... */
+ return 0;
+}
+
+
+/*---------------------------------------------------*/
+void BZ_API(BZ2_bzclose) (BZFILE* b)
+{
+ int bzerr;
+ FILE *fp;
+
+ if (b==NULL) {return;}
+ fp = ((bzFile *)b)->handle;
+ if(((bzFile*)b)->writing){
+ BZ2_bzWriteClose(&bzerr,b,0,NULL,NULL);
+ if(bzerr != BZ_OK){
+ BZ2_bzWriteClose(NULL,b,1,NULL,NULL);
+ }
+ }else{
+ BZ2_bzReadClose(&bzerr,b);
+ }
+ if(fp!=stdin && fp!=stdout){
+ fclose(fp);
+ }
+}
+
+
+/*---------------------------------------------------*/
+/*--
+ return last error code
+--*/
+static const char *bzerrorstrings[] = {
+ "OK"
+ ,"SEQUENCE_ERROR"
+ ,"PARAM_ERROR"
+ ,"MEM_ERROR"
+ ,"DATA_ERROR"
+ ,"DATA_ERROR_MAGIC"
+ ,"IO_ERROR"
+ ,"UNEXPECTED_EOF"
+ ,"OUTBUFF_FULL"
+ ,"CONFIG_ERROR"
+ ,"???" /* for future */
+ ,"???" /* for future */
+ ,"???" /* for future */
+ ,"???" /* for future */
+ ,"???" /* for future */
+ ,"???" /* for future */
+};
+
+
+const char * BZ_API(BZ2_bzerror) (BZFILE *b, int *errnum)
+{
+ int err = ((bzFile *)b)->lastErr;
+
+ if(err>0) err = 0;
+ *errnum = err;
+ return bzerrorstrings[err*-1];
+}
+#endif
+
+
+/*-------------------------------------------------------------*/
+/*--- end bzlib.c ---*/
+/*-------------------------------------------------------------*/
diff --git a/third-party/bzip2/bzlib.h b/third-party/bzip2/bzlib.h
new file mode 100644
index 0000000..8277123
--- /dev/null
+++ b/third-party/bzip2/bzlib.h
@@ -0,0 +1,282 @@
+
+/*-------------------------------------------------------------*/
+/*--- Public header file for the library. ---*/
+/*--- bzlib.h ---*/
+/*-------------------------------------------------------------*/
+
+/* ------------------------------------------------------------------
+ This file is part of bzip2/libbzip2, a program and library for
+ lossless, block-sorting data compression.
+
+ bzip2/libbzip2 version 1.0.6 of 6 September 2010
+ Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
+
+ Please read the WARNING, DISCLAIMER and PATENTS sections in the
+ README file.
+
+ This program is released under the terms of the license contained
+ in the file LICENSE.
+ ------------------------------------------------------------------ */
+
+
+#ifndef _BZLIB_H
+#define _BZLIB_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#define BZ_RUN 0
+#define BZ_FLUSH 1
+#define BZ_FINISH 2
+
+#define BZ_OK 0
+#define BZ_RUN_OK 1
+#define BZ_FLUSH_OK 2
+#define BZ_FINISH_OK 3
+#define BZ_STREAM_END 4
+#define BZ_SEQUENCE_ERROR (-1)
+#define BZ_PARAM_ERROR (-2)
+#define BZ_MEM_ERROR (-3)
+#define BZ_DATA_ERROR (-4)
+#define BZ_DATA_ERROR_MAGIC (-5)
+#define BZ_IO_ERROR (-6)
+#define BZ_UNEXPECTED_EOF (-7)
+#define BZ_OUTBUFF_FULL (-8)
+#define BZ_CONFIG_ERROR (-9)
+
+typedef
+ struct {
+ char *next_in;
+ unsigned int avail_in;
+ unsigned int total_in_lo32;
+ unsigned int total_in_hi32;
+
+ char *next_out;
+ unsigned int avail_out;
+ unsigned int total_out_lo32;
+ unsigned int total_out_hi32;
+
+ void *state;
+
+ void *(*bzalloc)(void *,int,int);
+ void (*bzfree)(void *,void *);
+ void *opaque;
+ }
+ bz_stream;
+
+
+#ifndef BZ_IMPORT
+#define BZ_EXPORT
+#endif
+
+#ifndef BZ_NO_STDIO
+/* Need a definitition for FILE */
+#include <stdio.h>
+#endif
+
+#ifdef _WIN32
+# include <windows.h>
+# ifdef small
+ /* windows.h define small to char */
+# undef small
+# endif
+# ifdef BZ_EXPORT
+# define BZ_API(func) WINAPI func
+# define BZ_EXTERN extern
+# else
+ /* import windows dll dynamically */
+# define BZ_API(func) (WINAPI * func)
+# define BZ_EXTERN
+# endif
+#else
+# define BZ_API(func) func
+# define BZ_EXTERN extern
+#endif
+
+
+/*-- Core (low-level) library functions --*/
+
+BZ_EXTERN int BZ_API(BZ2_bzCompressInit) (
+ bz_stream* strm,
+ int blockSize100k,
+ int verbosity,
+ int workFactor
+ );
+
+BZ_EXTERN int BZ_API(BZ2_bzCompress) (
+ bz_stream* strm,
+ int action
+ );
+
+BZ_EXTERN int BZ_API(BZ2_bzCompressEnd) (
+ bz_stream* strm
+ );
+
+BZ_EXTERN int BZ_API(BZ2_bzDecompressInit) (
+ bz_stream *strm,
+ int verbosity,
+ int small
+ );
+
+BZ_EXTERN int BZ_API(BZ2_bzDecompress) (
+ bz_stream* strm
+ );
+
+BZ_EXTERN int BZ_API(BZ2_bzDecompressEnd) (
+ bz_stream *strm
+ );
+
+
+
+/*-- High(er) level library functions --*/
+
+#ifndef BZ_NO_STDIO
+#define BZ_MAX_UNUSED 5000
+
+typedef void BZFILE;
+
+BZ_EXTERN BZFILE* BZ_API(BZ2_bzReadOpen) (
+ int* bzerror,
+ FILE* f,
+ int verbosity,
+ int small,
+ void* unused,
+ int nUnused
+ );
+
+BZ_EXTERN void BZ_API(BZ2_bzReadClose) (
+ int* bzerror,
+ BZFILE* b
+ );
+
+BZ_EXTERN void BZ_API(BZ2_bzReadGetUnused) (
+ int* bzerror,
+ BZFILE* b,
+ void** unused,
+ int* nUnused
+ );
+
+BZ_EXTERN int BZ_API(BZ2_bzRead) (
+ int* bzerror,
+ BZFILE* b,
+ void* buf,
+ int len
+ );
+
+BZ_EXTERN BZFILE* BZ_API(BZ2_bzWriteOpen) (
+ int* bzerror,
+ FILE* f,
+ int blockSize100k,
+ int verbosity,
+ int workFactor
+ );
+
+BZ_EXTERN void BZ_API(BZ2_bzWrite) (
+ int* bzerror,
+ BZFILE* b,
+ void* buf,
+ int len
+ );
+
+BZ_EXTERN void BZ_API(BZ2_bzWriteClose) (
+ int* bzerror,
+ BZFILE* b,
+ int abandon,
+ unsigned int* nbytes_in,
+ unsigned int* nbytes_out
+ );
+
+BZ_EXTERN void BZ_API(BZ2_bzWriteClose64) (
+ int* bzerror,
+ BZFILE* b,
+ int abandon,
+ unsigned int* nbytes_in_lo32,
+ unsigned int* nbytes_in_hi32,
+ unsigned int* nbytes_out_lo32,
+ unsigned int* nbytes_out_hi32
+ );
+#endif
+
+
+/*-- Utility functions --*/
+
+BZ_EXTERN int BZ_API(BZ2_bzBuffToBuffCompress) (
+ char* dest,
+ unsigned int* destLen,
+ char* source,
+ unsigned int sourceLen,
+ int blockSize100k,
+ int verbosity,
+ int workFactor
+ );
+
+BZ_EXTERN int BZ_API(BZ2_bzBuffToBuffDecompress) (
+ char* dest,
+ unsigned int* destLen,
+ char* source,
+ unsigned int sourceLen,
+ int small,
+ int verbosity
+ );
+
+
+/*--
+ Code contributed by Yoshioka Tsuneo (tsuneo at rr.iij4u.or.jp)
+ to support better zlib compatibility.
+ This code is not _officially_ part of libbzip2 (yet);
+ I haven't tested it, documented it, or considered the
+ threading-safeness of it.
+ If this code breaks, please contact both Yoshioka and me.
+--*/
+
+BZ_EXTERN const char * BZ_API(BZ2_bzlibVersion) (
+ void
+ );
+
+#ifndef BZ_NO_STDIO
+BZ_EXTERN BZFILE * BZ_API(BZ2_bzopen) (
+ const char *path,
+ const char *mode
+ );
+
+BZ_EXTERN BZFILE * BZ_API(BZ2_bzdopen) (
+ int fd,
+ const char *mode
+ );
+
+BZ_EXTERN int BZ_API(BZ2_bzread) (
+ BZFILE* b,
+ void* buf,
+ int len
+ );
+
+BZ_EXTERN int BZ_API(BZ2_bzwrite) (
+ BZFILE* b,
+ void* buf,
+ int len
+ );
+
+BZ_EXTERN int BZ_API(BZ2_bzflush) (
+ BZFILE* b
+ );
+
+BZ_EXTERN void BZ_API(BZ2_bzclose) (
+ BZFILE* b
+ );
+
+BZ_EXTERN const char * BZ_API(BZ2_bzerror) (
+ BZFILE *b,
+ int *errnum
+ );
+#endif
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
+
+/*-------------------------------------------------------------*/
+/*--- end bzlib.h ---*/
+/*-------------------------------------------------------------*/
diff --git a/third-party/bzip2/bzlib_private.h b/third-party/bzip2/bzlib_private.h
new file mode 100644
index 0000000..5d0217f
--- /dev/null
+++ b/third-party/bzip2/bzlib_private.h
@@ -0,0 +1,509 @@
+
+/*-------------------------------------------------------------*/
+/*--- Private header file for the library. ---*/
+/*--- bzlib_private.h ---*/
+/*-------------------------------------------------------------*/
+
+/* ------------------------------------------------------------------
+ This file is part of bzip2/libbzip2, a program and library for
+ lossless, block-sorting data compression.
+
+ bzip2/libbzip2 version 1.0.6 of 6 September 2010
+ Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
+
+ Please read the WARNING, DISCLAIMER and PATENTS sections in the
+ README file.
+
+ This program is released under the terms of the license contained
+ in the file LICENSE.
+ ------------------------------------------------------------------ */
+
+
+#ifndef _BZLIB_PRIVATE_H
+#define _BZLIB_PRIVATE_H
+
+#include <stdlib.h>
+
+#ifndef BZ_NO_STDIO
+#include <stdio.h>
+#include <ctype.h>
+#include <string.h>
+#endif
+
+#include "bzlib.h"
+
+
+
+/*-- General stuff. --*/
+
+#define BZ_VERSION "1.0.6, 6-Sept-2010"
+
+typedef char Char;
+typedef unsigned char Bool;
+typedef unsigned char UChar;
+typedef int Int32;
+typedef unsigned int UInt32;
+typedef short Int16;
+typedef unsigned short UInt16;
+
+#define True ((Bool)1)
+#define False ((Bool)0)
+
+#ifndef __GNUC__
+#define __inline__ /* */
+#endif
+
+#ifndef BZ_NO_STDIO
+
+extern void BZ2_bz__AssertH__fail ( int errcode );
+#define AssertH(cond,errcode) \
+ { if (!(cond)) BZ2_bz__AssertH__fail ( errcode ); }
+
+#if BZ_DEBUG
+#define AssertD(cond,msg) \
+ { if (!(cond)) { \
+ fprintf ( stderr, \
+ "\n\nlibbzip2(debug build): internal error\n\t%s\n", msg );\
+ exit(1); \
+ }}
+#else
+#define AssertD(cond,msg) /* */
+#endif
+
+#define VPrintf0(zf) \
+ fprintf(stderr,zf)
+#define VPrintf1(zf,za1) \
+ fprintf(stderr,zf,za1)
+#define VPrintf2(zf,za1,za2) \
+ fprintf(stderr,zf,za1,za2)
+#define VPrintf3(zf,za1,za2,za3) \
+ fprintf(stderr,zf,za1,za2,za3)
+#define VPrintf4(zf,za1,za2,za3,za4) \
+ fprintf(stderr,zf,za1,za2,za3,za4)
+#define VPrintf5(zf,za1,za2,za3,za4,za5) \
+ fprintf(stderr,zf,za1,za2,za3,za4,za5)
+
+#else
+
+extern void bz_internal_error ( int errcode );
+#define AssertH(cond,errcode) \
+ { if (!(cond)) bz_internal_error ( errcode ); }
+#define AssertD(cond,msg) do { } while (0)
+#define VPrintf0(zf) do { } while (0)
+#define VPrintf1(zf,za1) do { } while (0)
+#define VPrintf2(zf,za1,za2) do { } while (0)
+#define VPrintf3(zf,za1,za2,za3) do { } while (0)
+#define VPrintf4(zf,za1,za2,za3,za4) do { } while (0)
+#define VPrintf5(zf,za1,za2,za3,za4,za5) do { } while (0)
+
+#endif
+
+
+#define BZALLOC(nnn) (strm->bzalloc)(strm->opaque,(nnn),1)
+#define BZFREE(ppp) (strm->bzfree)(strm->opaque,(ppp))
+
+
+/*-- Header bytes. --*/
+
+#define BZ_HDR_B 0x42 /* 'B' */
+#define BZ_HDR_Z 0x5a /* 'Z' */
+#define BZ_HDR_h 0x68 /* 'h' */
+#define BZ_HDR_0 0x30 /* '0' */
+
+/*-- Constants for the back end. --*/
+
+#define BZ_MAX_ALPHA_SIZE 258
+#define BZ_MAX_CODE_LEN 23
+
+#define BZ_RUNA 0
+#define BZ_RUNB 1
+
+#define BZ_N_GROUPS 6
+#define BZ_G_SIZE 50
+#define BZ_N_ITERS 4
+
+#define BZ_MAX_SELECTORS (2 + (900000 / BZ_G_SIZE))
+
+
+
+/*-- Stuff for randomising repetitive blocks. --*/
+
+extern Int32 BZ2_rNums[512];
+
+#define BZ_RAND_DECLS \
+ Int32 rNToGo; \
+ Int32 rTPos \
+
+#define BZ_RAND_INIT_MASK \
+ s->rNToGo = 0; \
+ s->rTPos = 0 \
+
+#define BZ_RAND_MASK ((s->rNToGo == 1) ? 1 : 0)
+
+#define BZ_RAND_UPD_MASK \
+ if (s->rNToGo == 0) { \
+ s->rNToGo = BZ2_rNums[s->rTPos]; \
+ s->rTPos++; \
+ if (s->rTPos == 512) s->rTPos = 0; \
+ } \
+ s->rNToGo--;
+
+
+
+/*-- Stuff for doing CRCs. --*/
+
+extern UInt32 BZ2_crc32Table[256];
+
+#define BZ_INITIALISE_CRC(crcVar) \
+{ \
+ crcVar = 0xffffffffL; \
+}
+
+#define BZ_FINALISE_CRC(crcVar) \
+{ \
+ crcVar = ~(crcVar); \
+}
+
+#define BZ_UPDATE_CRC(crcVar,cha) \
+{ \
+ crcVar = (crcVar << 8) ^ \
+ BZ2_crc32Table[(crcVar >> 24) ^ \
+ ((UChar)cha)]; \
+}
+
+
+
+/*-- States and modes for compression. --*/
+
+#define BZ_M_IDLE 1
+#define BZ_M_RUNNING 2
+#define BZ_M_FLUSHING 3
+#define BZ_M_FINISHING 4
+
+#define BZ_S_OUTPUT 1
+#define BZ_S_INPUT 2
+
+#define BZ_N_RADIX 2
+#define BZ_N_QSORT 12
+#define BZ_N_SHELL 18
+#define BZ_N_OVERSHOOT (BZ_N_RADIX + BZ_N_QSORT + BZ_N_SHELL + 2)
+
+
+
+
+/*-- Structure holding all the compression-side stuff. --*/
+
+typedef
+ struct {
+ /* pointer back to the struct bz_stream */
+ bz_stream* strm;
+
+ /* mode this stream is in, and whether inputting */
+ /* or outputting data */
+ Int32 mode;
+ Int32 state;
+
+ /* remembers avail_in when flush/finish requested */
+ UInt32 avail_in_expect;
+
+ /* for doing the block sorting */
+ UInt32* arr1;
+ UInt32* arr2;
+ UInt32* ftab;
+ Int32 origPtr;
+
+ /* aliases for arr1 and arr2 */
+ UInt32* ptr;
+ UChar* block;
+ UInt16* mtfv;
+ UChar* zbits;
+
+ /* for deciding when to use the fallback sorting algorithm */
+ Int32 workFactor;
+
+ /* run-length-encoding of the input */
+ UInt32 state_in_ch;
+ Int32 state_in_len;
+ BZ_RAND_DECLS;
+
+ /* input and output limits and current posns */
+ Int32 nblock;
+ Int32 nblockMAX;
+ Int32 numZ;
+ Int32 state_out_pos;
+
+ /* map of bytes used in block */
+ Int32 nInUse;
+ Bool inUse[256];
+ UChar unseqToSeq[256];
+
+ /* the buffer for bit stream creation */
+ UInt32 bsBuff;
+ Int32 bsLive;
+
+ /* block and combined CRCs */
+ UInt32 blockCRC;
+ UInt32 combinedCRC;
+
+ /* misc administratium */
+ Int32 verbosity;
+ Int32 blockNo;
+ Int32 blockSize100k;
+
+ /* stuff for coding the MTF values */
+ Int32 nMTF;
+ Int32 mtfFreq [BZ_MAX_ALPHA_SIZE];
+ UChar selector [BZ_MAX_SELECTORS];
+ UChar selectorMtf[BZ_MAX_SELECTORS];
+
+ UChar len [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
+ Int32 code [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
+ Int32 rfreq [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
+ /* second dimension: only 3 needed; 4 makes index calculations faster */
+ UInt32 len_pack[BZ_MAX_ALPHA_SIZE][4];
+
+ }
+ EState;
+
+
+
+/*-- externs for compression. --*/
+
+extern void
+BZ2_blockSort ( EState* );
+
+extern void
+BZ2_compressBlock ( EState*, Bool );
+
+extern void
+BZ2_bsInitWrite ( EState* );
+
+extern void
+BZ2_hbAssignCodes ( Int32*, UChar*, Int32, Int32, Int32 );
+
+extern void
+BZ2_hbMakeCodeLengths ( UChar*, Int32*, Int32, Int32 );
+
+
+
+/*-- states for decompression. --*/
+
+#define BZ_X_IDLE 1
+#define BZ_X_OUTPUT 2
+
+#define BZ_X_MAGIC_1 10
+#define BZ_X_MAGIC_2 11
+#define BZ_X_MAGIC_3 12
+#define BZ_X_MAGIC_4 13
+#define BZ_X_BLKHDR_1 14
+#define BZ_X_BLKHDR_2 15
+#define BZ_X_BLKHDR_3 16
+#define BZ_X_BLKHDR_4 17
+#define BZ_X_BLKHDR_5 18
+#define BZ_X_BLKHDR_6 19
+#define BZ_X_BCRC_1 20
+#define BZ_X_BCRC_2 21
+#define BZ_X_BCRC_3 22
+#define BZ_X_BCRC_4 23
+#define BZ_X_RANDBIT 24
+#define BZ_X_ORIGPTR_1 25
+#define BZ_X_ORIGPTR_2 26
+#define BZ_X_ORIGPTR_3 27
+#define BZ_X_MAPPING_1 28
+#define BZ_X_MAPPING_2 29
+#define BZ_X_SELECTOR_1 30
+#define BZ_X_SELECTOR_2 31
+#define BZ_X_SELECTOR_3 32
+#define BZ_X_CODING_1 33
+#define BZ_X_CODING_2 34
+#define BZ_X_CODING_3 35
+#define BZ_X_MTF_1 36
+#define BZ_X_MTF_2 37
+#define BZ_X_MTF_3 38
+#define BZ_X_MTF_4 39
+#define BZ_X_MTF_5 40
+#define BZ_X_MTF_6 41
+#define BZ_X_ENDHDR_2 42
+#define BZ_X_ENDHDR_3 43
+#define BZ_X_ENDHDR_4 44
+#define BZ_X_ENDHDR_5 45
+#define BZ_X_ENDHDR_6 46
+#define BZ_X_CCRC_1 47
+#define BZ_X_CCRC_2 48
+#define BZ_X_CCRC_3 49
+#define BZ_X_CCRC_4 50
+
+
+
+/*-- Constants for the fast MTF decoder. --*/
+
+#define MTFA_SIZE 4096
+#define MTFL_SIZE 16
+
+
+
+/*-- Structure holding all the decompression-side stuff. --*/
+
+typedef
+ struct {
+ /* pointer back to the struct bz_stream */
+ bz_stream* strm;
+
+ /* state indicator for this stream */
+ Int32 state;
+
+ /* for doing the final run-length decoding */
+ UChar state_out_ch;
+ Int32 state_out_len;
+ Bool blockRandomised;
+ BZ_RAND_DECLS;
+
+ /* the buffer for bit stream reading */
+ UInt32 bsBuff;
+ Int32 bsLive;
+
+ /* misc administratium */
+ Int32 blockSize100k;
+ Bool smallDecompress;
+ Int32 currBlockNo;
+ Int32 verbosity;
+
+ /* for undoing the Burrows-Wheeler transform */
+ Int32 origPtr;
+ UInt32 tPos;
+ Int32 k0;
+ Int32 unzftab[256];
+ Int32 nblock_used;
+ Int32 cftab[257];
+ Int32 cftabCopy[257];
+
+ /* for undoing the Burrows-Wheeler transform (FAST) */
+ UInt32 *tt;
+
+ /* for undoing the Burrows-Wheeler transform (SMALL) */
+ UInt16 *ll16;
+ UChar *ll4;
+
+ /* stored and calculated CRCs */
+ UInt32 storedBlockCRC;
+ UInt32 storedCombinedCRC;
+ UInt32 calculatedBlockCRC;
+ UInt32 calculatedCombinedCRC;
+
+ /* map of bytes used in block */
+ Int32 nInUse;
+ Bool inUse[256];
+ Bool inUse16[16];
+ UChar seqToUnseq[256];
+
+ /* for decoding the MTF values */
+ UChar mtfa [MTFA_SIZE];
+ Int32 mtfbase[256 / MTFL_SIZE];
+ UChar selector [BZ_MAX_SELECTORS];
+ UChar selectorMtf[BZ_MAX_SELECTORS];
+ UChar len [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
+
+ Int32 limit [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
+ Int32 base [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
+ Int32 perm [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
+ Int32 minLens[BZ_N_GROUPS];
+
+ /* save area for scalars in the main decompress code */
+ Int32 save_i;
+ Int32 save_j;
+ Int32 save_t;
+ Int32 save_alphaSize;
+ Int32 save_nGroups;
+ Int32 save_nSelectors;
+ Int32 save_EOB;
+ Int32 save_groupNo;
+ Int32 save_groupPos;
+ Int32 save_nextSym;
+ Int32 save_nblockMAX;
+ Int32 save_nblock;
+ Int32 save_es;
+ Int32 save_N;
+ Int32 save_curr;
+ Int32 save_zt;
+ Int32 save_zn;
+ Int32 save_zvec;
+ Int32 save_zj;
+ Int32 save_gSel;
+ Int32 save_gMinlen;
+ Int32* save_gLimit;
+ Int32* save_gBase;
+ Int32* save_gPerm;
+
+ }
+ DState;
+
+
+
+/*-- Macros for decompression. --*/
+
+#define BZ_GET_FAST(cccc) \
+ /* c_tPos is unsigned, hence test < 0 is pointless. */ \
+ if (s->tPos >= (UInt32)100000 * (UInt32)s->blockSize100k) return True; \
+ s->tPos = s->tt[s->tPos]; \
+ cccc = (UChar)(s->tPos & 0xff); \
+ s->tPos >>= 8;
+
+#define BZ_GET_FAST_C(cccc) \
+ /* c_tPos is unsigned, hence test < 0 is pointless. */ \
+ if (c_tPos >= (UInt32)100000 * (UInt32)ro_blockSize100k) return True; \
+ c_tPos = c_tt[c_tPos]; \
+ cccc = (UChar)(c_tPos & 0xff); \
+ c_tPos >>= 8;
+
+#define SET_LL4(i,n) \
+ { if (((i) & 0x1) == 0) \
+ s->ll4[(i) >> 1] = (s->ll4[(i) >> 1] & 0xf0) | (n); else \
+ s->ll4[(i) >> 1] = (s->ll4[(i) >> 1] & 0x0f) | ((n) << 4); \
+ }
+
+#define GET_LL4(i) \
+ ((((UInt32)(s->ll4[(i) >> 1])) >> (((i) << 2) & 0x4)) & 0xF)
+
+#define SET_LL(i,n) \
+ { s->ll16[i] = (UInt16)(n & 0x0000ffff); \
+ SET_LL4(i, n >> 16); \
+ }
+
+#define GET_LL(i) \
+ (((UInt32)s->ll16[i]) | (GET_LL4(i) << 16))
+
+#define BZ_GET_SMALL(cccc) \
+ /* c_tPos is unsigned, hence test < 0 is pointless. */ \
+ if (s->tPos >= (UInt32)100000 * (UInt32)s->blockSize100k) return True; \
+ cccc = BZ2_indexIntoF ( s->tPos, s->cftab ); \
+ s->tPos = GET_LL(s->tPos);
+
+
+/*-- externs for decompression. --*/
+
+extern Int32
+BZ2_indexIntoF ( Int32, Int32* );
+
+extern Int32
+BZ2_decompress ( DState* );
+
+extern void
+BZ2_hbCreateDecodeTables ( Int32*, Int32*, Int32*, UChar*,
+ Int32, Int32, Int32 );
+
+
+#endif
+
+
+/*-- BZ_NO_STDIO seems to make NULL disappear on some platforms. --*/
+
+#ifdef BZ_NO_STDIO
+#ifndef NULL
+#define NULL 0
+#endif
+#endif
+
+
+/*-------------------------------------------------------------*/
+/*--- end bzlib_private.h ---*/
+/*-------------------------------------------------------------*/
diff --git a/third-party/bzip2/bzmore b/third-party/bzip2/bzmore
new file mode 100644
index 0000000..d314043
--- /dev/null
+++ b/third-party/bzip2/bzmore
@@ -0,0 +1,61 @@
+#!/bin/sh
+
+# Bzmore wrapped for bzip2,
+# adapted from zmore by Philippe Troin <phil at fifi.org> for Debian GNU/Linux.
+
+PATH="/usr/bin:$PATH"; export PATH
+
+prog=`echo $0 | sed 's|.*/||'`
+case "$prog" in
+ *less) more=less ;;
+ *) more=more ;;
+esac
+
+if test "`echo -n a`" = "-n a"; then
+ # looks like a SysV system:
+ n1=''; n2='\c'
+else
+ n1='-n'; n2=''
+fi
+oldtty=`stty -g 2>/dev/null`
+if stty -cbreak 2>/dev/null; then
+ cb='cbreak'; ncb='-cbreak'
+else
+ # 'stty min 1' resets eof to ^a on both SunOS and SysV!
+ cb='min 1 -icanon'; ncb='icanon eof ^d'
+fi
+if test $? -eq 0 -a -n "$oldtty"; then
+ trap 'stty $oldtty 2>/dev/null; exit' 0 2 3 5 10 13 15
+else
+ trap 'stty $ncb echo 2>/dev/null; exit' 0 2 3 5 10 13 15
+fi
+
+if test $# = 0; then
+ if test -t 0; then
+ echo usage: $prog files...
+ else
+ bzip2 -cdfq | eval $more
+ fi
+else
+ FIRST=1
+ for FILE
+ do
+ if test $FIRST -eq 0; then
+ echo $n1 "--More--(Next file: $FILE)$n2"
+ stty $cb -echo 2>/dev/null
+ ANS=`dd bs=1 count=1 2>/dev/null`
+ stty $ncb echo 2>/dev/null
+ echo " "
+ if test "$ANS" = 'e' -o "$ANS" = 'q'; then
+ exit
+ fi
+ fi
+ if test "$ANS" != 's'; then
+ echo "------> $FILE <------"
+ bzip2 -cdfq "$FILE" | eval $more
+ fi
+ if test -t; then
+ FIRST=0
+ fi
+ done
+fi
diff --git a/third-party/bzip2/bzmore.1 b/third-party/bzip2/bzmore.1
new file mode 100644
index 0000000..b437d3b
--- /dev/null
+++ b/third-party/bzip2/bzmore.1
@@ -0,0 +1,152 @@
+.\"Shamelessly copied from zmore.1 by Philippe Troin <phil at fifi.org>
+.\"for Debian GNU/Linux
+.TH BZMORE 1
+.SH NAME
+bzmore, bzless \- file perusal filter for crt viewing of bzip2 compressed text
+.SH SYNOPSIS
+.B bzmore
+[ name ... ]
+.br
+.B bzless
+[ name ... ]
+.SH NOTE
+In the following description,
+.I bzless
+and
+.I less
+can be used interchangeably with
+.I bzmore
+and
+.I more.
+.SH DESCRIPTION
+.I Bzmore
+is a filter which allows examination of compressed or plain text files
+one screenful at a time on a soft-copy terminal.
+.I bzmore
+works on files compressed with
+.I bzip2
+and also on uncompressed files.
+If a file does not exist,
+.I bzmore
+looks for a file of the same name with the addition of a .bz2 suffix.
+.PP
+.I Bzmore
+normally pauses after each screenful, printing --More--
+at the bottom of the screen.
+If the user then types a carriage return, one more line is displayed.
+If the user hits a space,
+another screenful is displayed. Other possibilities are enumerated later.
+.PP
+.I Bzmore
+looks in the file
+.I /etc/termcap
+to determine terminal characteristics,
+and to determine the default window size.
+On a terminal capable of displaying 24 lines,
+the default window size is 22 lines.
+Other sequences which may be typed when
+.I bzmore
+pauses, and their effects, are as follows (\fIi\fP is an optional integer
+argument, defaulting to 1) :
+.PP
+.IP \fIi\|\fP<space>
+display
+.I i
+more lines, (or another screenful if no argument is given)
+.PP
+.IP ^D
+display 11 more lines (a ``scroll'').
+If
+.I i
+is given, then the scroll size is set to \fIi\|\fP.
+.PP
+.IP d
+same as ^D (control-D)
+.PP
+.IP \fIi\|\fPz
+same as typing a space except that \fIi\|\fP, if present, becomes the new
+window size. Note that the window size reverts back to the default at the
+end of the current file.
+.PP
+.IP \fIi\|\fPs
+skip \fIi\|\fP lines and print a screenful of lines
+.PP
+.IP \fIi\|\fPf
+skip \fIi\fP screenfuls and print a screenful of lines
+.PP
+.IP "q or Q"
+quit reading the current file; go on to the next (if any)
+.PP
+.IP "e or q"
+When the prompt --More--(Next file:
+.IR file )
+is printed, this command causes bzmore to exit.
+.PP
+.IP s
+When the prompt --More--(Next file:
+.IR file )
+is printed, this command causes bzmore to skip the next file and continue.
+.PP
+.IP =
+Display the current line number.
+.PP
+.IP \fIi\|\fP/expr
+search for the \fIi\|\fP-th occurrence of the regular expression \fIexpr.\fP
+If the pattern is not found,
+.I bzmore
+goes on to the next file (if any).
+Otherwise, a screenful is displayed, starting two lines before the place
+where the expression was found.
+The user's erase and kill characters may be used to edit the regular
+expression.
+Erasing back past the first column cancels the search command.
+.PP
+.IP \fIi\|\fPn
+search for the \fIi\|\fP-th occurrence of the last regular expression entered.
+.PP
+.IP !command
+invoke a shell with \fIcommand\|\fP.
+The character `!' in "command" are replaced with the
+previous shell command. The sequence "\\!" is replaced by "!".
+.PP
+.IP ":q or :Q"
+quit reading the current file; go on to the next (if any)
+(same as q or Q).
+.PP
+.IP .
+(dot) repeat the previous command.
+.PP
+The commands take effect immediately, i.e., it is not necessary to
+type a carriage return.
+Up to the time when the command character itself is given,
+the user may hit the line kill character to cancel the numerical
+argument being formed.
+In addition, the user may hit the erase character to redisplay the
+--More-- message.
+.PP
+At any time when output is being sent to the terminal, the user can
+hit the quit key (normally control\-\\).
+.I Bzmore
+will stop sending output, and will display the usual --More--
+prompt.
+The user may then enter one of the above commands in the normal manner.
+Unfortunately, some output is lost when this is done, due to the
+fact that any characters waiting in the terminal's output queue
+are flushed when the quit signal occurs.
+.PP
+The terminal is set to
+.I noecho
+mode by this program so that the output can be continuous.
+What you type will thus not show on your terminal, except for the / and !
+commands.
+.PP
+If the standard output is not a teletype, then
+.I bzmore
+acts just like
+.I bzcat,
+except that a header is printed before each file.
+.SH FILES
+.DT
+/etc/termcap Terminal data base
+.SH "SEE ALSO"
+more(1), less(1), bzip2(1), bzdiff(1), bzgrep(1)
diff --git a/third-party/bzip2/compress.c b/third-party/bzip2/compress.c
new file mode 100644
index 0000000..caf7696
--- /dev/null
+++ b/third-party/bzip2/compress.c
@@ -0,0 +1,672 @@
+
+/*-------------------------------------------------------------*/
+/*--- Compression machinery (not incl block sorting) ---*/
+/*--- compress.c ---*/
+/*-------------------------------------------------------------*/
+
+/* ------------------------------------------------------------------
+ This file is part of bzip2/libbzip2, a program and library for
+ lossless, block-sorting data compression.
+
+ bzip2/libbzip2 version 1.0.6 of 6 September 2010
+ Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
+
+ Please read the WARNING, DISCLAIMER and PATENTS sections in the
+ README file.
+
+ This program is released under the terms of the license contained
+ in the file LICENSE.
+ ------------------------------------------------------------------ */
+
+
+/* CHANGES
+ 0.9.0 -- original version.
+ 0.9.0a/b -- no changes in this file.
+ 0.9.0c -- changed setting of nGroups in sendMTFValues()
+ so as to do a bit better on small files
+*/
+
+#include "bzlib_private.h"
+
+
+/*---------------------------------------------------*/
+/*--- Bit stream I/O ---*/
+/*---------------------------------------------------*/
+
+/*---------------------------------------------------*/
+void BZ2_bsInitWrite ( EState* s )
+{
+ s->bsLive = 0;
+ s->bsBuff = 0;
+}
+
+
+/*---------------------------------------------------*/
+static
+void bsFinishWrite ( EState* s )
+{
+ while (s->bsLive > 0) {
+ s->zbits[s->numZ] = (UChar)(s->bsBuff >> 24);
+ s->numZ++;
+ s->bsBuff <<= 8;
+ s->bsLive -= 8;
+ }
+}
+
+
+/*---------------------------------------------------*/
+#define bsNEEDW(nz) \
+{ \
+ while (s->bsLive >= 8) { \
+ s->zbits[s->numZ] \
+ = (UChar)(s->bsBuff >> 24); \
+ s->numZ++; \
+ s->bsBuff <<= 8; \
+ s->bsLive -= 8; \
+ } \
+}
+
+
+/*---------------------------------------------------*/
+static
+__inline__
+void bsW ( EState* s, Int32 n, UInt32 v )
+{
+ bsNEEDW ( n );
+ s->bsBuff |= (v << (32 - s->bsLive - n));
+ s->bsLive += n;
+}
+
+
+/*---------------------------------------------------*/
+static
+void bsPutUInt32 ( EState* s, UInt32 u )
+{
+ bsW ( s, 8, (u >> 24) & 0xffL );
+ bsW ( s, 8, (u >> 16) & 0xffL );
+ bsW ( s, 8, (u >> 8) & 0xffL );
+ bsW ( s, 8, u & 0xffL );
+}
+
+
+/*---------------------------------------------------*/
+static
+void bsPutUChar ( EState* s, UChar c )
+{
+ bsW( s, 8, (UInt32)c );
+}
+
+
+/*---------------------------------------------------*/
+/*--- The back end proper ---*/
+/*---------------------------------------------------*/
+
+/*---------------------------------------------------*/
+static
+void makeMaps_e ( EState* s )
+{
+ Int32 i;
+ s->nInUse = 0;
+ for (i = 0; i < 256; i++)
+ if (s->inUse[i]) {
+ s->unseqToSeq[i] = s->nInUse;
+ s->nInUse++;
+ }
+}
+
+
+/*---------------------------------------------------*/
+static
+void generateMTFValues ( EState* s )
+{
+ UChar yy[256];
+ Int32 i, j;
+ Int32 zPend;
+ Int32 wr;
+ Int32 EOB;
+
+ /*
+ After sorting (eg, here),
+ s->arr1 [ 0 .. s->nblock-1 ] holds sorted order,
+ and
+ ((UChar*)s->arr2) [ 0 .. s->nblock-1 ]
+ holds the original block data.
+
+ The first thing to do is generate the MTF values,
+ and put them in
+ ((UInt16*)s->arr1) [ 0 .. s->nblock-1 ].
+ Because there are strictly fewer or equal MTF values
+ than block values, ptr values in this area are overwritten
+ with MTF values only when they are no longer needed.
+
+ The final compressed bitstream is generated into the
+ area starting at
+ (UChar*) (&((UChar*)s->arr2)[s->nblock])
+
+ These storage aliases are set up in bzCompressInit(),
+ except for the last one, which is arranged in
+ compressBlock().
+ */
+ UInt32* ptr = s->ptr;
+ UChar* block = s->block;
+ UInt16* mtfv = s->mtfv;
+
+ makeMaps_e ( s );
+ EOB = s->nInUse+1;
+
+ for (i = 0; i <= EOB; i++) s->mtfFreq[i] = 0;
+
+ wr = 0;
+ zPend = 0;
+ for (i = 0; i < s->nInUse; i++) yy[i] = (UChar) i;
+
+ for (i = 0; i < s->nblock; i++) {
+ UChar ll_i;
+ AssertD ( wr <= i, "generateMTFValues(1)" );
+ j = ptr[i]-1; if (j < 0) j += s->nblock;
+ ll_i = s->unseqToSeq[block[j]];
+ AssertD ( ll_i < s->nInUse, "generateMTFValues(2a)" );
+
+ if (yy[0] == ll_i) {
+ zPend++;
+ } else {
+
+ if (zPend > 0) {
+ zPend--;
+ while (True) {
+ if (zPend & 1) {
+ mtfv[wr] = BZ_RUNB; wr++;
+ s->mtfFreq[BZ_RUNB]++;
+ } else {
+ mtfv[wr] = BZ_RUNA; wr++;
+ s->mtfFreq[BZ_RUNA]++;
+ }
+ if (zPend < 2) break;
+ zPend = (zPend - 2) / 2;
+ };
+ zPend = 0;
+ }
+ {
+ register UChar rtmp;
+ register UChar* ryy_j;
+ register UChar rll_i;
+ rtmp = yy[1];
+ yy[1] = yy[0];
+ ryy_j = &(yy[1]);
+ rll_i = ll_i;
+ while ( rll_i != rtmp ) {
+ register UChar rtmp2;
+ ryy_j++;
+ rtmp2 = rtmp;
+ rtmp = *ryy_j;
+ *ryy_j = rtmp2;
+ };
+ yy[0] = rtmp;
+ j = ryy_j - &(yy[0]);
+ mtfv[wr] = j+1; wr++; s->mtfFreq[j+1]++;
+ }
+
+ }
+ }
+
+ if (zPend > 0) {
+ zPend--;
+ while (True) {
+ if (zPend & 1) {
+ mtfv[wr] = BZ_RUNB; wr++;
+ s->mtfFreq[BZ_RUNB]++;
+ } else {
+ mtfv[wr] = BZ_RUNA; wr++;
+ s->mtfFreq[BZ_RUNA]++;
+ }
+ if (zPend < 2) break;
+ zPend = (zPend - 2) / 2;
+ };
+ zPend = 0;
+ }
+
+ mtfv[wr] = EOB; wr++; s->mtfFreq[EOB]++;
+
+ s->nMTF = wr;
+}
+
+
+/*---------------------------------------------------*/
+#define BZ_LESSER_ICOST 0
+#define BZ_GREATER_ICOST 15
+
+static
+void sendMTFValues ( EState* s )
+{
+ Int32 v, t, i, j, gs, ge, totc, bt, bc, iter;
+ Int32 nSelectors, alphaSize, minLen, maxLen, selCtr;
+ Int32 nGroups, nBytes;
+
+ /*--
+ UChar len [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
+ is a global since the decoder also needs it.
+
+ Int32 code[BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
+ Int32 rfreq[BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
+ are also globals only used in this proc.
+ Made global to keep stack frame size small.
+ --*/
+
+
+ UInt16 cost[BZ_N_GROUPS];
+ Int32 fave[BZ_N_GROUPS];
+
+ UInt16* mtfv = s->mtfv;
+
+ if (s->verbosity >= 3)
+ VPrintf3( " %d in block, %d after MTF & 1-2 coding, "
+ "%d+2 syms in use\n",
+ s->nblock, s->nMTF, s->nInUse );
+
+ alphaSize = s->nInUse+2;
+ for (t = 0; t < BZ_N_GROUPS; t++)
+ for (v = 0; v < alphaSize; v++)
+ s->len[t][v] = BZ_GREATER_ICOST;
+
+ /*--- Decide how many coding tables to use ---*/
+ AssertH ( s->nMTF > 0, 3001 );
+ if (s->nMTF < 200) nGroups = 2; else
+ if (s->nMTF < 600) nGroups = 3; else
+ if (s->nMTF < 1200) nGroups = 4; else
+ if (s->nMTF < 2400) nGroups = 5; else
+ nGroups = 6;
+
+ /*--- Generate an initial set of coding tables ---*/
+ {
+ Int32 nPart, remF, tFreq, aFreq;
+
+ nPart = nGroups;
+ remF = s->nMTF;
+ gs = 0;
+ while (nPart > 0) {
+ tFreq = remF / nPart;
+ ge = gs-1;
+ aFreq = 0;
+ while (aFreq < tFreq && ge < alphaSize-1) {
+ ge++;
+ aFreq += s->mtfFreq[ge];
+ }
+
+ if (ge > gs
+ && nPart != nGroups && nPart != 1
+ && ((nGroups-nPart) % 2 == 1)) {
+ aFreq -= s->mtfFreq[ge];
+ ge--;
+ }
+
+ if (s->verbosity >= 3)
+ VPrintf5( " initial group %d, [%d .. %d], "
+ "has %d syms (%4.1f%%)\n",
+ nPart, gs, ge, aFreq,
+ (100.0 * (float)aFreq) / (float)(s->nMTF) );
+
+ for (v = 0; v < alphaSize; v++)
+ if (v >= gs && v <= ge)
+ s->len[nPart-1][v] = BZ_LESSER_ICOST; else
+ s->len[nPart-1][v] = BZ_GREATER_ICOST;
+
+ nPart--;
+ gs = ge+1;
+ remF -= aFreq;
+ }
+ }
+
+ /*---
+ Iterate up to BZ_N_ITERS times to improve the tables.
+ ---*/
+ for (iter = 0; iter < BZ_N_ITERS; iter++) {
+
+ for (t = 0; t < nGroups; t++) fave[t] = 0;
+
+ for (t = 0; t < nGroups; t++)
+ for (v = 0; v < alphaSize; v++)
+ s->rfreq[t][v] = 0;
+
+ /*---
+ Set up an auxiliary length table which is used to fast-track
+ the common case (nGroups == 6).
+ ---*/
+ if (nGroups == 6) {
+ for (v = 0; v < alphaSize; v++) {
+ s->len_pack[v][0] = (s->len[1][v] << 16) | s->len[0][v];
+ s->len_pack[v][1] = (s->len[3][v] << 16) | s->len[2][v];
+ s->len_pack[v][2] = (s->len[5][v] << 16) | s->len[4][v];
+ }
+ }
+
+ nSelectors = 0;
+ totc = 0;
+ gs = 0;
+ while (True) {
+
+ /*--- Set group start & end marks. --*/
+ if (gs >= s->nMTF) break;
+ ge = gs + BZ_G_SIZE - 1;
+ if (ge >= s->nMTF) ge = s->nMTF-1;
+
+ /*--
+ Calculate the cost of this group as coded
+ by each of the coding tables.
+ --*/
+ for (t = 0; t < nGroups; t++) cost[t] = 0;
+
+ if (nGroups == 6 && 50 == ge-gs+1) {
+ /*--- fast track the common case ---*/
+ register UInt32 cost01, cost23, cost45;
+ register UInt16 icv;
+ cost01 = cost23 = cost45 = 0;
+
+# define BZ_ITER(nn) \
+ icv = mtfv[gs+(nn)]; \
+ cost01 += s->len_pack[icv][0]; \
+ cost23 += s->len_pack[icv][1]; \
+ cost45 += s->len_pack[icv][2]; \
+
+ BZ_ITER(0); BZ_ITER(1); BZ_ITER(2); BZ_ITER(3); BZ_ITER(4);
+ BZ_ITER(5); BZ_ITER(6); BZ_ITER(7); BZ_ITER(8); BZ_ITER(9);
+ BZ_ITER(10); BZ_ITER(11); BZ_ITER(12); BZ_ITER(13); BZ_ITER(14);
+ BZ_ITER(15); BZ_ITER(16); BZ_ITER(17); BZ_ITER(18); BZ_ITER(19);
+ BZ_ITER(20); BZ_ITER(21); BZ_ITER(22); BZ_ITER(23); BZ_ITER(24);
+ BZ_ITER(25); BZ_ITER(26); BZ_ITER(27); BZ_ITER(28); BZ_ITER(29);
+ BZ_ITER(30); BZ_ITER(31); BZ_ITER(32); BZ_ITER(33); BZ_ITER(34);
+ BZ_ITER(35); BZ_ITER(36); BZ_ITER(37); BZ_ITER(38); BZ_ITER(39);
+ BZ_ITER(40); BZ_ITER(41); BZ_ITER(42); BZ_ITER(43); BZ_ITER(44);
+ BZ_ITER(45); BZ_ITER(46); BZ_ITER(47); BZ_ITER(48); BZ_ITER(49);
+
+# undef BZ_ITER
+
+ cost[0] = cost01 & 0xffff; cost[1] = cost01 >> 16;
+ cost[2] = cost23 & 0xffff; cost[3] = cost23 >> 16;
+ cost[4] = cost45 & 0xffff; cost[5] = cost45 >> 16;
+
+ } else {
+ /*--- slow version which correctly handles all situations ---*/
+ for (i = gs; i <= ge; i++) {
+ UInt16 icv = mtfv[i];
+ for (t = 0; t < nGroups; t++) cost[t] += s->len[t][icv];
+ }
+ }
+
+ /*--
+ Find the coding table which is best for this group,
+ and record its identity in the selector table.
+ --*/
+ bc = 999999999; bt = -1;
+ for (t = 0; t < nGroups; t++)
+ if (cost[t] < bc) { bc = cost[t]; bt = t; };
+ totc += bc;
+ fave[bt]++;
+ s->selector[nSelectors] = bt;
+ nSelectors++;
+
+ /*--
+ Increment the symbol frequencies for the selected table.
+ --*/
+ if (nGroups == 6 && 50 == ge-gs+1) {
+ /*--- fast track the common case ---*/
+
+# define BZ_ITUR(nn) s->rfreq[bt][ mtfv[gs+(nn)] ]++
+
+ BZ_ITUR(0); BZ_ITUR(1); BZ_ITUR(2); BZ_ITUR(3); BZ_ITUR(4);
+ BZ_ITUR(5); BZ_ITUR(6); BZ_ITUR(7); BZ_ITUR(8); BZ_ITUR(9);
+ BZ_ITUR(10); BZ_ITUR(11); BZ_ITUR(12); BZ_ITUR(13); BZ_ITUR(14);
+ BZ_ITUR(15); BZ_ITUR(16); BZ_ITUR(17); BZ_ITUR(18); BZ_ITUR(19);
+ BZ_ITUR(20); BZ_ITUR(21); BZ_ITUR(22); BZ_ITUR(23); BZ_ITUR(24);
+ BZ_ITUR(25); BZ_ITUR(26); BZ_ITUR(27); BZ_ITUR(28); BZ_ITUR(29);
+ BZ_ITUR(30); BZ_ITUR(31); BZ_ITUR(32); BZ_ITUR(33); BZ_ITUR(34);
+ BZ_ITUR(35); BZ_ITUR(36); BZ_ITUR(37); BZ_ITUR(38); BZ_ITUR(39);
+ BZ_ITUR(40); BZ_ITUR(41); BZ_ITUR(42); BZ_ITUR(43); BZ_ITUR(44);
+ BZ_ITUR(45); BZ_ITUR(46); BZ_ITUR(47); BZ_ITUR(48); BZ_ITUR(49);
+
+# undef BZ_ITUR
+
+ } else {
+ /*--- slow version which correctly handles all situations ---*/
+ for (i = gs; i <= ge; i++)
+ s->rfreq[bt][ mtfv[i] ]++;
+ }
+
+ gs = ge+1;
+ }
+ if (s->verbosity >= 3) {
+ VPrintf2 ( " pass %d: size is %d, grp uses are ",
+ iter+1, totc/8 );
+ for (t = 0; t < nGroups; t++)
+ VPrintf1 ( "%d ", fave[t] );
+ VPrintf0 ( "\n" );
+ }
+
+ /*--
+ Recompute the tables based on the accumulated frequencies.
+ --*/
+ /* maxLen was changed from 20 to 17 in bzip2-1.0.3. See
+ comment in huffman.c for details. */
+ for (t = 0; t < nGroups; t++)
+ BZ2_hbMakeCodeLengths ( &(s->len[t][0]), &(s->rfreq[t][0]),
+ alphaSize, 17 /*20*/ );
+ }
+
+
+ AssertH( nGroups < 8, 3002 );
+ AssertH( nSelectors < 32768 &&
+ nSelectors <= (2 + (900000 / BZ_G_SIZE)),
+ 3003 );
+
+
+ /*--- Compute MTF values for the selectors. ---*/
+ {
+ UChar pos[BZ_N_GROUPS], ll_i, tmp2, tmp;
+ for (i = 0; i < nGroups; i++) pos[i] = i;
+ for (i = 0; i < nSelectors; i++) {
+ ll_i = s->selector[i];
+ j = 0;
+ tmp = pos[j];
+ while ( ll_i != tmp ) {
+ j++;
+ tmp2 = tmp;
+ tmp = pos[j];
+ pos[j] = tmp2;
+ };
+ pos[0] = tmp;
+ s->selectorMtf[i] = j;
+ }
+ };
+
+ /*--- Assign actual codes for the tables. --*/
+ for (t = 0; t < nGroups; t++) {
+ minLen = 32;
+ maxLen = 0;
+ for (i = 0; i < alphaSize; i++) {
+ if (s->len[t][i] > maxLen) maxLen = s->len[t][i];
+ if (s->len[t][i] < minLen) minLen = s->len[t][i];
+ }
+ AssertH ( !(maxLen > 17 /*20*/ ), 3004 );
+ AssertH ( !(minLen < 1), 3005 );
+ BZ2_hbAssignCodes ( &(s->code[t][0]), &(s->len[t][0]),
+ minLen, maxLen, alphaSize );
+ }
+
+ /*--- Transmit the mapping table. ---*/
+ {
+ Bool inUse16[16];
+ for (i = 0; i < 16; i++) {
+ inUse16[i] = False;
+ for (j = 0; j < 16; j++)
+ if (s->inUse[i * 16 + j]) inUse16[i] = True;
+ }
+
+ nBytes = s->numZ;
+ for (i = 0; i < 16; i++)
+ if (inUse16[i]) bsW(s,1,1); else bsW(s,1,0);
+
+ for (i = 0; i < 16; i++)
+ if (inUse16[i])
+ for (j = 0; j < 16; j++) {
+ if (s->inUse[i * 16 + j]) bsW(s,1,1); else bsW(s,1,0);
+ }
+
+ if (s->verbosity >= 3)
+ VPrintf1( " bytes: mapping %d, ", s->numZ-nBytes );
+ }
+
+ /*--- Now the selectors. ---*/
+ nBytes = s->numZ;
+ bsW ( s, 3, nGroups );
+ bsW ( s, 15, nSelectors );
+ for (i = 0; i < nSelectors; i++) {
+ for (j = 0; j < s->selectorMtf[i]; j++) bsW(s,1,1);
+ bsW(s,1,0);
+ }
+ if (s->verbosity >= 3)
+ VPrintf1( "selectors %d, ", s->numZ-nBytes );
+
+ /*--- Now the coding tables. ---*/
+ nBytes = s->numZ;
+
+ for (t = 0; t < nGroups; t++) {
+ Int32 curr = s->len[t][0];
+ bsW ( s, 5, curr );
+ for (i = 0; i < alphaSize; i++) {
+ while (curr < s->len[t][i]) { bsW(s,2,2); curr++; /* 10 */ };
+ while (curr > s->len[t][i]) { bsW(s,2,3); curr--; /* 11 */ };
+ bsW ( s, 1, 0 );
+ }
+ }
+
+ if (s->verbosity >= 3)
+ VPrintf1 ( "code lengths %d, ", s->numZ-nBytes );
+
+ /*--- And finally, the block data proper ---*/
+ nBytes = s->numZ;
+ selCtr = 0;
+ gs = 0;
+ while (True) {
+ if (gs >= s->nMTF) break;
+ ge = gs + BZ_G_SIZE - 1;
+ if (ge >= s->nMTF) ge = s->nMTF-1;
+ AssertH ( s->selector[selCtr] < nGroups, 3006 );
+
+ if (nGroups == 6 && 50 == ge-gs+1) {
+ /*--- fast track the common case ---*/
+ UInt16 mtfv_i;
+ UChar* s_len_sel_selCtr
+ = &(s->len[s->selector[selCtr]][0]);
+ Int32* s_code_sel_selCtr
+ = &(s->code[s->selector[selCtr]][0]);
+
+# define BZ_ITAH(nn) \
+ mtfv_i = mtfv[gs+(nn)]; \
+ bsW ( s, \
+ s_len_sel_selCtr[mtfv_i], \
+ s_code_sel_selCtr[mtfv_i] )
+
+ BZ_ITAH(0); BZ_ITAH(1); BZ_ITAH(2); BZ_ITAH(3); BZ_ITAH(4);
+ BZ_ITAH(5); BZ_ITAH(6); BZ_ITAH(7); BZ_ITAH(8); BZ_ITAH(9);
+ BZ_ITAH(10); BZ_ITAH(11); BZ_ITAH(12); BZ_ITAH(13); BZ_ITAH(14);
+ BZ_ITAH(15); BZ_ITAH(16); BZ_ITAH(17); BZ_ITAH(18); BZ_ITAH(19);
+ BZ_ITAH(20); BZ_ITAH(21); BZ_ITAH(22); BZ_ITAH(23); BZ_ITAH(24);
+ BZ_ITAH(25); BZ_ITAH(26); BZ_ITAH(27); BZ_ITAH(28); BZ_ITAH(29);
+ BZ_ITAH(30); BZ_ITAH(31); BZ_ITAH(32); BZ_ITAH(33); BZ_ITAH(34);
+ BZ_ITAH(35); BZ_ITAH(36); BZ_ITAH(37); BZ_ITAH(38); BZ_ITAH(39);
+ BZ_ITAH(40); BZ_ITAH(41); BZ_ITAH(42); BZ_ITAH(43); BZ_ITAH(44);
+ BZ_ITAH(45); BZ_ITAH(46); BZ_ITAH(47); BZ_ITAH(48); BZ_ITAH(49);
+
+# undef BZ_ITAH
+
+ } else {
+ /*--- slow version which correctly handles all situations ---*/
+ for (i = gs; i <= ge; i++) {
+ bsW ( s,
+ s->len [s->selector[selCtr]] [mtfv[i]],
+ s->code [s->selector[selCtr]] [mtfv[i]] );
+ }
+ }
+
+
+ gs = ge+1;
+ selCtr++;
+ }
+ AssertH( selCtr == nSelectors, 3007 );
+
+ if (s->verbosity >= 3)
+ VPrintf1( "codes %d\n", s->numZ-nBytes );
+}
+
+
+/*---------------------------------------------------*/
+void BZ2_compressBlock ( EState* s, Bool is_last_block )
+{
+ if (s->nblock > 0) {
+
+ BZ_FINALISE_CRC ( s->blockCRC );
+ s->combinedCRC = (s->combinedCRC << 1) | (s->combinedCRC >> 31);
+ s->combinedCRC ^= s->blockCRC;
+ if (s->blockNo > 1) s->numZ = 0;
+
+ if (s->verbosity >= 2)
+ VPrintf4( " block %d: crc = 0x%08x, "
+ "combined CRC = 0x%08x, size = %d\n",
+ s->blockNo, s->blockCRC, s->combinedCRC, s->nblock );
+
+ BZ2_blockSort ( s );
+ }
+
+ s->zbits = (UChar*) (&((UChar*)s->arr2)[s->nblock]);
+
+ /*-- If this is the first block, create the stream header. --*/
+ if (s->blockNo == 1) {
+ BZ2_bsInitWrite ( s );
+ bsPutUChar ( s, BZ_HDR_B );
+ bsPutUChar ( s, BZ_HDR_Z );
+ bsPutUChar ( s, BZ_HDR_h );
+ bsPutUChar ( s, (UChar)(BZ_HDR_0 + s->blockSize100k) );
+ }
+
+ if (s->nblock > 0) {
+
+ bsPutUChar ( s, 0x31 ); bsPutUChar ( s, 0x41 );
+ bsPutUChar ( s, 0x59 ); bsPutUChar ( s, 0x26 );
+ bsPutUChar ( s, 0x53 ); bsPutUChar ( s, 0x59 );
+
+ /*-- Now the block's CRC, so it is in a known place. --*/
+ bsPutUInt32 ( s, s->blockCRC );
+
+ /*--
+ Now a single bit indicating (non-)randomisation.
+ As of version 0.9.5, we use a better sorting algorithm
+ which makes randomisation unnecessary. So always set
+ the randomised bit to 'no'. Of course, the decoder
+ still needs to be able to handle randomised blocks
+ so as to maintain backwards compatibility with
+ older versions of bzip2.
+ --*/
+ bsW(s,1,0);
+
+ bsW ( s, 24, s->origPtr );
+ generateMTFValues ( s );
+ sendMTFValues ( s );
+ }
+
+
+ /*-- If this is the last block, add the stream trailer. --*/
+ if (is_last_block) {
+
+ bsPutUChar ( s, 0x17 ); bsPutUChar ( s, 0x72 );
+ bsPutUChar ( s, 0x45 ); bsPutUChar ( s, 0x38 );
+ bsPutUChar ( s, 0x50 ); bsPutUChar ( s, 0x90 );
+ bsPutUInt32 ( s, s->combinedCRC );
+ if (s->verbosity >= 2)
+ VPrintf1( " final combined CRC = 0x%08x\n ", s->combinedCRC );
+ bsFinishWrite ( s );
+ }
+}
+
+
+/*-------------------------------------------------------------*/
+/*--- end compress.c ---*/
+/*-------------------------------------------------------------*/
diff --git a/third-party/bzip2/crctable.c b/third-party/bzip2/crctable.c
new file mode 100644
index 0000000..1fea7e9
--- /dev/null
+++ b/third-party/bzip2/crctable.c
@@ -0,0 +1,104 @@
+
+/*-------------------------------------------------------------*/
+/*--- Table for doing CRCs ---*/
+/*--- crctable.c ---*/
+/*-------------------------------------------------------------*/
+
+/* ------------------------------------------------------------------
+ This file is part of bzip2/libbzip2, a program and library for
+ lossless, block-sorting data compression.
+
+ bzip2/libbzip2 version 1.0.6 of 6 September 2010
+ Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
+
+ Please read the WARNING, DISCLAIMER and PATENTS sections in the
+ README file.
+
+ This program is released under the terms of the license contained
+ in the file LICENSE.
+ ------------------------------------------------------------------ */
+
+
+#include "bzlib_private.h"
+
+/*--
+ I think this is an implementation of the AUTODIN-II,
+ Ethernet & FDDI 32-bit CRC standard. Vaguely derived
+ from code by Rob Warnock, in Section 51 of the
+ comp.compression FAQ.
+--*/
+
+UInt32 BZ2_crc32Table[256] = {
+
+ /*-- Ugly, innit? --*/
+
+ 0x00000000L, 0x04c11db7L, 0x09823b6eL, 0x0d4326d9L,
+ 0x130476dcL, 0x17c56b6bL, 0x1a864db2L, 0x1e475005L,
+ 0x2608edb8L, 0x22c9f00fL, 0x2f8ad6d6L, 0x2b4bcb61L,
+ 0x350c9b64L, 0x31cd86d3L, 0x3c8ea00aL, 0x384fbdbdL,
+ 0x4c11db70L, 0x48d0c6c7L, 0x4593e01eL, 0x4152fda9L,
+ 0x5f15adacL, 0x5bd4b01bL, 0x569796c2L, 0x52568b75L,
+ 0x6a1936c8L, 0x6ed82b7fL, 0x639b0da6L, 0x675a1011L,
+ 0x791d4014L, 0x7ddc5da3L, 0x709f7b7aL, 0x745e66cdL,
+ 0x9823b6e0L, 0x9ce2ab57L, 0x91a18d8eL, 0x95609039L,
+ 0x8b27c03cL, 0x8fe6dd8bL, 0x82a5fb52L, 0x8664e6e5L,
+ 0xbe2b5b58L, 0xbaea46efL, 0xb7a96036L, 0xb3687d81L,
+ 0xad2f2d84L, 0xa9ee3033L, 0xa4ad16eaL, 0xa06c0b5dL,
+ 0xd4326d90L, 0xd0f37027L, 0xddb056feL, 0xd9714b49L,
+ 0xc7361b4cL, 0xc3f706fbL, 0xceb42022L, 0xca753d95L,
+ 0xf23a8028L, 0xf6fb9d9fL, 0xfbb8bb46L, 0xff79a6f1L,
+ 0xe13ef6f4L, 0xe5ffeb43L, 0xe8bccd9aL, 0xec7dd02dL,
+ 0x34867077L, 0x30476dc0L, 0x3d044b19L, 0x39c556aeL,
+ 0x278206abL, 0x23431b1cL, 0x2e003dc5L, 0x2ac12072L,
+ 0x128e9dcfL, 0x164f8078L, 0x1b0ca6a1L, 0x1fcdbb16L,
+ 0x018aeb13L, 0x054bf6a4L, 0x0808d07dL, 0x0cc9cdcaL,
+ 0x7897ab07L, 0x7c56b6b0L, 0x71159069L, 0x75d48ddeL,
+ 0x6b93dddbL, 0x6f52c06cL, 0x6211e6b5L, 0x66d0fb02L,
+ 0x5e9f46bfL, 0x5a5e5b08L, 0x571d7dd1L, 0x53dc6066L,
+ 0x4d9b3063L, 0x495a2dd4L, 0x44190b0dL, 0x40d816baL,
+ 0xaca5c697L, 0xa864db20L, 0xa527fdf9L, 0xa1e6e04eL,
+ 0xbfa1b04bL, 0xbb60adfcL, 0xb6238b25L, 0xb2e29692L,
+ 0x8aad2b2fL, 0x8e6c3698L, 0x832f1041L, 0x87ee0df6L,
+ 0x99a95df3L, 0x9d684044L, 0x902b669dL, 0x94ea7b2aL,
+ 0xe0b41de7L, 0xe4750050L, 0xe9362689L, 0xedf73b3eL,
+ 0xf3b06b3bL, 0xf771768cL, 0xfa325055L, 0xfef34de2L,
+ 0xc6bcf05fL, 0xc27dede8L, 0xcf3ecb31L, 0xcbffd686L,
+ 0xd5b88683L, 0xd1799b34L, 0xdc3abdedL, 0xd8fba05aL,
+ 0x690ce0eeL, 0x6dcdfd59L, 0x608edb80L, 0x644fc637L,
+ 0x7a089632L, 0x7ec98b85L, 0x738aad5cL, 0x774bb0ebL,
+ 0x4f040d56L, 0x4bc510e1L, 0x46863638L, 0x42472b8fL,
+ 0x5c007b8aL, 0x58c1663dL, 0x558240e4L, 0x51435d53L,
+ 0x251d3b9eL, 0x21dc2629L, 0x2c9f00f0L, 0x285e1d47L,
+ 0x36194d42L, 0x32d850f5L, 0x3f9b762cL, 0x3b5a6b9bL,
+ 0x0315d626L, 0x07d4cb91L, 0x0a97ed48L, 0x0e56f0ffL,
+ 0x1011a0faL, 0x14d0bd4dL, 0x19939b94L, 0x1d528623L,
+ 0xf12f560eL, 0xf5ee4bb9L, 0xf8ad6d60L, 0xfc6c70d7L,
+ 0xe22b20d2L, 0xe6ea3d65L, 0xeba91bbcL, 0xef68060bL,
+ 0xd727bbb6L, 0xd3e6a601L, 0xdea580d8L, 0xda649d6fL,
+ 0xc423cd6aL, 0xc0e2d0ddL, 0xcda1f604L, 0xc960ebb3L,
+ 0xbd3e8d7eL, 0xb9ff90c9L, 0xb4bcb610L, 0xb07daba7L,
+ 0xae3afba2L, 0xaafbe615L, 0xa7b8c0ccL, 0xa379dd7bL,
+ 0x9b3660c6L, 0x9ff77d71L, 0x92b45ba8L, 0x9675461fL,
+ 0x8832161aL, 0x8cf30badL, 0x81b02d74L, 0x857130c3L,
+ 0x5d8a9099L, 0x594b8d2eL, 0x5408abf7L, 0x50c9b640L,
+ 0x4e8ee645L, 0x4a4ffbf2L, 0x470cdd2bL, 0x43cdc09cL,
+ 0x7b827d21L, 0x7f436096L, 0x7200464fL, 0x76c15bf8L,
+ 0x68860bfdL, 0x6c47164aL, 0x61043093L, 0x65c52d24L,
+ 0x119b4be9L, 0x155a565eL, 0x18197087L, 0x1cd86d30L,
+ 0x029f3d35L, 0x065e2082L, 0x0b1d065bL, 0x0fdc1becL,
+ 0x3793a651L, 0x3352bbe6L, 0x3e119d3fL, 0x3ad08088L,
+ 0x2497d08dL, 0x2056cd3aL, 0x2d15ebe3L, 0x29d4f654L,
+ 0xc5a92679L, 0xc1683bceL, 0xcc2b1d17L, 0xc8ea00a0L,
+ 0xd6ad50a5L, 0xd26c4d12L, 0xdf2f6bcbL, 0xdbee767cL,
+ 0xe3a1cbc1L, 0xe760d676L, 0xea23f0afL, 0xeee2ed18L,
+ 0xf0a5bd1dL, 0xf464a0aaL, 0xf9278673L, 0xfde69bc4L,
+ 0x89b8fd09L, 0x8d79e0beL, 0x803ac667L, 0x84fbdbd0L,
+ 0x9abc8bd5L, 0x9e7d9662L, 0x933eb0bbL, 0x97ffad0cL,
+ 0xafb010b1L, 0xab710d06L, 0xa6322bdfL, 0xa2f33668L,
+ 0xbcb4666dL, 0xb8757bdaL, 0xb5365d03L, 0xb1f740b4L
+};
+
+
+/*-------------------------------------------------------------*/
+/*--- end crctable.c ---*/
+/*-------------------------------------------------------------*/
diff --git a/third-party/bzip2/decompress.c b/third-party/bzip2/decompress.c
new file mode 100644
index 0000000..311f566
--- /dev/null
+++ b/third-party/bzip2/decompress.c
@@ -0,0 +1,646 @@
+
+/*-------------------------------------------------------------*/
+/*--- Decompression machinery ---*/
+/*--- decompress.c ---*/
+/*-------------------------------------------------------------*/
+
+/* ------------------------------------------------------------------
+ This file is part of bzip2/libbzip2, a program and library for
+ lossless, block-sorting data compression.
+
+ bzip2/libbzip2 version 1.0.6 of 6 September 2010
+ Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
+
+ Please read the WARNING, DISCLAIMER and PATENTS sections in the
+ README file.
+
+ This program is released under the terms of the license contained
+ in the file LICENSE.
+ ------------------------------------------------------------------ */
+
+
+#include "bzlib_private.h"
+
+
+/*---------------------------------------------------*/
+static
+void makeMaps_d ( DState* s )
+{
+ Int32 i;
+ s->nInUse = 0;
+ for (i = 0; i < 256; i++)
+ if (s->inUse[i]) {
+ s->seqToUnseq[s->nInUse] = i;
+ s->nInUse++;
+ }
+}
+
+
+/*---------------------------------------------------*/
+#define RETURN(rrr) \
+ { retVal = rrr; goto save_state_and_return; };
+
+#define GET_BITS(lll,vvv,nnn) \
+ case lll: s->state = lll; \
+ while (True) { \
+ if (s->bsLive >= nnn) { \
+ UInt32 v; \
+ v = (s->bsBuff >> \
+ (s->bsLive-nnn)) & ((1 << nnn)-1); \
+ s->bsLive -= nnn; \
+ vvv = v; \
+ break; \
+ } \
+ if (s->strm->avail_in == 0) RETURN(BZ_OK); \
+ s->bsBuff \
+ = (s->bsBuff << 8) | \
+ ((UInt32) \
+ (*((UChar*)(s->strm->next_in)))); \
+ s->bsLive += 8; \
+ s->strm->next_in++; \
+ s->strm->avail_in--; \
+ s->strm->total_in_lo32++; \
+ if (s->strm->total_in_lo32 == 0) \
+ s->strm->total_in_hi32++; \
+ }
+
+#define GET_UCHAR(lll,uuu) \
+ GET_BITS(lll,uuu,8)
+
+#define GET_BIT(lll,uuu) \
+ GET_BITS(lll,uuu,1)
+
+/*---------------------------------------------------*/
+#define GET_MTF_VAL(label1,label2,lval) \
+{ \
+ if (groupPos == 0) { \
+ groupNo++; \
+ if (groupNo >= nSelectors) \
+ RETURN(BZ_DATA_ERROR); \
+ groupPos = BZ_G_SIZE; \
+ gSel = s->selector[groupNo]; \
+ gMinlen = s->minLens[gSel]; \
+ gLimit = &(s->limit[gSel][0]); \
+ gPerm = &(s->perm[gSel][0]); \
+ gBase = &(s->base[gSel][0]); \
+ } \
+ groupPos--; \
+ zn = gMinlen; \
+ GET_BITS(label1, zvec, zn); \
+ while (1) { \
+ if (zn > 20 /* the longest code */) \
+ RETURN(BZ_DATA_ERROR); \
+ if (zvec <= gLimit[zn]) break; \
+ zn++; \
+ GET_BIT(label2, zj); \
+ zvec = (zvec << 1) | zj; \
+ }; \
+ if (zvec - gBase[zn] < 0 \
+ || zvec - gBase[zn] >= BZ_MAX_ALPHA_SIZE) \
+ RETURN(BZ_DATA_ERROR); \
+ lval = gPerm[zvec - gBase[zn]]; \
+}
+
+
+/*---------------------------------------------------*/
+Int32 BZ2_decompress ( DState* s )
+{
+ UChar uc;
+ Int32 retVal;
+ Int32 minLen, maxLen;
+ bz_stream* strm = s->strm;
+
+ /* stuff that needs to be saved/restored */
+ Int32 i;
+ Int32 j;
+ Int32 t;
+ Int32 alphaSize;
+ Int32 nGroups;
+ Int32 nSelectors;
+ Int32 EOB;
+ Int32 groupNo;
+ Int32 groupPos;
+ Int32 nextSym;
+ Int32 nblockMAX;
+ Int32 nblock;
+ Int32 es;
+ Int32 N;
+ Int32 curr;
+ Int32 zt;
+ Int32 zn;
+ Int32 zvec;
+ Int32 zj;
+ Int32 gSel;
+ Int32 gMinlen;
+ Int32* gLimit;
+ Int32* gBase;
+ Int32* gPerm;
+
+ if (s->state == BZ_X_MAGIC_1) {
+ /*initialise the save area*/
+ s->save_i = 0;
+ s->save_j = 0;
+ s->save_t = 0;
+ s->save_alphaSize = 0;
+ s->save_nGroups = 0;
+ s->save_nSelectors = 0;
+ s->save_EOB = 0;
+ s->save_groupNo = 0;
+ s->save_groupPos = 0;
+ s->save_nextSym = 0;
+ s->save_nblockMAX = 0;
+ s->save_nblock = 0;
+ s->save_es = 0;
+ s->save_N = 0;
+ s->save_curr = 0;
+ s->save_zt = 0;
+ s->save_zn = 0;
+ s->save_zvec = 0;
+ s->save_zj = 0;
+ s->save_gSel = 0;
+ s->save_gMinlen = 0;
+ s->save_gLimit = NULL;
+ s->save_gBase = NULL;
+ s->save_gPerm = NULL;
+ }
+
+ /*restore from the save area*/
+ i = s->save_i;
+ j = s->save_j;
+ t = s->save_t;
+ alphaSize = s->save_alphaSize;
+ nGroups = s->save_nGroups;
+ nSelectors = s->save_nSelectors;
+ EOB = s->save_EOB;
+ groupNo = s->save_groupNo;
+ groupPos = s->save_groupPos;
+ nextSym = s->save_nextSym;
+ nblockMAX = s->save_nblockMAX;
+ nblock = s->save_nblock;
+ es = s->save_es;
+ N = s->save_N;
+ curr = s->save_curr;
+ zt = s->save_zt;
+ zn = s->save_zn;
+ zvec = s->save_zvec;
+ zj = s->save_zj;
+ gSel = s->save_gSel;
+ gMinlen = s->save_gMinlen;
+ gLimit = s->save_gLimit;
+ gBase = s->save_gBase;
+ gPerm = s->save_gPerm;
+
+ retVal = BZ_OK;
+
+ switch (s->state) {
+
+ GET_UCHAR(BZ_X_MAGIC_1, uc);
+ if (uc != BZ_HDR_B) RETURN(BZ_DATA_ERROR_MAGIC);
+
+ GET_UCHAR(BZ_X_MAGIC_2, uc);
+ if (uc != BZ_HDR_Z) RETURN(BZ_DATA_ERROR_MAGIC);
+
+ GET_UCHAR(BZ_X_MAGIC_3, uc)
+ if (uc != BZ_HDR_h) RETURN(BZ_DATA_ERROR_MAGIC);
+
+ GET_BITS(BZ_X_MAGIC_4, s->blockSize100k, 8)
+ if (s->blockSize100k < (BZ_HDR_0 + 1) ||
+ s->blockSize100k > (BZ_HDR_0 + 9)) RETURN(BZ_DATA_ERROR_MAGIC);
+ s->blockSize100k -= BZ_HDR_0;
+
+ if (s->smallDecompress) {
+ s->ll16 = BZALLOC( s->blockSize100k * 100000 * sizeof(UInt16) );
+ s->ll4 = BZALLOC(
+ ((1 + s->blockSize100k * 100000) >> 1) * sizeof(UChar)
+ );
+ if (s->ll16 == NULL || s->ll4 == NULL) RETURN(BZ_MEM_ERROR);
+ } else {
+ s->tt = BZALLOC( s->blockSize100k * 100000 * sizeof(Int32) );
+ if (s->tt == NULL) RETURN(BZ_MEM_ERROR);
+ }
+
+ GET_UCHAR(BZ_X_BLKHDR_1, uc);
+
+ if (uc == 0x17) goto endhdr_2;
+ if (uc != 0x31) RETURN(BZ_DATA_ERROR);
+ GET_UCHAR(BZ_X_BLKHDR_2, uc);
+ if (uc != 0x41) RETURN(BZ_DATA_ERROR);
+ GET_UCHAR(BZ_X_BLKHDR_3, uc);
+ if (uc != 0x59) RETURN(BZ_DATA_ERROR);
+ GET_UCHAR(BZ_X_BLKHDR_4, uc);
+ if (uc != 0x26) RETURN(BZ_DATA_ERROR);
+ GET_UCHAR(BZ_X_BLKHDR_5, uc);
+ if (uc != 0x53) RETURN(BZ_DATA_ERROR);
+ GET_UCHAR(BZ_X_BLKHDR_6, uc);
+ if (uc != 0x59) RETURN(BZ_DATA_ERROR);
+
+ s->currBlockNo++;
+ if (s->verbosity >= 2)
+ VPrintf1 ( "\n [%d: huff+mtf ", s->currBlockNo );
+
+ s->storedBlockCRC = 0;
+ GET_UCHAR(BZ_X_BCRC_1, uc);
+ s->storedBlockCRC = (s->storedBlockCRC << 8) | ((UInt32)uc);
+ GET_UCHAR(BZ_X_BCRC_2, uc);
+ s->storedBlockCRC = (s->storedBlockCRC << 8) | ((UInt32)uc);
+ GET_UCHAR(BZ_X_BCRC_3, uc);
+ s->storedBlockCRC = (s->storedBlockCRC << 8) | ((UInt32)uc);
+ GET_UCHAR(BZ_X_BCRC_4, uc);
+ s->storedBlockCRC = (s->storedBlockCRC << 8) | ((UInt32)uc);
+
+ GET_BITS(BZ_X_RANDBIT, s->blockRandomised, 1);
+
+ s->origPtr = 0;
+ GET_UCHAR(BZ_X_ORIGPTR_1, uc);
+ s->origPtr = (s->origPtr << 8) | ((Int32)uc);
+ GET_UCHAR(BZ_X_ORIGPTR_2, uc);
+ s->origPtr = (s->origPtr << 8) | ((Int32)uc);
+ GET_UCHAR(BZ_X_ORIGPTR_3, uc);
+ s->origPtr = (s->origPtr << 8) | ((Int32)uc);
+
+ if (s->origPtr < 0)
+ RETURN(BZ_DATA_ERROR);
+ if (s->origPtr > 10 + 100000*s->blockSize100k)
+ RETURN(BZ_DATA_ERROR);
+
+ /*--- Receive the mapping table ---*/
+ for (i = 0; i < 16; i++) {
+ GET_BIT(BZ_X_MAPPING_1, uc);
+ if (uc == 1)
+ s->inUse16[i] = True; else
+ s->inUse16[i] = False;
+ }
+
+ for (i = 0; i < 256; i++) s->inUse[i] = False;
+
+ for (i = 0; i < 16; i++)
+ if (s->inUse16[i])
+ for (j = 0; j < 16; j++) {
+ GET_BIT(BZ_X_MAPPING_2, uc);
+ if (uc == 1) s->inUse[i * 16 + j] = True;
+ }
+ makeMaps_d ( s );
+ if (s->nInUse == 0) RETURN(BZ_DATA_ERROR);
+ alphaSize = s->nInUse+2;
+
+ /*--- Now the selectors ---*/
+ GET_BITS(BZ_X_SELECTOR_1, nGroups, 3);
+ if (nGroups < 2 || nGroups > 6) RETURN(BZ_DATA_ERROR);
+ GET_BITS(BZ_X_SELECTOR_2, nSelectors, 15);
+ if (nSelectors < 1) RETURN(BZ_DATA_ERROR);
+ for (i = 0; i < nSelectors; i++) {
+ j = 0;
+ while (True) {
+ GET_BIT(BZ_X_SELECTOR_3, uc);
+ if (uc == 0) break;
+ j++;
+ if (j >= nGroups) RETURN(BZ_DATA_ERROR);
+ }
+ s->selectorMtf[i] = j;
+ }
+
+ /*--- Undo the MTF values for the selectors. ---*/
+ {
+ UChar pos[BZ_N_GROUPS], tmp, v;
+ for (v = 0; v < nGroups; v++) pos[v] = v;
+
+ for (i = 0; i < nSelectors; i++) {
+ v = s->selectorMtf[i];
+ tmp = pos[v];
+ while (v > 0) { pos[v] = pos[v-1]; v--; }
+ pos[0] = tmp;
+ s->selector[i] = tmp;
+ }
+ }
+
+ /*--- Now the coding tables ---*/
+ for (t = 0; t < nGroups; t++) {
+ GET_BITS(BZ_X_CODING_1, curr, 5);
+ for (i = 0; i < alphaSize; i++) {
+ while (True) {
+ if (curr < 1 || curr > 20) RETURN(BZ_DATA_ERROR);
+ GET_BIT(BZ_X_CODING_2, uc);
+ if (uc == 0) break;
+ GET_BIT(BZ_X_CODING_3, uc);
+ if (uc == 0) curr++; else curr--;
+ }
+ s->len[t][i] = curr;
+ }
+ }
+
+ /*--- Create the Huffman decoding tables ---*/
+ for (t = 0; t < nGroups; t++) {
+ minLen = 32;
+ maxLen = 0;
+ for (i = 0; i < alphaSize; i++) {
+ if (s->len[t][i] > maxLen) maxLen = s->len[t][i];
+ if (s->len[t][i] < minLen) minLen = s->len[t][i];
+ }
+ BZ2_hbCreateDecodeTables (
+ &(s->limit[t][0]),
+ &(s->base[t][0]),
+ &(s->perm[t][0]),
+ &(s->len[t][0]),
+ minLen, maxLen, alphaSize
+ );
+ s->minLens[t] = minLen;
+ }
+
+ /*--- Now the MTF values ---*/
+
+ EOB = s->nInUse+1;
+ nblockMAX = 100000 * s->blockSize100k;
+ groupNo = -1;
+ groupPos = 0;
+
+ for (i = 0; i <= 255; i++) s->unzftab[i] = 0;
+
+ /*-- MTF init --*/
+ {
+ Int32 ii, jj, kk;
+ kk = MTFA_SIZE-1;
+ for (ii = 256 / MTFL_SIZE - 1; ii >= 0; ii--) {
+ for (jj = MTFL_SIZE-1; jj >= 0; jj--) {
+ s->mtfa[kk] = (UChar)(ii * MTFL_SIZE + jj);
+ kk--;
+ }
+ s->mtfbase[ii] = kk + 1;
+ }
+ }
+ /*-- end MTF init --*/
+
+ nblock = 0;
+ GET_MTF_VAL(BZ_X_MTF_1, BZ_X_MTF_2, nextSym);
+
+ while (True) {
+
+ if (nextSym == EOB) break;
+
+ if (nextSym == BZ_RUNA || nextSym == BZ_RUNB) {
+
+ es = -1;
+ N = 1;
+ do {
+ /* Check that N doesn't get too big, so that es doesn't
+ go negative. The maximum value that can be
+ RUNA/RUNB encoded is equal to the block size (post
+ the initial RLE), viz, 900k, so bounding N at 2
+ million should guard against overflow without
+ rejecting any legitimate inputs. */
+ if (N >= 2*1024*1024) RETURN(BZ_DATA_ERROR);
+ if (nextSym == BZ_RUNA) es = es + (0+1) * N; else
+ if (nextSym == BZ_RUNB) es = es + (1+1) * N;
+ N = N * 2;
+ GET_MTF_VAL(BZ_X_MTF_3, BZ_X_MTF_4, nextSym);
+ }
+ while (nextSym == BZ_RUNA || nextSym == BZ_RUNB);
+
+ es++;
+ uc = s->seqToUnseq[ s->mtfa[s->mtfbase[0]] ];
+ s->unzftab[uc] += es;
+
+ if (s->smallDecompress)
+ while (es > 0) {
+ if (nblock >= nblockMAX) RETURN(BZ_DATA_ERROR);
+ s->ll16[nblock] = (UInt16)uc;
+ nblock++;
+ es--;
+ }
+ else
+ while (es > 0) {
+ if (nblock >= nblockMAX) RETURN(BZ_DATA_ERROR);
+ s->tt[nblock] = (UInt32)uc;
+ nblock++;
+ es--;
+ };
+
+ continue;
+
+ } else {
+
+ if (nblock >= nblockMAX) RETURN(BZ_DATA_ERROR);
+
+ /*-- uc = MTF ( nextSym-1 ) --*/
+ {
+ Int32 ii, jj, kk, pp, lno, off;
+ UInt32 nn;
+ nn = (UInt32)(nextSym - 1);
+
+ if (nn < MTFL_SIZE) {
+ /* avoid general-case expense */
+ pp = s->mtfbase[0];
+ uc = s->mtfa[pp+nn];
+ while (nn > 3) {
+ Int32 z = pp+nn;
+ s->mtfa[(z) ] = s->mtfa[(z)-1];
+ s->mtfa[(z)-1] = s->mtfa[(z)-2];
+ s->mtfa[(z)-2] = s->mtfa[(z)-3];
+ s->mtfa[(z)-3] = s->mtfa[(z)-4];
+ nn -= 4;
+ }
+ while (nn > 0) {
+ s->mtfa[(pp+nn)] = s->mtfa[(pp+nn)-1]; nn--;
+ };
+ s->mtfa[pp] = uc;
+ } else {
+ /* general case */
+ lno = nn / MTFL_SIZE;
+ off = nn % MTFL_SIZE;
+ pp = s->mtfbase[lno] + off;
+ uc = s->mtfa[pp];
+ while (pp > s->mtfbase[lno]) {
+ s->mtfa[pp] = s->mtfa[pp-1]; pp--;
+ };
+ s->mtfbase[lno]++;
+ while (lno > 0) {
+ s->mtfbase[lno]--;
+ s->mtfa[s->mtfbase[lno]]
+ = s->mtfa[s->mtfbase[lno-1] + MTFL_SIZE - 1];
+ lno--;
+ }
+ s->mtfbase[0]--;
+ s->mtfa[s->mtfbase[0]] = uc;
+ if (s->mtfbase[0] == 0) {
+ kk = MTFA_SIZE-1;
+ for (ii = 256 / MTFL_SIZE-1; ii >= 0; ii--) {
+ for (jj = MTFL_SIZE-1; jj >= 0; jj--) {
+ s->mtfa[kk] = s->mtfa[s->mtfbase[ii] + jj];
+ kk--;
+ }
+ s->mtfbase[ii] = kk + 1;
+ }
+ }
+ }
+ }
+ /*-- end uc = MTF ( nextSym-1 ) --*/
+
+ s->unzftab[s->seqToUnseq[uc]]++;
+ if (s->smallDecompress)
+ s->ll16[nblock] = (UInt16)(s->seqToUnseq[uc]); else
+ s->tt[nblock] = (UInt32)(s->seqToUnseq[uc]);
+ nblock++;
+
+ GET_MTF_VAL(BZ_X_MTF_5, BZ_X_MTF_6, nextSym);
+ continue;
+ }
+ }
+
+ /* Now we know what nblock is, we can do a better sanity
+ check on s->origPtr.
+ */
+ if (s->origPtr < 0 || s->origPtr >= nblock)
+ RETURN(BZ_DATA_ERROR);
+
+ /*-- Set up cftab to facilitate generation of T^(-1) --*/
+ /* Check: unzftab entries in range. */
+ for (i = 0; i <= 255; i++) {
+ if (s->unzftab[i] < 0 || s->unzftab[i] > nblock)
+ RETURN(BZ_DATA_ERROR);
+ }
+ /* Actually generate cftab. */
+ s->cftab[0] = 0;
+ for (i = 1; i <= 256; i++) s->cftab[i] = s->unzftab[i-1];
+ for (i = 1; i <= 256; i++) s->cftab[i] += s->cftab[i-1];
+ /* Check: cftab entries in range. */
+ for (i = 0; i <= 256; i++) {
+ if (s->cftab[i] < 0 || s->cftab[i] > nblock) {
+ /* s->cftab[i] can legitimately be == nblock */
+ RETURN(BZ_DATA_ERROR);
+ }
+ }
+ /* Check: cftab entries non-descending. */
+ for (i = 1; i <= 256; i++) {
+ if (s->cftab[i-1] > s->cftab[i]) {
+ RETURN(BZ_DATA_ERROR);
+ }
+ }
+
+ s->state_out_len = 0;
+ s->state_out_ch = 0;
+ BZ_INITIALISE_CRC ( s->calculatedBlockCRC );
+ s->state = BZ_X_OUTPUT;
+ if (s->verbosity >= 2) VPrintf0 ( "rt+rld" );
+
+ if (s->smallDecompress) {
+
+ /*-- Make a copy of cftab, used in generation of T --*/
+ for (i = 0; i <= 256; i++) s->cftabCopy[i] = s->cftab[i];
+
+ /*-- compute the T vector --*/
+ for (i = 0; i < nblock; i++) {
+ uc = (UChar)(s->ll16[i]);
+ SET_LL(i, s->cftabCopy[uc]);
+ s->cftabCopy[uc]++;
+ }
+
+ /*-- Compute T^(-1) by pointer reversal on T --*/
+ i = s->origPtr;
+ j = GET_LL(i);
+ do {
+ Int32 tmp = GET_LL(j);
+ SET_LL(j, i);
+ i = j;
+ j = tmp;
+ }
+ while (i != s->origPtr);
+
+ s->tPos = s->origPtr;
+ s->nblock_used = 0;
+ if (s->blockRandomised) {
+ BZ_RAND_INIT_MASK;
+ BZ_GET_SMALL(s->k0); s->nblock_used++;
+ BZ_RAND_UPD_MASK; s->k0 ^= BZ_RAND_MASK;
+ } else {
+ BZ_GET_SMALL(s->k0); s->nblock_used++;
+ }
+
+ } else {
+
+ /*-- compute the T^(-1) vector --*/
+ for (i = 0; i < nblock; i++) {
+ uc = (UChar)(s->tt[i] & 0xff);
+ s->tt[s->cftab[uc]] |= (i << 8);
+ s->cftab[uc]++;
+ }
+
+ s->tPos = s->tt[s->origPtr] >> 8;
+ s->nblock_used = 0;
+ if (s->blockRandomised) {
+ BZ_RAND_INIT_MASK;
+ BZ_GET_FAST(s->k0); s->nblock_used++;
+ BZ_RAND_UPD_MASK; s->k0 ^= BZ_RAND_MASK;
+ } else {
+ BZ_GET_FAST(s->k0); s->nblock_used++;
+ }
+
+ }
+
+ RETURN(BZ_OK);
+
+
+
+ endhdr_2:
+
+ GET_UCHAR(BZ_X_ENDHDR_2, uc);
+ if (uc != 0x72) RETURN(BZ_DATA_ERROR);
+ GET_UCHAR(BZ_X_ENDHDR_3, uc);
+ if (uc != 0x45) RETURN(BZ_DATA_ERROR);
+ GET_UCHAR(BZ_X_ENDHDR_4, uc);
+ if (uc != 0x38) RETURN(BZ_DATA_ERROR);
+ GET_UCHAR(BZ_X_ENDHDR_5, uc);
+ if (uc != 0x50) RETURN(BZ_DATA_ERROR);
+ GET_UCHAR(BZ_X_ENDHDR_6, uc);
+ if (uc != 0x90) RETURN(BZ_DATA_ERROR);
+
+ s->storedCombinedCRC = 0;
+ GET_UCHAR(BZ_X_CCRC_1, uc);
+ s->storedCombinedCRC = (s->storedCombinedCRC << 8) | ((UInt32)uc);
+ GET_UCHAR(BZ_X_CCRC_2, uc);
+ s->storedCombinedCRC = (s->storedCombinedCRC << 8) | ((UInt32)uc);
+ GET_UCHAR(BZ_X_CCRC_3, uc);
+ s->storedCombinedCRC = (s->storedCombinedCRC << 8) | ((UInt32)uc);
+ GET_UCHAR(BZ_X_CCRC_4, uc);
+ s->storedCombinedCRC = (s->storedCombinedCRC << 8) | ((UInt32)uc);
+
+ s->state = BZ_X_IDLE;
+ RETURN(BZ_STREAM_END);
+
+ default: AssertH ( False, 4001 );
+ }
+
+ AssertH ( False, 4002 );
+
+ save_state_and_return:
+
+ s->save_i = i;
+ s->save_j = j;
+ s->save_t = t;
+ s->save_alphaSize = alphaSize;
+ s->save_nGroups = nGroups;
+ s->save_nSelectors = nSelectors;
+ s->save_EOB = EOB;
+ s->save_groupNo = groupNo;
+ s->save_groupPos = groupPos;
+ s->save_nextSym = nextSym;
+ s->save_nblockMAX = nblockMAX;
+ s->save_nblock = nblock;
+ s->save_es = es;
+ s->save_N = N;
+ s->save_curr = curr;
+ s->save_zt = zt;
+ s->save_zn = zn;
+ s->save_zvec = zvec;
+ s->save_zj = zj;
+ s->save_gSel = gSel;
+ s->save_gMinlen = gMinlen;
+ s->save_gLimit = gLimit;
+ s->save_gBase = gBase;
+ s->save_gPerm = gPerm;
+
+ return retVal;
+}
+
+
+/*-------------------------------------------------------------*/
+/*--- end decompress.c ---*/
+/*-------------------------------------------------------------*/
diff --git a/third-party/bzip2/dlltest.c b/third-party/bzip2/dlltest.c
new file mode 100644
index 0000000..03fa146
--- /dev/null
+++ b/third-party/bzip2/dlltest.c
@@ -0,0 +1,175 @@
+/*
+ minibz2
+ libbz2.dll test program.
+ by Yoshioka Tsuneo (tsuneo at rr.iij4u.or.jp)
+ This file is Public Domain. Welcome any email to me.
+
+ usage: minibz2 [-d] [-{1,2,..9}] [[srcfilename] destfilename]
+*/
+
+#define BZ_IMPORT
+#include <stdio.h>
+#include <stdlib.h>
+#include "bzlib.h"
+#ifdef _WIN32
+#include <io.h>
+#endif
+
+
+#ifdef _WIN32
+
+#define BZ2_LIBNAME "libbz2-1.0.2.DLL"
+
+#include <windows.h>
+static int BZ2DLLLoaded = 0;
+static HINSTANCE BZ2DLLhLib;
+int BZ2DLLLoadLibrary(void)
+{
+ HINSTANCE hLib;
+
+ if(BZ2DLLLoaded==1){return 0;}
+ hLib=LoadLibrary(BZ2_LIBNAME);
+ if(hLib == NULL){
+ fprintf(stderr,"Can't load %s\n",BZ2_LIBNAME);
+ return -1;
+ }
+ BZ2_bzlibVersion=GetProcAddress(hLib,"BZ2_bzlibVersion");
+ BZ2_bzopen=GetProcAddress(hLib,"BZ2_bzopen");
+ BZ2_bzdopen=GetProcAddress(hLib,"BZ2_bzdopen");
+ BZ2_bzread=GetProcAddress(hLib,"BZ2_bzread");
+ BZ2_bzwrite=GetProcAddress(hLib,"BZ2_bzwrite");
+ BZ2_bzflush=GetProcAddress(hLib,"BZ2_bzflush");
+ BZ2_bzclose=GetProcAddress(hLib,"BZ2_bzclose");
+ BZ2_bzerror=GetProcAddress(hLib,"BZ2_bzerror");
+
+ if (!BZ2_bzlibVersion || !BZ2_bzopen || !BZ2_bzdopen
+ || !BZ2_bzread || !BZ2_bzwrite || !BZ2_bzflush
+ || !BZ2_bzclose || !BZ2_bzerror) {
+ fprintf(stderr,"GetProcAddress failed.\n");
+ return -1;
+ }
+ BZ2DLLLoaded=1;
+ BZ2DLLhLib=hLib;
+ return 0;
+
+}
+int BZ2DLLFreeLibrary(void)
+{
+ if(BZ2DLLLoaded==0){return 0;}
+ FreeLibrary(BZ2DLLhLib);
+ BZ2DLLLoaded=0;
+}
+#endif /* WIN32 */
+
+void usage(void)
+{
+ puts("usage: minibz2 [-d] [-{1,2,..9}] [[srcfilename] destfilename]");
+}
+
+int main(int argc,char *argv[])
+{
+ int decompress = 0;
+ int level = 9;
+ char *fn_r = NULL;
+ char *fn_w = NULL;
+
+#ifdef _WIN32
+ if(BZ2DLLLoadLibrary()<0){
+ fprintf(stderr,"Loading of %s failed. Giving up.\n", BZ2_LIBNAME);
+ exit(1);
+ }
+ printf("Loading of %s succeeded. Library version is %s.\n",
+ BZ2_LIBNAME, BZ2_bzlibVersion() );
+#endif
+ while(++argv,--argc){
+ if(**argv =='-' || **argv=='/'){
+ char *p;
+
+ for(p=*argv+1;*p;p++){
+ if(*p=='d'){
+ decompress = 1;
+ }else if('1'<=*p && *p<='9'){
+ level = *p - '0';
+ }else{
+ usage();
+ exit(1);
+ }
+ }
+ }else{
+ break;
+ }
+ }
+ if(argc>=1){
+ fn_r = *argv;
+ argc--;argv++;
+ }else{
+ fn_r = NULL;
+ }
+ if(argc>=1){
+ fn_w = *argv;
+ argc--;argv++;
+ }else{
+ fn_w = NULL;
+ }
+ {
+ int len;
+ char buff[0x1000];
+ char mode[10];
+
+ if(decompress){
+ BZFILE *BZ2fp_r = NULL;
+ FILE *fp_w = NULL;
+
+ if(fn_w){
+ if((fp_w = fopen(fn_w,"wb"))==NULL){
+ printf("can't open [%s]\n",fn_w);
+ perror("reason:");
+ exit(1);
+ }
+ }else{
+ fp_w = stdout;
+ }
+ if((fn_r == NULL && (BZ2fp_r = BZ2_bzdopen(fileno(stdin),"rb"))==NULL)
+ || (fn_r != NULL && (BZ2fp_r = BZ2_bzopen(fn_r,"rb"))==NULL)){
+ printf("can't bz2openstream\n");
+ exit(1);
+ }
+ while((len=BZ2_bzread(BZ2fp_r,buff,0x1000))>0){
+ fwrite(buff,1,len,fp_w);
+ }
+ BZ2_bzclose(BZ2fp_r);
+ if(fp_w != stdout) fclose(fp_w);
+ }else{
+ BZFILE *BZ2fp_w = NULL;
+ FILE *fp_r = NULL;
+
+ if(fn_r){
+ if((fp_r = fopen(fn_r,"rb"))==NULL){
+ printf("can't open [%s]\n",fn_r);
+ perror("reason:");
+ exit(1);
+ }
+ }else{
+ fp_r = stdin;
+ }
+ mode[0]='w';
+ mode[1] = '0' + level;
+ mode[2] = '\0';
+
+ if((fn_w == NULL && (BZ2fp_w = BZ2_bzdopen(fileno(stdout),mode))==NULL)
+ || (fn_w !=NULL && (BZ2fp_w = BZ2_bzopen(fn_w,mode))==NULL)){
+ printf("can't bz2openstream\n");
+ exit(1);
+ }
+ while((len=fread(buff,1,0x1000,fp_r))>0){
+ BZ2_bzwrite(BZ2fp_w,buff,len);
+ }
+ BZ2_bzclose(BZ2fp_w);
+ if(fp_r!=stdin)fclose(fp_r);
+ }
+ }
+#ifdef _WIN32
+ BZ2DLLFreeLibrary();
+#endif
+ return 0;
+}
diff --git a/third-party/bzip2/dlltest.dsp b/third-party/bzip2/dlltest.dsp
new file mode 100644
index 0000000..4b1615e
--- /dev/null
+++ b/third-party/bzip2/dlltest.dsp
@@ -0,0 +1,93 @@
+# Microsoft Developer Studio Project File - Name="dlltest" - Package Owner=<4>
+# Microsoft Developer Studio Generated Build File, Format Version 5.00
+# ** �ҏW���Ȃ��ł������� **
+
+# TARGTYPE "Win32 (x86) Console Application" 0x0103
+
+CFG=dlltest - Win32 Debug
+!MESSAGE ����͗L����Ҳ�̧�قł͂���܂���B ������ۼު�Ă�����ނ��邽�߂ɂ� NMAKE ��g�p���Ă��������B
+!MESSAGE [Ҳ�̧�ق̴���߰�] ����ނ�g�p���Ď��s���Ă�������
+!MESSAGE
+!MESSAGE NMAKE /f "dlltest.mak".
+!MESSAGE
+!MESSAGE NMAKE �̎��s���ɍ\����w��ł��܂�
+!MESSAGE ����� ײݏ��ϸۂ̐ݒ���`���܂��B��:
+!MESSAGE
+!MESSAGE NMAKE /f "dlltest.mak" CFG="dlltest - Win32 Debug"
+!MESSAGE
+!MESSAGE �I��”\������� Ӱ��:
+!MESSAGE
+!MESSAGE "dlltest - Win32 Release" ("Win32 (x86) Console Application" �p)
+!MESSAGE "dlltest - Win32 Debug" ("Win32 (x86) Console Application" �p)
+!MESSAGE
+
+# Begin Project
+# PROP Scc_ProjName ""
+# PROP Scc_LocalPath ""
+CPP=cl.exe
+RSC=rc.exe
+
+!IF "$(CFG)" == "dlltest - Win32 Release"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 0
+# PROP BASE Output_Dir "Release"
+# PROP BASE Intermediate_Dir "Release"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 0
+# PROP Output_Dir "Release"
+# PROP Intermediate_Dir "Release"
+# PROP Ignore_Export_Lib 0
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /c
+# ADD CPP /nologo /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /c
+# ADD BASE RSC /l 0x411 /d "NDEBUG"
+# ADD RSC /l 0x411 /d "NDEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LINK32=link.exe
+# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /machine:I386
+# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /machine:I386 /out:"minibz2.exe"
+
+!ELSEIF "$(CFG)" == "dlltest - Win32 Debug"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "dlltest_"
+# PROP BASE Intermediate_Dir "dlltest_"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "dlltest_"
+# PROP Intermediate_Dir "dlltest_"
+# PROP Ignore_Export_Lib 0
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /W3 /Gm /GX /Zi /Od /D "WIN32" /D "_DEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /c
+# ADD CPP /nologo /W3 /Gm /GX /Zi /Od /D "WIN32" /D "_DEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /c
+# ADD BASE RSC /l 0x411 /d "_DEBUG"
+# ADD RSC /l 0x411 /d "_DEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LINK32=link.exe
+# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /debug /machine:I386 /pdbtype:sept
+# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /debug /machine:I386 /out:"minibz2.exe" /pdbtype:sept
+
+!ENDIF
+
+# Begin Target
+
+# Name "dlltest - Win32 Release"
+# Name "dlltest - Win32 Debug"
+# Begin Source File
+
+SOURCE=.\bzlib.h
+# End Source File
+# Begin Source File
+
+SOURCE=.\dlltest.c
+# End Source File
+# End Target
+# End Project
diff --git a/third-party/bzip2/entities.xml b/third-party/bzip2/entities.xml
new file mode 100644
index 0000000..4b28f34
--- /dev/null
+++ b/third-party/bzip2/entities.xml
@@ -0,0 +1,9 @@
+<!-- misc. strings -->
+<!ENTITY bz-url "http://www.bzip.org">
+<!ENTITY bz-email "jseward at bzip.org">
+<!ENTITY bz-lifespan "1996-2010">
+
+<!ENTITY bz-version "1.0.6">
+<!ENTITY bz-date "6 September 2010">
+
+<!ENTITY manual-title "bzip2 Manual">
diff --git a/third-party/bzip2/format.pl b/third-party/bzip2/format.pl
new file mode 100755
index 0000000..f169fd9
--- /dev/null
+++ b/third-party/bzip2/format.pl
@@ -0,0 +1,68 @@
+#!/usr/bin/perl -w
+#
+# ------------------------------------------------------------------
+# This file is part of bzip2/libbzip2, a program and library for
+# lossless, block-sorting data compression.
+#
+# bzip2/libbzip2 version 1.0.6 of 6 September 2010
+# Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
+#
+# Please read the WARNING, DISCLAIMER and PATENTS sections in the
+# README file.
+#
+# This program is released under the terms of the license contained
+# in the file LICENSE.
+# ------------------------------------------------------------------
+#
+use strict;
+
+# get command line values:
+if ( $#ARGV !=1 ) {
+ die "Usage: $0 xml_infile xml_outfile\n";
+}
+
+my $infile = shift;
+# check infile exists
+die "Can't find file \"$infile\""
+ unless -f $infile;
+# check we can read infile
+if (! -r $infile) {
+ die "Can't read input $infile\n";
+}
+# check we can open infile
+open( INFILE,"<$infile" ) or
+ die "Can't input $infile $!";
+
+#my $outfile = 'fmt-manual.xml';
+my $outfile = shift;
+#print "Infile: $infile, Outfile: $outfile\n";
+# check we can write to outfile
+open( OUTFILE,">$outfile" ) or
+ die "Can't output $outfile $! for writing";
+
+my ($prev, $curr, $str);
+$prev = ''; $curr = '';
+while ( <INFILE> ) {
+
+ print OUTFILE $prev;
+ $prev = $curr;
+ $curr = $_;
+ $str = '';
+
+ if ( $prev =~ /<programlisting>$|<screen>$/ ) {
+ chomp $prev;
+ $curr = join( '', $prev, "<![CDATA[", $curr );
+ $prev = '';
+ next;
+ }
+ elsif ( $curr =~ /<\/programlisting>|<\/screen>/ ) {
+ chomp $prev;
+ $curr = join( '', $prev, "]]>", $curr );
+ $prev = '';
+ next;
+ }
+}
+print OUTFILE $curr;
+close INFILE;
+close OUTFILE;
+exit;
diff --git a/third-party/bzip2/huffman.c b/third-party/bzip2/huffman.c
new file mode 100644
index 0000000..2283fdb
--- /dev/null
+++ b/third-party/bzip2/huffman.c
@@ -0,0 +1,205 @@
+
+/*-------------------------------------------------------------*/
+/*--- Huffman coding low-level stuff ---*/
+/*--- huffman.c ---*/
+/*-------------------------------------------------------------*/
+
+/* ------------------------------------------------------------------
+ This file is part of bzip2/libbzip2, a program and library for
+ lossless, block-sorting data compression.
+
+ bzip2/libbzip2 version 1.0.6 of 6 September 2010
+ Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
+
+ Please read the WARNING, DISCLAIMER and PATENTS sections in the
+ README file.
+
+ This program is released under the terms of the license contained
+ in the file LICENSE.
+ ------------------------------------------------------------------ */
+
+
+#include "bzlib_private.h"
+
+/*---------------------------------------------------*/
+#define WEIGHTOF(zz0) ((zz0) & 0xffffff00)
+#define DEPTHOF(zz1) ((zz1) & 0x000000ff)
+#define MYMAX(zz2,zz3) ((zz2) > (zz3) ? (zz2) : (zz3))
+
+#define ADDWEIGHTS(zw1,zw2) \
+ (WEIGHTOF(zw1)+WEIGHTOF(zw2)) | \
+ (1 + MYMAX(DEPTHOF(zw1),DEPTHOF(zw2)))
+
+#define UPHEAP(z) \
+{ \
+ Int32 zz, tmp; \
+ zz = z; tmp = heap[zz]; \
+ while (weight[tmp] < weight[heap[zz >> 1]]) { \
+ heap[zz] = heap[zz >> 1]; \
+ zz >>= 1; \
+ } \
+ heap[zz] = tmp; \
+}
+
+#define DOWNHEAP(z) \
+{ \
+ Int32 zz, yy, tmp; \
+ zz = z; tmp = heap[zz]; \
+ while (True) { \
+ yy = zz << 1; \
+ if (yy > nHeap) break; \
+ if (yy < nHeap && \
+ weight[heap[yy+1]] < weight[heap[yy]]) \
+ yy++; \
+ if (weight[tmp] < weight[heap[yy]]) break; \
+ heap[zz] = heap[yy]; \
+ zz = yy; \
+ } \
+ heap[zz] = tmp; \
+}
+
+
+/*---------------------------------------------------*/
+void BZ2_hbMakeCodeLengths ( UChar *len,
+ Int32 *freq,
+ Int32 alphaSize,
+ Int32 maxLen )
+{
+ /*--
+ Nodes and heap entries run from 1. Entry 0
+ for both the heap and nodes is a sentinel.
+ --*/
+ Int32 nNodes, nHeap, n1, n2, i, j, k;
+ Bool tooLong;
+
+ Int32 heap [ BZ_MAX_ALPHA_SIZE + 2 ];
+ Int32 weight [ BZ_MAX_ALPHA_SIZE * 2 ];
+ Int32 parent [ BZ_MAX_ALPHA_SIZE * 2 ];
+
+ for (i = 0; i < alphaSize; i++)
+ weight[i+1] = (freq[i] == 0 ? 1 : freq[i]) << 8;
+
+ while (True) {
+
+ nNodes = alphaSize;
+ nHeap = 0;
+
+ heap[0] = 0;
+ weight[0] = 0;
+ parent[0] = -2;
+
+ for (i = 1; i <= alphaSize; i++) {
+ parent[i] = -1;
+ nHeap++;
+ heap[nHeap] = i;
+ UPHEAP(nHeap);
+ }
+
+ AssertH( nHeap < (BZ_MAX_ALPHA_SIZE+2), 2001 );
+
+ while (nHeap > 1) {
+ n1 = heap[1]; heap[1] = heap[nHeap]; nHeap--; DOWNHEAP(1);
+ n2 = heap[1]; heap[1] = heap[nHeap]; nHeap--; DOWNHEAP(1);
+ nNodes++;
+ parent[n1] = parent[n2] = nNodes;
+ weight[nNodes] = ADDWEIGHTS(weight[n1], weight[n2]);
+ parent[nNodes] = -1;
+ nHeap++;
+ heap[nHeap] = nNodes;
+ UPHEAP(nHeap);
+ }
+
+ AssertH( nNodes < (BZ_MAX_ALPHA_SIZE * 2), 2002 );
+
+ tooLong = False;
+ for (i = 1; i <= alphaSize; i++) {
+ j = 0;
+ k = i;
+ while (parent[k] >= 0) { k = parent[k]; j++; }
+ len[i-1] = j;
+ if (j > maxLen) tooLong = True;
+ }
+
+ if (! tooLong) break;
+
+ /* 17 Oct 04: keep-going condition for the following loop used
+ to be 'i < alphaSize', which missed the last element,
+ theoretically leading to the possibility of the compressor
+ looping. However, this count-scaling step is only needed if
+ one of the generated Huffman code words is longer than
+ maxLen, which up to and including version 1.0.2 was 20 bits,
+ which is extremely unlikely. In version 1.0.3 maxLen was
+ changed to 17 bits, which has minimal effect on compression
+ ratio, but does mean this scaling step is used from time to
+ time, enough to verify that it works.
+
+ This means that bzip2-1.0.3 and later will only produce
+ Huffman codes with a maximum length of 17 bits. However, in
+ order to preserve backwards compatibility with bitstreams
+ produced by versions pre-1.0.3, the decompressor must still
+ handle lengths of up to 20. */
+
+ for (i = 1; i <= alphaSize; i++) {
+ j = weight[i] >> 8;
+ j = 1 + (j / 2);
+ weight[i] = j << 8;
+ }
+ }
+}
+
+
+/*---------------------------------------------------*/
+void BZ2_hbAssignCodes ( Int32 *code,
+ UChar *length,
+ Int32 minLen,
+ Int32 maxLen,
+ Int32 alphaSize )
+{
+ Int32 n, vec, i;
+
+ vec = 0;
+ for (n = minLen; n <= maxLen; n++) {
+ for (i = 0; i < alphaSize; i++)
+ if (length[i] == n) { code[i] = vec; vec++; };
+ vec <<= 1;
+ }
+}
+
+
+/*---------------------------------------------------*/
+void BZ2_hbCreateDecodeTables ( Int32 *limit,
+ Int32 *base,
+ Int32 *perm,
+ UChar *length,
+ Int32 minLen,
+ Int32 maxLen,
+ Int32 alphaSize )
+{
+ Int32 pp, i, j, vec;
+
+ pp = 0;
+ for (i = minLen; i <= maxLen; i++)
+ for (j = 0; j < alphaSize; j++)
+ if (length[j] == i) { perm[pp] = j; pp++; };
+
+ for (i = 0; i < BZ_MAX_CODE_LEN; i++) base[i] = 0;
+ for (i = 0; i < alphaSize; i++) base[length[i]+1]++;
+
+ for (i = 1; i < BZ_MAX_CODE_LEN; i++) base[i] += base[i-1];
+
+ for (i = 0; i < BZ_MAX_CODE_LEN; i++) limit[i] = 0;
+ vec = 0;
+
+ for (i = minLen; i <= maxLen; i++) {
+ vec += (base[i+1] - base[i]);
+ limit[i] = vec-1;
+ vec <<= 1;
+ }
+ for (i = minLen + 1; i <= maxLen; i++)
+ base[i] = ((limit[i-1] + 1) << 1) - base[i];
+}
+
+
+/*-------------------------------------------------------------*/
+/*--- end huffman.c ---*/
+/*-------------------------------------------------------------*/
diff --git a/third-party/bzip2/libbz2.def b/third-party/bzip2/libbz2.def
new file mode 100644
index 0000000..2dc0dd8
--- /dev/null
+++ b/third-party/bzip2/libbz2.def
@@ -0,0 +1,27 @@
+LIBRARY LIBBZ2
+DESCRIPTION "libbzip2: library for data compression"
+EXPORTS
+ BZ2_bzCompressInit
+ BZ2_bzCompress
+ BZ2_bzCompressEnd
+ BZ2_bzDecompressInit
+ BZ2_bzDecompress
+ BZ2_bzDecompressEnd
+ BZ2_bzReadOpen
+ BZ2_bzReadClose
+ BZ2_bzReadGetUnused
+ BZ2_bzRead
+ BZ2_bzWriteOpen
+ BZ2_bzWrite
+ BZ2_bzWriteClose
+ BZ2_bzWriteClose64
+ BZ2_bzBuffToBuffCompress
+ BZ2_bzBuffToBuffDecompress
+ BZ2_bzlibVersion
+ BZ2_bzopen
+ BZ2_bzdopen
+ BZ2_bzread
+ BZ2_bzwrite
+ BZ2_bzflush
+ BZ2_bzclose
+ BZ2_bzerror
diff --git a/third-party/bzip2/libbz2.dsp b/third-party/bzip2/libbz2.dsp
new file mode 100644
index 0000000..a21a20f
--- /dev/null
+++ b/third-party/bzip2/libbz2.dsp
@@ -0,0 +1,130 @@
+# Microsoft Developer Studio Project File - Name="libbz2" - Package Owner=<4>
+# Microsoft Developer Studio Generated Build File, Format Version 5.00
+# ** �ҏW���Ȃ��ł������� **
+
+# TARGTYPE "Win32 (x86) Dynamic-Link Library" 0x0102
+
+CFG=libbz2 - Win32 Debug
+!MESSAGE ����͗L����Ҳ�̧�قł͂���܂���B ������ۼު�Ă�����ނ��邽�߂ɂ� NMAKE ��g�p���Ă��������B
+!MESSAGE [Ҳ�̧�ق̴���߰�] ����ނ�g�p���Ď��s���Ă�������
+!MESSAGE
+!MESSAGE NMAKE /f "libbz2.mak".
+!MESSAGE
+!MESSAGE NMAKE �̎��s���ɍ\����w��ł��܂�
+!MESSAGE ����� ײݏ��ϸۂ̐ݒ���`���܂��B��:
+!MESSAGE
+!MESSAGE NMAKE /f "libbz2.mak" CFG="libbz2 - Win32 Debug"
+!MESSAGE
+!MESSAGE �I��”\������� Ӱ��:
+!MESSAGE
+!MESSAGE "libbz2 - Win32 Release" ("Win32 (x86) Dynamic-Link Library" �p)
+!MESSAGE "libbz2 - Win32 Debug" ("Win32 (x86) Dynamic-Link Library" �p)
+!MESSAGE
+
+# Begin Project
+# PROP Scc_ProjName ""
+# PROP Scc_LocalPath ""
+CPP=cl.exe
+MTL=midl.exe
+RSC=rc.exe
+
+!IF "$(CFG)" == "libbz2 - Win32 Release"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 0
+# PROP BASE Output_Dir "Release"
+# PROP BASE Intermediate_Dir "Release"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 0
+# PROP Output_Dir "Release"
+# PROP Intermediate_Dir "Release"
+# PROP Ignore_Export_Lib 0
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /MT /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /YX /FD /c
+# ADD CPP /nologo /MT /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /YX /FD /c
+# ADD BASE MTL /nologo /D "NDEBUG" /mktyplib203 /o NUL /win32
+# ADD MTL /nologo /D "NDEBUG" /mktyplib203 /o NUL /win32
+# ADD BASE RSC /l 0x411 /d "NDEBUG"
+# ADD RSC /l 0x411 /d "NDEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LINK32=link.exe
+# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:windows /dll /machine:I386
+# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:windows /dll /machine:I386 /out:"libbz2.dll"
+
+!ELSEIF "$(CFG)" == "libbz2 - Win32 Debug"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "Debug"
+# PROP BASE Intermediate_Dir "Debug"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "Debug"
+# PROP Intermediate_Dir "Debug"
+# PROP Ignore_Export_Lib 0
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /MTd /W3 /Gm /GX /Zi /Od /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /YX /FD /c
+# ADD CPP /nologo /MTd /W3 /Gm /GX /Zi /Od /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /YX /FD /c
+# ADD BASE MTL /nologo /D "_DEBUG" /mktyplib203 /o NUL /win32
+# ADD MTL /nologo /D "_DEBUG" /mktyplib203 /o NUL /win32
+# ADD BASE RSC /l 0x411 /d "_DEBUG"
+# ADD RSC /l 0x411 /d "_DEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LINK32=link.exe
+# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:windows /dll /debug /machine:I386 /pdbtype:sept
+# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:windows /dll /debug /machine:I386 /out:"libbz2.dll" /pdbtype:sept
+
+!ENDIF
+
+# Begin Target
+
+# Name "libbz2 - Win32 Release"
+# Name "libbz2 - Win32 Debug"
+# Begin Source File
+
+SOURCE=.\blocksort.c
+# End Source File
+# Begin Source File
+
+SOURCE=.\bzlib.c
+# End Source File
+# Begin Source File
+
+SOURCE=.\bzlib.h
+# End Source File
+# Begin Source File
+
+SOURCE=.\bzlib_private.h
+# End Source File
+# Begin Source File
+
+SOURCE=.\compress.c
+# End Source File
+# Begin Source File
+
+SOURCE=.\crctable.c
+# End Source File
+# Begin Source File
+
+SOURCE=.\decompress.c
+# End Source File
+# Begin Source File
+
+SOURCE=.\huffman.c
+# End Source File
+# Begin Source File
+
+SOURCE=.\libbz2.def
+# End Source File
+# Begin Source File
+
+SOURCE=.\randtable.c
+# End Source File
+# End Target
+# End Project
diff --git a/third-party/bzip2/makefile.msc b/third-party/bzip2/makefile.msc
new file mode 100644
index 0000000..799a18a
--- /dev/null
+++ b/third-party/bzip2/makefile.msc
@@ -0,0 +1,63 @@
+# Makefile for Microsoft Visual C++ 6.0
+# usage: nmake -f makefile.msc
+# K.M. Syring (syring at gsf.de)
+# Fixed up by JRS for bzip2-0.9.5d release.
+
+CC=cl
+CFLAGS= -DWIN32 -MD -Ox -D_FILE_OFFSET_BITS=64 -nologo
+
+OBJS= blocksort.obj \
+ huffman.obj \
+ crctable.obj \
+ randtable.obj \
+ compress.obj \
+ decompress.obj \
+ bzlib.obj
+
+all: lib bzip2 test
+
+bzip2: lib
+ $(CC) $(CFLAGS) -o bzip2 bzip2.c libbz2.lib setargv.obj
+ $(CC) $(CFLAGS) -o bzip2recover bzip2recover.c
+
+lib: $(OBJS)
+ lib /out:libbz2.lib $(OBJS)
+
+test: bzip2
+ type words1
+ .\\bzip2 -1 < sample1.ref > sample1.rb2
+ .\\bzip2 -2 < sample2.ref > sample2.rb2
+ .\\bzip2 -3 < sample3.ref > sample3.rb2
+ .\\bzip2 -d < sample1.bz2 > sample1.tst
+ .\\bzip2 -d < sample2.bz2 > sample2.tst
+ .\\bzip2 -ds < sample3.bz2 > sample3.tst
+ @echo All six of the fc's should find no differences.
+ @echo If fc finds an error on sample3.bz2, this could be
+ @echo because WinZip's 'TAR file smart CR/LF conversion'
+ @echo is too clever for its own good. Disable this option.
+ @echo The correct size for sample3.ref is 120,244. If it
+ @echo is 150,251, WinZip has messed it up.
+ fc sample1.bz2 sample1.rb2
+ fc sample2.bz2 sample2.rb2
+ fc sample3.bz2 sample3.rb2
+ fc sample1.tst sample1.ref
+ fc sample2.tst sample2.ref
+ fc sample3.tst sample3.ref
+
+
+
+clean:
+ del *.obj
+ del libbz2.lib
+ del bzip2.exe
+ del bzip2recover.exe
+ del sample1.rb2
+ del sample2.rb2
+ del sample3.rb2
+ del sample1.tst
+ del sample2.tst
+ del sample3.tst
+
+.c.obj:
+ $(CC) $(CFLAGS) -c $*.c -o $*.obj
+
diff --git a/third-party/bzip2/manual.html b/third-party/bzip2/manual.html
new file mode 100644
index 0000000..f59427f
--- /dev/null
+++ b/third-party/bzip2/manual.html
@@ -0,0 +1,2540 @@
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
+<title>bzip2 and libbzip2, version 1.0.6</title>
+<meta name="generator" content="DocBook XSL Stylesheets V1.75.2">
+<style type="text/css" media="screen">/* Colours:
+#74240f dark brown h1, h2, h3, h4
+#336699 medium blue links
+#339999 turquoise link hover colour
+#202020 almost black general text
+#761596 purple md5sum text
+#626262 dark gray pre border
+#eeeeee very light gray pre background
+#f2f2f9 very light blue nav table background
+#3366cc medium blue nav table border
+*/
+
+a, a:link, a:visited, a:active { color: #336699; }
+a:hover { color: #339999; }
+
+body { font: 80%/126% sans-serif; }
+h1, h2, h3, h4 { color: #74240f; }
+
+dt { color: #336699; font-weight: bold }
+dd {
+ margin-left: 1.5em;
+ padding-bottom: 0.8em;
+}
+
+/* -- ruler -- */
+div.hr_blue {
+ height: 3px;
+ background:#ffffff url("/images/hr_blue.png") repeat-x; }
+div.hr_blue hr { display:none; }
+
+/* release styles */
+#release p { margin-top: 0.4em; }
+#release .md5sum { color: #761596; }
+
+
+/* ------ styles for docs|manuals|howto ------ */
+/* -- lists -- */
+ul {
+ margin: 0px 4px 16px 16px;
+ padding: 0px;
+ list-style: url("/images/li-blue.png");
+}
+ul li {
+ margin-bottom: 10px;
+}
+ul ul {
+ list-style-type: none;
+ list-style-image: none;
+ margin-left: 0px;
+}
+
+/* header / footer nav tables */
+table.nav {
+ border: solid 1px #3366cc;
+ background: #f2f2f9;
+ background-color: #f2f2f9;
+ margin-bottom: 0.5em;
+}
+/* don't have underlined links in chunked nav menus */
+table.nav a { text-decoration: none; }
+table.nav a:hover { text-decoration: underline; }
+table.nav td { font-size: 85%; }
+
+code, tt, pre { font-size: 120%; }
+code, tt { color: #761596; }
+
+div.literallayout, pre.programlisting, pre.screen {
+ color: #000000;
+ padding: 0.5em;
+ background: #eeeeee;
+ border: 1px solid #626262;
+ background-color: #eeeeee;
+ margin: 4px 0px 4px 0px;
+}
+</style>
+</head>
+<body bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><div lang="en" class="book" title="bzip2 and libbzip2, version 1.0.6">
+<div class="titlepage">
+<div>
+<div><h1 class="title">
+<a name="userman"></a>bzip2 and libbzip2, version 1.0.6</h1></div>
+<div><h2 class="subtitle">A program and library for data compression</h2></div>
+<div><div class="authorgroup"><div class="author">
+<h3 class="author">
+<span class="firstname">Julian</span> <span class="surname">Seward</span>
+</h3>
+<div class="affiliation"><span class="orgname">http://www.bzip.org<br></span></div>
+</div></div></div>
+<div><p class="releaseinfo">Version 1.0.6 of 6 September 2010</p></div>
+<div><p class="copyright">Copyright � 1996-2010 Julian Seward</p></div>
+<div><div class="legalnotice" title="Legal Notice">
+<a name="id537185"></a><p>This program, <code class="computeroutput">bzip2</code>, the
+ associated library <code class="computeroutput">libbzip2</code>, and
+ all documentation, are copyright � 1996-2010 Julian Seward.
+ All rights reserved.</p>
+<p>Redistribution and use in source and binary forms, with
+ or without modification, are permitted provided that the
+ following conditions are met:</p>
+<div class="itemizedlist"><ul class="itemizedlist" type="bullet">
+<li class="listitem" style="list-style-type: disc"><p>Redistributions of source code must retain the
+ above copyright notice, this list of conditions and the
+ following disclaimer.</p></li>
+<li class="listitem" style="list-style-type: disc"><p>The origin of this software must not be
+ misrepresented; you must not claim that you wrote the original
+ software. If you use this software in a product, an
+ acknowledgment in the product documentation would be
+ appreciated but is not required.</p></li>
+<li class="listitem" style="list-style-type: disc"><p>Altered source versions must be plainly marked
+ as such, and must not be misrepresented as being the original
+ software.</p></li>
+<li class="listitem" style="list-style-type: disc"><p>The name of the author may not be used to
+ endorse or promote products derived from this software without
+ specific prior written permission.</p></li>
+</ul></div>
+<p>THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY
+ EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+ THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+ PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+ AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+ TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+ IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
+ THE POSSIBILITY OF SUCH DAMAGE.</p>
+<p>PATENTS: To the best of my knowledge,
+ <code class="computeroutput">bzip2</code> and
+ <code class="computeroutput">libbzip2</code> do not use any patented
+ algorithms. However, I do not have the resources to carry
+ out a patent search. Therefore I cannot give any guarantee of
+ the above statement.
+ </p>
+</div></div>
+</div>
+<hr>
+</div>
+<div class="toc">
+<p><b>Table of Contents</b></p>
+<dl>
+<dt><span class="chapter"><a href="#intro">1. Introduction</a></span></dt>
+<dt><span class="chapter"><a href="#using">2. How to use bzip2</a></span></dt>
+<dd><dl>
+<dt><span class="sect1"><a href="#name">2.1. NAME</a></span></dt>
+<dt><span class="sect1"><a href="#synopsis">2.2. SYNOPSIS</a></span></dt>
+<dt><span class="sect1"><a href="#description">2.3. DESCRIPTION</a></span></dt>
+<dt><span class="sect1"><a href="#options">2.4. OPTIONS</a></span></dt>
+<dt><span class="sect1"><a href="#memory-management">2.5. MEMORY MANAGEMENT</a></span></dt>
+<dt><span class="sect1"><a href="#recovering">2.6. RECOVERING DATA FROM DAMAGED FILES</a></span></dt>
+<dt><span class="sect1"><a href="#performance">2.7. PERFORMANCE NOTES</a></span></dt>
+<dt><span class="sect1"><a href="#caveats">2.8. CAVEATS</a></span></dt>
+<dt><span class="sect1"><a href="#author">2.9. AUTHOR</a></span></dt>
+</dl></dd>
+<dt><span class="chapter"><a href="#libprog">3.
+Programming with <code class="computeroutput">libbzip2</code>
+</a></span></dt>
+<dd><dl>
+<dt><span class="sect1"><a href="#top-level">3.1. Top-level structure</a></span></dt>
+<dd><dl>
+<dt><span class="sect2"><a href="#ll-summary">3.1.1. Low-level summary</a></span></dt>
+<dt><span class="sect2"><a href="#hl-summary">3.1.2. High-level summary</a></span></dt>
+<dt><span class="sect2"><a href="#util-fns-summary">3.1.3. Utility functions summary</a></span></dt>
+</dl></dd>
+<dt><span class="sect1"><a href="#err-handling">3.2. Error handling</a></span></dt>
+<dt><span class="sect1"><a href="#low-level">3.3. Low-level interface</a></span></dt>
+<dd><dl>
+<dt><span class="sect2"><a href="#bzcompress-init">3.3.1. BZ2_bzCompressInit</a></span></dt>
+<dt><span class="sect2"><a href="#bzCompress">3.3.2. BZ2_bzCompress</a></span></dt>
+<dt><span class="sect2"><a href="#bzCompress-end">3.3.3. BZ2_bzCompressEnd</a></span></dt>
+<dt><span class="sect2"><a href="#bzDecompress-init">3.3.4. BZ2_bzDecompressInit</a></span></dt>
+<dt><span class="sect2"><a href="#bzDecompress">3.3.5. BZ2_bzDecompress</a></span></dt>
+<dt><span class="sect2"><a href="#bzDecompress-end">3.3.6. BZ2_bzDecompressEnd</a></span></dt>
+</dl></dd>
+<dt><span class="sect1"><a href="#hl-interface">3.4. High-level interface</a></span></dt>
+<dd><dl>
+<dt><span class="sect2"><a href="#bzreadopen">3.4.1. BZ2_bzReadOpen</a></span></dt>
+<dt><span class="sect2"><a href="#bzread">3.4.2. BZ2_bzRead</a></span></dt>
+<dt><span class="sect2"><a href="#bzreadgetunused">3.4.3. BZ2_bzReadGetUnused</a></span></dt>
+<dt><span class="sect2"><a href="#bzreadclose">3.4.4. BZ2_bzReadClose</a></span></dt>
+<dt><span class="sect2"><a href="#bzwriteopen">3.4.5. BZ2_bzWriteOpen</a></span></dt>
+<dt><span class="sect2"><a href="#bzwrite">3.4.6. BZ2_bzWrite</a></span></dt>
+<dt><span class="sect2"><a href="#bzwriteclose">3.4.7. BZ2_bzWriteClose</a></span></dt>
+<dt><span class="sect2"><a href="#embed">3.4.8. Handling embedded compressed data streams</a></span></dt>
+<dt><span class="sect2"><a href="#std-rdwr">3.4.9. Standard file-reading/writing code</a></span></dt>
+</dl></dd>
+<dt><span class="sect1"><a href="#util-fns">3.5. Utility functions</a></span></dt>
+<dd><dl>
+<dt><span class="sect2"><a href="#bzbufftobuffcompress">3.5.1. BZ2_bzBuffToBuffCompress</a></span></dt>
+<dt><span class="sect2"><a href="#bzbufftobuffdecompress">3.5.2. BZ2_bzBuffToBuffDecompress</a></span></dt>
+</dl></dd>
+<dt><span class="sect1"><a href="#zlib-compat">3.6. zlib compatibility functions</a></span></dt>
+<dt><span class="sect1"><a href="#stdio-free">3.7. Using the library in a stdio-free environment</a></span></dt>
+<dd><dl>
+<dt><span class="sect2"><a href="#stdio-bye">3.7.1. Getting rid of stdio</a></span></dt>
+<dt><span class="sect2"><a href="#critical-error">3.7.2. Critical error handling</a></span></dt>
+</dl></dd>
+<dt><span class="sect1"><a href="#win-dll">3.8. Making a Windows DLL</a></span></dt>
+</dl></dd>
+<dt><span class="chapter"><a href="#misc">4. Miscellanea</a></span></dt>
+<dd><dl>
+<dt><span class="sect1"><a href="#limits">4.1. Limitations of the compressed file format</a></span></dt>
+<dt><span class="sect1"><a href="#port-issues">4.2. Portability issues</a></span></dt>
+<dt><span class="sect1"><a href="#bugs">4.3. Reporting bugs</a></span></dt>
+<dt><span class="sect1"><a href="#package">4.4. Did you get the right package?</a></span></dt>
+<dt><span class="sect1"><a href="#reading">4.5. Further Reading</a></span></dt>
+</dl></dd>
+</dl>
+</div>
+<div class="chapter" title="1.�Introduction">
+<div class="titlepage"><div><div><h2 class="title">
+<a name="intro"></a>1.�Introduction</h2></div></div></div>
+<p><code class="computeroutput">bzip2</code> compresses files
+using the Burrows-Wheeler block-sorting text compression
+algorithm, and Huffman coding. Compression is generally
+considerably better than that achieved by more conventional
+LZ77/LZ78-based compressors, and approaches the performance of
+the PPM family of statistical compressors.</p>
+<p><code class="computeroutput">bzip2</code> is built on top of
+<code class="computeroutput">libbzip2</code>, a flexible library for
+handling compressed data in the
+<code class="computeroutput">bzip2</code> format. This manual
+describes both how to use the program and how to work with the
+library interface. Most of the manual is devoted to this
+library, not the program, which is good news if your interest is
+only in the program.</p>
+<div class="itemizedlist"><ul class="itemizedlist" type="bullet">
+<li class="listitem" style="list-style-type: disc"><p><a class="xref" href="#using" title="2.�How to use bzip2">How to use bzip2</a> describes how to use
+ <code class="computeroutput">bzip2</code>; this is the only part
+ you need to read if you just want to know how to operate the
+ program.</p></li>
+<li class="listitem" style="list-style-type: disc"><p><a class="xref" href="#libprog" title="3.� Programming with libbzip2">Programming with libbzip2</a> describes the
+ programming interfaces in detail, and</p></li>
+<li class="listitem" style="list-style-type: disc"><p><a class="xref" href="#misc" title="4.�Miscellanea">Miscellanea</a> records some
+ miscellaneous notes which I thought ought to be recorded
+ somewhere.</p></li>
+</ul></div>
+</div>
+<div class="chapter" title="2.�How to use bzip2">
+<div class="titlepage"><div><div><h2 class="title">
+<a name="using"></a>2.�How to use bzip2</h2></div></div></div>
+<div class="toc">
+<p><b>Table of Contents</b></p>
+<dl>
+<dt><span class="sect1"><a href="#name">2.1. NAME</a></span></dt>
+<dt><span class="sect1"><a href="#synopsis">2.2. SYNOPSIS</a></span></dt>
+<dt><span class="sect1"><a href="#description">2.3. DESCRIPTION</a></span></dt>
+<dt><span class="sect1"><a href="#options">2.4. OPTIONS</a></span></dt>
+<dt><span class="sect1"><a href="#memory-management">2.5. MEMORY MANAGEMENT</a></span></dt>
+<dt><span class="sect1"><a href="#recovering">2.6. RECOVERING DATA FROM DAMAGED FILES</a></span></dt>
+<dt><span class="sect1"><a href="#performance">2.7. PERFORMANCE NOTES</a></span></dt>
+<dt><span class="sect1"><a href="#caveats">2.8. CAVEATS</a></span></dt>
+<dt><span class="sect1"><a href="#author">2.9. AUTHOR</a></span></dt>
+</dl>
+</div>
+<p>This chapter contains a copy of the
+<code class="computeroutput">bzip2</code> man page, and nothing
+else.</p>
+<div class="sect1" title="2.1.�NAME">
+<div class="titlepage"><div><div><h2 class="title" style="clear: both">
+<a name="name"></a>2.1.�NAME</h2></div></div></div>
+<div class="itemizedlist"><ul class="itemizedlist" type="bullet">
+<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">bzip2</code>,
+ <code class="computeroutput">bunzip2</code> - a block-sorting file
+ compressor, v1.0.6</p></li>
+<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">bzcat</code> -
+ decompresses files to stdout</p></li>
+<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">bzip2recover</code> -
+ recovers data from damaged bzip2 files</p></li>
+</ul></div>
+</div>
+<div class="sect1" title="2.2.�SYNOPSIS">
+<div class="titlepage"><div><div><h2 class="title" style="clear: both">
+<a name="synopsis"></a>2.2.�SYNOPSIS</h2></div></div></div>
+<div class="itemizedlist"><ul class="itemizedlist" type="bullet">
+<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">bzip2</code> [
+ -cdfkqstvzVL123456789 ] [ filenames ... ]</p></li>
+<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">bunzip2</code> [
+ -fkvsVL ] [ filenames ... ]</p></li>
+<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">bzcat</code> [ -s ] [
+ filenames ... ]</p></li>
+<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">bzip2recover</code>
+ filename</p></li>
+</ul></div>
+</div>
+<div class="sect1" title="2.3.�DESCRIPTION">
+<div class="titlepage"><div><div><h2 class="title" style="clear: both">
+<a name="description"></a>2.3.�DESCRIPTION</h2></div></div></div>
+<p><code class="computeroutput">bzip2</code> compresses files
+using the Burrows-Wheeler block sorting text compression
+algorithm, and Huffman coding. Compression is generally
+considerably better than that achieved by more conventional
+LZ77/LZ78-based compressors, and approaches the performance of
+the PPM family of statistical compressors.</p>
+<p>The command-line options are deliberately very similar to
+those of GNU <code class="computeroutput">gzip</code>, but they are
+not identical.</p>
+<p><code class="computeroutput">bzip2</code> expects a list of
+file names to accompany the command-line flags. Each file is
+replaced by a compressed version of itself, with the name
+<code class="computeroutput">original_name.bz2</code>. Each
+compressed file has the same modification date, permissions, and,
+when possible, ownership as the corresponding original, so that
+these properties can be correctly restored at decompression time.
+File name handling is naive in the sense that there is no
+mechanism for preserving original file names, permissions,
+ownerships or dates in filesystems which lack these concepts, or
+have serious file name length restrictions, such as
+MS-DOS.</p>
+<p><code class="computeroutput">bzip2</code> and
+<code class="computeroutput">bunzip2</code> will by default not
+overwrite existing files. If you want this to happen, specify
+the <code class="computeroutput">-f</code> flag.</p>
+<p>If no file names are specified,
+<code class="computeroutput">bzip2</code> compresses from standard
+input to standard output. In this case,
+<code class="computeroutput">bzip2</code> will decline to write
+compressed output to a terminal, as this would be entirely
+incomprehensible and therefore pointless.</p>
+<p><code class="computeroutput">bunzip2</code> (or
+<code class="computeroutput">bzip2 -d</code>) decompresses all
+specified files. Files which were not created by
+<code class="computeroutput">bzip2</code> will be detected and
+ignored, and a warning issued.
+<code class="computeroutput">bzip2</code> attempts to guess the
+filename for the decompressed file from that of the compressed
+file as follows:</p>
+<div class="itemizedlist"><ul class="itemizedlist" type="bullet">
+<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">filename.bz2 </code>
+ becomes
+ <code class="computeroutput">filename</code></p></li>
+<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">filename.bz </code>
+ becomes
+ <code class="computeroutput">filename</code></p></li>
+<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">filename.tbz2</code>
+ becomes
+ <code class="computeroutput">filename.tar</code></p></li>
+<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">filename.tbz </code>
+ becomes
+ <code class="computeroutput">filename.tar</code></p></li>
+<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">anyothername </code>
+ becomes
+ <code class="computeroutput">anyothername.out</code></p></li>
+</ul></div>
+<p>If the file does not end in one of the recognised endings,
+<code class="computeroutput">.bz2</code>,
+<code class="computeroutput">.bz</code>,
+<code class="computeroutput">.tbz2</code> or
+<code class="computeroutput">.tbz</code>,
+<code class="computeroutput">bzip2</code> complains that it cannot
+guess the name of the original file, and uses the original name
+with <code class="computeroutput">.out</code> appended.</p>
+<p>As with compression, supplying no filenames causes
+decompression from standard input to standard output.</p>
+<p><code class="computeroutput">bunzip2</code> will correctly
+decompress a file which is the concatenation of two or more
+compressed files. The result is the concatenation of the
+corresponding uncompressed files. Integrity testing
+(<code class="computeroutput">-t</code>) of concatenated compressed
+files is also supported.</p>
+<p>You can also compress or decompress files to the standard
+output by giving the <code class="computeroutput">-c</code> flag.
+Multiple files may be compressed and decompressed like this. The
+resulting outputs are fed sequentially to stdout. Compression of
+multiple files in this manner generates a stream containing
+multiple compressed file representations. Such a stream can be
+decompressed correctly only by
+<code class="computeroutput">bzip2</code> version 0.9.0 or later.
+Earlier versions of <code class="computeroutput">bzip2</code> will
+stop after decompressing the first file in the stream.</p>
+<p><code class="computeroutput">bzcat</code> (or
+<code class="computeroutput">bzip2 -dc</code>) decompresses all
+specified files to the standard output.</p>
+<p><code class="computeroutput">bzip2</code> will read arguments
+from the environment variables
+<code class="computeroutput">BZIP2</code> and
+<code class="computeroutput">BZIP</code>, in that order, and will
+process them before any arguments read from the command line.
+This gives a convenient way to supply default arguments.</p>
+<p>Compression is always performed, even if the compressed
+file is slightly larger than the original. Files of less than
+about one hundred bytes tend to get larger, since the compression
+mechanism has a constant overhead in the region of 50 bytes.
+Random data (including the output of most file compressors) is
+coded at about 8.05 bits per byte, giving an expansion of around
+0.5%.</p>
+<p>As a self-check for your protection,
+<code class="computeroutput">bzip2</code> uses 32-bit CRCs to make
+sure that the decompressed version of a file is identical to the
+original. This guards against corruption of the compressed data,
+and against undetected bugs in
+<code class="computeroutput">bzip2</code> (hopefully very unlikely).
+The chances of data corruption going undetected is microscopic,
+about one chance in four billion for each file processed. Be
+aware, though, that the check occurs upon decompression, so it
+can only tell you that something is wrong. It can't help you
+recover the original uncompressed data. You can use
+<code class="computeroutput">bzip2recover</code> to try to recover
+data from damaged files.</p>
+<p>Return values: 0 for a normal exit, 1 for environmental
+problems (file not found, invalid flags, I/O errors, etc.), 2
+to indicate a corrupt compressed file, 3 for an internal
+consistency error (eg, bug) which caused
+<code class="computeroutput">bzip2</code> to panic.</p>
+</div>
+<div class="sect1" title="2.4.�OPTIONS">
+<div class="titlepage"><div><div><h2 class="title" style="clear: both">
+<a name="options"></a>2.4.�OPTIONS</h2></div></div></div>
+<div class="variablelist"><dl>
+<dt><span class="term"><code class="computeroutput">-c --stdout</code></span></dt>
+<dd><p>Compress or decompress to standard
+ output.</p></dd>
+<dt><span class="term"><code class="computeroutput">-d --decompress</code></span></dt>
+<dd><p>Force decompression.
+ <code class="computeroutput">bzip2</code>,
+ <code class="computeroutput">bunzip2</code> and
+ <code class="computeroutput">bzcat</code> are really the same
+ program, and the decision about what actions to take is done on
+ the basis of which name is used. This flag overrides that
+ mechanism, and forces bzip2 to decompress.</p></dd>
+<dt><span class="term"><code class="computeroutput">-z --compress</code></span></dt>
+<dd><p>The complement to
+ <code class="computeroutput">-d</code>: forces compression,
+ regardless of the invokation name.</p></dd>
+<dt><span class="term"><code class="computeroutput">-t --test</code></span></dt>
+<dd><p>Check integrity of the specified file(s), but
+ don't decompress them. This really performs a trial
+ decompression and throws away the result.</p></dd>
+<dt><span class="term"><code class="computeroutput">-f --force</code></span></dt>
+<dd>
+<p>Force overwrite of output files. Normally,
+ <code class="computeroutput">bzip2</code> will not overwrite
+ existing output files. Also forces
+ <code class="computeroutput">bzip2</code> to break hard links to
+ files, which it otherwise wouldn't do.</p>
+<p><code class="computeroutput">bzip2</code> normally declines
+ to decompress files which don't have the correct magic header
+ bytes. If forced (<code class="computeroutput">-f</code>),
+ however, it will pass such files through unmodified. This is
+ how GNU <code class="computeroutput">gzip</code> behaves.</p>
+</dd>
+<dt><span class="term"><code class="computeroutput">-k --keep</code></span></dt>
+<dd><p>Keep (don't delete) input files during
+ compression or decompression.</p></dd>
+<dt><span class="term"><code class="computeroutput">-s --small</code></span></dt>
+<dd>
+<p>Reduce memory usage, for compression,
+ decompression and testing. Files are decompressed and tested
+ using a modified algorithm which only requires 2.5 bytes per
+ block byte. This means any file can be decompressed in 2300k
+ of memory, albeit at about half the normal speed.</p>
+<p>During compression, <code class="computeroutput">-s</code>
+ selects a block size of 200k, which limits memory use to around
+ the same figure, at the expense of your compression ratio. In
+ short, if your machine is low on memory (8 megabytes or less),
+ use <code class="computeroutput">-s</code> for everything. See
+ <a class="xref" href="#memory-management" title="2.5.�MEMORY MANAGEMENT">MEMORY MANAGEMENT</a> below.</p>
+</dd>
+<dt><span class="term"><code class="computeroutput">-q --quiet</code></span></dt>
+<dd><p>Suppress non-essential warning messages.
+ Messages pertaining to I/O errors and other critical events
+ will not be suppressed.</p></dd>
+<dt><span class="term"><code class="computeroutput">-v --verbose</code></span></dt>
+<dd><p>Verbose mode -- show the compression ratio for
+ each file processed. Further
+ <code class="computeroutput">-v</code>'s increase the verbosity
+ level, spewing out lots of information which is primarily of
+ interest for diagnostic purposes.</p></dd>
+<dt><span class="term"><code class="computeroutput">-L --license -V --version</code></span></dt>
+<dd><p>Display the software version, license terms and
+ conditions.</p></dd>
+<dt><span class="term"><code class="computeroutput">-1</code> (or
+ <code class="computeroutput">--fast</code>) to
+ <code class="computeroutput">-9</code> (or
+ <code class="computeroutput">-best</code>)</span></dt>
+<dd><p>Set the block size to 100 k, 200 k ... 900 k
+ when compressing. Has no effect when decompressing. See <a class="xref" href="#memory-management" title="2.5.�MEMORY MANAGEMENT">MEMORY MANAGEMENT</a> below. The
+ <code class="computeroutput">--fast</code> and
+ <code class="computeroutput">--best</code> aliases are primarily
+ for GNU <code class="computeroutput">gzip</code> compatibility.
+ In particular, <code class="computeroutput">--fast</code> doesn't
+ make things significantly faster. And
+ <code class="computeroutput">--best</code> merely selects the
+ default behaviour.</p></dd>
+<dt><span class="term"><code class="computeroutput">--</code></span></dt>
+<dd><p>Treats all subsequent arguments as file names,
+ even if they start with a dash. This is so you can handle
+ files with names beginning with a dash, for example:
+ <code class="computeroutput">bzip2 --
+ -myfilename</code>.</p></dd>
+<dt>
+<span class="term"><code class="computeroutput">--repetitive-fast</code>, </span><span class="term"><code class="computeroutput">--repetitive-best</code></span>
+</dt>
+<dd><p>These flags are redundant in versions 0.9.5 and
+ above. They provided some coarse control over the behaviour of
+ the sorting algorithm in earlier versions, which was sometimes
+ useful. 0.9.5 and above have an improved algorithm which
+ renders these flags irrelevant.</p></dd>
+</dl></div>
+</div>
+<div class="sect1" title="2.5.�MEMORY MANAGEMENT">
+<div class="titlepage"><div><div><h2 class="title" style="clear: both">
+<a name="memory-management"></a>2.5.�MEMORY MANAGEMENT</h2></div></div></div>
+<p><code class="computeroutput">bzip2</code> compresses large
+files in blocks. The block size affects both the compression
+ratio achieved, and the amount of memory needed for compression
+and decompression. The flags <code class="computeroutput">-1</code>
+through <code class="computeroutput">-9</code> specify the block
+size to be 100,000 bytes through 900,000 bytes (the default)
+respectively. At decompression time, the block size used for
+compression is read from the header of the compressed file, and
+<code class="computeroutput">bunzip2</code> then allocates itself
+just enough memory to decompress the file. Since block sizes are
+stored in compressed files, it follows that the flags
+<code class="computeroutput">-1</code> to
+<code class="computeroutput">-9</code> are irrelevant to and so
+ignored during decompression.</p>
+<p>Compression and decompression requirements, in bytes, can be
+estimated as:</p>
+<pre class="programlisting">Compression: 400k + ( 8 x block size )
+
+Decompression: 100k + ( 4 x block size ), or
+ 100k + ( 2.5 x block size )</pre>
+<p>Larger block sizes give rapidly diminishing marginal
+returns. Most of the compression comes from the first two or
+three hundred k of block size, a fact worth bearing in mind when
+using <code class="computeroutput">bzip2</code> on small machines.
+It is also important to appreciate that the decompression memory
+requirement is set at compression time by the choice of block
+size.</p>
+<p>For files compressed with the default 900k block size,
+<code class="computeroutput">bunzip2</code> will require about 3700
+kbytes to decompress. To support decompression of any file on a
+4 megabyte machine, <code class="computeroutput">bunzip2</code> has
+an option to decompress using approximately half this amount of
+memory, about 2300 kbytes. Decompression speed is also halved,
+so you should use this option only where necessary. The relevant
+flag is <code class="computeroutput">-s</code>.</p>
+<p>In general, try and use the largest block size memory
+constraints allow, since that maximises the compression achieved.
+Compression and decompression speed are virtually unaffected by
+block size.</p>
+<p>Another significant point applies to files which fit in a
+single block -- that means most files you'd encounter using a
+large block size. The amount of real memory touched is
+proportional to the size of the file, since the file is smaller
+than a block. For example, compressing a file 20,000 bytes long
+with the flag <code class="computeroutput">-9</code> will cause the
+compressor to allocate around 7600k of memory, but only touch
+400k + 20000 * 8 = 560 kbytes of it. Similarly, the decompressor
+will allocate 3700k but only touch 100k + 20000 * 4 = 180
+kbytes.</p>
+<p>Here is a table which summarises the maximum memory usage
+for different block sizes. Also recorded is the total compressed
+size for 14 files of the Calgary Text Compression Corpus
+totalling 3,141,622 bytes. This column gives some feel for how
+compression varies with block size. These figures tend to
+understate the advantage of larger block sizes for larger files,
+since the Corpus is dominated by smaller files.</p>
+<pre class="programlisting"> Compress Decompress Decompress Corpus
+Flag usage usage -s usage Size
+
+ -1 1200k 500k 350k 914704
+ -2 2000k 900k 600k 877703
+ -3 2800k 1300k 850k 860338
+ -4 3600k 1700k 1100k 846899
+ -5 4400k 2100k 1350k 845160
+ -6 5200k 2500k 1600k 838626
+ -7 6100k 2900k 1850k 834096
+ -8 6800k 3300k 2100k 828642
+ -9 7600k 3700k 2350k 828642</pre>
+</div>
+<div class="sect1" title="2.6.�RECOVERING DATA FROM DAMAGED FILES">
+<div class="titlepage"><div><div><h2 class="title" style="clear: both">
+<a name="recovering"></a>2.6.�RECOVERING DATA FROM DAMAGED FILES</h2></div></div></div>
+<p><code class="computeroutput">bzip2</code> compresses files in
+blocks, usually 900kbytes long. Each block is handled
+independently. If a media or transmission error causes a
+multi-block <code class="computeroutput">.bz2</code> file to become
+damaged, it may be possible to recover data from the undamaged
+blocks in the file.</p>
+<p>The compressed representation of each block is delimited by
+a 48-bit pattern, which makes it possible to find the block
+boundaries with reasonable certainty. Each block also carries
+its own 32-bit CRC, so damaged blocks can be distinguished from
+undamaged ones.</p>
+<p><code class="computeroutput">bzip2recover</code> is a simple
+program whose purpose is to search for blocks in
+<code class="computeroutput">.bz2</code> files, and write each block
+out into its own <code class="computeroutput">.bz2</code> file. You
+can then use <code class="computeroutput">bzip2 -t</code> to test
+the integrity of the resulting files, and decompress those which
+are undamaged.</p>
+<p><code class="computeroutput">bzip2recover</code> takes a
+single argument, the name of the damaged file, and writes a
+number of files <code class="computeroutput">rec0001file.bz2</code>,
+<code class="computeroutput">rec0002file.bz2</code>, etc, containing
+the extracted blocks. The output filenames are designed so that
+the use of wildcards in subsequent processing -- for example,
+<code class="computeroutput">bzip2 -dc rec*file.bz2 >
+recovered_data</code> -- lists the files in the correct
+order.</p>
+<p><code class="computeroutput">bzip2recover</code> should be of
+most use dealing with large <code class="computeroutput">.bz2</code>
+files, as these will contain many blocks. It is clearly futile
+to use it on damaged single-block files, since a damaged block
+cannot be recovered. If you wish to minimise any potential data
+loss through media or transmission errors, you might consider
+compressing with a smaller block size.</p>
+</div>
+<div class="sect1" title="2.7.�PERFORMANCE NOTES">
+<div class="titlepage"><div><div><h2 class="title" style="clear: both">
+<a name="performance"></a>2.7.�PERFORMANCE NOTES</h2></div></div></div>
+<p>The sorting phase of compression gathers together similar
+strings in the file. Because of this, files containing very long
+runs of repeated symbols, like "aabaabaabaab ..." (repeated
+several hundred times) may compress more slowly than normal.
+Versions 0.9.5 and above fare much better than previous versions
+in this respect. The ratio between worst-case and average-case
+compression time is in the region of 10:1. For previous
+versions, this figure was more like 100:1. You can use the
+<code class="computeroutput">-vvvv</code> option to monitor progress
+in great detail, if you want.</p>
+<p>Decompression speed is unaffected by these
+phenomena.</p>
+<p><code class="computeroutput">bzip2</code> usually allocates
+several megabytes of memory to operate in, and then charges all
+over it in a fairly random fashion. This means that performance,
+both for compressing and decompressing, is largely determined by
+the speed at which your machine can service cache misses.
+Because of this, small changes to the code to reduce the miss
+rate have been observed to give disproportionately large
+performance improvements. I imagine
+<code class="computeroutput">bzip2</code> will perform best on
+machines with very large caches.</p>
+</div>
+<div class="sect1" title="2.8.�CAVEATS">
+<div class="titlepage"><div><div><h2 class="title" style="clear: both">
+<a name="caveats"></a>2.8.�CAVEATS</h2></div></div></div>
+<p>I/O error messages are not as helpful as they could be.
+<code class="computeroutput">bzip2</code> tries hard to detect I/O
+errors and exit cleanly, but the details of what the problem is
+sometimes seem rather misleading.</p>
+<p>This manual page pertains to version 1.0.6 of
+<code class="computeroutput">bzip2</code>. Compressed data created by
+this version is entirely forwards and backwards compatible with the
+previous public releases, versions 0.1pl2, 0.9.0 and 0.9.5, 1.0.0,
+1.0.1, 1.0.2 and 1.0.3, but with the following exception: 0.9.0 and
+above can correctly decompress multiple concatenated compressed files.
+0.1pl2 cannot do this; it will stop after decompressing just the first
+file in the stream.</p>
+<p><code class="computeroutput">bzip2recover</code> versions
+prior to 1.0.2 used 32-bit integers to represent bit positions in
+compressed files, so it could not handle compressed files more
+than 512 megabytes long. Versions 1.0.2 and above use 64-bit ints
+on some platforms which support them (GNU supported targets, and
+Windows). To establish whether or not
+<code class="computeroutput">bzip2recover</code> was built with such
+a limitation, run it without arguments. In any event you can
+build yourself an unlimited version if you can recompile it with
+<code class="computeroutput">MaybeUInt64</code> set to be an
+unsigned 64-bit integer.</p>
+</div>
+<div class="sect1" title="2.9.�AUTHOR">
+<div class="titlepage"><div><div><h2 class="title" style="clear: both">
+<a name="author"></a>2.9.�AUTHOR</h2></div></div></div>
+<p>Julian Seward,
+<code class="computeroutput">jseward at bzip.org</code></p>
+<p>The ideas embodied in
+<code class="computeroutput">bzip2</code> are due to (at least) the
+following people: Michael Burrows and David Wheeler (for the
+block sorting transformation), David Wheeler (again, for the
+Huffman coder), Peter Fenwick (for the structured coding model in
+the original <code class="computeroutput">bzip</code>, and many
+refinements), and Alistair Moffat, Radford Neal and Ian Witten
+(for the arithmetic coder in the original
+<code class="computeroutput">bzip</code>). I am much indebted for
+their help, support and advice. See the manual in the source
+distribution for pointers to sources of documentation. Christian
+von Roques encouraged me to look for faster sorting algorithms,
+so as to speed up compression. Bela Lubkin encouraged me to
+improve the worst-case compression performance.
+Donna Robinson XMLised the documentation.
+Many people sent
+patches, helped with portability problems, lent machines, gave
+advice and were generally helpful.</p>
+</div>
+</div>
+<div class="chapter" title="3.� Programming with libbzip2">
+<div class="titlepage"><div><div><h2 class="title">
+<a name="libprog"></a>3.�
+Programming with <code class="computeroutput">libbzip2</code>
+</h2></div></div></div>
+<div class="toc">
+<p><b>Table of Contents</b></p>
+<dl>
+<dt><span class="sect1"><a href="#top-level">3.1. Top-level structure</a></span></dt>
+<dd><dl>
+<dt><span class="sect2"><a href="#ll-summary">3.1.1. Low-level summary</a></span></dt>
+<dt><span class="sect2"><a href="#hl-summary">3.1.2. High-level summary</a></span></dt>
+<dt><span class="sect2"><a href="#util-fns-summary">3.1.3. Utility functions summary</a></span></dt>
+</dl></dd>
+<dt><span class="sect1"><a href="#err-handling">3.2. Error handling</a></span></dt>
+<dt><span class="sect1"><a href="#low-level">3.3. Low-level interface</a></span></dt>
+<dd><dl>
+<dt><span class="sect2"><a href="#bzcompress-init">3.3.1. BZ2_bzCompressInit</a></span></dt>
+<dt><span class="sect2"><a href="#bzCompress">3.3.2. BZ2_bzCompress</a></span></dt>
+<dt><span class="sect2"><a href="#bzCompress-end">3.3.3. BZ2_bzCompressEnd</a></span></dt>
+<dt><span class="sect2"><a href="#bzDecompress-init">3.3.4. BZ2_bzDecompressInit</a></span></dt>
+<dt><span class="sect2"><a href="#bzDecompress">3.3.5. BZ2_bzDecompress</a></span></dt>
+<dt><span class="sect2"><a href="#bzDecompress-end">3.3.6. BZ2_bzDecompressEnd</a></span></dt>
+</dl></dd>
+<dt><span class="sect1"><a href="#hl-interface">3.4. High-level interface</a></span></dt>
+<dd><dl>
+<dt><span class="sect2"><a href="#bzreadopen">3.4.1. BZ2_bzReadOpen</a></span></dt>
+<dt><span class="sect2"><a href="#bzread">3.4.2. BZ2_bzRead</a></span></dt>
+<dt><span class="sect2"><a href="#bzreadgetunused">3.4.3. BZ2_bzReadGetUnused</a></span></dt>
+<dt><span class="sect2"><a href="#bzreadclose">3.4.4. BZ2_bzReadClose</a></span></dt>
+<dt><span class="sect2"><a href="#bzwriteopen">3.4.5. BZ2_bzWriteOpen</a></span></dt>
+<dt><span class="sect2"><a href="#bzwrite">3.4.6. BZ2_bzWrite</a></span></dt>
+<dt><span class="sect2"><a href="#bzwriteclose">3.4.7. BZ2_bzWriteClose</a></span></dt>
+<dt><span class="sect2"><a href="#embed">3.4.8. Handling embedded compressed data streams</a></span></dt>
+<dt><span class="sect2"><a href="#std-rdwr">3.4.9. Standard file-reading/writing code</a></span></dt>
+</dl></dd>
+<dt><span class="sect1"><a href="#util-fns">3.5. Utility functions</a></span></dt>
+<dd><dl>
+<dt><span class="sect2"><a href="#bzbufftobuffcompress">3.5.1. BZ2_bzBuffToBuffCompress</a></span></dt>
+<dt><span class="sect2"><a href="#bzbufftobuffdecompress">3.5.2. BZ2_bzBuffToBuffDecompress</a></span></dt>
+</dl></dd>
+<dt><span class="sect1"><a href="#zlib-compat">3.6. zlib compatibility functions</a></span></dt>
+<dt><span class="sect1"><a href="#stdio-free">3.7. Using the library in a stdio-free environment</a></span></dt>
+<dd><dl>
+<dt><span class="sect2"><a href="#stdio-bye">3.7.1. Getting rid of stdio</a></span></dt>
+<dt><span class="sect2"><a href="#critical-error">3.7.2. Critical error handling</a></span></dt>
+</dl></dd>
+<dt><span class="sect1"><a href="#win-dll">3.8. Making a Windows DLL</a></span></dt>
+</dl>
+</div>
+<p>This chapter describes the programming interface to
+<code class="computeroutput">libbzip2</code>.</p>
+<p>For general background information, particularly about
+memory use and performance aspects, you'd be well advised to read
+<a class="xref" href="#using" title="2.�How to use bzip2">How to use bzip2</a> as well.</p>
+<div class="sect1" title="3.1.�Top-level structure">
+<div class="titlepage"><div><div><h2 class="title" style="clear: both">
+<a name="top-level"></a>3.1.�Top-level structure</h2></div></div></div>
+<p><code class="computeroutput">libbzip2</code> is a flexible
+library for compressing and decompressing data in the
+<code class="computeroutput">bzip2</code> data format. Although
+packaged as a single entity, it helps to regard the library as
+three separate parts: the low level interface, and the high level
+interface, and some utility functions.</p>
+<p>The structure of
+<code class="computeroutput">libbzip2</code>'s interfaces is similar
+to that of Jean-loup Gailly's and Mark Adler's excellent
+<code class="computeroutput">zlib</code> library.</p>
+<p>All externally visible symbols have names beginning
+<code class="computeroutput">BZ2_</code>. This is new in version
+1.0. The intention is to minimise pollution of the namespaces of
+library clients.</p>
+<p>To use any part of the library, you need to
+<code class="computeroutput">#include <bzlib.h></code>
+into your sources.</p>
+<div class="sect2" title="3.1.1.�Low-level summary">
+<div class="titlepage"><div><div><h3 class="title">
+<a name="ll-summary"></a>3.1.1.�Low-level summary</h3></div></div></div>
+<p>This interface provides services for compressing and
+decompressing data in memory. There's no provision for dealing
+with files, streams or any other I/O mechanisms, just straight
+memory-to-memory work. In fact, this part of the library can be
+compiled without inclusion of
+<code class="computeroutput">stdio.h</code>, which may be helpful
+for embedded applications.</p>
+<p>The low-level part of the library has no global variables
+and is therefore thread-safe.</p>
+<p>Six routines make up the low level interface:
+<code class="computeroutput">BZ2_bzCompressInit</code>,
+<code class="computeroutput">BZ2_bzCompress</code>, and
+<code class="computeroutput">BZ2_bzCompressEnd</code> for
+compression, and a corresponding trio
+<code class="computeroutput">BZ2_bzDecompressInit</code>,
+<code class="computeroutput">BZ2_bzDecompress</code> and
+<code class="computeroutput">BZ2_bzDecompressEnd</code> for
+decompression. The <code class="computeroutput">*Init</code>
+functions allocate memory for compression/decompression and do
+other initialisations, whilst the
+<code class="computeroutput">*End</code> functions close down
+operations and release memory.</p>
+<p>The real work is done by
+<code class="computeroutput">BZ2_bzCompress</code> and
+<code class="computeroutput">BZ2_bzDecompress</code>. These
+compress and decompress data from a user-supplied input buffer to
+a user-supplied output buffer. These buffers can be any size;
+arbitrary quantities of data are handled by making repeated calls
+to these functions. This is a flexible mechanism allowing a
+consumer-pull style of activity, or producer-push, or a mixture
+of both.</p>
+</div>
+<div class="sect2" title="3.1.2.�High-level summary">
+<div class="titlepage"><div><div><h3 class="title">
+<a name="hl-summary"></a>3.1.2.�High-level summary</h3></div></div></div>
+<p>This interface provides some handy wrappers around the
+low-level interface to facilitate reading and writing
+<code class="computeroutput">bzip2</code> format files
+(<code class="computeroutput">.bz2</code> files). The routines
+provide hooks to facilitate reading files in which the
+<code class="computeroutput">bzip2</code> data stream is embedded
+within some larger-scale file structure, or where there are
+multiple <code class="computeroutput">bzip2</code> data streams
+concatenated end-to-end.</p>
+<p>For reading files,
+<code class="computeroutput">BZ2_bzReadOpen</code>,
+<code class="computeroutput">BZ2_bzRead</code>,
+<code class="computeroutput">BZ2_bzReadClose</code> and
+<code class="computeroutput">BZ2_bzReadGetUnused</code> are
+supplied. For writing files,
+<code class="computeroutput">BZ2_bzWriteOpen</code>,
+<code class="computeroutput">BZ2_bzWrite</code> and
+<code class="computeroutput">BZ2_bzWriteFinish</code> are
+available.</p>
+<p>As with the low-level library, no global variables are used
+so the library is per se thread-safe. However, if I/O errors
+occur whilst reading or writing the underlying compressed files,
+you may have to consult <code class="computeroutput">errno</code> to
+determine the cause of the error. In that case, you'd need a C
+library which correctly supports
+<code class="computeroutput">errno</code> in a multithreaded
+environment.</p>
+<p>To make the library a little simpler and more portable,
+<code class="computeroutput">BZ2_bzReadOpen</code> and
+<code class="computeroutput">BZ2_bzWriteOpen</code> require you to
+pass them file handles (<code class="computeroutput">FILE*</code>s)
+which have previously been opened for reading or writing
+respectively. That avoids portability problems associated with
+file operations and file attributes, whilst not being much of an
+imposition on the programmer.</p>
+</div>
+<div class="sect2" title="3.1.3.�Utility functions summary">
+<div class="titlepage"><div><div><h3 class="title">
+<a name="util-fns-summary"></a>3.1.3.�Utility functions summary</h3></div></div></div>
+<p>For very simple needs,
+<code class="computeroutput">BZ2_bzBuffToBuffCompress</code> and
+<code class="computeroutput">BZ2_bzBuffToBuffDecompress</code> are
+provided. These compress data in memory from one buffer to
+another buffer in a single function call. You should assess
+whether these functions fulfill your memory-to-memory
+compression/decompression requirements before investing effort in
+understanding the more general but more complex low-level
+interface.</p>
+<p>Yoshioka Tsuneo
+(<code class="computeroutput">tsuneo at rr.iij4u.or.jp</code>) has
+contributed some functions to give better
+<code class="computeroutput">zlib</code> compatibility. These
+functions are <code class="computeroutput">BZ2_bzopen</code>,
+<code class="computeroutput">BZ2_bzread</code>,
+<code class="computeroutput">BZ2_bzwrite</code>,
+<code class="computeroutput">BZ2_bzflush</code>,
+<code class="computeroutput">BZ2_bzclose</code>,
+<code class="computeroutput">BZ2_bzerror</code> and
+<code class="computeroutput">BZ2_bzlibVersion</code>. You may find
+these functions more convenient for simple file reading and
+writing, than those in the high-level interface. These functions
+are not (yet) officially part of the library, and are minimally
+documented here. If they break, you get to keep all the pieces.
+I hope to document them properly when time permits.</p>
+<p>Yoshioka also contributed modifications to allow the
+library to be built as a Windows DLL.</p>
+</div>
+</div>
+<div class="sect1" title="3.2.�Error handling">
+<div class="titlepage"><div><div><h2 class="title" style="clear: both">
+<a name="err-handling"></a>3.2.�Error handling</h2></div></div></div>
+<p>The library is designed to recover cleanly in all
+situations, including the worst-case situation of decompressing
+random data. I'm not 100% sure that it can always do this, so
+you might want to add a signal handler to catch segmentation
+violations during decompression if you are feeling especially
+paranoid. I would be interested in hearing more about the
+robustness of the library to corrupted compressed data.</p>
+<p>Version 1.0.3 more robust in this respect than any
+previous version. Investigations with Valgrind (a tool for detecting
+problems with memory management) indicate
+that, at least for the few files I tested, all single-bit errors
+in the decompressed data are caught properly, with no
+segmentation faults, no uses of uninitialised data, no out of
+range reads or writes, and no infinite looping in the decompressor.
+So it's certainly pretty robust, although
+I wouldn't claim it to be totally bombproof.</p>
+<p>The file <code class="computeroutput">bzlib.h</code> contains
+all definitions needed to use the library. In particular, you
+should definitely not include
+<code class="computeroutput">bzlib_private.h</code>.</p>
+<p>In <code class="computeroutput">bzlib.h</code>, the various
+return values are defined. The following list is not intended as
+an exhaustive description of the circumstances in which a given
+value may be returned -- those descriptions are given later.
+Rather, it is intended to convey the rough meaning of each return
+value. The first five actions are normal and not intended to
+denote an error situation.</p>
+<div class="variablelist"><dl>
+<dt><span class="term"><code class="computeroutput">BZ_OK</code></span></dt>
+<dd><p>The requested action was completed
+ successfully.</p></dd>
+<dt><span class="term"><code class="computeroutput">BZ_RUN_OK, BZ_FLUSH_OK,
+ BZ_FINISH_OK</code></span></dt>
+<dd><p>In
+ <code class="computeroutput">BZ2_bzCompress</code>, the requested
+ flush/finish/nothing-special action was completed
+ successfully.</p></dd>
+<dt><span class="term"><code class="computeroutput">BZ_STREAM_END</code></span></dt>
+<dd><p>Compression of data was completed, or the
+ logical stream end was detected during
+ decompression.</p></dd>
+</dl></div>
+<p>The following return values indicate an error of some
+kind.</p>
+<div class="variablelist"><dl>
+<dt><span class="term"><code class="computeroutput">BZ_CONFIG_ERROR</code></span></dt>
+<dd><p>Indicates that the library has been improperly
+ compiled on your platform -- a major configuration error.
+ Specifically, it means that
+ <code class="computeroutput">sizeof(char)</code>,
+ <code class="computeroutput">sizeof(short)</code> and
+ <code class="computeroutput">sizeof(int)</code> are not 1, 2 and
+ 4 respectively, as they should be. Note that the library
+ should still work properly on 64-bit platforms which follow
+ the LP64 programming model -- that is, where
+ <code class="computeroutput">sizeof(long)</code> and
+ <code class="computeroutput">sizeof(void*)</code> are 8. Under
+ LP64, <code class="computeroutput">sizeof(int)</code> is still 4,
+ so <code class="computeroutput">libbzip2</code>, which doesn't
+ use the <code class="computeroutput">long</code> type, is
+ OK.</p></dd>
+<dt><span class="term"><code class="computeroutput">BZ_SEQUENCE_ERROR</code></span></dt>
+<dd><p>When using the library, it is important to call
+ the functions in the correct sequence and with data structures
+ (buffers etc) in the correct states.
+ <code class="computeroutput">libbzip2</code> checks as much as it
+ can to ensure this is happening, and returns
+ <code class="computeroutput">BZ_SEQUENCE_ERROR</code> if not.
+ Code which complies precisely with the function semantics, as
+ detailed below, should never receive this value; such an event
+ denotes buggy code which you should
+ investigate.</p></dd>
+<dt><span class="term"><code class="computeroutput">BZ_PARAM_ERROR</code></span></dt>
+<dd><p>Returned when a parameter to a function call is
+ out of range or otherwise manifestly incorrect. As with
+ <code class="computeroutput">BZ_SEQUENCE_ERROR</code>, this
+ denotes a bug in the client code. The distinction between
+ <code class="computeroutput">BZ_PARAM_ERROR</code> and
+ <code class="computeroutput">BZ_SEQUENCE_ERROR</code> is a bit
+ hazy, but still worth making.</p></dd>
+<dt><span class="term"><code class="computeroutput">BZ_MEM_ERROR</code></span></dt>
+<dd><p>Returned when a request to allocate memory
+ failed. Note that the quantity of memory needed to decompress
+ a stream cannot be determined until the stream's header has
+ been read. So
+ <code class="computeroutput">BZ2_bzDecompress</code> and
+ <code class="computeroutput">BZ2_bzRead</code> may return
+ <code class="computeroutput">BZ_MEM_ERROR</code> even though some
+ of the compressed data has been read. The same is not true
+ for compression; once
+ <code class="computeroutput">BZ2_bzCompressInit</code> or
+ <code class="computeroutput">BZ2_bzWriteOpen</code> have
+ successfully completed,
+ <code class="computeroutput">BZ_MEM_ERROR</code> cannot
+ occur.</p></dd>
+<dt><span class="term"><code class="computeroutput">BZ_DATA_ERROR</code></span></dt>
+<dd><p>Returned when a data integrity error is
+ detected during decompression. Most importantly, this means
+ when stored and computed CRCs for the data do not match. This
+ value is also returned upon detection of any other anomaly in
+ the compressed data.</p></dd>
+<dt><span class="term"><code class="computeroutput">BZ_DATA_ERROR_MAGIC</code></span></dt>
+<dd><p>As a special case of
+ <code class="computeroutput">BZ_DATA_ERROR</code>, it is
+ sometimes useful to know when the compressed stream does not
+ start with the correct magic bytes (<code class="computeroutput">'B' 'Z'
+ 'h'</code>).</p></dd>
+<dt><span class="term"><code class="computeroutput">BZ_IO_ERROR</code></span></dt>
+<dd><p>Returned by
+ <code class="computeroutput">BZ2_bzRead</code> and
+ <code class="computeroutput">BZ2_bzWrite</code> when there is an
+ error reading or writing in the compressed file, and by
+ <code class="computeroutput">BZ2_bzReadOpen</code> and
+ <code class="computeroutput">BZ2_bzWriteOpen</code> for attempts
+ to use a file for which the error indicator (viz,
+ <code class="computeroutput">ferror(f)</code>) is set. On
+ receipt of <code class="computeroutput">BZ_IO_ERROR</code>, the
+ caller should consult <code class="computeroutput">errno</code>
+ and/or <code class="computeroutput">perror</code> to acquire
+ operating-system specific information about the
+ problem.</p></dd>
+<dt><span class="term"><code class="computeroutput">BZ_UNEXPECTED_EOF</code></span></dt>
+<dd><p>Returned by
+ <code class="computeroutput">BZ2_bzRead</code> when the
+ compressed file finishes before the logical end of stream is
+ detected.</p></dd>
+<dt><span class="term"><code class="computeroutput">BZ_OUTBUFF_FULL</code></span></dt>
+<dd><p>Returned by
+ <code class="computeroutput">BZ2_bzBuffToBuffCompress</code> and
+ <code class="computeroutput">BZ2_bzBuffToBuffDecompress</code> to
+ indicate that the output data will not fit into the output
+ buffer provided.</p></dd>
+</dl></div>
+</div>
+<div class="sect1" title="3.3.�Low-level interface">
+<div class="titlepage"><div><div><h2 class="title" style="clear: both">
+<a name="low-level"></a>3.3.�Low-level interface</h2></div></div></div>
+<div class="sect2" title="3.3.1.�BZ2_bzCompressInit">
+<div class="titlepage"><div><div><h3 class="title">
+<a name="bzcompress-init"></a>3.3.1.�BZ2_bzCompressInit</h3></div></div></div>
+<pre class="programlisting">typedef struct {
+ char *next_in;
+ unsigned int avail_in;
+ unsigned int total_in_lo32;
+ unsigned int total_in_hi32;
+
+ char *next_out;
+ unsigned int avail_out;
+ unsigned int total_out_lo32;
+ unsigned int total_out_hi32;
+
+ void *state;
+
+ void *(*bzalloc)(void *,int,int);
+ void (*bzfree)(void *,void *);
+ void *opaque;
+} bz_stream;
+
+int BZ2_bzCompressInit ( bz_stream *strm,
+ int blockSize100k,
+ int verbosity,
+ int workFactor );</pre>
+<p>Prepares for compression. The
+<code class="computeroutput">bz_stream</code> structure holds all
+data pertaining to the compression activity. A
+<code class="computeroutput">bz_stream</code> structure should be
+allocated and initialised prior to the call. The fields of
+<code class="computeroutput">bz_stream</code> comprise the entirety
+of the user-visible data. <code class="computeroutput">state</code>
+is a pointer to the private data structures required for
+compression.</p>
+<p>Custom memory allocators are supported, via fields
+<code class="computeroutput">bzalloc</code>,
+<code class="computeroutput">bzfree</code>, and
+<code class="computeroutput">opaque</code>. The value
+<code class="computeroutput">opaque</code> is passed to as the first
+argument to all calls to <code class="computeroutput">bzalloc</code>
+and <code class="computeroutput">bzfree</code>, but is otherwise
+ignored by the library. The call <code class="computeroutput">bzalloc (
+opaque, n, m )</code> is expected to return a pointer
+<code class="computeroutput">p</code> to <code class="computeroutput">n *
+m</code> bytes of memory, and <code class="computeroutput">bzfree (
+opaque, p )</code> should free that memory.</p>
+<p>If you don't want to use a custom memory allocator, set
+<code class="computeroutput">bzalloc</code>,
+<code class="computeroutput">bzfree</code> and
+<code class="computeroutput">opaque</code> to
+<code class="computeroutput">NULL</code>, and the library will then
+use the standard <code class="computeroutput">malloc</code> /
+<code class="computeroutput">free</code> routines.</p>
+<p>Before calling
+<code class="computeroutput">BZ2_bzCompressInit</code>, fields
+<code class="computeroutput">bzalloc</code>,
+<code class="computeroutput">bzfree</code> and
+<code class="computeroutput">opaque</code> should be filled
+appropriately, as just described. Upon return, the internal
+state will have been allocated and initialised, and
+<code class="computeroutput">total_in_lo32</code>,
+<code class="computeroutput">total_in_hi32</code>,
+<code class="computeroutput">total_out_lo32</code> and
+<code class="computeroutput">total_out_hi32</code> will have been
+set to zero. These four fields are used by the library to inform
+the caller of the total amount of data passed into and out of the
+library, respectively. You should not try to change them. As of
+version 1.0, 64-bit counts are maintained, even on 32-bit
+platforms, using the <code class="computeroutput">_hi32</code>
+fields to store the upper 32 bits of the count. So, for example,
+the total amount of data in is <code class="computeroutput">(total_in_hi32
+<< 32) + total_in_lo32</code>.</p>
+<p>Parameter <code class="computeroutput">blockSize100k</code>
+specifies the block size to be used for compression. It should
+be a value between 1 and 9 inclusive, and the actual block size
+used is 100000 x this figure. 9 gives the best compression but
+takes most memory.</p>
+<p>Parameter <code class="computeroutput">verbosity</code> should
+be set to a number between 0 and 4 inclusive. 0 is silent, and
+greater numbers give increasingly verbose monitoring/debugging
+output. If the library has been compiled with
+<code class="computeroutput">-DBZ_NO_STDIO</code>, no such output
+will appear for any verbosity setting.</p>
+<p>Parameter <code class="computeroutput">workFactor</code>
+controls how the compression phase behaves when presented with
+worst case, highly repetitive, input data. If compression runs
+into difficulties caused by repetitive data, the library switches
+from the standard sorting algorithm to a fallback algorithm. The
+fallback is slower than the standard algorithm by perhaps a
+factor of three, but always behaves reasonably, no matter how bad
+the input.</p>
+<p>Lower values of <code class="computeroutput">workFactor</code>
+reduce the amount of effort the standard algorithm will expend
+before resorting to the fallback. You should set this parameter
+carefully; too low, and many inputs will be handled by the
+fallback algorithm and so compress rather slowly, too high, and
+your average-to-worst case compression times can become very
+large. The default value of 30 gives reasonable behaviour over a
+wide range of circumstances.</p>
+<p>Allowable values range from 0 to 250 inclusive. 0 is a
+special case, equivalent to using the default value of 30.</p>
+<p>Note that the compressed output generated is the same
+regardless of whether or not the fallback algorithm is
+used.</p>
+<p>Be aware also that this parameter may disappear entirely in
+future versions of the library. In principle it should be
+possible to devise a good way to automatically choose which
+algorithm to use. Such a mechanism would render the parameter
+obsolete.</p>
+<p>Possible return values:</p>
+<pre class="programlisting">BZ_CONFIG_ERROR
+ if the library has been mis-compiled
+BZ_PARAM_ERROR
+ if strm is NULL
+ or blockSize < 1 or blockSize > 9
+ or verbosity < 0 or verbosity > 4
+ or workFactor < 0 or workFactor > 250
+BZ_MEM_ERROR
+ if not enough memory is available
+BZ_OK
+ otherwise</pre>
+<p>Allowable next actions:</p>
+<pre class="programlisting">BZ2_bzCompress
+ if BZ_OK is returned
+ no specific action needed in case of error</pre>
+</div>
+<div class="sect2" title="3.3.2.�BZ2_bzCompress">
+<div class="titlepage"><div><div><h3 class="title">
+<a name="bzCompress"></a>3.3.2.�BZ2_bzCompress</h3></div></div></div>
+<pre class="programlisting">int BZ2_bzCompress ( bz_stream *strm, int action );</pre>
+<p>Provides more input and/or output buffer space for the
+library. The caller maintains input and output buffers, and
+calls <code class="computeroutput">BZ2_bzCompress</code> to transfer
+data between them.</p>
+<p>Before each call to
+<code class="computeroutput">BZ2_bzCompress</code>,
+<code class="computeroutput">next_in</code> should point at the data
+to be compressed, and <code class="computeroutput">avail_in</code>
+should indicate how many bytes the library may read.
+<code class="computeroutput">BZ2_bzCompress</code> updates
+<code class="computeroutput">next_in</code>,
+<code class="computeroutput">avail_in</code> and
+<code class="computeroutput">total_in</code> to reflect the number
+of bytes it has read.</p>
+<p>Similarly, <code class="computeroutput">next_out</code> should
+point to a buffer in which the compressed data is to be placed,
+with <code class="computeroutput">avail_out</code> indicating how
+much output space is available.
+<code class="computeroutput">BZ2_bzCompress</code> updates
+<code class="computeroutput">next_out</code>,
+<code class="computeroutput">avail_out</code> and
+<code class="computeroutput">total_out</code> to reflect the number
+of bytes output.</p>
+<p>You may provide and remove as little or as much data as you
+like on each call of
+<code class="computeroutput">BZ2_bzCompress</code>. In the limit,
+it is acceptable to supply and remove data one byte at a time,
+although this would be terribly inefficient. You should always
+ensure that at least one byte of output space is available at
+each call.</p>
+<p>A second purpose of
+<code class="computeroutput">BZ2_bzCompress</code> is to request a
+change of mode of the compressed stream.</p>
+<p>Conceptually, a compressed stream can be in one of four
+states: IDLE, RUNNING, FLUSHING and FINISHING. Before
+initialisation
+(<code class="computeroutput">BZ2_bzCompressInit</code>) and after
+termination (<code class="computeroutput">BZ2_bzCompressEnd</code>),
+a stream is regarded as IDLE.</p>
+<p>Upon initialisation
+(<code class="computeroutput">BZ2_bzCompressInit</code>), the stream
+is placed in the RUNNING state. Subsequent calls to
+<code class="computeroutput">BZ2_bzCompress</code> should pass
+<code class="computeroutput">BZ_RUN</code> as the requested action;
+other actions are illegal and will result in
+<code class="computeroutput">BZ_SEQUENCE_ERROR</code>.</p>
+<p>At some point, the calling program will have provided all
+the input data it wants to. It will then want to finish up -- in
+effect, asking the library to process any data it might have
+buffered internally. In this state,
+<code class="computeroutput">BZ2_bzCompress</code> will no longer
+attempt to read data from
+<code class="computeroutput">next_in</code>, but it will want to
+write data to <code class="computeroutput">next_out</code>. Because
+the output buffer supplied by the user can be arbitrarily small,
+the finishing-up operation cannot necessarily be done with a
+single call of
+<code class="computeroutput">BZ2_bzCompress</code>.</p>
+<p>Instead, the calling program passes
+<code class="computeroutput">BZ_FINISH</code> as an action to
+<code class="computeroutput">BZ2_bzCompress</code>. This changes
+the stream's state to FINISHING. Any remaining input (ie,
+<code class="computeroutput">next_in[0 .. avail_in-1]</code>) is
+compressed and transferred to the output buffer. To do this,
+<code class="computeroutput">BZ2_bzCompress</code> must be called
+repeatedly until all the output has been consumed. At that
+point, <code class="computeroutput">BZ2_bzCompress</code> returns
+<code class="computeroutput">BZ_STREAM_END</code>, and the stream's
+state is set back to IDLE.
+<code class="computeroutput">BZ2_bzCompressEnd</code> should then be
+called.</p>
+<p>Just to make sure the calling program does not cheat, the
+library makes a note of <code class="computeroutput">avail_in</code>
+at the time of the first call to
+<code class="computeroutput">BZ2_bzCompress</code> which has
+<code class="computeroutput">BZ_FINISH</code> as an action (ie, at
+the time the program has announced its intention to not supply
+any more input). By comparing this value with that of
+<code class="computeroutput">avail_in</code> over subsequent calls
+to <code class="computeroutput">BZ2_bzCompress</code>, the library
+can detect any attempts to slip in more data to compress. Any
+calls for which this is detected will return
+<code class="computeroutput">BZ_SEQUENCE_ERROR</code>. This
+indicates a programming mistake which should be corrected.</p>
+<p>Instead of asking to finish, the calling program may ask
+<code class="computeroutput">BZ2_bzCompress</code> to take all the
+remaining input, compress it and terminate the current
+(Burrows-Wheeler) compression block. This could be useful for
+error control purposes. The mechanism is analogous to that for
+finishing: call <code class="computeroutput">BZ2_bzCompress</code>
+with an action of <code class="computeroutput">BZ_FLUSH</code>,
+remove output data, and persist with the
+<code class="computeroutput">BZ_FLUSH</code> action until the value
+<code class="computeroutput">BZ_RUN</code> is returned. As with
+finishing, <code class="computeroutput">BZ2_bzCompress</code>
+detects any attempt to provide more input data once the flush has
+begun.</p>
+<p>Once the flush is complete, the stream returns to the
+normal RUNNING state.</p>
+<p>This all sounds pretty complex, but isn't really. Here's a
+table which shows which actions are allowable in each state, what
+action will be taken, what the next state is, and what the
+non-error return values are. Note that you can't explicitly ask
+what state the stream is in, but nor do you need to -- it can be
+inferred from the values returned by
+<code class="computeroutput">BZ2_bzCompress</code>.</p>
+<pre class="programlisting">IDLE/any
+ Illegal. IDLE state only exists after BZ2_bzCompressEnd or
+ before BZ2_bzCompressInit.
+ Return value = BZ_SEQUENCE_ERROR
+
+RUNNING/BZ_RUN
+ Compress from next_in to next_out as much as possible.
+ Next state = RUNNING
+ Return value = BZ_RUN_OK
+
+RUNNING/BZ_FLUSH
+ Remember current value of next_in. Compress from next_in
+ to next_out as much as possible, but do not accept any more input.
+ Next state = FLUSHING
+ Return value = BZ_FLUSH_OK
+
+RUNNING/BZ_FINISH
+ Remember current value of next_in. Compress from next_in
+ to next_out as much as possible, but do not accept any more input.
+ Next state = FINISHING
+ Return value = BZ_FINISH_OK
+
+FLUSHING/BZ_FLUSH
+ Compress from next_in to next_out as much as possible,
+ but do not accept any more input.
+ If all the existing input has been used up and all compressed
+ output has been removed
+ Next state = RUNNING; Return value = BZ_RUN_OK
+ else
+ Next state = FLUSHING; Return value = BZ_FLUSH_OK
+
+FLUSHING/other
+ Illegal.
+ Return value = BZ_SEQUENCE_ERROR
+
+FINISHING/BZ_FINISH
+ Compress from next_in to next_out as much as possible,
+ but to not accept any more input.
+ If all the existing input has been used up and all compressed
+ output has been removed
+ Next state = IDLE; Return value = BZ_STREAM_END
+ else
+ Next state = FINISHING; Return value = BZ_FINISH_OK
+
+FINISHING/other
+ Illegal.
+ Return value = BZ_SEQUENCE_ERROR</pre>
+<p>That still looks complicated? Well, fair enough. The
+usual sequence of calls for compressing a load of data is:</p>
+<div class="orderedlist"><ol class="orderedlist" type="1">
+<li class="listitem"><p>Get started with
+ <code class="computeroutput">BZ2_bzCompressInit</code>.</p></li>
+<li class="listitem"><p>Shovel data in and shlurp out its compressed form
+ using zero or more calls of
+ <code class="computeroutput">BZ2_bzCompress</code> with action =
+ <code class="computeroutput">BZ_RUN</code>.</p></li>
+<li class="listitem"><p>Finish up. Repeatedly call
+ <code class="computeroutput">BZ2_bzCompress</code> with action =
+ <code class="computeroutput">BZ_FINISH</code>, copying out the
+ compressed output, until
+ <code class="computeroutput">BZ_STREAM_END</code> is
+ returned.</p></li>
+<li class="listitem"><p>Close up and go home. Call
+ <code class="computeroutput">BZ2_bzCompressEnd</code>.</p></li>
+</ol></div>
+<p>If the data you want to compress fits into your input
+buffer all at once, you can skip the calls of
+<code class="computeroutput">BZ2_bzCompress ( ..., BZ_RUN )</code>
+and just do the <code class="computeroutput">BZ2_bzCompress ( ..., BZ_FINISH
+)</code> calls.</p>
+<p>All required memory is allocated by
+<code class="computeroutput">BZ2_bzCompressInit</code>. The
+compression library can accept any data at all (obviously). So
+you shouldn't get any error return values from the
+<code class="computeroutput">BZ2_bzCompress</code> calls. If you
+do, they will be
+<code class="computeroutput">BZ_SEQUENCE_ERROR</code>, and indicate
+a bug in your programming.</p>
+<p>Trivial other possible return values:</p>
+<pre class="programlisting">BZ_PARAM_ERROR
+ if strm is NULL, or strm->s is NULL</pre>
+</div>
+<div class="sect2" title="3.3.3.�BZ2_bzCompressEnd">
+<div class="titlepage"><div><div><h3 class="title">
+<a name="bzCompress-end"></a>3.3.3.�BZ2_bzCompressEnd</h3></div></div></div>
+<pre class="programlisting">int BZ2_bzCompressEnd ( bz_stream *strm );</pre>
+<p>Releases all memory associated with a compression
+stream.</p>
+<p>Possible return values:</p>
+<pre class="programlisting">BZ_PARAM_ERROR if strm is NULL or strm->s is NULL
+BZ_OK otherwise</pre>
+</div>
+<div class="sect2" title="3.3.4.�BZ2_bzDecompressInit">
+<div class="titlepage"><div><div><h3 class="title">
+<a name="bzDecompress-init"></a>3.3.4.�BZ2_bzDecompressInit</h3></div></div></div>
+<pre class="programlisting">int BZ2_bzDecompressInit ( bz_stream *strm, int verbosity, int small );</pre>
+<p>Prepares for decompression. As with
+<code class="computeroutput">BZ2_bzCompressInit</code>, a
+<code class="computeroutput">bz_stream</code> record should be
+allocated and initialised before the call. Fields
+<code class="computeroutput">bzalloc</code>,
+<code class="computeroutput">bzfree</code> and
+<code class="computeroutput">opaque</code> should be set if a custom
+memory allocator is required, or made
+<code class="computeroutput">NULL</code> for the normal
+<code class="computeroutput">malloc</code> /
+<code class="computeroutput">free</code> routines. Upon return, the
+internal state will have been initialised, and
+<code class="computeroutput">total_in</code> and
+<code class="computeroutput">total_out</code> will be zero.</p>
+<p>For the meaning of parameter
+<code class="computeroutput">verbosity</code>, see
+<code class="computeroutput">BZ2_bzCompressInit</code>.</p>
+<p>If <code class="computeroutput">small</code> is nonzero, the
+library will use an alternative decompression algorithm which
+uses less memory but at the cost of decompressing more slowly
+(roughly speaking, half the speed, but the maximum memory
+requirement drops to around 2300k). See <a class="xref" href="#using" title="2.�How to use bzip2">How to use bzip2</a>
+for more information on memory management.</p>
+<p>Note that the amount of memory needed to decompress a
+stream cannot be determined until the stream's header has been
+read, so even if
+<code class="computeroutput">BZ2_bzDecompressInit</code> succeeds, a
+subsequent <code class="computeroutput">BZ2_bzDecompress</code>
+could fail with
+<code class="computeroutput">BZ_MEM_ERROR</code>.</p>
+<p>Possible return values:</p>
+<pre class="programlisting">BZ_CONFIG_ERROR
+ if the library has been mis-compiled
+BZ_PARAM_ERROR
+ if ( small != 0 && small != 1 )
+ or (verbosity <; 0 || verbosity > 4)
+BZ_MEM_ERROR
+ if insufficient memory is available</pre>
+<p>Allowable next actions:</p>
+<pre class="programlisting">BZ2_bzDecompress
+ if BZ_OK was returned
+ no specific action required in case of error</pre>
+</div>
+<div class="sect2" title="3.3.5.�BZ2_bzDecompress">
+<div class="titlepage"><div><div><h3 class="title">
+<a name="bzDecompress"></a>3.3.5.�BZ2_bzDecompress</h3></div></div></div>
+<pre class="programlisting">int BZ2_bzDecompress ( bz_stream *strm );</pre>
+<p>Provides more input and/out output buffer space for the
+library. The caller maintains input and output buffers, and uses
+<code class="computeroutput">BZ2_bzDecompress</code> to transfer
+data between them.</p>
+<p>Before each call to
+<code class="computeroutput">BZ2_bzDecompress</code>,
+<code class="computeroutput">next_in</code> should point at the
+compressed data, and <code class="computeroutput">avail_in</code>
+should indicate how many bytes the library may read.
+<code class="computeroutput">BZ2_bzDecompress</code> updates
+<code class="computeroutput">next_in</code>,
+<code class="computeroutput">avail_in</code> and
+<code class="computeroutput">total_in</code> to reflect the number
+of bytes it has read.</p>
+<p>Similarly, <code class="computeroutput">next_out</code> should
+point to a buffer in which the uncompressed output is to be
+placed, with <code class="computeroutput">avail_out</code>
+indicating how much output space is available.
+<code class="computeroutput">BZ2_bzCompress</code> updates
+<code class="computeroutput">next_out</code>,
+<code class="computeroutput">avail_out</code> and
+<code class="computeroutput">total_out</code> to reflect the number
+of bytes output.</p>
+<p>You may provide and remove as little or as much data as you
+like on each call of
+<code class="computeroutput">BZ2_bzDecompress</code>. In the limit,
+it is acceptable to supply and remove data one byte at a time,
+although this would be terribly inefficient. You should always
+ensure that at least one byte of output space is available at
+each call.</p>
+<p>Use of <code class="computeroutput">BZ2_bzDecompress</code> is
+simpler than
+<code class="computeroutput">BZ2_bzCompress</code>.</p>
+<p>You should provide input and remove output as described
+above, and repeatedly call
+<code class="computeroutput">BZ2_bzDecompress</code> until
+<code class="computeroutput">BZ_STREAM_END</code> is returned.
+Appearance of <code class="computeroutput">BZ_STREAM_END</code>
+denotes that <code class="computeroutput">BZ2_bzDecompress</code>
+has detected the logical end of the compressed stream.
+<code class="computeroutput">BZ2_bzDecompress</code> will not
+produce <code class="computeroutput">BZ_STREAM_END</code> until all
+output data has been placed into the output buffer, so once
+<code class="computeroutput">BZ_STREAM_END</code> appears, you are
+guaranteed to have available all the decompressed output, and
+<code class="computeroutput">BZ2_bzDecompressEnd</code> can safely
+be called.</p>
+<p>If case of an error return value, you should call
+<code class="computeroutput">BZ2_bzDecompressEnd</code> to clean up
+and release memory.</p>
+<p>Possible return values:</p>
+<pre class="programlisting">BZ_PARAM_ERROR
+ if strm is NULL or strm->s is NULL
+ or strm->avail_out < 1
+BZ_DATA_ERROR
+ if a data integrity error is detected in the compressed stream
+BZ_DATA_ERROR_MAGIC
+ if the compressed stream doesn't begin with the right magic bytes
+BZ_MEM_ERROR
+ if there wasn't enough memory available
+BZ_STREAM_END
+ if the logical end of the data stream was detected and all
+ output in has been consumed, eg s-->avail_out > 0
+BZ_OK
+ otherwise</pre>
+<p>Allowable next actions:</p>
+<pre class="programlisting">BZ2_bzDecompress
+ if BZ_OK was returned
+BZ2_bzDecompressEnd
+ otherwise</pre>
+</div>
+<div class="sect2" title="3.3.6.�BZ2_bzDecompressEnd">
+<div class="titlepage"><div><div><h3 class="title">
+<a name="bzDecompress-end"></a>3.3.6.�BZ2_bzDecompressEnd</h3></div></div></div>
+<pre class="programlisting">int BZ2_bzDecompressEnd ( bz_stream *strm );</pre>
+<p>Releases all memory associated with a decompression
+stream.</p>
+<p>Possible return values:</p>
+<pre class="programlisting">BZ_PARAM_ERROR
+ if strm is NULL or strm->s is NULL
+BZ_OK
+ otherwise</pre>
+<p>Allowable next actions:</p>
+<pre class="programlisting"> None.</pre>
+</div>
+</div>
+<div class="sect1" title="3.4.�High-level interface">
+<div class="titlepage"><div><div><h2 class="title" style="clear: both">
+<a name="hl-interface"></a>3.4.�High-level interface</h2></div></div></div>
+<p>This interface provides functions for reading and writing
+<code class="computeroutput">bzip2</code> format files. First, some
+general points.</p>
+<div class="itemizedlist"><ul class="itemizedlist" type="bullet">
+<li class="listitem" style="list-style-type: disc"><p>All of the functions take an
+ <code class="computeroutput">int*</code> first argument,
+ <code class="computeroutput">bzerror</code>. After each call,
+ <code class="computeroutput">bzerror</code> should be consulted
+ first to determine the outcome of the call. If
+ <code class="computeroutput">bzerror</code> is
+ <code class="computeroutput">BZ_OK</code>, the call completed
+ successfully, and only then should the return value of the
+ function (if any) be consulted. If
+ <code class="computeroutput">bzerror</code> is
+ <code class="computeroutput">BZ_IO_ERROR</code>, there was an
+ error reading/writing the underlying compressed file, and you
+ should then consult <code class="computeroutput">errno</code> /
+ <code class="computeroutput">perror</code> to determine the cause
+ of the difficulty. <code class="computeroutput">bzerror</code>
+ may also be set to various other values; precise details are
+ given on a per-function basis below.</p></li>
+<li class="listitem" style="list-style-type: disc"><p>If <code class="computeroutput">bzerror</code> indicates
+ an error (ie, anything except
+ <code class="computeroutput">BZ_OK</code> and
+ <code class="computeroutput">BZ_STREAM_END</code>), you should
+ immediately call
+ <code class="computeroutput">BZ2_bzReadClose</code> (or
+ <code class="computeroutput">BZ2_bzWriteClose</code>, depending on
+ whether you are attempting to read or to write) to free up all
+ resources associated with the stream. Once an error has been
+ indicated, behaviour of all calls except
+ <code class="computeroutput">BZ2_bzReadClose</code>
+ (<code class="computeroutput">BZ2_bzWriteClose</code>) is
+ undefined. The implication is that (1)
+ <code class="computeroutput">bzerror</code> should be checked
+ after each call, and (2) if
+ <code class="computeroutput">bzerror</code> indicates an error,
+ <code class="computeroutput">BZ2_bzReadClose</code>
+ (<code class="computeroutput">BZ2_bzWriteClose</code>) should then
+ be called to clean up.</p></li>
+<li class="listitem" style="list-style-type: disc"><p>The <code class="computeroutput">FILE*</code> arguments
+ passed to <code class="computeroutput">BZ2_bzReadOpen</code> /
+ <code class="computeroutput">BZ2_bzWriteOpen</code> should be set
+ to binary mode. Most Unix systems will do this by default, but
+ other platforms, including Windows and Mac, will not. If you
+ omit this, you may encounter problems when moving code to new
+ platforms.</p></li>
+<li class="listitem" style="list-style-type: disc"><p>Memory allocation requests are handled by
+ <code class="computeroutput">malloc</code> /
+ <code class="computeroutput">free</code>. At present there is no
+ facility for user-defined memory allocators in the file I/O
+ functions (could easily be added, though).</p></li>
+</ul></div>
+<div class="sect2" title="3.4.1.�BZ2_bzReadOpen">
+<div class="titlepage"><div><div><h3 class="title">
+<a name="bzreadopen"></a>3.4.1.�BZ2_bzReadOpen</h3></div></div></div>
+<pre class="programlisting">typedef void BZFILE;
+
+BZFILE *BZ2_bzReadOpen( int *bzerror, FILE *f,
+ int verbosity, int small,
+ void *unused, int nUnused );</pre>
+<p>Prepare to read compressed data from file handle
+<code class="computeroutput">f</code>.
+<code class="computeroutput">f</code> should refer to a file which
+has been opened for reading, and for which the error indicator
+(<code class="computeroutput">ferror(f)</code>)is not set. If
+<code class="computeroutput">small</code> is 1, the library will try
+to decompress using less memory, at the expense of speed.</p>
+<p>For reasons explained below,
+<code class="computeroutput">BZ2_bzRead</code> will decompress the
+<code class="computeroutput">nUnused</code> bytes starting at
+<code class="computeroutput">unused</code>, before starting to read
+from the file <code class="computeroutput">f</code>. At most
+<code class="computeroutput">BZ_MAX_UNUSED</code> bytes may be
+supplied like this. If this facility is not required, you should
+pass <code class="computeroutput">NULL</code> and
+<code class="computeroutput">0</code> for
+<code class="computeroutput">unused</code> and
+n<code class="computeroutput">Unused</code> respectively.</p>
+<p>For the meaning of parameters
+<code class="computeroutput">small</code> and
+<code class="computeroutput">verbosity</code>, see
+<code class="computeroutput">BZ2_bzDecompressInit</code>.</p>
+<p>The amount of memory needed to decompress a file cannot be
+determined until the file's header has been read. So it is
+possible that <code class="computeroutput">BZ2_bzReadOpen</code>
+returns <code class="computeroutput">BZ_OK</code> but a subsequent
+call of <code class="computeroutput">BZ2_bzRead</code> will return
+<code class="computeroutput">BZ_MEM_ERROR</code>.</p>
+<p>Possible assignments to
+<code class="computeroutput">bzerror</code>:</p>
+<pre class="programlisting">BZ_CONFIG_ERROR
+ if the library has been mis-compiled
+BZ_PARAM_ERROR
+ if f is NULL
+ or small is neither 0 nor 1
+ or ( unused == NULL && nUnused != 0 )
+ or ( unused != NULL && !(0 <= nUnused <= BZ_MAX_UNUSED) )
+BZ_IO_ERROR
+ if ferror(f) is nonzero
+BZ_MEM_ERROR
+ if insufficient memory is available
+BZ_OK
+ otherwise.</pre>
+<p>Possible return values:</p>
+<pre class="programlisting">Pointer to an abstract BZFILE
+ if bzerror is BZ_OK
+NULL
+ otherwise</pre>
+<p>Allowable next actions:</p>
+<pre class="programlisting">BZ2_bzRead
+ if bzerror is BZ_OK
+BZ2_bzClose
+ otherwise</pre>
+</div>
+<div class="sect2" title="3.4.2.�BZ2_bzRead">
+<div class="titlepage"><div><div><h3 class="title">
+<a name="bzread"></a>3.4.2.�BZ2_bzRead</h3></div></div></div>
+<pre class="programlisting">int BZ2_bzRead ( int *bzerror, BZFILE *b, void *buf, int len );</pre>
+<p>Reads up to <code class="computeroutput">len</code>
+(uncompressed) bytes from the compressed file
+<code class="computeroutput">b</code> into the buffer
+<code class="computeroutput">buf</code>. If the read was
+successful, <code class="computeroutput">bzerror</code> is set to
+<code class="computeroutput">BZ_OK</code> and the number of bytes
+read is returned. If the logical end-of-stream was detected,
+<code class="computeroutput">bzerror</code> will be set to
+<code class="computeroutput">BZ_STREAM_END</code>, and the number of
+bytes read is returned. All other
+<code class="computeroutput">bzerror</code> values denote an
+error.</p>
+<p><code class="computeroutput">BZ2_bzRead</code> will supply
+<code class="computeroutput">len</code> bytes, unless the logical
+stream end is detected or an error occurs. Because of this, it
+is possible to detect the stream end by observing when the number
+of bytes returned is less than the number requested.
+Nevertheless, this is regarded as inadvisable; you should instead
+check <code class="computeroutput">bzerror</code> after every call
+and watch out for
+<code class="computeroutput">BZ_STREAM_END</code>.</p>
+<p>Internally, <code class="computeroutput">BZ2_bzRead</code>
+copies data from the compressed file in chunks of size
+<code class="computeroutput">BZ_MAX_UNUSED</code> bytes before
+decompressing it. If the file contains more bytes than strictly
+needed to reach the logical end-of-stream,
+<code class="computeroutput">BZ2_bzRead</code> will almost certainly
+read some of the trailing data before signalling
+<code class="computeroutput">BZ_SEQUENCE_END</code>. To collect the
+read but unused data once
+<code class="computeroutput">BZ_SEQUENCE_END</code> has appeared,
+call <code class="computeroutput">BZ2_bzReadGetUnused</code>
+immediately before
+<code class="computeroutput">BZ2_bzReadClose</code>.</p>
+<p>Possible assignments to
+<code class="computeroutput">bzerror</code>:</p>
+<pre class="programlisting">BZ_PARAM_ERROR
+ if b is NULL or buf is NULL or len < 0
+BZ_SEQUENCE_ERROR
+ if b was opened with BZ2_bzWriteOpen
+BZ_IO_ERROR
+ if there is an error reading from the compressed file
+BZ_UNEXPECTED_EOF
+ if the compressed file ended before
+ the logical end-of-stream was detected
+BZ_DATA_ERROR
+ if a data integrity error was detected in the compressed stream
+BZ_DATA_ERROR_MAGIC
+ if the stream does not begin with the requisite header bytes
+ (ie, is not a bzip2 data file). This is really
+ a special case of BZ_DATA_ERROR.
+BZ_MEM_ERROR
+ if insufficient memory was available
+BZ_STREAM_END
+ if the logical end of stream was detected.
+BZ_OK
+ otherwise.</pre>
+<p>Possible return values:</p>
+<pre class="programlisting">number of bytes read
+ if bzerror is BZ_OK or BZ_STREAM_END
+undefined
+ otherwise</pre>
+<p>Allowable next actions:</p>
+<pre class="programlisting">collect data from buf, then BZ2_bzRead or BZ2_bzReadClose
+ if bzerror is BZ_OK
+collect data from buf, then BZ2_bzReadClose or BZ2_bzReadGetUnused
+ if bzerror is BZ_SEQUENCE_END
+BZ2_bzReadClose
+ otherwise</pre>
+</div>
+<div class="sect2" title="3.4.3.�BZ2_bzReadGetUnused">
+<div class="titlepage"><div><div><h3 class="title">
+<a name="bzreadgetunused"></a>3.4.3.�BZ2_bzReadGetUnused</h3></div></div></div>
+<pre class="programlisting">void BZ2_bzReadGetUnused( int* bzerror, BZFILE *b,
+ void** unused, int* nUnused );</pre>
+<p>Returns data which was read from the compressed file but
+was not needed to get to the logical end-of-stream.
+<code class="computeroutput">*unused</code> is set to the address of
+the data, and <code class="computeroutput">*nUnused</code> to the
+number of bytes. <code class="computeroutput">*nUnused</code> will
+be set to a value between <code class="computeroutput">0</code> and
+<code class="computeroutput">BZ_MAX_UNUSED</code> inclusive.</p>
+<p>This function may only be called once
+<code class="computeroutput">BZ2_bzRead</code> has signalled
+<code class="computeroutput">BZ_STREAM_END</code> but before
+<code class="computeroutput">BZ2_bzReadClose</code>.</p>
+<p>Possible assignments to
+<code class="computeroutput">bzerror</code>:</p>
+<pre class="programlisting">BZ_PARAM_ERROR
+ if b is NULL
+ or unused is NULL or nUnused is NULL
+BZ_SEQUENCE_ERROR
+ if BZ_STREAM_END has not been signalled
+ or if b was opened with BZ2_bzWriteOpen
+BZ_OK
+ otherwise</pre>
+<p>Allowable next actions:</p>
+<pre class="programlisting">BZ2_bzReadClose</pre>
+</div>
+<div class="sect2" title="3.4.4.�BZ2_bzReadClose">
+<div class="titlepage"><div><div><h3 class="title">
+<a name="bzreadclose"></a>3.4.4.�BZ2_bzReadClose</h3></div></div></div>
+<pre class="programlisting">void BZ2_bzReadClose ( int *bzerror, BZFILE *b );</pre>
+<p>Releases all memory pertaining to the compressed file
+<code class="computeroutput">b</code>.
+<code class="computeroutput">BZ2_bzReadClose</code> does not call
+<code class="computeroutput">fclose</code> on the underlying file
+handle, so you should do that yourself if appropriate.
+<code class="computeroutput">BZ2_bzReadClose</code> should be called
+to clean up after all error situations.</p>
+<p>Possible assignments to
+<code class="computeroutput">bzerror</code>:</p>
+<pre class="programlisting">BZ_SEQUENCE_ERROR
+ if b was opened with BZ2_bzOpenWrite
+BZ_OK
+ otherwise</pre>
+<p>Allowable next actions:</p>
+<pre class="programlisting">none</pre>
+</div>
+<div class="sect2" title="3.4.5.�BZ2_bzWriteOpen">
+<div class="titlepage"><div><div><h3 class="title">
+<a name="bzwriteopen"></a>3.4.5.�BZ2_bzWriteOpen</h3></div></div></div>
+<pre class="programlisting">BZFILE *BZ2_bzWriteOpen( int *bzerror, FILE *f,
+ int blockSize100k, int verbosity,
+ int workFactor );</pre>
+<p>Prepare to write compressed data to file handle
+<code class="computeroutput">f</code>.
+<code class="computeroutput">f</code> should refer to a file which
+has been opened for writing, and for which the error indicator
+(<code class="computeroutput">ferror(f)</code>)is not set.</p>
+<p>For the meaning of parameters
+<code class="computeroutput">blockSize100k</code>,
+<code class="computeroutput">verbosity</code> and
+<code class="computeroutput">workFactor</code>, see
+<code class="computeroutput">BZ2_bzCompressInit</code>.</p>
+<p>All required memory is allocated at this stage, so if the
+call completes successfully,
+<code class="computeroutput">BZ_MEM_ERROR</code> cannot be signalled
+by a subsequent call to
+<code class="computeroutput">BZ2_bzWrite</code>.</p>
+<p>Possible assignments to
+<code class="computeroutput">bzerror</code>:</p>
+<pre class="programlisting">BZ_CONFIG_ERROR
+ if the library has been mis-compiled
+BZ_PARAM_ERROR
+ if f is NULL
+ or blockSize100k < 1 or blockSize100k > 9
+BZ_IO_ERROR
+ if ferror(f) is nonzero
+BZ_MEM_ERROR
+ if insufficient memory is available
+BZ_OK
+ otherwise</pre>
+<p>Possible return values:</p>
+<pre class="programlisting">Pointer to an abstract BZFILE
+ if bzerror is BZ_OK
+NULL
+ otherwise</pre>
+<p>Allowable next actions:</p>
+<pre class="programlisting">BZ2_bzWrite
+ if bzerror is BZ_OK
+ (you could go directly to BZ2_bzWriteClose, but this would be pretty pointless)
+BZ2_bzWriteClose
+ otherwise</pre>
+</div>
+<div class="sect2" title="3.4.6.�BZ2_bzWrite">
+<div class="titlepage"><div><div><h3 class="title">
+<a name="bzwrite"></a>3.4.6.�BZ2_bzWrite</h3></div></div></div>
+<pre class="programlisting">void BZ2_bzWrite ( int *bzerror, BZFILE *b, void *buf, int len );</pre>
+<p>Absorbs <code class="computeroutput">len</code> bytes from the
+buffer <code class="computeroutput">buf</code>, eventually to be
+compressed and written to the file.</p>
+<p>Possible assignments to
+<code class="computeroutput">bzerror</code>:</p>
+<pre class="programlisting">BZ_PARAM_ERROR
+ if b is NULL or buf is NULL or len < 0
+BZ_SEQUENCE_ERROR
+ if b was opened with BZ2_bzReadOpen
+BZ_IO_ERROR
+ if there is an error writing the compressed file.
+BZ_OK
+ otherwise</pre>
+</div>
+<div class="sect2" title="3.4.7.�BZ2_bzWriteClose">
+<div class="titlepage"><div><div><h3 class="title">
+<a name="bzwriteclose"></a>3.4.7.�BZ2_bzWriteClose</h3></div></div></div>
+<pre class="programlisting">void BZ2_bzWriteClose( int *bzerror, BZFILE* f,
+ int abandon,
+ unsigned int* nbytes_in,
+ unsigned int* nbytes_out );
+
+void BZ2_bzWriteClose64( int *bzerror, BZFILE* f,
+ int abandon,
+ unsigned int* nbytes_in_lo32,
+ unsigned int* nbytes_in_hi32,
+ unsigned int* nbytes_out_lo32,
+ unsigned int* nbytes_out_hi32 );</pre>
+<p>Compresses and flushes to the compressed file all data so
+far supplied by <code class="computeroutput">BZ2_bzWrite</code>.
+The logical end-of-stream markers are also written, so subsequent
+calls to <code class="computeroutput">BZ2_bzWrite</code> are
+illegal. All memory associated with the compressed file
+<code class="computeroutput">b</code> is released.
+<code class="computeroutput">fflush</code> is called on the
+compressed file, but it is not
+<code class="computeroutput">fclose</code>'d.</p>
+<p>If <code class="computeroutput">BZ2_bzWriteClose</code> is
+called to clean up after an error, the only action is to release
+the memory. The library records the error codes issued by
+previous calls, so this situation will be detected automatically.
+There is no attempt to complete the compression operation, nor to
+<code class="computeroutput">fflush</code> the compressed file. You
+can force this behaviour to happen even in the case of no error,
+by passing a nonzero value to
+<code class="computeroutput">abandon</code>.</p>
+<p>If <code class="computeroutput">nbytes_in</code> is non-null,
+<code class="computeroutput">*nbytes_in</code> will be set to be the
+total volume of uncompressed data handled. Similarly,
+<code class="computeroutput">nbytes_out</code> will be set to the
+total volume of compressed data written. For compatibility with
+older versions of the library,
+<code class="computeroutput">BZ2_bzWriteClose</code> only yields the
+lower 32 bits of these counts. Use
+<code class="computeroutput">BZ2_bzWriteClose64</code> if you want
+the full 64 bit counts. These two functions are otherwise
+absolutely identical.</p>
+<p>Possible assignments to
+<code class="computeroutput">bzerror</code>:</p>
+<pre class="programlisting">BZ_SEQUENCE_ERROR
+ if b was opened with BZ2_bzReadOpen
+BZ_IO_ERROR
+ if there is an error writing the compressed file
+BZ_OK
+ otherwise</pre>
+</div>
+<div class="sect2" title="3.4.8.�Handling embedded compressed data streams">
+<div class="titlepage"><div><div><h3 class="title">
+<a name="embed"></a>3.4.8.�Handling embedded compressed data streams</h3></div></div></div>
+<p>The high-level library facilitates use of
+<code class="computeroutput">bzip2</code> data streams which form
+some part of a surrounding, larger data stream.</p>
+<div class="itemizedlist"><ul class="itemizedlist" type="bullet">
+<li class="listitem" style="list-style-type: disc"><p>For writing, the library takes an open file handle,
+ writes compressed data to it,
+ <code class="computeroutput">fflush</code>es it but does not
+ <code class="computeroutput">fclose</code> it. The calling
+ application can write its own data before and after the
+ compressed data stream, using that same file handle.</p></li>
+<li class="listitem" style="list-style-type: disc"><p>Reading is more complex, and the facilities are not as
+ general as they could be since generality is hard to reconcile
+ with efficiency. <code class="computeroutput">BZ2_bzRead</code>
+ reads from the compressed file in blocks of size
+ <code class="computeroutput">BZ_MAX_UNUSED</code> bytes, and in
+ doing so probably will overshoot the logical end of compressed
+ stream. To recover this data once decompression has ended,
+ call <code class="computeroutput">BZ2_bzReadGetUnused</code> after
+ the last call of <code class="computeroutput">BZ2_bzRead</code>
+ (the one returning
+ <code class="computeroutput">BZ_STREAM_END</code>) but before
+ calling
+ <code class="computeroutput">BZ2_bzReadClose</code>.</p></li>
+</ul></div>
+<p>This mechanism makes it easy to decompress multiple
+<code class="computeroutput">bzip2</code> streams placed end-to-end.
+As the end of one stream, when
+<code class="computeroutput">BZ2_bzRead</code> returns
+<code class="computeroutput">BZ_STREAM_END</code>, call
+<code class="computeroutput">BZ2_bzReadGetUnused</code> to collect
+the unused data (copy it into your own buffer somewhere). That
+data forms the start of the next compressed stream. To start
+uncompressing that next stream, call
+<code class="computeroutput">BZ2_bzReadOpen</code> again, feeding in
+the unused data via the <code class="computeroutput">unused</code> /
+<code class="computeroutput">nUnused</code> parameters. Keep doing
+this until <code class="computeroutput">BZ_STREAM_END</code> return
+coincides with the physical end of file
+(<code class="computeroutput">feof(f)</code>). In this situation
+<code class="computeroutput">BZ2_bzReadGetUnused</code> will of
+course return no data.</p>
+<p>This should give some feel for how the high-level interface
+can be used. If you require extra flexibility, you'll have to
+bite the bullet and get to grips with the low-level
+interface.</p>
+</div>
+<div class="sect2" title="3.4.9.�Standard file-reading/writing code">
+<div class="titlepage"><div><div><h3 class="title">
+<a name="std-rdwr"></a>3.4.9.�Standard file-reading/writing code</h3></div></div></div>
+<p>Here's how you'd write data to a compressed file:</p>
+<pre class="programlisting">FILE* f;
+BZFILE* b;
+int nBuf;
+char buf[ /* whatever size you like */ ];
+int bzerror;
+int nWritten;
+
+f = fopen ( "myfile.bz2", "w" );
+if ( !f ) {
+ /* handle error */
+}
+b = BZ2_bzWriteOpen( &bzerror, f, 9 );
+if (bzerror != BZ_OK) {
+ BZ2_bzWriteClose ( b );
+ /* handle error */
+}
+
+while ( /* condition */ ) {
+ /* get data to write into buf, and set nBuf appropriately */
+ nWritten = BZ2_bzWrite ( &bzerror, b, buf, nBuf );
+ if (bzerror == BZ_IO_ERROR) {
+ BZ2_bzWriteClose ( &bzerror, b );
+ /* handle error */
+ }
+}
+
+BZ2_bzWriteClose( &bzerror, b );
+if (bzerror == BZ_IO_ERROR) {
+ /* handle error */
+}</pre>
+<p>And to read from a compressed file:</p>
+<pre class="programlisting">FILE* f;
+BZFILE* b;
+int nBuf;
+char buf[ /* whatever size you like */ ];
+int bzerror;
+int nWritten;
+
+f = fopen ( "myfile.bz2", "r" );
+if ( !f ) {
+ /* handle error */
+}
+b = BZ2_bzReadOpen ( &bzerror, f, 0, NULL, 0 );
+if ( bzerror != BZ_OK ) {
+ BZ2_bzReadClose ( &bzerror, b );
+ /* handle error */
+}
+
+bzerror = BZ_OK;
+while ( bzerror == BZ_OK && /* arbitrary other conditions */) {
+ nBuf = BZ2_bzRead ( &bzerror, b, buf, /* size of buf */ );
+ if ( bzerror == BZ_OK ) {
+ /* do something with buf[0 .. nBuf-1] */
+ }
+}
+if ( bzerror != BZ_STREAM_END ) {
+ BZ2_bzReadClose ( &bzerror, b );
+ /* handle error */
+} else {
+ BZ2_bzReadClose ( &bzerror, b );
+}</pre>
+</div>
+</div>
+<div class="sect1" title="3.5.�Utility functions">
+<div class="titlepage"><div><div><h2 class="title" style="clear: both">
+<a name="util-fns"></a>3.5.�Utility functions</h2></div></div></div>
+<div class="sect2" title="3.5.1.�BZ2_bzBuffToBuffCompress">
+<div class="titlepage"><div><div><h3 class="title">
+<a name="bzbufftobuffcompress"></a>3.5.1.�BZ2_bzBuffToBuffCompress</h3></div></div></div>
+<pre class="programlisting">int BZ2_bzBuffToBuffCompress( char* dest,
+ unsigned int* destLen,
+ char* source,
+ unsigned int sourceLen,
+ int blockSize100k,
+ int verbosity,
+ int workFactor );</pre>
+<p>Attempts to compress the data in <code class="computeroutput">source[0
+.. sourceLen-1]</code> into the destination buffer,
+<code class="computeroutput">dest[0 .. *destLen-1]</code>. If the
+destination buffer is big enough,
+<code class="computeroutput">*destLen</code> is set to the size of
+the compressed data, and <code class="computeroutput">BZ_OK</code>
+is returned. If the compressed data won't fit,
+<code class="computeroutput">*destLen</code> is unchanged, and
+<code class="computeroutput">BZ_OUTBUFF_FULL</code> is
+returned.</p>
+<p>Compression in this manner is a one-shot event, done with a
+single call to this function. The resulting compressed data is a
+complete <code class="computeroutput">bzip2</code> format data
+stream. There is no mechanism for making additional calls to
+provide extra input data. If you want that kind of mechanism,
+use the low-level interface.</p>
+<p>For the meaning of parameters
+<code class="computeroutput">blockSize100k</code>,
+<code class="computeroutput">verbosity</code> and
+<code class="computeroutput">workFactor</code>, see
+<code class="computeroutput">BZ2_bzCompressInit</code>.</p>
+<p>To guarantee that the compressed data will fit in its
+buffer, allocate an output buffer of size 1% larger than the
+uncompressed data, plus six hundred extra bytes.</p>
+<p><code class="computeroutput">BZ2_bzBuffToBuffDecompress</code>
+will not write data at or beyond
+<code class="computeroutput">dest[*destLen]</code>, even in case of
+buffer overflow.</p>
+<p>Possible return values:</p>
+<pre class="programlisting">BZ_CONFIG_ERROR
+ if the library has been mis-compiled
+BZ_PARAM_ERROR
+ if dest is NULL or destLen is NULL
+ or blockSize100k < 1 or blockSize100k > 9
+ or verbosity < 0 or verbosity > 4
+ or workFactor < 0 or workFactor > 250
+BZ_MEM_ERROR
+ if insufficient memory is available
+BZ_OUTBUFF_FULL
+ if the size of the compressed data exceeds *destLen
+BZ_OK
+ otherwise</pre>
+</div>
+<div class="sect2" title="3.5.2.�BZ2_bzBuffToBuffDecompress">
+<div class="titlepage"><div><div><h3 class="title">
+<a name="bzbufftobuffdecompress"></a>3.5.2.�BZ2_bzBuffToBuffDecompress</h3></div></div></div>
+<pre class="programlisting">int BZ2_bzBuffToBuffDecompress( char* dest,
+ unsigned int* destLen,
+ char* source,
+ unsigned int sourceLen,
+ int small,
+ int verbosity );</pre>
+<p>Attempts to decompress the data in <code class="computeroutput">source[0
+.. sourceLen-1]</code> into the destination buffer,
+<code class="computeroutput">dest[0 .. *destLen-1]</code>. If the
+destination buffer is big enough,
+<code class="computeroutput">*destLen</code> is set to the size of
+the uncompressed data, and <code class="computeroutput">BZ_OK</code>
+is returned. If the compressed data won't fit,
+<code class="computeroutput">*destLen</code> is unchanged, and
+<code class="computeroutput">BZ_OUTBUFF_FULL</code> is
+returned.</p>
+<p><code class="computeroutput">source</code> is assumed to hold
+a complete <code class="computeroutput">bzip2</code> format data
+stream.
+<code class="computeroutput">BZ2_bzBuffToBuffDecompress</code> tries
+to decompress the entirety of the stream into the output
+buffer.</p>
+<p>For the meaning of parameters
+<code class="computeroutput">small</code> and
+<code class="computeroutput">verbosity</code>, see
+<code class="computeroutput">BZ2_bzDecompressInit</code>.</p>
+<p>Because the compression ratio of the compressed data cannot
+be known in advance, there is no easy way to guarantee that the
+output buffer will be big enough. You may of course make
+arrangements in your code to record the size of the uncompressed
+data, but such a mechanism is beyond the scope of this
+library.</p>
+<p><code class="computeroutput">BZ2_bzBuffToBuffDecompress</code>
+will not write data at or beyond
+<code class="computeroutput">dest[*destLen]</code>, even in case of
+buffer overflow.</p>
+<p>Possible return values:</p>
+<pre class="programlisting">BZ_CONFIG_ERROR
+ if the library has been mis-compiled
+BZ_PARAM_ERROR
+ if dest is NULL or destLen is NULL
+ or small != 0 && small != 1
+ or verbosity < 0 or verbosity > 4
+BZ_MEM_ERROR
+ if insufficient memory is available
+BZ_OUTBUFF_FULL
+ if the size of the compressed data exceeds *destLen
+BZ_DATA_ERROR
+ if a data integrity error was detected in the compressed data
+BZ_DATA_ERROR_MAGIC
+ if the compressed data doesn't begin with the right magic bytes
+BZ_UNEXPECTED_EOF
+ if the compressed data ends unexpectedly
+BZ_OK
+ otherwise</pre>
+</div>
+</div>
+<div class="sect1" title="3.6.�zlib compatibility functions">
+<div class="titlepage"><div><div><h2 class="title" style="clear: both">
+<a name="zlib-compat"></a>3.6.�zlib compatibility functions</h2></div></div></div>
+<p>Yoshioka Tsuneo has contributed some functions to give
+better <code class="computeroutput">zlib</code> compatibility.
+These functions are <code class="computeroutput">BZ2_bzopen</code>,
+<code class="computeroutput">BZ2_bzread</code>,
+<code class="computeroutput">BZ2_bzwrite</code>,
+<code class="computeroutput">BZ2_bzflush</code>,
+<code class="computeroutput">BZ2_bzclose</code>,
+<code class="computeroutput">BZ2_bzerror</code> and
+<code class="computeroutput">BZ2_bzlibVersion</code>. These
+functions are not (yet) officially part of the library. If they
+break, you get to keep all the pieces. Nevertheless, I think
+they work ok.</p>
+<pre class="programlisting">typedef void BZFILE;
+
+const char * BZ2_bzlibVersion ( void );</pre>
+<p>Returns a string indicating the library version.</p>
+<pre class="programlisting">BZFILE * BZ2_bzopen ( const char *path, const char *mode );
+BZFILE * BZ2_bzdopen ( int fd, const char *mode );</pre>
+<p>Opens a <code class="computeroutput">.bz2</code> file for
+reading or writing, using either its name or a pre-existing file
+descriptor. Analogous to <code class="computeroutput">fopen</code>
+and <code class="computeroutput">fdopen</code>.</p>
+<pre class="programlisting">int BZ2_bzread ( BZFILE* b, void* buf, int len );
+int BZ2_bzwrite ( BZFILE* b, void* buf, int len );</pre>
+<p>Reads/writes data from/to a previously opened
+<code class="computeroutput">BZFILE</code>. Analogous to
+<code class="computeroutput">fread</code> and
+<code class="computeroutput">fwrite</code>.</p>
+<pre class="programlisting">int BZ2_bzflush ( BZFILE* b );
+void BZ2_bzclose ( BZFILE* b );</pre>
+<p>Flushes/closes a <code class="computeroutput">BZFILE</code>.
+<code class="computeroutput">BZ2_bzflush</code> doesn't actually do
+anything. Analogous to <code class="computeroutput">fflush</code>
+and <code class="computeroutput">fclose</code>.</p>
+<pre class="programlisting">const char * BZ2_bzerror ( BZFILE *b, int *errnum )</pre>
+<p>Returns a string describing the more recent error status of
+<code class="computeroutput">b</code>, and also sets
+<code class="computeroutput">*errnum</code> to its numerical
+value.</p>
+</div>
+<div class="sect1" title="3.7.�Using the library in a stdio-free environment">
+<div class="titlepage"><div><div><h2 class="title" style="clear: both">
+<a name="stdio-free"></a>3.7.�Using the library in a stdio-free environment</h2></div></div></div>
+<div class="sect2" title="3.7.1.�Getting rid of stdio">
+<div class="titlepage"><div><div><h3 class="title">
+<a name="stdio-bye"></a>3.7.1.�Getting rid of stdio</h3></div></div></div>
+<p>In a deeply embedded application, you might want to use
+just the memory-to-memory functions. You can do this
+conveniently by compiling the library with preprocessor symbol
+<code class="computeroutput">BZ_NO_STDIO</code> defined. Doing this
+gives you a library containing only the following eight
+functions:</p>
+<p><code class="computeroutput">BZ2_bzCompressInit</code>,
+<code class="computeroutput">BZ2_bzCompress</code>,
+<code class="computeroutput">BZ2_bzCompressEnd</code>
+<code class="computeroutput">BZ2_bzDecompressInit</code>,
+<code class="computeroutput">BZ2_bzDecompress</code>,
+<code class="computeroutput">BZ2_bzDecompressEnd</code>
+<code class="computeroutput">BZ2_bzBuffToBuffCompress</code>,
+<code class="computeroutput">BZ2_bzBuffToBuffDecompress</code></p>
+<p>When compiled like this, all functions will ignore
+<code class="computeroutput">verbosity</code> settings.</p>
+</div>
+<div class="sect2" title="3.7.2.�Critical error handling">
+<div class="titlepage"><div><div><h3 class="title">
+<a name="critical-error"></a>3.7.2.�Critical error handling</h3></div></div></div>
+<p><code class="computeroutput">libbzip2</code> contains a number
+of internal assertion checks which should, needless to say, never
+be activated. Nevertheless, if an assertion should fail,
+behaviour depends on whether or not the library was compiled with
+<code class="computeroutput">BZ_NO_STDIO</code> set.</p>
+<p>For a normal compile, an assertion failure yields the
+message:</p>
+<div class="blockquote"><blockquote class="blockquote">
+<p>bzip2/libbzip2: internal error number N.</p>
+<p>This is a bug in bzip2/libbzip2, 1.0.6 of 6 September 2010.
+Please report it to me at: jseward at bzip.org. If this happened
+when you were using some program which uses libbzip2 as a
+component, you should also report this bug to the author(s)
+of that program. Please make an effort to report this bug;
+timely and accurate bug reports eventually lead to higher
+quality software. Thanks. Julian Seward, 6 September 2010.
+</p>
+</blockquote></div>
+<p>where <code class="computeroutput">N</code> is some error code
+number. If <code class="computeroutput">N == 1007</code>, it also
+prints some extra text advising the reader that unreliable memory
+is often associated with internal error 1007. (This is a
+frequently-observed-phenomenon with versions 1.0.0/1.0.1).</p>
+<p><code class="computeroutput">exit(3)</code> is then
+called.</p>
+<p>For a <code class="computeroutput">stdio</code>-free library,
+assertion failures result in a call to a function declared
+as:</p>
+<pre class="programlisting">extern void bz_internal_error ( int errcode );</pre>
+<p>The relevant code is passed as a parameter. You should
+supply such a function.</p>
+<p>In either case, once an assertion failure has occurred, any
+<code class="computeroutput">bz_stream</code> records involved can
+be regarded as invalid. You should not attempt to resume normal
+operation with them.</p>
+<p>You may, of course, change critical error handling to suit
+your needs. As I said above, critical errors indicate bugs in
+the library and should not occur. All "normal" error situations
+are indicated via error return codes from functions, and can be
+recovered from.</p>
+</div>
+</div>
+<div class="sect1" title="3.8.�Making a Windows DLL">
+<div class="titlepage"><div><div><h2 class="title" style="clear: both">
+<a name="win-dll"></a>3.8.�Making a Windows DLL</h2></div></div></div>
+<p>Everything related to Windows has been contributed by
+Yoshioka Tsuneo
+(<code class="computeroutput">tsuneo at rr.iij4u.or.jp</code>), so
+you should send your queries to him (but perhaps Cc: me,
+<code class="computeroutput">jseward at bzip.org</code>).</p>
+<p>My vague understanding of what to do is: using Visual C++
+5.0, open the project file
+<code class="computeroutput">libbz2.dsp</code>, and build. That's
+all.</p>
+<p>If you can't open the project file for some reason, make a
+new one, naming these files:
+<code class="computeroutput">blocksort.c</code>,
+<code class="computeroutput">bzlib.c</code>,
+<code class="computeroutput">compress.c</code>,
+<code class="computeroutput">crctable.c</code>,
+<code class="computeroutput">decompress.c</code>,
+<code class="computeroutput">huffman.c</code>,
+<code class="computeroutput">randtable.c</code> and
+<code class="computeroutput">libbz2.def</code>. You will also need
+to name the header files <code class="computeroutput">bzlib.h</code>
+and <code class="computeroutput">bzlib_private.h</code>.</p>
+<p>If you don't use VC++, you may need to define the
+proprocessor symbol
+<code class="computeroutput">_WIN32</code>.</p>
+<p>Finally, <code class="computeroutput">dlltest.c</code> is a
+sample program using the DLL. It has a project file,
+<code class="computeroutput">dlltest.dsp</code>.</p>
+<p>If you just want a makefile for Visual C, have a look at
+<code class="computeroutput">makefile.msc</code>.</p>
+<p>Be aware that if you compile
+<code class="computeroutput">bzip2</code> itself on Win32, you must
+set <code class="computeroutput">BZ_UNIX</code> to 0 and
+<code class="computeroutput">BZ_LCCWIN32</code> to 1, in the file
+<code class="computeroutput">bzip2.c</code>, before compiling.
+Otherwise the resulting binary won't work correctly.</p>
+<p>I haven't tried any of this stuff myself, but it all looks
+plausible.</p>
+</div>
+</div>
+<div class="chapter" title="4.�Miscellanea">
+<div class="titlepage"><div><div><h2 class="title">
+<a name="misc"></a>4.�Miscellanea</h2></div></div></div>
+<div class="toc">
+<p><b>Table of Contents</b></p>
+<dl>
+<dt><span class="sect1"><a href="#limits">4.1. Limitations of the compressed file format</a></span></dt>
+<dt><span class="sect1"><a href="#port-issues">4.2. Portability issues</a></span></dt>
+<dt><span class="sect1"><a href="#bugs">4.3. Reporting bugs</a></span></dt>
+<dt><span class="sect1"><a href="#package">4.4. Did you get the right package?</a></span></dt>
+<dt><span class="sect1"><a href="#reading">4.5. Further Reading</a></span></dt>
+</dl>
+</div>
+<p>These are just some random thoughts of mine. Your mileage
+may vary.</p>
+<div class="sect1" title="4.1.�Limitations of the compressed file format">
+<div class="titlepage"><div><div><h2 class="title" style="clear: both">
+<a name="limits"></a>4.1.�Limitations of the compressed file format</h2></div></div></div>
+<p><code class="computeroutput">bzip2-1.0.X</code>,
+<code class="computeroutput">0.9.5</code> and
+<code class="computeroutput">0.9.0</code> use exactly the same file
+format as the original version,
+<code class="computeroutput">bzip2-0.1</code>. This decision was
+made in the interests of stability. Creating yet another
+incompatible compressed file format would create further
+confusion and disruption for users.</p>
+<p>Nevertheless, this is not a painless decision. Development
+work since the release of
+<code class="computeroutput">bzip2-0.1</code> in August 1997 has
+shown complexities in the file format which slow down
+decompression and, in retrospect, are unnecessary. These
+are:</p>
+<div class="itemizedlist"><ul class="itemizedlist" type="bullet">
+<li class="listitem" style="list-style-type: disc"><p>The run-length encoder, which is the first of the
+ compression transformations, is entirely irrelevant. The
+ original purpose was to protect the sorting algorithm from the
+ very worst case input: a string of repeated symbols. But
+ algorithm steps Q6a and Q6b in the original Burrows-Wheeler
+ technical report (SRC-124) show how repeats can be handled
+ without difficulty in block sorting.</p></li>
+<li class="listitem" style="list-style-type: disc">
+<p>The randomisation mechanism doesn't really need to be
+ there. Udi Manber and Gene Myers published a suffix array
+ construction algorithm a few years back, which can be employed
+ to sort any block, no matter how repetitive, in O(N log N)
+ time. Subsequent work by Kunihiko Sadakane has produced a
+ derivative O(N (log N)^2) algorithm which usually outperforms
+ the Manber-Myers algorithm.</p>
+<p>I could have changed to Sadakane's algorithm, but I find
+ it to be slower than <code class="computeroutput">bzip2</code>'s
+ existing algorithm for most inputs, and the randomisation
+ mechanism protects adequately against bad cases. I didn't
+ think it was a good tradeoff to make. Partly this is due to
+ the fact that I was not flooded with email complaints about
+ <code class="computeroutput">bzip2-0.1</code>'s performance on
+ repetitive data, so perhaps it isn't a problem for real
+ inputs.</p>
+<p>Probably the best long-term solution, and the one I have
+ incorporated into 0.9.5 and above, is to use the existing
+ sorting algorithm initially, and fall back to a O(N (log N)^2)
+ algorithm if the standard algorithm gets into
+ difficulties.</p>
+</li>
+<li class="listitem" style="list-style-type: disc"><p>The compressed file format was never designed to be
+ handled by a library, and I have had to jump though some hoops
+ to produce an efficient implementation of decompression. It's
+ a bit hairy. Try passing
+ <code class="computeroutput">decompress.c</code> through the C
+ preprocessor and you'll see what I mean. Much of this
+ complexity could have been avoided if the compressed size of
+ each block of data was recorded in the data stream.</p></li>
+<li class="listitem" style="list-style-type: disc"><p>An Adler-32 checksum, rather than a CRC32 checksum,
+ would be faster to compute.</p></li>
+</ul></div>
+<p>It would be fair to say that the
+<code class="computeroutput">bzip2</code> format was frozen before I
+properly and fully understood the performance consequences of
+doing so.</p>
+<p>Improvements which I was able to incorporate into 0.9.0,
+despite using the same file format, are:</p>
+<div class="itemizedlist"><ul class="itemizedlist" type="bullet">
+<li class="listitem" style="list-style-type: disc"><p>Single array implementation of the inverse BWT. This
+ significantly speeds up decompression, presumably because it
+ reduces the number of cache misses.</p></li>
+<li class="listitem" style="list-style-type: disc"><p>Faster inverse MTF transform for large MTF values.
+ The new implementation is based on the notion of sliding blocks
+ of values.</p></li>
+<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">bzip2-0.9.0</code> now reads
+ and writes files with <code class="computeroutput">fread</code>
+ and <code class="computeroutput">fwrite</code>; version 0.1 used
+ <code class="computeroutput">putc</code> and
+ <code class="computeroutput">getc</code>. Duh! Well, you live
+ and learn.</p></li>
+</ul></div>
+<p>Further ahead, it would be nice to be able to do random
+access into files. This will require some careful design of
+compressed file formats.</p>
+</div>
+<div class="sect1" title="4.2.�Portability issues">
+<div class="titlepage"><div><div><h2 class="title" style="clear: both">
+<a name="port-issues"></a>4.2.�Portability issues</h2></div></div></div>
+<p>After some consideration, I have decided not to use GNU
+<code class="computeroutput">autoconf</code> to configure 0.9.5 or
+1.0.</p>
+<p><code class="computeroutput">autoconf</code>, admirable and
+wonderful though it is, mainly assists with portability problems
+between Unix-like platforms. But
+<code class="computeroutput">bzip2</code> doesn't have much in the
+way of portability problems on Unix; most of the difficulties
+appear when porting to the Mac, or to Microsoft's operating
+systems. <code class="computeroutput">autoconf</code> doesn't help
+in those cases, and brings in a whole load of new
+complexity.</p>
+<p>Most people should be able to compile the library and
+program under Unix straight out-of-the-box, so to speak,
+especially if you have a version of GNU C available.</p>
+<p>There are a couple of
+<code class="computeroutput">__inline__</code> directives in the
+code. GNU C (<code class="computeroutput">gcc</code>) should be
+able to handle them. If you're not using GNU C, your C compiler
+shouldn't see them at all. If your compiler does, for some
+reason, see them and doesn't like them, just
+<code class="computeroutput">#define</code>
+<code class="computeroutput">__inline__</code> to be
+<code class="computeroutput">/* */</code>. One easy way to do this
+is to compile with the flag
+<code class="computeroutput">-D__inline__=</code>, which should be
+understood by most Unix compilers.</p>
+<p>If you still have difficulties, try compiling with the
+macro <code class="computeroutput">BZ_STRICT_ANSI</code> defined.
+This should enable you to build the library in a strictly ANSI
+compliant environment. Building the program itself like this is
+dangerous and not supported, since you remove
+<code class="computeroutput">bzip2</code>'s checks against
+compressing directories, symbolic links, devices, and other
+not-really-a-file entities. This could cause filesystem
+corruption!</p>
+<p>One other thing: if you create a
+<code class="computeroutput">bzip2</code> binary for public distribution,
+please consider linking it statically (<code class="computeroutput">gcc
+-static</code>). This avoids all sorts of library-version
+issues that others may encounter later on.</p>
+<p>If you build <code class="computeroutput">bzip2</code> on
+Win32, you must set <code class="computeroutput">BZ_UNIX</code> to 0
+and <code class="computeroutput">BZ_LCCWIN32</code> to 1, in the
+file <code class="computeroutput">bzip2.c</code>, before compiling.
+Otherwise the resulting binary won't work correctly.</p>
+</div>
+<div class="sect1" title="4.3.�Reporting bugs">
+<div class="titlepage"><div><div><h2 class="title" style="clear: both">
+<a name="bugs"></a>4.3.�Reporting bugs</h2></div></div></div>
+<p>I tried pretty hard to make sure
+<code class="computeroutput">bzip2</code> is bug free, both by
+design and by testing. Hopefully you'll never need to read this
+section for real.</p>
+<p>Nevertheless, if <code class="computeroutput">bzip2</code> dies
+with a segmentation fault, a bus error or an internal assertion
+failure, it will ask you to email me a bug report. Experience from
+years of feedback of bzip2 users indicates that almost all these
+problems can be traced to either compiler bugs or hardware
+problems.</p>
+<div class="itemizedlist"><ul class="itemizedlist" type="bullet">
+<li class="listitem" style="list-style-type: disc">
+<p>Recompile the program with no optimisation, and
+ see if it works. And/or try a different compiler. I heard all
+ sorts of stories about various flavours of GNU C (and other
+ compilers) generating bad code for
+ <code class="computeroutput">bzip2</code>, and I've run across two
+ such examples myself.</p>
+<p>2.7.X versions of GNU C are known to generate bad code
+ from time to time, at high optimisation levels. If you get
+ problems, try using the flags
+ <code class="computeroutput">-O2</code>
+ <code class="computeroutput">-fomit-frame-pointer</code>
+ <code class="computeroutput">-fno-strength-reduce</code>. You
+ should specifically <span class="emphasis"><em>not</em></span> use
+ <code class="computeroutput">-funroll-loops</code>.</p>
+<p>You may notice that the Makefile runs six tests as part
+ of the build process. If the program passes all of these, it's
+ a pretty good (but not 100%) indication that the compiler has
+ done its job correctly.</p>
+</li>
+<li class="listitem" style="list-style-type: disc">
+<p>If <code class="computeroutput">bzip2</code>
+ crashes randomly, and the crashes are not repeatable, you may
+ have a flaky memory subsystem.
+ <code class="computeroutput">bzip2</code> really hammers your
+ memory hierarchy, and if it's a bit marginal, you may get these
+ problems. Ditto if your disk or I/O subsystem is slowly
+ failing. Yup, this really does happen.</p>
+<p>Try using a different machine of the same type, and see
+ if you can repeat the problem.</p>
+</li>
+<li class="listitem" style="list-style-type: disc"><p>This isn't really a bug, but ... If
+ <code class="computeroutput">bzip2</code> tells you your file is
+ corrupted on decompression, and you obtained the file via FTP,
+ there is a possibility that you forgot to tell FTP to do a
+ binary mode transfer. That absolutely will cause the file to
+ be non-decompressible. You'll have to transfer it
+ again.</p></li>
+</ul></div>
+<p>If you've incorporated
+<code class="computeroutput">libbzip2</code> into your own program
+and are getting problems, please, please, please, check that the
+parameters you are passing in calls to the library, are correct,
+and in accordance with what the documentation says is allowable.
+I have tried to make the library robust against such problems,
+but I'm sure I haven't succeeded.</p>
+<p>Finally, if the above comments don't help, you'll have to
+send me a bug report. Now, it's just amazing how many people
+will send me a bug report saying something like:</p>
+<pre class="programlisting">bzip2 crashed with segmentation fault on my machine</pre>
+<p>and absolutely nothing else. Needless to say, a such a
+report is <span class="emphasis"><em>totally, utterly, completely and
+comprehensively 100% useless; a waste of your time, my time, and
+net bandwidth</em></span>. With no details at all, there's no way
+I can possibly begin to figure out what the problem is.</p>
+<p>The rules of the game are: facts, facts, facts. Don't omit
+them because "oh, they won't be relevant". At the bare
+minimum:</p>
+<pre class="programlisting">Machine type. Operating system version.
+Exact version of bzip2 (do bzip2 -V).
+Exact version of the compiler used.
+Flags passed to the compiler.</pre>
+<p>However, the most important single thing that will help me
+is the file that you were trying to compress or decompress at the
+time the problem happened. Without that, my ability to do
+anything more than speculate about the cause, is limited.</p>
+</div>
+<div class="sect1" title="4.4.�Did you get the right package?">
+<div class="titlepage"><div><div><h2 class="title" style="clear: both">
+<a name="package"></a>4.4.�Did you get the right package?</h2></div></div></div>
+<p><code class="computeroutput">bzip2</code> is a resource hog.
+It soaks up large amounts of CPU cycles and memory. Also, it
+gives very large latencies. In the worst case, you can feed many
+megabytes of uncompressed data into the library before getting
+any compressed output, so this probably rules out applications
+requiring interactive behaviour.</p>
+<p>These aren't faults of my implementation, I hope, but more
+an intrinsic property of the Burrows-Wheeler transform
+(unfortunately). Maybe this isn't what you want.</p>
+<p>If you want a compressor and/or library which is faster,
+uses less memory but gets pretty good compression, and has
+minimal latency, consider Jean-loup Gailly's and Mark Adler's
+work, <code class="computeroutput">zlib-1.2.1</code> and
+<code class="computeroutput">gzip-1.2.4</code>. Look for them at
+<a class="ulink" href="http://www.zlib.org" target="_top">http://www.zlib.org</a> and
+<a class="ulink" href="http://www.gzip.org" target="_top">http://www.gzip.org</a>
+respectively.</p>
+<p>For something faster and lighter still, you might try Markus F
+X J Oberhumer's <code class="computeroutput">LZO</code> real-time
+compression/decompression library, at
+<a class="ulink" href="http://www.oberhumer.com/opensource" target="_top">http://www.oberhumer.com/opensource</a>.</p>
+</div>
+<div class="sect1" title="4.5.�Further Reading">
+<div class="titlepage"><div><div><h2 class="title" style="clear: both">
+<a name="reading"></a>4.5.�Further Reading</h2></div></div></div>
+<p><code class="computeroutput">bzip2</code> is not research
+work, in the sense that it doesn't present any new ideas.
+Rather, it's an engineering exercise based on existing
+ideas.</p>
+<p>Four documents describe essentially all the ideas behind
+<code class="computeroutput">bzip2</code>:</p>
+<div class="literallayout"><p>Michael�Burrows�and�D.�J.�Wheeler:<br>
+��"A�block-sorting�lossless�data�compression�algorithm"<br>
+���10th�May�1994.�<br>
+���Digital�SRC�Research�Report�124.<br>
+���ftp://ftp.digital.com/pub/DEC/SRC/research-reports/SRC-124.ps.gz<br>
+���If�you�have�trouble�finding�it,�try�searching�at�the<br>
+���New�Zealand�Digital�Library,�http://www.nzdl.org.<br>
+<br>
+Daniel�S.�Hirschberg�and�Debra�A.�LeLewer<br>
+��"Efficient�Decoding�of�Prefix�Codes"<br>
+���Communications�of�the�ACM,�April�1990,�Vol�33,�Number�4.<br>
+���You�might�be�able�to�get�an�electronic�copy�of�this<br>
+���from�the�ACM�Digital�Library.<br>
+<br>
+David�J.�Wheeler<br>
+���Program�bred3.c�and�accompanying�document�bred3.ps.<br>
+���This�contains�the�idea�behind�the�multi-table�Huffman�coding�scheme.<br>
+���ftp://ftp.cl.cam.ac.uk/users/djw3/<br>
+<br>
+Jon�L.�Bentley�and�Robert�Sedgewick<br>
+��"Fast�Algorithms�for�Sorting�and�Searching�Strings"<br>
+���Available�from�Sedgewick's�web�page,<br>
+���www.cs.princeton.edu/~rs<br>
+</p></div>
+<p>The following paper gives valuable additional insights into
+the algorithm, but is not immediately the basis of any code used
+in bzip2.</p>
+<div class="literallayout"><p>Peter�Fenwick:<br>
+���Block�Sorting�Text�Compression<br>
+���Proceedings�of�the�19th�Australasian�Computer�Science�Conference,<br>
+�����Melbourne,�Australia.��Jan�31�-�Feb�2,�1996.<br>
+���ftp://ftp.cs.auckland.ac.nz/pub/peter-f/ACSC96paper.ps</p></div>
+<p>Kunihiko Sadakane's sorting algorithm, mentioned above, is
+available from:</p>
+<div class="literallayout"><p>http://naomi.is.s.u-tokyo.ac.jp/~sada/papers/Sada98b.ps.gz<br>
+</p></div>
+<p>The Manber-Myers suffix array construction algorithm is
+described in a paper available from:</p>
+<div class="literallayout"><p>http://www.cs.arizona.edu/people/gene/PAPERS/suffix.ps<br>
+</p></div>
+<p>Finally, the following papers document some
+investigations I made into the performance of sorting
+and decompression algorithms:</p>
+<div class="literallayout"><p>Julian�Seward<br>
+���On�the�Performance�of�BWT�Sorting�Algorithms<br>
+���Proceedings�of�the�IEEE�Data�Compression�Conference�2000<br>
+�����Snowbird,�Utah.��28-30�March�2000.<br>
+<br>
+Julian�Seward<br>
+���Space-time�Tradeoffs�in�the�Inverse�B-W�Transform<br>
+���Proceedings�of�the�IEEE�Data�Compression�Conference�2001<br>
+�����Snowbird,�Utah.��27-29�March�2001.<br>
+</p></div>
+</div>
+</div>
+</div></body>
+</html>
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+ pdfWordSpacing pdfHorizScaling mul 0 pdfTextMat dtransform 32
+ 4 3 roll pdfCharSpacing pdfHorizScaling mul add 0
+ pdfTextMat dtransform
+ 6 5 roll Tj1
+} def
+/Tj16V {
+ fCol
+ 2 index stringwidth pdfTextMat idtransform exch pop
+ sub exch div
+ 0 pdfWordSpacing pdfTextMat dtransform 32
+ 4 3 roll pdfCharSpacing add 0 exch
+ pdfTextMat dtransform
+ 6 5 roll Tj1
+} def
+/Tj1 {
+ 0 pdfTextRise pdfTextMat dtransform rmoveto
+ currentpoint 8 2 roll
+ pdfTextRender 1 and 0 eq {
+ 6 copy awidthshow
+ } if
+ pdfTextRender 3 and dup 1 eq exch 2 eq or {
+ 7 index 7 index moveto
+ 6 copy
+ currentfont /FontType get 3 eq { fCol } { sCol } ifelse
+ false awcp currentpoint stroke moveto
+ } if
+ pdfTextRender 4 and 0 ne {
+ 8 6 roll moveto
+ false awcp
+ /pdfTextClipPath [ pdfTextClipPath aload pop
+ {/moveto cvx}
+ {/lineto cvx}
+ {/curveto cvx}
+ {/closepath cvx}
+ pathforall ] def
+ currentpoint newpath moveto
+ } {
+ 8 {pop} repeat
+ } ifelse
+ 0 pdfTextRise neg pdfTextMat dtransform rmoveto
+} def
+/TJm { pdfFontSize 0.001 mul mul neg 0
+ pdfTextMat dtransform rmoveto } def
+/TJmV { pdfFontSize 0.001 mul mul neg 0 exch
+ pdfTextMat dtransform rmoveto } def
+/Tclip { pdfTextClipPath cvx exec clip newpath
+ /pdfTextClipPath [] def } def
+/Tclip* { pdfTextClipPath cvx exec eoclip newpath
+ /pdfTextClipPath [] def } def
+% Level 2 image operators
+/pdfImBuf 100 string def
+/pdfIm {
+ image
+ { currentfile pdfImBuf readline
+ not { pop exit } if
+ (%-EOD-) eq { exit } if } loop
+} def
+/pdfImM {
+ fCol imagemask
+ { currentfile pdfImBuf readline
+ not { pop exit } if
+ (%-EOD-) eq { exit } if } loop
+} def
+/pr { 2 index 2 index 3 2 roll putinterval 4 add } def
+/pdfImClip {
+ gsave
+ 0 2 4 index length 1 sub {
+ dup 4 index exch 2 copy
+ get 5 index div put
+ 1 add 3 index exch 2 copy
+ get 3 index div put
+ } for
+ pop pop rectclip
+} def
+/pdfImClipEnd { grestore } def
+% shading operators
+/colordelta {
+ false 0 1 3 index length 1 sub {
+ dup 4 index exch get 3 index 3 2 roll get sub abs 0.004 gt {
+ pop true
+ } if
+ } for
+ exch pop exch pop
+} def
+/funcCol { func n array astore } def
+/funcSH {
+ dup 0 eq {
+ true
+ } {
+ dup 6 eq {
+ false
+ } {
+ 4 index 4 index funcCol dup
+ 6 index 4 index funcCol dup
+ 3 1 roll colordelta 3 1 roll
+ 5 index 5 index funcCol dup
+ 3 1 roll colordelta 3 1 roll
+ 6 index 8 index funcCol dup
+ 3 1 roll colordelta 3 1 roll
+ colordelta or or or
+ } ifelse
+ } ifelse
+ {
+ 1 add
+ 4 index 3 index add 0.5 mul exch 4 index 3 index add 0.5 mul exch
+ 6 index 6 index 4 index 4 index 4 index funcSH
+ 2 index 6 index 6 index 4 index 4 index funcSH
+ 6 index 2 index 4 index 6 index 4 index funcSH
+ 5 3 roll 3 2 roll funcSH pop pop
+ } {
+ pop 3 index 2 index add 0.5 mul 3 index 2 index add 0.5 mul
+ funcCol sc
+ dup 4 index exch mat transform m
+ 3 index 3 index mat transform l
+ 1 index 3 index mat transform l
+ mat transform l pop pop h f*
+ } ifelse
+} def
+/axialCol {
+ dup 0 lt {
+ pop t0
+ } {
+ dup 1 gt {
+ pop t1
+ } {
+ dt mul t0 add
+ } ifelse
+ } ifelse
+ func n array astore
+} def
+/axialSH {
+ dup 0 eq {
+ true
+ } {
+ dup 8 eq {
+ false
+ } {
+ 2 index axialCol 2 index axialCol colordelta
+ } ifelse
+ } ifelse
+ {
+ 1 add 3 1 roll 2 copy add 0.5 mul
+ dup 4 3 roll exch 4 index axialSH
+ exch 3 2 roll axialSH
+ } {
+ pop 2 copy add 0.5 mul
+ axialCol sc
+ exch dup dx mul x0 add exch dy mul y0 add
+ 3 2 roll dup dx mul x0 add exch dy mul y0 add
+ dx abs dy abs ge {
+ 2 copy yMin sub dy mul dx div add yMin m
+ yMax sub dy mul dx div add yMax l
+ 2 copy yMax sub dy mul dx div add yMax l
+ yMin sub dy mul dx div add yMin l
+ h f*
+ } {
+ exch 2 copy xMin sub dx mul dy div add xMin exch m
+ xMax sub dx mul dy div add xMax exch l
+ exch 2 copy xMax sub dx mul dy div add xMax exch l
+ xMin sub dx mul dy div add xMin exch l
+ h f*
+ } ifelse
+ } ifelse
+} def
+/radialCol {
+ dup t0 lt {
+ pop t0
+ } {
+ dup t1 gt {
+ pop t1
+ } if
+ } ifelse
+ func n array astore
+} def
+/radialSH {
+ dup 0 eq {
+ true
+ } {
+ dup 8 eq {
+ false
+ } {
+ 2 index dt mul t0 add radialCol
+ 2 index dt mul t0 add radialCol colordelta
+ } ifelse
+ } ifelse
+ {
+ 1 add 3 1 roll 2 copy add 0.5 mul
+ dup 4 3 roll exch 4 index radialSH
+ exch 3 2 roll radialSH
+ } {
+ pop 2 copy add 0.5 mul dt mul t0 add
+ radialCol sc
+ encl {
+ exch dup dx mul x0 add exch dup dy mul y0 add exch dr mul r0 add
+ 0 360 arc h
+ dup dx mul x0 add exch dup dy mul y0 add exch dr mul r0 add
+ 360 0 arcn h f
+ } {
+ 2 copy
+ dup dx mul x0 add exch dup dy mul y0 add exch dr mul r0 add
+ a1 a2 arcn
+ dup dx mul x0 add exch dup dy mul y0 add exch dr mul r0 add
+ a2 a1 arcn h
+ dup dx mul x0 add exch dup dy mul y0 add exch dr mul r0 add
+ a1 a2 arc
+ dup dx mul x0 add exch dup dy mul y0 add exch dr mul r0 add
+ a2 a1 arc h f
+ } ifelse
+ } ifelse
+} def
+end
+%%EndResource
+%%EndProlog
+%%BeginSetup
+xpdf begin
+%%BeginResource: font PYRIYB+NimbusSanL-Bold
+%!PS-AdobeFont-1.0: NimbusSanL-Bold 1.05
+%%CreationDate: Wed Dec 22 1999
+% Copyright (URW)++,Copyright 1999 by (URW)++ Design & Development
+% (URW)++,Copyright 1999 by (URW)++ Design & Development
+% See the file COPYING (GNU General Public License) for license conditions.
+% As a special exception, permission is granted to include this font
+% program in a Postscript or PDF file that consists of a document that
+% contains text to be displayed or printed using this font, regardless
+% of the conditions or license applying to the document itself.
+12 dict begin
+/FontInfo 10 dict dup begin
+/version (1.05) readonly def
+/Notice ((URW)++,Copyright 1999 by (URW)++ Design & Development. See the file COPYING (GNU General Public License) for license conditions. As a special exception, permission is granted to include this font program in a Postscript or PDF file that consists of a document that contains text to be displayed or printed using this font, regardless of the conditions or license applying to the document itself.) readonly def
+/Copyright (Copyright (URW)++,Copyright 1999 by (URW)++ Design & Development) readonly def
+/FullName (Nimbus Sans L Bold) readonly def
+/FamilyName (Nimbus Sans L) readonly def
+/Weight (Bold) readonly def
+/ItalicAngle 0.0 def
+/isFixedPitch false def
+/UnderlinePosition -155 def
+/UnderlineThickness 69 def
+end readonly def
+/FontName /PYRIYB+NimbusSanL-Bold def
+/PaintType 0 def
+/WMode 0 def
+/FontBBox {-173 -307 1003 949} readonly def
+/FontType 1 def
+/FontMatrix [0.001 0.0 0.0 0.001 0.0 0.0] readonly def
+/Encoding StandardEncoding def
+currentdict end
+currentfile eexec
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+%%EndResource
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+[ /.notdef/.notdef/fi/fl/.notdef/.notdef/.notdef/.notdef
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+ /space/exclam/quotedbl/numbersign/dollar/percent/ampersand/quoteright
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+ /currency/copyright/quotedblleft/guillemotleft/guilsinglleft/guilsinglright/fi/fl
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+ /emdash/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef
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+ /.notdef/AE/.notdef/ordfeminine/.notdef/.notdef/.notdef/.notdef
+ /Lslash/Oslash/OE/ordmasculine/.notdef/.notdef/.notdef/.notdef
+ /.notdef/ae/.notdef/.notdef/.notdef/dotlessi/.notdef/.notdef
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+pdfMakeFont
+%%BeginResource: font XDVKOU+NimbusRomNo9L-Regu
+%!PS-AdobeFont-1.0: NimbusRomNo9L-Regu 1.05
+%%CreationDate: Wed Dec 22 1999
+% Copyright (URW)++,Copyright 1999 by (URW)++ Design & Development
+% (URW)++,Copyright 1999 by (URW)++ Design & Development
+% See the file COPYING (GNU General Public License) for license conditions.
+% As a special exception, permission is granted to include this font
+% program in a Postscript or PDF file that consists of a document that
+% contains text to be displayed or printed using this font, regardless
+% of the conditions or license applying to the document itself.
+12 dict begin
+/FontInfo 10 dict dup begin
+/version (1.05) readonly def
+/Notice ((URW)++,Copyright 1999 by (URW)++ Design & Development. See the file COPYING (GNU General Public License) for license conditions. As a special exception, permission is granted to include this font program in a Postscript or PDF file that consists of a document that contains text to be displayed or printed using this font, regardless of the conditions or license applying to the document itself.) readonly def
+/Copyright (Copyright (URW)++,Copyright 1999 by (URW)++ Design & Development) readonly def
+/FullName (Nimbus Roman No9 L Regular) readonly def
+/FamilyName (Nimbus Roman No9 L) readonly def
+/Weight (Regular) readonly def
+/ItalicAngle 0.0 def
+/isFixedPitch false def
+/UnderlinePosition -100 def
+/UnderlineThickness 50 def
+end readonly def
+/FontName /XDVKOU+NimbusRomNo9L-Regu def
+/PaintType 0 def
+/WMode 0 def
+/FontBBox {-168 -281 1000 924} readonly def
+/FontType 1 def
+/FontMatrix [0.001 0.0 0.0 0.001 0.0 0.0] readonly def
+/Encoding StandardEncoding def
+currentdict end
+currentfile eexec
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+pdfMakeFont
+%%BeginResource: font QYKIKI+NimbusMonL-Regu
+%!PS-AdobeFont-1.0: NimbusMonL-Regu 1.05
+%%CreationDate: Wed Dec 22 1999
+% Copyright (URW)++,Copyright 1999 by (URW)++ Design & Development
+% (URW)++,Copyright 1999 by (URW)++ Design & Development
+% See the file COPYING (GNU General Public License) for license conditions.
+% As a special exception, permission is granted to include this font
+% program in a Postscript or PDF file that consists of a document that
+% contains text to be displayed or printed using this font, regardless
+% of the conditions or license applying to the document itself.
+12 dict begin
+/FontInfo 10 dict dup begin
+/version (1.05) readonly def
+/Notice ((URW)++,Copyright 1999 by (URW)++ Design & Development. See the file COPYING (GNU General Public License) for license conditions. As a special exception, permission is granted to include this font program in a Postscript or PDF file that consists of a document that contains text to be displayed or printed using this font, regardless of the conditions or license applying to the document itself.) readonly def
+/Copyright (Copyright (URW)++,Copyright 1999 by (URW)++ Design & Development) readonly def
+/FullName (Nimbus Mono L Regular) readonly def
+/FamilyName (Nimbus Mono L) readonly def
+/Weight (Regular) readonly def
+/ItalicAngle 0.0 def
+/isFixedPitch false def
+/UnderlinePosition -100 def
+/UnderlineThickness 50 def
+end readonly def
+/FontName /QYKIKI+NimbusMonL-Regu def
+/PaintType 0 def
+/WMode 0 def
+/FontBBox {-12 -237 650 811} readonly def
+/FontType 1 def
+/FontMatrix [0.001 0.0 0.0 0.001 0.0 0.0] readonly def
+/Encoding StandardEncoding def
+currentdict end
+currentfile eexec
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+%%EndResource
+/F230_0 /BITXNG+CMMI10 1 1
+[ /.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef
+ /.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef
+ /.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef
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+ /.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef
+ /.notdef/.notdef/.notdef/.notdef/.notdef/arrowhookright/.notdef/.notdef
+ /.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef
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+ /.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef
+ /.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef
+ /.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef
+ /.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef]
+pdfMakeFont
+%%BeginResource: font ZWXELK+NimbusMonL-Bold
+%!PS-AdobeFont-1.0: NimbusMonL-Bold 1.05
+%%CreationDate: Wed Dec 22 1999
+% Copyright (URW)++,Copyright 1999 by (URW)++ Design & Development
+% (URW)++,Copyright 1999 by (URW)++ Design & Development
+% See the file COPYING (GNU General Public License) for license conditions.
+% As a special exception, permission is granted to include this font
+% program in a Postscript or PDF file that consists of a document that
+% contains text to be displayed or printed using this font, regardless
+% of the conditions or license applying to the document itself.
+12 dict begin
+/FontInfo 10 dict dup begin
+/version (1.05) readonly def
+/Notice ((URW)++,Copyright 1999 by (URW)++ Design & Development. See the file COPYING (GNU General Public License) for license conditions. As a special exception, permission is granted to include this font program in a Postscript or PDF file that consists of a document that contains text to be displayed or printed using this font, regardless of the conditions or license applying to the document itself.) readonly def
+/Copyright (Copyright (URW)++,Copyright 1999 by (URW)++ Design & Development) readonly def
+/FullName (Nimbus Mono L Bold) readonly def
+/FamilyName (Nimbus Mono L) readonly def
+/Weight (Bold) readonly def
+/ItalicAngle 0.0 def
+/isFixedPitch false def
+/UnderlinePosition -100 def
+/UnderlineThickness 50 def
+end readonly def
+/FontName /ZWXELK+NimbusMonL-Bold def
+/PaintType 0 def
+/WMode 0 def
+/FontBBox {-43 -278 681 871} readonly def
+/FontType 1 def
+/FontMatrix [0.001 0.0 0.0 0.001 0.0 0.0] readonly def
+/Encoding StandardEncoding def
+currentdict end
+currentfile eexec
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+%%Title: CMSY10
+%Version: 003.002
+%%CreationDate: Mon Jul 13 16:17:00 2009
+%%Creator: David M. Jones
+%Copyright: Copyright (c) 1997, 2009 American Mathematical Society
+%Copyright: (<http://www.ams.org>), with Reserved Font Name CMSY10.
+% This Font Software is licensed under the SIL Open Font License, Version 1.1.
+% This license is in the accompanying file OFL.txt, and is also
+% available with a FAQ at: http://scripts.sil.org/OFL.
+%%EndComments
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+12 dict begin
+/FontInfo 10 dict dup begin
+/version (1.05) readonly def
+/Notice ((URW)++,Copyright 1999 by (URW)++ Design & Development. See the file COPYING (GNU General Public License) for license conditions. As a special exception, permission is granted to include this font program in a Postscript or PDF file that consists of a document that contains text to be displayed or printed using this font, regardless of the conditions or license applying to the document itself.) readonly def
+/Copyright (Copyright (URW)++,Copyright 1999 by (URW)++ Design & Development) readonly def
+/FullName (Nimbus Roman No9 L Regular Italic) readonly def
+/FamilyName (Nimbus Roman No9 L) readonly def
+/Weight (Regular) readonly def
+/ItalicAngle -15.5 def
+/isFixedPitch false def
+/UnderlinePosition -100 def
+/UnderlineThickness 50 def
+end readonly def
+/FontName /AMYDOG+NimbusRomNo9L-ReguItal def
+/PaintType 0 def
+/WMode 0 def
+/FontBBox {-169 -270 1010 924} readonly def
+/FontType 1 def
+/FontMatrix [0.001 0.0 0.0 0.001 0.0 0.0] readonly def
+/Encoding StandardEncoding def
+currentdict end
+currentfile eexec
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+<?xml version="1.0"?> <!-- -*- sgml -*- -->
+<!DOCTYPE book PUBLIC "-//OASIS//DTD DocBook XML V4.2//EN"
+ "http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd"[
+
+<!-- various strings, dates etc. common to all docs -->
+<!ENTITY % common-ents SYSTEM "entities.xml"> %common-ents;
+]>
+
+<book lang="en" id="userman" xreflabel="bzip2 Manual">
+
+ <bookinfo>
+ <title>bzip2 and libbzip2, version 1.0.6</title>
+ <subtitle>A program and library for data compression</subtitle>
+ <copyright>
+ <year>&bz-lifespan;</year>
+ <holder>Julian Seward</holder>
+ </copyright>
+ <releaseinfo>Version &bz-version; of &bz-date;</releaseinfo>
+
+ <authorgroup>
+ <author>
+ <firstname>Julian</firstname>
+ <surname>Seward</surname>
+ <affiliation>
+ <orgname>&bz-url;</orgname>
+ </affiliation>
+ </author>
+ </authorgroup>
+
+ <legalnotice>
+
+ <para>This program, <computeroutput>bzip2</computeroutput>, the
+ associated library <computeroutput>libbzip2</computeroutput>, and
+ all documentation, are copyright © &bz-lifespan; Julian Seward.
+ All rights reserved.</para>
+
+ <para>Redistribution and use in source and binary forms, with
+ or without modification, are permitted provided that the
+ following conditions are met:</para>
+
+ <itemizedlist mark='bullet'>
+
+ <listitem><para>Redistributions of source code must retain the
+ above copyright notice, this list of conditions and the
+ following disclaimer.</para></listitem>
+
+ <listitem><para>The origin of this software must not be
+ misrepresented; you must not claim that you wrote the original
+ software. If you use this software in a product, an
+ acknowledgment in the product documentation would be
+ appreciated but is not required.</para></listitem>
+
+ <listitem><para>Altered source versions must be plainly marked
+ as such, and must not be misrepresented as being the original
+ software.</para></listitem>
+
+ <listitem><para>The name of the author may not be used to
+ endorse or promote products derived from this software without
+ specific prior written permission.</para></listitem>
+
+ </itemizedlist>
+
+ <para>THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY
+ EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+ THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+ PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+ AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+ TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+ IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
+ THE POSSIBILITY OF SUCH DAMAGE.</para>
+
+ <para>PATENTS: To the best of my knowledge,
+ <computeroutput>bzip2</computeroutput> and
+ <computeroutput>libbzip2</computeroutput> do not use any patented
+ algorithms. However, I do not have the resources to carry
+ out a patent search. Therefore I cannot give any guarantee of
+ the above statement.
+ </para>
+
+</legalnotice>
+
+</bookinfo>
+
+
+
+<chapter id="intro" xreflabel="Introduction">
+<title>Introduction</title>
+
+<para><computeroutput>bzip2</computeroutput> compresses files
+using the Burrows-Wheeler block-sorting text compression
+algorithm, and Huffman coding. Compression is generally
+considerably better than that achieved by more conventional
+LZ77/LZ78-based compressors, and approaches the performance of
+the PPM family of statistical compressors.</para>
+
+<para><computeroutput>bzip2</computeroutput> is built on top of
+<computeroutput>libbzip2</computeroutput>, a flexible library for
+handling compressed data in the
+<computeroutput>bzip2</computeroutput> format. This manual
+describes both how to use the program and how to work with the
+library interface. Most of the manual is devoted to this
+library, not the program, which is good news if your interest is
+only in the program.</para>
+
+<itemizedlist mark='bullet'>
+
+ <listitem><para><xref linkend="using"/> describes how to use
+ <computeroutput>bzip2</computeroutput>; this is the only part
+ you need to read if you just want to know how to operate the
+ program.</para></listitem>
+
+ <listitem><para><xref linkend="libprog"/> describes the
+ programming interfaces in detail, and</para></listitem>
+
+ <listitem><para><xref linkend="misc"/> records some
+ miscellaneous notes which I thought ought to be recorded
+ somewhere.</para></listitem>
+
+</itemizedlist>
+
+</chapter>
+
+
+<chapter id="using" xreflabel="How to use bzip2">
+<title>How to use bzip2</title>
+
+<para>This chapter contains a copy of the
+<computeroutput>bzip2</computeroutput> man page, and nothing
+else.</para>
+
+<sect1 id="name" xreflabel="NAME">
+<title>NAME</title>
+
+<itemizedlist mark='bullet'>
+
+ <listitem><para><computeroutput>bzip2</computeroutput>,
+ <computeroutput>bunzip2</computeroutput> - a block-sorting file
+ compressor, v1.0.6</para></listitem>
+
+ <listitem><para><computeroutput>bzcat</computeroutput> -
+ decompresses files to stdout</para></listitem>
+
+ <listitem><para><computeroutput>bzip2recover</computeroutput> -
+ recovers data from damaged bzip2 files</para></listitem>
+
+</itemizedlist>
+
+</sect1>
+
+
+<sect1 id="synopsis" xreflabel="SYNOPSIS">
+<title>SYNOPSIS</title>
+
+<itemizedlist mark='bullet'>
+
+ <listitem><para><computeroutput>bzip2</computeroutput> [
+ -cdfkqstvzVL123456789 ] [ filenames ... ]</para></listitem>
+
+ <listitem><para><computeroutput>bunzip2</computeroutput> [
+ -fkvsVL ] [ filenames ... ]</para></listitem>
+
+ <listitem><para><computeroutput>bzcat</computeroutput> [ -s ] [
+ filenames ... ]</para></listitem>
+
+ <listitem><para><computeroutput>bzip2recover</computeroutput>
+ filename</para></listitem>
+
+</itemizedlist>
+
+</sect1>
+
+
+<sect1 id="description" xreflabel="DESCRIPTION">
+<title>DESCRIPTION</title>
+
+<para><computeroutput>bzip2</computeroutput> compresses files
+using the Burrows-Wheeler block sorting text compression
+algorithm, and Huffman coding. Compression is generally
+considerably better than that achieved by more conventional
+LZ77/LZ78-based compressors, and approaches the performance of
+the PPM family of statistical compressors.</para>
+
+<para>The command-line options are deliberately very similar to
+those of GNU <computeroutput>gzip</computeroutput>, but they are
+not identical.</para>
+
+<para><computeroutput>bzip2</computeroutput> expects a list of
+file names to accompany the command-line flags. Each file is
+replaced by a compressed version of itself, with the name
+<computeroutput>original_name.bz2</computeroutput>. Each
+compressed file has the same modification date, permissions, and,
+when possible, ownership as the corresponding original, so that
+these properties can be correctly restored at decompression time.
+File name handling is naive in the sense that there is no
+mechanism for preserving original file names, permissions,
+ownerships or dates in filesystems which lack these concepts, or
+have serious file name length restrictions, such as
+MS-DOS.</para>
+
+<para><computeroutput>bzip2</computeroutput> and
+<computeroutput>bunzip2</computeroutput> will by default not
+overwrite existing files. If you want this to happen, specify
+the <computeroutput>-f</computeroutput> flag.</para>
+
+<para>If no file names are specified,
+<computeroutput>bzip2</computeroutput> compresses from standard
+input to standard output. In this case,
+<computeroutput>bzip2</computeroutput> will decline to write
+compressed output to a terminal, as this would be entirely
+incomprehensible and therefore pointless.</para>
+
+<para><computeroutput>bunzip2</computeroutput> (or
+<computeroutput>bzip2 -d</computeroutput>) decompresses all
+specified files. Files which were not created by
+<computeroutput>bzip2</computeroutput> will be detected and
+ignored, and a warning issued.
+<computeroutput>bzip2</computeroutput> attempts to guess the
+filename for the decompressed file from that of the compressed
+file as follows:</para>
+
+<itemizedlist mark='bullet'>
+
+ <listitem><para><computeroutput>filename.bz2 </computeroutput>
+ becomes
+ <computeroutput>filename</computeroutput></para></listitem>
+
+ <listitem><para><computeroutput>filename.bz </computeroutput>
+ becomes
+ <computeroutput>filename</computeroutput></para></listitem>
+
+ <listitem><para><computeroutput>filename.tbz2</computeroutput>
+ becomes
+ <computeroutput>filename.tar</computeroutput></para></listitem>
+
+ <listitem><para><computeroutput>filename.tbz </computeroutput>
+ becomes
+ <computeroutput>filename.tar</computeroutput></para></listitem>
+
+ <listitem><para><computeroutput>anyothername </computeroutput>
+ becomes
+ <computeroutput>anyothername.out</computeroutput></para></listitem>
+
+</itemizedlist>
+
+<para>If the file does not end in one of the recognised endings,
+<computeroutput>.bz2</computeroutput>,
+<computeroutput>.bz</computeroutput>,
+<computeroutput>.tbz2</computeroutput> or
+<computeroutput>.tbz</computeroutput>,
+<computeroutput>bzip2</computeroutput> complains that it cannot
+guess the name of the original file, and uses the original name
+with <computeroutput>.out</computeroutput> appended.</para>
+
+<para>As with compression, supplying no filenames causes
+decompression from standard input to standard output.</para>
+
+<para><computeroutput>bunzip2</computeroutput> will correctly
+decompress a file which is the concatenation of two or more
+compressed files. The result is the concatenation of the
+corresponding uncompressed files. Integrity testing
+(<computeroutput>-t</computeroutput>) of concatenated compressed
+files is also supported.</para>
+
+<para>You can also compress or decompress files to the standard
+output by giving the <computeroutput>-c</computeroutput> flag.
+Multiple files may be compressed and decompressed like this. The
+resulting outputs are fed sequentially to stdout. Compression of
+multiple files in this manner generates a stream containing
+multiple compressed file representations. Such a stream can be
+decompressed correctly only by
+<computeroutput>bzip2</computeroutput> version 0.9.0 or later.
+Earlier versions of <computeroutput>bzip2</computeroutput> will
+stop after decompressing the first file in the stream.</para>
+
+<para><computeroutput>bzcat</computeroutput> (or
+<computeroutput>bzip2 -dc</computeroutput>) decompresses all
+specified files to the standard output.</para>
+
+<para><computeroutput>bzip2</computeroutput> will read arguments
+from the environment variables
+<computeroutput>BZIP2</computeroutput> and
+<computeroutput>BZIP</computeroutput>, in that order, and will
+process them before any arguments read from the command line.
+This gives a convenient way to supply default arguments.</para>
+
+<para>Compression is always performed, even if the compressed
+file is slightly larger than the original. Files of less than
+about one hundred bytes tend to get larger, since the compression
+mechanism has a constant overhead in the region of 50 bytes.
+Random data (including the output of most file compressors) is
+coded at about 8.05 bits per byte, giving an expansion of around
+0.5%.</para>
+
+<para>As a self-check for your protection,
+<computeroutput>bzip2</computeroutput> uses 32-bit CRCs to make
+sure that the decompressed version of a file is identical to the
+original. This guards against corruption of the compressed data,
+and against undetected bugs in
+<computeroutput>bzip2</computeroutput> (hopefully very unlikely).
+The chances of data corruption going undetected is microscopic,
+about one chance in four billion for each file processed. Be
+aware, though, that the check occurs upon decompression, so it
+can only tell you that something is wrong. It can't help you
+recover the original uncompressed data. You can use
+<computeroutput>bzip2recover</computeroutput> to try to recover
+data from damaged files.</para>
+
+<para>Return values: 0 for a normal exit, 1 for environmental
+problems (file not found, invalid flags, I/O errors, etc.), 2
+to indicate a corrupt compressed file, 3 for an internal
+consistency error (eg, bug) which caused
+<computeroutput>bzip2</computeroutput> to panic.</para>
+
+</sect1>
+
+
+<sect1 id="options" xreflabel="OPTIONS">
+<title>OPTIONS</title>
+
+<variablelist>
+
+ <varlistentry>
+ <term><computeroutput>-c --stdout</computeroutput></term>
+ <listitem><para>Compress or decompress to standard
+ output.</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><computeroutput>-d --decompress</computeroutput></term>
+ <listitem><para>Force decompression.
+ <computeroutput>bzip2</computeroutput>,
+ <computeroutput>bunzip2</computeroutput> and
+ <computeroutput>bzcat</computeroutput> are really the same
+ program, and the decision about what actions to take is done on
+ the basis of which name is used. This flag overrides that
+ mechanism, and forces bzip2 to decompress.</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><computeroutput>-z --compress</computeroutput></term>
+ <listitem><para>The complement to
+ <computeroutput>-d</computeroutput>: forces compression,
+ regardless of the invokation name.</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><computeroutput>-t --test</computeroutput></term>
+ <listitem><para>Check integrity of the specified file(s), but
+ don't decompress them. This really performs a trial
+ decompression and throws away the result.</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><computeroutput>-f --force</computeroutput></term>
+ <listitem><para>Force overwrite of output files. Normally,
+ <computeroutput>bzip2</computeroutput> will not overwrite
+ existing output files. Also forces
+ <computeroutput>bzip2</computeroutput> to break hard links to
+ files, which it otherwise wouldn't do.</para>
+ <para><computeroutput>bzip2</computeroutput> normally declines
+ to decompress files which don't have the correct magic header
+ bytes. If forced (<computeroutput>-f</computeroutput>),
+ however, it will pass such files through unmodified. This is
+ how GNU <computeroutput>gzip</computeroutput> behaves.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><computeroutput>-k --keep</computeroutput></term>
+ <listitem><para>Keep (don't delete) input files during
+ compression or decompression.</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><computeroutput>-s --small</computeroutput></term>
+ <listitem><para>Reduce memory usage, for compression,
+ decompression and testing. Files are decompressed and tested
+ using a modified algorithm which only requires 2.5 bytes per
+ block byte. This means any file can be decompressed in 2300k
+ of memory, albeit at about half the normal speed.</para>
+ <para>During compression, <computeroutput>-s</computeroutput>
+ selects a block size of 200k, which limits memory use to around
+ the same figure, at the expense of your compression ratio. In
+ short, if your machine is low on memory (8 megabytes or less),
+ use <computeroutput>-s</computeroutput> for everything. See
+ <xref linkend="memory-management"/> below.</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><computeroutput>-q --quiet</computeroutput></term>
+ <listitem><para>Suppress non-essential warning messages.
+ Messages pertaining to I/O errors and other critical events
+ will not be suppressed.</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><computeroutput>-v --verbose</computeroutput></term>
+ <listitem><para>Verbose mode -- show the compression ratio for
+ each file processed. Further
+ <computeroutput>-v</computeroutput>'s increase the verbosity
+ level, spewing out lots of information which is primarily of
+ interest for diagnostic purposes.</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><computeroutput>-L --license -V --version</computeroutput></term>
+ <listitem><para>Display the software version, license terms and
+ conditions.</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><computeroutput>-1</computeroutput> (or
+ <computeroutput>--fast</computeroutput>) to
+ <computeroutput>-9</computeroutput> (or
+ <computeroutput>-best</computeroutput>)</term>
+ <listitem><para>Set the block size to 100 k, 200 k ... 900 k
+ when compressing. Has no effect when decompressing. See <xref
+ linkend="memory-management" /> below. The
+ <computeroutput>--fast</computeroutput> and
+ <computeroutput>--best</computeroutput> aliases are primarily
+ for GNU <computeroutput>gzip</computeroutput> compatibility.
+ In particular, <computeroutput>--fast</computeroutput> doesn't
+ make things significantly faster. And
+ <computeroutput>--best</computeroutput> merely selects the
+ default behaviour.</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><computeroutput>--</computeroutput></term>
+ <listitem><para>Treats all subsequent arguments as file names,
+ even if they start with a dash. This is so you can handle
+ files with names beginning with a dash, for example:
+ <computeroutput>bzip2 --
+ -myfilename</computeroutput>.</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><computeroutput>--repetitive-fast</computeroutput></term>
+ <term><computeroutput>--repetitive-best</computeroutput></term>
+ <listitem><para>These flags are redundant in versions 0.9.5 and
+ above. They provided some coarse control over the behaviour of
+ the sorting algorithm in earlier versions, which was sometimes
+ useful. 0.9.5 and above have an improved algorithm which
+ renders these flags irrelevant.</para></listitem>
+ </varlistentry>
+
+</variablelist>
+
+</sect1>
+
+
+<sect1 id="memory-management" xreflabel="MEMORY MANAGEMENT">
+<title>MEMORY MANAGEMENT</title>
+
+<para><computeroutput>bzip2</computeroutput> compresses large
+files in blocks. The block size affects both the compression
+ratio achieved, and the amount of memory needed for compression
+and decompression. The flags <computeroutput>-1</computeroutput>
+through <computeroutput>-9</computeroutput> specify the block
+size to be 100,000 bytes through 900,000 bytes (the default)
+respectively. At decompression time, the block size used for
+compression is read from the header of the compressed file, and
+<computeroutput>bunzip2</computeroutput> then allocates itself
+just enough memory to decompress the file. Since block sizes are
+stored in compressed files, it follows that the flags
+<computeroutput>-1</computeroutput> to
+<computeroutput>-9</computeroutput> are irrelevant to and so
+ignored during decompression.</para>
+
+<para>Compression and decompression requirements, in bytes, can be
+estimated as:</para>
+<programlisting>
+Compression: 400k + ( 8 x block size )
+
+Decompression: 100k + ( 4 x block size ), or
+ 100k + ( 2.5 x block size )
+</programlisting>
+
+<para>Larger block sizes give rapidly diminishing marginal
+returns. Most of the compression comes from the first two or
+three hundred k of block size, a fact worth bearing in mind when
+using <computeroutput>bzip2</computeroutput> on small machines.
+It is also important to appreciate that the decompression memory
+requirement is set at compression time by the choice of block
+size.</para>
+
+<para>For files compressed with the default 900k block size,
+<computeroutput>bunzip2</computeroutput> will require about 3700
+kbytes to decompress. To support decompression of any file on a
+4 megabyte machine, <computeroutput>bunzip2</computeroutput> has
+an option to decompress using approximately half this amount of
+memory, about 2300 kbytes. Decompression speed is also halved,
+so you should use this option only where necessary. The relevant
+flag is <computeroutput>-s</computeroutput>.</para>
+
+<para>In general, try and use the largest block size memory
+constraints allow, since that maximises the compression achieved.
+Compression and decompression speed are virtually unaffected by
+block size.</para>
+
+<para>Another significant point applies to files which fit in a
+single block -- that means most files you'd encounter using a
+large block size. The amount of real memory touched is
+proportional to the size of the file, since the file is smaller
+than a block. For example, compressing a file 20,000 bytes long
+with the flag <computeroutput>-9</computeroutput> will cause the
+compressor to allocate around 7600k of memory, but only touch
+400k + 20000 * 8 = 560 kbytes of it. Similarly, the decompressor
+will allocate 3700k but only touch 100k + 20000 * 4 = 180
+kbytes.</para>
+
+<para>Here is a table which summarises the maximum memory usage
+for different block sizes. Also recorded is the total compressed
+size for 14 files of the Calgary Text Compression Corpus
+totalling 3,141,622 bytes. This column gives some feel for how
+compression varies with block size. These figures tend to
+understate the advantage of larger block sizes for larger files,
+since the Corpus is dominated by smaller files.</para>
+
+<programlisting>
+ Compress Decompress Decompress Corpus
+Flag usage usage -s usage Size
+
+ -1 1200k 500k 350k 914704
+ -2 2000k 900k 600k 877703
+ -3 2800k 1300k 850k 860338
+ -4 3600k 1700k 1100k 846899
+ -5 4400k 2100k 1350k 845160
+ -6 5200k 2500k 1600k 838626
+ -7 6100k 2900k 1850k 834096
+ -8 6800k 3300k 2100k 828642
+ -9 7600k 3700k 2350k 828642
+</programlisting>
+
+</sect1>
+
+
+<sect1 id="recovering" xreflabel="RECOVERING DATA FROM DAMAGED FILES">
+<title>RECOVERING DATA FROM DAMAGED FILES</title>
+
+<para><computeroutput>bzip2</computeroutput> compresses files in
+blocks, usually 900kbytes long. Each block is handled
+independently. If a media or transmission error causes a
+multi-block <computeroutput>.bz2</computeroutput> file to become
+damaged, it may be possible to recover data from the undamaged
+blocks in the file.</para>
+
+<para>The compressed representation of each block is delimited by
+a 48-bit pattern, which makes it possible to find the block
+boundaries with reasonable certainty. Each block also carries
+its own 32-bit CRC, so damaged blocks can be distinguished from
+undamaged ones.</para>
+
+<para><computeroutput>bzip2recover</computeroutput> is a simple
+program whose purpose is to search for blocks in
+<computeroutput>.bz2</computeroutput> files, and write each block
+out into its own <computeroutput>.bz2</computeroutput> file. You
+can then use <computeroutput>bzip2 -t</computeroutput> to test
+the integrity of the resulting files, and decompress those which
+are undamaged.</para>
+
+<para><computeroutput>bzip2recover</computeroutput> takes a
+single argument, the name of the damaged file, and writes a
+number of files <computeroutput>rec0001file.bz2</computeroutput>,
+<computeroutput>rec0002file.bz2</computeroutput>, etc, containing
+the extracted blocks. The output filenames are designed so that
+the use of wildcards in subsequent processing -- for example,
+<computeroutput>bzip2 -dc rec*file.bz2 >
+recovered_data</computeroutput> -- lists the files in the correct
+order.</para>
+
+<para><computeroutput>bzip2recover</computeroutput> should be of
+most use dealing with large <computeroutput>.bz2</computeroutput>
+files, as these will contain many blocks. It is clearly futile
+to use it on damaged single-block files, since a damaged block
+cannot be recovered. If you wish to minimise any potential data
+loss through media or transmission errors, you might consider
+compressing with a smaller block size.</para>
+
+</sect1>
+
+
+<sect1 id="performance" xreflabel="PERFORMANCE NOTES">
+<title>PERFORMANCE NOTES</title>
+
+<para>The sorting phase of compression gathers together similar
+strings in the file. Because of this, files containing very long
+runs of repeated symbols, like "aabaabaabaab ..." (repeated
+several hundred times) may compress more slowly than normal.
+Versions 0.9.5 and above fare much better than previous versions
+in this respect. The ratio between worst-case and average-case
+compression time is in the region of 10:1. For previous
+versions, this figure was more like 100:1. You can use the
+<computeroutput>-vvvv</computeroutput> option to monitor progress
+in great detail, if you want.</para>
+
+<para>Decompression speed is unaffected by these
+phenomena.</para>
+
+<para><computeroutput>bzip2</computeroutput> usually allocates
+several megabytes of memory to operate in, and then charges all
+over it in a fairly random fashion. This means that performance,
+both for compressing and decompressing, is largely determined by
+the speed at which your machine can service cache misses.
+Because of this, small changes to the code to reduce the miss
+rate have been observed to give disproportionately large
+performance improvements. I imagine
+<computeroutput>bzip2</computeroutput> will perform best on
+machines with very large caches.</para>
+
+</sect1>
+
+
+
+<sect1 id="caveats" xreflabel="CAVEATS">
+<title>CAVEATS</title>
+
+<para>I/O error messages are not as helpful as they could be.
+<computeroutput>bzip2</computeroutput> tries hard to detect I/O
+errors and exit cleanly, but the details of what the problem is
+sometimes seem rather misleading.</para>
+
+<para>This manual page pertains to version &bz-version; of
+<computeroutput>bzip2</computeroutput>. Compressed data created by
+this version is entirely forwards and backwards compatible with the
+previous public releases, versions 0.1pl2, 0.9.0 and 0.9.5, 1.0.0,
+1.0.1, 1.0.2 and 1.0.3, but with the following exception: 0.9.0 and
+above can correctly decompress multiple concatenated compressed files.
+0.1pl2 cannot do this; it will stop after decompressing just the first
+file in the stream.</para>
+
+<para><computeroutput>bzip2recover</computeroutput> versions
+prior to 1.0.2 used 32-bit integers to represent bit positions in
+compressed files, so it could not handle compressed files more
+than 512 megabytes long. Versions 1.0.2 and above use 64-bit ints
+on some platforms which support them (GNU supported targets, and
+Windows). To establish whether or not
+<computeroutput>bzip2recover</computeroutput> was built with such
+a limitation, run it without arguments. In any event you can
+build yourself an unlimited version if you can recompile it with
+<computeroutput>MaybeUInt64</computeroutput> set to be an
+unsigned 64-bit integer.</para>
+
+</sect1>
+
+
+
+<sect1 id="author" xreflabel="AUTHOR">
+<title>AUTHOR</title>
+
+<para>Julian Seward,
+<computeroutput>&bz-email;</computeroutput></para>
+
+<para>The ideas embodied in
+<computeroutput>bzip2</computeroutput> are due to (at least) the
+following people: Michael Burrows and David Wheeler (for the
+block sorting transformation), David Wheeler (again, for the
+Huffman coder), Peter Fenwick (for the structured coding model in
+the original <computeroutput>bzip</computeroutput>, and many
+refinements), and Alistair Moffat, Radford Neal and Ian Witten
+(for the arithmetic coder in the original
+<computeroutput>bzip</computeroutput>). I am much indebted for
+their help, support and advice. See the manual in the source
+distribution for pointers to sources of documentation. Christian
+von Roques encouraged me to look for faster sorting algorithms,
+so as to speed up compression. Bela Lubkin encouraged me to
+improve the worst-case compression performance.
+Donna Robinson XMLised the documentation.
+Many people sent
+patches, helped with portability problems, lent machines, gave
+advice and were generally helpful.</para>
+
+</sect1>
+
+</chapter>
+
+
+
+<chapter id="libprog" xreflabel="Programming with libbzip2">
+<title>
+Programming with <computeroutput>libbzip2</computeroutput>
+</title>
+
+<para>This chapter describes the programming interface to
+<computeroutput>libbzip2</computeroutput>.</para>
+
+<para>For general background information, particularly about
+memory use and performance aspects, you'd be well advised to read
+<xref linkend="using"/> as well.</para>
+
+
+<sect1 id="top-level" xreflabel="Top-level structure">
+<title>Top-level structure</title>
+
+<para><computeroutput>libbzip2</computeroutput> is a flexible
+library for compressing and decompressing data in the
+<computeroutput>bzip2</computeroutput> data format. Although
+packaged as a single entity, it helps to regard the library as
+three separate parts: the low level interface, and the high level
+interface, and some utility functions.</para>
+
+<para>The structure of
+<computeroutput>libbzip2</computeroutput>'s interfaces is similar
+to that of Jean-loup Gailly's and Mark Adler's excellent
+<computeroutput>zlib</computeroutput> library.</para>
+
+<para>All externally visible symbols have names beginning
+<computeroutput>BZ2_</computeroutput>. This is new in version
+1.0. The intention is to minimise pollution of the namespaces of
+library clients.</para>
+
+<para>To use any part of the library, you need to
+<computeroutput>#include <bzlib.h></computeroutput>
+into your sources.</para>
+
+
+
+<sect2 id="ll-summary" xreflabel="Low-level summary">
+<title>Low-level summary</title>
+
+<para>This interface provides services for compressing and
+decompressing data in memory. There's no provision for dealing
+with files, streams or any other I/O mechanisms, just straight
+memory-to-memory work. In fact, this part of the library can be
+compiled without inclusion of
+<computeroutput>stdio.h</computeroutput>, which may be helpful
+for embedded applications.</para>
+
+<para>The low-level part of the library has no global variables
+and is therefore thread-safe.</para>
+
+<para>Six routines make up the low level interface:
+<computeroutput>BZ2_bzCompressInit</computeroutput>,
+<computeroutput>BZ2_bzCompress</computeroutput>, and
+<computeroutput>BZ2_bzCompressEnd</computeroutput> for
+compression, and a corresponding trio
+<computeroutput>BZ2_bzDecompressInit</computeroutput>,
+<computeroutput>BZ2_bzDecompress</computeroutput> and
+<computeroutput>BZ2_bzDecompressEnd</computeroutput> for
+decompression. The <computeroutput>*Init</computeroutput>
+functions allocate memory for compression/decompression and do
+other initialisations, whilst the
+<computeroutput>*End</computeroutput> functions close down
+operations and release memory.</para>
+
+<para>The real work is done by
+<computeroutput>BZ2_bzCompress</computeroutput> and
+<computeroutput>BZ2_bzDecompress</computeroutput>. These
+compress and decompress data from a user-supplied input buffer to
+a user-supplied output buffer. These buffers can be any size;
+arbitrary quantities of data are handled by making repeated calls
+to these functions. This is a flexible mechanism allowing a
+consumer-pull style of activity, or producer-push, or a mixture
+of both.</para>
+
+</sect2>
+
+
+<sect2 id="hl-summary" xreflabel="High-level summary">
+<title>High-level summary</title>
+
+<para>This interface provides some handy wrappers around the
+low-level interface to facilitate reading and writing
+<computeroutput>bzip2</computeroutput> format files
+(<computeroutput>.bz2</computeroutput> files). The routines
+provide hooks to facilitate reading files in which the
+<computeroutput>bzip2</computeroutput> data stream is embedded
+within some larger-scale file structure, or where there are
+multiple <computeroutput>bzip2</computeroutput> data streams
+concatenated end-to-end.</para>
+
+<para>For reading files,
+<computeroutput>BZ2_bzReadOpen</computeroutput>,
+<computeroutput>BZ2_bzRead</computeroutput>,
+<computeroutput>BZ2_bzReadClose</computeroutput> and
+<computeroutput>BZ2_bzReadGetUnused</computeroutput> are
+supplied. For writing files,
+<computeroutput>BZ2_bzWriteOpen</computeroutput>,
+<computeroutput>BZ2_bzWrite</computeroutput> and
+<computeroutput>BZ2_bzWriteFinish</computeroutput> are
+available.</para>
+
+<para>As with the low-level library, no global variables are used
+so the library is per se thread-safe. However, if I/O errors
+occur whilst reading or writing the underlying compressed files,
+you may have to consult <computeroutput>errno</computeroutput> to
+determine the cause of the error. In that case, you'd need a C
+library which correctly supports
+<computeroutput>errno</computeroutput> in a multithreaded
+environment.</para>
+
+<para>To make the library a little simpler and more portable,
+<computeroutput>BZ2_bzReadOpen</computeroutput> and
+<computeroutput>BZ2_bzWriteOpen</computeroutput> require you to
+pass them file handles (<computeroutput>FILE*</computeroutput>s)
+which have previously been opened for reading or writing
+respectively. That avoids portability problems associated with
+file operations and file attributes, whilst not being much of an
+imposition on the programmer.</para>
+
+</sect2>
+
+
+<sect2 id="util-fns-summary" xreflabel="Utility functions summary">
+<title>Utility functions summary</title>
+
+<para>For very simple needs,
+<computeroutput>BZ2_bzBuffToBuffCompress</computeroutput> and
+<computeroutput>BZ2_bzBuffToBuffDecompress</computeroutput> are
+provided. These compress data in memory from one buffer to
+another buffer in a single function call. You should assess
+whether these functions fulfill your memory-to-memory
+compression/decompression requirements before investing effort in
+understanding the more general but more complex low-level
+interface.</para>
+
+<para>Yoshioka Tsuneo
+(<computeroutput>tsuneo at rr.iij4u.or.jp</computeroutput>) has
+contributed some functions to give better
+<computeroutput>zlib</computeroutput> compatibility. These
+functions are <computeroutput>BZ2_bzopen</computeroutput>,
+<computeroutput>BZ2_bzread</computeroutput>,
+<computeroutput>BZ2_bzwrite</computeroutput>,
+<computeroutput>BZ2_bzflush</computeroutput>,
+<computeroutput>BZ2_bzclose</computeroutput>,
+<computeroutput>BZ2_bzerror</computeroutput> and
+<computeroutput>BZ2_bzlibVersion</computeroutput>. You may find
+these functions more convenient for simple file reading and
+writing, than those in the high-level interface. These functions
+are not (yet) officially part of the library, and are minimally
+documented here. If they break, you get to keep all the pieces.
+I hope to document them properly when time permits.</para>
+
+<para>Yoshioka also contributed modifications to allow the
+library to be built as a Windows DLL.</para>
+
+</sect2>
+
+</sect1>
+
+
+<sect1 id="err-handling" xreflabel="Error handling">
+<title>Error handling</title>
+
+<para>The library is designed to recover cleanly in all
+situations, including the worst-case situation of decompressing
+random data. I'm not 100% sure that it can always do this, so
+you might want to add a signal handler to catch segmentation
+violations during decompression if you are feeling especially
+paranoid. I would be interested in hearing more about the
+robustness of the library to corrupted compressed data.</para>
+
+<para>Version 1.0.3 more robust in this respect than any
+previous version. Investigations with Valgrind (a tool for detecting
+problems with memory management) indicate
+that, at least for the few files I tested, all single-bit errors
+in the decompressed data are caught properly, with no
+segmentation faults, no uses of uninitialised data, no out of
+range reads or writes, and no infinite looping in the decompressor.
+So it's certainly pretty robust, although
+I wouldn't claim it to be totally bombproof.</para>
+
+<para>The file <computeroutput>bzlib.h</computeroutput> contains
+all definitions needed to use the library. In particular, you
+should definitely not include
+<computeroutput>bzlib_private.h</computeroutput>.</para>
+
+<para>In <computeroutput>bzlib.h</computeroutput>, the various
+return values are defined. The following list is not intended as
+an exhaustive description of the circumstances in which a given
+value may be returned -- those descriptions are given later.
+Rather, it is intended to convey the rough meaning of each return
+value. The first five actions are normal and not intended to
+denote an error situation.</para>
+
+<variablelist>
+
+ <varlistentry>
+ <term><computeroutput>BZ_OK</computeroutput></term>
+ <listitem><para>The requested action was completed
+ successfully.</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><computeroutput>BZ_RUN_OK, BZ_FLUSH_OK,
+ BZ_FINISH_OK</computeroutput></term>
+ <listitem><para>In
+ <computeroutput>BZ2_bzCompress</computeroutput>, the requested
+ flush/finish/nothing-special action was completed
+ successfully.</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><computeroutput>BZ_STREAM_END</computeroutput></term>
+ <listitem><para>Compression of data was completed, or the
+ logical stream end was detected during
+ decompression.</para></listitem>
+ </varlistentry>
+
+</variablelist>
+
+<para>The following return values indicate an error of some
+kind.</para>
+
+<variablelist>
+
+ <varlistentry>
+ <term><computeroutput>BZ_CONFIG_ERROR</computeroutput></term>
+ <listitem><para>Indicates that the library has been improperly
+ compiled on your platform -- a major configuration error.
+ Specifically, it means that
+ <computeroutput>sizeof(char)</computeroutput>,
+ <computeroutput>sizeof(short)</computeroutput> and
+ <computeroutput>sizeof(int)</computeroutput> are not 1, 2 and
+ 4 respectively, as they should be. Note that the library
+ should still work properly on 64-bit platforms which follow
+ the LP64 programming model -- that is, where
+ <computeroutput>sizeof(long)</computeroutput> and
+ <computeroutput>sizeof(void*)</computeroutput> are 8. Under
+ LP64, <computeroutput>sizeof(int)</computeroutput> is still 4,
+ so <computeroutput>libbzip2</computeroutput>, which doesn't
+ use the <computeroutput>long</computeroutput> type, is
+ OK.</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><computeroutput>BZ_SEQUENCE_ERROR</computeroutput></term>
+ <listitem><para>When using the library, it is important to call
+ the functions in the correct sequence and with data structures
+ (buffers etc) in the correct states.
+ <computeroutput>libbzip2</computeroutput> checks as much as it
+ can to ensure this is happening, and returns
+ <computeroutput>BZ_SEQUENCE_ERROR</computeroutput> if not.
+ Code which complies precisely with the function semantics, as
+ detailed below, should never receive this value; such an event
+ denotes buggy code which you should
+ investigate.</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><computeroutput>BZ_PARAM_ERROR</computeroutput></term>
+ <listitem><para>Returned when a parameter to a function call is
+ out of range or otherwise manifestly incorrect. As with
+ <computeroutput>BZ_SEQUENCE_ERROR</computeroutput>, this
+ denotes a bug in the client code. The distinction between
+ <computeroutput>BZ_PARAM_ERROR</computeroutput> and
+ <computeroutput>BZ_SEQUENCE_ERROR</computeroutput> is a bit
+ hazy, but still worth making.</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><computeroutput>BZ_MEM_ERROR</computeroutput></term>
+ <listitem><para>Returned when a request to allocate memory
+ failed. Note that the quantity of memory needed to decompress
+ a stream cannot be determined until the stream's header has
+ been read. So
+ <computeroutput>BZ2_bzDecompress</computeroutput> and
+ <computeroutput>BZ2_bzRead</computeroutput> may return
+ <computeroutput>BZ_MEM_ERROR</computeroutput> even though some
+ of the compressed data has been read. The same is not true
+ for compression; once
+ <computeroutput>BZ2_bzCompressInit</computeroutput> or
+ <computeroutput>BZ2_bzWriteOpen</computeroutput> have
+ successfully completed,
+ <computeroutput>BZ_MEM_ERROR</computeroutput> cannot
+ occur.</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><computeroutput>BZ_DATA_ERROR</computeroutput></term>
+ <listitem><para>Returned when a data integrity error is
+ detected during decompression. Most importantly, this means
+ when stored and computed CRCs for the data do not match. This
+ value is also returned upon detection of any other anomaly in
+ the compressed data.</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><computeroutput>BZ_DATA_ERROR_MAGIC</computeroutput></term>
+ <listitem><para>As a special case of
+ <computeroutput>BZ_DATA_ERROR</computeroutput>, it is
+ sometimes useful to know when the compressed stream does not
+ start with the correct magic bytes (<computeroutput>'B' 'Z'
+ 'h'</computeroutput>).</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><computeroutput>BZ_IO_ERROR</computeroutput></term>
+ <listitem><para>Returned by
+ <computeroutput>BZ2_bzRead</computeroutput> and
+ <computeroutput>BZ2_bzWrite</computeroutput> when there is an
+ error reading or writing in the compressed file, and by
+ <computeroutput>BZ2_bzReadOpen</computeroutput> and
+ <computeroutput>BZ2_bzWriteOpen</computeroutput> for attempts
+ to use a file for which the error indicator (viz,
+ <computeroutput>ferror(f)</computeroutput>) is set. On
+ receipt of <computeroutput>BZ_IO_ERROR</computeroutput>, the
+ caller should consult <computeroutput>errno</computeroutput>
+ and/or <computeroutput>perror</computeroutput> to acquire
+ operating-system specific information about the
+ problem.</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><computeroutput>BZ_UNEXPECTED_EOF</computeroutput></term>
+ <listitem><para>Returned by
+ <computeroutput>BZ2_bzRead</computeroutput> when the
+ compressed file finishes before the logical end of stream is
+ detected.</para></listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><computeroutput>BZ_OUTBUFF_FULL</computeroutput></term>
+ <listitem><para>Returned by
+ <computeroutput>BZ2_bzBuffToBuffCompress</computeroutput> and
+ <computeroutput>BZ2_bzBuffToBuffDecompress</computeroutput> to
+ indicate that the output data will not fit into the output
+ buffer provided.</para></listitem>
+ </varlistentry>
+
+</variablelist>
+
+</sect1>
+
+
+
+<sect1 id="low-level" xreflabel=">Low-level interface">
+<title>Low-level interface</title>
+
+
+<sect2 id="bzcompress-init" xreflabel="BZ2_bzCompressInit">
+<title>BZ2_bzCompressInit</title>
+
+<programlisting>
+typedef struct {
+ char *next_in;
+ unsigned int avail_in;
+ unsigned int total_in_lo32;
+ unsigned int total_in_hi32;
+
+ char *next_out;
+ unsigned int avail_out;
+ unsigned int total_out_lo32;
+ unsigned int total_out_hi32;
+
+ void *state;
+
+ void *(*bzalloc)(void *,int,int);
+ void (*bzfree)(void *,void *);
+ void *opaque;
+} bz_stream;
+
+int BZ2_bzCompressInit ( bz_stream *strm,
+ int blockSize100k,
+ int verbosity,
+ int workFactor );
+</programlisting>
+
+<para>Prepares for compression. The
+<computeroutput>bz_stream</computeroutput> structure holds all
+data pertaining to the compression activity. A
+<computeroutput>bz_stream</computeroutput> structure should be
+allocated and initialised prior to the call. The fields of
+<computeroutput>bz_stream</computeroutput> comprise the entirety
+of the user-visible data. <computeroutput>state</computeroutput>
+is a pointer to the private data structures required for
+compression.</para>
+
+<para>Custom memory allocators are supported, via fields
+<computeroutput>bzalloc</computeroutput>,
+<computeroutput>bzfree</computeroutput>, and
+<computeroutput>opaque</computeroutput>. The value
+<computeroutput>opaque</computeroutput> is passed to as the first
+argument to all calls to <computeroutput>bzalloc</computeroutput>
+and <computeroutput>bzfree</computeroutput>, but is otherwise
+ignored by the library. The call <computeroutput>bzalloc (
+opaque, n, m )</computeroutput> is expected to return a pointer
+<computeroutput>p</computeroutput> to <computeroutput>n *
+m</computeroutput> bytes of memory, and <computeroutput>bzfree (
+opaque, p )</computeroutput> should free that memory.</para>
+
+<para>If you don't want to use a custom memory allocator, set
+<computeroutput>bzalloc</computeroutput>,
+<computeroutput>bzfree</computeroutput> and
+<computeroutput>opaque</computeroutput> to
+<computeroutput>NULL</computeroutput>, and the library will then
+use the standard <computeroutput>malloc</computeroutput> /
+<computeroutput>free</computeroutput> routines.</para>
+
+<para>Before calling
+<computeroutput>BZ2_bzCompressInit</computeroutput>, fields
+<computeroutput>bzalloc</computeroutput>,
+<computeroutput>bzfree</computeroutput> and
+<computeroutput>opaque</computeroutput> should be filled
+appropriately, as just described. Upon return, the internal
+state will have been allocated and initialised, and
+<computeroutput>total_in_lo32</computeroutput>,
+<computeroutput>total_in_hi32</computeroutput>,
+<computeroutput>total_out_lo32</computeroutput> and
+<computeroutput>total_out_hi32</computeroutput> will have been
+set to zero. These four fields are used by the library to inform
+the caller of the total amount of data passed into and out of the
+library, respectively. You should not try to change them. As of
+version 1.0, 64-bit counts are maintained, even on 32-bit
+platforms, using the <computeroutput>_hi32</computeroutput>
+fields to store the upper 32 bits of the count. So, for example,
+the total amount of data in is <computeroutput>(total_in_hi32
+<< 32) + total_in_lo32</computeroutput>.</para>
+
+<para>Parameter <computeroutput>blockSize100k</computeroutput>
+specifies the block size to be used for compression. It should
+be a value between 1 and 9 inclusive, and the actual block size
+used is 100000 x this figure. 9 gives the best compression but
+takes most memory.</para>
+
+<para>Parameter <computeroutput>verbosity</computeroutput> should
+be set to a number between 0 and 4 inclusive. 0 is silent, and
+greater numbers give increasingly verbose monitoring/debugging
+output. If the library has been compiled with
+<computeroutput>-DBZ_NO_STDIO</computeroutput>, no such output
+will appear for any verbosity setting.</para>
+
+<para>Parameter <computeroutput>workFactor</computeroutput>
+controls how the compression phase behaves when presented with
+worst case, highly repetitive, input data. If compression runs
+into difficulties caused by repetitive data, the library switches
+from the standard sorting algorithm to a fallback algorithm. The
+fallback is slower than the standard algorithm by perhaps a
+factor of three, but always behaves reasonably, no matter how bad
+the input.</para>
+
+<para>Lower values of <computeroutput>workFactor</computeroutput>
+reduce the amount of effort the standard algorithm will expend
+before resorting to the fallback. You should set this parameter
+carefully; too low, and many inputs will be handled by the
+fallback algorithm and so compress rather slowly, too high, and
+your average-to-worst case compression times can become very
+large. The default value of 30 gives reasonable behaviour over a
+wide range of circumstances.</para>
+
+<para>Allowable values range from 0 to 250 inclusive. 0 is a
+special case, equivalent to using the default value of 30.</para>
+
+<para>Note that the compressed output generated is the same
+regardless of whether or not the fallback algorithm is
+used.</para>
+
+<para>Be aware also that this parameter may disappear entirely in
+future versions of the library. In principle it should be
+possible to devise a good way to automatically choose which
+algorithm to use. Such a mechanism would render the parameter
+obsolete.</para>
+
+<para>Possible return values:</para>
+
+<programlisting>
+BZ_CONFIG_ERROR
+ if the library has been mis-compiled
+BZ_PARAM_ERROR
+ if strm is NULL
+ or blockSize < 1 or blockSize > 9
+ or verbosity < 0 or verbosity > 4
+ or workFactor < 0 or workFactor > 250
+BZ_MEM_ERROR
+ if not enough memory is available
+BZ_OK
+ otherwise
+</programlisting>
+
+<para>Allowable next actions:</para>
+
+<programlisting>
+BZ2_bzCompress
+ if BZ_OK is returned
+ no specific action needed in case of error
+</programlisting>
+
+</sect2>
+
+
+<sect2 id="bzCompress" xreflabel="BZ2_bzCompress">
+<title>BZ2_bzCompress</title>
+
+<programlisting>
+int BZ2_bzCompress ( bz_stream *strm, int action );
+</programlisting>
+
+<para>Provides more input and/or output buffer space for the
+library. The caller maintains input and output buffers, and
+calls <computeroutput>BZ2_bzCompress</computeroutput> to transfer
+data between them.</para>
+
+<para>Before each call to
+<computeroutput>BZ2_bzCompress</computeroutput>,
+<computeroutput>next_in</computeroutput> should point at the data
+to be compressed, and <computeroutput>avail_in</computeroutput>
+should indicate how many bytes the library may read.
+<computeroutput>BZ2_bzCompress</computeroutput> updates
+<computeroutput>next_in</computeroutput>,
+<computeroutput>avail_in</computeroutput> and
+<computeroutput>total_in</computeroutput> to reflect the number
+of bytes it has read.</para>
+
+<para>Similarly, <computeroutput>next_out</computeroutput> should
+point to a buffer in which the compressed data is to be placed,
+with <computeroutput>avail_out</computeroutput> indicating how
+much output space is available.
+<computeroutput>BZ2_bzCompress</computeroutput> updates
+<computeroutput>next_out</computeroutput>,
+<computeroutput>avail_out</computeroutput> and
+<computeroutput>total_out</computeroutput> to reflect the number
+of bytes output.</para>
+
+<para>You may provide and remove as little or as much data as you
+like on each call of
+<computeroutput>BZ2_bzCompress</computeroutput>. In the limit,
+it is acceptable to supply and remove data one byte at a time,
+although this would be terribly inefficient. You should always
+ensure that at least one byte of output space is available at
+each call.</para>
+
+<para>A second purpose of
+<computeroutput>BZ2_bzCompress</computeroutput> is to request a
+change of mode of the compressed stream.</para>
+
+<para>Conceptually, a compressed stream can be in one of four
+states: IDLE, RUNNING, FLUSHING and FINISHING. Before
+initialisation
+(<computeroutput>BZ2_bzCompressInit</computeroutput>) and after
+termination (<computeroutput>BZ2_bzCompressEnd</computeroutput>),
+a stream is regarded as IDLE.</para>
+
+<para>Upon initialisation
+(<computeroutput>BZ2_bzCompressInit</computeroutput>), the stream
+is placed in the RUNNING state. Subsequent calls to
+<computeroutput>BZ2_bzCompress</computeroutput> should pass
+<computeroutput>BZ_RUN</computeroutput> as the requested action;
+other actions are illegal and will result in
+<computeroutput>BZ_SEQUENCE_ERROR</computeroutput>.</para>
+
+<para>At some point, the calling program will have provided all
+the input data it wants to. It will then want to finish up -- in
+effect, asking the library to process any data it might have
+buffered internally. In this state,
+<computeroutput>BZ2_bzCompress</computeroutput> will no longer
+attempt to read data from
+<computeroutput>next_in</computeroutput>, but it will want to
+write data to <computeroutput>next_out</computeroutput>. Because
+the output buffer supplied by the user can be arbitrarily small,
+the finishing-up operation cannot necessarily be done with a
+single call of
+<computeroutput>BZ2_bzCompress</computeroutput>.</para>
+
+<para>Instead, the calling program passes
+<computeroutput>BZ_FINISH</computeroutput> as an action to
+<computeroutput>BZ2_bzCompress</computeroutput>. This changes
+the stream's state to FINISHING. Any remaining input (ie,
+<computeroutput>next_in[0 .. avail_in-1]</computeroutput>) is
+compressed and transferred to the output buffer. To do this,
+<computeroutput>BZ2_bzCompress</computeroutput> must be called
+repeatedly until all the output has been consumed. At that
+point, <computeroutput>BZ2_bzCompress</computeroutput> returns
+<computeroutput>BZ_STREAM_END</computeroutput>, and the stream's
+state is set back to IDLE.
+<computeroutput>BZ2_bzCompressEnd</computeroutput> should then be
+called.</para>
+
+<para>Just to make sure the calling program does not cheat, the
+library makes a note of <computeroutput>avail_in</computeroutput>
+at the time of the first call to
+<computeroutput>BZ2_bzCompress</computeroutput> which has
+<computeroutput>BZ_FINISH</computeroutput> as an action (ie, at
+the time the program has announced its intention to not supply
+any more input). By comparing this value with that of
+<computeroutput>avail_in</computeroutput> over subsequent calls
+to <computeroutput>BZ2_bzCompress</computeroutput>, the library
+can detect any attempts to slip in more data to compress. Any
+calls for which this is detected will return
+<computeroutput>BZ_SEQUENCE_ERROR</computeroutput>. This
+indicates a programming mistake which should be corrected.</para>
+
+<para>Instead of asking to finish, the calling program may ask
+<computeroutput>BZ2_bzCompress</computeroutput> to take all the
+remaining input, compress it and terminate the current
+(Burrows-Wheeler) compression block. This could be useful for
+error control purposes. The mechanism is analogous to that for
+finishing: call <computeroutput>BZ2_bzCompress</computeroutput>
+with an action of <computeroutput>BZ_FLUSH</computeroutput>,
+remove output data, and persist with the
+<computeroutput>BZ_FLUSH</computeroutput> action until the value
+<computeroutput>BZ_RUN</computeroutput> is returned. As with
+finishing, <computeroutput>BZ2_bzCompress</computeroutput>
+detects any attempt to provide more input data once the flush has
+begun.</para>
+
+<para>Once the flush is complete, the stream returns to the
+normal RUNNING state.</para>
+
+<para>This all sounds pretty complex, but isn't really. Here's a
+table which shows which actions are allowable in each state, what
+action will be taken, what the next state is, and what the
+non-error return values are. Note that you can't explicitly ask
+what state the stream is in, but nor do you need to -- it can be
+inferred from the values returned by
+<computeroutput>BZ2_bzCompress</computeroutput>.</para>
+
+<programlisting>
+IDLE/any
+ Illegal. IDLE state only exists after BZ2_bzCompressEnd or
+ before BZ2_bzCompressInit.
+ Return value = BZ_SEQUENCE_ERROR
+
+RUNNING/BZ_RUN
+ Compress from next_in to next_out as much as possible.
+ Next state = RUNNING
+ Return value = BZ_RUN_OK
+
+RUNNING/BZ_FLUSH
+ Remember current value of next_in. Compress from next_in
+ to next_out as much as possible, but do not accept any more input.
+ Next state = FLUSHING
+ Return value = BZ_FLUSH_OK
+
+RUNNING/BZ_FINISH
+ Remember current value of next_in. Compress from next_in
+ to next_out as much as possible, but do not accept any more input.
+ Next state = FINISHING
+ Return value = BZ_FINISH_OK
+
+FLUSHING/BZ_FLUSH
+ Compress from next_in to next_out as much as possible,
+ but do not accept any more input.
+ If all the existing input has been used up and all compressed
+ output has been removed
+ Next state = RUNNING; Return value = BZ_RUN_OK
+ else
+ Next state = FLUSHING; Return value = BZ_FLUSH_OK
+
+FLUSHING/other
+ Illegal.
+ Return value = BZ_SEQUENCE_ERROR
+
+FINISHING/BZ_FINISH
+ Compress from next_in to next_out as much as possible,
+ but to not accept any more input.
+ If all the existing input has been used up and all compressed
+ output has been removed
+ Next state = IDLE; Return value = BZ_STREAM_END
+ else
+ Next state = FINISHING; Return value = BZ_FINISH_OK
+
+FINISHING/other
+ Illegal.
+ Return value = BZ_SEQUENCE_ERROR
+</programlisting>
+
+
+<para>That still looks complicated? Well, fair enough. The
+usual sequence of calls for compressing a load of data is:</para>
+
+<orderedlist>
+
+ <listitem><para>Get started with
+ <computeroutput>BZ2_bzCompressInit</computeroutput>.</para></listitem>
+
+ <listitem><para>Shovel data in and shlurp out its compressed form
+ using zero or more calls of
+ <computeroutput>BZ2_bzCompress</computeroutput> with action =
+ <computeroutput>BZ_RUN</computeroutput>.</para></listitem>
+
+ <listitem><para>Finish up. Repeatedly call
+ <computeroutput>BZ2_bzCompress</computeroutput> with action =
+ <computeroutput>BZ_FINISH</computeroutput>, copying out the
+ compressed output, until
+ <computeroutput>BZ_STREAM_END</computeroutput> is
+ returned.</para></listitem> <listitem><para>Close up and go home. Call
+ <computeroutput>BZ2_bzCompressEnd</computeroutput>.</para></listitem>
+
+</orderedlist>
+
+<para>If the data you want to compress fits into your input
+buffer all at once, you can skip the calls of
+<computeroutput>BZ2_bzCompress ( ..., BZ_RUN )</computeroutput>
+and just do the <computeroutput>BZ2_bzCompress ( ..., BZ_FINISH
+)</computeroutput> calls.</para>
+
+<para>All required memory is allocated by
+<computeroutput>BZ2_bzCompressInit</computeroutput>. The
+compression library can accept any data at all (obviously). So
+you shouldn't get any error return values from the
+<computeroutput>BZ2_bzCompress</computeroutput> calls. If you
+do, they will be
+<computeroutput>BZ_SEQUENCE_ERROR</computeroutput>, and indicate
+a bug in your programming.</para>
+
+<para>Trivial other possible return values:</para>
+
+<programlisting>
+BZ_PARAM_ERROR
+ if strm is NULL, or strm->s is NULL
+</programlisting>
+
+</sect2>
+
+
+<sect2 id="bzCompress-end" xreflabel="BZ2_bzCompressEnd">
+<title>BZ2_bzCompressEnd</title>
+
+<programlisting>
+int BZ2_bzCompressEnd ( bz_stream *strm );
+</programlisting>
+
+<para>Releases all memory associated with a compression
+stream.</para>
+
+<para>Possible return values:</para>
+
+<programlisting>
+BZ_PARAM_ERROR if strm is NULL or strm->s is NULL
+BZ_OK otherwise
+</programlisting>
+
+</sect2>
+
+
+<sect2 id="bzDecompress-init" xreflabel="BZ2_bzDecompressInit">
+<title>BZ2_bzDecompressInit</title>
+
+<programlisting>
+int BZ2_bzDecompressInit ( bz_stream *strm, int verbosity, int small );
+</programlisting>
+
+<para>Prepares for decompression. As with
+<computeroutput>BZ2_bzCompressInit</computeroutput>, a
+<computeroutput>bz_stream</computeroutput> record should be
+allocated and initialised before the call. Fields
+<computeroutput>bzalloc</computeroutput>,
+<computeroutput>bzfree</computeroutput> and
+<computeroutput>opaque</computeroutput> should be set if a custom
+memory allocator is required, or made
+<computeroutput>NULL</computeroutput> for the normal
+<computeroutput>malloc</computeroutput> /
+<computeroutput>free</computeroutput> routines. Upon return, the
+internal state will have been initialised, and
+<computeroutput>total_in</computeroutput> and
+<computeroutput>total_out</computeroutput> will be zero.</para>
+
+<para>For the meaning of parameter
+<computeroutput>verbosity</computeroutput>, see
+<computeroutput>BZ2_bzCompressInit</computeroutput>.</para>
+
+<para>If <computeroutput>small</computeroutput> is nonzero, the
+library will use an alternative decompression algorithm which
+uses less memory but at the cost of decompressing more slowly
+(roughly speaking, half the speed, but the maximum memory
+requirement drops to around 2300k). See <xref linkend="using"/>
+for more information on memory management.</para>
+
+<para>Note that the amount of memory needed to decompress a
+stream cannot be determined until the stream's header has been
+read, so even if
+<computeroutput>BZ2_bzDecompressInit</computeroutput> succeeds, a
+subsequent <computeroutput>BZ2_bzDecompress</computeroutput>
+could fail with
+<computeroutput>BZ_MEM_ERROR</computeroutput>.</para>
+
+<para>Possible return values:</para>
+
+<programlisting>
+BZ_CONFIG_ERROR
+ if the library has been mis-compiled
+BZ_PARAM_ERROR
+ if ( small != 0 && small != 1 )
+ or (verbosity <; 0 || verbosity > 4)
+BZ_MEM_ERROR
+ if insufficient memory is available
+</programlisting>
+
+<para>Allowable next actions:</para>
+
+<programlisting>
+BZ2_bzDecompress
+ if BZ_OK was returned
+ no specific action required in case of error
+</programlisting>
+
+</sect2>
+
+
+<sect2 id="bzDecompress" xreflabel="BZ2_bzDecompress">
+<title>BZ2_bzDecompress</title>
+
+<programlisting>
+int BZ2_bzDecompress ( bz_stream *strm );
+</programlisting>
+
+<para>Provides more input and/out output buffer space for the
+library. The caller maintains input and output buffers, and uses
+<computeroutput>BZ2_bzDecompress</computeroutput> to transfer
+data between them.</para>
+
+<para>Before each call to
+<computeroutput>BZ2_bzDecompress</computeroutput>,
+<computeroutput>next_in</computeroutput> should point at the
+compressed data, and <computeroutput>avail_in</computeroutput>
+should indicate how many bytes the library may read.
+<computeroutput>BZ2_bzDecompress</computeroutput> updates
+<computeroutput>next_in</computeroutput>,
+<computeroutput>avail_in</computeroutput> and
+<computeroutput>total_in</computeroutput> to reflect the number
+of bytes it has read.</para>
+
+<para>Similarly, <computeroutput>next_out</computeroutput> should
+point to a buffer in which the uncompressed output is to be
+placed, with <computeroutput>avail_out</computeroutput>
+indicating how much output space is available.
+<computeroutput>BZ2_bzCompress</computeroutput> updates
+<computeroutput>next_out</computeroutput>,
+<computeroutput>avail_out</computeroutput> and
+<computeroutput>total_out</computeroutput> to reflect the number
+of bytes output.</para>
+
+<para>You may provide and remove as little or as much data as you
+like on each call of
+<computeroutput>BZ2_bzDecompress</computeroutput>. In the limit,
+it is acceptable to supply and remove data one byte at a time,
+although this would be terribly inefficient. You should always
+ensure that at least one byte of output space is available at
+each call.</para>
+
+<para>Use of <computeroutput>BZ2_bzDecompress</computeroutput> is
+simpler than
+<computeroutput>BZ2_bzCompress</computeroutput>.</para>
+
+<para>You should provide input and remove output as described
+above, and repeatedly call
+<computeroutput>BZ2_bzDecompress</computeroutput> until
+<computeroutput>BZ_STREAM_END</computeroutput> is returned.
+Appearance of <computeroutput>BZ_STREAM_END</computeroutput>
+denotes that <computeroutput>BZ2_bzDecompress</computeroutput>
+has detected the logical end of the compressed stream.
+<computeroutput>BZ2_bzDecompress</computeroutput> will not
+produce <computeroutput>BZ_STREAM_END</computeroutput> until all
+output data has been placed into the output buffer, so once
+<computeroutput>BZ_STREAM_END</computeroutput> appears, you are
+guaranteed to have available all the decompressed output, and
+<computeroutput>BZ2_bzDecompressEnd</computeroutput> can safely
+be called.</para>
+
+<para>If case of an error return value, you should call
+<computeroutput>BZ2_bzDecompressEnd</computeroutput> to clean up
+and release memory.</para>
+
+<para>Possible return values:</para>
+
+<programlisting>
+BZ_PARAM_ERROR
+ if strm is NULL or strm->s is NULL
+ or strm->avail_out < 1
+BZ_DATA_ERROR
+ if a data integrity error is detected in the compressed stream
+BZ_DATA_ERROR_MAGIC
+ if the compressed stream doesn't begin with the right magic bytes
+BZ_MEM_ERROR
+ if there wasn't enough memory available
+BZ_STREAM_END
+ if the logical end of the data stream was detected and all
+ output in has been consumed, eg s-->avail_out > 0
+BZ_OK
+ otherwise
+</programlisting>
+
+<para>Allowable next actions:</para>
+
+<programlisting>
+BZ2_bzDecompress
+ if BZ_OK was returned
+BZ2_bzDecompressEnd
+ otherwise
+</programlisting>
+
+</sect2>
+
+
+<sect2 id="bzDecompress-end" xreflabel="BZ2_bzDecompressEnd">
+<title>BZ2_bzDecompressEnd</title>
+
+<programlisting>
+int BZ2_bzDecompressEnd ( bz_stream *strm );
+</programlisting>
+
+<para>Releases all memory associated with a decompression
+stream.</para>
+
+<para>Possible return values:</para>
+
+<programlisting>
+BZ_PARAM_ERROR
+ if strm is NULL or strm->s is NULL
+BZ_OK
+ otherwise
+</programlisting>
+
+<para>Allowable next actions:</para>
+
+<programlisting>
+ None.
+</programlisting>
+
+</sect2>
+
+</sect1>
+
+
+<sect1 id="hl-interface" xreflabel="High-level interface">
+<title>High-level interface</title>
+
+<para>This interface provides functions for reading and writing
+<computeroutput>bzip2</computeroutput> format files. First, some
+general points.</para>
+
+<itemizedlist mark='bullet'>
+
+ <listitem><para>All of the functions take an
+ <computeroutput>int*</computeroutput> first argument,
+ <computeroutput>bzerror</computeroutput>. After each call,
+ <computeroutput>bzerror</computeroutput> should be consulted
+ first to determine the outcome of the call. If
+ <computeroutput>bzerror</computeroutput> is
+ <computeroutput>BZ_OK</computeroutput>, the call completed
+ successfully, and only then should the return value of the
+ function (if any) be consulted. If
+ <computeroutput>bzerror</computeroutput> is
+ <computeroutput>BZ_IO_ERROR</computeroutput>, there was an
+ error reading/writing the underlying compressed file, and you
+ should then consult <computeroutput>errno</computeroutput> /
+ <computeroutput>perror</computeroutput> to determine the cause
+ of the difficulty. <computeroutput>bzerror</computeroutput>
+ may also be set to various other values; precise details are
+ given on a per-function basis below.</para></listitem>
+
+ <listitem><para>If <computeroutput>bzerror</computeroutput> indicates
+ an error (ie, anything except
+ <computeroutput>BZ_OK</computeroutput> and
+ <computeroutput>BZ_STREAM_END</computeroutput>), you should
+ immediately call
+ <computeroutput>BZ2_bzReadClose</computeroutput> (or
+ <computeroutput>BZ2_bzWriteClose</computeroutput>, depending on
+ whether you are attempting to read or to write) to free up all
+ resources associated with the stream. Once an error has been
+ indicated, behaviour of all calls except
+ <computeroutput>BZ2_bzReadClose</computeroutput>
+ (<computeroutput>BZ2_bzWriteClose</computeroutput>) is
+ undefined. The implication is that (1)
+ <computeroutput>bzerror</computeroutput> should be checked
+ after each call, and (2) if
+ <computeroutput>bzerror</computeroutput> indicates an error,
+ <computeroutput>BZ2_bzReadClose</computeroutput>
+ (<computeroutput>BZ2_bzWriteClose</computeroutput>) should then
+ be called to clean up.</para></listitem>
+
+ <listitem><para>The <computeroutput>FILE*</computeroutput> arguments
+ passed to <computeroutput>BZ2_bzReadOpen</computeroutput> /
+ <computeroutput>BZ2_bzWriteOpen</computeroutput> should be set
+ to binary mode. Most Unix systems will do this by default, but
+ other platforms, including Windows and Mac, will not. If you
+ omit this, you may encounter problems when moving code to new
+ platforms.</para></listitem>
+
+ <listitem><para>Memory allocation requests are handled by
+ <computeroutput>malloc</computeroutput> /
+ <computeroutput>free</computeroutput>. At present there is no
+ facility for user-defined memory allocators in the file I/O
+ functions (could easily be added, though).</para></listitem>
+
+</itemizedlist>
+
+
+
+<sect2 id="bzreadopen" xreflabel="BZ2_bzReadOpen">
+<title>BZ2_bzReadOpen</title>
+
+<programlisting>
+typedef void BZFILE;
+
+BZFILE *BZ2_bzReadOpen( int *bzerror, FILE *f,
+ int verbosity, int small,
+ void *unused, int nUnused );
+</programlisting>
+
+<para>Prepare to read compressed data from file handle
+<computeroutput>f</computeroutput>.
+<computeroutput>f</computeroutput> should refer to a file which
+has been opened for reading, and for which the error indicator
+(<computeroutput>ferror(f)</computeroutput>)is not set. If
+<computeroutput>small</computeroutput> is 1, the library will try
+to decompress using less memory, at the expense of speed.</para>
+
+<para>For reasons explained below,
+<computeroutput>BZ2_bzRead</computeroutput> will decompress the
+<computeroutput>nUnused</computeroutput> bytes starting at
+<computeroutput>unused</computeroutput>, before starting to read
+from the file <computeroutput>f</computeroutput>. At most
+<computeroutput>BZ_MAX_UNUSED</computeroutput> bytes may be
+supplied like this. If this facility is not required, you should
+pass <computeroutput>NULL</computeroutput> and
+<computeroutput>0</computeroutput> for
+<computeroutput>unused</computeroutput> and
+n<computeroutput>Unused</computeroutput> respectively.</para>
+
+<para>For the meaning of parameters
+<computeroutput>small</computeroutput> and
+<computeroutput>verbosity</computeroutput>, see
+<computeroutput>BZ2_bzDecompressInit</computeroutput>.</para>
+
+<para>The amount of memory needed to decompress a file cannot be
+determined until the file's header has been read. So it is
+possible that <computeroutput>BZ2_bzReadOpen</computeroutput>
+returns <computeroutput>BZ_OK</computeroutput> but a subsequent
+call of <computeroutput>BZ2_bzRead</computeroutput> will return
+<computeroutput>BZ_MEM_ERROR</computeroutput>.</para>
+
+<para>Possible assignments to
+<computeroutput>bzerror</computeroutput>:</para>
+
+<programlisting>
+BZ_CONFIG_ERROR
+ if the library has been mis-compiled
+BZ_PARAM_ERROR
+ if f is NULL
+ or small is neither 0 nor 1
+ or ( unused == NULL && nUnused != 0 )
+ or ( unused != NULL && !(0 <= nUnused <= BZ_MAX_UNUSED) )
+BZ_IO_ERROR
+ if ferror(f) is nonzero
+BZ_MEM_ERROR
+ if insufficient memory is available
+BZ_OK
+ otherwise.
+</programlisting>
+
+<para>Possible return values:</para>
+
+<programlisting>
+Pointer to an abstract BZFILE
+ if bzerror is BZ_OK
+NULL
+ otherwise
+</programlisting>
+
+<para>Allowable next actions:</para>
+
+<programlisting>
+BZ2_bzRead
+ if bzerror is BZ_OK
+BZ2_bzClose
+ otherwise
+</programlisting>
+
+</sect2>
+
+
+<sect2 id="bzread" xreflabel="BZ2_bzRead">
+<title>BZ2_bzRead</title>
+
+<programlisting>
+int BZ2_bzRead ( int *bzerror, BZFILE *b, void *buf, int len );
+</programlisting>
+
+<para>Reads up to <computeroutput>len</computeroutput>
+(uncompressed) bytes from the compressed file
+<computeroutput>b</computeroutput> into the buffer
+<computeroutput>buf</computeroutput>. If the read was
+successful, <computeroutput>bzerror</computeroutput> is set to
+<computeroutput>BZ_OK</computeroutput> and the number of bytes
+read is returned. If the logical end-of-stream was detected,
+<computeroutput>bzerror</computeroutput> will be set to
+<computeroutput>BZ_STREAM_END</computeroutput>, and the number of
+bytes read is returned. All other
+<computeroutput>bzerror</computeroutput> values denote an
+error.</para>
+
+<para><computeroutput>BZ2_bzRead</computeroutput> will supply
+<computeroutput>len</computeroutput> bytes, unless the logical
+stream end is detected or an error occurs. Because of this, it
+is possible to detect the stream end by observing when the number
+of bytes returned is less than the number requested.
+Nevertheless, this is regarded as inadvisable; you should instead
+check <computeroutput>bzerror</computeroutput> after every call
+and watch out for
+<computeroutput>BZ_STREAM_END</computeroutput>.</para>
+
+<para>Internally, <computeroutput>BZ2_bzRead</computeroutput>
+copies data from the compressed file in chunks of size
+<computeroutput>BZ_MAX_UNUSED</computeroutput> bytes before
+decompressing it. If the file contains more bytes than strictly
+needed to reach the logical end-of-stream,
+<computeroutput>BZ2_bzRead</computeroutput> will almost certainly
+read some of the trailing data before signalling
+<computeroutput>BZ_SEQUENCE_END</computeroutput>. To collect the
+read but unused data once
+<computeroutput>BZ_SEQUENCE_END</computeroutput> has appeared,
+call <computeroutput>BZ2_bzReadGetUnused</computeroutput>
+immediately before
+<computeroutput>BZ2_bzReadClose</computeroutput>.</para>
+
+<para>Possible assignments to
+<computeroutput>bzerror</computeroutput>:</para>
+
+<programlisting>
+BZ_PARAM_ERROR
+ if b is NULL or buf is NULL or len < 0
+BZ_SEQUENCE_ERROR
+ if b was opened with BZ2_bzWriteOpen
+BZ_IO_ERROR
+ if there is an error reading from the compressed file
+BZ_UNEXPECTED_EOF
+ if the compressed file ended before
+ the logical end-of-stream was detected
+BZ_DATA_ERROR
+ if a data integrity error was detected in the compressed stream
+BZ_DATA_ERROR_MAGIC
+ if the stream does not begin with the requisite header bytes
+ (ie, is not a bzip2 data file). This is really
+ a special case of BZ_DATA_ERROR.
+BZ_MEM_ERROR
+ if insufficient memory was available
+BZ_STREAM_END
+ if the logical end of stream was detected.
+BZ_OK
+ otherwise.
+</programlisting>
+
+<para>Possible return values:</para>
+
+<programlisting>
+number of bytes read
+ if bzerror is BZ_OK or BZ_STREAM_END
+undefined
+ otherwise
+</programlisting>
+
+<para>Allowable next actions:</para>
+
+<programlisting>
+collect data from buf, then BZ2_bzRead or BZ2_bzReadClose
+ if bzerror is BZ_OK
+collect data from buf, then BZ2_bzReadClose or BZ2_bzReadGetUnused
+ if bzerror is BZ_SEQUENCE_END
+BZ2_bzReadClose
+ otherwise
+</programlisting>
+
+</sect2>
+
+
+<sect2 id="bzreadgetunused" xreflabel="BZ2_bzReadGetUnused">
+<title>BZ2_bzReadGetUnused</title>
+
+<programlisting>
+void BZ2_bzReadGetUnused( int* bzerror, BZFILE *b,
+ void** unused, int* nUnused );
+</programlisting>
+
+<para>Returns data which was read from the compressed file but
+was not needed to get to the logical end-of-stream.
+<computeroutput>*unused</computeroutput> is set to the address of
+the data, and <computeroutput>*nUnused</computeroutput> to the
+number of bytes. <computeroutput>*nUnused</computeroutput> will
+be set to a value between <computeroutput>0</computeroutput> and
+<computeroutput>BZ_MAX_UNUSED</computeroutput> inclusive.</para>
+
+<para>This function may only be called once
+<computeroutput>BZ2_bzRead</computeroutput> has signalled
+<computeroutput>BZ_STREAM_END</computeroutput> but before
+<computeroutput>BZ2_bzReadClose</computeroutput>.</para>
+
+<para>Possible assignments to
+<computeroutput>bzerror</computeroutput>:</para>
+
+<programlisting>
+BZ_PARAM_ERROR
+ if b is NULL
+ or unused is NULL or nUnused is NULL
+BZ_SEQUENCE_ERROR
+ if BZ_STREAM_END has not been signalled
+ or if b was opened with BZ2_bzWriteOpen
+BZ_OK
+ otherwise
+</programlisting>
+
+<para>Allowable next actions:</para>
+
+<programlisting>
+BZ2_bzReadClose
+</programlisting>
+
+</sect2>
+
+
+<sect2 id="bzreadclose" xreflabel="BZ2_bzReadClose">
+<title>BZ2_bzReadClose</title>
+
+<programlisting>
+void BZ2_bzReadClose ( int *bzerror, BZFILE *b );
+</programlisting>
+
+<para>Releases all memory pertaining to the compressed file
+<computeroutput>b</computeroutput>.
+<computeroutput>BZ2_bzReadClose</computeroutput> does not call
+<computeroutput>fclose</computeroutput> on the underlying file
+handle, so you should do that yourself if appropriate.
+<computeroutput>BZ2_bzReadClose</computeroutput> should be called
+to clean up after all error situations.</para>
+
+<para>Possible assignments to
+<computeroutput>bzerror</computeroutput>:</para>
+
+<programlisting>
+BZ_SEQUENCE_ERROR
+ if b was opened with BZ2_bzOpenWrite
+BZ_OK
+ otherwise
+</programlisting>
+
+<para>Allowable next actions:</para>
+
+<programlisting>
+none
+</programlisting>
+
+</sect2>
+
+
+<sect2 id="bzwriteopen" xreflabel="BZ2_bzWriteOpen">
+<title>BZ2_bzWriteOpen</title>
+
+<programlisting>
+BZFILE *BZ2_bzWriteOpen( int *bzerror, FILE *f,
+ int blockSize100k, int verbosity,
+ int workFactor );
+</programlisting>
+
+<para>Prepare to write compressed data to file handle
+<computeroutput>f</computeroutput>.
+<computeroutput>f</computeroutput> should refer to a file which
+has been opened for writing, and for which the error indicator
+(<computeroutput>ferror(f)</computeroutput>)is not set.</para>
+
+<para>For the meaning of parameters
+<computeroutput>blockSize100k</computeroutput>,
+<computeroutput>verbosity</computeroutput> and
+<computeroutput>workFactor</computeroutput>, see
+<computeroutput>BZ2_bzCompressInit</computeroutput>.</para>
+
+<para>All required memory is allocated at this stage, so if the
+call completes successfully,
+<computeroutput>BZ_MEM_ERROR</computeroutput> cannot be signalled
+by a subsequent call to
+<computeroutput>BZ2_bzWrite</computeroutput>.</para>
+
+<para>Possible assignments to
+<computeroutput>bzerror</computeroutput>:</para>
+
+<programlisting>
+BZ_CONFIG_ERROR
+ if the library has been mis-compiled
+BZ_PARAM_ERROR
+ if f is NULL
+ or blockSize100k < 1 or blockSize100k > 9
+BZ_IO_ERROR
+ if ferror(f) is nonzero
+BZ_MEM_ERROR
+ if insufficient memory is available
+BZ_OK
+ otherwise
+</programlisting>
+
+<para>Possible return values:</para>
+
+<programlisting>
+Pointer to an abstract BZFILE
+ if bzerror is BZ_OK
+NULL
+ otherwise
+</programlisting>
+
+<para>Allowable next actions:</para>
+
+<programlisting>
+BZ2_bzWrite
+ if bzerror is BZ_OK
+ (you could go directly to BZ2_bzWriteClose, but this would be pretty pointless)
+BZ2_bzWriteClose
+ otherwise
+</programlisting>
+
+</sect2>
+
+
+<sect2 id="bzwrite" xreflabel="BZ2_bzWrite">
+<title>BZ2_bzWrite</title>
+
+<programlisting>
+void BZ2_bzWrite ( int *bzerror, BZFILE *b, void *buf, int len );
+</programlisting>
+
+<para>Absorbs <computeroutput>len</computeroutput> bytes from the
+buffer <computeroutput>buf</computeroutput>, eventually to be
+compressed and written to the file.</para>
+
+<para>Possible assignments to
+<computeroutput>bzerror</computeroutput>:</para>
+
+<programlisting>
+BZ_PARAM_ERROR
+ if b is NULL or buf is NULL or len < 0
+BZ_SEQUENCE_ERROR
+ if b was opened with BZ2_bzReadOpen
+BZ_IO_ERROR
+ if there is an error writing the compressed file.
+BZ_OK
+ otherwise
+</programlisting>
+
+</sect2>
+
+
+<sect2 id="bzwriteclose" xreflabel="BZ2_bzWriteClose">
+<title>BZ2_bzWriteClose</title>
+
+<programlisting>
+void BZ2_bzWriteClose( int *bzerror, BZFILE* f,
+ int abandon,
+ unsigned int* nbytes_in,
+ unsigned int* nbytes_out );
+
+void BZ2_bzWriteClose64( int *bzerror, BZFILE* f,
+ int abandon,
+ unsigned int* nbytes_in_lo32,
+ unsigned int* nbytes_in_hi32,
+ unsigned int* nbytes_out_lo32,
+ unsigned int* nbytes_out_hi32 );
+</programlisting>
+
+<para>Compresses and flushes to the compressed file all data so
+far supplied by <computeroutput>BZ2_bzWrite</computeroutput>.
+The logical end-of-stream markers are also written, so subsequent
+calls to <computeroutput>BZ2_bzWrite</computeroutput> are
+illegal. All memory associated with the compressed file
+<computeroutput>b</computeroutput> is released.
+<computeroutput>fflush</computeroutput> is called on the
+compressed file, but it is not
+<computeroutput>fclose</computeroutput>'d.</para>
+
+<para>If <computeroutput>BZ2_bzWriteClose</computeroutput> is
+called to clean up after an error, the only action is to release
+the memory. The library records the error codes issued by
+previous calls, so this situation will be detected automatically.
+There is no attempt to complete the compression operation, nor to
+<computeroutput>fflush</computeroutput> the compressed file. You
+can force this behaviour to happen even in the case of no error,
+by passing a nonzero value to
+<computeroutput>abandon</computeroutput>.</para>
+
+<para>If <computeroutput>nbytes_in</computeroutput> is non-null,
+<computeroutput>*nbytes_in</computeroutput> will be set to be the
+total volume of uncompressed data handled. Similarly,
+<computeroutput>nbytes_out</computeroutput> will be set to the
+total volume of compressed data written. For compatibility with
+older versions of the library,
+<computeroutput>BZ2_bzWriteClose</computeroutput> only yields the
+lower 32 bits of these counts. Use
+<computeroutput>BZ2_bzWriteClose64</computeroutput> if you want
+the full 64 bit counts. These two functions are otherwise
+absolutely identical.</para>
+
+<para>Possible assignments to
+<computeroutput>bzerror</computeroutput>:</para>
+
+<programlisting>
+BZ_SEQUENCE_ERROR
+ if b was opened with BZ2_bzReadOpen
+BZ_IO_ERROR
+ if there is an error writing the compressed file
+BZ_OK
+ otherwise
+</programlisting>
+
+</sect2>
+
+
+<sect2 id="embed" xreflabel="Handling embedded compressed data streams">
+<title>Handling embedded compressed data streams</title>
+
+<para>The high-level library facilitates use of
+<computeroutput>bzip2</computeroutput> data streams which form
+some part of a surrounding, larger data stream.</para>
+
+<itemizedlist mark='bullet'>
+
+ <listitem><para>For writing, the library takes an open file handle,
+ writes compressed data to it,
+ <computeroutput>fflush</computeroutput>es it but does not
+ <computeroutput>fclose</computeroutput> it. The calling
+ application can write its own data before and after the
+ compressed data stream, using that same file handle.</para></listitem>
+
+ <listitem><para>Reading is more complex, and the facilities are not as
+ general as they could be since generality is hard to reconcile
+ with efficiency. <computeroutput>BZ2_bzRead</computeroutput>
+ reads from the compressed file in blocks of size
+ <computeroutput>BZ_MAX_UNUSED</computeroutput> bytes, and in
+ doing so probably will overshoot the logical end of compressed
+ stream. To recover this data once decompression has ended,
+ call <computeroutput>BZ2_bzReadGetUnused</computeroutput> after
+ the last call of <computeroutput>BZ2_bzRead</computeroutput>
+ (the one returning
+ <computeroutput>BZ_STREAM_END</computeroutput>) but before
+ calling
+ <computeroutput>BZ2_bzReadClose</computeroutput>.</para></listitem>
+
+</itemizedlist>
+
+<para>This mechanism makes it easy to decompress multiple
+<computeroutput>bzip2</computeroutput> streams placed end-to-end.
+As the end of one stream, when
+<computeroutput>BZ2_bzRead</computeroutput> returns
+<computeroutput>BZ_STREAM_END</computeroutput>, call
+<computeroutput>BZ2_bzReadGetUnused</computeroutput> to collect
+the unused data (copy it into your own buffer somewhere). That
+data forms the start of the next compressed stream. To start
+uncompressing that next stream, call
+<computeroutput>BZ2_bzReadOpen</computeroutput> again, feeding in
+the unused data via the <computeroutput>unused</computeroutput> /
+<computeroutput>nUnused</computeroutput> parameters. Keep doing
+this until <computeroutput>BZ_STREAM_END</computeroutput> return
+coincides with the physical end of file
+(<computeroutput>feof(f)</computeroutput>). In this situation
+<computeroutput>BZ2_bzReadGetUnused</computeroutput> will of
+course return no data.</para>
+
+<para>This should give some feel for how the high-level interface
+can be used. If you require extra flexibility, you'll have to
+bite the bullet and get to grips with the low-level
+interface.</para>
+
+</sect2>
+
+
+<sect2 id="std-rdwr" xreflabel="Standard file-reading/writing code">
+<title>Standard file-reading/writing code</title>
+
+<para>Here's how you'd write data to a compressed file:</para>
+
+<programlisting>
+FILE* f;
+BZFILE* b;
+int nBuf;
+char buf[ /* whatever size you like */ ];
+int bzerror;
+int nWritten;
+
+f = fopen ( "myfile.bz2", "w" );
+if ( !f ) {
+ /* handle error */
+}
+b = BZ2_bzWriteOpen( &bzerror, f, 9 );
+if (bzerror != BZ_OK) {
+ BZ2_bzWriteClose ( b );
+ /* handle error */
+}
+
+while ( /* condition */ ) {
+ /* get data to write into buf, and set nBuf appropriately */
+ nWritten = BZ2_bzWrite ( &bzerror, b, buf, nBuf );
+ if (bzerror == BZ_IO_ERROR) {
+ BZ2_bzWriteClose ( &bzerror, b );
+ /* handle error */
+ }
+}
+
+BZ2_bzWriteClose( &bzerror, b );
+if (bzerror == BZ_IO_ERROR) {
+ /* handle error */
+}
+</programlisting>
+
+<para>And to read from a compressed file:</para>
+
+<programlisting>
+FILE* f;
+BZFILE* b;
+int nBuf;
+char buf[ /* whatever size you like */ ];
+int bzerror;
+int nWritten;
+
+f = fopen ( "myfile.bz2", "r" );
+if ( !f ) {
+ /* handle error */
+}
+b = BZ2_bzReadOpen ( &bzerror, f, 0, NULL, 0 );
+if ( bzerror != BZ_OK ) {
+ BZ2_bzReadClose ( &bzerror, b );
+ /* handle error */
+}
+
+bzerror = BZ_OK;
+while ( bzerror == BZ_OK && /* arbitrary other conditions */) {
+ nBuf = BZ2_bzRead ( &bzerror, b, buf, /* size of buf */ );
+ if ( bzerror == BZ_OK ) {
+ /* do something with buf[0 .. nBuf-1] */
+ }
+}
+if ( bzerror != BZ_STREAM_END ) {
+ BZ2_bzReadClose ( &bzerror, b );
+ /* handle error */
+} else {
+ BZ2_bzReadClose ( &bzerror, b );
+}
+</programlisting>
+
+</sect2>
+
+</sect1>
+
+
+<sect1 id="util-fns" xreflabel="Utility functions">
+<title>Utility functions</title>
+
+
+<sect2 id="bzbufftobuffcompress" xreflabel="BZ2_bzBuffToBuffCompress">
+<title>BZ2_bzBuffToBuffCompress</title>
+
+<programlisting>
+int BZ2_bzBuffToBuffCompress( char* dest,
+ unsigned int* destLen,
+ char* source,
+ unsigned int sourceLen,
+ int blockSize100k,
+ int verbosity,
+ int workFactor );
+</programlisting>
+
+<para>Attempts to compress the data in <computeroutput>source[0
+.. sourceLen-1]</computeroutput> into the destination buffer,
+<computeroutput>dest[0 .. *destLen-1]</computeroutput>. If the
+destination buffer is big enough,
+<computeroutput>*destLen</computeroutput> is set to the size of
+the compressed data, and <computeroutput>BZ_OK</computeroutput>
+is returned. If the compressed data won't fit,
+<computeroutput>*destLen</computeroutput> is unchanged, and
+<computeroutput>BZ_OUTBUFF_FULL</computeroutput> is
+returned.</para>
+
+<para>Compression in this manner is a one-shot event, done with a
+single call to this function. The resulting compressed data is a
+complete <computeroutput>bzip2</computeroutput> format data
+stream. There is no mechanism for making additional calls to
+provide extra input data. If you want that kind of mechanism,
+use the low-level interface.</para>
+
+<para>For the meaning of parameters
+<computeroutput>blockSize100k</computeroutput>,
+<computeroutput>verbosity</computeroutput> and
+<computeroutput>workFactor</computeroutput>, see
+<computeroutput>BZ2_bzCompressInit</computeroutput>.</para>
+
+<para>To guarantee that the compressed data will fit in its
+buffer, allocate an output buffer of size 1% larger than the
+uncompressed data, plus six hundred extra bytes.</para>
+
+<para><computeroutput>BZ2_bzBuffToBuffDecompress</computeroutput>
+will not write data at or beyond
+<computeroutput>dest[*destLen]</computeroutput>, even in case of
+buffer overflow.</para>
+
+<para>Possible return values:</para>
+
+<programlisting>
+BZ_CONFIG_ERROR
+ if the library has been mis-compiled
+BZ_PARAM_ERROR
+ if dest is NULL or destLen is NULL
+ or blockSize100k < 1 or blockSize100k > 9
+ or verbosity < 0 or verbosity > 4
+ or workFactor < 0 or workFactor > 250
+BZ_MEM_ERROR
+ if insufficient memory is available
+BZ_OUTBUFF_FULL
+ if the size of the compressed data exceeds *destLen
+BZ_OK
+ otherwise
+</programlisting>
+
+</sect2>
+
+
+<sect2 id="bzbufftobuffdecompress" xreflabel="BZ2_bzBuffToBuffDecompress">
+<title>BZ2_bzBuffToBuffDecompress</title>
+
+<programlisting>
+int BZ2_bzBuffToBuffDecompress( char* dest,
+ unsigned int* destLen,
+ char* source,
+ unsigned int sourceLen,
+ int small,
+ int verbosity );
+</programlisting>
+
+<para>Attempts to decompress the data in <computeroutput>source[0
+.. sourceLen-1]</computeroutput> into the destination buffer,
+<computeroutput>dest[0 .. *destLen-1]</computeroutput>. If the
+destination buffer is big enough,
+<computeroutput>*destLen</computeroutput> is set to the size of
+the uncompressed data, and <computeroutput>BZ_OK</computeroutput>
+is returned. If the compressed data won't fit,
+<computeroutput>*destLen</computeroutput> is unchanged, and
+<computeroutput>BZ_OUTBUFF_FULL</computeroutput> is
+returned.</para>
+
+<para><computeroutput>source</computeroutput> is assumed to hold
+a complete <computeroutput>bzip2</computeroutput> format data
+stream.
+<computeroutput>BZ2_bzBuffToBuffDecompress</computeroutput> tries
+to decompress the entirety of the stream into the output
+buffer.</para>
+
+<para>For the meaning of parameters
+<computeroutput>small</computeroutput> and
+<computeroutput>verbosity</computeroutput>, see
+<computeroutput>BZ2_bzDecompressInit</computeroutput>.</para>
+
+<para>Because the compression ratio of the compressed data cannot
+be known in advance, there is no easy way to guarantee that the
+output buffer will be big enough. You may of course make
+arrangements in your code to record the size of the uncompressed
+data, but such a mechanism is beyond the scope of this
+library.</para>
+
+<para><computeroutput>BZ2_bzBuffToBuffDecompress</computeroutput>
+will not write data at or beyond
+<computeroutput>dest[*destLen]</computeroutput>, even in case of
+buffer overflow.</para>
+
+<para>Possible return values:</para>
+
+<programlisting>
+BZ_CONFIG_ERROR
+ if the library has been mis-compiled
+BZ_PARAM_ERROR
+ if dest is NULL or destLen is NULL
+ or small != 0 && small != 1
+ or verbosity < 0 or verbosity > 4
+BZ_MEM_ERROR
+ if insufficient memory is available
+BZ_OUTBUFF_FULL
+ if the size of the compressed data exceeds *destLen
+BZ_DATA_ERROR
+ if a data integrity error was detected in the compressed data
+BZ_DATA_ERROR_MAGIC
+ if the compressed data doesn't begin with the right magic bytes
+BZ_UNEXPECTED_EOF
+ if the compressed data ends unexpectedly
+BZ_OK
+ otherwise
+</programlisting>
+
+</sect2>
+
+</sect1>
+
+
+<sect1 id="zlib-compat" xreflabel="zlib compatibility functions">
+<title>zlib compatibility functions</title>
+
+<para>Yoshioka Tsuneo has contributed some functions to give
+better <computeroutput>zlib</computeroutput> compatibility.
+These functions are <computeroutput>BZ2_bzopen</computeroutput>,
+<computeroutput>BZ2_bzread</computeroutput>,
+<computeroutput>BZ2_bzwrite</computeroutput>,
+<computeroutput>BZ2_bzflush</computeroutput>,
+<computeroutput>BZ2_bzclose</computeroutput>,
+<computeroutput>BZ2_bzerror</computeroutput> and
+<computeroutput>BZ2_bzlibVersion</computeroutput>. These
+functions are not (yet) officially part of the library. If they
+break, you get to keep all the pieces. Nevertheless, I think
+they work ok.</para>
+
+<programlisting>
+typedef void BZFILE;
+
+const char * BZ2_bzlibVersion ( void );
+</programlisting>
+
+<para>Returns a string indicating the library version.</para>
+
+<programlisting>
+BZFILE * BZ2_bzopen ( const char *path, const char *mode );
+BZFILE * BZ2_bzdopen ( int fd, const char *mode );
+</programlisting>
+
+<para>Opens a <computeroutput>.bz2</computeroutput> file for
+reading or writing, using either its name or a pre-existing file
+descriptor. Analogous to <computeroutput>fopen</computeroutput>
+and <computeroutput>fdopen</computeroutput>.</para>
+
+<programlisting>
+int BZ2_bzread ( BZFILE* b, void* buf, int len );
+int BZ2_bzwrite ( BZFILE* b, void* buf, int len );
+</programlisting>
+
+<para>Reads/writes data from/to a previously opened
+<computeroutput>BZFILE</computeroutput>. Analogous to
+<computeroutput>fread</computeroutput> and
+<computeroutput>fwrite</computeroutput>.</para>
+
+<programlisting>
+int BZ2_bzflush ( BZFILE* b );
+void BZ2_bzclose ( BZFILE* b );
+</programlisting>
+
+<para>Flushes/closes a <computeroutput>BZFILE</computeroutput>.
+<computeroutput>BZ2_bzflush</computeroutput> doesn't actually do
+anything. Analogous to <computeroutput>fflush</computeroutput>
+and <computeroutput>fclose</computeroutput>.</para>
+
+<programlisting>
+const char * BZ2_bzerror ( BZFILE *b, int *errnum )
+</programlisting>
+
+<para>Returns a string describing the more recent error status of
+<computeroutput>b</computeroutput>, and also sets
+<computeroutput>*errnum</computeroutput> to its numerical
+value.</para>
+
+</sect1>
+
+
+<sect1 id="stdio-free"
+ xreflabel="Using the library in a stdio-free environment">
+<title>Using the library in a stdio-free environment</title>
+
+
+<sect2 id="stdio-bye" xreflabel="Getting rid of stdio">
+<title>Getting rid of stdio</title>
+
+<para>In a deeply embedded application, you might want to use
+just the memory-to-memory functions. You can do this
+conveniently by compiling the library with preprocessor symbol
+<computeroutput>BZ_NO_STDIO</computeroutput> defined. Doing this
+gives you a library containing only the following eight
+functions:</para>
+
+<para><computeroutput>BZ2_bzCompressInit</computeroutput>,
+<computeroutput>BZ2_bzCompress</computeroutput>,
+<computeroutput>BZ2_bzCompressEnd</computeroutput>
+<computeroutput>BZ2_bzDecompressInit</computeroutput>,
+<computeroutput>BZ2_bzDecompress</computeroutput>,
+<computeroutput>BZ2_bzDecompressEnd</computeroutput>
+<computeroutput>BZ2_bzBuffToBuffCompress</computeroutput>,
+<computeroutput>BZ2_bzBuffToBuffDecompress</computeroutput></para>
+
+<para>When compiled like this, all functions will ignore
+<computeroutput>verbosity</computeroutput> settings.</para>
+
+</sect2>
+
+
+<sect2 id="critical-error" xreflabel="Critical error handling">
+<title>Critical error handling</title>
+
+<para><computeroutput>libbzip2</computeroutput> contains a number
+of internal assertion checks which should, needless to say, never
+be activated. Nevertheless, if an assertion should fail,
+behaviour depends on whether or not the library was compiled with
+<computeroutput>BZ_NO_STDIO</computeroutput> set.</para>
+
+<para>For a normal compile, an assertion failure yields the
+message:</para>
+
+<blockquote>
+<para>bzip2/libbzip2: internal error number N.</para>
+<para>This is a bug in bzip2/libbzip2, &bz-version; of &bz-date;.
+Please report it to me at: &bz-email;. If this happened
+when you were using some program which uses libbzip2 as a
+component, you should also report this bug to the author(s)
+of that program. Please make an effort to report this bug;
+timely and accurate bug reports eventually lead to higher
+quality software. Thanks. Julian Seward, &bz-date;.
+</para></blockquote>
+
+<para>where <computeroutput>N</computeroutput> is some error code
+number. If <computeroutput>N == 1007</computeroutput>, it also
+prints some extra text advising the reader that unreliable memory
+is often associated with internal error 1007. (This is a
+frequently-observed-phenomenon with versions 1.0.0/1.0.1).</para>
+
+<para><computeroutput>exit(3)</computeroutput> is then
+called.</para>
+
+<para>For a <computeroutput>stdio</computeroutput>-free library,
+assertion failures result in a call to a function declared
+as:</para>
+
+<programlisting>
+extern void bz_internal_error ( int errcode );
+</programlisting>
+
+<para>The relevant code is passed as a parameter. You should
+supply such a function.</para>
+
+<para>In either case, once an assertion failure has occurred, any
+<computeroutput>bz_stream</computeroutput> records involved can
+be regarded as invalid. You should not attempt to resume normal
+operation with them.</para>
+
+<para>You may, of course, change critical error handling to suit
+your needs. As I said above, critical errors indicate bugs in
+the library and should not occur. All "normal" error situations
+are indicated via error return codes from functions, and can be
+recovered from.</para>
+
+</sect2>
+
+</sect1>
+
+
+<sect1 id="win-dll" xreflabel="Making a Windows DLL">
+<title>Making a Windows DLL</title>
+
+<para>Everything related to Windows has been contributed by
+Yoshioka Tsuneo
+(<computeroutput>tsuneo at rr.iij4u.or.jp</computeroutput>), so
+you should send your queries to him (but perhaps Cc: me,
+<computeroutput>&bz-email;</computeroutput>).</para>
+
+<para>My vague understanding of what to do is: using Visual C++
+5.0, open the project file
+<computeroutput>libbz2.dsp</computeroutput>, and build. That's
+all.</para>
+
+<para>If you can't open the project file for some reason, make a
+new one, naming these files:
+<computeroutput>blocksort.c</computeroutput>,
+<computeroutput>bzlib.c</computeroutput>,
+<computeroutput>compress.c</computeroutput>,
+<computeroutput>crctable.c</computeroutput>,
+<computeroutput>decompress.c</computeroutput>,
+<computeroutput>huffman.c</computeroutput>,
+<computeroutput>randtable.c</computeroutput> and
+<computeroutput>libbz2.def</computeroutput>. You will also need
+to name the header files <computeroutput>bzlib.h</computeroutput>
+and <computeroutput>bzlib_private.h</computeroutput>.</para>
+
+<para>If you don't use VC++, you may need to define the
+proprocessor symbol
+<computeroutput>_WIN32</computeroutput>.</para>
+
+<para>Finally, <computeroutput>dlltest.c</computeroutput> is a
+sample program using the DLL. It has a project file,
+<computeroutput>dlltest.dsp</computeroutput>.</para>
+
+<para>If you just want a makefile for Visual C, have a look at
+<computeroutput>makefile.msc</computeroutput>.</para>
+
+<para>Be aware that if you compile
+<computeroutput>bzip2</computeroutput> itself on Win32, you must
+set <computeroutput>BZ_UNIX</computeroutput> to 0 and
+<computeroutput>BZ_LCCWIN32</computeroutput> to 1, in the file
+<computeroutput>bzip2.c</computeroutput>, before compiling.
+Otherwise the resulting binary won't work correctly.</para>
+
+<para>I haven't tried any of this stuff myself, but it all looks
+plausible.</para>
+
+</sect1>
+
+</chapter>
+
+
+
+<chapter id="misc" xreflabel="Miscellanea">
+<title>Miscellanea</title>
+
+<para>These are just some random thoughts of mine. Your mileage
+may vary.</para>
+
+
+<sect1 id="limits" xreflabel="Limitations of the compressed file format">
+<title>Limitations of the compressed file format</title>
+
+<para><computeroutput>bzip2-1.0.X</computeroutput>,
+<computeroutput>0.9.5</computeroutput> and
+<computeroutput>0.9.0</computeroutput> use exactly the same file
+format as the original version,
+<computeroutput>bzip2-0.1</computeroutput>. This decision was
+made in the interests of stability. Creating yet another
+incompatible compressed file format would create further
+confusion and disruption for users.</para>
+
+<para>Nevertheless, this is not a painless decision. Development
+work since the release of
+<computeroutput>bzip2-0.1</computeroutput> in August 1997 has
+shown complexities in the file format which slow down
+decompression and, in retrospect, are unnecessary. These
+are:</para>
+
+<itemizedlist mark='bullet'>
+
+ <listitem><para>The run-length encoder, which is the first of the
+ compression transformations, is entirely irrelevant. The
+ original purpose was to protect the sorting algorithm from the
+ very worst case input: a string of repeated symbols. But
+ algorithm steps Q6a and Q6b in the original Burrows-Wheeler
+ technical report (SRC-124) show how repeats can be handled
+ without difficulty in block sorting.</para></listitem>
+
+ <listitem><para>The randomisation mechanism doesn't really need to be
+ there. Udi Manber and Gene Myers published a suffix array
+ construction algorithm a few years back, which can be employed
+ to sort any block, no matter how repetitive, in O(N log N)
+ time. Subsequent work by Kunihiko Sadakane has produced a
+ derivative O(N (log N)^2) algorithm which usually outperforms
+ the Manber-Myers algorithm.</para>
+
+ <para>I could have changed to Sadakane's algorithm, but I find
+ it to be slower than <computeroutput>bzip2</computeroutput>'s
+ existing algorithm for most inputs, and the randomisation
+ mechanism protects adequately against bad cases. I didn't
+ think it was a good tradeoff to make. Partly this is due to
+ the fact that I was not flooded with email complaints about
+ <computeroutput>bzip2-0.1</computeroutput>'s performance on
+ repetitive data, so perhaps it isn't a problem for real
+ inputs.</para>
+
+ <para>Probably the best long-term solution, and the one I have
+ incorporated into 0.9.5 and above, is to use the existing
+ sorting algorithm initially, and fall back to a O(N (log N)^2)
+ algorithm if the standard algorithm gets into
+ difficulties.</para></listitem>
+
+ <listitem><para>The compressed file format was never designed to be
+ handled by a library, and I have had to jump though some hoops
+ to produce an efficient implementation of decompression. It's
+ a bit hairy. Try passing
+ <computeroutput>decompress.c</computeroutput> through the C
+ preprocessor and you'll see what I mean. Much of this
+ complexity could have been avoided if the compressed size of
+ each block of data was recorded in the data stream.</para></listitem>
+
+ <listitem><para>An Adler-32 checksum, rather than a CRC32 checksum,
+ would be faster to compute.</para></listitem>
+
+</itemizedlist>
+
+<para>It would be fair to say that the
+<computeroutput>bzip2</computeroutput> format was frozen before I
+properly and fully understood the performance consequences of
+doing so.</para>
+
+<para>Improvements which I was able to incorporate into 0.9.0,
+despite using the same file format, are:</para>
+
+<itemizedlist mark='bullet'>
+
+ <listitem><para>Single array implementation of the inverse BWT. This
+ significantly speeds up decompression, presumably because it
+ reduces the number of cache misses.</para></listitem>
+
+ <listitem><para>Faster inverse MTF transform for large MTF values.
+ The new implementation is based on the notion of sliding blocks
+ of values.</para></listitem>
+
+ <listitem><para><computeroutput>bzip2-0.9.0</computeroutput> now reads
+ and writes files with <computeroutput>fread</computeroutput>
+ and <computeroutput>fwrite</computeroutput>; version 0.1 used
+ <computeroutput>putc</computeroutput> and
+ <computeroutput>getc</computeroutput>. Duh! Well, you live
+ and learn.</para></listitem>
+
+</itemizedlist>
+
+<para>Further ahead, it would be nice to be able to do random
+access into files. This will require some careful design of
+compressed file formats.</para>
+
+</sect1>
+
+
+<sect1 id="port-issues" xreflabel="Portability issues">
+<title>Portability issues</title>
+
+<para>After some consideration, I have decided not to use GNU
+<computeroutput>autoconf</computeroutput> to configure 0.9.5 or
+1.0.</para>
+
+<para><computeroutput>autoconf</computeroutput>, admirable and
+wonderful though it is, mainly assists with portability problems
+between Unix-like platforms. But
+<computeroutput>bzip2</computeroutput> doesn't have much in the
+way of portability problems on Unix; most of the difficulties
+appear when porting to the Mac, or to Microsoft's operating
+systems. <computeroutput>autoconf</computeroutput> doesn't help
+in those cases, and brings in a whole load of new
+complexity.</para>
+
+<para>Most people should be able to compile the library and
+program under Unix straight out-of-the-box, so to speak,
+especially if you have a version of GNU C available.</para>
+
+<para>There are a couple of
+<computeroutput>__inline__</computeroutput> directives in the
+code. GNU C (<computeroutput>gcc</computeroutput>) should be
+able to handle them. If you're not using GNU C, your C compiler
+shouldn't see them at all. If your compiler does, for some
+reason, see them and doesn't like them, just
+<computeroutput>#define</computeroutput>
+<computeroutput>__inline__</computeroutput> to be
+<computeroutput>/* */</computeroutput>. One easy way to do this
+is to compile with the flag
+<computeroutput>-D__inline__=</computeroutput>, which should be
+understood by most Unix compilers.</para>
+
+<para>If you still have difficulties, try compiling with the
+macro <computeroutput>BZ_STRICT_ANSI</computeroutput> defined.
+This should enable you to build the library in a strictly ANSI
+compliant environment. Building the program itself like this is
+dangerous and not supported, since you remove
+<computeroutput>bzip2</computeroutput>'s checks against
+compressing directories, symbolic links, devices, and other
+not-really-a-file entities. This could cause filesystem
+corruption!</para>
+
+<para>One other thing: if you create a
+<computeroutput>bzip2</computeroutput> binary for public distribution,
+please consider linking it statically (<computeroutput>gcc
+-static</computeroutput>). This avoids all sorts of library-version
+issues that others may encounter later on.</para>
+
+<para>If you build <computeroutput>bzip2</computeroutput> on
+Win32, you must set <computeroutput>BZ_UNIX</computeroutput> to 0
+and <computeroutput>BZ_LCCWIN32</computeroutput> to 1, in the
+file <computeroutput>bzip2.c</computeroutput>, before compiling.
+Otherwise the resulting binary won't work correctly.</para>
+
+</sect1>
+
+
+<sect1 id="bugs" xreflabel="Reporting bugs">
+<title>Reporting bugs</title>
+
+<para>I tried pretty hard to make sure
+<computeroutput>bzip2</computeroutput> is bug free, both by
+design and by testing. Hopefully you'll never need to read this
+section for real.</para>
+
+<para>Nevertheless, if <computeroutput>bzip2</computeroutput> dies
+with a segmentation fault, a bus error or an internal assertion
+failure, it will ask you to email me a bug report. Experience from
+years of feedback of bzip2 users indicates that almost all these
+problems can be traced to either compiler bugs or hardware
+problems.</para>
+
+<itemizedlist mark='bullet'>
+
+ <listitem><para>Recompile the program with no optimisation, and
+ see if it works. And/or try a different compiler. I heard all
+ sorts of stories about various flavours of GNU C (and other
+ compilers) generating bad code for
+ <computeroutput>bzip2</computeroutput>, and I've run across two
+ such examples myself.</para>
+
+ <para>2.7.X versions of GNU C are known to generate bad code
+ from time to time, at high optimisation levels. If you get
+ problems, try using the flags
+ <computeroutput>-O2</computeroutput>
+ <computeroutput>-fomit-frame-pointer</computeroutput>
+ <computeroutput>-fno-strength-reduce</computeroutput>. You
+ should specifically <emphasis>not</emphasis> use
+ <computeroutput>-funroll-loops</computeroutput>.</para>
+
+ <para>You may notice that the Makefile runs six tests as part
+ of the build process. If the program passes all of these, it's
+ a pretty good (but not 100%) indication that the compiler has
+ done its job correctly.</para></listitem>
+
+ <listitem><para>If <computeroutput>bzip2</computeroutput>
+ crashes randomly, and the crashes are not repeatable, you may
+ have a flaky memory subsystem.
+ <computeroutput>bzip2</computeroutput> really hammers your
+ memory hierarchy, and if it's a bit marginal, you may get these
+ problems. Ditto if your disk or I/O subsystem is slowly
+ failing. Yup, this really does happen.</para>
+
+ <para>Try using a different machine of the same type, and see
+ if you can repeat the problem.</para></listitem>
+
+ <listitem><para>This isn't really a bug, but ... If
+ <computeroutput>bzip2</computeroutput> tells you your file is
+ corrupted on decompression, and you obtained the file via FTP,
+ there is a possibility that you forgot to tell FTP to do a
+ binary mode transfer. That absolutely will cause the file to
+ be non-decompressible. You'll have to transfer it
+ again.</para></listitem>
+
+</itemizedlist>
+
+<para>If you've incorporated
+<computeroutput>libbzip2</computeroutput> into your own program
+and are getting problems, please, please, please, check that the
+parameters you are passing in calls to the library, are correct,
+and in accordance with what the documentation says is allowable.
+I have tried to make the library robust against such problems,
+but I'm sure I haven't succeeded.</para>
+
+<para>Finally, if the above comments don't help, you'll have to
+send me a bug report. Now, it's just amazing how many people
+will send me a bug report saying something like:</para>
+
+<programlisting>
+bzip2 crashed with segmentation fault on my machine
+</programlisting>
+
+<para>and absolutely nothing else. Needless to say, a such a
+report is <emphasis>totally, utterly, completely and
+comprehensively 100% useless; a waste of your time, my time, and
+net bandwidth</emphasis>. With no details at all, there's no way
+I can possibly begin to figure out what the problem is.</para>
+
+<para>The rules of the game are: facts, facts, facts. Don't omit
+them because "oh, they won't be relevant". At the bare
+minimum:</para>
+
+<programlisting>
+Machine type. Operating system version.
+Exact version of bzip2 (do bzip2 -V).
+Exact version of the compiler used.
+Flags passed to the compiler.
+</programlisting>
+
+<para>However, the most important single thing that will help me
+is the file that you were trying to compress or decompress at the
+time the problem happened. Without that, my ability to do
+anything more than speculate about the cause, is limited.</para>
+
+</sect1>
+
+
+<sect1 id="package" xreflabel="Did you get the right package?">
+<title>Did you get the right package?</title>
+
+<para><computeroutput>bzip2</computeroutput> is a resource hog.
+It soaks up large amounts of CPU cycles and memory. Also, it
+gives very large latencies. In the worst case, you can feed many
+megabytes of uncompressed data into the library before getting
+any compressed output, so this probably rules out applications
+requiring interactive behaviour.</para>
+
+<para>These aren't faults of my implementation, I hope, but more
+an intrinsic property of the Burrows-Wheeler transform
+(unfortunately). Maybe this isn't what you want.</para>
+
+<para>If you want a compressor and/or library which is faster,
+uses less memory but gets pretty good compression, and has
+minimal latency, consider Jean-loup Gailly's and Mark Adler's
+work, <computeroutput>zlib-1.2.1</computeroutput> and
+<computeroutput>gzip-1.2.4</computeroutput>. Look for them at
+<ulink url="http://www.zlib.org">http://www.zlib.org</ulink> and
+<ulink url="http://www.gzip.org">http://www.gzip.org</ulink>
+respectively.</para>
+
+<para>For something faster and lighter still, you might try Markus F
+X J Oberhumer's <computeroutput>LZO</computeroutput> real-time
+compression/decompression library, at
+<ulink url="http://www.oberhumer.com/opensource">http://www.oberhumer.com/opensource</ulink>.</para>
+
+</sect1>
+
+
+
+<sect1 id="reading" xreflabel="Further Reading">
+<title>Further Reading</title>
+
+<para><computeroutput>bzip2</computeroutput> is not research
+work, in the sense that it doesn't present any new ideas.
+Rather, it's an engineering exercise based on existing
+ideas.</para>
+
+<para>Four documents describe essentially all the ideas behind
+<computeroutput>bzip2</computeroutput>:</para>
+
+<literallayout>Michael Burrows and D. J. Wheeler:
+ "A block-sorting lossless data compression algorithm"
+ 10th May 1994.
+ Digital SRC Research Report 124.
+ ftp://ftp.digital.com/pub/DEC/SRC/research-reports/SRC-124.ps.gz
+ If you have trouble finding it, try searching at the
+ New Zealand Digital Library, http://www.nzdl.org.
+
+Daniel S. Hirschberg and Debra A. LeLewer
+ "Efficient Decoding of Prefix Codes"
+ Communications of the ACM, April 1990, Vol 33, Number 4.
+ You might be able to get an electronic copy of this
+ from the ACM Digital Library.
+
+David J. Wheeler
+ Program bred3.c and accompanying document bred3.ps.
+ This contains the idea behind the multi-table Huffman coding scheme.
+ ftp://ftp.cl.cam.ac.uk/users/djw3/
+
+Jon L. Bentley and Robert Sedgewick
+ "Fast Algorithms for Sorting and Searching Strings"
+ Available from Sedgewick's web page,
+ www.cs.princeton.edu/~rs
+</literallayout>
+
+<para>The following paper gives valuable additional insights into
+the algorithm, but is not immediately the basis of any code used
+in bzip2.</para>
+
+<literallayout>Peter Fenwick:
+ Block Sorting Text Compression
+ Proceedings of the 19th Australasian Computer Science Conference,
+ Melbourne, Australia. Jan 31 - Feb 2, 1996.
+ ftp://ftp.cs.auckland.ac.nz/pub/peter-f/ACSC96paper.ps</literallayout>
+
+<para>Kunihiko Sadakane's sorting algorithm, mentioned above, is
+available from:</para>
+
+<literallayout>http://naomi.is.s.u-tokyo.ac.jp/~sada/papers/Sada98b.ps.gz
+</literallayout>
+
+<para>The Manber-Myers suffix array construction algorithm is
+described in a paper available from:</para>
+
+<literallayout>http://www.cs.arizona.edu/people/gene/PAPERS/suffix.ps
+</literallayout>
+
+<para>Finally, the following papers document some
+investigations I made into the performance of sorting
+and decompression algorithms:</para>
+
+<literallayout>Julian Seward
+ On the Performance of BWT Sorting Algorithms
+ Proceedings of the IEEE Data Compression Conference 2000
+ Snowbird, Utah. 28-30 March 2000.
+
+Julian Seward
+ Space-time Tradeoffs in the Inverse B-W Transform
+ Proceedings of the IEEE Data Compression Conference 2001
+ Snowbird, Utah. 27-29 March 2001.
+</literallayout>
+
+</sect1>
+
+</chapter>
+
+</book>
diff --git a/third-party/bzip2/mk251.c b/third-party/bzip2/mk251.c
new file mode 100644
index 0000000..c9c36f6
--- /dev/null
+++ b/third-party/bzip2/mk251.c
@@ -0,0 +1,31 @@
+
+/* Spew out a long sequence of the byte 251. When fed to bzip2
+ versions 1.0.0 or 1.0.1, causes it to die with internal error
+ 1007 in blocksort.c. This assertion misses an extremely rare
+ case, which is fixed in this version (1.0.2) and above.
+*/
+
+/* ------------------------------------------------------------------
+ This file is part of bzip2/libbzip2, a program and library for
+ lossless, block-sorting data compression.
+
+ bzip2/libbzip2 version 1.0.6 of 6 September 2010
+ Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
+
+ Please read the WARNING, DISCLAIMER and PATENTS sections in the
+ README file.
+
+ This program is released under the terms of the license contained
+ in the file LICENSE.
+ ------------------------------------------------------------------ */
+
+
+#include <stdio.h>
+
+int main ()
+{
+ int i;
+ for (i = 0; i < 48500000 ; i++)
+ putchar(251);
+ return 0;
+}
diff --git a/third-party/bzip2/randtable.c b/third-party/bzip2/randtable.c
new file mode 100644
index 0000000..6d62459
--- /dev/null
+++ b/third-party/bzip2/randtable.c
@@ -0,0 +1,84 @@
+
+/*-------------------------------------------------------------*/
+/*--- Table for randomising repetitive blocks ---*/
+/*--- randtable.c ---*/
+/*-------------------------------------------------------------*/
+
+/* ------------------------------------------------------------------
+ This file is part of bzip2/libbzip2, a program and library for
+ lossless, block-sorting data compression.
+
+ bzip2/libbzip2 version 1.0.6 of 6 September 2010
+ Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
+
+ Please read the WARNING, DISCLAIMER and PATENTS sections in the
+ README file.
+
+ This program is released under the terms of the license contained
+ in the file LICENSE.
+ ------------------------------------------------------------------ */
+
+
+#include "bzlib_private.h"
+
+
+/*---------------------------------------------*/
+Int32 BZ2_rNums[512] = {
+ 619, 720, 127, 481, 931, 816, 813, 233, 566, 247,
+ 985, 724, 205, 454, 863, 491, 741, 242, 949, 214,
+ 733, 859, 335, 708, 621, 574, 73, 654, 730, 472,
+ 419, 436, 278, 496, 867, 210, 399, 680, 480, 51,
+ 878, 465, 811, 169, 869, 675, 611, 697, 867, 561,
+ 862, 687, 507, 283, 482, 129, 807, 591, 733, 623,
+ 150, 238, 59, 379, 684, 877, 625, 169, 643, 105,
+ 170, 607, 520, 932, 727, 476, 693, 425, 174, 647,
+ 73, 122, 335, 530, 442, 853, 695, 249, 445, 515,
+ 909, 545, 703, 919, 874, 474, 882, 500, 594, 612,
+ 641, 801, 220, 162, 819, 984, 589, 513, 495, 799,
+ 161, 604, 958, 533, 221, 400, 386, 867, 600, 782,
+ 382, 596, 414, 171, 516, 375, 682, 485, 911, 276,
+ 98, 553, 163, 354, 666, 933, 424, 341, 533, 870,
+ 227, 730, 475, 186, 263, 647, 537, 686, 600, 224,
+ 469, 68, 770, 919, 190, 373, 294, 822, 808, 206,
+ 184, 943, 795, 384, 383, 461, 404, 758, 839, 887,
+ 715, 67, 618, 276, 204, 918, 873, 777, 604, 560,
+ 951, 160, 578, 722, 79, 804, 96, 409, 713, 940,
+ 652, 934, 970, 447, 318, 353, 859, 672, 112, 785,
+ 645, 863, 803, 350, 139, 93, 354, 99, 820, 908,
+ 609, 772, 154, 274, 580, 184, 79, 626, 630, 742,
+ 653, 282, 762, 623, 680, 81, 927, 626, 789, 125,
+ 411, 521, 938, 300, 821, 78, 343, 175, 128, 250,
+ 170, 774, 972, 275, 999, 639, 495, 78, 352, 126,
+ 857, 956, 358, 619, 580, 124, 737, 594, 701, 612,
+ 669, 112, 134, 694, 363, 992, 809, 743, 168, 974,
+ 944, 375, 748, 52, 600, 747, 642, 182, 862, 81,
+ 344, 805, 988, 739, 511, 655, 814, 334, 249, 515,
+ 897, 955, 664, 981, 649, 113, 974, 459, 893, 228,
+ 433, 837, 553, 268, 926, 240, 102, 654, 459, 51,
+ 686, 754, 806, 760, 493, 403, 415, 394, 687, 700,
+ 946, 670, 656, 610, 738, 392, 760, 799, 887, 653,
+ 978, 321, 576, 617, 626, 502, 894, 679, 243, 440,
+ 680, 879, 194, 572, 640, 724, 926, 56, 204, 700,
+ 707, 151, 457, 449, 797, 195, 791, 558, 945, 679,
+ 297, 59, 87, 824, 713, 663, 412, 693, 342, 606,
+ 134, 108, 571, 364, 631, 212, 174, 643, 304, 329,
+ 343, 97, 430, 751, 497, 314, 983, 374, 822, 928,
+ 140, 206, 73, 263, 980, 736, 876, 478, 430, 305,
+ 170, 514, 364, 692, 829, 82, 855, 953, 676, 246,
+ 369, 970, 294, 750, 807, 827, 150, 790, 288, 923,
+ 804, 378, 215, 828, 592, 281, 565, 555, 710, 82,
+ 896, 831, 547, 261, 524, 462, 293, 465, 502, 56,
+ 661, 821, 976, 991, 658, 869, 905, 758, 745, 193,
+ 768, 550, 608, 933, 378, 286, 215, 979, 792, 961,
+ 61, 688, 793, 644, 986, 403, 106, 366, 905, 644,
+ 372, 567, 466, 434, 645, 210, 389, 550, 919, 135,
+ 780, 773, 635, 389, 707, 100, 626, 958, 165, 504,
+ 920, 176, 193, 713, 857, 265, 203, 50, 668, 108,
+ 645, 990, 626, 197, 510, 357, 358, 850, 858, 364,
+ 936, 638
+};
+
+
+/*-------------------------------------------------------------*/
+/*--- end randtable.c ---*/
+/*-------------------------------------------------------------*/
diff --git a/third-party/bzip2/sample1.bz2 b/third-party/bzip2/sample1.bz2
new file mode 100644
index 0000000..18dea60
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diff --git a/third-party/bzip2/sample1.ref b/third-party/bzip2/sample1.ref
new file mode 100644
index 0000000..a56e52b
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diff --git a/third-party/bzip2/sample2.bz2 b/third-party/bzip2/sample2.bz2
new file mode 100644
index 0000000..d5a6160
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diff --git a/third-party/bzip2/sample2.ref b/third-party/bzip2/sample2.ref
new file mode 100644
index 0000000..34af958
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diff --git a/third-party/bzip2/sample3.bz2 b/third-party/bzip2/sample3.bz2
new file mode 100644
index 0000000..d90cff9
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diff --git a/third-party/bzip2/sample3.ref b/third-party/bzip2/sample3.ref
new file mode 100644
index 0000000..775a2f6
--- /dev/null
+++ b/third-party/bzip2/sample3.ref
@@ -0,0 +1,30007 @@
+This file is exceedingly boring. If you find yourself
+reading it, please (1) take it from me that you can safely
+guess what the rest of the file says, and (2) seek professional
+help.
+
+ps. there are no further sarcastic remarks in this file.
+
+ugh
+ugh
+ugh
+ugh
+ugh
+ugh
+ugh
+ugh
+ugh
+ugh
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diff --git a/third-party/bzip2/spewG.c b/third-party/bzip2/spewG.c
new file mode 100644
index 0000000..14a3649
--- /dev/null
+++ b/third-party/bzip2/spewG.c
@@ -0,0 +1,54 @@
+
+/* spew out a thoroughly gigantic file designed so that bzip2
+ can compress it reasonably rapidly. This is to help test
+ support for large files (> 2GB) in a reasonable amount of time.
+ I suggest you use the undocumented --exponential option to
+ bzip2 when compressing the resulting file; this saves a bit of
+ time. Note: *don't* bother with --exponential when compressing
+ Real Files; it'll just waste a lot of CPU time :-)
+ (but is otherwise harmless).
+*/
+
+/* ------------------------------------------------------------------
+ This file is part of bzip2/libbzip2, a program and library for
+ lossless, block-sorting data compression.
+
+ bzip2/libbzip2 version 1.0.6 of 6 September 2010
+ Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
+
+ Please read the WARNING, DISCLAIMER and PATENTS sections in the
+ README file.
+
+ This program is released under the terms of the license contained
+ in the file LICENSE.
+ ------------------------------------------------------------------ */
+
+
+#define _FILE_OFFSET_BITS 64
+
+#include <stdio.h>
+#include <stdlib.h>
+
+/* The number of megabytes of junk to spew out (roughly) */
+#define MEGABYTES 5000
+
+#define N_BUF 1000000
+char buf[N_BUF];
+
+int main ( int argc, char** argv )
+{
+ int ii, kk, p;
+ srandom(1);
+ setbuffer ( stdout, buf, N_BUF );
+ for (kk = 0; kk < MEGABYTES * 515; kk+=3) {
+ p = 25+random()%50;
+ for (ii = 0; ii < p; ii++)
+ printf ( "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa" );
+ for (ii = 0; ii < p-1; ii++)
+ printf ( "bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb" );
+ for (ii = 0; ii < p+1; ii++)
+ printf ( "ccccccccccccccccccccccccccccccccccccc" );
+ }
+ fflush(stdout);
+ return 0;
+}
diff --git a/third-party/bzip2/unzcrash.c b/third-party/bzip2/unzcrash.c
new file mode 100644
index 0000000..7041da5
--- /dev/null
+++ b/third-party/bzip2/unzcrash.c
@@ -0,0 +1,141 @@
+
+/* A test program written to test robustness to decompression of
+ corrupted data. Usage is
+ unzcrash filename
+ and the program will read the specified file, compress it (in memory),
+ and then repeatedly decompress it, each time with a different bit of
+ the compressed data inverted, so as to test all possible one-bit errors.
+ This should not cause any invalid memory accesses. If it does,
+ I want to know about it!
+
+ PS. As you can see from the above description, the process is
+ incredibly slow. A file of size eg 5KB will cause it to run for
+ many hours.
+*/
+
+/* ------------------------------------------------------------------
+ This file is part of bzip2/libbzip2, a program and library for
+ lossless, block-sorting data compression.
+
+ bzip2/libbzip2 version 1.0.6 of 6 September 2010
+ Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
+
+ Please read the WARNING, DISCLAIMER and PATENTS sections in the
+ README file.
+
+ This program is released under the terms of the license contained
+ in the file LICENSE.
+ ------------------------------------------------------------------ */
+
+
+#include <stdio.h>
+#include <assert.h>
+#include "bzlib.h"
+
+#define M_BLOCK 1000000
+
+typedef unsigned char uchar;
+
+#define M_BLOCK_OUT (M_BLOCK + 1000000)
+uchar inbuf[M_BLOCK];
+uchar outbuf[M_BLOCK_OUT];
+uchar zbuf[M_BLOCK + 600 + (M_BLOCK / 100)];
+
+int nIn, nOut, nZ;
+
+static char *bzerrorstrings[] = {
+ "OK"
+ ,"SEQUENCE_ERROR"
+ ,"PARAM_ERROR"
+ ,"MEM_ERROR"
+ ,"DATA_ERROR"
+ ,"DATA_ERROR_MAGIC"
+ ,"IO_ERROR"
+ ,"UNEXPECTED_EOF"
+ ,"OUTBUFF_FULL"
+ ,"???" /* for future */
+ ,"???" /* for future */
+ ,"???" /* for future */
+ ,"???" /* for future */
+ ,"???" /* for future */
+ ,"???" /* for future */
+};
+
+void flip_bit ( int bit )
+{
+ int byteno = bit / 8;
+ int bitno = bit % 8;
+ uchar mask = 1 << bitno;
+ //fprintf ( stderr, "(byte %d bit %d mask %d)",
+ // byteno, bitno, (int)mask );
+ zbuf[byteno] ^= mask;
+}
+
+int main ( int argc, char** argv )
+{
+ FILE* f;
+ int r;
+ int bit;
+ int i;
+
+ if (argc != 2) {
+ fprintf ( stderr, "usage: unzcrash filename\n" );
+ return 1;
+ }
+
+ f = fopen ( argv[1], "r" );
+ if (!f) {
+ fprintf ( stderr, "unzcrash: can't open %s\n", argv[1] );
+ return 1;
+ }
+
+ nIn = fread ( inbuf, 1, M_BLOCK, f );
+ fprintf ( stderr, "%d bytes read\n", nIn );
+
+ nZ = M_BLOCK;
+ r = BZ2_bzBuffToBuffCompress (
+ zbuf, &nZ, inbuf, nIn, 9, 0, 30 );
+
+ assert (r == BZ_OK);
+ fprintf ( stderr, "%d after compression\n", nZ );
+
+ for (bit = 0; bit < nZ*8; bit++) {
+ fprintf ( stderr, "bit %d ", bit );
+ flip_bit ( bit );
+ nOut = M_BLOCK_OUT;
+ r = BZ2_bzBuffToBuffDecompress (
+ outbuf, &nOut, zbuf, nZ, 0, 0 );
+ fprintf ( stderr, " %d %s ", r, bzerrorstrings[-r] );
+
+ if (r != BZ_OK) {
+ fprintf ( stderr, "\n" );
+ } else {
+ if (nOut != nIn) {
+ fprintf(stderr, "nIn/nOut mismatch %d %d\n", nIn, nOut );
+ return 1;
+ } else {
+ for (i = 0; i < nOut; i++)
+ if (inbuf[i] != outbuf[i]) {
+ fprintf(stderr, "mismatch at %d\n", i );
+ return 1;
+ }
+ if (i == nOut) fprintf(stderr, "really ok!\n" );
+ }
+ }
+
+ flip_bit ( bit );
+ }
+
+#if 0
+ assert (nOut == nIn);
+ for (i = 0; i < nOut; i++) {
+ if (inbuf[i] != outbuf[i]) {
+ fprintf ( stderr, "difference at %d !\n", i );
+ return 1;
+ }
+ }
+#endif
+
+ fprintf ( stderr, "all ok\n" );
+ return 0;
+}
diff --git a/third-party/bzip2/words0 b/third-party/bzip2/words0
new file mode 100644
index 0000000..fbf442a
--- /dev/null
+++ b/third-party/bzip2/words0
@@ -0,0 +1,9 @@
+
+If compilation produces errors, or a large number of warnings,
+please read README.COMPILATION.PROBLEMS -- you might be able to
+adjust the flags in this Makefile to improve matters.
+
+Also in README.COMPILATION.PROBLEMS are some hints that may help
+if your build produces an executable which is unable to correctly
+handle so-called 'large files' -- files of size 2GB or more.
+
diff --git a/third-party/bzip2/words1 b/third-party/bzip2/words1
new file mode 100644
index 0000000..2e83de9
--- /dev/null
+++ b/third-party/bzip2/words1
@@ -0,0 +1,4 @@
+
+Doing 6 tests (3 compress, 3 uncompress) ...
+If there's a problem, things might stop at this point.
+
diff --git a/third-party/bzip2/words2 b/third-party/bzip2/words2
new file mode 100644
index 0000000..caddcf4
--- /dev/null
+++ b/third-party/bzip2/words2
@@ -0,0 +1,5 @@
+
+Checking test results. If any of the four "cmp"s which follow
+report any differences, something is wrong. If you can't easily
+figure out what, please let me know (jseward at bzip.org).
+
diff --git a/third-party/bzip2/words3 b/third-party/bzip2/words3
new file mode 100644
index 0000000..6972669
--- /dev/null
+++ b/third-party/bzip2/words3
@@ -0,0 +1,30 @@
+
+If you got this far and the 'cmp's didn't complain, it looks
+like you're in business.
+
+To install in /usr/local/bin, /usr/local/lib, /usr/local/man and
+/usr/local/include, type
+
+ make install
+
+To install somewhere else, eg, /xxx/yyy/{bin,lib,man,include}, type
+
+ make install PREFIX=/xxx/yyy
+
+If you are (justifiably) paranoid and want to see what 'make install'
+is going to do, you can first do
+
+ make -n install or
+ make -n install PREFIX=/xxx/yyy respectively.
+
+The -n instructs make to show the commands it would execute, but
+not actually execute them.
+
+Instructions for use are in the preformatted manual page, in the file
+bzip2.txt. For more detailed documentation, read the full manual.
+It is available in Postscript form (manual.ps), PDF form (manual.pdf),
+and HTML form (manual.html).
+
+You can also do "bzip2 --help" to see some helpful information.
+"bzip2 -L" displays the software license.
+
diff --git a/third-party/bzip2/xmlproc.sh b/third-party/bzip2/xmlproc.sh
new file mode 100755
index 0000000..ca284ea
--- /dev/null
+++ b/third-party/bzip2/xmlproc.sh
@@ -0,0 +1,114 @@
+#!/bin/bash
+# see the README file for usage etc.
+#
+# ------------------------------------------------------------------
+# This file is part of bzip2/libbzip2, a program and library for
+# lossless, block-sorting data compression.
+#
+# bzip2/libbzip2 version 1.0.6 of 6 September 2010
+# Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
+#
+# Please read the WARNING, DISCLAIMER and PATENTS sections in the
+# README file.
+#
+# This program is released under the terms of the license contained
+# in the file LICENSE.
+# ----------------------------------------------------------------
+
+
+usage() {
+ echo '';
+ echo 'Usage: xmlproc.sh -[option] <filename.xml>';
+ echo 'Specify a target from:';
+ echo '-v verify xml file conforms to dtd';
+ echo '-html output in html format (single file)';
+ echo '-ps output in postscript format';
+ echo '-pdf output in pdf format';
+ exit;
+}
+
+if test $# -ne 2; then
+ usage
+fi
+# assign the variable for the output type
+action=$1; shift
+# assign the output filename
+xmlfile=$1; shift
+# and check user input it correct
+if !(test -f $xmlfile); then
+ echo "No such file: $xmlfile";
+ exit;
+fi
+# some other stuff we will use
+OUT=output
+xsl_fo=bz-fo.xsl
+xsl_html=bz-html.xsl
+
+basename=$xmlfile
+basename=${basename//'.xml'/''}
+
+fofile="${basename}.fo"
+htmlfile="${basename}.html"
+pdffile="${basename}.pdf"
+psfile="${basename}.ps"
+xmlfmtfile="${basename}.fmt"
+
+# first process the xmlfile with CDATA tags
+./format.pl $xmlfile $xmlfmtfile
+# so the shell knows where the catalogs live
+export XML_CATALOG_FILES=/etc/xml/catalog
+
+# post-processing tidy up
+cleanup() {
+ echo "Cleaning up: $@"
+ while [ $# != 0 ]
+ do
+ arg=$1; shift;
+ echo " deleting $arg";
+ rm $arg
+ done
+}
+
+case $action in
+ -v)
+ flags='--noout --xinclude --noblanks --postvalid'
+ dtd='--dtdvalid http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd'
+ xmllint $flags $dtd $xmlfmtfile 2> $OUT
+ egrep 'error' $OUT
+ rm $OUT
+ ;;
+
+ -html)
+ echo "Creating $htmlfile ..."
+ xsltproc --nonet --xinclude -o $htmlfile $xsl_html $xmlfmtfile
+ cleanup $xmlfmtfile
+ ;;
+
+ -pdf)
+ echo "Creating $pdffile ..."
+ xsltproc --nonet --xinclude -o $fofile $xsl_fo $xmlfmtfile
+ pdfxmltex $fofile >$OUT </dev/null
+ pdfxmltex $fofile >$OUT </dev/null
+ pdfxmltex $fofile >$OUT </dev/null
+ cleanup $OUT $xmlfmtfile *.aux *.fo *.log *.out
+ ;;
+
+ -ps)
+ echo "Creating $psfile ..."
+ xsltproc --nonet --xinclude -o $fofile $xsl_fo $xmlfmtfile
+ pdfxmltex $fofile >$OUT </dev/null
+ pdfxmltex $fofile >$OUT </dev/null
+ pdfxmltex $fofile >$OUT </dev/null
+ pdftops $pdffile $psfile
+ cleanup $OUT $xmlfmtfile $pdffile *.aux *.fo *.log *.out
+# passivetex is broken, so we can't go this route yet.
+# xmltex $fofile >$OUT </dev/null
+# xmltex $fofile >$OUT </dev/null
+# xmltex $fofile >$OUT </dev/null
+# dvips -R -q -o bzip-manual.ps *.dvi
+ ;;
+
+ *)
+ usage
+ ;;
+esac
diff --git a/third-party/seqan/ChangeLog b/third-party/seqan/ChangeLog
index 7322d49..f161dda 100644
--- a/third-party/seqan/ChangeLog
+++ b/third-party/seqan/ChangeLog
@@ -1,3 +1,8 @@
+2015-08-14 Michael R. Crusoe <crusoe at ucdavis.edu>
+
+ * third-party/seqan/core/include/seqan/basic/debug_test_system.h: disable
+ unfullifable #include
+
2014-12-02 Michael R. Crusoe <mcrusoe at msu.edu>
* core/include/seqan/seq_io/sequence_stream_impl.h: don't memory map plain
diff --git a/third-party/seqan/core/include/seqan/basic/debug_test_system.h b/third-party/seqan/core/include/seqan/basic/debug_test_system.h
index b6b8bc7..ae9e7ac 100644
--- a/third-party/seqan/core/include/seqan/basic/debug_test_system.h
+++ b/third-party/seqan/core/include/seqan/basic/debug_test_system.h
@@ -233,7 +233,7 @@ bool foo(MyEnum x) {
// Any SeqAn headers or headers including SeqAn headers have to come AFTER the
// definition of SEQAN_ENABLE_CHECKPOINT above.
-#include <seqan/base.h>
+// #include <seqan/base.h>
int main(int argc, char const ** argv)
{
diff --git a/third-party/zlib/.gitignore b/third-party/zlib/.gitignore
new file mode 100644
index 0000000..676d6e2
--- /dev/null
+++ b/third-party/zlib/.gitignore
@@ -0,0 +1,5 @@
+libz.so.*
+libz.*dylib
+libz.a
+Makefile
+zconf.h
diff --git a/third-party/zlib/CMakeLists.txt b/third-party/zlib/CMakeLists.txt
new file mode 100644
index 0000000..0c0247c
--- /dev/null
+++ b/third-party/zlib/CMakeLists.txt
@@ -0,0 +1,249 @@
+cmake_minimum_required(VERSION 2.4.4)
+set(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS ON)
+
+project(zlib C)
+
+set(VERSION "1.2.8")
+
+option(ASM686 "Enable building i686 assembly implementation")
+option(AMD64 "Enable building amd64 assembly implementation")
+
+set(INSTALL_BIN_DIR "${CMAKE_INSTALL_PREFIX}/bin" CACHE PATH "Installation directory for executables")
+set(INSTALL_LIB_DIR "${CMAKE_INSTALL_PREFIX}/lib" CACHE PATH "Installation directory for libraries")
+set(INSTALL_INC_DIR "${CMAKE_INSTALL_PREFIX}/include" CACHE PATH "Installation directory for headers")
+set(INSTALL_MAN_DIR "${CMAKE_INSTALL_PREFIX}/share/man" CACHE PATH "Installation directory for manual pages")
+set(INSTALL_PKGCONFIG_DIR "${CMAKE_INSTALL_PREFIX}/share/pkgconfig" CACHE PATH "Installation directory for pkgconfig (.pc) files")
+
+include(CheckTypeSize)
+include(CheckFunctionExists)
+include(CheckIncludeFile)
+include(CheckCSourceCompiles)
+enable_testing()
+
+check_include_file(sys/types.h HAVE_SYS_TYPES_H)
+check_include_file(stdint.h HAVE_STDINT_H)
+check_include_file(stddef.h HAVE_STDDEF_H)
+
+#
+# Check to see if we have large file support
+#
+set(CMAKE_REQUIRED_DEFINITIONS -D_LARGEFILE64_SOURCE=1)
+# We add these other definitions here because CheckTypeSize.cmake
+# in CMake 2.4.x does not automatically do so and we want
+# compatibility with CMake 2.4.x.
+if(HAVE_SYS_TYPES_H)
+ list(APPEND CMAKE_REQUIRED_DEFINITIONS -DHAVE_SYS_TYPES_H)
+endif()
+if(HAVE_STDINT_H)
+ list(APPEND CMAKE_REQUIRED_DEFINITIONS -DHAVE_STDINT_H)
+endif()
+if(HAVE_STDDEF_H)
+ list(APPEND CMAKE_REQUIRED_DEFINITIONS -DHAVE_STDDEF_H)
+endif()
+check_type_size(off64_t OFF64_T)
+if(HAVE_OFF64_T)
+ add_definitions(-D_LARGEFILE64_SOURCE=1)
+endif()
+set(CMAKE_REQUIRED_DEFINITIONS) # clear variable
+
+#
+# Check for fseeko
+#
+check_function_exists(fseeko HAVE_FSEEKO)
+if(NOT HAVE_FSEEKO)
+ add_definitions(-DNO_FSEEKO)
+endif()
+
+#
+# Check for unistd.h
+#
+check_include_file(unistd.h Z_HAVE_UNISTD_H)
+
+if(MSVC)
+ set(CMAKE_DEBUG_POSTFIX "d")
+ add_definitions(-D_CRT_SECURE_NO_DEPRECATE)
+ add_definitions(-D_CRT_NONSTDC_NO_DEPRECATE)
+ include_directories(${CMAKE_CURRENT_SOURCE_DIR})
+endif()
+
+if(NOT CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_CURRENT_BINARY_DIR)
+ # If we're doing an out of source build and the user has a zconf.h
+ # in their source tree...
+ if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h)
+ message(STATUS "Renaming")
+ message(STATUS " ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h")
+ message(STATUS "to 'zconf.h.included' because this file is included with zlib")
+ message(STATUS "but CMake generates it automatically in the build directory.")
+ file(RENAME ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h.included)
+ endif()
+endif()
+
+set(ZLIB_PC ${CMAKE_CURRENT_BINARY_DIR}/zlib.pc)
+configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/zlib.pc.cmakein
+ ${ZLIB_PC} @ONLY)
+configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h.cmakein
+ ${CMAKE_CURRENT_BINARY_DIR}/zconf.h @ONLY)
+include_directories(${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_SOURCE_DIR})
+
+
+#============================================================================
+# zlib
+#============================================================================
+
+set(ZLIB_PUBLIC_HDRS
+ ${CMAKE_CURRENT_BINARY_DIR}/zconf.h
+ zlib.h
+)
+set(ZLIB_PRIVATE_HDRS
+ crc32.h
+ deflate.h
+ gzguts.h
+ inffast.h
+ inffixed.h
+ inflate.h
+ inftrees.h
+ trees.h
+ zutil.h
+)
+set(ZLIB_SRCS
+ adler32.c
+ compress.c
+ crc32.c
+ deflate.c
+ gzclose.c
+ gzlib.c
+ gzread.c
+ gzwrite.c
+ inflate.c
+ infback.c
+ inftrees.c
+ inffast.c
+ trees.c
+ uncompr.c
+ zutil.c
+)
+
+if(NOT MINGW)
+ set(ZLIB_DLL_SRCS
+ win32/zlib1.rc # If present will override custom build rule below.
+ )
+endif()
+
+if(CMAKE_COMPILER_IS_GNUCC)
+ if(ASM686)
+ set(ZLIB_ASMS contrib/asm686/match.S)
+ elseif (AMD64)
+ set(ZLIB_ASMS contrib/amd64/amd64-match.S)
+ endif ()
+
+ if(ZLIB_ASMS)
+ add_definitions(-DASMV)
+ set_source_files_properties(${ZLIB_ASMS} PROPERTIES LANGUAGE C COMPILE_FLAGS -DNO_UNDERLINE)
+ endif()
+endif()
+
+if(MSVC)
+ if(ASM686)
+ ENABLE_LANGUAGE(ASM_MASM)
+ set(ZLIB_ASMS
+ contrib/masmx86/inffas32.asm
+ contrib/masmx86/match686.asm
+ )
+ elseif (AMD64)
+ ENABLE_LANGUAGE(ASM_MASM)
+ set(ZLIB_ASMS
+ contrib/masmx64/gvmat64.asm
+ contrib/masmx64/inffasx64.asm
+ )
+ endif()
+
+ if(ZLIB_ASMS)
+ add_definitions(-DASMV -DASMINF)
+ endif()
+endif()
+
+# parse the full version number from zlib.h and include in ZLIB_FULL_VERSION
+file(READ ${CMAKE_CURRENT_SOURCE_DIR}/zlib.h _zlib_h_contents)
+string(REGEX REPLACE ".*#define[ \t]+ZLIB_VERSION[ \t]+\"([-0-9A-Za-z.]+)\".*"
+ "\\1" ZLIB_FULL_VERSION ${_zlib_h_contents})
+
+if(MINGW)
+ # This gets us DLL resource information when compiling on MinGW.
+ if(NOT CMAKE_RC_COMPILER)
+ set(CMAKE_RC_COMPILER windres.exe)
+ endif()
+
+ add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/zlib1rc.obj
+ COMMAND ${CMAKE_RC_COMPILER}
+ -D GCC_WINDRES
+ -I ${CMAKE_CURRENT_SOURCE_DIR}
+ -I ${CMAKE_CURRENT_BINARY_DIR}
+ -o ${CMAKE_CURRENT_BINARY_DIR}/zlib1rc.obj
+ -i ${CMAKE_CURRENT_SOURCE_DIR}/win32/zlib1.rc)
+ set(ZLIB_DLL_SRCS ${CMAKE_CURRENT_BINARY_DIR}/zlib1rc.obj)
+endif(MINGW)
+
+add_library(zlib SHARED ${ZLIB_SRCS} ${ZLIB_ASMS} ${ZLIB_DLL_SRCS} ${ZLIB_PUBLIC_HDRS} ${ZLIB_PRIVATE_HDRS})
+add_library(zlibstatic STATIC ${ZLIB_SRCS} ${ZLIB_ASMS} ${ZLIB_PUBLIC_HDRS} ${ZLIB_PRIVATE_HDRS})
+set_target_properties(zlib PROPERTIES DEFINE_SYMBOL ZLIB_DLL)
+set_target_properties(zlib PROPERTIES SOVERSION 1)
+
+if(NOT CYGWIN)
+ # This property causes shared libraries on Linux to have the full version
+ # encoded into their final filename. We disable this on Cygwin because
+ # it causes cygz-${ZLIB_FULL_VERSION}.dll to be created when cygz.dll
+ # seems to be the default.
+ #
+ # This has no effect with MSVC, on that platform the version info for
+ # the DLL comes from the resource file win32/zlib1.rc
+ set_target_properties(zlib PROPERTIES VERSION ${ZLIB_FULL_VERSION})
+endif()
+
+if(UNIX)
+ # On unix-like platforms the library is almost always called libz
+ set_target_properties(zlib zlibstatic PROPERTIES OUTPUT_NAME z)
+ if(NOT APPLE)
+ set_target_properties(zlib PROPERTIES LINK_FLAGS "-Wl,--version-script,\"${CMAKE_CURRENT_SOURCE_DIR}/zlib.map\"")
+ endif()
+elseif(BUILD_SHARED_LIBS AND WIN32)
+ # Creates zlib1.dll when building shared library version
+ set_target_properties(zlib PROPERTIES SUFFIX "1.dll")
+endif()
+
+if(NOT SKIP_INSTALL_LIBRARIES AND NOT SKIP_INSTALL_ALL )
+ install(TARGETS zlib zlibstatic
+ RUNTIME DESTINATION "${INSTALL_BIN_DIR}"
+ ARCHIVE DESTINATION "${INSTALL_LIB_DIR}"
+ LIBRARY DESTINATION "${INSTALL_LIB_DIR}" )
+endif()
+if(NOT SKIP_INSTALL_HEADERS AND NOT SKIP_INSTALL_ALL )
+ install(FILES ${ZLIB_PUBLIC_HDRS} DESTINATION "${INSTALL_INC_DIR}")
+endif()
+if(NOT SKIP_INSTALL_FILES AND NOT SKIP_INSTALL_ALL )
+ install(FILES zlib.3 DESTINATION "${INSTALL_MAN_DIR}/man3")
+endif()
+if(NOT SKIP_INSTALL_FILES AND NOT SKIP_INSTALL_ALL )
+ install(FILES ${ZLIB_PC} DESTINATION "${INSTALL_PKGCONFIG_DIR}")
+endif()
+
+#============================================================================
+# Example binaries
+#============================================================================
+
+add_executable(example test/example.c)
+target_link_libraries(example zlib)
+add_test(example example)
+
+add_executable(minigzip test/minigzip.c)
+target_link_libraries(minigzip zlib)
+
+if(HAVE_OFF64_T)
+ add_executable(example64 test/example.c)
+ target_link_libraries(example64 zlib)
+ set_target_properties(example64 PROPERTIES COMPILE_FLAGS "-D_FILE_OFFSET_BITS=64")
+ add_test(example64 example64)
+
+ add_executable(minigzip64 test/minigzip.c)
+ target_link_libraries(minigzip64 zlib)
+ set_target_properties(minigzip64 PROPERTIES COMPILE_FLAGS "-D_FILE_OFFSET_BITS=64")
+endif()
diff --git a/third-party/zlib/ChangeLog b/third-party/zlib/ChangeLog
new file mode 100644
index 0000000..f22aaba
--- /dev/null
+++ b/third-party/zlib/ChangeLog
@@ -0,0 +1,1472 @@
+
+ ChangeLog file for zlib
+
+Changes in 1.2.8 (28 Apr 2013)
+- Update contrib/minizip/iowin32.c for Windows RT [Vollant]
+- Do not force Z_CONST for C++
+- Clean up contrib/vstudio [Ro�]
+- Correct spelling error in zlib.h
+- Fix mixed line endings in contrib/vstudio
+
+Changes in 1.2.7.3 (13 Apr 2013)
+- Fix version numbers and DLL names in contrib/vstudio/*/zlib.rc
+
+Changes in 1.2.7.2 (13 Apr 2013)
+- Change check for a four-byte type back to hexadecimal
+- Fix typo in win32/Makefile.msc
+- Add casts in gzwrite.c for pointer differences
+
+Changes in 1.2.7.1 (24 Mar 2013)
+- Replace use of unsafe string functions with snprintf if available
+- Avoid including stddef.h on Windows for Z_SOLO compile [Niessink]
+- Fix gzgetc undefine when Z_PREFIX set [Turk]
+- Eliminate use of mktemp in Makefile (not always available)
+- Fix bug in 'F' mode for gzopen()
+- Add inflateGetDictionary() function
+- Correct comment in deflate.h
+- Use _snprintf for snprintf in Microsoft C
+- On Darwin, only use /usr/bin/libtool if libtool is not Apple
+- Delete "--version" file if created by "ar --version" [Richard G.]
+- Fix configure check for veracity of compiler error return codes
+- Fix CMake compilation of static lib for MSVC2010 x64
+- Remove unused variable in infback9.c
+- Fix argument checks in gzlog_compress() and gzlog_write()
+- Clean up the usage of z_const and respect const usage within zlib
+- Clean up examples/gzlog.[ch] comparisons of different types
+- Avoid shift equal to bits in type (caused endless loop)
+- Fix unintialized value bug in gzputc() introduced by const patches
+- Fix memory allocation error in examples/zran.c [Nor]
+- Fix bug where gzopen(), gzclose() would write an empty file
+- Fix bug in gzclose() when gzwrite() runs out of memory
+- Check for input buffer malloc failure in examples/gzappend.c
+- Add note to contrib/blast to use binary mode in stdio
+- Fix comparisons of differently signed integers in contrib/blast
+- Check for invalid code length codes in contrib/puff
+- Fix serious but very rare decompression bug in inftrees.c
+- Update inflateBack() comments, since inflate() can be faster
+- Use underscored I/O function names for WINAPI_FAMILY
+- Add _tr_flush_bits to the external symbols prefixed by --zprefix
+- Add contrib/vstudio/vc10 pre-build step for static only
+- Quote --version-script argument in CMakeLists.txt
+- Don't specify --version-script on Apple platforms in CMakeLists.txt
+- Fix casting error in contrib/testzlib/testzlib.c
+- Fix types in contrib/minizip to match result of get_crc_table()
+- Simplify contrib/vstudio/vc10 with 'd' suffix
+- Add TOP support to win32/Makefile.msc
+- Suport i686 and amd64 assembler builds in CMakeLists.txt
+- Fix typos in the use of _LARGEFILE64_SOURCE in zconf.h
+- Add vc11 and vc12 build files to contrib/vstudio
+- Add gzvprintf() as an undocumented function in zlib
+- Fix configure for Sun shell
+- Remove runtime check in configure for four-byte integer type
+- Add casts and consts to ease user conversion to C++
+- Add man pages for minizip and miniunzip
+- In Makefile uninstall, don't rm if preceding cd fails
+- Do not return Z_BUF_ERROR if deflateParam() has nothing to write
+
+Changes in 1.2.7 (2 May 2012)
+- Replace use of memmove() with a simple copy for portability
+- Test for existence of strerror
+- Restore gzgetc_ for backward compatibility with 1.2.6
+- Fix build with non-GNU make on Solaris
+- Require gcc 4.0 or later on Mac OS X to use the hidden attribute
+- Include unistd.h for Watcom C
+- Use __WATCOMC__ instead of __WATCOM__
+- Do not use the visibility attribute if NO_VIZ defined
+- Improve the detection of no hidden visibility attribute
+- Avoid using __int64 for gcc or solo compilation
+- Cast to char * in gzprintf to avoid warnings [Zinser]
+- Fix make_vms.com for VAX [Zinser]
+- Don't use library or built-in byte swaps
+- Simplify test and use of gcc hidden attribute
+- Fix bug in gzclose_w() when gzwrite() fails to allocate memory
+- Add "x" (O_EXCL) and "e" (O_CLOEXEC) modes support to gzopen()
+- Fix bug in test/minigzip.c for configure --solo
+- Fix contrib/vstudio project link errors [Mohanathas]
+- Add ability to choose the builder in make_vms.com [Schweda]
+- Add DESTDIR support to mingw32 win32/Makefile.gcc
+- Fix comments in win32/Makefile.gcc for proper usage
+- Allow overriding the default install locations for cmake
+- Generate and install the pkg-config file with cmake
+- Build both a static and a shared version of zlib with cmake
+- Include version symbols for cmake builds
+- If using cmake with MSVC, add the source directory to the includes
+- Remove unneeded EXTRA_CFLAGS from win32/Makefile.gcc [Truta]
+- Move obsolete emx makefile to old [Truta]
+- Allow the use of -Wundef when compiling or using zlib
+- Avoid the use of the -u option with mktemp
+- Improve inflate() documentation on the use of Z_FINISH
+- Recognize clang as gcc
+- Add gzopen_w() in Windows for wide character path names
+- Rename zconf.h in CMakeLists.txt to move it out of the way
+- Add source directory in CMakeLists.txt for building examples
+- Look in build directory for zlib.pc in CMakeLists.txt
+- Remove gzflags from zlibvc.def in vc9 and vc10
+- Fix contrib/minizip compilation in the MinGW environment
+- Update ./configure for Solaris, support --64 [Mooney]
+- Remove -R. from Solaris shared build (possible security issue)
+- Avoid race condition for parallel make (-j) running example
+- Fix type mismatch between get_crc_table() and crc_table
+- Fix parsing of version with "-" in CMakeLists.txt [Snider, Ziegler]
+- Fix the path to zlib.map in CMakeLists.txt
+- Force the native libtool in Mac OS X to avoid GNU libtool [Beebe]
+- Add instructions to win32/Makefile.gcc for shared install [Torri]
+
+Changes in 1.2.6.1 (12 Feb 2012)
+- Avoid the use of the Objective-C reserved name "id"
+- Include io.h in gzguts.h for Microsoft compilers
+- Fix problem with ./configure --prefix and gzgetc macro
+- Include gz_header definition when compiling zlib solo
+- Put gzflags() functionality back in zutil.c
+- Avoid library header include in crc32.c for Z_SOLO
+- Use name in GCC_CLASSIC as C compiler for coverage testing, if set
+- Minor cleanup in contrib/minizip/zip.c [Vollant]
+- Update make_vms.com [Zinser]
+- Remove unnecessary gzgetc_ function
+- Use optimized byte swap operations for Microsoft and GNU [Snyder]
+- Fix minor typo in zlib.h comments [Rzesniowiecki]
+
+Changes in 1.2.6 (29 Jan 2012)
+- Update the Pascal interface in contrib/pascal
+- Fix function numbers for gzgetc_ in zlibvc.def files
+- Fix configure.ac for contrib/minizip [Schiffer]
+- Fix large-entry detection in minizip on 64-bit systems [Schiffer]
+- Have ./configure use the compiler return code for error indication
+- Fix CMakeLists.txt for cross compilation [McClure]
+- Fix contrib/minizip/zip.c for 64-bit architectures [Dalsnes]
+- Fix compilation of contrib/minizip on FreeBSD [Marquez]
+- Correct suggested usages in win32/Makefile.msc [Shachar, Horvath]
+- Include io.h for Turbo C / Borland C on all platforms [Truta]
+- Make version explicit in contrib/minizip/configure.ac [Bosmans]
+- Avoid warning for no encryption in contrib/minizip/zip.c [Vollant]
+- Minor cleanup up contrib/minizip/unzip.c [Vollant]
+- Fix bug when compiling minizip with C++ [Vollant]
+- Protect for long name and extra fields in contrib/minizip [Vollant]
+- Avoid some warnings in contrib/minizip [Vollant]
+- Add -I../.. -L../.. to CFLAGS for minizip and miniunzip
+- Add missing libs to minizip linker command
+- Add support for VPATH builds in contrib/minizip
+- Add an --enable-demos option to contrib/minizip/configure
+- Add the generation of configure.log by ./configure
+- Exit when required parameters not provided to win32/Makefile.gcc
+- Have gzputc return the character written instead of the argument
+- Use the -m option on ldconfig for BSD systems [Tobias]
+- Correct in zlib.map when deflateResetKeep was added
+
+Changes in 1.2.5.3 (15 Jan 2012)
+- Restore gzgetc function for binary compatibility
+- Do not use _lseeki64 under Borland C++ [Truta]
+- Update win32/Makefile.msc to build test/*.c [Truta]
+- Remove old/visualc6 given CMakefile and other alternatives
+- Update AS400 build files and documentation [Monnerat]
+- Update win32/Makefile.gcc to build test/*.c [Truta]
+- Permit stronger flushes after Z_BLOCK flushes
+- Avoid extraneous empty blocks when doing empty flushes
+- Permit Z_NULL arguments to deflatePending
+- Allow deflatePrime() to insert bits in the middle of a stream
+- Remove second empty static block for Z_PARTIAL_FLUSH
+- Write out all of the available bits when using Z_BLOCK
+- Insert the first two strings in the hash table after a flush
+
+Changes in 1.2.5.2 (17 Dec 2011)
+- fix ld error: unable to find version dependency 'ZLIB_1.2.5'
+- use relative symlinks for shared libs
+- Avoid searching past window for Z_RLE strategy
+- Assure that high-water mark initialization is always applied in deflate
+- Add assertions to fill_window() in deflate.c to match comments
+- Update python link in README
+- Correct spelling error in gzread.c
+- Fix bug in gzgets() for a concatenated empty gzip stream
+- Correct error in comment for gz_make()
+- Change gzread() and related to ignore junk after gzip streams
+- Allow gzread() and related to continue after gzclearerr()
+- Allow gzrewind() and gzseek() after a premature end-of-file
+- Simplify gzseek() now that raw after gzip is ignored
+- Change gzgetc() to a macro for speed (~40% speedup in testing)
+- Fix gzclose() to return the actual error last encountered
+- Always add large file support for windows
+- Include zconf.h for windows large file support
+- Include zconf.h.cmakein for windows large file support
+- Update zconf.h.cmakein on make distclean
+- Merge vestigial vsnprintf determination from zutil.h to gzguts.h
+- Clarify how gzopen() appends in zlib.h comments
+- Correct documentation of gzdirect() since junk at end now ignored
+- Add a transparent write mode to gzopen() when 'T' is in the mode
+- Update python link in zlib man page
+- Get inffixed.h and MAKEFIXED result to match
+- Add a ./config --solo option to make zlib subset with no libary use
+- Add undocumented inflateResetKeep() function for CAB file decoding
+- Add --cover option to ./configure for gcc coverage testing
+- Add #define ZLIB_CONST option to use const in the z_stream interface
+- Add comment to gzdopen() in zlib.h to use dup() when using fileno()
+- Note behavior of uncompress() to provide as much data as it can
+- Add files in contrib/minizip to aid in building libminizip
+- Split off AR options in Makefile.in and configure
+- Change ON macro to Z_ARG to avoid application conflicts
+- Facilitate compilation with Borland C++ for pragmas and vsnprintf
+- Include io.h for Turbo C / Borland C++
+- Move example.c and minigzip.c to test/
+- Simplify incomplete code table filling in inflate_table()
+- Remove code from inflate.c and infback.c that is impossible to execute
+- Test the inflate code with full coverage
+- Allow deflateSetDictionary, inflateSetDictionary at any time (in raw)
+- Add deflateResetKeep and fix inflateResetKeep to retain dictionary
+- Fix gzwrite.c to accommodate reduced memory zlib compilation
+- Have inflate() with Z_FINISH avoid the allocation of a window
+- Do not set strm->adler when doing raw inflate
+- Fix gzeof() to behave just like feof() when read is not past end of file
+- Fix bug in gzread.c when end-of-file is reached
+- Avoid use of Z_BUF_ERROR in gz* functions except for premature EOF
+- Document gzread() capability to read concurrently written files
+- Remove hard-coding of resource compiler in CMakeLists.txt [Blammo]
+
+Changes in 1.2.5.1 (10 Sep 2011)
+- Update FAQ entry on shared builds (#13)
+- Avoid symbolic argument to chmod in Makefile.in
+- Fix bug and add consts in contrib/puff [Oberhumer]
+- Update contrib/puff/zeros.raw test file to have all block types
+- Add full coverage test for puff in contrib/puff/Makefile
+- Fix static-only-build install in Makefile.in
+- Fix bug in unzGetCurrentFileInfo() in contrib/minizip [Kuno]
+- Add libz.a dependency to shared in Makefile.in for parallel builds
+- Spell out "number" (instead of "nb") in zlib.h for total_in, total_out
+- Replace $(...) with `...` in configure for non-bash sh [Bowler]
+- Add darwin* to Darwin* and solaris* to SunOS\ 5* in configure [Groffen]
+- Add solaris* to Linux* in configure to allow gcc use [Groffen]
+- Add *bsd* to Linux* case in configure [Bar-Lev]
+- Add inffast.obj to dependencies in win32/Makefile.msc
+- Correct spelling error in deflate.h [Kohler]
+- Change libzdll.a again to libz.dll.a (!) in win32/Makefile.gcc
+- Add test to configure for GNU C looking for gcc in output of $cc -v
+- Add zlib.pc generation to win32/Makefile.gcc [Weigelt]
+- Fix bug in zlib.h for _FILE_OFFSET_BITS set and _LARGEFILE64_SOURCE not
+- Add comment in zlib.h that adler32_combine with len2 < 0 makes no sense
+- Make NO_DIVIDE option in adler32.c much faster (thanks to John Reiser)
+- Make stronger test in zconf.h to include unistd.h for LFS
+- Apply Darwin patches for 64-bit file offsets to contrib/minizip [Slack]
+- Fix zlib.h LFS support when Z_PREFIX used
+- Add updated as400 support (removed from old) [Monnerat]
+- Avoid deflate sensitivity to volatile input data
+- Avoid division in adler32_combine for NO_DIVIDE
+- Clarify the use of Z_FINISH with deflateBound() amount of space
+- Set binary for output file in puff.c
+- Use u4 type for crc_table to avoid conversion warnings
+- Apply casts in zlib.h to avoid conversion warnings
+- Add OF to prototypes for adler32_combine_ and crc32_combine_ [Miller]
+- Improve inflateSync() documentation to note indeterminancy
+- Add deflatePending() function to return the amount of pending output
+- Correct the spelling of "specification" in FAQ [Randers-Pehrson]
+- Add a check in configure for stdarg.h, use for gzprintf()
+- Check that pointers fit in ints when gzprint() compiled old style
+- Add dummy name before $(SHAREDLIBV) in Makefile [Bar-Lev, Bowler]
+- Delete line in configure that adds -L. libz.a to LDFLAGS [Weigelt]
+- Add debug records in assmebler code [Londer]
+- Update RFC references to use http://tools.ietf.org/html/... [Li]
+- Add --archs option, use of libtool to configure for Mac OS X [Borstel]
+
+Changes in 1.2.5 (19 Apr 2010)
+- Disable visibility attribute in win32/Makefile.gcc [Bar-Lev]
+- Default to libdir as sharedlibdir in configure [Nieder]
+- Update copyright dates on modified source files
+- Update trees.c to be able to generate modified trees.h
+- Exit configure for MinGW, suggesting win32/Makefile.gcc
+- Check for NULL path in gz_open [Homurlu]
+
+Changes in 1.2.4.5 (18 Apr 2010)
+- Set sharedlibdir in configure [Torok]
+- Set LDFLAGS in Makefile.in [Bar-Lev]
+- Avoid mkdir objs race condition in Makefile.in [Bowler]
+- Add ZLIB_INTERNAL in front of internal inter-module functions and arrays
+- Define ZLIB_INTERNAL to hide internal functions and arrays for GNU C
+- Don't use hidden attribute when it is a warning generator (e.g. Solaris)
+
+Changes in 1.2.4.4 (18 Apr 2010)
+- Fix CROSS_PREFIX executable testing, CHOST extract, mingw* [Torok]
+- Undefine _LARGEFILE64_SOURCE in zconf.h if it is zero, but not if empty
+- Try to use bash or ksh regardless of functionality of /bin/sh
+- Fix configure incompatibility with NetBSD sh
+- Remove attempt to run under bash or ksh since have better NetBSD fix
+- Fix win32/Makefile.gcc for MinGW [Bar-Lev]
+- Add diagnostic messages when using CROSS_PREFIX in configure
+- Added --sharedlibdir option to configure [Weigelt]
+- Use hidden visibility attribute when available [Frysinger]
+
+Changes in 1.2.4.3 (10 Apr 2010)
+- Only use CROSS_PREFIX in configure for ar and ranlib if they exist
+- Use CROSS_PREFIX for nm [Bar-Lev]
+- Assume _LARGEFILE64_SOURCE defined is equivalent to true
+- Avoid use of undefined symbols in #if with && and ||
+- Make *64 prototypes in gzguts.h consistent with functions
+- Add -shared load option for MinGW in configure [Bowler]
+- Move z_off64_t to public interface, use instead of off64_t
+- Remove ! from shell test in configure (not portable to Solaris)
+- Change +0 macro tests to -0 for possibly increased portability
+
+Changes in 1.2.4.2 (9 Apr 2010)
+- Add consistent carriage returns to readme.txt's in masmx86 and masmx64
+- Really provide prototypes for *64 functions when building without LFS
+- Only define unlink() in minigzip.c if unistd.h not included
+- Update README to point to contrib/vstudio project files
+- Move projects/vc6 to old/ and remove projects/
+- Include stdlib.h in minigzip.c for setmode() definition under WinCE
+- Clean up assembler builds in win32/Makefile.msc [Rowe]
+- Include sys/types.h for Microsoft for off_t definition
+- Fix memory leak on error in gz_open()
+- Symbolize nm as $NM in configure [Weigelt]
+- Use TEST_LDSHARED instead of LDSHARED to link test programs [Weigelt]
+- Add +0 to _FILE_OFFSET_BITS and _LFS64_LARGEFILE in case not defined
+- Fix bug in gzeof() to take into account unused input data
+- Avoid initialization of structures with variables in puff.c
+- Updated win32/README-WIN32.txt [Rowe]
+
+Changes in 1.2.4.1 (28 Mar 2010)
+- Remove the use of [a-z] constructs for sed in configure [gentoo 310225]
+- Remove $(SHAREDLIB) from LIBS in Makefile.in [Creech]
+- Restore "for debugging" comment on sprintf() in gzlib.c
+- Remove fdopen for MVS from gzguts.h
+- Put new README-WIN32.txt in win32 [Rowe]
+- Add check for shell to configure and invoke another shell if needed
+- Fix big fat stinking bug in gzseek() on uncompressed files
+- Remove vestigial F_OPEN64 define in zutil.h
+- Set and check the value of _LARGEFILE_SOURCE and _LARGEFILE64_SOURCE
+- Avoid errors on non-LFS systems when applications define LFS macros
+- Set EXE to ".exe" in configure for MINGW [Kahle]
+- Match crc32() in crc32.c exactly to the prototype in zlib.h [Sherrill]
+- Add prefix for cross-compilation in win32/makefile.gcc [Bar-Lev]
+- Add DLL install in win32/makefile.gcc [Bar-Lev]
+- Allow Linux* or linux* from uname in configure [Bar-Lev]
+- Allow ldconfig to be redefined in configure and Makefile.in [Bar-Lev]
+- Add cross-compilation prefixes to configure [Bar-Lev]
+- Match type exactly in gz_load() invocation in gzread.c
+- Match type exactly of zcalloc() in zutil.c to zlib.h alloc_func
+- Provide prototypes for *64 functions when building zlib without LFS
+- Don't use -lc when linking shared library on MinGW
+- Remove errno.h check in configure and vestigial errno code in zutil.h
+
+Changes in 1.2.4 (14 Mar 2010)
+- Fix VER3 extraction in configure for no fourth subversion
+- Update zlib.3, add docs to Makefile.in to make .pdf out of it
+- Add zlib.3.pdf to distribution
+- Don't set error code in gzerror() if passed pointer is NULL
+- Apply destination directory fixes to CMakeLists.txt [Lowman]
+- Move #cmakedefine's to a new zconf.in.cmakein
+- Restore zconf.h for builds that don't use configure or cmake
+- Add distclean to dummy Makefile for convenience
+- Update and improve INDEX, README, and FAQ
+- Update CMakeLists.txt for the return of zconf.h [Lowman]
+- Update contrib/vstudio/vc9 and vc10 [Vollant]
+- Change libz.dll.a back to libzdll.a in win32/Makefile.gcc
+- Apply license and readme changes to contrib/asm686 [Raiter]
+- Check file name lengths and add -c option in minigzip.c [Li]
+- Update contrib/amd64 and contrib/masmx86/ [Vollant]
+- Avoid use of "eof" parameter in trees.c to not shadow library variable
+- Update make_vms.com for removal of zlibdefs.h [Zinser]
+- Update assembler code and vstudio projects in contrib [Vollant]
+- Remove outdated assembler code contrib/masm686 and contrib/asm586
+- Remove old vc7 and vc8 from contrib/vstudio
+- Update win32/Makefile.msc, add ZLIB_VER_SUBREVISION [Rowe]
+- Fix memory leaks in gzclose_r() and gzclose_w(), file leak in gz_open()
+- Add contrib/gcc_gvmat64 for longest_match and inflate_fast [Vollant]
+- Remove *64 functions from win32/zlib.def (they're not 64-bit yet)
+- Fix bug in void-returning vsprintf() case in gzwrite.c
+- Fix name change from inflate.h in contrib/inflate86/inffas86.c
+- Check if temporary file exists before removing in make_vms.com [Zinser]
+- Fix make install and uninstall for --static option
+- Fix usage of _MSC_VER in gzguts.h and zutil.h [Truta]
+- Update readme.txt in contrib/masmx64 and masmx86 to assemble
+
+Changes in 1.2.3.9 (21 Feb 2010)
+- Expunge gzio.c
+- Move as400 build information to old
+- Fix updates in contrib/minizip and contrib/vstudio
+- Add const to vsnprintf test in configure to avoid warnings [Weigelt]
+- Delete zconf.h (made by configure) [Weigelt]
+- Change zconf.in.h to zconf.h.in per convention [Weigelt]
+- Check for NULL buf in gzgets()
+- Return empty string for gzgets() with len == 1 (like fgets())
+- Fix description of gzgets() in zlib.h for end-of-file, NULL return
+- Update minizip to 1.1 [Vollant]
+- Avoid MSVC loss of data warnings in gzread.c, gzwrite.c
+- Note in zlib.h that gzerror() should be used to distinguish from EOF
+- Remove use of snprintf() from gzlib.c
+- Fix bug in gzseek()
+- Update contrib/vstudio, adding vc9 and vc10 [Kuno, Vollant]
+- Fix zconf.h generation in CMakeLists.txt [Lowman]
+- Improve comments in zconf.h where modified by configure
+
+Changes in 1.2.3.8 (13 Feb 2010)
+- Clean up text files (tabs, trailing whitespace, etc.) [Oberhumer]
+- Use z_off64_t in gz_zero() and gz_skip() to match state->skip
+- Avoid comparison problem when sizeof(int) == sizeof(z_off64_t)
+- Revert to Makefile.in from 1.2.3.6 (live with the clutter)
+- Fix missing error return in gzflush(), add zlib.h note
+- Add *64 functions to zlib.map [Levin]
+- Fix signed/unsigned comparison in gz_comp()
+- Use SFLAGS when testing shared linking in configure
+- Add --64 option to ./configure to use -m64 with gcc
+- Fix ./configure --help to correctly name options
+- Have make fail if a test fails [Levin]
+- Avoid buffer overrun in contrib/masmx64/gvmat64.asm [Simpson]
+- Remove assembler object files from contrib
+
+Changes in 1.2.3.7 (24 Jan 2010)
+- Always gzopen() with O_LARGEFILE if available
+- Fix gzdirect() to work immediately after gzopen() or gzdopen()
+- Make gzdirect() more precise when the state changes while reading
+- Improve zlib.h documentation in many places
+- Catch memory allocation failure in gz_open()
+- Complete close operation if seek forward in gzclose_w() fails
+- Return Z_ERRNO from gzclose_r() if close() fails
+- Return Z_STREAM_ERROR instead of EOF for gzclose() being passed NULL
+- Return zero for gzwrite() errors to match zlib.h description
+- Return -1 on gzputs() error to match zlib.h description
+- Add zconf.in.h to allow recovery from configure modification [Weigelt]
+- Fix static library permissions in Makefile.in [Weigelt]
+- Avoid warnings in configure tests that hide functionality [Weigelt]
+- Add *BSD and DragonFly to Linux case in configure [gentoo 123571]
+- Change libzdll.a to libz.dll.a in win32/Makefile.gcc [gentoo 288212]
+- Avoid access of uninitialized data for first inflateReset2 call [Gomes]
+- Keep object files in subdirectories to reduce the clutter somewhat
+- Remove default Makefile and zlibdefs.h, add dummy Makefile
+- Add new external functions to Z_PREFIX, remove duplicates, z_z_ -> z_
+- Remove zlibdefs.h completely -- modify zconf.h instead
+
+Changes in 1.2.3.6 (17 Jan 2010)
+- Avoid void * arithmetic in gzread.c and gzwrite.c
+- Make compilers happier with const char * for gz_error message
+- Avoid unused parameter warning in inflate.c
+- Avoid signed-unsigned comparison warning in inflate.c
+- Indent #pragma's for traditional C
+- Fix usage of strwinerror() in glib.c, change to gz_strwinerror()
+- Correct email address in configure for system options
+- Update make_vms.com and add make_vms.com to contrib/minizip [Zinser]
+- Update zlib.map [Brown]
+- Fix Makefile.in for Solaris 10 make of example64 and minizip64 [Torok]
+- Apply various fixes to CMakeLists.txt [Lowman]
+- Add checks on len in gzread() and gzwrite()
+- Add error message for no more room for gzungetc()
+- Remove zlib version check in gzwrite()
+- Defer compression of gzprintf() result until need to
+- Use snprintf() in gzdopen() if available
+- Remove USE_MMAP configuration determination (only used by minigzip)
+- Remove examples/pigz.c (available separately)
+- Update examples/gun.c to 1.6
+
+Changes in 1.2.3.5 (8 Jan 2010)
+- Add space after #if in zutil.h for some compilers
+- Fix relatively harmless bug in deflate_fast() [Exarevsky]
+- Fix same problem in deflate_slow()
+- Add $(SHAREDLIBV) to LIBS in Makefile.in [Brown]
+- Add deflate_rle() for faster Z_RLE strategy run-length encoding
+- Add deflate_huff() for faster Z_HUFFMAN_ONLY encoding
+- Change name of "write" variable in inffast.c to avoid library collisions
+- Fix premature EOF from gzread() in gzio.c [Brown]
+- Use zlib header window size if windowBits is 0 in inflateInit2()
+- Remove compressBound() call in deflate.c to avoid linking compress.o
+- Replace use of errno in gz* with functions, support WinCE [Alves]
+- Provide alternative to perror() in minigzip.c for WinCE [Alves]
+- Don't use _vsnprintf on later versions of MSVC [Lowman]
+- Add CMake build script and input file [Lowman]
+- Update contrib/minizip to 1.1 [Svensson, Vollant]
+- Moved nintendods directory from contrib to .
+- Replace gzio.c with a new set of routines with the same functionality
+- Add gzbuffer(), gzoffset(), gzclose_r(), gzclose_w() as part of above
+- Update contrib/minizip to 1.1b
+- Change gzeof() to return 0 on error instead of -1 to agree with zlib.h
+
+Changes in 1.2.3.4 (21 Dec 2009)
+- Use old school .SUFFIXES in Makefile.in for FreeBSD compatibility
+- Update comments in configure and Makefile.in for default --shared
+- Fix test -z's in configure [Marquess]
+- Build examplesh and minigzipsh when not testing
+- Change NULL's to Z_NULL's in deflate.c and in comments in zlib.h
+- Import LDFLAGS from the environment in configure
+- Fix configure to populate SFLAGS with discovered CFLAGS options
+- Adapt make_vms.com to the new Makefile.in [Zinser]
+- Add zlib2ansi script for C++ compilation [Marquess]
+- Add _FILE_OFFSET_BITS=64 test to make test (when applicable)
+- Add AMD64 assembler code for longest match to contrib [Teterin]
+- Include options from $SFLAGS when doing $LDSHARED
+- Simplify 64-bit file support by introducing z_off64_t type
+- Make shared object files in objs directory to work around old Sun cc
+- Use only three-part version number for Darwin shared compiles
+- Add rc option to ar in Makefile.in for when ./configure not run
+- Add -WI,-rpath,. to LDFLAGS for OSF 1 V4*
+- Set LD_LIBRARYN32_PATH for SGI IRIX shared compile
+- Protect against _FILE_OFFSET_BITS being defined when compiling zlib
+- Rename Makefile.in targets allstatic to static and allshared to shared
+- Fix static and shared Makefile.in targets to be independent
+- Correct error return bug in gz_open() by setting state [Brown]
+- Put spaces before ;;'s in configure for better sh compatibility
+- Add pigz.c (parallel implementation of gzip) to examples/
+- Correct constant in crc32.c to UL [Leventhal]
+- Reject negative lengths in crc32_combine()
+- Add inflateReset2() function to work like inflateEnd()/inflateInit2()
+- Include sys/types.h for _LARGEFILE64_SOURCE [Brown]
+- Correct typo in doc/algorithm.txt [Janik]
+- Fix bug in adler32_combine() [Zhu]
+- Catch missing-end-of-block-code error in all inflates and in puff
+ Assures that random input to inflate eventually results in an error
+- Added enough.c (calculation of ENOUGH for inftrees.h) to examples/
+- Update ENOUGH and its usage to reflect discovered bounds
+- Fix gzerror() error report on empty input file [Brown]
+- Add ush casts in trees.c to avoid pedantic runtime errors
+- Fix typo in zlib.h uncompress() description [Reiss]
+- Correct inflate() comments with regard to automatic header detection
+- Remove deprecation comment on Z_PARTIAL_FLUSH (it stays)
+- Put new version of gzlog (2.0) in examples with interruption recovery
+- Add puff compile option to permit invalid distance-too-far streams
+- Add puff TEST command options, ability to read piped input
+- Prototype the *64 functions in zlib.h when _FILE_OFFSET_BITS == 64, but
+ _LARGEFILE64_SOURCE not defined
+- Fix Z_FULL_FLUSH to truly erase the past by resetting s->strstart
+- Fix deflateSetDictionary() to use all 32K for output consistency
+- Remove extraneous #define MIN_LOOKAHEAD in deflate.c (in deflate.h)
+- Clear bytes after deflate lookahead to avoid use of uninitialized data
+- Change a limit in inftrees.c to be more transparent to Coverity Prevent
+- Update win32/zlib.def with exported symbols from zlib.h
+- Correct spelling errors in zlib.h [Willem, Sobrado]
+- Allow Z_BLOCK for deflate() to force a new block
+- Allow negative bits in inflatePrime() to delete existing bit buffer
+- Add Z_TREES flush option to inflate() to return at end of trees
+- Add inflateMark() to return current state information for random access
+- Add Makefile for NintendoDS to contrib [Costa]
+- Add -w in configure compile tests to avoid spurious warnings [Beucler]
+- Fix typos in zlib.h comments for deflateSetDictionary()
+- Fix EOF detection in transparent gzread() [Maier]
+
+Changes in 1.2.3.3 (2 October 2006)
+- Make --shared the default for configure, add a --static option
+- Add compile option to permit invalid distance-too-far streams
+- Add inflateUndermine() function which is required to enable above
+- Remove use of "this" variable name for C++ compatibility [Marquess]
+- Add testing of shared library in make test, if shared library built
+- Use ftello() and fseeko() if available instead of ftell() and fseek()
+- Provide two versions of all functions that use the z_off_t type for
+ binary compatibility -- a normal version and a 64-bit offset version,
+ per the Large File Support Extension when _LARGEFILE64_SOURCE is
+ defined; use the 64-bit versions by default when _FILE_OFFSET_BITS
+ is defined to be 64
+- Add a --uname= option to configure to perhaps help with cross-compiling
+
+Changes in 1.2.3.2 (3 September 2006)
+- Turn off silly Borland warnings [Hay]
+- Use off64_t and define _LARGEFILE64_SOURCE when present
+- Fix missing dependency on inffixed.h in Makefile.in
+- Rig configure --shared to build both shared and static [Teredesai, Truta]
+- Remove zconf.in.h and instead create a new zlibdefs.h file
+- Fix contrib/minizip/unzip.c non-encrypted after encrypted [Vollant]
+- Add treebuild.xml (see http://treebuild.metux.de/) [Weigelt]
+
+Changes in 1.2.3.1 (16 August 2006)
+- Add watcom directory with OpenWatcom make files [Daniel]
+- Remove #undef of FAR in zconf.in.h for MVS [Fedtke]
+- Update make_vms.com [Zinser]
+- Use -fPIC for shared build in configure [Teredesai, Nicholson]
+- Use only major version number for libz.so on IRIX and OSF1 [Reinholdtsen]
+- Use fdopen() (not _fdopen()) for Interix in zutil.h [B�ck]
+- Add some FAQ entries about the contrib directory
+- Update the MVS question in the FAQ
+- Avoid extraneous reads after EOF in gzio.c [Brown]
+- Correct spelling of "successfully" in gzio.c [Randers-Pehrson]
+- Add comments to zlib.h about gzerror() usage [Brown]
+- Set extra flags in gzip header in gzopen() like deflate() does
+- Make configure options more compatible with double-dash conventions
+ [Weigelt]
+- Clean up compilation under Solaris SunStudio cc [Rowe, Reinholdtsen]
+- Fix uninstall target in Makefile.in [Truta]
+- Add pkgconfig support [Weigelt]
+- Use $(DESTDIR) macro in Makefile.in [Reinholdtsen, Weigelt]
+- Replace set_data_type() with a more accurate detect_data_type() in
+ trees.c, according to the txtvsbin.txt document [Truta]
+- Swap the order of #include <stdio.h> and #include "zlib.h" in
+ gzio.c, example.c and minigzip.c [Truta]
+- Shut up annoying VS2005 warnings about standard C deprecation [Rowe,
+ Truta] (where?)
+- Fix target "clean" from win32/Makefile.bor [Truta]
+- Create .pdb and .manifest files in win32/makefile.msc [Ziegler, Rowe]
+- Update zlib www home address in win32/DLL_FAQ.txt [Truta]
+- Update contrib/masmx86/inffas32.asm for VS2005 [Vollant, Van Wassenhove]
+- Enable browse info in the "Debug" and "ASM Debug" configurations in
+ the Visual C++ 6 project, and set (non-ASM) "Debug" as default [Truta]
+- Add pkgconfig support [Weigelt]
+- Add ZLIB_VER_MAJOR, ZLIB_VER_MINOR and ZLIB_VER_REVISION in zlib.h,
+ for use in win32/zlib1.rc [Polushin, Rowe, Truta]
+- Add a document that explains the new text detection scheme to
+ doc/txtvsbin.txt [Truta]
+- Add rfc1950.txt, rfc1951.txt and rfc1952.txt to doc/ [Truta]
+- Move algorithm.txt into doc/ [Truta]
+- Synchronize FAQ with website
+- Fix compressBound(), was low for some pathological cases [Fearnley]
+- Take into account wrapper variations in deflateBound()
+- Set examples/zpipe.c input and output to binary mode for Windows
+- Update examples/zlib_how.html with new zpipe.c (also web site)
+- Fix some warnings in examples/gzlog.c and examples/zran.c (it seems
+ that gcc became pickier in 4.0)
+- Add zlib.map for Linux: "All symbols from zlib-1.1.4 remain
+ un-versioned, the patch adds versioning only for symbols introduced in
+ zlib-1.2.0 or later. It also declares as local those symbols which are
+ not designed to be exported." [Levin]
+- Update Z_PREFIX list in zconf.in.h, add --zprefix option to configure
+- Do not initialize global static by default in trees.c, add a response
+ NO_INIT_GLOBAL_POINTERS to initialize them if needed [Marquess]
+- Don't use strerror() in gzio.c under WinCE [Yakimov]
+- Don't use errno.h in zutil.h under WinCE [Yakimov]
+- Move arguments for AR to its usage to allow replacing ar [Marot]
+- Add HAVE_VISIBILITY_PRAGMA in zconf.in.h for Mozilla [Randers-Pehrson]
+- Improve inflateInit() and inflateInit2() documentation
+- Fix structure size comment in inflate.h
+- Change configure help option from --h* to --help [Santos]
+
+Changes in 1.2.3 (18 July 2005)
+- Apply security vulnerability fixes to contrib/infback9 as well
+- Clean up some text files (carriage returns, trailing space)
+- Update testzlib, vstudio, masmx64, and masmx86 in contrib [Vollant]
+
+Changes in 1.2.2.4 (11 July 2005)
+- Add inflatePrime() function for starting inflation at bit boundary
+- Avoid some Visual C warnings in deflate.c
+- Avoid more silly Visual C warnings in inflate.c and inftrees.c for 64-bit
+ compile
+- Fix some spelling errors in comments [Betts]
+- Correct inflateInit2() error return documentation in zlib.h
+- Add zran.c example of compressed data random access to examples
+ directory, shows use of inflatePrime()
+- Fix cast for assignments to strm->state in inflate.c and infback.c
+- Fix zlibCompileFlags() in zutil.c to use 1L for long shifts [Oberhumer]
+- Move declarations of gf2 functions to right place in crc32.c [Oberhumer]
+- Add cast in trees.c t avoid a warning [Oberhumer]
+- Avoid some warnings in fitblk.c, gun.c, gzjoin.c in examples [Oberhumer]
+- Update make_vms.com [Zinser]
+- Initialize state->write in inflateReset() since copied in inflate_fast()
+- Be more strict on incomplete code sets in inflate_table() and increase
+ ENOUGH and MAXD -- this repairs a possible security vulnerability for
+ invalid inflate input. Thanks to Tavis Ormandy and Markus Oberhumer for
+ discovering the vulnerability and providing test cases.
+- Add ia64 support to configure for HP-UX [Smith]
+- Add error return to gzread() for format or i/o error [Levin]
+- Use malloc.h for OS/2 [Necasek]
+
+Changes in 1.2.2.3 (27 May 2005)
+- Replace 1U constants in inflate.c and inftrees.c for 64-bit compile
+- Typecast fread() return values in gzio.c [Vollant]
+- Remove trailing space in minigzip.c outmode (VC++ can't deal with it)
+- Fix crc check bug in gzread() after gzungetc() [Heiner]
+- Add the deflateTune() function to adjust internal compression parameters
+- Add a fast gzip decompressor, gun.c, to examples (use of inflateBack)
+- Remove an incorrect assertion in examples/zpipe.c
+- Add C++ wrapper in infback9.h [Donais]
+- Fix bug in inflateCopy() when decoding fixed codes
+- Note in zlib.h how much deflateSetDictionary() actually uses
+- Remove USE_DICT_HEAD in deflate.c (would mess up inflate if used)
+- Add _WIN32_WCE to define WIN32 in zconf.in.h [Spencer]
+- Don't include stderr.h or errno.h for _WIN32_WCE in zutil.h [Spencer]
+- Add gzdirect() function to indicate transparent reads
+- Update contrib/minizip [Vollant]
+- Fix compilation of deflate.c when both ASMV and FASTEST [Oberhumer]
+- Add casts in crc32.c to avoid warnings [Oberhumer]
+- Add contrib/masmx64 [Vollant]
+- Update contrib/asm586, asm686, masmx86, testzlib, vstudio [Vollant]
+
+Changes in 1.2.2.2 (30 December 2004)
+- Replace structure assignments in deflate.c and inflate.c with zmemcpy to
+ avoid implicit memcpy calls (portability for no-library compilation)
+- Increase sprintf() buffer size in gzdopen() to allow for large numbers
+- Add INFLATE_STRICT to check distances against zlib header
+- Improve WinCE errno handling and comments [Chang]
+- Remove comment about no gzip header processing in FAQ
+- Add Z_FIXED strategy option to deflateInit2() to force fixed trees
+- Add updated make_vms.com [Coghlan], update README
+- Create a new "examples" directory, move gzappend.c there, add zpipe.c,
+ fitblk.c, gzlog.[ch], gzjoin.c, and zlib_how.html.
+- Add FAQ entry and comments in deflate.c on uninitialized memory access
+- Add Solaris 9 make options in configure [Gilbert]
+- Allow strerror() usage in gzio.c for STDC
+- Fix DecompressBuf in contrib/delphi/ZLib.pas [ManChesTer]
+- Update contrib/masmx86/inffas32.asm and gvmat32.asm [Vollant]
+- Use z_off_t for adler32_combine() and crc32_combine() lengths
+- Make adler32() much faster for small len
+- Use OS_CODE in deflate() default gzip header
+
+Changes in 1.2.2.1 (31 October 2004)
+- Allow inflateSetDictionary() call for raw inflate
+- Fix inflate header crc check bug for file names and comments
+- Add deflateSetHeader() and gz_header structure for custom gzip headers
+- Add inflateGetheader() to retrieve gzip headers
+- Add crc32_combine() and adler32_combine() functions
+- Add alloc_func, free_func, in_func, out_func to Z_PREFIX list
+- Use zstreamp consistently in zlib.h (inflate_back functions)
+- Remove GUNZIP condition from definition of inflate_mode in inflate.h
+ and in contrib/inflate86/inffast.S [Truta, Anderson]
+- Add support for AMD64 in contrib/inflate86/inffas86.c [Anderson]
+- Update projects/README.projects and projects/visualc6 [Truta]
+- Update win32/DLL_FAQ.txt [Truta]
+- Avoid warning under NO_GZCOMPRESS in gzio.c; fix typo [Truta]
+- Deprecate Z_ASCII; use Z_TEXT instead [Truta]
+- Use a new algorithm for setting strm->data_type in trees.c [Truta]
+- Do not define an exit() prototype in zutil.c unless DEBUG defined
+- Remove prototype of exit() from zutil.c, example.c, minigzip.c [Truta]
+- Add comment in zlib.h for Z_NO_FLUSH parameter to deflate()
+- Fix Darwin build version identification [Peterson]
+
+Changes in 1.2.2 (3 October 2004)
+- Update zlib.h comments on gzip in-memory processing
+- Set adler to 1 in inflateReset() to support Java test suite [Walles]
+- Add contrib/dotzlib [Ravn]
+- Update win32/DLL_FAQ.txt [Truta]
+- Update contrib/minizip [Vollant]
+- Move contrib/visual-basic.txt to old/ [Truta]
+- Fix assembler builds in projects/visualc6/ [Truta]
+
+Changes in 1.2.1.2 (9 September 2004)
+- Update INDEX file
+- Fix trees.c to update strm->data_type (no one ever noticed!)
+- Fix bug in error case in inflate.c, infback.c, and infback9.c [Brown]
+- Add "volatile" to crc table flag declaration (for DYNAMIC_CRC_TABLE)
+- Add limited multitasking protection to DYNAMIC_CRC_TABLE
+- Add NO_vsnprintf for VMS in zutil.h [Mozilla]
+- Don't declare strerror() under VMS [Mozilla]
+- Add comment to DYNAMIC_CRC_TABLE to use get_crc_table() to initialize
+- Update contrib/ada [Anisimkov]
+- Update contrib/minizip [Vollant]
+- Fix configure to not hardcode directories for Darwin [Peterson]
+- Fix gzio.c to not return error on empty files [Brown]
+- Fix indentation; update version in contrib/delphi/ZLib.pas and
+ contrib/pascal/zlibpas.pas [Truta]
+- Update mkasm.bat in contrib/masmx86 [Truta]
+- Update contrib/untgz [Truta]
+- Add projects/README.projects [Truta]
+- Add project for MS Visual C++ 6.0 in projects/visualc6 [Cadieux, Truta]
+- Update win32/DLL_FAQ.txt [Truta]
+- Update list of Z_PREFIX symbols in zconf.h [Randers-Pehrson, Truta]
+- Remove an unnecessary assignment to curr in inftrees.c [Truta]
+- Add OS/2 to exe builds in configure [Poltorak]
+- Remove err dummy parameter in zlib.h [Kientzle]
+
+Changes in 1.2.1.1 (9 January 2004)
+- Update email address in README
+- Several FAQ updates
+- Fix a big fat bug in inftrees.c that prevented decoding valid
+ dynamic blocks with only literals and no distance codes --
+ Thanks to "Hot Emu" for the bug report and sample file
+- Add a note to puff.c on no distance codes case.
+
+Changes in 1.2.1 (17 November 2003)
+- Remove a tab in contrib/gzappend/gzappend.c
+- Update some interfaces in contrib for new zlib functions
+- Update zlib version number in some contrib entries
+- Add Windows CE definition for ptrdiff_t in zutil.h [Mai, Truta]
+- Support shared libraries on Hurd and KFreeBSD [Brown]
+- Fix error in NO_DIVIDE option of adler32.c
+
+Changes in 1.2.0.8 (4 November 2003)
+- Update version in contrib/delphi/ZLib.pas and contrib/pascal/zlibpas.pas
+- Add experimental NO_DIVIDE #define in adler32.c
+ - Possibly faster on some processors (let me know if it is)
+- Correct Z_BLOCK to not return on first inflate call if no wrap
+- Fix strm->data_type on inflate() return to correctly indicate EOB
+- Add deflatePrime() function for appending in the middle of a byte
+- Add contrib/gzappend for an example of appending to a stream
+- Update win32/DLL_FAQ.txt [Truta]
+- Delete Turbo C comment in README [Truta]
+- Improve some indentation in zconf.h [Truta]
+- Fix infinite loop on bad input in configure script [Church]
+- Fix gzeof() for concatenated gzip files [Johnson]
+- Add example to contrib/visual-basic.txt [Michael B.]
+- Add -p to mkdir's in Makefile.in [vda]
+- Fix configure to properly detect presence or lack of printf functions
+- Add AS400 support [Monnerat]
+- Add a little Cygwin support [Wilson]
+
+Changes in 1.2.0.7 (21 September 2003)
+- Correct some debug formats in contrib/infback9
+- Cast a type in a debug statement in trees.c
+- Change search and replace delimiter in configure from % to # [Beebe]
+- Update contrib/untgz to 0.2 with various fixes [Truta]
+- Add build support for Amiga [Nikl]
+- Remove some directories in old that have been updated to 1.2
+- Add dylib building for Mac OS X in configure and Makefile.in
+- Remove old distribution stuff from Makefile
+- Update README to point to DLL_FAQ.txt, and add comment on Mac OS X
+- Update links in README
+
+Changes in 1.2.0.6 (13 September 2003)
+- Minor FAQ updates
+- Update contrib/minizip to 1.00 [Vollant]
+- Remove test of gz functions in example.c when GZ_COMPRESS defined [Truta]
+- Update POSTINC comment for 68060 [Nikl]
+- Add contrib/infback9 with deflate64 decoding (unsupported)
+- For MVS define NO_vsnprintf and undefine FAR [van Burik]
+- Add pragma for fdopen on MVS [van Burik]
+
+Changes in 1.2.0.5 (8 September 2003)
+- Add OF to inflateBackEnd() declaration in zlib.h
+- Remember start when using gzdopen in the middle of a file
+- Use internal off_t counters in gz* functions to properly handle seeks
+- Perform more rigorous check for distance-too-far in inffast.c
+- Add Z_BLOCK flush option to return from inflate at block boundary
+- Set strm->data_type on return from inflate
+ - Indicate bits unused, if at block boundary, and if in last block
+- Replace size_t with ptrdiff_t in crc32.c, and check for correct size
+- Add condition so old NO_DEFLATE define still works for compatibility
+- FAQ update regarding the Windows DLL [Truta]
+- INDEX update: add qnx entry, remove aix entry [Truta]
+- Install zlib.3 into mandir [Wilson]
+- Move contrib/zlib_dll_FAQ.txt to win32/DLL_FAQ.txt; update [Truta]
+- Adapt the zlib interface to the new DLL convention guidelines [Truta]
+- Introduce ZLIB_WINAPI macro to allow the export of functions using
+ the WINAPI calling convention, for Visual Basic [Vollant, Truta]
+- Update msdos and win32 scripts and makefiles [Truta]
+- Export symbols by name, not by ordinal, in win32/zlib.def [Truta]
+- Add contrib/ada [Anisimkov]
+- Move asm files from contrib/vstudio/vc70_32 to contrib/asm386 [Truta]
+- Rename contrib/asm386 to contrib/masmx86 [Truta, Vollant]
+- Add contrib/masm686 [Truta]
+- Fix offsets in contrib/inflate86 and contrib/masmx86/inffas32.asm
+ [Truta, Vollant]
+- Update contrib/delphi; rename to contrib/pascal; add example [Truta]
+- Remove contrib/delphi2; add a new contrib/delphi [Truta]
+- Avoid inclusion of the nonstandard <memory.h> in contrib/iostream,
+ and fix some method prototypes [Truta]
+- Fix the ZCR_SEED2 constant to avoid warnings in contrib/minizip
+ [Truta]
+- Avoid the use of backslash (\) in contrib/minizip [Vollant]
+- Fix file time handling in contrib/untgz; update makefiles [Truta]
+- Update contrib/vstudio/vc70_32 to comply with the new DLL guidelines
+ [Vollant]
+- Remove contrib/vstudio/vc15_16 [Vollant]
+- Rename contrib/vstudio/vc70_32 to contrib/vstudio/vc7 [Truta]
+- Update README.contrib [Truta]
+- Invert the assignment order of match_head and s->prev[...] in
+ INSERT_STRING [Truta]
+- Compare TOO_FAR with 32767 instead of 32768, to avoid 16-bit warnings
+ [Truta]
+- Compare function pointers with 0, not with NULL or Z_NULL [Truta]
+- Fix prototype of syncsearch in inflate.c [Truta]
+- Introduce ASMINF macro to be enabled when using an ASM implementation
+ of inflate_fast [Truta]
+- Change NO_DEFLATE to NO_GZCOMPRESS [Truta]
+- Modify test_gzio in example.c to take a single file name as a
+ parameter [Truta]
+- Exit the example.c program if gzopen fails [Truta]
+- Add type casts around strlen in example.c [Truta]
+- Remove casting to sizeof in minigzip.c; give a proper type
+ to the variable compared with SUFFIX_LEN [Truta]
+- Update definitions of STDC and STDC99 in zconf.h [Truta]
+- Synchronize zconf.h with the new Windows DLL interface [Truta]
+- Use SYS16BIT instead of __32BIT__ to distinguish between
+ 16- and 32-bit platforms [Truta]
+- Use far memory allocators in small 16-bit memory models for
+ Turbo C [Truta]
+- Add info about the use of ASMV, ASMINF and ZLIB_WINAPI in
+ zlibCompileFlags [Truta]
+- Cygwin has vsnprintf [Wilson]
+- In Windows16, OS_CODE is 0, as in MSDOS [Truta]
+- In Cygwin, OS_CODE is 3 (Unix), not 11 (Windows32) [Wilson]
+
+Changes in 1.2.0.4 (10 August 2003)
+- Minor FAQ updates
+- Be more strict when checking inflateInit2's windowBits parameter
+- Change NO_GUNZIP compile option to NO_GZIP to cover deflate as well
+- Add gzip wrapper option to deflateInit2 using windowBits
+- Add updated QNX rule in configure and qnx directory [Bonnefoy]
+- Make inflate distance-too-far checks more rigorous
+- Clean up FAR usage in inflate
+- Add casting to sizeof() in gzio.c and minigzip.c
+
+Changes in 1.2.0.3 (19 July 2003)
+- Fix silly error in gzungetc() implementation [Vollant]
+- Update contrib/minizip and contrib/vstudio [Vollant]
+- Fix printf format in example.c
+- Correct cdecl support in zconf.in.h [Anisimkov]
+- Minor FAQ updates
+
+Changes in 1.2.0.2 (13 July 2003)
+- Add ZLIB_VERNUM in zlib.h for numerical preprocessor comparisons
+- Attempt to avoid warnings in crc32.c for pointer-int conversion
+- Add AIX to configure, remove aix directory [Bakker]
+- Add some casts to minigzip.c
+- Improve checking after insecure sprintf() or vsprintf() calls
+- Remove #elif's from crc32.c
+- Change leave label to inf_leave in inflate.c and infback.c to avoid
+ library conflicts
+- Remove inflate gzip decoding by default--only enable gzip decoding by
+ special request for stricter backward compatibility
+- Add zlibCompileFlags() function to return compilation information
+- More typecasting in deflate.c to avoid warnings
+- Remove leading underscore from _Capital #defines [Truta]
+- Fix configure to link shared library when testing
+- Add some Windows CE target adjustments [Mai]
+- Remove #define ZLIB_DLL in zconf.h [Vollant]
+- Add zlib.3 [Rodgers]
+- Update RFC URL in deflate.c and algorithm.txt [Mai]
+- Add zlib_dll_FAQ.txt to contrib [Truta]
+- Add UL to some constants [Truta]
+- Update minizip and vstudio [Vollant]
+- Remove vestigial NEED_DUMMY_RETURN from zconf.in.h
+- Expand use of NO_DUMMY_DECL to avoid all dummy structures
+- Added iostream3 to contrib [Schwardt]
+- Replace rewind() with fseek() for WinCE [Truta]
+- Improve setting of zlib format compression level flags
+ - Report 0 for huffman and rle strategies and for level == 0 or 1
+ - Report 2 only for level == 6
+- Only deal with 64K limit when necessary at compile time [Truta]
+- Allow TOO_FAR check to be turned off at compile time [Truta]
+- Add gzclearerr() function [Souza]
+- Add gzungetc() function
+
+Changes in 1.2.0.1 (17 March 2003)
+- Add Z_RLE strategy for run-length encoding [Truta]
+ - When Z_RLE requested, restrict matches to distance one
+ - Update zlib.h, minigzip.c, gzopen(), gzdopen() for Z_RLE
+- Correct FASTEST compilation to allow level == 0
+- Clean up what gets compiled for FASTEST
+- Incorporate changes to zconf.in.h [Vollant]
+ - Refine detection of Turbo C need for dummy returns
+ - Refine ZLIB_DLL compilation
+ - Include additional header file on VMS for off_t typedef
+- Try to use _vsnprintf where it supplants vsprintf [Vollant]
+- Add some casts in inffast.c
+- Enchance comments in zlib.h on what happens if gzprintf() tries to
+ write more than 4095 bytes before compression
+- Remove unused state from inflateBackEnd()
+- Remove exit(0) from minigzip.c, example.c
+- Get rid of all those darn tabs
+- Add "check" target to Makefile.in that does the same thing as "test"
+- Add "mostlyclean" and "maintainer-clean" targets to Makefile.in
+- Update contrib/inflate86 [Anderson]
+- Update contrib/testzlib, contrib/vstudio, contrib/minizip [Vollant]
+- Add msdos and win32 directories with makefiles [Truta]
+- More additions and improvements to the FAQ
+
+Changes in 1.2.0 (9 March 2003)
+- New and improved inflate code
+ - About 20% faster
+ - Does not allocate 32K window unless and until needed
+ - Automatically detects and decompresses gzip streams
+ - Raw inflate no longer needs an extra dummy byte at end
+ - Added inflateBack functions using a callback interface--even faster
+ than inflate, useful for file utilities (gzip, zip)
+ - Added inflateCopy() function to record state for random access on
+ externally generated deflate streams (e.g. in gzip files)
+ - More readable code (I hope)
+- New and improved crc32()
+ - About 50% faster, thanks to suggestions from Rodney Brown
+- Add deflateBound() and compressBound() functions
+- Fix memory leak in deflateInit2()
+- Permit setting dictionary for raw deflate (for parallel deflate)
+- Fix const declaration for gzwrite()
+- Check for some malloc() failures in gzio.c
+- Fix bug in gzopen() on single-byte file 0x1f
+- Fix bug in gzread() on concatenated file with 0x1f at end of buffer
+ and next buffer doesn't start with 0x8b
+- Fix uncompress() to return Z_DATA_ERROR on truncated input
+- Free memory at end of example.c
+- Remove MAX #define in trees.c (conflicted with some libraries)
+- Fix static const's in deflate.c, gzio.c, and zutil.[ch]
+- Declare malloc() and free() in gzio.c if STDC not defined
+- Use malloc() instead of calloc() in zutil.c if int big enough
+- Define STDC for AIX
+- Add aix/ with approach for compiling shared library on AIX
+- Add HP-UX support for shared libraries in configure
+- Add OpenUNIX support for shared libraries in configure
+- Use $cc instead of gcc to build shared library
+- Make prefix directory if needed when installing
+- Correct Macintosh avoidance of typedef Byte in zconf.h
+- Correct Turbo C memory allocation when under Linux
+- Use libz.a instead of -lz in Makefile (assure use of compiled library)
+- Update configure to check for snprintf or vsnprintf functions and their
+ return value, warn during make if using an insecure function
+- Fix configure problem with compile-time knowledge of HAVE_UNISTD_H that
+ is lost when library is used--resolution is to build new zconf.h
+- Documentation improvements (in zlib.h):
+ - Document raw deflate and inflate
+ - Update RFCs URL
+ - Point out that zlib and gzip formats are different
+ - Note that Z_BUF_ERROR is not fatal
+ - Document string limit for gzprintf() and possible buffer overflow
+ - Note requirement on avail_out when flushing
+ - Note permitted values of flush parameter of inflate()
+- Add some FAQs (and even answers) to the FAQ
+- Add contrib/inflate86/ for x86 faster inflate
+- Add contrib/blast/ for PKWare Data Compression Library decompression
+- Add contrib/puff/ simple inflate for deflate format description
+
+Changes in 1.1.4 (11 March 2002)
+- ZFREE was repeated on same allocation on some error conditions.
+ This creates a security problem described in
+ http://www.zlib.org/advisory-2002-03-11.txt
+- Returned incorrect error (Z_MEM_ERROR) on some invalid data
+- Avoid accesses before window for invalid distances with inflate window
+ less than 32K.
+- force windowBits > 8 to avoid a bug in the encoder for a window size
+ of 256 bytes. (A complete fix will be available in 1.1.5).
+
+Changes in 1.1.3 (9 July 1998)
+- fix "an inflate input buffer bug that shows up on rare but persistent
+ occasions" (Mark)
+- fix gzread and gztell for concatenated .gz files (Didier Le Botlan)
+- fix gzseek(..., SEEK_SET) in write mode
+- fix crc check after a gzeek (Frank Faubert)
+- fix miniunzip when the last entry in a zip file is itself a zip file
+ (J Lillge)
+- add contrib/asm586 and contrib/asm686 (Brian Raiter)
+ See http://www.muppetlabs.com/~breadbox/software/assembly.html
+- add support for Delphi 3 in contrib/delphi (Bob Dellaca)
+- add support for C++Builder 3 and Delphi 3 in contrib/delphi2 (Davide Moretti)
+- do not exit prematurely in untgz if 0 at start of block (Magnus Holmgren)
+- use macro EXTERN instead of extern to support DLL for BeOS (Sander Stoks)
+- added a FAQ file
+
+- Support gzdopen on Mac with Metrowerks (Jason Linhart)
+- Do not redefine Byte on Mac (Brad Pettit & Jason Linhart)
+- define SEEK_END too if SEEK_SET is not defined (Albert Chin-A-Young)
+- avoid some warnings with Borland C (Tom Tanner)
+- fix a problem in contrib/minizip/zip.c for 16-bit MSDOS (Gilles Vollant)
+- emulate utime() for WIN32 in contrib/untgz (Gilles Vollant)
+- allow several arguments to configure (Tim Mooney, Frodo Looijaard)
+- use libdir and includedir in Makefile.in (Tim Mooney)
+- support shared libraries on OSF1 V4 (Tim Mooney)
+- remove so_locations in "make clean" (Tim Mooney)
+- fix maketree.c compilation error (Glenn, Mark)
+- Python interface to zlib now in Python 1.5 (Jeremy Hylton)
+- new Makefile.riscos (Rich Walker)
+- initialize static descriptors in trees.c for embedded targets (Nick Smith)
+- use "foo-gz" in example.c for RISCOS and VMS (Nick Smith)
+- add the OS/2 files in Makefile.in too (Andrew Zabolotny)
+- fix fdopen and halloc macros for Microsoft C 6.0 (Tom Lane)
+- fix maketree.c to allow clean compilation of inffixed.h (Mark)
+- fix parameter check in deflateCopy (Gunther Nikl)
+- cleanup trees.c, use compressed_len only in debug mode (Christian Spieler)
+- Many portability patches by Christian Spieler:
+ . zutil.c, zutil.h: added "const" for zmem*
+ . Make_vms.com: fixed some typos
+ . Make_vms.com: msdos/Makefile.*: removed zutil.h from some dependency lists
+ . msdos/Makefile.msc: remove "default rtl link library" info from obj files
+ . msdos/Makefile.*: use model-dependent name for the built zlib library
+ . msdos/Makefile.emx, nt/Makefile.emx, nt/Makefile.gcc:
+ new makefiles, for emx (DOS/OS2), emx&rsxnt and mingw32 (Windows 9x / NT)
+- use define instead of typedef for Bytef also for MSC small/medium (Tom Lane)
+- replace __far with _far for better portability (Christian Spieler, Tom Lane)
+- fix test for errno.h in configure (Tim Newsham)
+
+Changes in 1.1.2 (19 March 98)
+- added contrib/minzip, mini zip and unzip based on zlib (Gilles Vollant)
+ See http://www.winimage.com/zLibDll/unzip.html
+- preinitialize the inflate tables for fixed codes, to make the code
+ completely thread safe (Mark)
+- some simplifications and slight speed-up to the inflate code (Mark)
+- fix gzeof on non-compressed files (Allan Schrum)
+- add -std1 option in configure for OSF1 to fix gzprintf (Martin Mokrejs)
+- use default value of 4K for Z_BUFSIZE for 16-bit MSDOS (Tim Wegner + Glenn)
+- added os2/Makefile.def and os2/zlib.def (Andrew Zabolotny)
+- add shared lib support for UNIX_SV4.2MP (MATSUURA Takanori)
+- do not wrap extern "C" around system includes (Tom Lane)
+- mention zlib binding for TCL in README (Andreas Kupries)
+- added amiga/Makefile.pup for Amiga powerUP SAS/C PPC (Andreas Kleinert)
+- allow "make install prefix=..." even after configure (Glenn Randers-Pehrson)
+- allow "configure --prefix $HOME" (Tim Mooney)
+- remove warnings in example.c and gzio.c (Glenn Randers-Pehrson)
+- move Makefile.sas to amiga/Makefile.sas
+
+Changes in 1.1.1 (27 Feb 98)
+- fix macros _tr_tally_* in deflate.h for debug mode (Glenn Randers-Pehrson)
+- remove block truncation heuristic which had very marginal effect for zlib
+ (smaller lit_bufsize than in gzip 1.2.4) and degraded a little the
+ compression ratio on some files. This also allows inlining _tr_tally for
+ matches in deflate_slow.
+- added msdos/Makefile.w32 for WIN32 Microsoft Visual C++ (Bob Frazier)
+
+Changes in 1.1.0 (24 Feb 98)
+- do not return STREAM_END prematurely in inflate (John Bowler)
+- revert to the zlib 1.0.8 inflate to avoid the gcc 2.8.0 bug (Jeremy Buhler)
+- compile with -DFASTEST to get compression code optimized for speed only
+- in minigzip, try mmap'ing the input file first (Miguel Albrecht)
+- increase size of I/O buffers in minigzip.c and gzio.c (not a big gain
+ on Sun but significant on HP)
+
+- add a pointer to experimental unzip library in README (Gilles Vollant)
+- initialize variable gcc in configure (Chris Herborth)
+
+Changes in 1.0.9 (17 Feb 1998)
+- added gzputs and gzgets functions
+- do not clear eof flag in gzseek (Mark Diekhans)
+- fix gzseek for files in transparent mode (Mark Diekhans)
+- do not assume that vsprintf returns the number of bytes written (Jens Krinke)
+- replace EXPORT with ZEXPORT to avoid conflict with other programs
+- added compress2 in zconf.h, zlib.def, zlib.dnt
+- new asm code from Gilles Vollant in contrib/asm386
+- simplify the inflate code (Mark):
+ . Replace ZALLOC's in huft_build() with single ZALLOC in inflate_blocks_new()
+ . ZALLOC the length list in inflate_trees_fixed() instead of using stack
+ . ZALLOC the value area for huft_build() instead of using stack
+ . Simplify Z_FINISH check in inflate()
+
+- Avoid gcc 2.8.0 comparison bug a little differently than zlib 1.0.8
+- in inftrees.c, avoid cc -O bug on HP (Farshid Elahi)
+- in zconf.h move the ZLIB_DLL stuff earlier to avoid problems with
+ the declaration of FAR (Gilles VOllant)
+- install libz.so* with mode 755 (executable) instead of 644 (Marc Lehmann)
+- read_buf buf parameter of type Bytef* instead of charf*
+- zmemcpy parameters are of type Bytef*, not charf* (Joseph Strout)
+- do not redeclare unlink in minigzip.c for WIN32 (John Bowler)
+- fix check for presence of directories in "make install" (Ian Willis)
+
+Changes in 1.0.8 (27 Jan 1998)
+- fixed offsets in contrib/asm386/gvmat32.asm (Gilles Vollant)
+- fix gzgetc and gzputc for big endian systems (Markus Oberhumer)
+- added compress2() to allow setting the compression level
+- include sys/types.h to get off_t on some systems (Marc Lehmann & QingLong)
+- use constant arrays for the static trees in trees.c instead of computing
+ them at run time (thanks to Ken Raeburn for this suggestion). To create
+ trees.h, compile with GEN_TREES_H and run "make test".
+- check return code of example in "make test" and display result
+- pass minigzip command line options to file_compress
+- simplifying code of inflateSync to avoid gcc 2.8 bug
+
+- support CC="gcc -Wall" in configure -s (QingLong)
+- avoid a flush caused by ftell in gzopen for write mode (Ken Raeburn)
+- fix test for shared library support to avoid compiler warnings
+- zlib.lib -> zlib.dll in msdos/zlib.rc (Gilles Vollant)
+- check for TARGET_OS_MAC in addition to MACOS (Brad Pettit)
+- do not use fdopen for Metrowerks on Mac (Brad Pettit))
+- add checks for gzputc and gzputc in example.c
+- avoid warnings in gzio.c and deflate.c (Andreas Kleinert)
+- use const for the CRC table (Ken Raeburn)
+- fixed "make uninstall" for shared libraries
+- use Tracev instead of Trace in infblock.c
+- in example.c use correct compressed length for test_sync
+- suppress +vnocompatwarnings in configure for HPUX (not always supported)
+
+Changes in 1.0.7 (20 Jan 1998)
+- fix gzseek which was broken in write mode
+- return error for gzseek to negative absolute position
+- fix configure for Linux (Chun-Chung Chen)
+- increase stack space for MSC (Tim Wegner)
+- get_crc_table and inflateSyncPoint are EXPORTed (Gilles Vollant)
+- define EXPORTVA for gzprintf (Gilles Vollant)
+- added man page zlib.3 (Rick Rodgers)
+- for contrib/untgz, fix makedir() and improve Makefile
+
+- check gzseek in write mode in example.c
+- allocate extra buffer for seeks only if gzseek is actually called
+- avoid signed/unsigned comparisons (Tim Wegner, Gilles Vollant)
+- add inflateSyncPoint in zconf.h
+- fix list of exported functions in nt/zlib.dnt and mdsos/zlib.def
+
+Changes in 1.0.6 (19 Jan 1998)
+- add functions gzprintf, gzputc, gzgetc, gztell, gzeof, gzseek, gzrewind and
+ gzsetparams (thanks to Roland Giersig and Kevin Ruland for some of this code)
+- Fix a deflate bug occurring only with compression level 0 (thanks to
+ Andy Buckler for finding this one).
+- In minigzip, pass transparently also the first byte for .Z files.
+- return Z_BUF_ERROR instead of Z_OK if output buffer full in uncompress()
+- check Z_FINISH in inflate (thanks to Marc Schluper)
+- Implement deflateCopy (thanks to Adam Costello)
+- make static libraries by default in configure, add --shared option.
+- move MSDOS or Windows specific files to directory msdos
+- suppress the notion of partial flush to simplify the interface
+ (but the symbol Z_PARTIAL_FLUSH is kept for compatibility with 1.0.4)
+- suppress history buffer provided by application to simplify the interface
+ (this feature was not implemented anyway in 1.0.4)
+- next_in and avail_in must be initialized before calling inflateInit or
+ inflateInit2
+- add EXPORT in all exported functions (for Windows DLL)
+- added Makefile.nt (thanks to Stephen Williams)
+- added the unsupported "contrib" directory:
+ contrib/asm386/ by Gilles Vollant <info at winimage.com>
+ 386 asm code replacing longest_match().
+ contrib/iostream/ by Kevin Ruland <kevin at rodin.wustl.edu>
+ A C++ I/O streams interface to the zlib gz* functions
+ contrib/iostream2/ by Tyge L�vset <Tyge.Lovset at cmr.no>
+ Another C++ I/O streams interface
+ contrib/untgz/ by "Pedro A. Aranda Guti\irrez" <paag at tid.es>
+ A very simple tar.gz file extractor using zlib
+ contrib/visual-basic.txt by Carlos Rios <c_rios at sonda.cl>
+ How to use compress(), uncompress() and the gz* functions from VB.
+- pass params -f (filtered data), -h (huffman only), -1 to -9 (compression
+ level) in minigzip (thanks to Tom Lane)
+
+- use const for rommable constants in deflate
+- added test for gzseek and gztell in example.c
+- add undocumented function inflateSyncPoint() (hack for Paul Mackerras)
+- add undocumented function zError to convert error code to string
+ (for Tim Smithers)
+- Allow compilation of gzio with -DNO_DEFLATE to avoid the compression code.
+- Use default memcpy for Symantec MSDOS compiler.
+- Add EXPORT keyword for check_func (needed for Windows DLL)
+- add current directory to LD_LIBRARY_PATH for "make test"
+- create also a link for libz.so.1
+- added support for FUJITSU UXP/DS (thanks to Toshiaki Nomura)
+- use $(SHAREDLIB) instead of libz.so in Makefile.in (for HPUX)
+- added -soname for Linux in configure (Chun-Chung Chen,
+- assign numbers to the exported functions in zlib.def (for Windows DLL)
+- add advice in zlib.h for best usage of deflateSetDictionary
+- work around compiler bug on Atari (cast Z_NULL in call of s->checkfn)
+- allow compilation with ANSI keywords only enabled for TurboC in large model
+- avoid "versionString"[0] (Borland bug)
+- add NEED_DUMMY_RETURN for Borland
+- use variable z_verbose for tracing in debug mode (L. Peter Deutsch).
+- allow compilation with CC
+- defined STDC for OS/2 (David Charlap)
+- limit external names to 8 chars for MVS (Thomas Lund)
+- in minigzip.c, use static buffers only for 16-bit systems
+- fix suffix check for "minigzip -d foo.gz"
+- do not return an error for the 2nd of two consecutive gzflush() (Felix Lee)
+- use _fdopen instead of fdopen for MSC >= 6.0 (Thomas Fanslau)
+- added makelcc.bat for lcc-win32 (Tom St Denis)
+- in Makefile.dj2, use copy and del instead of install and rm (Frank Donahoe)
+- Avoid expanded $Id$. Use "rcs -kb" or "cvs admin -kb" to avoid Id expansion.
+- check for unistd.h in configure (for off_t)
+- remove useless check parameter in inflate_blocks_free
+- avoid useless assignment of s->check to itself in inflate_blocks_new
+- do not flush twice in gzclose (thanks to Ken Raeburn)
+- rename FOPEN as F_OPEN to avoid clash with /usr/include/sys/file.h
+- use NO_ERRNO_H instead of enumeration of operating systems with errno.h
+- work around buggy fclose on pipes for HP/UX
+- support zlib DLL with BORLAND C++ 5.0 (thanks to Glenn Randers-Pehrson)
+- fix configure if CC is already equal to gcc
+
+Changes in 1.0.5 (3 Jan 98)
+- Fix inflate to terminate gracefully when fed corrupted or invalid data
+- Use const for rommable constants in inflate
+- Eliminate memory leaks on error conditions in inflate
+- Removed some vestigial code in inflate
+- Update web address in README
+
+Changes in 1.0.4 (24 Jul 96)
+- In very rare conditions, deflate(s, Z_FINISH) could fail to produce an EOF
+ bit, so the decompressor could decompress all the correct data but went
+ on to attempt decompressing extra garbage data. This affected minigzip too.
+- zlibVersion and gzerror return const char* (needed for DLL)
+- port to RISCOS (no fdopen, no multiple dots, no unlink, no fileno)
+- use z_error only for DEBUG (avoid problem with DLLs)
+
+Changes in 1.0.3 (2 Jul 96)
+- use z_streamp instead of z_stream *, which is now a far pointer in MSDOS
+ small and medium models; this makes the library incompatible with previous
+ versions for these models. (No effect in large model or on other systems.)
+- return OK instead of BUF_ERROR if previous deflate call returned with
+ avail_out as zero but there is nothing to do
+- added memcmp for non STDC compilers
+- define NO_DUMMY_DECL for more Mac compilers (.h files merged incorrectly)
+- define __32BIT__ if __386__ or i386 is defined (pb. with Watcom and SCO)
+- better check for 16-bit mode MSC (avoids problem with Symantec)
+
+Changes in 1.0.2 (23 May 96)
+- added Windows DLL support
+- added a function zlibVersion (for the DLL support)
+- fixed declarations using Bytef in infutil.c (pb with MSDOS medium model)
+- Bytef is define's instead of typedef'd only for Borland C
+- avoid reading uninitialized memory in example.c
+- mention in README that the zlib format is now RFC1950
+- updated Makefile.dj2
+- added algorithm.doc
+
+Changes in 1.0.1 (20 May 96) [1.0 skipped to avoid confusion]
+- fix array overlay in deflate.c which sometimes caused bad compressed data
+- fix inflate bug with empty stored block
+- fix MSDOS medium model which was broken in 0.99
+- fix deflateParams() which could generated bad compressed data.
+- Bytef is define'd instead of typedef'ed (work around Borland bug)
+- added an INDEX file
+- new makefiles for DJGPP (Makefile.dj2), 32-bit Borland (Makefile.b32),
+ Watcom (Makefile.wat), Amiga SAS/C (Makefile.sas)
+- speed up adler32 for modern machines without auto-increment
+- added -ansi for IRIX in configure
+- static_init_done in trees.c is an int
+- define unlink as delete for VMS
+- fix configure for QNX
+- add configure branch for SCO and HPUX
+- avoid many warnings (unused variables, dead assignments, etc...)
+- no fdopen for BeOS
+- fix the Watcom fix for 32 bit mode (define FAR as empty)
+- removed redefinition of Byte for MKWERKS
+- work around an MWKERKS bug (incorrect merge of all .h files)
+
+Changes in 0.99 (27 Jan 96)
+- allow preset dictionary shared between compressor and decompressor
+- allow compression level 0 (no compression)
+- add deflateParams in zlib.h: allow dynamic change of compression level
+ and compression strategy.
+- test large buffers and deflateParams in example.c
+- add optional "configure" to build zlib as a shared library
+- suppress Makefile.qnx, use configure instead
+- fixed deflate for 64-bit systems (detected on Cray)
+- fixed inflate_blocks for 64-bit systems (detected on Alpha)
+- declare Z_DEFLATED in zlib.h (possible parameter for deflateInit2)
+- always return Z_BUF_ERROR when deflate() has nothing to do
+- deflateInit and inflateInit are now macros to allow version checking
+- prefix all global functions and types with z_ with -DZ_PREFIX
+- make falloc completely reentrant (inftrees.c)
+- fixed very unlikely race condition in ct_static_init
+- free in reverse order of allocation to help memory manager
+- use zlib-1.0/* instead of zlib/* inside the tar.gz
+- make zlib warning-free with "gcc -O3 -Wall -Wwrite-strings -Wpointer-arith
+ -Wconversion -Wstrict-prototypes -Wmissing-prototypes"
+- allow gzread on concatenated .gz files
+- deflateEnd now returns Z_DATA_ERROR if it was premature
+- deflate is finally (?) fully deterministic (no matches beyond end of input)
+- Document Z_SYNC_FLUSH
+- add uninstall in Makefile
+- Check for __cpluplus in zlib.h
+- Better test in ct_align for partial flush
+- avoid harmless warnings for Borland C++
+- initialize hash_head in deflate.c
+- avoid warning on fdopen (gzio.c) for HP cc -Aa
+- include stdlib.h for STDC compilers
+- include errno.h for Cray
+- ignore error if ranlib doesn't exist
+- call ranlib twice for NeXTSTEP
+- use exec_prefix instead of prefix for libz.a
+- renamed ct_* as _tr_* to avoid conflict with applications
+- clear z->msg in inflateInit2 before any error return
+- initialize opaque in example.c, gzio.c, deflate.c and inflate.c
+- fixed typo in zconf.h (_GNUC__ => __GNUC__)
+- check for WIN32 in zconf.h and zutil.c (avoid farmalloc in 32-bit mode)
+- fix typo in Make_vms.com (f$trnlnm -> f$getsyi)
+- in fcalloc, normalize pointer if size > 65520 bytes
+- don't use special fcalloc for 32 bit Borland C++
+- use STDC instead of __GO32__ to avoid redeclaring exit, calloc, etc...
+- use Z_BINARY instead of BINARY
+- document that gzclose after gzdopen will close the file
+- allow "a" as mode in gzopen.
+- fix error checking in gzread
+- allow skipping .gz extra-field on pipes
+- added reference to Perl interface in README
+- put the crc table in FAR data (I dislike more and more the medium model :)
+- added get_crc_table
+- added a dimension to all arrays (Borland C can't count).
+- workaround Borland C bug in declaration of inflate_codes_new & inflate_fast
+- guard against multiple inclusion of *.h (for precompiled header on Mac)
+- Watcom C pretends to be Microsoft C small model even in 32 bit mode.
+- don't use unsized arrays to avoid silly warnings by Visual C++:
+ warning C4746: 'inflate_mask' : unsized array treated as '__far'
+ (what's wrong with far data in far model?).
+- define enum out of inflate_blocks_state to allow compilation with C++
+
+Changes in 0.95 (16 Aug 95)
+- fix MSDOS small and medium model (now easier to adapt to any compiler)
+- inlined send_bits
+- fix the final (:-) bug for deflate with flush (output was correct but
+ not completely flushed in rare occasions).
+- default window size is same for compression and decompression
+ (it's now sufficient to set MAX_WBITS in zconf.h).
+- voidp -> voidpf and voidnp -> voidp (for consistency with other
+ typedefs and because voidnp was not near in large model).
+
+Changes in 0.94 (13 Aug 95)
+- support MSDOS medium model
+- fix deflate with flush (could sometimes generate bad output)
+- fix deflateReset (zlib header was incorrectly suppressed)
+- added support for VMS
+- allow a compression level in gzopen()
+- gzflush now calls fflush
+- For deflate with flush, flush even if no more input is provided.
+- rename libgz.a as libz.a
+- avoid complex expression in infcodes.c triggering Turbo C bug
+- work around a problem with gcc on Alpha (in INSERT_STRING)
+- don't use inline functions (problem with some gcc versions)
+- allow renaming of Byte, uInt, etc... with #define.
+- avoid warning about (unused) pointer before start of array in deflate.c
+- avoid various warnings in gzio.c, example.c, infblock.c, adler32.c, zutil.c
+- avoid reserved word 'new' in trees.c
+
+Changes in 0.93 (25 June 95)
+- temporarily disable inline functions
+- make deflate deterministic
+- give enough lookahead for PARTIAL_FLUSH
+- Set binary mode for stdin/stdout in minigzip.c for OS/2
+- don't even use signed char in inflate (not portable enough)
+- fix inflate memory leak for segmented architectures
+
+Changes in 0.92 (3 May 95)
+- don't assume that char is signed (problem on SGI)
+- Clear bit buffer when starting a stored block
+- no memcpy on Pyramid
+- suppressed inftest.c
+- optimized fill_window, put longest_match inline for gcc
+- optimized inflate on stored blocks.
+- untabify all sources to simplify patches
+
+Changes in 0.91 (2 May 95)
+- Default MEM_LEVEL is 8 (not 9 for Unix) as documented in zlib.h
+- Document the memory requirements in zconf.h
+- added "make install"
+- fix sync search logic in inflateSync
+- deflate(Z_FULL_FLUSH) now works even if output buffer too short
+- after inflateSync, don't scare people with just "lo world"
+- added support for DJGPP
+
+Changes in 0.9 (1 May 95)
+- don't assume that zalloc clears the allocated memory (the TurboC bug
+ was Mark's bug after all :)
+- let again gzread copy uncompressed data unchanged (was working in 0.71)
+- deflate(Z_FULL_FLUSH), inflateReset and inflateSync are now fully implemented
+- added a test of inflateSync in example.c
+- moved MAX_WBITS to zconf.h because users might want to change that.
+- document explicitly that zalloc(64K) on MSDOS must return a normalized
+ pointer (zero offset)
+- added Makefiles for Microsoft C, Turbo C, Borland C++
+- faster crc32()
+
+Changes in 0.8 (29 April 95)
+- added fast inflate (inffast.c)
+- deflate(Z_FINISH) now returns Z_STREAM_END when done. Warning: this
+ is incompatible with previous versions of zlib which returned Z_OK.
+- work around a TurboC compiler bug (bad code for b << 0, see infutil.h)
+ (actually that was not a compiler bug, see 0.81 above)
+- gzread no longer reads one extra byte in certain cases
+- In gzio destroy(), don't reference a freed structure
+- avoid many warnings for MSDOS
+- avoid the ERROR symbol which is used by MS Windows
+
+Changes in 0.71 (14 April 95)
+- Fixed more MSDOS compilation problems :( There is still a bug with
+ TurboC large model.
+
+Changes in 0.7 (14 April 95)
+- Added full inflate support.
+- Simplified the crc32() interface. The pre- and post-conditioning
+ (one's complement) is now done inside crc32(). WARNING: this is
+ incompatible with previous versions; see zlib.h for the new usage.
+
+Changes in 0.61 (12 April 95)
+- workaround for a bug in TurboC. example and minigzip now work on MSDOS.
+
+Changes in 0.6 (11 April 95)
+- added minigzip.c
+- added gzdopen to reopen a file descriptor as gzFile
+- added transparent reading of non-gziped files in gzread.
+- fixed bug in gzread (don't read crc as data)
+- fixed bug in destroy (gzio.c) (don't return Z_STREAM_END for gzclose).
+- don't allocate big arrays in the stack (for MSDOS)
+- fix some MSDOS compilation problems
+
+Changes in 0.5:
+- do real compression in deflate.c. Z_PARTIAL_FLUSH is supported but
+ not yet Z_FULL_FLUSH.
+- support decompression but only in a single step (forced Z_FINISH)
+- added opaque object for zalloc and zfree.
+- added deflateReset and inflateReset
+- added a variable zlib_version for consistency checking.
+- renamed the 'filter' parameter of deflateInit2 as 'strategy'.
+ Added Z_FILTERED and Z_HUFFMAN_ONLY constants.
+
+Changes in 0.4:
+- avoid "zip" everywhere, use zlib instead of ziplib.
+- suppress Z_BLOCK_FLUSH, interpret Z_PARTIAL_FLUSH as block flush
+ if compression method == 8.
+- added adler32 and crc32
+- renamed deflateOptions as deflateInit2, call one or the other but not both
+- added the method parameter for deflateInit2.
+- added inflateInit2
+- simplied considerably deflateInit and inflateInit by not supporting
+ user-provided history buffer. This is supported only in deflateInit2
+ and inflateInit2.
+
+Changes in 0.3:
+- prefix all macro names with Z_
+- use Z_FINISH instead of deflateEnd to finish compression.
+- added Z_HUFFMAN_ONLY
+- added gzerror()
diff --git a/third-party/zlib/FAQ b/third-party/zlib/FAQ
new file mode 100644
index 0000000..99b7cf9
--- /dev/null
+++ b/third-party/zlib/FAQ
@@ -0,0 +1,368 @@
+
+ Frequently Asked Questions about zlib
+
+
+If your question is not there, please check the zlib home page
+http://zlib.net/ which may have more recent information.
+The lastest zlib FAQ is at http://zlib.net/zlib_faq.html
+
+
+ 1. Is zlib Y2K-compliant?
+
+ Yes. zlib doesn't handle dates.
+
+ 2. Where can I get a Windows DLL version?
+
+ The zlib sources can be compiled without change to produce a DLL. See the
+ file win32/DLL_FAQ.txt in the zlib distribution. Pointers to the
+ precompiled DLL are found in the zlib web site at http://zlib.net/ .
+
+ 3. Where can I get a Visual Basic interface to zlib?
+
+ See
+ * http://marknelson.us/1997/01/01/zlib-engine/
+ * win32/DLL_FAQ.txt in the zlib distribution
+
+ 4. compress() returns Z_BUF_ERROR.
+
+ Make sure that before the call of compress(), the length of the compressed
+ buffer is equal to the available size of the compressed buffer and not
+ zero. For Visual Basic, check that this parameter is passed by reference
+ ("as any"), not by value ("as long").
+
+ 5. deflate() or inflate() returns Z_BUF_ERROR.
+
+ Before making the call, make sure that avail_in and avail_out are not zero.
+ When setting the parameter flush equal to Z_FINISH, also make sure that
+ avail_out is big enough to allow processing all pending input. Note that a
+ Z_BUF_ERROR is not fatal--another call to deflate() or inflate() can be
+ made with more input or output space. A Z_BUF_ERROR may in fact be
+ unavoidable depending on how the functions are used, since it is not
+ possible to tell whether or not there is more output pending when
+ strm.avail_out returns with zero. See http://zlib.net/zlib_how.html for a
+ heavily annotated example.
+
+ 6. Where's the zlib documentation (man pages, etc.)?
+
+ It's in zlib.h . Examples of zlib usage are in the files test/example.c
+ and test/minigzip.c, with more in examples/ .
+
+ 7. Why don't you use GNU autoconf or libtool or ...?
+
+ Because we would like to keep zlib as a very small and simple package.
+ zlib is rather portable and doesn't need much configuration.
+
+ 8. I found a bug in zlib.
+
+ Most of the time, such problems are due to an incorrect usage of zlib.
+ Please try to reproduce the problem with a small program and send the
+ corresponding source to us at zlib at gzip.org . Do not send multi-megabyte
+ data files without prior agreement.
+
+ 9. Why do I get "undefined reference to gzputc"?
+
+ If "make test" produces something like
+
+ example.o(.text+0x154): undefined reference to `gzputc'
+
+ check that you don't have old files libz.* in /usr/lib, /usr/local/lib or
+ /usr/X11R6/lib. Remove any old versions, then do "make install".
+
+10. I need a Delphi interface to zlib.
+
+ See the contrib/delphi directory in the zlib distribution.
+
+11. Can zlib handle .zip archives?
+
+ Not by itself, no. See the directory contrib/minizip in the zlib
+ distribution.
+
+12. Can zlib handle .Z files?
+
+ No, sorry. You have to spawn an uncompress or gunzip subprocess, or adapt
+ the code of uncompress on your own.
+
+13. How can I make a Unix shared library?
+
+ By default a shared (and a static) library is built for Unix. So:
+
+ make distclean
+ ./configure
+ make
+
+14. How do I install a shared zlib library on Unix?
+
+ After the above, then:
+
+ make install
+
+ However, many flavors of Unix come with a shared zlib already installed.
+ Before going to the trouble of compiling a shared version of zlib and
+ trying to install it, you may want to check if it's already there! If you
+ can #include <zlib.h>, it's there. The -lz option will probably link to
+ it. You can check the version at the top of zlib.h or with the
+ ZLIB_VERSION symbol defined in zlib.h .
+
+15. I have a question about OttoPDF.
+
+ We are not the authors of OttoPDF. The real author is on the OttoPDF web
+ site: Joel Hainley, jhainley at myndkryme.com.
+
+16. Can zlib decode Flate data in an Adobe PDF file?
+
+ Yes. See http://www.pdflib.com/ . To modify PDF forms, see
+ http://sourceforge.net/projects/acroformtool/ .
+
+17. Why am I getting this "register_frame_info not found" error on Solaris?
+
+ After installing zlib 1.1.4 on Solaris 2.6, running applications using zlib
+ generates an error such as:
+
+ ld.so.1: rpm: fatal: relocation error: file /usr/local/lib/libz.so:
+ symbol __register_frame_info: referenced symbol not found
+
+ The symbol __register_frame_info is not part of zlib, it is generated by
+ the C compiler (cc or gcc). You must recompile applications using zlib
+ which have this problem. This problem is specific to Solaris. See
+ http://www.sunfreeware.com for Solaris versions of zlib and applications
+ using zlib.
+
+18. Why does gzip give an error on a file I make with compress/deflate?
+
+ The compress and deflate functions produce data in the zlib format, which
+ is different and incompatible with the gzip format. The gz* functions in
+ zlib on the other hand use the gzip format. Both the zlib and gzip formats
+ use the same compressed data format internally, but have different headers
+ and trailers around the compressed data.
+
+19. Ok, so why are there two different formats?
+
+ The gzip format was designed to retain the directory information about a
+ single file, such as the name and last modification date. The zlib format
+ on the other hand was designed for in-memory and communication channel
+ applications, and has a much more compact header and trailer and uses a
+ faster integrity check than gzip.
+
+20. Well that's nice, but how do I make a gzip file in memory?
+
+ You can request that deflate write the gzip format instead of the zlib
+ format using deflateInit2(). You can also request that inflate decode the
+ gzip format using inflateInit2(). Read zlib.h for more details.
+
+21. Is zlib thread-safe?
+
+ Yes. However any library routines that zlib uses and any application-
+ provided memory allocation routines must also be thread-safe. zlib's gz*
+ functions use stdio library routines, and most of zlib's functions use the
+ library memory allocation routines by default. zlib's *Init* functions
+ allow for the application to provide custom memory allocation routines.
+
+ Of course, you should only operate on any given zlib or gzip stream from a
+ single thread at a time.
+
+22. Can I use zlib in my commercial application?
+
+ Yes. Please read the license in zlib.h.
+
+23. Is zlib under the GNU license?
+
+ No. Please read the license in zlib.h.
+
+24. The license says that altered source versions must be "plainly marked". So
+ what exactly do I need to do to meet that requirement?
+
+ You need to change the ZLIB_VERSION and ZLIB_VERNUM #defines in zlib.h. In
+ particular, the final version number needs to be changed to "f", and an
+ identification string should be appended to ZLIB_VERSION. Version numbers
+ x.x.x.f are reserved for modifications to zlib by others than the zlib
+ maintainers. For example, if the version of the base zlib you are altering
+ is "1.2.3.4", then in zlib.h you should change ZLIB_VERNUM to 0x123f, and
+ ZLIB_VERSION to something like "1.2.3.f-zachary-mods-v3". You can also
+ update the version strings in deflate.c and inftrees.c.
+
+ For altered source distributions, you should also note the origin and
+ nature of the changes in zlib.h, as well as in ChangeLog and README, along
+ with the dates of the alterations. The origin should include at least your
+ name (or your company's name), and an email address to contact for help or
+ issues with the library.
+
+ Note that distributing a compiled zlib library along with zlib.h and
+ zconf.h is also a source distribution, and so you should change
+ ZLIB_VERSION and ZLIB_VERNUM and note the origin and nature of the changes
+ in zlib.h as you would for a full source distribution.
+
+25. Will zlib work on a big-endian or little-endian architecture, and can I
+ exchange compressed data between them?
+
+ Yes and yes.
+
+26. Will zlib work on a 64-bit machine?
+
+ Yes. It has been tested on 64-bit machines, and has no dependence on any
+ data types being limited to 32-bits in length. If you have any
+ difficulties, please provide a complete problem report to zlib at gzip.org
+
+27. Will zlib decompress data from the PKWare Data Compression Library?
+
+ No. The PKWare DCL uses a completely different compressed data format than
+ does PKZIP and zlib. However, you can look in zlib's contrib/blast
+ directory for a possible solution to your problem.
+
+28. Can I access data randomly in a compressed stream?
+
+ No, not without some preparation. If when compressing you periodically use
+ Z_FULL_FLUSH, carefully write all the pending data at those points, and
+ keep an index of those locations, then you can start decompression at those
+ points. You have to be careful to not use Z_FULL_FLUSH too often, since it
+ can significantly degrade compression. Alternatively, you can scan a
+ deflate stream once to generate an index, and then use that index for
+ random access. See examples/zran.c .
+
+29. Does zlib work on MVS, OS/390, CICS, etc.?
+
+ It has in the past, but we have not heard of any recent evidence. There
+ were working ports of zlib 1.1.4 to MVS, but those links no longer work.
+ If you know of recent, successful applications of zlib on these operating
+ systems, please let us know. Thanks.
+
+30. Is there some simpler, easier to read version of inflate I can look at to
+ understand the deflate format?
+
+ First off, you should read RFC 1951. Second, yes. Look in zlib's
+ contrib/puff directory.
+
+31. Does zlib infringe on any patents?
+
+ As far as we know, no. In fact, that was originally the whole point behind
+ zlib. Look here for some more information:
+
+ http://www.gzip.org/#faq11
+
+32. Can zlib work with greater than 4 GB of data?
+
+ Yes. inflate() and deflate() will process any amount of data correctly.
+ Each call of inflate() or deflate() is limited to input and output chunks
+ of the maximum value that can be stored in the compiler's "unsigned int"
+ type, but there is no limit to the number of chunks. Note however that the
+ strm.total_in and strm_total_out counters may be limited to 4 GB. These
+ counters are provided as a convenience and are not used internally by
+ inflate() or deflate(). The application can easily set up its own counters
+ updated after each call of inflate() or deflate() to count beyond 4 GB.
+ compress() and uncompress() may be limited to 4 GB, since they operate in a
+ single call. gzseek() and gztell() may be limited to 4 GB depending on how
+ zlib is compiled. See the zlibCompileFlags() function in zlib.h.
+
+ The word "may" appears several times above since there is a 4 GB limit only
+ if the compiler's "long" type is 32 bits. If the compiler's "long" type is
+ 64 bits, then the limit is 16 exabytes.
+
+33. Does zlib have any security vulnerabilities?
+
+ The only one that we are aware of is potentially in gzprintf(). If zlib is
+ compiled to use sprintf() or vsprintf(), then there is no protection
+ against a buffer overflow of an 8K string space (or other value as set by
+ gzbuffer()), other than the caller of gzprintf() assuring that the output
+ will not exceed 8K. On the other hand, if zlib is compiled to use
+ snprintf() or vsnprintf(), which should normally be the case, then there is
+ no vulnerability. The ./configure script will display warnings if an
+ insecure variation of sprintf() will be used by gzprintf(). Also the
+ zlibCompileFlags() function will return information on what variant of
+ sprintf() is used by gzprintf().
+
+ If you don't have snprintf() or vsnprintf() and would like one, you can
+ find a portable implementation here:
+
+ http://www.ijs.si/software/snprintf/
+
+ Note that you should be using the most recent version of zlib. Versions
+ 1.1.3 and before were subject to a double-free vulnerability, and versions
+ 1.2.1 and 1.2.2 were subject to an access exception when decompressing
+ invalid compressed data.
+
+34. Is there a Java version of zlib?
+
+ Probably what you want is to use zlib in Java. zlib is already included
+ as part of the Java SDK in the java.util.zip package. If you really want
+ a version of zlib written in the Java language, look on the zlib home
+ page for links: http://zlib.net/ .
+
+35. I get this or that compiler or source-code scanner warning when I crank it
+ up to maximally-pedantic. Can't you guys write proper code?
+
+ Many years ago, we gave up attempting to avoid warnings on every compiler
+ in the universe. It just got to be a waste of time, and some compilers
+ were downright silly as well as contradicted each other. So now, we simply
+ make sure that the code always works.
+
+36. Valgrind (or some similar memory access checker) says that deflate is
+ performing a conditional jump that depends on an uninitialized value.
+ Isn't that a bug?
+
+ No. That is intentional for performance reasons, and the output of deflate
+ is not affected. This only started showing up recently since zlib 1.2.x
+ uses malloc() by default for allocations, whereas earlier versions used
+ calloc(), which zeros out the allocated memory. Even though the code was
+ correct, versions 1.2.4 and later was changed to not stimulate these
+ checkers.
+
+37. Will zlib read the (insert any ancient or arcane format here) compressed
+ data format?
+
+ Probably not. Look in the comp.compression FAQ for pointers to various
+ formats and associated software.
+
+38. How can I encrypt/decrypt zip files with zlib?
+
+ zlib doesn't support encryption. The original PKZIP encryption is very
+ weak and can be broken with freely available programs. To get strong
+ encryption, use GnuPG, http://www.gnupg.org/ , which already includes zlib
+ compression. For PKZIP compatible "encryption", look at
+ http://www.info-zip.org/
+
+39. What's the difference between the "gzip" and "deflate" HTTP 1.1 encodings?
+
+ "gzip" is the gzip format, and "deflate" is the zlib format. They should
+ probably have called the second one "zlib" instead to avoid confusion with
+ the raw deflate compressed data format. While the HTTP 1.1 RFC 2616
+ correctly points to the zlib specification in RFC 1950 for the "deflate"
+ transfer encoding, there have been reports of servers and browsers that
+ incorrectly produce or expect raw deflate data per the deflate
+ specification in RFC 1951, most notably Microsoft. So even though the
+ "deflate" transfer encoding using the zlib format would be the more
+ efficient approach (and in fact exactly what the zlib format was designed
+ for), using the "gzip" transfer encoding is probably more reliable due to
+ an unfortunate choice of name on the part of the HTTP 1.1 authors.
+
+ Bottom line: use the gzip format for HTTP 1.1 encoding.
+
+40. Does zlib support the new "Deflate64" format introduced by PKWare?
+
+ No. PKWare has apparently decided to keep that format proprietary, since
+ they have not documented it as they have previous compression formats. In
+ any case, the compression improvements are so modest compared to other more
+ modern approaches, that it's not worth the effort to implement.
+
+41. I'm having a problem with the zip functions in zlib, can you help?
+
+ There are no zip functions in zlib. You are probably using minizip by
+ Giles Vollant, which is found in the contrib directory of zlib. It is not
+ part of zlib. In fact none of the stuff in contrib is part of zlib. The
+ files in there are not supported by the zlib authors. You need to contact
+ the authors of the respective contribution for help.
+
+42. The match.asm code in contrib is under the GNU General Public License.
+ Since it's part of zlib, doesn't that mean that all of zlib falls under the
+ GNU GPL?
+
+ No. The files in contrib are not part of zlib. They were contributed by
+ other authors and are provided as a convenience to the user within the zlib
+ distribution. Each item in contrib has its own license.
+
+43. Is zlib subject to export controls? What is its ECCN?
+
+ zlib is not subject to export controls, and so is classified as EAR99.
+
+44. Can you please sign these lengthy legal documents and fax them back to us
+ so that we can use your software in our product?
+
+ No. Go away. Shoo.
diff --git a/third-party/zlib/INDEX b/third-party/zlib/INDEX
new file mode 100644
index 0000000..2ba0641
--- /dev/null
+++ b/third-party/zlib/INDEX
@@ -0,0 +1,68 @@
+CMakeLists.txt cmake build file
+ChangeLog history of changes
+FAQ Frequently Asked Questions about zlib
+INDEX this file
+Makefile dummy Makefile that tells you to ./configure
+Makefile.in template for Unix Makefile
+README guess what
+configure configure script for Unix
+make_vms.com makefile for VMS
+test/example.c zlib usages examples for build testing
+test/minigzip.c minimal gzip-like functionality for build testing
+test/infcover.c inf*.c code coverage for build coverage testing
+treebuild.xml XML description of source file dependencies
+zconf.h.cmakein zconf.h template for cmake
+zconf.h.in zconf.h template for configure
+zlib.3 Man page for zlib
+zlib.3.pdf Man page in PDF format
+zlib.map Linux symbol information
+zlib.pc.in Template for pkg-config descriptor
+zlib.pc.cmakein zlib.pc template for cmake
+zlib2ansi perl script to convert source files for C++ compilation
+
+amiga/ makefiles for Amiga SAS C
+as400/ makefiles for AS/400
+doc/ documentation for formats and algorithms
+msdos/ makefiles for MSDOS
+nintendods/ makefile for Nintendo DS
+old/ makefiles for various architectures and zlib documentation
+ files that have not yet been updated for zlib 1.2.x
+qnx/ makefiles for QNX
+watcom/ makefiles for OpenWatcom
+win32/ makefiles for Windows
+
+ zlib public header files (required for library use):
+zconf.h
+zlib.h
+
+ private source files used to build the zlib library:
+adler32.c
+compress.c
+crc32.c
+crc32.h
+deflate.c
+deflate.h
+gzclose.c
+gzguts.h
+gzlib.c
+gzread.c
+gzwrite.c
+infback.c
+inffast.c
+inffast.h
+inffixed.h
+inflate.c
+inflate.h
+inftrees.c
+inftrees.h
+trees.c
+trees.h
+uncompr.c
+zutil.c
+zutil.h
+
+ source files for sample programs
+See examples/README.examples
+
+ unsupported contributions by third parties
+See contrib/README.contrib
diff --git a/third-party/zlib/Makefile.in b/third-party/zlib/Makefile.in
new file mode 100644
index 0000000..c61aa30
--- /dev/null
+++ b/third-party/zlib/Makefile.in
@@ -0,0 +1,288 @@
+# Makefile for zlib
+# Copyright (C) 1995-2013 Jean-loup Gailly, Mark Adler
+# For conditions of distribution and use, see copyright notice in zlib.h
+
+# To compile and test, type:
+# ./configure; make test
+# Normally configure builds both a static and a shared library.
+# If you want to build just a static library, use: ./configure --static
+
+# To use the asm code, type:
+# cp contrib/asm?86/match.S ./match.S
+# make LOC=-DASMV OBJA=match.o
+
+# To install /usr/local/lib/libz.* and /usr/local/include/zlib.h, type:
+# make install
+# To install in $HOME instead of /usr/local, use:
+# make install prefix=$HOME
+
+CC=cc
+
+CFLAGS=-O
+#CFLAGS=-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7
+#CFLAGS=-g -DDEBUG
+#CFLAGS=-O3 -Wall -Wwrite-strings -Wpointer-arith -Wconversion \
+# -Wstrict-prototypes -Wmissing-prototypes
+
+SFLAGS=-O
+LDFLAGS=
+TEST_LDFLAGS=-L. libz.a
+LDSHARED=$(CC)
+CPP=$(CC) -E
+
+STATICLIB=libz.a
+SHAREDLIB=libz.so
+SHAREDLIBV=libz.so.1.2.8
+SHAREDLIBM=libz.so.1
+LIBS=$(STATICLIB) $(SHAREDLIBV)
+
+AR=ar
+ARFLAGS=rc
+RANLIB=ranlib
+LDCONFIG=ldconfig
+LDSHAREDLIBC=-lc
+TAR=tar
+SHELL=/bin/sh
+EXE=
+
+prefix = /usr/local
+exec_prefix = ${prefix}
+libdir = ${exec_prefix}/lib
+sharedlibdir = ${libdir}
+includedir = ${prefix}/include
+mandir = ${prefix}/share/man
+man3dir = ${mandir}/man3
+pkgconfigdir = ${libdir}/pkgconfig
+
+OBJZ = adler32.o crc32.o deflate.o infback.o inffast.o inflate.o inftrees.o trees.o zutil.o
+OBJG = compress.o uncompr.o gzclose.o gzlib.o gzread.o gzwrite.o
+OBJC = $(OBJZ) $(OBJG)
+
+PIC_OBJZ = adler32.lo crc32.lo deflate.lo infback.lo inffast.lo inflate.lo inftrees.lo trees.lo zutil.lo
+PIC_OBJG = compress.lo uncompr.lo gzclose.lo gzlib.lo gzread.lo gzwrite.lo
+PIC_OBJC = $(PIC_OBJZ) $(PIC_OBJG)
+
+# to use the asm code: make OBJA=match.o, PIC_OBJA=match.lo
+OBJA =
+PIC_OBJA =
+
+OBJS = $(OBJC) $(OBJA)
+
+PIC_OBJS = $(PIC_OBJC) $(PIC_OBJA)
+
+all: static shared
+
+static: example$(EXE) minigzip$(EXE)
+
+shared: examplesh$(EXE) minigzipsh$(EXE)
+
+all64: example64$(EXE) minigzip64$(EXE)
+
+check: test
+
+test: all teststatic testshared
+
+teststatic: static
+ @TMPST=tmpst_$$; \
+ if echo hello world | ./minigzip | ./minigzip -d && ./example $$TMPST ; then \
+ echo ' *** zlib test OK ***'; \
+ else \
+ echo ' *** zlib test FAILED ***'; false; \
+ fi; \
+ rm -f $$TMPST
+
+testshared: shared
+ @LD_LIBRARY_PATH=`pwd`:$(LD_LIBRARY_PATH) ; export LD_LIBRARY_PATH; \
+ LD_LIBRARYN32_PATH=`pwd`:$(LD_LIBRARYN32_PATH) ; export LD_LIBRARYN32_PATH; \
+ DYLD_LIBRARY_PATH=`pwd`:$(DYLD_LIBRARY_PATH) ; export DYLD_LIBRARY_PATH; \
+ SHLIB_PATH=`pwd`:$(SHLIB_PATH) ; export SHLIB_PATH; \
+ TMPSH=tmpsh_$$; \
+ if echo hello world | ./minigzipsh | ./minigzipsh -d && ./examplesh $$TMPSH; then \
+ echo ' *** zlib shared test OK ***'; \
+ else \
+ echo ' *** zlib shared test FAILED ***'; false; \
+ fi; \
+ rm -f $$TMPSH
+
+test64: all64
+ @TMP64=tmp64_$$; \
+ if echo hello world | ./minigzip64 | ./minigzip64 -d && ./example64 $$TMP64; then \
+ echo ' *** zlib 64-bit test OK ***'; \
+ else \
+ echo ' *** zlib 64-bit test FAILED ***'; false; \
+ fi; \
+ rm -f $$TMP64
+
+infcover.o: test/infcover.c zlib.h zconf.h
+ $(CC) $(CFLAGS) -I. -c -o $@ test/infcover.c
+
+infcover: infcover.o libz.a
+ $(CC) $(CFLAGS) -o $@ infcover.o libz.a
+
+cover: infcover
+ rm -f *.gcda
+ ./infcover
+ gcov inf*.c
+
+libz.a: $(OBJS)
+ $(AR) $(ARFLAGS) $@ $(OBJS)
+ -@ ($(RANLIB) $@ || true) >/dev/null 2>&1
+
+match.o: match.S
+ $(CPP) match.S > _match.s
+ $(CC) -c _match.s
+ mv _match.o match.o
+ rm -f _match.s
+
+match.lo: match.S
+ $(CPP) match.S > _match.s
+ $(CC) -c -fPIC _match.s
+ mv _match.o match.lo
+ rm -f _match.s
+
+example.o: test/example.c zlib.h zconf.h
+ $(CC) $(CFLAGS) -I. -c -o $@ test/example.c
+
+minigzip.o: test/minigzip.c zlib.h zconf.h
+ $(CC) $(CFLAGS) -I. -c -o $@ test/minigzip.c
+
+example64.o: test/example.c zlib.h zconf.h
+ $(CC) $(CFLAGS) -I. -D_FILE_OFFSET_BITS=64 -c -o $@ test/example.c
+
+minigzip64.o: test/minigzip.c zlib.h zconf.h
+ $(CC) $(CFLAGS) -I. -D_FILE_OFFSET_BITS=64 -c -o $@ test/minigzip.c
+
+.SUFFIXES: .lo
+
+.c.lo:
+ - at mkdir objs 2>/dev/null || test -d objs
+ $(CC) $(SFLAGS) -DPIC -c -o objs/$*.o $<
+ - at mv objs/$*.o $@
+
+placebo $(SHAREDLIBV): $(PIC_OBJS) libz.a
+ $(LDSHARED) $(SFLAGS) -o $@ $(PIC_OBJS) $(LDSHAREDLIBC) $(LDFLAGS)
+ rm -f $(SHAREDLIB) $(SHAREDLIBM)
+ ln -s $@ $(SHAREDLIB)
+ ln -s $@ $(SHAREDLIBM)
+ - at rmdir objs
+
+example$(EXE): example.o $(STATICLIB)
+ $(CC) $(CFLAGS) -o $@ example.o $(TEST_LDFLAGS)
+
+minigzip$(EXE): minigzip.o $(STATICLIB)
+ $(CC) $(CFLAGS) -o $@ minigzip.o $(TEST_LDFLAGS)
+
+examplesh$(EXE): example.o $(SHAREDLIBV)
+ $(CC) $(CFLAGS) -o $@ example.o -L. $(SHAREDLIBV)
+
+minigzipsh$(EXE): minigzip.o $(SHAREDLIBV)
+ $(CC) $(CFLAGS) -o $@ minigzip.o -L. $(SHAREDLIBV)
+
+example64$(EXE): example64.o $(STATICLIB)
+ $(CC) $(CFLAGS) -o $@ example64.o $(TEST_LDFLAGS)
+
+minigzip64$(EXE): minigzip64.o $(STATICLIB)
+ $(CC) $(CFLAGS) -o $@ minigzip64.o $(TEST_LDFLAGS)
+
+install-libs: $(LIBS)
+ - at if [ ! -d $(DESTDIR)$(exec_prefix) ]; then mkdir -p $(DESTDIR)$(exec_prefix); fi
+ - at if [ ! -d $(DESTDIR)$(libdir) ]; then mkdir -p $(DESTDIR)$(libdir); fi
+ - at if [ ! -d $(DESTDIR)$(sharedlibdir) ]; then mkdir -p $(DESTDIR)$(sharedlibdir); fi
+ - at if [ ! -d $(DESTDIR)$(man3dir) ]; then mkdir -p $(DESTDIR)$(man3dir); fi
+ - at if [ ! -d $(DESTDIR)$(pkgconfigdir) ]; then mkdir -p $(DESTDIR)$(pkgconfigdir); fi
+ cp $(STATICLIB) $(DESTDIR)$(libdir)
+ chmod 644 $(DESTDIR)$(libdir)/$(STATICLIB)
+ -@($(RANLIB) $(DESTDIR)$(libdir)/libz.a || true) >/dev/null 2>&1
+ - at if test -n "$(SHAREDLIBV)"; then \
+ cp $(SHAREDLIBV) $(DESTDIR)$(sharedlibdir); \
+ echo "cp $(SHAREDLIBV) $(DESTDIR)$(sharedlibdir)"; \
+ chmod 755 $(DESTDIR)$(sharedlibdir)/$(SHAREDLIBV); \
+ echo "chmod 755 $(DESTDIR)$(sharedlibdir)/$(SHAREDLIBV)"; \
+ rm -f $(DESTDIR)$(sharedlibdir)/$(SHAREDLIB) $(DESTDIR)$(sharedlibdir)/$(SHAREDLIBM); \
+ ln -s $(SHAREDLIBV) $(DESTDIR)$(sharedlibdir)/$(SHAREDLIB); \
+ ln -s $(SHAREDLIBV) $(DESTDIR)$(sharedlibdir)/$(SHAREDLIBM); \
+ ($(LDCONFIG) || true) >/dev/null 2>&1; \
+ fi
+ cp zlib.3 $(DESTDIR)$(man3dir)
+ chmod 644 $(DESTDIR)$(man3dir)/zlib.3
+ cp zlib.pc $(DESTDIR)$(pkgconfigdir)
+ chmod 644 $(DESTDIR)$(pkgconfigdir)/zlib.pc
+# The ranlib in install is needed on NeXTSTEP which checks file times
+# ldconfig is for Linux
+
+install: install-libs
+ - at if [ ! -d $(DESTDIR)$(includedir) ]; then mkdir -p $(DESTDIR)$(includedir); fi
+ cp zlib.h zconf.h $(DESTDIR)$(includedir)
+ chmod 644 $(DESTDIR)$(includedir)/zlib.h $(DESTDIR)$(includedir)/zconf.h
+
+uninstall:
+ cd $(DESTDIR)$(includedir) && rm -f zlib.h zconf.h
+ cd $(DESTDIR)$(libdir) && rm -f libz.a; \
+ if test -n "$(SHAREDLIBV)" -a -f $(SHAREDLIBV); then \
+ rm -f $(SHAREDLIBV) $(SHAREDLIB) $(SHAREDLIBM); \
+ fi
+ cd $(DESTDIR)$(man3dir) && rm -f zlib.3
+ cd $(DESTDIR)$(pkgconfigdir) && rm -f zlib.pc
+
+docs: zlib.3.pdf
+
+zlib.3.pdf: zlib.3
+ groff -mandoc -f H -T ps zlib.3 | ps2pdf - zlib.3.pdf
+
+zconf.h.cmakein: zconf.h.in
+ -@ TEMPFILE=zconfh_$$; \
+ echo "/#define ZCONF_H/ a\\\\\n#cmakedefine Z_PREFIX\\\\\n#cmakedefine Z_HAVE_UNISTD_H\n" >> $$TEMPFILE &&\
+ sed -f $$TEMPFILE zconf.h.in > zconf.h.cmakein &&\
+ touch -r zconf.h.in zconf.h.cmakein &&\
+ rm $$TEMPFILE
+
+zconf: zconf.h.in
+ cp -p zconf.h.in zconf.h
+
+mostlyclean: clean
+clean:
+ rm -f *.o *.lo *~ \
+ example$(EXE) minigzip$(EXE) examplesh$(EXE) minigzipsh$(EXE) \
+ example64$(EXE) minigzip64$(EXE) \
+ infcover \
+ libz.* foo.gz so_locations \
+ _match.s maketree contrib/infback9/*.o
+ rm -rf objs
+ rm -f *.gcda *.gcno *.gcov
+ rm -f contrib/infback9/*.gcda contrib/infback9/*.gcno contrib/infback9/*.gcov
+
+maintainer-clean: distclean
+distclean: clean zconf zconf.h.cmakein docs
+ rm -f Makefile zlib.pc configure.log
+ - at rm -f .DS_Store
+ - at printf 'all:\n\t- at echo "Please use ./configure first. Thank you."\n' > Makefile
+ - at printf '\ndistclean:\n\tmake -f Makefile.in distclean\n' >> Makefile
+ - at touch -r Makefile.in Makefile
+
+tags:
+ etags *.[ch]
+
+depend:
+ makedepend -- $(CFLAGS) -- *.[ch]
+
+# DO NOT DELETE THIS LINE -- make depend depends on it.
+
+adler32.o zutil.o: zutil.h zlib.h zconf.h
+gzclose.o gzlib.o gzread.o gzwrite.o: zlib.h zconf.h gzguts.h
+compress.o example.o minigzip.o uncompr.o: zlib.h zconf.h
+crc32.o: zutil.h zlib.h zconf.h crc32.h
+deflate.o: deflate.h zutil.h zlib.h zconf.h
+infback.o inflate.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h inffixed.h
+inffast.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
+inftrees.o: zutil.h zlib.h zconf.h inftrees.h
+trees.o: deflate.h zutil.h zlib.h zconf.h trees.h
+
+adler32.lo zutil.lo: zutil.h zlib.h zconf.h
+gzclose.lo gzlib.lo gzread.lo gzwrite.lo: zlib.h zconf.h gzguts.h
+compress.lo example.lo minigzip.lo uncompr.lo: zlib.h zconf.h
+crc32.lo: zutil.h zlib.h zconf.h crc32.h
+deflate.lo: deflate.h zutil.h zlib.h zconf.h
+infback.lo inflate.lo: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h inffixed.h
+inffast.lo: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
+inftrees.lo: zutil.h zlib.h zconf.h inftrees.h
+trees.lo: deflate.h zutil.h zlib.h zconf.h trees.h
diff --git a/third-party/zlib/Makefile.pic b/third-party/zlib/Makefile.pic
new file mode 100644
index 0000000..1d4d914
--- /dev/null
+++ b/third-party/zlib/Makefile.pic
@@ -0,0 +1,3 @@
+include Makefile
+
+PIC: $(PIC_OBJS)
diff --git a/third-party/zlib/README b/third-party/zlib/README
new file mode 100644
index 0000000..5ca9d12
--- /dev/null
+++ b/third-party/zlib/README
@@ -0,0 +1,115 @@
+ZLIB DATA COMPRESSION LIBRARY
+
+zlib 1.2.8 is a general purpose data compression library. All the code is
+thread safe. The data format used by the zlib library is described by RFCs
+(Request for Comments) 1950 to 1952 in the files
+http://tools.ietf.org/html/rfc1950 (zlib format), rfc1951 (deflate format) and
+rfc1952 (gzip format).
+
+All functions of the compression library are documented in the file zlib.h
+(volunteer to write man pages welcome, contact zlib at gzip.org). A usage example
+of the library is given in the file test/example.c which also tests that
+the library is working correctly. Another example is given in the file
+test/minigzip.c. The compression library itself is composed of all source
+files in the root directory.
+
+To compile all files and run the test program, follow the instructions given at
+the top of Makefile.in. In short "./configure; make test", and if that goes
+well, "make install" should work for most flavors of Unix. For Windows, use
+one of the special makefiles in win32/ or contrib/vstudio/ . For VMS, use
+make_vms.com.
+
+Questions about zlib should be sent to <zlib at gzip.org>, or to Gilles Vollant
+<info at winimage.com> for the Windows DLL version. The zlib home page is
+http://zlib.net/ . Before reporting a problem, please check this site to
+verify that you have the latest version of zlib; otherwise get the latest
+version and check whether the problem still exists or not.
+
+PLEASE read the zlib FAQ http://zlib.net/zlib_faq.html before asking for help.
+
+Mark Nelson <markn at ieee.org> wrote an article about zlib for the Jan. 1997
+issue of Dr. Dobb's Journal; a copy of the article is available at
+http://marknelson.us/1997/01/01/zlib-engine/ .
+
+The changes made in version 1.2.8 are documented in the file ChangeLog.
+
+Unsupported third party contributions are provided in directory contrib/ .
+
+zlib is available in Java using the java.util.zip package, documented at
+http://java.sun.com/developer/technicalArticles/Programming/compression/ .
+
+A Perl interface to zlib written by Paul Marquess <pmqs at cpan.org> is available
+at CPAN (Comprehensive Perl Archive Network) sites, including
+http://search.cpan.org/~pmqs/IO-Compress-Zlib/ .
+
+A Python interface to zlib written by A.M. Kuchling <amk at amk.ca> is
+available in Python 1.5 and later versions, see
+http://docs.python.org/library/zlib.html .
+
+zlib is built into tcl: http://wiki.tcl.tk/4610 .
+
+An experimental package to read and write files in .zip format, written on top
+of zlib by Gilles Vollant <info at winimage.com>, is available in the
+contrib/minizip directory of zlib.
+
+
+Notes for some targets:
+
+- For Windows DLL versions, please see win32/DLL_FAQ.txt
+
+- For 64-bit Irix, deflate.c must be compiled without any optimization. With
+ -O, one libpng test fails. The test works in 32 bit mode (with the -n32
+ compiler flag). The compiler bug has been reported to SGI.
+
+- zlib doesn't work with gcc 2.6.3 on a DEC 3000/300LX under OSF/1 2.1 it works
+ when compiled with cc.
+
+- On Digital Unix 4.0D (formely OSF/1) on AlphaServer, the cc option -std1 is
+ necessary to get gzprintf working correctly. This is done by configure.
+
+- zlib doesn't work on HP-UX 9.05 with some versions of /bin/cc. It works with
+ other compilers. Use "make test" to check your compiler.
+
+- gzdopen is not supported on RISCOS or BEOS.
+
+- For PalmOs, see http://palmzlib.sourceforge.net/
+
+
+Acknowledgments:
+
+ The deflate format used by zlib was defined by Phil Katz. The deflate and
+ zlib specifications were written by L. Peter Deutsch. Thanks to all the
+ people who reported problems and suggested various improvements in zlib; they
+ are too numerous to cite here.
+
+Copyright notice:
+
+ (C) 1995-2013 Jean-loup Gailly and Mark Adler
+
+ This software is provided 'as-is', without any express or implied
+ warranty. In no event will the authors be held liable for any damages
+ arising from the use of this software.
+
+ Permission is granted to anyone to use this software for any purpose,
+ including commercial applications, and to alter it and redistribute it
+ freely, subject to the following restrictions:
+
+ 1. The origin of this software must not be misrepresented; you must not
+ claim that you wrote the original software. If you use this software
+ in a product, an acknowledgment in the product documentation would be
+ appreciated but is not required.
+ 2. Altered source versions must be plainly marked as such, and must not be
+ misrepresented as being the original software.
+ 3. This notice may not be removed or altered from any source distribution.
+
+ Jean-loup Gailly Mark Adler
+ jloup at gzip.org madler at alumni.caltech.edu
+
+If you use the zlib library in a product, we would appreciate *not* receiving
+lengthy legal documents to sign. The sources are provided for free but without
+warranty of any kind. The library has been entirely written by Jean-loup
+Gailly and Mark Adler; it does not include third-party code.
+
+If you redistribute modified sources, we would appreciate that you include in
+the file ChangeLog history information documenting your changes. Please read
+the FAQ for more information on the distribution of modified source versions.
diff --git a/third-party/zlib/adler32.c b/third-party/zlib/adler32.c
new file mode 100644
index 0000000..a868f07
--- /dev/null
+++ b/third-party/zlib/adler32.c
@@ -0,0 +1,179 @@
+/* adler32.c -- compute the Adler-32 checksum of a data stream
+ * Copyright (C) 1995-2011 Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* @(#) $Id$ */
+
+#include "zutil.h"
+
+#define local static
+
+local uLong adler32_combine_ OF((uLong adler1, uLong adler2, z_off64_t len2));
+
+#define BASE 65521 /* largest prime smaller than 65536 */
+#define NMAX 5552
+/* NMAX is the largest n such that 255n(n+1)/2 + (n+1)(BASE-1) <= 2^32-1 */
+
+#define DO1(buf,i) {adler += (buf)[i]; sum2 += adler;}
+#define DO2(buf,i) DO1(buf,i); DO1(buf,i+1);
+#define DO4(buf,i) DO2(buf,i); DO2(buf,i+2);
+#define DO8(buf,i) DO4(buf,i); DO4(buf,i+4);
+#define DO16(buf) DO8(buf,0); DO8(buf,8);
+
+/* use NO_DIVIDE if your processor does not do division in hardware --
+ try it both ways to see which is faster */
+#ifdef NO_DIVIDE
+/* note that this assumes BASE is 65521, where 65536 % 65521 == 15
+ (thank you to John Reiser for pointing this out) */
+# define CHOP(a) \
+ do { \
+ unsigned long tmp = a >> 16; \
+ a &= 0xffffUL; \
+ a += (tmp << 4) - tmp; \
+ } while (0)
+# define MOD28(a) \
+ do { \
+ CHOP(a); \
+ if (a >= BASE) a -= BASE; \
+ } while (0)
+# define MOD(a) \
+ do { \
+ CHOP(a); \
+ MOD28(a); \
+ } while (0)
+# define MOD63(a) \
+ do { /* this assumes a is not negative */ \
+ z_off64_t tmp = a >> 32; \
+ a &= 0xffffffffL; \
+ a += (tmp << 8) - (tmp << 5) + tmp; \
+ tmp = a >> 16; \
+ a &= 0xffffL; \
+ a += (tmp << 4) - tmp; \
+ tmp = a >> 16; \
+ a &= 0xffffL; \
+ a += (tmp << 4) - tmp; \
+ if (a >= BASE) a -= BASE; \
+ } while (0)
+#else
+# define MOD(a) a %= BASE
+# define MOD28(a) a %= BASE
+# define MOD63(a) a %= BASE
+#endif
+
+/* ========================================================================= */
+uLong ZEXPORT adler32(adler, buf, len)
+ uLong adler;
+ const Bytef *buf;
+ uInt len;
+{
+ unsigned long sum2;
+ unsigned n;
+
+ /* split Adler-32 into component sums */
+ sum2 = (adler >> 16) & 0xffff;
+ adler &= 0xffff;
+
+ /* in case user likes doing a byte at a time, keep it fast */
+ if (len == 1) {
+ adler += buf[0];
+ if (adler >= BASE)
+ adler -= BASE;
+ sum2 += adler;
+ if (sum2 >= BASE)
+ sum2 -= BASE;
+ return adler | (sum2 << 16);
+ }
+
+ /* initial Adler-32 value (deferred check for len == 1 speed) */
+ if (buf == Z_NULL)
+ return 1L;
+
+ /* in case short lengths are provided, keep it somewhat fast */
+ if (len < 16) {
+ while (len--) {
+ adler += *buf++;
+ sum2 += adler;
+ }
+ if (adler >= BASE)
+ adler -= BASE;
+ MOD28(sum2); /* only added so many BASE's */
+ return adler | (sum2 << 16);
+ }
+
+ /* do length NMAX blocks -- requires just one modulo operation */
+ while (len >= NMAX) {
+ len -= NMAX;
+ n = NMAX / 16; /* NMAX is divisible by 16 */
+ do {
+ DO16(buf); /* 16 sums unrolled */
+ buf += 16;
+ } while (--n);
+ MOD(adler);
+ MOD(sum2);
+ }
+
+ /* do remaining bytes (less than NMAX, still just one modulo) */
+ if (len) { /* avoid modulos if none remaining */
+ while (len >= 16) {
+ len -= 16;
+ DO16(buf);
+ buf += 16;
+ }
+ while (len--) {
+ adler += *buf++;
+ sum2 += adler;
+ }
+ MOD(adler);
+ MOD(sum2);
+ }
+
+ /* return recombined sums */
+ return adler | (sum2 << 16);
+}
+
+/* ========================================================================= */
+local uLong adler32_combine_(adler1, adler2, len2)
+ uLong adler1;
+ uLong adler2;
+ z_off64_t len2;
+{
+ unsigned long sum1;
+ unsigned long sum2;
+ unsigned rem;
+
+ /* for negative len, return invalid adler32 as a clue for debugging */
+ if (len2 < 0)
+ return 0xffffffffUL;
+
+ /* the derivation of this formula is left as an exercise for the reader */
+ MOD63(len2); /* assumes len2 >= 0 */
+ rem = (unsigned)len2;
+ sum1 = adler1 & 0xffff;
+ sum2 = rem * sum1;
+ MOD(sum2);
+ sum1 += (adler2 & 0xffff) + BASE - 1;
+ sum2 += ((adler1 >> 16) & 0xffff) + ((adler2 >> 16) & 0xffff) + BASE - rem;
+ if (sum1 >= BASE) sum1 -= BASE;
+ if (sum1 >= BASE) sum1 -= BASE;
+ if (sum2 >= (BASE << 1)) sum2 -= (BASE << 1);
+ if (sum2 >= BASE) sum2 -= BASE;
+ return sum1 | (sum2 << 16);
+}
+
+/* ========================================================================= */
+uLong ZEXPORT adler32_combine(adler1, adler2, len2)
+ uLong adler1;
+ uLong adler2;
+ z_off_t len2;
+{
+ return adler32_combine_(adler1, adler2, len2);
+}
+
+uLong ZEXPORT adler32_combine64(adler1, adler2, len2)
+ uLong adler1;
+ uLong adler2;
+ z_off64_t len2;
+{
+ return adler32_combine_(adler1, adler2, len2);
+}
diff --git a/third-party/zlib/compress.c b/third-party/zlib/compress.c
new file mode 100644
index 0000000..6e97626
--- /dev/null
+++ b/third-party/zlib/compress.c
@@ -0,0 +1,80 @@
+/* compress.c -- compress a memory buffer
+ * Copyright (C) 1995-2005 Jean-loup Gailly.
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* @(#) $Id$ */
+
+#define ZLIB_INTERNAL
+#include "zlib.h"
+
+/* ===========================================================================
+ Compresses the source buffer into the destination buffer. The level
+ parameter has the same meaning as in deflateInit. sourceLen is the byte
+ length of the source buffer. Upon entry, destLen is the total size of the
+ destination buffer, which must be at least 0.1% larger than sourceLen plus
+ 12 bytes. Upon exit, destLen is the actual size of the compressed buffer.
+
+ compress2 returns Z_OK if success, Z_MEM_ERROR if there was not enough
+ memory, Z_BUF_ERROR if there was not enough room in the output buffer,
+ Z_STREAM_ERROR if the level parameter is invalid.
+*/
+int ZEXPORT compress2 (dest, destLen, source, sourceLen, level)
+ Bytef *dest;
+ uLongf *destLen;
+ const Bytef *source;
+ uLong sourceLen;
+ int level;
+{
+ z_stream stream;
+ int err;
+
+ stream.next_in = (z_const Bytef *)source;
+ stream.avail_in = (uInt)sourceLen;
+#ifdef MAXSEG_64K
+ /* Check for source > 64K on 16-bit machine: */
+ if ((uLong)stream.avail_in != sourceLen) return Z_BUF_ERROR;
+#endif
+ stream.next_out = dest;
+ stream.avail_out = (uInt)*destLen;
+ if ((uLong)stream.avail_out != *destLen) return Z_BUF_ERROR;
+
+ stream.zalloc = (alloc_func)0;
+ stream.zfree = (free_func)0;
+ stream.opaque = (voidpf)0;
+
+ err = deflateInit(&stream, level);
+ if (err != Z_OK) return err;
+
+ err = deflate(&stream, Z_FINISH);
+ if (err != Z_STREAM_END) {
+ deflateEnd(&stream);
+ return err == Z_OK ? Z_BUF_ERROR : err;
+ }
+ *destLen = stream.total_out;
+
+ err = deflateEnd(&stream);
+ return err;
+}
+
+/* ===========================================================================
+ */
+int ZEXPORT compress (dest, destLen, source, sourceLen)
+ Bytef *dest;
+ uLongf *destLen;
+ const Bytef *source;
+ uLong sourceLen;
+{
+ return compress2(dest, destLen, source, sourceLen, Z_DEFAULT_COMPRESSION);
+}
+
+/* ===========================================================================
+ If the default memLevel or windowBits for deflateInit() is changed, then
+ this function needs to be updated.
+ */
+uLong ZEXPORT compressBound (sourceLen)
+ uLong sourceLen;
+{
+ return sourceLen + (sourceLen >> 12) + (sourceLen >> 14) +
+ (sourceLen >> 25) + 13;
+}
diff --git a/third-party/zlib/configure b/third-party/zlib/configure
new file mode 100755
index 0000000..b77a8a8
--- /dev/null
+++ b/third-party/zlib/configure
@@ -0,0 +1,831 @@
+#!/bin/sh
+# configure script for zlib.
+#
+# Normally configure builds both a static and a shared library.
+# If you want to build just a static library, use: ./configure --static
+#
+# To impose specific compiler or flags or install directory, use for example:
+# prefix=$HOME CC=cc CFLAGS="-O4" ./configure
+# or for csh/tcsh users:
+# (setenv prefix $HOME; setenv CC cc; setenv CFLAGS "-O4"; ./configure)
+
+# Incorrect settings of CC or CFLAGS may prevent creating a shared library.
+# If you have problems, try without defining CC and CFLAGS before reporting
+# an error.
+
+# start off configure.log
+echo -------------------- >> configure.log
+echo $0 $* >> configure.log
+date >> configure.log
+
+# set command prefix for cross-compilation
+if [ -n "${CHOST}" ]; then
+ uname="`echo "${CHOST}" | sed -e 's/^[^-]*-\([^-]*\)$/\1/' -e 's/^[^-]*-[^-]*-\([^-]*\)$/\1/' -e 's/^[^-]*-[^-]*-\([^-]*\)-.*$/\1/'`"
+ CROSS_PREFIX="${CHOST}-"
+fi
+
+# destination name for static library
+STATICLIB=libz.a
+
+# extract zlib version numbers from zlib.h
+VER=`sed -n -e '/VERSION "/s/.*"\(.*\)".*/\1/p' < zlib.h`
+VER3=`sed -n -e '/VERSION "/s/.*"\([0-9]*\\.[0-9]*\\.[0-9]*\).*/\1/p' < zlib.h`
+VER2=`sed -n -e '/VERSION "/s/.*"\([0-9]*\\.[0-9]*\)\\..*/\1/p' < zlib.h`
+VER1=`sed -n -e '/VERSION "/s/.*"\([0-9]*\)\\..*/\1/p' < zlib.h`
+
+# establish commands for library building
+if "${CROSS_PREFIX}ar" --version >/dev/null 2>/dev/null || test $? -lt 126; then
+ AR=${AR-"${CROSS_PREFIX}ar"}
+ test -n "${CROSS_PREFIX}" && echo Using ${AR} | tee -a configure.log
+else
+ AR=${AR-"ar"}
+ test -n "${CROSS_PREFIX}" && echo Using ${AR} | tee -a configure.log
+fi
+ARFLAGS=${ARFLAGS-"rc"}
+if "${CROSS_PREFIX}ranlib" --version >/dev/null 2>/dev/null || test $? -lt 126; then
+ RANLIB=${RANLIB-"${CROSS_PREFIX}ranlib"}
+ test -n "${CROSS_PREFIX}" && echo Using ${RANLIB} | tee -a configure.log
+else
+ RANLIB=${RANLIB-"ranlib"}
+fi
+if "${CROSS_PREFIX}nm" --version >/dev/null 2>/dev/null || test $? -lt 126; then
+ NM=${NM-"${CROSS_PREFIX}nm"}
+ test -n "${CROSS_PREFIX}" && echo Using ${NM} | tee -a configure.log
+else
+ NM=${NM-"nm"}
+fi
+
+# set defaults before processing command line options
+LDCONFIG=${LDCONFIG-"ldconfig"}
+LDSHAREDLIBC="${LDSHAREDLIBC--lc}"
+ARCHS=
+prefix=${prefix-/usr/local}
+exec_prefix=${exec_prefix-'${prefix}'}
+libdir=${libdir-'${exec_prefix}/lib'}
+sharedlibdir=${sharedlibdir-'${libdir}'}
+includedir=${includedir-'${prefix}/include'}
+mandir=${mandir-'${prefix}/share/man'}
+shared_ext='.so'
+shared=1
+solo=0
+cover=0
+zprefix=0
+zconst=0
+build64=0
+gcc=0
+old_cc="$CC"
+old_cflags="$CFLAGS"
+OBJC='$(OBJZ) $(OBJG)'
+PIC_OBJC='$(PIC_OBJZ) $(PIC_OBJG)'
+
+# leave this script, optionally in a bad way
+leave()
+{
+ if test "$*" != "0"; then
+ echo "** $0 aborting." | tee -a configure.log
+ fi
+ rm -f $test.[co] $test $test$shared_ext $test.gcno ./--version
+ echo -------------------- >> configure.log
+ echo >> configure.log
+ echo >> configure.log
+ exit $1
+}
+
+# process command line options
+while test $# -ge 1
+do
+case "$1" in
+ -h* | --help)
+ echo 'usage:' | tee -a configure.log
+ echo ' configure [--const] [--zprefix] [--prefix=PREFIX] [--eprefix=EXPREFIX]' | tee -a configure.log
+ echo ' [--static] [--64] [--libdir=LIBDIR] [--sharedlibdir=LIBDIR]' | tee -a configure.log
+ echo ' [--includedir=INCLUDEDIR] [--archs="-arch i386 -arch x86_64"]' | tee -a configure.log
+ exit 0 ;;
+ -p*=* | --prefix=*) prefix=`echo $1 | sed 's/.*=//'`; shift ;;
+ -e*=* | --eprefix=*) exec_prefix=`echo $1 | sed 's/.*=//'`; shift ;;
+ -l*=* | --libdir=*) libdir=`echo $1 | sed 's/.*=//'`; shift ;;
+ --sharedlibdir=*) sharedlibdir=`echo $1 | sed 's/.*=//'`; shift ;;
+ -i*=* | --includedir=*) includedir=`echo $1 | sed 's/.*=//'`;shift ;;
+ -u*=* | --uname=*) uname=`echo $1 | sed 's/.*=//'`;shift ;;
+ -p* | --prefix) prefix="$2"; shift; shift ;;
+ -e* | --eprefix) exec_prefix="$2"; shift; shift ;;
+ -l* | --libdir) libdir="$2"; shift; shift ;;
+ -i* | --includedir) includedir="$2"; shift; shift ;;
+ -s* | --shared | --enable-shared) shared=1; shift ;;
+ -t | --static) shared=0; shift ;;
+ --solo) solo=1; shift ;;
+ --cover) cover=1; shift ;;
+ -z* | --zprefix) zprefix=1; shift ;;
+ -6* | --64) build64=1; shift ;;
+ -a*=* | --archs=*) ARCHS=`echo $1 | sed 's/.*=//'`; shift ;;
+ --sysconfdir=*) echo "ignored option: --sysconfdir" | tee -a configure.log; shift ;;
+ --localstatedir=*) echo "ignored option: --localstatedir" | tee -a configure.log; shift ;;
+ -c* | --const) zconst=1; shift ;;
+ *)
+ echo "unknown option: $1" | tee -a configure.log
+ echo "$0 --help for help" | tee -a configure.log
+ leave 1;;
+ esac
+done
+
+# temporary file name
+test=ztest$$
+
+# put arguments in log, also put test file in log if used in arguments
+show()
+{
+ case "$*" in
+ *$test.c*)
+ echo === $test.c === >> configure.log
+ cat $test.c >> configure.log
+ echo === >> configure.log;;
+ esac
+ echo $* >> configure.log
+}
+
+# check for gcc vs. cc and set compile and link flags based on the system identified by uname
+cat > $test.c <<EOF
+extern int getchar();
+int hello() {return getchar();}
+EOF
+
+test -z "$CC" && echo Checking for ${CROSS_PREFIX}gcc... | tee -a configure.log
+cc=${CC-${CROSS_PREFIX}gcc}
+cflags=${CFLAGS-"-O3"}
+# to force the asm version use: CFLAGS="-O3 -DASMV" ./configure
+case "$cc" in
+ *gcc*) gcc=1 ;;
+ *clang*) gcc=1 ;;
+esac
+case `$cc -v 2>&1` in
+ *gcc*) gcc=1 ;;
+esac
+
+show $cc -c $test.c
+if test "$gcc" -eq 1 && ($cc -c $test.c) >> configure.log 2>&1; then
+ echo ... using gcc >> configure.log
+ CC="$cc"
+ CFLAGS="${CFLAGS--O3} ${ARCHS}"
+ SFLAGS="${CFLAGS--O3} -fPIC"
+ LDFLAGS="${LDFLAGS} ${ARCHS}"
+ if test $build64 -eq 1; then
+ CFLAGS="${CFLAGS} -m64"
+ SFLAGS="${SFLAGS} -m64"
+ fi
+ if test "${ZLIBGCCWARN}" = "YES"; then
+ if test "$zconst" -eq 1; then
+ CFLAGS="${CFLAGS} -Wall -Wextra -Wcast-qual -pedantic -DZLIB_CONST"
+ else
+ CFLAGS="${CFLAGS} -Wall -Wextra -pedantic"
+ fi
+ fi
+ if test -z "$uname"; then
+ uname=`(uname -s || echo unknown) 2>/dev/null`
+ fi
+ case "$uname" in
+ Linux* | linux* | GNU | GNU/* | solaris*)
+ LDSHARED=${LDSHARED-"$cc -shared -Wl,-soname,libz.so.1,--version-script,zlib.map"} ;;
+ *BSD | *bsd* | DragonFly)
+ LDSHARED=${LDSHARED-"$cc -shared -Wl,-soname,libz.so.1,--version-script,zlib.map"}
+ LDCONFIG="ldconfig -m" ;;
+ CYGWIN* | Cygwin* | cygwin* | OS/2*)
+ EXE='.exe' ;;
+ MINGW* | mingw*)
+# temporary bypass
+ rm -f $test.[co] $test $test$shared_ext
+ echo "Please use win32/Makefile.gcc instead." | tee -a configure.log
+ leave 1
+ LDSHARED=${LDSHARED-"$cc -shared"}
+ LDSHAREDLIBC=""
+ EXE='.exe' ;;
+ QNX*) # This is for QNX6. I suppose that the QNX rule below is for QNX2,QNX4
+ # (alain.bonnefoy at icbt.com)
+ LDSHARED=${LDSHARED-"$cc -shared -Wl,-hlibz.so.1"} ;;
+ HP-UX*)
+ LDSHARED=${LDSHARED-"$cc -shared $SFLAGS"}
+ case `(uname -m || echo unknown) 2>/dev/null` in
+ ia64)
+ shared_ext='.so'
+ SHAREDLIB='libz.so' ;;
+ *)
+ shared_ext='.sl'
+ SHAREDLIB='libz.sl' ;;
+ esac ;;
+ Darwin* | darwin*)
+ shared_ext='.dylib'
+ SHAREDLIB=libz$shared_ext
+ SHAREDLIBV=libz.$VER$shared_ext
+ SHAREDLIBM=libz.$VER1$shared_ext
+ LDSHARED=${LDSHARED-"$cc -dynamiclib -install_name $libdir/$SHAREDLIBM -compatibility_version $VER1 -current_version $VER3"}
+ if libtool -V 2>&1 | grep Apple > /dev/null; then
+ AR="libtool"
+ else
+ AR="/usr/bin/libtool"
+ fi
+ ARFLAGS="-o" ;;
+ *) LDSHARED=${LDSHARED-"$cc -shared"} ;;
+ esac
+else
+ # find system name and corresponding cc options
+ CC=${CC-cc}
+ gcc=0
+ echo ... using $CC >> configure.log
+ if test -z "$uname"; then
+ uname=`(uname -sr || echo unknown) 2>/dev/null`
+ fi
+ case "$uname" in
+ HP-UX*) SFLAGS=${CFLAGS-"-O +z"}
+ CFLAGS=${CFLAGS-"-O"}
+# LDSHARED=${LDSHARED-"ld -b +vnocompatwarnings"}
+ LDSHARED=${LDSHARED-"ld -b"}
+ case `(uname -m || echo unknown) 2>/dev/null` in
+ ia64)
+ shared_ext='.so'
+ SHAREDLIB='libz.so' ;;
+ *)
+ shared_ext='.sl'
+ SHAREDLIB='libz.sl' ;;
+ esac ;;
+ IRIX*) SFLAGS=${CFLAGS-"-ansi -O2 -rpath ."}
+ CFLAGS=${CFLAGS-"-ansi -O2"}
+ LDSHARED=${LDSHARED-"cc -shared -Wl,-soname,libz.so.1"} ;;
+ OSF1\ V4*) SFLAGS=${CFLAGS-"-O -std1"}
+ CFLAGS=${CFLAGS-"-O -std1"}
+ LDFLAGS="${LDFLAGS} -Wl,-rpath,."
+ LDSHARED=${LDSHARED-"cc -shared -Wl,-soname,libz.so -Wl,-msym -Wl,-rpath,$(libdir) -Wl,-set_version,${VER}:1.0"} ;;
+ OSF1*) SFLAGS=${CFLAGS-"-O -std1"}
+ CFLAGS=${CFLAGS-"-O -std1"}
+ LDSHARED=${LDSHARED-"cc -shared -Wl,-soname,libz.so.1"} ;;
+ QNX*) SFLAGS=${CFLAGS-"-4 -O"}
+ CFLAGS=${CFLAGS-"-4 -O"}
+ LDSHARED=${LDSHARED-"cc"}
+ RANLIB=${RANLIB-"true"}
+ AR="cc"
+ ARFLAGS="-A" ;;
+ SCO_SV\ 3.2*) SFLAGS=${CFLAGS-"-O3 -dy -KPIC "}
+ CFLAGS=${CFLAGS-"-O3"}
+ LDSHARED=${LDSHARED-"cc -dy -KPIC -G"} ;;
+ SunOS\ 5* | solaris*)
+ LDSHARED=${LDSHARED-"cc -G -h libz$shared_ext.$VER1"}
+ SFLAGS=${CFLAGS-"-fast -KPIC"}
+ CFLAGS=${CFLAGS-"-fast"}
+ if test $build64 -eq 1; then
+ # old versions of SunPRO/Workshop/Studio don't support -m64,
+ # but newer ones do. Check for it.
+ flag64=`$CC -flags | egrep -- '^-m64'`
+ if test x"$flag64" != x"" ; then
+ CFLAGS="${CFLAGS} -m64"
+ SFLAGS="${SFLAGS} -m64"
+ else
+ case `(uname -m || echo unknown) 2>/dev/null` in
+ i86*)
+ SFLAGS="$SFLAGS -xarch=amd64"
+ CFLAGS="$CFLAGS -xarch=amd64" ;;
+ *)
+ SFLAGS="$SFLAGS -xarch=v9"
+ CFLAGS="$CFLAGS -xarch=v9" ;;
+ esac
+ fi
+ fi
+ ;;
+ SunOS\ 4*) SFLAGS=${CFLAGS-"-O2 -PIC"}
+ CFLAGS=${CFLAGS-"-O2"}
+ LDSHARED=${LDSHARED-"ld"} ;;
+ SunStudio\ 9*) SFLAGS=${CFLAGS-"-fast -xcode=pic32 -xtarget=ultra3 -xarch=v9b"}
+ CFLAGS=${CFLAGS-"-fast -xtarget=ultra3 -xarch=v9b"}
+ LDSHARED=${LDSHARED-"cc -xarch=v9b"} ;;
+ UNIX_System_V\ 4.2.0)
+ SFLAGS=${CFLAGS-"-KPIC -O"}
+ CFLAGS=${CFLAGS-"-O"}
+ LDSHARED=${LDSHARED-"cc -G"} ;;
+ UNIX_SV\ 4.2MP)
+ SFLAGS=${CFLAGS-"-Kconform_pic -O"}
+ CFLAGS=${CFLAGS-"-O"}
+ LDSHARED=${LDSHARED-"cc -G"} ;;
+ OpenUNIX\ 5)
+ SFLAGS=${CFLAGS-"-KPIC -O"}
+ CFLAGS=${CFLAGS-"-O"}
+ LDSHARED=${LDSHARED-"cc -G"} ;;
+ AIX*) # Courtesy of dbakker at arrayasolutions.com
+ SFLAGS=${CFLAGS-"-O -qmaxmem=8192"}
+ CFLAGS=${CFLAGS-"-O -qmaxmem=8192"}
+ LDSHARED=${LDSHARED-"xlc -G"} ;;
+ # send working options for other systems to zlib at gzip.org
+ *) SFLAGS=${CFLAGS-"-O"}
+ CFLAGS=${CFLAGS-"-O"}
+ LDSHARED=${LDSHARED-"cc -shared"} ;;
+ esac
+fi
+
+# destination names for shared library if not defined above
+SHAREDLIB=${SHAREDLIB-"libz$shared_ext"}
+SHAREDLIBV=${SHAREDLIBV-"libz$shared_ext.$VER"}
+SHAREDLIBM=${SHAREDLIBM-"libz$shared_ext.$VER1"}
+
+echo >> configure.log
+
+# define functions for testing compiler and library characteristics and logging the results
+
+cat > $test.c <<EOF
+#error error
+EOF
+if ($CC -c $CFLAGS $test.c) 2>/dev/null; then
+ try()
+ {
+ show $*
+ test "`( $* ) 2>&1 | tee -a configure.log`" = ""
+ }
+ echo - using any output from compiler to indicate an error >> configure.log
+else
+try()
+{
+ show $*
+ ( $* ) >> configure.log 2>&1
+ ret=$?
+ if test $ret -ne 0; then
+ echo "(exit code "$ret")" >> configure.log
+ fi
+ return $ret
+}
+fi
+
+tryboth()
+{
+ show $*
+ got=`( $* ) 2>&1`
+ ret=$?
+ printf %s "$got" >> configure.log
+ if test $ret -ne 0; then
+ return $ret
+ fi
+ test "$got" = ""
+}
+
+cat > $test.c << EOF
+int foo() { return 0; }
+EOF
+echo "Checking for obsessive-compulsive compiler options..." >> configure.log
+if try $CC -c $CFLAGS $test.c; then
+ :
+else
+ echo "Compiler error reporting is too harsh for $0 (perhaps remove -Werror)." | tee -a configure.log
+ leave 1
+fi
+
+echo >> configure.log
+
+# see if shared library build supported
+cat > $test.c <<EOF
+extern int getchar();
+int hello() {return getchar();}
+EOF
+if test $shared -eq 1; then
+ echo Checking for shared library support... | tee -a configure.log
+ # we must test in two steps (cc then ld), required at least on SunOS 4.x
+ if try $CC -w -c $SFLAGS $test.c &&
+ try $LDSHARED $SFLAGS -o $test$shared_ext $test.o; then
+ echo Building shared library $SHAREDLIBV with $CC. | tee -a configure.log
+ elif test -z "$old_cc" -a -z "$old_cflags"; then
+ echo No shared library support. | tee -a configure.log
+ shared=0;
+ else
+ echo 'No shared library support; try without defining CC and CFLAGS' | tee -a configure.log
+ shared=0;
+ fi
+fi
+if test $shared -eq 0; then
+ LDSHARED="$CC"
+ ALL="static"
+ TEST="all teststatic"
+ SHAREDLIB=""
+ SHAREDLIBV=""
+ SHAREDLIBM=""
+ echo Building static library $STATICLIB version $VER with $CC. | tee -a configure.log
+else
+ ALL="static shared"
+ TEST="all teststatic testshared"
+fi
+
+# check for underscores in external names for use by assembler code
+CPP=${CPP-"$CC -E"}
+case $CFLAGS in
+ *ASMV*)
+ echo >> configure.log
+ show "$NM $test.o | grep _hello"
+ if test "`$NM $test.o | grep _hello | tee -a configure.log`" = ""; then
+ CPP="$CPP -DNO_UNDERLINE"
+ echo Checking for underline in external names... No. | tee -a configure.log
+ else
+ echo Checking for underline in external names... Yes. | tee -a configure.log
+ fi ;;
+esac
+
+echo >> configure.log
+
+# check for large file support, and if none, check for fseeko()
+cat > $test.c <<EOF
+#include <sys/types.h>
+off64_t dummy = 0;
+EOF
+if try $CC -c $CFLAGS -D_LARGEFILE64_SOURCE=1 $test.c; then
+ CFLAGS="${CFLAGS} -D_LARGEFILE64_SOURCE=1"
+ SFLAGS="${SFLAGS} -D_LARGEFILE64_SOURCE=1"
+ ALL="${ALL} all64"
+ TEST="${TEST} test64"
+ echo "Checking for off64_t... Yes." | tee -a configure.log
+ echo "Checking for fseeko... Yes." | tee -a configure.log
+else
+ echo "Checking for off64_t... No." | tee -a configure.log
+ echo >> configure.log
+ cat > $test.c <<EOF
+#include <stdio.h>
+int main(void) {
+ fseeko(NULL, 0, 0);
+ return 0;
+}
+EOF
+ if try $CC $CFLAGS -o $test $test.c; then
+ echo "Checking for fseeko... Yes." | tee -a configure.log
+ else
+ CFLAGS="${CFLAGS} -DNO_FSEEKO"
+ SFLAGS="${SFLAGS} -DNO_FSEEKO"
+ echo "Checking for fseeko... No." | tee -a configure.log
+ fi
+fi
+
+echo >> configure.log
+
+# check for strerror() for use by gz* functions
+cat > $test.c <<EOF
+#include <string.h>
+#include <errno.h>
+int main() { return strlen(strerror(errno)); }
+EOF
+if try $CC $CFLAGS -o $test $test.c; then
+ echo "Checking for strerror... Yes." | tee -a configure.log
+else
+ CFLAGS="${CFLAGS} -DNO_STRERROR"
+ SFLAGS="${SFLAGS} -DNO_STRERROR"
+ echo "Checking for strerror... No." | tee -a configure.log
+fi
+
+# copy clean zconf.h for subsequent edits
+cp -p zconf.h.in zconf.h
+
+echo >> configure.log
+
+# check for unistd.h and save result in zconf.h
+cat > $test.c <<EOF
+#include <unistd.h>
+int main() { return 0; }
+EOF
+if try $CC -c $CFLAGS $test.c; then
+ sed < zconf.h "/^#ifdef HAVE_UNISTD_H.* may be/s/def HAVE_UNISTD_H\(.*\) may be/ 1\1 was/" > zconf.temp.h
+ mv zconf.temp.h zconf.h
+ echo "Checking for unistd.h... Yes." | tee -a configure.log
+else
+ echo "Checking for unistd.h... No." | tee -a configure.log
+fi
+
+echo >> configure.log
+
+# check for stdarg.h and save result in zconf.h
+cat > $test.c <<EOF
+#include <stdarg.h>
+int main() { return 0; }
+EOF
+if try $CC -c $CFLAGS $test.c; then
+ sed < zconf.h "/^#ifdef HAVE_STDARG_H.* may be/s/def HAVE_STDARG_H\(.*\) may be/ 1\1 was/" > zconf.temp.h
+ mv zconf.temp.h zconf.h
+ echo "Checking for stdarg.h... Yes." | tee -a configure.log
+else
+ echo "Checking for stdarg.h... No." | tee -a configure.log
+fi
+
+# if the z_ prefix was requested, save that in zconf.h
+if test $zprefix -eq 1; then
+ sed < zconf.h "/#ifdef Z_PREFIX.* may be/s/def Z_PREFIX\(.*\) may be/ 1\1 was/" > zconf.temp.h
+ mv zconf.temp.h zconf.h
+ echo >> configure.log
+ echo "Using z_ prefix on all symbols." | tee -a configure.log
+fi
+
+# if --solo compilation was requested, save that in zconf.h and remove gz stuff from object lists
+if test $solo -eq 1; then
+ sed '/#define ZCONF_H/a\
+#define Z_SOLO
+
+' < zconf.h > zconf.temp.h
+ mv zconf.temp.h zconf.h
+OBJC='$(OBJZ)'
+PIC_OBJC='$(PIC_OBJZ)'
+fi
+
+# if code coverage testing was requested, use older gcc if defined, e.g. "gcc-4.2" on Mac OS X
+if test $cover -eq 1; then
+ CFLAGS="${CFLAGS} -fprofile-arcs -ftest-coverage"
+ if test -n "$GCC_CLASSIC"; then
+ CC=$GCC_CLASSIC
+ fi
+fi
+
+echo >> configure.log
+
+# conduct a series of tests to resolve eight possible cases of using "vs" or "s" printf functions
+# (using stdarg or not), with or without "n" (proving size of buffer), and with or without a
+# return value. The most secure result is vsnprintf() with a return value. snprintf() with a
+# return value is secure as well, but then gzprintf() will be limited to 20 arguments.
+cat > $test.c <<EOF
+#include <stdio.h>
+#include <stdarg.h>
+#include "zconf.h"
+int main()
+{
+#ifndef STDC
+ choke me
+#endif
+ return 0;
+}
+EOF
+if try $CC -c $CFLAGS $test.c; then
+ echo "Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf()." | tee -a configure.log
+
+ echo >> configure.log
+ cat > $test.c <<EOF
+#include <stdio.h>
+#include <stdarg.h>
+int mytest(const char *fmt, ...)
+{
+ char buf[20];
+ va_list ap;
+ va_start(ap, fmt);
+ vsnprintf(buf, sizeof(buf), fmt, ap);
+ va_end(ap);
+ return 0;
+}
+int main()
+{
+ return (mytest("Hello%d\n", 1));
+}
+EOF
+ if try $CC $CFLAGS -o $test $test.c; then
+ echo "Checking for vsnprintf() in stdio.h... Yes." | tee -a configure.log
+
+ echo >> configure.log
+ cat >$test.c <<EOF
+#include <stdio.h>
+#include <stdarg.h>
+int mytest(const char *fmt, ...)
+{
+ int n;
+ char buf[20];
+ va_list ap;
+ va_start(ap, fmt);
+ n = vsnprintf(buf, sizeof(buf), fmt, ap);
+ va_end(ap);
+ return n;
+}
+int main()
+{
+ return (mytest("Hello%d\n", 1));
+}
+EOF
+
+ if try $CC -c $CFLAGS $test.c; then
+ echo "Checking for return value of vsnprintf()... Yes." | tee -a configure.log
+ else
+ CFLAGS="$CFLAGS -DHAS_vsnprintf_void"
+ SFLAGS="$SFLAGS -DHAS_vsnprintf_void"
+ echo "Checking for return value of vsnprintf()... No." | tee -a configure.log
+ echo " WARNING: apparently vsnprintf() does not return a value. zlib" | tee -a configure.log
+ echo " can build but will be open to possible string-format security" | tee -a configure.log
+ echo " vulnerabilities." | tee -a configure.log
+ fi
+ else
+ CFLAGS="$CFLAGS -DNO_vsnprintf"
+ SFLAGS="$SFLAGS -DNO_vsnprintf"
+ echo "Checking for vsnprintf() in stdio.h... No." | tee -a configure.log
+ echo " WARNING: vsnprintf() not found, falling back to vsprintf(). zlib" | tee -a configure.log
+ echo " can build but will be open to possible buffer-overflow security" | tee -a configure.log
+ echo " vulnerabilities." | tee -a configure.log
+
+ echo >> configure.log
+ cat >$test.c <<EOF
+#include <stdio.h>
+#include <stdarg.h>
+int mytest(const char *fmt, ...)
+{
+ int n;
+ char buf[20];
+ va_list ap;
+ va_start(ap, fmt);
+ n = vsprintf(buf, fmt, ap);
+ va_end(ap);
+ return n;
+}
+int main()
+{
+ return (mytest("Hello%d\n", 1));
+}
+EOF
+
+ if try $CC -c $CFLAGS $test.c; then
+ echo "Checking for return value of vsprintf()... Yes." | tee -a configure.log
+ else
+ CFLAGS="$CFLAGS -DHAS_vsprintf_void"
+ SFLAGS="$SFLAGS -DHAS_vsprintf_void"
+ echo "Checking for return value of vsprintf()... No." | tee -a configure.log
+ echo " WARNING: apparently vsprintf() does not return a value. zlib" | tee -a configure.log
+ echo " can build but will be open to possible string-format security" | tee -a configure.log
+ echo " vulnerabilities." | tee -a configure.log
+ fi
+ fi
+else
+ echo "Checking whether to use vs[n]printf() or s[n]printf()... using s[n]printf()." | tee -a configure.log
+
+ echo >> configure.log
+ cat >$test.c <<EOF
+#include <stdio.h>
+int mytest()
+{
+ char buf[20];
+ snprintf(buf, sizeof(buf), "%s", "foo");
+ return 0;
+}
+int main()
+{
+ return (mytest());
+}
+EOF
+
+ if try $CC $CFLAGS -o $test $test.c; then
+ echo "Checking for snprintf() in stdio.h... Yes." | tee -a configure.log
+
+ echo >> configure.log
+ cat >$test.c <<EOF
+#include <stdio.h>
+int mytest()
+{
+ char buf[20];
+ return snprintf(buf, sizeof(buf), "%s", "foo");
+}
+int main()
+{
+ return (mytest());
+}
+EOF
+
+ if try $CC -c $CFLAGS $test.c; then
+ echo "Checking for return value of snprintf()... Yes." | tee -a configure.log
+ else
+ CFLAGS="$CFLAGS -DHAS_snprintf_void"
+ SFLAGS="$SFLAGS -DHAS_snprintf_void"
+ echo "Checking for return value of snprintf()... No." | tee -a configure.log
+ echo " WARNING: apparently snprintf() does not return a value. zlib" | tee -a configure.log
+ echo " can build but will be open to possible string-format security" | tee -a configure.log
+ echo " vulnerabilities." | tee -a configure.log
+ fi
+ else
+ CFLAGS="$CFLAGS -DNO_snprintf"
+ SFLAGS="$SFLAGS -DNO_snprintf"
+ echo "Checking for snprintf() in stdio.h... No." | tee -a configure.log
+ echo " WARNING: snprintf() not found, falling back to sprintf(). zlib" | tee -a configure.log
+ echo " can build but will be open to possible buffer-overflow security" | tee -a configure.log
+ echo " vulnerabilities." | tee -a configure.log
+
+ echo >> configure.log
+ cat >$test.c <<EOF
+#include <stdio.h>
+int mytest()
+{
+ char buf[20];
+ return sprintf(buf, "%s", "foo");
+}
+int main()
+{
+ return (mytest());
+}
+EOF
+
+ if try $CC -c $CFLAGS $test.c; then
+ echo "Checking for return value of sprintf()... Yes." | tee -a configure.log
+ else
+ CFLAGS="$CFLAGS -DHAS_sprintf_void"
+ SFLAGS="$SFLAGS -DHAS_sprintf_void"
+ echo "Checking for return value of sprintf()... No." | tee -a configure.log
+ echo " WARNING: apparently sprintf() does not return a value. zlib" | tee -a configure.log
+ echo " can build but will be open to possible string-format security" | tee -a configure.log
+ echo " vulnerabilities." | tee -a configure.log
+ fi
+ fi
+fi
+
+# see if we can hide zlib internal symbols that are linked between separate source files
+if test "$gcc" -eq 1; then
+ echo >> configure.log
+ cat > $test.c <<EOF
+#define ZLIB_INTERNAL __attribute__((visibility ("hidden")))
+int ZLIB_INTERNAL foo;
+int main()
+{
+ return 0;
+}
+EOF
+ if tryboth $CC -c $CFLAGS $test.c; then
+ CFLAGS="$CFLAGS -DHAVE_HIDDEN"
+ SFLAGS="$SFLAGS -DHAVE_HIDDEN"
+ echo "Checking for attribute(visibility) support... Yes." | tee -a configure.log
+ else
+ echo "Checking for attribute(visibility) support... No." | tee -a configure.log
+ fi
+fi
+
+# show the results in the log
+echo >> configure.log
+echo ALL = $ALL >> configure.log
+echo AR = $AR >> configure.log
+echo ARFLAGS = $ARFLAGS >> configure.log
+echo CC = $CC >> configure.log
+echo CFLAGS = $CFLAGS >> configure.log
+echo CPP = $CPP >> configure.log
+echo EXE = $EXE >> configure.log
+echo LDCONFIG = $LDCONFIG >> configure.log
+echo LDFLAGS = $LDFLAGS >> configure.log
+echo LDSHARED = $LDSHARED >> configure.log
+echo LDSHAREDLIBC = $LDSHAREDLIBC >> configure.log
+echo OBJC = $OBJC >> configure.log
+echo PIC_OBJC = $PIC_OBJC >> configure.log
+echo RANLIB = $RANLIB >> configure.log
+echo SFLAGS = $SFLAGS >> configure.log
+echo SHAREDLIB = $SHAREDLIB >> configure.log
+echo SHAREDLIBM = $SHAREDLIBM >> configure.log
+echo SHAREDLIBV = $SHAREDLIBV >> configure.log
+echo STATICLIB = $STATICLIB >> configure.log
+echo TEST = $TEST >> configure.log
+echo VER = $VER >> configure.log
+echo Z_U4 = $Z_U4 >> configure.log
+echo exec_prefix = $exec_prefix >> configure.log
+echo includedir = $includedir >> configure.log
+echo libdir = $libdir >> configure.log
+echo mandir = $mandir >> configure.log
+echo prefix = $prefix >> configure.log
+echo sharedlibdir = $sharedlibdir >> configure.log
+echo uname = $uname >> configure.log
+
+# udpate Makefile with the configure results
+sed < Makefile.in "
+/^CC *=/s#=.*#=$CC#
+/^CFLAGS *=/s#=.*#=$CFLAGS#
+/^SFLAGS *=/s#=.*#=$SFLAGS#
+/^LDFLAGS *=/s#=.*#=$LDFLAGS#
+/^LDSHARED *=/s#=.*#=$LDSHARED#
+/^CPP *=/s#=.*#=$CPP#
+/^STATICLIB *=/s#=.*#=$STATICLIB#
+/^SHAREDLIB *=/s#=.*#=$SHAREDLIB#
+/^SHAREDLIBV *=/s#=.*#=$SHAREDLIBV#
+/^SHAREDLIBM *=/s#=.*#=$SHAREDLIBM#
+/^AR *=/s#=.*#=$AR#
+/^ARFLAGS *=/s#=.*#=$ARFLAGS#
+/^RANLIB *=/s#=.*#=$RANLIB#
+/^LDCONFIG *=/s#=.*#=$LDCONFIG#
+/^LDSHAREDLIBC *=/s#=.*#=$LDSHAREDLIBC#
+/^EXE *=/s#=.*#=$EXE#
+/^prefix *=/s#=.*#=$prefix#
+/^exec_prefix *=/s#=.*#=$exec_prefix#
+/^libdir *=/s#=.*#=$libdir#
+/^sharedlibdir *=/s#=.*#=$sharedlibdir#
+/^includedir *=/s#=.*#=$includedir#
+/^mandir *=/s#=.*#=$mandir#
+/^OBJC *=/s#=.*#= $OBJC#
+/^PIC_OBJC *=/s#=.*#= $PIC_OBJC#
+/^all: */s#:.*#: $ALL#
+/^test: */s#:.*#: $TEST#
+" > Makefile
+
+# create zlib.pc with the configure results
+sed < zlib.pc.in "
+/^CC *=/s#=.*#=$CC#
+/^CFLAGS *=/s#=.*#=$CFLAGS#
+/^CPP *=/s#=.*#=$CPP#
+/^LDSHARED *=/s#=.*#=$LDSHARED#
+/^STATICLIB *=/s#=.*#=$STATICLIB#
+/^SHAREDLIB *=/s#=.*#=$SHAREDLIB#
+/^SHAREDLIBV *=/s#=.*#=$SHAREDLIBV#
+/^SHAREDLIBM *=/s#=.*#=$SHAREDLIBM#
+/^AR *=/s#=.*#=$AR#
+/^ARFLAGS *=/s#=.*#=$ARFLAGS#
+/^RANLIB *=/s#=.*#=$RANLIB#
+/^EXE *=/s#=.*#=$EXE#
+/^prefix *=/s#=.*#=$prefix#
+/^exec_prefix *=/s#=.*#=$exec_prefix#
+/^libdir *=/s#=.*#=$libdir#
+/^sharedlibdir *=/s#=.*#=$sharedlibdir#
+/^includedir *=/s#=.*#=$includedir#
+/^mandir *=/s#=.*#=$mandir#
+/^LDFLAGS *=/s#=.*#=$LDFLAGS#
+" | sed -e "
+s/\@VERSION\@/$VER/g;
+" > zlib.pc
+
+# done
+leave 0
diff --git a/third-party/zlib/crc32.c b/third-party/zlib/crc32.c
new file mode 100644
index 0000000..979a719
--- /dev/null
+++ b/third-party/zlib/crc32.c
@@ -0,0 +1,425 @@
+/* crc32.c -- compute the CRC-32 of a data stream
+ * Copyright (C) 1995-2006, 2010, 2011, 2012 Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ *
+ * Thanks to Rodney Brown <rbrown64 at csc.com.au> for his contribution of faster
+ * CRC methods: exclusive-oring 32 bits of data at a time, and pre-computing
+ * tables for updating the shift register in one step with three exclusive-ors
+ * instead of four steps with four exclusive-ors. This results in about a
+ * factor of two increase in speed on a Power PC G4 (PPC7455) using gcc -O3.
+ */
+
+/* @(#) $Id$ */
+
+/*
+ Note on the use of DYNAMIC_CRC_TABLE: there is no mutex or semaphore
+ protection on the static variables used to control the first-use generation
+ of the crc tables. Therefore, if you #define DYNAMIC_CRC_TABLE, you should
+ first call get_crc_table() to initialize the tables before allowing more than
+ one thread to use crc32().
+
+ DYNAMIC_CRC_TABLE and MAKECRCH can be #defined to write out crc32.h.
+ */
+
+#ifdef MAKECRCH
+# include <stdio.h>
+# ifndef DYNAMIC_CRC_TABLE
+# define DYNAMIC_CRC_TABLE
+# endif /* !DYNAMIC_CRC_TABLE */
+#endif /* MAKECRCH */
+
+#include "zutil.h" /* for STDC and FAR definitions */
+
+#define local static
+
+/* Definitions for doing the crc four data bytes at a time. */
+#if !defined(NOBYFOUR) && defined(Z_U4)
+# define BYFOUR
+#endif
+#ifdef BYFOUR
+ local unsigned long crc32_little OF((unsigned long,
+ const unsigned char FAR *, unsigned));
+ local unsigned long crc32_big OF((unsigned long,
+ const unsigned char FAR *, unsigned));
+# define TBLS 8
+#else
+# define TBLS 1
+#endif /* BYFOUR */
+
+/* Local functions for crc concatenation */
+local unsigned long gf2_matrix_times OF((unsigned long *mat,
+ unsigned long vec));
+local void gf2_matrix_square OF((unsigned long *square, unsigned long *mat));
+local uLong crc32_combine_ OF((uLong crc1, uLong crc2, z_off64_t len2));
+
+
+#ifdef DYNAMIC_CRC_TABLE
+
+local volatile int crc_table_empty = 1;
+local z_crc_t FAR crc_table[TBLS][256];
+local void make_crc_table OF((void));
+#ifdef MAKECRCH
+ local void write_table OF((FILE *, const z_crc_t FAR *));
+#endif /* MAKECRCH */
+/*
+ Generate tables for a byte-wise 32-bit CRC calculation on the polynomial:
+ x^32+x^26+x^23+x^22+x^16+x^12+x^11+x^10+x^8+x^7+x^5+x^4+x^2+x+1.
+
+ Polynomials over GF(2) are represented in binary, one bit per coefficient,
+ with the lowest powers in the most significant bit. Then adding polynomials
+ is just exclusive-or, and multiplying a polynomial by x is a right shift by
+ one. If we call the above polynomial p, and represent a byte as the
+ polynomial q, also with the lowest power in the most significant bit (so the
+ byte 0xb1 is the polynomial x^7+x^3+x+1), then the CRC is (q*x^32) mod p,
+ where a mod b means the remainder after dividing a by b.
+
+ This calculation is done using the shift-register method of multiplying and
+ taking the remainder. The register is initialized to zero, and for each
+ incoming bit, x^32 is added mod p to the register if the bit is a one (where
+ x^32 mod p is p+x^32 = x^26+...+1), and the register is multiplied mod p by
+ x (which is shifting right by one and adding x^32 mod p if the bit shifted
+ out is a one). We start with the highest power (least significant bit) of
+ q and repeat for all eight bits of q.
+
+ The first table is simply the CRC of all possible eight bit values. This is
+ all the information needed to generate CRCs on data a byte at a time for all
+ combinations of CRC register values and incoming bytes. The remaining tables
+ allow for word-at-a-time CRC calculation for both big-endian and little-
+ endian machines, where a word is four bytes.
+*/
+local void make_crc_table()
+{
+ z_crc_t c;
+ int n, k;
+ z_crc_t poly; /* polynomial exclusive-or pattern */
+ /* terms of polynomial defining this crc (except x^32): */
+ static volatile int first = 1; /* flag to limit concurrent making */
+ static const unsigned char p[] = {0,1,2,4,5,7,8,10,11,12,16,22,23,26};
+
+ /* See if another task is already doing this (not thread-safe, but better
+ than nothing -- significantly reduces duration of vulnerability in
+ case the advice about DYNAMIC_CRC_TABLE is ignored) */
+ if (first) {
+ first = 0;
+
+ /* make exclusive-or pattern from polynomial (0xedb88320UL) */
+ poly = 0;
+ for (n = 0; n < (int)(sizeof(p)/sizeof(unsigned char)); n++)
+ poly |= (z_crc_t)1 << (31 - p[n]);
+
+ /* generate a crc for every 8-bit value */
+ for (n = 0; n < 256; n++) {
+ c = (z_crc_t)n;
+ for (k = 0; k < 8; k++)
+ c = c & 1 ? poly ^ (c >> 1) : c >> 1;
+ crc_table[0][n] = c;
+ }
+
+#ifdef BYFOUR
+ /* generate crc for each value followed by one, two, and three zeros,
+ and then the byte reversal of those as well as the first table */
+ for (n = 0; n < 256; n++) {
+ c = crc_table[0][n];
+ crc_table[4][n] = ZSWAP32(c);
+ for (k = 1; k < 4; k++) {
+ c = crc_table[0][c & 0xff] ^ (c >> 8);
+ crc_table[k][n] = c;
+ crc_table[k + 4][n] = ZSWAP32(c);
+ }
+ }
+#endif /* BYFOUR */
+
+ crc_table_empty = 0;
+ }
+ else { /* not first */
+ /* wait for the other guy to finish (not efficient, but rare) */
+ while (crc_table_empty)
+ ;
+ }
+
+#ifdef MAKECRCH
+ /* write out CRC tables to crc32.h */
+ {
+ FILE *out;
+
+ out = fopen("crc32.h", "w");
+ if (out == NULL) return;
+ fprintf(out, "/* crc32.h -- tables for rapid CRC calculation\n");
+ fprintf(out, " * Generated automatically by crc32.c\n */\n\n");
+ fprintf(out, "local const z_crc_t FAR ");
+ fprintf(out, "crc_table[TBLS][256] =\n{\n {\n");
+ write_table(out, crc_table[0]);
+# ifdef BYFOUR
+ fprintf(out, "#ifdef BYFOUR\n");
+ for (k = 1; k < 8; k++) {
+ fprintf(out, " },\n {\n");
+ write_table(out, crc_table[k]);
+ }
+ fprintf(out, "#endif\n");
+# endif /* BYFOUR */
+ fprintf(out, " }\n};\n");
+ fclose(out);
+ }
+#endif /* MAKECRCH */
+}
+
+#ifdef MAKECRCH
+local void write_table(out, table)
+ FILE *out;
+ const z_crc_t FAR *table;
+{
+ int n;
+
+ for (n = 0; n < 256; n++)
+ fprintf(out, "%s0x%08lxUL%s", n % 5 ? "" : " ",
+ (unsigned long)(table[n]),
+ n == 255 ? "\n" : (n % 5 == 4 ? ",\n" : ", "));
+}
+#endif /* MAKECRCH */
+
+#else /* !DYNAMIC_CRC_TABLE */
+/* ========================================================================
+ * Tables of CRC-32s of all single-byte values, made by make_crc_table().
+ */
+#include "crc32.h"
+#endif /* DYNAMIC_CRC_TABLE */
+
+/* =========================================================================
+ * This function can be used by asm versions of crc32()
+ */
+const z_crc_t FAR * ZEXPORT get_crc_table()
+{
+#ifdef DYNAMIC_CRC_TABLE
+ if (crc_table_empty)
+ make_crc_table();
+#endif /* DYNAMIC_CRC_TABLE */
+ return (const z_crc_t FAR *)crc_table;
+}
+
+/* ========================================================================= */
+#define DO1 crc = crc_table[0][((int)crc ^ (*buf++)) & 0xff] ^ (crc >> 8)
+#define DO8 DO1; DO1; DO1; DO1; DO1; DO1; DO1; DO1
+
+/* ========================================================================= */
+unsigned long ZEXPORT crc32(crc, buf, len)
+ unsigned long crc;
+ const unsigned char FAR *buf;
+ uInt len;
+{
+ if (buf == Z_NULL) return 0UL;
+
+#ifdef DYNAMIC_CRC_TABLE
+ if (crc_table_empty)
+ make_crc_table();
+#endif /* DYNAMIC_CRC_TABLE */
+
+#ifdef BYFOUR
+ if (sizeof(void *) == sizeof(ptrdiff_t)) {
+ z_crc_t endian;
+
+ endian = 1;
+ if (*((unsigned char *)(&endian)))
+ return crc32_little(crc, buf, len);
+ else
+ return crc32_big(crc, buf, len);
+ }
+#endif /* BYFOUR */
+ crc = crc ^ 0xffffffffUL;
+ while (len >= 8) {
+ DO8;
+ len -= 8;
+ }
+ if (len) do {
+ DO1;
+ } while (--len);
+ return crc ^ 0xffffffffUL;
+}
+
+#ifdef BYFOUR
+
+/* ========================================================================= */
+#define DOLIT4 c ^= *buf4++; \
+ c = crc_table[3][c & 0xff] ^ crc_table[2][(c >> 8) & 0xff] ^ \
+ crc_table[1][(c >> 16) & 0xff] ^ crc_table[0][c >> 24]
+#define DOLIT32 DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4
+
+/* ========================================================================= */
+local unsigned long crc32_little(crc, buf, len)
+ unsigned long crc;
+ const unsigned char FAR *buf;
+ unsigned len;
+{
+ register z_crc_t c;
+ register const z_crc_t FAR *buf4;
+
+ c = (z_crc_t)crc;
+ c = ~c;
+ while (len && ((ptrdiff_t)buf & 3)) {
+ c = crc_table[0][(c ^ *buf++) & 0xff] ^ (c >> 8);
+ len--;
+ }
+
+ buf4 = (const z_crc_t FAR *)(const void FAR *)buf;
+ while (len >= 32) {
+ DOLIT32;
+ len -= 32;
+ }
+ while (len >= 4) {
+ DOLIT4;
+ len -= 4;
+ }
+ buf = (const unsigned char FAR *)buf4;
+
+ if (len) do {
+ c = crc_table[0][(c ^ *buf++) & 0xff] ^ (c >> 8);
+ } while (--len);
+ c = ~c;
+ return (unsigned long)c;
+}
+
+/* ========================================================================= */
+#define DOBIG4 c ^= *++buf4; \
+ c = crc_table[4][c & 0xff] ^ crc_table[5][(c >> 8) & 0xff] ^ \
+ crc_table[6][(c >> 16) & 0xff] ^ crc_table[7][c >> 24]
+#define DOBIG32 DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4
+
+/* ========================================================================= */
+local unsigned long crc32_big(crc, buf, len)
+ unsigned long crc;
+ const unsigned char FAR *buf;
+ unsigned len;
+{
+ register z_crc_t c;
+ register const z_crc_t FAR *buf4;
+
+ c = ZSWAP32((z_crc_t)crc);
+ c = ~c;
+ while (len && ((ptrdiff_t)buf & 3)) {
+ c = crc_table[4][(c >> 24) ^ *buf++] ^ (c << 8);
+ len--;
+ }
+
+ buf4 = (const z_crc_t FAR *)(const void FAR *)buf;
+ buf4--;
+ while (len >= 32) {
+ DOBIG32;
+ len -= 32;
+ }
+ while (len >= 4) {
+ DOBIG4;
+ len -= 4;
+ }
+ buf4++;
+ buf = (const unsigned char FAR *)buf4;
+
+ if (len) do {
+ c = crc_table[4][(c >> 24) ^ *buf++] ^ (c << 8);
+ } while (--len);
+ c = ~c;
+ return (unsigned long)(ZSWAP32(c));
+}
+
+#endif /* BYFOUR */
+
+#define GF2_DIM 32 /* dimension of GF(2) vectors (length of CRC) */
+
+/* ========================================================================= */
+local unsigned long gf2_matrix_times(mat, vec)
+ unsigned long *mat;
+ unsigned long vec;
+{
+ unsigned long sum;
+
+ sum = 0;
+ while (vec) {
+ if (vec & 1)
+ sum ^= *mat;
+ vec >>= 1;
+ mat++;
+ }
+ return sum;
+}
+
+/* ========================================================================= */
+local void gf2_matrix_square(square, mat)
+ unsigned long *square;
+ unsigned long *mat;
+{
+ int n;
+
+ for (n = 0; n < GF2_DIM; n++)
+ square[n] = gf2_matrix_times(mat, mat[n]);
+}
+
+/* ========================================================================= */
+local uLong crc32_combine_(crc1, crc2, len2)
+ uLong crc1;
+ uLong crc2;
+ z_off64_t len2;
+{
+ int n;
+ unsigned long row;
+ unsigned long even[GF2_DIM]; /* even-power-of-two zeros operator */
+ unsigned long odd[GF2_DIM]; /* odd-power-of-two zeros operator */
+
+ /* degenerate case (also disallow negative lengths) */
+ if (len2 <= 0)
+ return crc1;
+
+ /* put operator for one zero bit in odd */
+ odd[0] = 0xedb88320UL; /* CRC-32 polynomial */
+ row = 1;
+ for (n = 1; n < GF2_DIM; n++) {
+ odd[n] = row;
+ row <<= 1;
+ }
+
+ /* put operator for two zero bits in even */
+ gf2_matrix_square(even, odd);
+
+ /* put operator for four zero bits in odd */
+ gf2_matrix_square(odd, even);
+
+ /* apply len2 zeros to crc1 (first square will put the operator for one
+ zero byte, eight zero bits, in even) */
+ do {
+ /* apply zeros operator for this bit of len2 */
+ gf2_matrix_square(even, odd);
+ if (len2 & 1)
+ crc1 = gf2_matrix_times(even, crc1);
+ len2 >>= 1;
+
+ /* if no more bits set, then done */
+ if (len2 == 0)
+ break;
+
+ /* another iteration of the loop with odd and even swapped */
+ gf2_matrix_square(odd, even);
+ if (len2 & 1)
+ crc1 = gf2_matrix_times(odd, crc1);
+ len2 >>= 1;
+
+ /* if no more bits set, then done */
+ } while (len2 != 0);
+
+ /* return combined crc */
+ crc1 ^= crc2;
+ return crc1;
+}
+
+/* ========================================================================= */
+uLong ZEXPORT crc32_combine(crc1, crc2, len2)
+ uLong crc1;
+ uLong crc2;
+ z_off_t len2;
+{
+ return crc32_combine_(crc1, crc2, len2);
+}
+
+uLong ZEXPORT crc32_combine64(crc1, crc2, len2)
+ uLong crc1;
+ uLong crc2;
+ z_off64_t len2;
+{
+ return crc32_combine_(crc1, crc2, len2);
+}
diff --git a/third-party/zlib/crc32.h b/third-party/zlib/crc32.h
new file mode 100644
index 0000000..9e0c778
--- /dev/null
+++ b/third-party/zlib/crc32.h
@@ -0,0 +1,441 @@
+/* crc32.h -- tables for rapid CRC calculation
+ * Generated automatically by crc32.c
+ */
+
+local const z_crc_t FAR crc_table[TBLS][256] =
+{
+ {
+ 0x00000000UL, 0x77073096UL, 0xee0e612cUL, 0x990951baUL, 0x076dc419UL,
+ 0x706af48fUL, 0xe963a535UL, 0x9e6495a3UL, 0x0edb8832UL, 0x79dcb8a4UL,
+ 0xe0d5e91eUL, 0x97d2d988UL, 0x09b64c2bUL, 0x7eb17cbdUL, 0xe7b82d07UL,
+ 0x90bf1d91UL, 0x1db71064UL, 0x6ab020f2UL, 0xf3b97148UL, 0x84be41deUL,
+ 0x1adad47dUL, 0x6ddde4ebUL, 0xf4d4b551UL, 0x83d385c7UL, 0x136c9856UL,
+ 0x646ba8c0UL, 0xfd62f97aUL, 0x8a65c9ecUL, 0x14015c4fUL, 0x63066cd9UL,
+ 0xfa0f3d63UL, 0x8d080df5UL, 0x3b6e20c8UL, 0x4c69105eUL, 0xd56041e4UL,
+ 0xa2677172UL, 0x3c03e4d1UL, 0x4b04d447UL, 0xd20d85fdUL, 0xa50ab56bUL,
+ 0x35b5a8faUL, 0x42b2986cUL, 0xdbbbc9d6UL, 0xacbcf940UL, 0x32d86ce3UL,
+ 0x45df5c75UL, 0xdcd60dcfUL, 0xabd13d59UL, 0x26d930acUL, 0x51de003aUL,
+ 0xc8d75180UL, 0xbfd06116UL, 0x21b4f4b5UL, 0x56b3c423UL, 0xcfba9599UL,
+ 0xb8bda50fUL, 0x2802b89eUL, 0x5f058808UL, 0xc60cd9b2UL, 0xb10be924UL,
+ 0x2f6f7c87UL, 0x58684c11UL, 0xc1611dabUL, 0xb6662d3dUL, 0x76dc4190UL,
+ 0x01db7106UL, 0x98d220bcUL, 0xefd5102aUL, 0x71b18589UL, 0x06b6b51fUL,
+ 0x9fbfe4a5UL, 0xe8b8d433UL, 0x7807c9a2UL, 0x0f00f934UL, 0x9609a88eUL,
+ 0xe10e9818UL, 0x7f6a0dbbUL, 0x086d3d2dUL, 0x91646c97UL, 0xe6635c01UL,
+ 0x6b6b51f4UL, 0x1c6c6162UL, 0x856530d8UL, 0xf262004eUL, 0x6c0695edUL,
+ 0x1b01a57bUL, 0x8208f4c1UL, 0xf50fc457UL, 0x65b0d9c6UL, 0x12b7e950UL,
+ 0x8bbeb8eaUL, 0xfcb9887cUL, 0x62dd1ddfUL, 0x15da2d49UL, 0x8cd37cf3UL,
+ 0xfbd44c65UL, 0x4db26158UL, 0x3ab551ceUL, 0xa3bc0074UL, 0xd4bb30e2UL,
+ 0x4adfa541UL, 0x3dd895d7UL, 0xa4d1c46dUL, 0xd3d6f4fbUL, 0x4369e96aUL,
+ 0x346ed9fcUL, 0xad678846UL, 0xda60b8d0UL, 0x44042d73UL, 0x33031de5UL,
+ 0xaa0a4c5fUL, 0xdd0d7cc9UL, 0x5005713cUL, 0x270241aaUL, 0xbe0b1010UL,
+ 0xc90c2086UL, 0x5768b525UL, 0x206f85b3UL, 0xb966d409UL, 0xce61e49fUL,
+ 0x5edef90eUL, 0x29d9c998UL, 0xb0d09822UL, 0xc7d7a8b4UL, 0x59b33d17UL,
+ 0x2eb40d81UL, 0xb7bd5c3bUL, 0xc0ba6cadUL, 0xedb88320UL, 0x9abfb3b6UL,
+ 0x03b6e20cUL, 0x74b1d29aUL, 0xead54739UL, 0x9dd277afUL, 0x04db2615UL,
+ 0x73dc1683UL, 0xe3630b12UL, 0x94643b84UL, 0x0d6d6a3eUL, 0x7a6a5aa8UL,
+ 0xe40ecf0bUL, 0x9309ff9dUL, 0x0a00ae27UL, 0x7d079eb1UL, 0xf00f9344UL,
+ 0x8708a3d2UL, 0x1e01f268UL, 0x6906c2feUL, 0xf762575dUL, 0x806567cbUL,
+ 0x196c3671UL, 0x6e6b06e7UL, 0xfed41b76UL, 0x89d32be0UL, 0x10da7a5aUL,
+ 0x67dd4accUL, 0xf9b9df6fUL, 0x8ebeeff9UL, 0x17b7be43UL, 0x60b08ed5UL,
+ 0xd6d6a3e8UL, 0xa1d1937eUL, 0x38d8c2c4UL, 0x4fdff252UL, 0xd1bb67f1UL,
+ 0xa6bc5767UL, 0x3fb506ddUL, 0x48b2364bUL, 0xd80d2bdaUL, 0xaf0a1b4cUL,
+ 0x36034af6UL, 0x41047a60UL, 0xdf60efc3UL, 0xa867df55UL, 0x316e8eefUL,
+ 0x4669be79UL, 0xcb61b38cUL, 0xbc66831aUL, 0x256fd2a0UL, 0x5268e236UL,
+ 0xcc0c7795UL, 0xbb0b4703UL, 0x220216b9UL, 0x5505262fUL, 0xc5ba3bbeUL,
+ 0xb2bd0b28UL, 0x2bb45a92UL, 0x5cb36a04UL, 0xc2d7ffa7UL, 0xb5d0cf31UL,
+ 0x2cd99e8bUL, 0x5bdeae1dUL, 0x9b64c2b0UL, 0xec63f226UL, 0x756aa39cUL,
+ 0x026d930aUL, 0x9c0906a9UL, 0xeb0e363fUL, 0x72076785UL, 0x05005713UL,
+ 0x95bf4a82UL, 0xe2b87a14UL, 0x7bb12baeUL, 0x0cb61b38UL, 0x92d28e9bUL,
+ 0xe5d5be0dUL, 0x7cdcefb7UL, 0x0bdbdf21UL, 0x86d3d2d4UL, 0xf1d4e242UL,
+ 0x68ddb3f8UL, 0x1fda836eUL, 0x81be16cdUL, 0xf6b9265bUL, 0x6fb077e1UL,
+ 0x18b74777UL, 0x88085ae6UL, 0xff0f6a70UL, 0x66063bcaUL, 0x11010b5cUL,
+ 0x8f659effUL, 0xf862ae69UL, 0x616bffd3UL, 0x166ccf45UL, 0xa00ae278UL,
+ 0xd70dd2eeUL, 0x4e048354UL, 0x3903b3c2UL, 0xa7672661UL, 0xd06016f7UL,
+ 0x4969474dUL, 0x3e6e77dbUL, 0xaed16a4aUL, 0xd9d65adcUL, 0x40df0b66UL,
+ 0x37d83bf0UL, 0xa9bcae53UL, 0xdebb9ec5UL, 0x47b2cf7fUL, 0x30b5ffe9UL,
+ 0xbdbdf21cUL, 0xcabac28aUL, 0x53b39330UL, 0x24b4a3a6UL, 0xbad03605UL,
+ 0xcdd70693UL, 0x54de5729UL, 0x23d967bfUL, 0xb3667a2eUL, 0xc4614ab8UL,
+ 0x5d681b02UL, 0x2a6f2b94UL, 0xb40bbe37UL, 0xc30c8ea1UL, 0x5a05df1bUL,
+ 0x2d02ef8dUL
+#ifdef BYFOUR
+ },
+ {
+ 0x00000000UL, 0x191b3141UL, 0x32366282UL, 0x2b2d53c3UL, 0x646cc504UL,
+ 0x7d77f445UL, 0x565aa786UL, 0x4f4196c7UL, 0xc8d98a08UL, 0xd1c2bb49UL,
+ 0xfaefe88aUL, 0xe3f4d9cbUL, 0xacb54f0cUL, 0xb5ae7e4dUL, 0x9e832d8eUL,
+ 0x87981ccfUL, 0x4ac21251UL, 0x53d92310UL, 0x78f470d3UL, 0x61ef4192UL,
+ 0x2eaed755UL, 0x37b5e614UL, 0x1c98b5d7UL, 0x05838496UL, 0x821b9859UL,
+ 0x9b00a918UL, 0xb02dfadbUL, 0xa936cb9aUL, 0xe6775d5dUL, 0xff6c6c1cUL,
+ 0xd4413fdfUL, 0xcd5a0e9eUL, 0x958424a2UL, 0x8c9f15e3UL, 0xa7b24620UL,
+ 0xbea97761UL, 0xf1e8e1a6UL, 0xe8f3d0e7UL, 0xc3de8324UL, 0xdac5b265UL,
+ 0x5d5daeaaUL, 0x44469febUL, 0x6f6bcc28UL, 0x7670fd69UL, 0x39316baeUL,
+ 0x202a5aefUL, 0x0b07092cUL, 0x121c386dUL, 0xdf4636f3UL, 0xc65d07b2UL,
+ 0xed705471UL, 0xf46b6530UL, 0xbb2af3f7UL, 0xa231c2b6UL, 0x891c9175UL,
+ 0x9007a034UL, 0x179fbcfbUL, 0x0e848dbaUL, 0x25a9de79UL, 0x3cb2ef38UL,
+ 0x73f379ffUL, 0x6ae848beUL, 0x41c51b7dUL, 0x58de2a3cUL, 0xf0794f05UL,
+ 0xe9627e44UL, 0xc24f2d87UL, 0xdb541cc6UL, 0x94158a01UL, 0x8d0ebb40UL,
+ 0xa623e883UL, 0xbf38d9c2UL, 0x38a0c50dUL, 0x21bbf44cUL, 0x0a96a78fUL,
+ 0x138d96ceUL, 0x5ccc0009UL, 0x45d73148UL, 0x6efa628bUL, 0x77e153caUL,
+ 0xbabb5d54UL, 0xa3a06c15UL, 0x888d3fd6UL, 0x91960e97UL, 0xded79850UL,
+ 0xc7cca911UL, 0xece1fad2UL, 0xf5facb93UL, 0x7262d75cUL, 0x6b79e61dUL,
+ 0x4054b5deUL, 0x594f849fUL, 0x160e1258UL, 0x0f152319UL, 0x243870daUL,
+ 0x3d23419bUL, 0x65fd6ba7UL, 0x7ce65ae6UL, 0x57cb0925UL, 0x4ed03864UL,
+ 0x0191aea3UL, 0x188a9fe2UL, 0x33a7cc21UL, 0x2abcfd60UL, 0xad24e1afUL,
+ 0xb43fd0eeUL, 0x9f12832dUL, 0x8609b26cUL, 0xc94824abUL, 0xd05315eaUL,
+ 0xfb7e4629UL, 0xe2657768UL, 0x2f3f79f6UL, 0x362448b7UL, 0x1d091b74UL,
+ 0x04122a35UL, 0x4b53bcf2UL, 0x52488db3UL, 0x7965de70UL, 0x607eef31UL,
+ 0xe7e6f3feUL, 0xfefdc2bfUL, 0xd5d0917cUL, 0xcccba03dUL, 0x838a36faUL,
+ 0x9a9107bbUL, 0xb1bc5478UL, 0xa8a76539UL, 0x3b83984bUL, 0x2298a90aUL,
+ 0x09b5fac9UL, 0x10aecb88UL, 0x5fef5d4fUL, 0x46f46c0eUL, 0x6dd93fcdUL,
+ 0x74c20e8cUL, 0xf35a1243UL, 0xea412302UL, 0xc16c70c1UL, 0xd8774180UL,
+ 0x9736d747UL, 0x8e2de606UL, 0xa500b5c5UL, 0xbc1b8484UL, 0x71418a1aUL,
+ 0x685abb5bUL, 0x4377e898UL, 0x5a6cd9d9UL, 0x152d4f1eUL, 0x0c367e5fUL,
+ 0x271b2d9cUL, 0x3e001cddUL, 0xb9980012UL, 0xa0833153UL, 0x8bae6290UL,
+ 0x92b553d1UL, 0xddf4c516UL, 0xc4eff457UL, 0xefc2a794UL, 0xf6d996d5UL,
+ 0xae07bce9UL, 0xb71c8da8UL, 0x9c31de6bUL, 0x852aef2aUL, 0xca6b79edUL,
+ 0xd37048acUL, 0xf85d1b6fUL, 0xe1462a2eUL, 0x66de36e1UL, 0x7fc507a0UL,
+ 0x54e85463UL, 0x4df36522UL, 0x02b2f3e5UL, 0x1ba9c2a4UL, 0x30849167UL,
+ 0x299fa026UL, 0xe4c5aeb8UL, 0xfdde9ff9UL, 0xd6f3cc3aUL, 0xcfe8fd7bUL,
+ 0x80a96bbcUL, 0x99b25afdUL, 0xb29f093eUL, 0xab84387fUL, 0x2c1c24b0UL,
+ 0x350715f1UL, 0x1e2a4632UL, 0x07317773UL, 0x4870e1b4UL, 0x516bd0f5UL,
+ 0x7a468336UL, 0x635db277UL, 0xcbfad74eUL, 0xd2e1e60fUL, 0xf9ccb5ccUL,
+ 0xe0d7848dUL, 0xaf96124aUL, 0xb68d230bUL, 0x9da070c8UL, 0x84bb4189UL,
+ 0x03235d46UL, 0x1a386c07UL, 0x31153fc4UL, 0x280e0e85UL, 0x674f9842UL,
+ 0x7e54a903UL, 0x5579fac0UL, 0x4c62cb81UL, 0x8138c51fUL, 0x9823f45eUL,
+ 0xb30ea79dUL, 0xaa1596dcUL, 0xe554001bUL, 0xfc4f315aUL, 0xd7626299UL,
+ 0xce7953d8UL, 0x49e14f17UL, 0x50fa7e56UL, 0x7bd72d95UL, 0x62cc1cd4UL,
+ 0x2d8d8a13UL, 0x3496bb52UL, 0x1fbbe891UL, 0x06a0d9d0UL, 0x5e7ef3ecUL,
+ 0x4765c2adUL, 0x6c48916eUL, 0x7553a02fUL, 0x3a1236e8UL, 0x230907a9UL,
+ 0x0824546aUL, 0x113f652bUL, 0x96a779e4UL, 0x8fbc48a5UL, 0xa4911b66UL,
+ 0xbd8a2a27UL, 0xf2cbbce0UL, 0xebd08da1UL, 0xc0fdde62UL, 0xd9e6ef23UL,
+ 0x14bce1bdUL, 0x0da7d0fcUL, 0x268a833fUL, 0x3f91b27eUL, 0x70d024b9UL,
+ 0x69cb15f8UL, 0x42e6463bUL, 0x5bfd777aUL, 0xdc656bb5UL, 0xc57e5af4UL,
+ 0xee530937UL, 0xf7483876UL, 0xb809aeb1UL, 0xa1129ff0UL, 0x8a3fcc33UL,
+ 0x9324fd72UL
+ },
+ {
+ 0x00000000UL, 0x01c26a37UL, 0x0384d46eUL, 0x0246be59UL, 0x0709a8dcUL,
+ 0x06cbc2ebUL, 0x048d7cb2UL, 0x054f1685UL, 0x0e1351b8UL, 0x0fd13b8fUL,
+ 0x0d9785d6UL, 0x0c55efe1UL, 0x091af964UL, 0x08d89353UL, 0x0a9e2d0aUL,
+ 0x0b5c473dUL, 0x1c26a370UL, 0x1de4c947UL, 0x1fa2771eUL, 0x1e601d29UL,
+ 0x1b2f0bacUL, 0x1aed619bUL, 0x18abdfc2UL, 0x1969b5f5UL, 0x1235f2c8UL,
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+ 0xeed03fb4UL, 0x2d83129fUL, 0x6cb20986UL, 0xab2448c9UL, 0xea1553d0UL,
+ 0x29467efbUL, 0x687765e2UL, 0xf6793f2fUL, 0xb7482436UL, 0x741b091dUL,
+ 0x352a1204UL, 0xf2bc534bUL, 0xb38d4852UL, 0x70de6579UL, 0x31ef7e60UL,
+ 0xfef3e6e7UL, 0xbfc2fdfeUL, 0x7c91d0d5UL, 0x3da0cbccUL, 0xfa368a83UL,
+ 0xbb07919aUL, 0x7854bcb1UL, 0x3965a7a8UL, 0x4b98833bUL, 0x0aa99822UL,
+ 0xc9fab509UL, 0x88cbae10UL, 0x4f5def5fUL, 0x0e6cf446UL, 0xcd3fd96dUL,
+ 0x8c0ec274UL, 0x43125af3UL, 0x022341eaUL, 0xc1706cc1UL, 0x804177d8UL,
+ 0x47d73697UL, 0x06e62d8eUL, 0xc5b500a5UL, 0x84841bbcUL, 0x1a8a4171UL,
+ 0x5bbb5a68UL, 0x98e87743UL, 0xd9d96c5aUL, 0x1e4f2d15UL, 0x5f7e360cUL,
+ 0x9c2d1b27UL, 0xdd1c003eUL, 0x120098b9UL, 0x533183a0UL, 0x9062ae8bUL,
+ 0xd153b592UL, 0x16c5f4ddUL, 0x57f4efc4UL, 0x94a7c2efUL, 0xd596d9f6UL,
+ 0xe9bc07aeUL, 0xa88d1cb7UL, 0x6bde319cUL, 0x2aef2a85UL, 0xed796bcaUL,
+ 0xac4870d3UL, 0x6f1b5df8UL, 0x2e2a46e1UL, 0xe136de66UL, 0xa007c57fUL,
+ 0x6354e854UL, 0x2265f34dUL, 0xe5f3b202UL, 0xa4c2a91bUL, 0x67918430UL,
+ 0x26a09f29UL, 0xb8aec5e4UL, 0xf99fdefdUL, 0x3accf3d6UL, 0x7bfde8cfUL,
+ 0xbc6ba980UL, 0xfd5ab299UL, 0x3e099fb2UL, 0x7f3884abUL, 0xb0241c2cUL,
+ 0xf1150735UL, 0x32462a1eUL, 0x73773107UL, 0xb4e17048UL, 0xf5d06b51UL,
+ 0x3683467aUL, 0x77b25d63UL, 0x4ed7facbUL, 0x0fe6e1d2UL, 0xccb5ccf9UL,
+ 0x8d84d7e0UL, 0x4a1296afUL, 0x0b238db6UL, 0xc870a09dUL, 0x8941bb84UL,
+ 0x465d2303UL, 0x076c381aUL, 0xc43f1531UL, 0x850e0e28UL, 0x42984f67UL,
+ 0x03a9547eUL, 0xc0fa7955UL, 0x81cb624cUL, 0x1fc53881UL, 0x5ef42398UL,
+ 0x9da70eb3UL, 0xdc9615aaUL, 0x1b0054e5UL, 0x5a314ffcUL, 0x996262d7UL,
+ 0xd85379ceUL, 0x174fe149UL, 0x567efa50UL, 0x952dd77bUL, 0xd41ccc62UL,
+ 0x138a8d2dUL, 0x52bb9634UL, 0x91e8bb1fUL, 0xd0d9a006UL, 0xecf37e5eUL,
+ 0xadc26547UL, 0x6e91486cUL, 0x2fa05375UL, 0xe836123aUL, 0xa9070923UL,
+ 0x6a542408UL, 0x2b653f11UL, 0xe479a796UL, 0xa548bc8fUL, 0x661b91a4UL,
+ 0x272a8abdUL, 0xe0bccbf2UL, 0xa18dd0ebUL, 0x62defdc0UL, 0x23efe6d9UL,
+ 0xbde1bc14UL, 0xfcd0a70dUL, 0x3f838a26UL, 0x7eb2913fUL, 0xb924d070UL,
+ 0xf815cb69UL, 0x3b46e642UL, 0x7a77fd5bUL, 0xb56b65dcUL, 0xf45a7ec5UL,
+ 0x370953eeUL, 0x763848f7UL, 0xb1ae09b8UL, 0xf09f12a1UL, 0x33cc3f8aUL,
+ 0x72fd2493UL
+ },
+ {
+ 0x00000000UL, 0x376ac201UL, 0x6ed48403UL, 0x59be4602UL, 0xdca80907UL,
+ 0xebc2cb06UL, 0xb27c8d04UL, 0x85164f05UL, 0xb851130eUL, 0x8f3bd10fUL,
+ 0xd685970dUL, 0xe1ef550cUL, 0x64f91a09UL, 0x5393d808UL, 0x0a2d9e0aUL,
+ 0x3d475c0bUL, 0x70a3261cUL, 0x47c9e41dUL, 0x1e77a21fUL, 0x291d601eUL,
+ 0xac0b2f1bUL, 0x9b61ed1aUL, 0xc2dfab18UL, 0xf5b56919UL, 0xc8f23512UL,
+ 0xff98f713UL, 0xa626b111UL, 0x914c7310UL, 0x145a3c15UL, 0x2330fe14UL,
+ 0x7a8eb816UL, 0x4de47a17UL, 0xe0464d38UL, 0xd72c8f39UL, 0x8e92c93bUL,
+ 0xb9f80b3aUL, 0x3cee443fUL, 0x0b84863eUL, 0x523ac03cUL, 0x6550023dUL,
+ 0x58175e36UL, 0x6f7d9c37UL, 0x36c3da35UL, 0x01a91834UL, 0x84bf5731UL,
+ 0xb3d59530UL, 0xea6bd332UL, 0xdd011133UL, 0x90e56b24UL, 0xa78fa925UL,
+ 0xfe31ef27UL, 0xc95b2d26UL, 0x4c4d6223UL, 0x7b27a022UL, 0x2299e620UL,
+ 0x15f32421UL, 0x28b4782aUL, 0x1fdeba2bUL, 0x4660fc29UL, 0x710a3e28UL,
+ 0xf41c712dUL, 0xc376b32cUL, 0x9ac8f52eUL, 0xada2372fUL, 0xc08d9a70UL,
+ 0xf7e75871UL, 0xae591e73UL, 0x9933dc72UL, 0x1c259377UL, 0x2b4f5176UL,
+ 0x72f11774UL, 0x459bd575UL, 0x78dc897eUL, 0x4fb64b7fUL, 0x16080d7dUL,
+ 0x2162cf7cUL, 0xa4748079UL, 0x931e4278UL, 0xcaa0047aUL, 0xfdcac67bUL,
+ 0xb02ebc6cUL, 0x87447e6dUL, 0xdefa386fUL, 0xe990fa6eUL, 0x6c86b56bUL,
+ 0x5bec776aUL, 0x02523168UL, 0x3538f369UL, 0x087faf62UL, 0x3f156d63UL,
+ 0x66ab2b61UL, 0x51c1e960UL, 0xd4d7a665UL, 0xe3bd6464UL, 0xba032266UL,
+ 0x8d69e067UL, 0x20cbd748UL, 0x17a11549UL, 0x4e1f534bUL, 0x7975914aUL,
+ 0xfc63de4fUL, 0xcb091c4eUL, 0x92b75a4cUL, 0xa5dd984dUL, 0x989ac446UL,
+ 0xaff00647UL, 0xf64e4045UL, 0xc1248244UL, 0x4432cd41UL, 0x73580f40UL,
+ 0x2ae64942UL, 0x1d8c8b43UL, 0x5068f154UL, 0x67023355UL, 0x3ebc7557UL,
+ 0x09d6b756UL, 0x8cc0f853UL, 0xbbaa3a52UL, 0xe2147c50UL, 0xd57ebe51UL,
+ 0xe839e25aUL, 0xdf53205bUL, 0x86ed6659UL, 0xb187a458UL, 0x3491eb5dUL,
+ 0x03fb295cUL, 0x5a456f5eUL, 0x6d2fad5fUL, 0x801b35e1UL, 0xb771f7e0UL,
+ 0xeecfb1e2UL, 0xd9a573e3UL, 0x5cb33ce6UL, 0x6bd9fee7UL, 0x3267b8e5UL,
+ 0x050d7ae4UL, 0x384a26efUL, 0x0f20e4eeUL, 0x569ea2ecUL, 0x61f460edUL,
+ 0xe4e22fe8UL, 0xd388ede9UL, 0x8a36abebUL, 0xbd5c69eaUL, 0xf0b813fdUL,
+ 0xc7d2d1fcUL, 0x9e6c97feUL, 0xa90655ffUL, 0x2c101afaUL, 0x1b7ad8fbUL,
+ 0x42c49ef9UL, 0x75ae5cf8UL, 0x48e900f3UL, 0x7f83c2f2UL, 0x263d84f0UL,
+ 0x115746f1UL, 0x944109f4UL, 0xa32bcbf5UL, 0xfa958df7UL, 0xcdff4ff6UL,
+ 0x605d78d9UL, 0x5737bad8UL, 0x0e89fcdaUL, 0x39e33edbUL, 0xbcf571deUL,
+ 0x8b9fb3dfUL, 0xd221f5ddUL, 0xe54b37dcUL, 0xd80c6bd7UL, 0xef66a9d6UL,
+ 0xb6d8efd4UL, 0x81b22dd5UL, 0x04a462d0UL, 0x33cea0d1UL, 0x6a70e6d3UL,
+ 0x5d1a24d2UL, 0x10fe5ec5UL, 0x27949cc4UL, 0x7e2adac6UL, 0x494018c7UL,
+ 0xcc5657c2UL, 0xfb3c95c3UL, 0xa282d3c1UL, 0x95e811c0UL, 0xa8af4dcbUL,
+ 0x9fc58fcaUL, 0xc67bc9c8UL, 0xf1110bc9UL, 0x740744ccUL, 0x436d86cdUL,
+ 0x1ad3c0cfUL, 0x2db902ceUL, 0x4096af91UL, 0x77fc6d90UL, 0x2e422b92UL,
+ 0x1928e993UL, 0x9c3ea696UL, 0xab546497UL, 0xf2ea2295UL, 0xc580e094UL,
+ 0xf8c7bc9fUL, 0xcfad7e9eUL, 0x9613389cUL, 0xa179fa9dUL, 0x246fb598UL,
+ 0x13057799UL, 0x4abb319bUL, 0x7dd1f39aUL, 0x3035898dUL, 0x075f4b8cUL,
+ 0x5ee10d8eUL, 0x698bcf8fUL, 0xec9d808aUL, 0xdbf7428bUL, 0x82490489UL,
+ 0xb523c688UL, 0x88649a83UL, 0xbf0e5882UL, 0xe6b01e80UL, 0xd1dadc81UL,
+ 0x54cc9384UL, 0x63a65185UL, 0x3a181787UL, 0x0d72d586UL, 0xa0d0e2a9UL,
+ 0x97ba20a8UL, 0xce0466aaUL, 0xf96ea4abUL, 0x7c78ebaeUL, 0x4b1229afUL,
+ 0x12ac6fadUL, 0x25c6adacUL, 0x1881f1a7UL, 0x2feb33a6UL, 0x765575a4UL,
+ 0x413fb7a5UL, 0xc429f8a0UL, 0xf3433aa1UL, 0xaafd7ca3UL, 0x9d97bea2UL,
+ 0xd073c4b5UL, 0xe71906b4UL, 0xbea740b6UL, 0x89cd82b7UL, 0x0cdbcdb2UL,
+ 0x3bb10fb3UL, 0x620f49b1UL, 0x55658bb0UL, 0x6822d7bbUL, 0x5f4815baUL,
+ 0x06f653b8UL, 0x319c91b9UL, 0xb48adebcUL, 0x83e01cbdUL, 0xda5e5abfUL,
+ 0xed3498beUL
+ },
+ {
+ 0x00000000UL, 0x6567bcb8UL, 0x8bc809aaUL, 0xeeafb512UL, 0x5797628fUL,
+ 0x32f0de37UL, 0xdc5f6b25UL, 0xb938d79dUL, 0xef28b4c5UL, 0x8a4f087dUL,
+ 0x64e0bd6fUL, 0x018701d7UL, 0xb8bfd64aUL, 0xddd86af2UL, 0x3377dfe0UL,
+ 0x56106358UL, 0x9f571950UL, 0xfa30a5e8UL, 0x149f10faUL, 0x71f8ac42UL,
+ 0xc8c07bdfUL, 0xada7c767UL, 0x43087275UL, 0x266fcecdUL, 0x707fad95UL,
+ 0x1518112dUL, 0xfbb7a43fUL, 0x9ed01887UL, 0x27e8cf1aUL, 0x428f73a2UL,
+ 0xac20c6b0UL, 0xc9477a08UL, 0x3eaf32a0UL, 0x5bc88e18UL, 0xb5673b0aUL,
+ 0xd00087b2UL, 0x6938502fUL, 0x0c5fec97UL, 0xe2f05985UL, 0x8797e53dUL,
+ 0xd1878665UL, 0xb4e03addUL, 0x5a4f8fcfUL, 0x3f283377UL, 0x8610e4eaUL,
+ 0xe3775852UL, 0x0dd8ed40UL, 0x68bf51f8UL, 0xa1f82bf0UL, 0xc49f9748UL,
+ 0x2a30225aUL, 0x4f579ee2UL, 0xf66f497fUL, 0x9308f5c7UL, 0x7da740d5UL,
+ 0x18c0fc6dUL, 0x4ed09f35UL, 0x2bb7238dUL, 0xc518969fUL, 0xa07f2a27UL,
+ 0x1947fdbaUL, 0x7c204102UL, 0x928ff410UL, 0xf7e848a8UL, 0x3d58149bUL,
+ 0x583fa823UL, 0xb6901d31UL, 0xd3f7a189UL, 0x6acf7614UL, 0x0fa8caacUL,
+ 0xe1077fbeUL, 0x8460c306UL, 0xd270a05eUL, 0xb7171ce6UL, 0x59b8a9f4UL,
+ 0x3cdf154cUL, 0x85e7c2d1UL, 0xe0807e69UL, 0x0e2fcb7bUL, 0x6b4877c3UL,
+ 0xa20f0dcbUL, 0xc768b173UL, 0x29c70461UL, 0x4ca0b8d9UL, 0xf5986f44UL,
+ 0x90ffd3fcUL, 0x7e5066eeUL, 0x1b37da56UL, 0x4d27b90eUL, 0x284005b6UL,
+ 0xc6efb0a4UL, 0xa3880c1cUL, 0x1ab0db81UL, 0x7fd76739UL, 0x9178d22bUL,
+ 0xf41f6e93UL, 0x03f7263bUL, 0x66909a83UL, 0x883f2f91UL, 0xed589329UL,
+ 0x546044b4UL, 0x3107f80cUL, 0xdfa84d1eUL, 0xbacff1a6UL, 0xecdf92feUL,
+ 0x89b82e46UL, 0x67179b54UL, 0x027027ecUL, 0xbb48f071UL, 0xde2f4cc9UL,
+ 0x3080f9dbUL, 0x55e74563UL, 0x9ca03f6bUL, 0xf9c783d3UL, 0x176836c1UL,
+ 0x720f8a79UL, 0xcb375de4UL, 0xae50e15cUL, 0x40ff544eUL, 0x2598e8f6UL,
+ 0x73888baeUL, 0x16ef3716UL, 0xf8408204UL, 0x9d273ebcUL, 0x241fe921UL,
+ 0x41785599UL, 0xafd7e08bUL, 0xcab05c33UL, 0x3bb659edUL, 0x5ed1e555UL,
+ 0xb07e5047UL, 0xd519ecffUL, 0x6c213b62UL, 0x094687daUL, 0xe7e932c8UL,
+ 0x828e8e70UL, 0xd49eed28UL, 0xb1f95190UL, 0x5f56e482UL, 0x3a31583aUL,
+ 0x83098fa7UL, 0xe66e331fUL, 0x08c1860dUL, 0x6da63ab5UL, 0xa4e140bdUL,
+ 0xc186fc05UL, 0x2f294917UL, 0x4a4ef5afUL, 0xf3762232UL, 0x96119e8aUL,
+ 0x78be2b98UL, 0x1dd99720UL, 0x4bc9f478UL, 0x2eae48c0UL, 0xc001fdd2UL,
+ 0xa566416aUL, 0x1c5e96f7UL, 0x79392a4fUL, 0x97969f5dUL, 0xf2f123e5UL,
+ 0x05196b4dUL, 0x607ed7f5UL, 0x8ed162e7UL, 0xebb6de5fUL, 0x528e09c2UL,
+ 0x37e9b57aUL, 0xd9460068UL, 0xbc21bcd0UL, 0xea31df88UL, 0x8f566330UL,
+ 0x61f9d622UL, 0x049e6a9aUL, 0xbda6bd07UL, 0xd8c101bfUL, 0x366eb4adUL,
+ 0x53090815UL, 0x9a4e721dUL, 0xff29cea5UL, 0x11867bb7UL, 0x74e1c70fUL,
+ 0xcdd91092UL, 0xa8beac2aUL, 0x46111938UL, 0x2376a580UL, 0x7566c6d8UL,
+ 0x10017a60UL, 0xfeaecf72UL, 0x9bc973caUL, 0x22f1a457UL, 0x479618efUL,
+ 0xa939adfdUL, 0xcc5e1145UL, 0x06ee4d76UL, 0x6389f1ceUL, 0x8d2644dcUL,
+ 0xe841f864UL, 0x51792ff9UL, 0x341e9341UL, 0xdab12653UL, 0xbfd69aebUL,
+ 0xe9c6f9b3UL, 0x8ca1450bUL, 0x620ef019UL, 0x07694ca1UL, 0xbe519b3cUL,
+ 0xdb362784UL, 0x35999296UL, 0x50fe2e2eUL, 0x99b95426UL, 0xfcdee89eUL,
+ 0x12715d8cUL, 0x7716e134UL, 0xce2e36a9UL, 0xab498a11UL, 0x45e63f03UL,
+ 0x208183bbUL, 0x7691e0e3UL, 0x13f65c5bUL, 0xfd59e949UL, 0x983e55f1UL,
+ 0x2106826cUL, 0x44613ed4UL, 0xaace8bc6UL, 0xcfa9377eUL, 0x38417fd6UL,
+ 0x5d26c36eUL, 0xb389767cUL, 0xd6eecac4UL, 0x6fd61d59UL, 0x0ab1a1e1UL,
+ 0xe41e14f3UL, 0x8179a84bUL, 0xd769cb13UL, 0xb20e77abUL, 0x5ca1c2b9UL,
+ 0x39c67e01UL, 0x80fea99cUL, 0xe5991524UL, 0x0b36a036UL, 0x6e511c8eUL,
+ 0xa7166686UL, 0xc271da3eUL, 0x2cde6f2cUL, 0x49b9d394UL, 0xf0810409UL,
+ 0x95e6b8b1UL, 0x7b490da3UL, 0x1e2eb11bUL, 0x483ed243UL, 0x2d596efbUL,
+ 0xc3f6dbe9UL, 0xa6916751UL, 0x1fa9b0ccUL, 0x7ace0c74UL, 0x9461b966UL,
+ 0xf10605deUL
+#endif
+ }
+};
diff --git a/third-party/zlib/deflate.c b/third-party/zlib/deflate.c
new file mode 100644
index 0000000..6969577
--- /dev/null
+++ b/third-party/zlib/deflate.c
@@ -0,0 +1,1967 @@
+/* deflate.c -- compress data using the deflation algorithm
+ * Copyright (C) 1995-2013 Jean-loup Gailly and Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/*
+ * ALGORITHM
+ *
+ * The "deflation" process depends on being able to identify portions
+ * of the input text which are identical to earlier input (within a
+ * sliding window trailing behind the input currently being processed).
+ *
+ * The most straightforward technique turns out to be the fastest for
+ * most input files: try all possible matches and select the longest.
+ * The key feature of this algorithm is that insertions into the string
+ * dictionary are very simple and thus fast, and deletions are avoided
+ * completely. Insertions are performed at each input character, whereas
+ * string matches are performed only when the previous match ends. So it
+ * is preferable to spend more time in matches to allow very fast string
+ * insertions and avoid deletions. The matching algorithm for small
+ * strings is inspired from that of Rabin & Karp. A brute force approach
+ * is used to find longer strings when a small match has been found.
+ * A similar algorithm is used in comic (by Jan-Mark Wams) and freeze
+ * (by Leonid Broukhis).
+ * A previous version of this file used a more sophisticated algorithm
+ * (by Fiala and Greene) which is guaranteed to run in linear amortized
+ * time, but has a larger average cost, uses more memory and is patented.
+ * However the F&G algorithm may be faster for some highly redundant
+ * files if the parameter max_chain_length (described below) is too large.
+ *
+ * ACKNOWLEDGEMENTS
+ *
+ * The idea of lazy evaluation of matches is due to Jan-Mark Wams, and
+ * I found it in 'freeze' written by Leonid Broukhis.
+ * Thanks to many people for bug reports and testing.
+ *
+ * REFERENCES
+ *
+ * Deutsch, L.P.,"DEFLATE Compressed Data Format Specification".
+ * Available in http://tools.ietf.org/html/rfc1951
+ *
+ * A description of the Rabin and Karp algorithm is given in the book
+ * "Algorithms" by R. Sedgewick, Addison-Wesley, p252.
+ *
+ * Fiala,E.R., and Greene,D.H.
+ * Data Compression with Finite Windows, Comm.ACM, 32,4 (1989) 490-595
+ *
+ */
+
+/* @(#) $Id$ */
+
+#include "deflate.h"
+
+const char deflate_copyright[] =
+ " deflate 1.2.8 Copyright 1995-2013 Jean-loup Gailly and Mark Adler ";
+/*
+ If you use the zlib library in a product, an acknowledgment is welcome
+ in the documentation of your product. If for some reason you cannot
+ include such an acknowledgment, I would appreciate that you keep this
+ copyright string in the executable of your product.
+ */
+
+/* ===========================================================================
+ * Function prototypes.
+ */
+typedef enum {
+ need_more, /* block not completed, need more input or more output */
+ block_done, /* block flush performed */
+ finish_started, /* finish started, need only more output at next deflate */
+ finish_done /* finish done, accept no more input or output */
+} block_state;
+
+typedef block_state (*compress_func) OF((deflate_state *s, int flush));
+/* Compression function. Returns the block state after the call. */
+
+local void fill_window OF((deflate_state *s));
+local block_state deflate_stored OF((deflate_state *s, int flush));
+local block_state deflate_fast OF((deflate_state *s, int flush));
+#ifndef FASTEST
+local block_state deflate_slow OF((deflate_state *s, int flush));
+#endif
+local block_state deflate_rle OF((deflate_state *s, int flush));
+local block_state deflate_huff OF((deflate_state *s, int flush));
+local void lm_init OF((deflate_state *s));
+local void putShortMSB OF((deflate_state *s, uInt b));
+local void flush_pending OF((z_streamp strm));
+local int read_buf OF((z_streamp strm, Bytef *buf, unsigned size));
+#ifdef ASMV
+ void match_init OF((void)); /* asm code initialization */
+ uInt longest_match OF((deflate_state *s, IPos cur_match));
+#else
+local uInt longest_match OF((deflate_state *s, IPos cur_match));
+#endif
+
+#ifdef DEBUG
+local void check_match OF((deflate_state *s, IPos start, IPos match,
+ int length));
+#endif
+
+/* ===========================================================================
+ * Local data
+ */
+
+#define NIL 0
+/* Tail of hash chains */
+
+#ifndef TOO_FAR
+# define TOO_FAR 4096
+#endif
+/* Matches of length 3 are discarded if their distance exceeds TOO_FAR */
+
+/* Values for max_lazy_match, good_match and max_chain_length, depending on
+ * the desired pack level (0..9). The values given below have been tuned to
+ * exclude worst case performance for pathological files. Better values may be
+ * found for specific files.
+ */
+typedef struct config_s {
+ ush good_length; /* reduce lazy search above this match length */
+ ush max_lazy; /* do not perform lazy search above this match length */
+ ush nice_length; /* quit search above this match length */
+ ush max_chain;
+ compress_func func;
+} config;
+
+#ifdef FASTEST
+local const config configuration_table[2] = {
+/* good lazy nice chain */
+/* 0 */ {0, 0, 0, 0, deflate_stored}, /* store only */
+/* 1 */ {4, 4, 8, 4, deflate_fast}}; /* max speed, no lazy matches */
+#else
+local const config configuration_table[10] = {
+/* good lazy nice chain */
+/* 0 */ {0, 0, 0, 0, deflate_stored}, /* store only */
+/* 1 */ {4, 4, 8, 4, deflate_fast}, /* max speed, no lazy matches */
+/* 2 */ {4, 5, 16, 8, deflate_fast},
+/* 3 */ {4, 6, 32, 32, deflate_fast},
+
+/* 4 */ {4, 4, 16, 16, deflate_slow}, /* lazy matches */
+/* 5 */ {8, 16, 32, 32, deflate_slow},
+/* 6 */ {8, 16, 128, 128, deflate_slow},
+/* 7 */ {8, 32, 128, 256, deflate_slow},
+/* 8 */ {32, 128, 258, 1024, deflate_slow},
+/* 9 */ {32, 258, 258, 4096, deflate_slow}}; /* max compression */
+#endif
+
+/* Note: the deflate() code requires max_lazy >= MIN_MATCH and max_chain >= 4
+ * For deflate_fast() (levels <= 3) good is ignored and lazy has a different
+ * meaning.
+ */
+
+#define EQUAL 0
+/* result of memcmp for equal strings */
+
+#ifndef NO_DUMMY_DECL
+struct static_tree_desc_s {int dummy;}; /* for buggy compilers */
+#endif
+
+/* rank Z_BLOCK between Z_NO_FLUSH and Z_PARTIAL_FLUSH */
+#define RANK(f) (((f) << 1) - ((f) > 4 ? 9 : 0))
+
+/* ===========================================================================
+ * Update a hash value with the given input byte
+ * IN assertion: all calls to to UPDATE_HASH are made with consecutive
+ * input characters, so that a running hash key can be computed from the
+ * previous key instead of complete recalculation each time.
+ */
+#define UPDATE_HASH(s,h,c) (h = (((h)<<s->hash_shift) ^ (c)) & s->hash_mask)
+
+
+/* ===========================================================================
+ * Insert string str in the dictionary and set match_head to the previous head
+ * of the hash chain (the most recent string with same hash key). Return
+ * the previous length of the hash chain.
+ * If this file is compiled with -DFASTEST, the compression level is forced
+ * to 1, and no hash chains are maintained.
+ * IN assertion: all calls to to INSERT_STRING are made with consecutive
+ * input characters and the first MIN_MATCH bytes of str are valid
+ * (except for the last MIN_MATCH-1 bytes of the input file).
+ */
+#ifdef FASTEST
+#define INSERT_STRING(s, str, match_head) \
+ (UPDATE_HASH(s, s->ins_h, s->window[(str) + (MIN_MATCH-1)]), \
+ match_head = s->head[s->ins_h], \
+ s->head[s->ins_h] = (Pos)(str))
+#else
+#define INSERT_STRING(s, str, match_head) \
+ (UPDATE_HASH(s, s->ins_h, s->window[(str) + (MIN_MATCH-1)]), \
+ match_head = s->prev[(str) & s->w_mask] = s->head[s->ins_h], \
+ s->head[s->ins_h] = (Pos)(str))
+#endif
+
+/* ===========================================================================
+ * Initialize the hash table (avoiding 64K overflow for 16 bit systems).
+ * prev[] will be initialized on the fly.
+ */
+#define CLEAR_HASH(s) \
+ s->head[s->hash_size-1] = NIL; \
+ zmemzero((Bytef *)s->head, (unsigned)(s->hash_size-1)*sizeof(*s->head));
+
+/* ========================================================================= */
+int ZEXPORT deflateInit_(strm, level, version, stream_size)
+ z_streamp strm;
+ int level;
+ const char *version;
+ int stream_size;
+{
+ return deflateInit2_(strm, level, Z_DEFLATED, MAX_WBITS, DEF_MEM_LEVEL,
+ Z_DEFAULT_STRATEGY, version, stream_size);
+ /* To do: ignore strm->next_in if we use it as window */
+}
+
+/* ========================================================================= */
+int ZEXPORT deflateInit2_(strm, level, method, windowBits, memLevel, strategy,
+ version, stream_size)
+ z_streamp strm;
+ int level;
+ int method;
+ int windowBits;
+ int memLevel;
+ int strategy;
+ const char *version;
+ int stream_size;
+{
+ deflate_state *s;
+ int wrap = 1;
+ static const char my_version[] = ZLIB_VERSION;
+
+ ushf *overlay;
+ /* We overlay pending_buf and d_buf+l_buf. This works since the average
+ * output size for (length,distance) codes is <= 24 bits.
+ */
+
+ if (version == Z_NULL || version[0] != my_version[0] ||
+ stream_size != sizeof(z_stream)) {
+ return Z_VERSION_ERROR;
+ }
+ if (strm == Z_NULL) return Z_STREAM_ERROR;
+
+ strm->msg = Z_NULL;
+ if (strm->zalloc == (alloc_func)0) {
+#ifdef Z_SOLO
+ return Z_STREAM_ERROR;
+#else
+ strm->zalloc = zcalloc;
+ strm->opaque = (voidpf)0;
+#endif
+ }
+ if (strm->zfree == (free_func)0)
+#ifdef Z_SOLO
+ return Z_STREAM_ERROR;
+#else
+ strm->zfree = zcfree;
+#endif
+
+#ifdef FASTEST
+ if (level != 0) level = 1;
+#else
+ if (level == Z_DEFAULT_COMPRESSION) level = 6;
+#endif
+
+ if (windowBits < 0) { /* suppress zlib wrapper */
+ wrap = 0;
+ windowBits = -windowBits;
+ }
+#ifdef GZIP
+ else if (windowBits > 15) {
+ wrap = 2; /* write gzip wrapper instead */
+ windowBits -= 16;
+ }
+#endif
+ if (memLevel < 1 || memLevel > MAX_MEM_LEVEL || method != Z_DEFLATED ||
+ windowBits < 8 || windowBits > 15 || level < 0 || level > 9 ||
+ strategy < 0 || strategy > Z_FIXED) {
+ return Z_STREAM_ERROR;
+ }
+ if (windowBits == 8) windowBits = 9; /* until 256-byte window bug fixed */
+ s = (deflate_state *) ZALLOC(strm, 1, sizeof(deflate_state));
+ if (s == Z_NULL) return Z_MEM_ERROR;
+ strm->state = (struct internal_state FAR *)s;
+ s->strm = strm;
+
+ s->wrap = wrap;
+ s->gzhead = Z_NULL;
+ s->w_bits = windowBits;
+ s->w_size = 1 << s->w_bits;
+ s->w_mask = s->w_size - 1;
+
+ s->hash_bits = memLevel + 7;
+ s->hash_size = 1 << s->hash_bits;
+ s->hash_mask = s->hash_size - 1;
+ s->hash_shift = ((s->hash_bits+MIN_MATCH-1)/MIN_MATCH);
+
+ s->window = (Bytef *) ZALLOC(strm, s->w_size, 2*sizeof(Byte));
+ s->prev = (Posf *) ZALLOC(strm, s->w_size, sizeof(Pos));
+ s->head = (Posf *) ZALLOC(strm, s->hash_size, sizeof(Pos));
+
+ s->high_water = 0; /* nothing written to s->window yet */
+
+ s->lit_bufsize = 1 << (memLevel + 6); /* 16K elements by default */
+
+ overlay = (ushf *) ZALLOC(strm, s->lit_bufsize, sizeof(ush)+2);
+ s->pending_buf = (uchf *) overlay;
+ s->pending_buf_size = (ulg)s->lit_bufsize * (sizeof(ush)+2L);
+
+ if (s->window == Z_NULL || s->prev == Z_NULL || s->head == Z_NULL ||
+ s->pending_buf == Z_NULL) {
+ s->status = FINISH_STATE;
+ strm->msg = ERR_MSG(Z_MEM_ERROR);
+ deflateEnd (strm);
+ return Z_MEM_ERROR;
+ }
+ s->d_buf = overlay + s->lit_bufsize/sizeof(ush);
+ s->l_buf = s->pending_buf + (1+sizeof(ush))*s->lit_bufsize;
+
+ s->level = level;
+ s->strategy = strategy;
+ s->method = (Byte)method;
+
+ return deflateReset(strm);
+}
+
+/* ========================================================================= */
+int ZEXPORT deflateSetDictionary (strm, dictionary, dictLength)
+ z_streamp strm;
+ const Bytef *dictionary;
+ uInt dictLength;
+{
+ deflate_state *s;
+ uInt str, n;
+ int wrap;
+ unsigned avail;
+ z_const unsigned char *next;
+
+ if (strm == Z_NULL || strm->state == Z_NULL || dictionary == Z_NULL)
+ return Z_STREAM_ERROR;
+ s = strm->state;
+ wrap = s->wrap;
+ if (wrap == 2 || (wrap == 1 && s->status != INIT_STATE) || s->lookahead)
+ return Z_STREAM_ERROR;
+
+ /* when using zlib wrappers, compute Adler-32 for provided dictionary */
+ if (wrap == 1)
+ strm->adler = adler32(strm->adler, dictionary, dictLength);
+ s->wrap = 0; /* avoid computing Adler-32 in read_buf */
+
+ /* if dictionary would fill window, just replace the history */
+ if (dictLength >= s->w_size) {
+ if (wrap == 0) { /* already empty otherwise */
+ CLEAR_HASH(s);
+ s->strstart = 0;
+ s->block_start = 0L;
+ s->insert = 0;
+ }
+ dictionary += dictLength - s->w_size; /* use the tail */
+ dictLength = s->w_size;
+ }
+
+ /* insert dictionary into window and hash */
+ avail = strm->avail_in;
+ next = strm->next_in;
+ strm->avail_in = dictLength;
+ strm->next_in = (z_const Bytef *)dictionary;
+ fill_window(s);
+ while (s->lookahead >= MIN_MATCH) {
+ str = s->strstart;
+ n = s->lookahead - (MIN_MATCH-1);
+ do {
+ UPDATE_HASH(s, s->ins_h, s->window[str + MIN_MATCH-1]);
+#ifndef FASTEST
+ s->prev[str & s->w_mask] = s->head[s->ins_h];
+#endif
+ s->head[s->ins_h] = (Pos)str;
+ str++;
+ } while (--n);
+ s->strstart = str;
+ s->lookahead = MIN_MATCH-1;
+ fill_window(s);
+ }
+ s->strstart += s->lookahead;
+ s->block_start = (long)s->strstart;
+ s->insert = s->lookahead;
+ s->lookahead = 0;
+ s->match_length = s->prev_length = MIN_MATCH-1;
+ s->match_available = 0;
+ strm->next_in = next;
+ strm->avail_in = avail;
+ s->wrap = wrap;
+ return Z_OK;
+}
+
+/* ========================================================================= */
+int ZEXPORT deflateResetKeep (strm)
+ z_streamp strm;
+{
+ deflate_state *s;
+
+ if (strm == Z_NULL || strm->state == Z_NULL ||
+ strm->zalloc == (alloc_func)0 || strm->zfree == (free_func)0) {
+ return Z_STREAM_ERROR;
+ }
+
+ strm->total_in = strm->total_out = 0;
+ strm->msg = Z_NULL; /* use zfree if we ever allocate msg dynamically */
+ strm->data_type = Z_UNKNOWN;
+
+ s = (deflate_state *)strm->state;
+ s->pending = 0;
+ s->pending_out = s->pending_buf;
+
+ if (s->wrap < 0) {
+ s->wrap = -s->wrap; /* was made negative by deflate(..., Z_FINISH); */
+ }
+ s->status = s->wrap ? INIT_STATE : BUSY_STATE;
+ strm->adler =
+#ifdef GZIP
+ s->wrap == 2 ? crc32(0L, Z_NULL, 0) :
+#endif
+ adler32(0L, Z_NULL, 0);
+ s->last_flush = Z_NO_FLUSH;
+
+ _tr_init(s);
+
+ return Z_OK;
+}
+
+/* ========================================================================= */
+int ZEXPORT deflateReset (strm)
+ z_streamp strm;
+{
+ int ret;
+
+ ret = deflateResetKeep(strm);
+ if (ret == Z_OK)
+ lm_init(strm->state);
+ return ret;
+}
+
+/* ========================================================================= */
+int ZEXPORT deflateSetHeader (strm, head)
+ z_streamp strm;
+ gz_headerp head;
+{
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ if (strm->state->wrap != 2) return Z_STREAM_ERROR;
+ strm->state->gzhead = head;
+ return Z_OK;
+}
+
+/* ========================================================================= */
+int ZEXPORT deflatePending (strm, pending, bits)
+ unsigned *pending;
+ int *bits;
+ z_streamp strm;
+{
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ if (pending != Z_NULL)
+ *pending = strm->state->pending;
+ if (bits != Z_NULL)
+ *bits = strm->state->bi_valid;
+ return Z_OK;
+}
+
+/* ========================================================================= */
+int ZEXPORT deflatePrime (strm, bits, value)
+ z_streamp strm;
+ int bits;
+ int value;
+{
+ deflate_state *s;
+ int put;
+
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ s = strm->state;
+ if ((Bytef *)(s->d_buf) < s->pending_out + ((Buf_size + 7) >> 3))
+ return Z_BUF_ERROR;
+ do {
+ put = Buf_size - s->bi_valid;
+ if (put > bits)
+ put = bits;
+ s->bi_buf |= (ush)((value & ((1 << put) - 1)) << s->bi_valid);
+ s->bi_valid += put;
+ _tr_flush_bits(s);
+ value >>= put;
+ bits -= put;
+ } while (bits);
+ return Z_OK;
+}
+
+/* ========================================================================= */
+int ZEXPORT deflateParams(strm, level, strategy)
+ z_streamp strm;
+ int level;
+ int strategy;
+{
+ deflate_state *s;
+ compress_func func;
+ int err = Z_OK;
+
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ s = strm->state;
+
+#ifdef FASTEST
+ if (level != 0) level = 1;
+#else
+ if (level == Z_DEFAULT_COMPRESSION) level = 6;
+#endif
+ if (level < 0 || level > 9 || strategy < 0 || strategy > Z_FIXED) {
+ return Z_STREAM_ERROR;
+ }
+ func = configuration_table[s->level].func;
+
+ if ((strategy != s->strategy || func != configuration_table[level].func) &&
+ strm->total_in != 0) {
+ /* Flush the last buffer: */
+ err = deflate(strm, Z_BLOCK);
+ if (err == Z_BUF_ERROR && s->pending == 0)
+ err = Z_OK;
+ }
+ if (s->level != level) {
+ s->level = level;
+ s->max_lazy_match = configuration_table[level].max_lazy;
+ s->good_match = configuration_table[level].good_length;
+ s->nice_match = configuration_table[level].nice_length;
+ s->max_chain_length = configuration_table[level].max_chain;
+ }
+ s->strategy = strategy;
+ return err;
+}
+
+/* ========================================================================= */
+int ZEXPORT deflateTune(strm, good_length, max_lazy, nice_length, max_chain)
+ z_streamp strm;
+ int good_length;
+ int max_lazy;
+ int nice_length;
+ int max_chain;
+{
+ deflate_state *s;
+
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ s = strm->state;
+ s->good_match = good_length;
+ s->max_lazy_match = max_lazy;
+ s->nice_match = nice_length;
+ s->max_chain_length = max_chain;
+ return Z_OK;
+}
+
+/* =========================================================================
+ * For the default windowBits of 15 and memLevel of 8, this function returns
+ * a close to exact, as well as small, upper bound on the compressed size.
+ * They are coded as constants here for a reason--if the #define's are
+ * changed, then this function needs to be changed as well. The return
+ * value for 15 and 8 only works for those exact settings.
+ *
+ * For any setting other than those defaults for windowBits and memLevel,
+ * the value returned is a conservative worst case for the maximum expansion
+ * resulting from using fixed blocks instead of stored blocks, which deflate
+ * can emit on compressed data for some combinations of the parameters.
+ *
+ * This function could be more sophisticated to provide closer upper bounds for
+ * every combination of windowBits and memLevel. But even the conservative
+ * upper bound of about 14% expansion does not seem onerous for output buffer
+ * allocation.
+ */
+uLong ZEXPORT deflateBound(strm, sourceLen)
+ z_streamp strm;
+ uLong sourceLen;
+{
+ deflate_state *s;
+ uLong complen, wraplen;
+ Bytef *str;
+
+ /* conservative upper bound for compressed data */
+ complen = sourceLen +
+ ((sourceLen + 7) >> 3) + ((sourceLen + 63) >> 6) + 5;
+
+ /* if can't get parameters, return conservative bound plus zlib wrapper */
+ if (strm == Z_NULL || strm->state == Z_NULL)
+ return complen + 6;
+
+ /* compute wrapper length */
+ s = strm->state;
+ switch (s->wrap) {
+ case 0: /* raw deflate */
+ wraplen = 0;
+ break;
+ case 1: /* zlib wrapper */
+ wraplen = 6 + (s->strstart ? 4 : 0);
+ break;
+ case 2: /* gzip wrapper */
+ wraplen = 18;
+ if (s->gzhead != Z_NULL) { /* user-supplied gzip header */
+ if (s->gzhead->extra != Z_NULL)
+ wraplen += 2 + s->gzhead->extra_len;
+ str = s->gzhead->name;
+ if (str != Z_NULL)
+ do {
+ wraplen++;
+ } while (*str++);
+ str = s->gzhead->comment;
+ if (str != Z_NULL)
+ do {
+ wraplen++;
+ } while (*str++);
+ if (s->gzhead->hcrc)
+ wraplen += 2;
+ }
+ break;
+ default: /* for compiler happiness */
+ wraplen = 6;
+ }
+
+ /* if not default parameters, return conservative bound */
+ if (s->w_bits != 15 || s->hash_bits != 8 + 7)
+ return complen + wraplen;
+
+ /* default settings: return tight bound for that case */
+ return sourceLen + (sourceLen >> 12) + (sourceLen >> 14) +
+ (sourceLen >> 25) + 13 - 6 + wraplen;
+}
+
+/* =========================================================================
+ * Put a short in the pending buffer. The 16-bit value is put in MSB order.
+ * IN assertion: the stream state is correct and there is enough room in
+ * pending_buf.
+ */
+local void putShortMSB (s, b)
+ deflate_state *s;
+ uInt b;
+{
+ put_byte(s, (Byte)(b >> 8));
+ put_byte(s, (Byte)(b & 0xff));
+}
+
+/* =========================================================================
+ * Flush as much pending output as possible. All deflate() output goes
+ * through this function so some applications may wish to modify it
+ * to avoid allocating a large strm->next_out buffer and copying into it.
+ * (See also read_buf()).
+ */
+local void flush_pending(strm)
+ z_streamp strm;
+{
+ unsigned len;
+ deflate_state *s = strm->state;
+
+ _tr_flush_bits(s);
+ len = s->pending;
+ if (len > strm->avail_out) len = strm->avail_out;
+ if (len == 0) return;
+
+ zmemcpy(strm->next_out, s->pending_out, len);
+ strm->next_out += len;
+ s->pending_out += len;
+ strm->total_out += len;
+ strm->avail_out -= len;
+ s->pending -= len;
+ if (s->pending == 0) {
+ s->pending_out = s->pending_buf;
+ }
+}
+
+/* ========================================================================= */
+int ZEXPORT deflate (strm, flush)
+ z_streamp strm;
+ int flush;
+{
+ int old_flush; /* value of flush param for previous deflate call */
+ deflate_state *s;
+
+ if (strm == Z_NULL || strm->state == Z_NULL ||
+ flush > Z_BLOCK || flush < 0) {
+ return Z_STREAM_ERROR;
+ }
+ s = strm->state;
+
+ if (strm->next_out == Z_NULL ||
+ (strm->next_in == Z_NULL && strm->avail_in != 0) ||
+ (s->status == FINISH_STATE && flush != Z_FINISH)) {
+ ERR_RETURN(strm, Z_STREAM_ERROR);
+ }
+ if (strm->avail_out == 0) ERR_RETURN(strm, Z_BUF_ERROR);
+
+ s->strm = strm; /* just in case */
+ old_flush = s->last_flush;
+ s->last_flush = flush;
+
+ /* Write the header */
+ if (s->status == INIT_STATE) {
+#ifdef GZIP
+ if (s->wrap == 2) {
+ strm->adler = crc32(0L, Z_NULL, 0);
+ put_byte(s, 31);
+ put_byte(s, 139);
+ put_byte(s, 8);
+ if (s->gzhead == Z_NULL) {
+ put_byte(s, 0);
+ put_byte(s, 0);
+ put_byte(s, 0);
+ put_byte(s, 0);
+ put_byte(s, 0);
+ put_byte(s, s->level == 9 ? 2 :
+ (s->strategy >= Z_HUFFMAN_ONLY || s->level < 2 ?
+ 4 : 0));
+ put_byte(s, OS_CODE);
+ s->status = BUSY_STATE;
+ }
+ else {
+ put_byte(s, (s->gzhead->text ? 1 : 0) +
+ (s->gzhead->hcrc ? 2 : 0) +
+ (s->gzhead->extra == Z_NULL ? 0 : 4) +
+ (s->gzhead->name == Z_NULL ? 0 : 8) +
+ (s->gzhead->comment == Z_NULL ? 0 : 16)
+ );
+ put_byte(s, (Byte)(s->gzhead->time & 0xff));
+ put_byte(s, (Byte)((s->gzhead->time >> 8) & 0xff));
+ put_byte(s, (Byte)((s->gzhead->time >> 16) & 0xff));
+ put_byte(s, (Byte)((s->gzhead->time >> 24) & 0xff));
+ put_byte(s, s->level == 9 ? 2 :
+ (s->strategy >= Z_HUFFMAN_ONLY || s->level < 2 ?
+ 4 : 0));
+ put_byte(s, s->gzhead->os & 0xff);
+ if (s->gzhead->extra != Z_NULL) {
+ put_byte(s, s->gzhead->extra_len & 0xff);
+ put_byte(s, (s->gzhead->extra_len >> 8) & 0xff);
+ }
+ if (s->gzhead->hcrc)
+ strm->adler = crc32(strm->adler, s->pending_buf,
+ s->pending);
+ s->gzindex = 0;
+ s->status = EXTRA_STATE;
+ }
+ }
+ else
+#endif
+ {
+ uInt header = (Z_DEFLATED + ((s->w_bits-8)<<4)) << 8;
+ uInt level_flags;
+
+ if (s->strategy >= Z_HUFFMAN_ONLY || s->level < 2)
+ level_flags = 0;
+ else if (s->level < 6)
+ level_flags = 1;
+ else if (s->level == 6)
+ level_flags = 2;
+ else
+ level_flags = 3;
+ header |= (level_flags << 6);
+ if (s->strstart != 0) header |= PRESET_DICT;
+ header += 31 - (header % 31);
+
+ s->status = BUSY_STATE;
+ putShortMSB(s, header);
+
+ /* Save the adler32 of the preset dictionary: */
+ if (s->strstart != 0) {
+ putShortMSB(s, (uInt)(strm->adler >> 16));
+ putShortMSB(s, (uInt)(strm->adler & 0xffff));
+ }
+ strm->adler = adler32(0L, Z_NULL, 0);
+ }
+ }
+#ifdef GZIP
+ if (s->status == EXTRA_STATE) {
+ if (s->gzhead->extra != Z_NULL) {
+ uInt beg = s->pending; /* start of bytes to update crc */
+
+ while (s->gzindex < (s->gzhead->extra_len & 0xffff)) {
+ if (s->pending == s->pending_buf_size) {
+ if (s->gzhead->hcrc && s->pending > beg)
+ strm->adler = crc32(strm->adler, s->pending_buf + beg,
+ s->pending - beg);
+ flush_pending(strm);
+ beg = s->pending;
+ if (s->pending == s->pending_buf_size)
+ break;
+ }
+ put_byte(s, s->gzhead->extra[s->gzindex]);
+ s->gzindex++;
+ }
+ if (s->gzhead->hcrc && s->pending > beg)
+ strm->adler = crc32(strm->adler, s->pending_buf + beg,
+ s->pending - beg);
+ if (s->gzindex == s->gzhead->extra_len) {
+ s->gzindex = 0;
+ s->status = NAME_STATE;
+ }
+ }
+ else
+ s->status = NAME_STATE;
+ }
+ if (s->status == NAME_STATE) {
+ if (s->gzhead->name != Z_NULL) {
+ uInt beg = s->pending; /* start of bytes to update crc */
+ int val;
+
+ do {
+ if (s->pending == s->pending_buf_size) {
+ if (s->gzhead->hcrc && s->pending > beg)
+ strm->adler = crc32(strm->adler, s->pending_buf + beg,
+ s->pending - beg);
+ flush_pending(strm);
+ beg = s->pending;
+ if (s->pending == s->pending_buf_size) {
+ val = 1;
+ break;
+ }
+ }
+ val = s->gzhead->name[s->gzindex++];
+ put_byte(s, val);
+ } while (val != 0);
+ if (s->gzhead->hcrc && s->pending > beg)
+ strm->adler = crc32(strm->adler, s->pending_buf + beg,
+ s->pending - beg);
+ if (val == 0) {
+ s->gzindex = 0;
+ s->status = COMMENT_STATE;
+ }
+ }
+ else
+ s->status = COMMENT_STATE;
+ }
+ if (s->status == COMMENT_STATE) {
+ if (s->gzhead->comment != Z_NULL) {
+ uInt beg = s->pending; /* start of bytes to update crc */
+ int val;
+
+ do {
+ if (s->pending == s->pending_buf_size) {
+ if (s->gzhead->hcrc && s->pending > beg)
+ strm->adler = crc32(strm->adler, s->pending_buf + beg,
+ s->pending - beg);
+ flush_pending(strm);
+ beg = s->pending;
+ if (s->pending == s->pending_buf_size) {
+ val = 1;
+ break;
+ }
+ }
+ val = s->gzhead->comment[s->gzindex++];
+ put_byte(s, val);
+ } while (val != 0);
+ if (s->gzhead->hcrc && s->pending > beg)
+ strm->adler = crc32(strm->adler, s->pending_buf + beg,
+ s->pending - beg);
+ if (val == 0)
+ s->status = HCRC_STATE;
+ }
+ else
+ s->status = HCRC_STATE;
+ }
+ if (s->status == HCRC_STATE) {
+ if (s->gzhead->hcrc) {
+ if (s->pending + 2 > s->pending_buf_size)
+ flush_pending(strm);
+ if (s->pending + 2 <= s->pending_buf_size) {
+ put_byte(s, (Byte)(strm->adler & 0xff));
+ put_byte(s, (Byte)((strm->adler >> 8) & 0xff));
+ strm->adler = crc32(0L, Z_NULL, 0);
+ s->status = BUSY_STATE;
+ }
+ }
+ else
+ s->status = BUSY_STATE;
+ }
+#endif
+
+ /* Flush as much pending output as possible */
+ if (s->pending != 0) {
+ flush_pending(strm);
+ if (strm->avail_out == 0) {
+ /* Since avail_out is 0, deflate will be called again with
+ * more output space, but possibly with both pending and
+ * avail_in equal to zero. There won't be anything to do,
+ * but this is not an error situation so make sure we
+ * return OK instead of BUF_ERROR at next call of deflate:
+ */
+ s->last_flush = -1;
+ return Z_OK;
+ }
+
+ /* Make sure there is something to do and avoid duplicate consecutive
+ * flushes. For repeated and useless calls with Z_FINISH, we keep
+ * returning Z_STREAM_END instead of Z_BUF_ERROR.
+ */
+ } else if (strm->avail_in == 0 && RANK(flush) <= RANK(old_flush) &&
+ flush != Z_FINISH) {
+ ERR_RETURN(strm, Z_BUF_ERROR);
+ }
+
+ /* User must not provide more input after the first FINISH: */
+ if (s->status == FINISH_STATE && strm->avail_in != 0) {
+ ERR_RETURN(strm, Z_BUF_ERROR);
+ }
+
+ /* Start a new block or continue the current one.
+ */
+ if (strm->avail_in != 0 || s->lookahead != 0 ||
+ (flush != Z_NO_FLUSH && s->status != FINISH_STATE)) {
+ block_state bstate;
+
+ bstate = s->strategy == Z_HUFFMAN_ONLY ? deflate_huff(s, flush) :
+ (s->strategy == Z_RLE ? deflate_rle(s, flush) :
+ (*(configuration_table[s->level].func))(s, flush));
+
+ if (bstate == finish_started || bstate == finish_done) {
+ s->status = FINISH_STATE;
+ }
+ if (bstate == need_more || bstate == finish_started) {
+ if (strm->avail_out == 0) {
+ s->last_flush = -1; /* avoid BUF_ERROR next call, see above */
+ }
+ return Z_OK;
+ /* If flush != Z_NO_FLUSH && avail_out == 0, the next call
+ * of deflate should use the same flush parameter to make sure
+ * that the flush is complete. So we don't have to output an
+ * empty block here, this will be done at next call. This also
+ * ensures that for a very small output buffer, we emit at most
+ * one empty block.
+ */
+ }
+ if (bstate == block_done) {
+ if (flush == Z_PARTIAL_FLUSH) {
+ _tr_align(s);
+ } else if (flush != Z_BLOCK) { /* FULL_FLUSH or SYNC_FLUSH */
+ _tr_stored_block(s, (char*)0, 0L, 0);
+ /* For a full flush, this empty block will be recognized
+ * as a special marker by inflate_sync().
+ */
+ if (flush == Z_FULL_FLUSH) {
+ CLEAR_HASH(s); /* forget history */
+ if (s->lookahead == 0) {
+ s->strstart = 0;
+ s->block_start = 0L;
+ s->insert = 0;
+ }
+ }
+ }
+ flush_pending(strm);
+ if (strm->avail_out == 0) {
+ s->last_flush = -1; /* avoid BUF_ERROR at next call, see above */
+ return Z_OK;
+ }
+ }
+ }
+ Assert(strm->avail_out > 0, "bug2");
+
+ if (flush != Z_FINISH) return Z_OK;
+ if (s->wrap <= 0) return Z_STREAM_END;
+
+ /* Write the trailer */
+#ifdef GZIP
+ if (s->wrap == 2) {
+ put_byte(s, (Byte)(strm->adler & 0xff));
+ put_byte(s, (Byte)((strm->adler >> 8) & 0xff));
+ put_byte(s, (Byte)((strm->adler >> 16) & 0xff));
+ put_byte(s, (Byte)((strm->adler >> 24) & 0xff));
+ put_byte(s, (Byte)(strm->total_in & 0xff));
+ put_byte(s, (Byte)((strm->total_in >> 8) & 0xff));
+ put_byte(s, (Byte)((strm->total_in >> 16) & 0xff));
+ put_byte(s, (Byte)((strm->total_in >> 24) & 0xff));
+ }
+ else
+#endif
+ {
+ putShortMSB(s, (uInt)(strm->adler >> 16));
+ putShortMSB(s, (uInt)(strm->adler & 0xffff));
+ }
+ flush_pending(strm);
+ /* If avail_out is zero, the application will call deflate again
+ * to flush the rest.
+ */
+ if (s->wrap > 0) s->wrap = -s->wrap; /* write the trailer only once! */
+ return s->pending != 0 ? Z_OK : Z_STREAM_END;
+}
+
+/* ========================================================================= */
+int ZEXPORT deflateEnd (strm)
+ z_streamp strm;
+{
+ int status;
+
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+
+ status = strm->state->status;
+ if (status != INIT_STATE &&
+ status != EXTRA_STATE &&
+ status != NAME_STATE &&
+ status != COMMENT_STATE &&
+ status != HCRC_STATE &&
+ status != BUSY_STATE &&
+ status != FINISH_STATE) {
+ return Z_STREAM_ERROR;
+ }
+
+ /* Deallocate in reverse order of allocations: */
+ TRY_FREE(strm, strm->state->pending_buf);
+ TRY_FREE(strm, strm->state->head);
+ TRY_FREE(strm, strm->state->prev);
+ TRY_FREE(strm, strm->state->window);
+
+ ZFREE(strm, strm->state);
+ strm->state = Z_NULL;
+
+ return status == BUSY_STATE ? Z_DATA_ERROR : Z_OK;
+}
+
+/* =========================================================================
+ * Copy the source state to the destination state.
+ * To simplify the source, this is not supported for 16-bit MSDOS (which
+ * doesn't have enough memory anyway to duplicate compression states).
+ */
+int ZEXPORT deflateCopy (dest, source)
+ z_streamp dest;
+ z_streamp source;
+{
+#ifdef MAXSEG_64K
+ return Z_STREAM_ERROR;
+#else
+ deflate_state *ds;
+ deflate_state *ss;
+ ushf *overlay;
+
+
+ if (source == Z_NULL || dest == Z_NULL || source->state == Z_NULL) {
+ return Z_STREAM_ERROR;
+ }
+
+ ss = source->state;
+
+ zmemcpy((voidpf)dest, (voidpf)source, sizeof(z_stream));
+
+ ds = (deflate_state *) ZALLOC(dest, 1, sizeof(deflate_state));
+ if (ds == Z_NULL) return Z_MEM_ERROR;
+ dest->state = (struct internal_state FAR *) ds;
+ zmemcpy((voidpf)ds, (voidpf)ss, sizeof(deflate_state));
+ ds->strm = dest;
+
+ ds->window = (Bytef *) ZALLOC(dest, ds->w_size, 2*sizeof(Byte));
+ ds->prev = (Posf *) ZALLOC(dest, ds->w_size, sizeof(Pos));
+ ds->head = (Posf *) ZALLOC(dest, ds->hash_size, sizeof(Pos));
+ overlay = (ushf *) ZALLOC(dest, ds->lit_bufsize, sizeof(ush)+2);
+ ds->pending_buf = (uchf *) overlay;
+
+ if (ds->window == Z_NULL || ds->prev == Z_NULL || ds->head == Z_NULL ||
+ ds->pending_buf == Z_NULL) {
+ deflateEnd (dest);
+ return Z_MEM_ERROR;
+ }
+ /* following zmemcpy do not work for 16-bit MSDOS */
+ zmemcpy(ds->window, ss->window, ds->w_size * 2 * sizeof(Byte));
+ zmemcpy((voidpf)ds->prev, (voidpf)ss->prev, ds->w_size * sizeof(Pos));
+ zmemcpy((voidpf)ds->head, (voidpf)ss->head, ds->hash_size * sizeof(Pos));
+ zmemcpy(ds->pending_buf, ss->pending_buf, (uInt)ds->pending_buf_size);
+
+ ds->pending_out = ds->pending_buf + (ss->pending_out - ss->pending_buf);
+ ds->d_buf = overlay + ds->lit_bufsize/sizeof(ush);
+ ds->l_buf = ds->pending_buf + (1+sizeof(ush))*ds->lit_bufsize;
+
+ ds->l_desc.dyn_tree = ds->dyn_ltree;
+ ds->d_desc.dyn_tree = ds->dyn_dtree;
+ ds->bl_desc.dyn_tree = ds->bl_tree;
+
+ return Z_OK;
+#endif /* MAXSEG_64K */
+}
+
+/* ===========================================================================
+ * Read a new buffer from the current input stream, update the adler32
+ * and total number of bytes read. All deflate() input goes through
+ * this function so some applications may wish to modify it to avoid
+ * allocating a large strm->next_in buffer and copying from it.
+ * (See also flush_pending()).
+ */
+local int read_buf(strm, buf, size)
+ z_streamp strm;
+ Bytef *buf;
+ unsigned size;
+{
+ unsigned len = strm->avail_in;
+
+ if (len > size) len = size;
+ if (len == 0) return 0;
+
+ strm->avail_in -= len;
+
+ zmemcpy(buf, strm->next_in, len);
+ if (strm->state->wrap == 1) {
+ strm->adler = adler32(strm->adler, buf, len);
+ }
+#ifdef GZIP
+ else if (strm->state->wrap == 2) {
+ strm->adler = crc32(strm->adler, buf, len);
+ }
+#endif
+ strm->next_in += len;
+ strm->total_in += len;
+
+ return (int)len;
+}
+
+/* ===========================================================================
+ * Initialize the "longest match" routines for a new zlib stream
+ */
+local void lm_init (s)
+ deflate_state *s;
+{
+ s->window_size = (ulg)2L*s->w_size;
+
+ CLEAR_HASH(s);
+
+ /* Set the default configuration parameters:
+ */
+ s->max_lazy_match = configuration_table[s->level].max_lazy;
+ s->good_match = configuration_table[s->level].good_length;
+ s->nice_match = configuration_table[s->level].nice_length;
+ s->max_chain_length = configuration_table[s->level].max_chain;
+
+ s->strstart = 0;
+ s->block_start = 0L;
+ s->lookahead = 0;
+ s->insert = 0;
+ s->match_length = s->prev_length = MIN_MATCH-1;
+ s->match_available = 0;
+ s->ins_h = 0;
+#ifndef FASTEST
+#ifdef ASMV
+ match_init(); /* initialize the asm code */
+#endif
+#endif
+}
+
+#ifndef FASTEST
+/* ===========================================================================
+ * Set match_start to the longest match starting at the given string and
+ * return its length. Matches shorter or equal to prev_length are discarded,
+ * in which case the result is equal to prev_length and match_start is
+ * garbage.
+ * IN assertions: cur_match is the head of the hash chain for the current
+ * string (strstart) and its distance is <= MAX_DIST, and prev_length >= 1
+ * OUT assertion: the match length is not greater than s->lookahead.
+ */
+#ifndef ASMV
+/* For 80x86 and 680x0, an optimized version will be provided in match.asm or
+ * match.S. The code will be functionally equivalent.
+ */
+local uInt longest_match(s, cur_match)
+ deflate_state *s;
+ IPos cur_match; /* current match */
+{
+ unsigned chain_length = s->max_chain_length;/* max hash chain length */
+ register Bytef *scan = s->window + s->strstart; /* current string */
+ register Bytef *match; /* matched string */
+ register int len; /* length of current match */
+ int best_len = s->prev_length; /* best match length so far */
+ int nice_match = s->nice_match; /* stop if match long enough */
+ IPos limit = s->strstart > (IPos)MAX_DIST(s) ?
+ s->strstart - (IPos)MAX_DIST(s) : NIL;
+ /* Stop when cur_match becomes <= limit. To simplify the code,
+ * we prevent matches with the string of window index 0.
+ */
+ Posf *prev = s->prev;
+ uInt wmask = s->w_mask;
+
+#ifdef UNALIGNED_OK
+ /* Compare two bytes at a time. Note: this is not always beneficial.
+ * Try with and without -DUNALIGNED_OK to check.
+ */
+ register Bytef *strend = s->window + s->strstart + MAX_MATCH - 1;
+ register ush scan_start = *(ushf*)scan;
+ register ush scan_end = *(ushf*)(scan+best_len-1);
+#else
+ register Bytef *strend = s->window + s->strstart + MAX_MATCH;
+ register Byte scan_end1 = scan[best_len-1];
+ register Byte scan_end = scan[best_len];
+#endif
+
+ /* The code is optimized for HASH_BITS >= 8 and MAX_MATCH-2 multiple of 16.
+ * It is easy to get rid of this optimization if necessary.
+ */
+ Assert(s->hash_bits >= 8 && MAX_MATCH == 258, "Code too clever");
+
+ /* Do not waste too much time if we already have a good match: */
+ if (s->prev_length >= s->good_match) {
+ chain_length >>= 2;
+ }
+ /* Do not look for matches beyond the end of the input. This is necessary
+ * to make deflate deterministic.
+ */
+ if ((uInt)nice_match > s->lookahead) nice_match = s->lookahead;
+
+ Assert((ulg)s->strstart <= s->window_size-MIN_LOOKAHEAD, "need lookahead");
+
+ do {
+ Assert(cur_match < s->strstart, "no future");
+ match = s->window + cur_match;
+
+ /* Skip to next match if the match length cannot increase
+ * or if the match length is less than 2. Note that the checks below
+ * for insufficient lookahead only occur occasionally for performance
+ * reasons. Therefore uninitialized memory will be accessed, and
+ * conditional jumps will be made that depend on those values.
+ * However the length of the match is limited to the lookahead, so
+ * the output of deflate is not affected by the uninitialized values.
+ */
+#if (defined(UNALIGNED_OK) && MAX_MATCH == 258)
+ /* This code assumes sizeof(unsigned short) == 2. Do not use
+ * UNALIGNED_OK if your compiler uses a different size.
+ */
+ if (*(ushf*)(match+best_len-1) != scan_end ||
+ *(ushf*)match != scan_start) continue;
+
+ /* It is not necessary to compare scan[2] and match[2] since they are
+ * always equal when the other bytes match, given that the hash keys
+ * are equal and that HASH_BITS >= 8. Compare 2 bytes at a time at
+ * strstart+3, +5, ... up to strstart+257. We check for insufficient
+ * lookahead only every 4th comparison; the 128th check will be made
+ * at strstart+257. If MAX_MATCH-2 is not a multiple of 8, it is
+ * necessary to put more guard bytes at the end of the window, or
+ * to check more often for insufficient lookahead.
+ */
+ Assert(scan[2] == match[2], "scan[2]?");
+ scan++, match++;
+ do {
+ } while (*(ushf*)(scan+=2) == *(ushf*)(match+=2) &&
+ *(ushf*)(scan+=2) == *(ushf*)(match+=2) &&
+ *(ushf*)(scan+=2) == *(ushf*)(match+=2) &&
+ *(ushf*)(scan+=2) == *(ushf*)(match+=2) &&
+ scan < strend);
+ /* The funny "do {}" generates better code on most compilers */
+
+ /* Here, scan <= window+strstart+257 */
+ Assert(scan <= s->window+(unsigned)(s->window_size-1), "wild scan");
+ if (*scan == *match) scan++;
+
+ len = (MAX_MATCH - 1) - (int)(strend-scan);
+ scan = strend - (MAX_MATCH-1);
+
+#else /* UNALIGNED_OK */
+
+ if (match[best_len] != scan_end ||
+ match[best_len-1] != scan_end1 ||
+ *match != *scan ||
+ *++match != scan[1]) continue;
+
+ /* The check at best_len-1 can be removed because it will be made
+ * again later. (This heuristic is not always a win.)
+ * It is not necessary to compare scan[2] and match[2] since they
+ * are always equal when the other bytes match, given that
+ * the hash keys are equal and that HASH_BITS >= 8.
+ */
+ scan += 2, match++;
+ Assert(*scan == *match, "match[2]?");
+
+ /* We check for insufficient lookahead only every 8th comparison;
+ * the 256th check will be made at strstart+258.
+ */
+ do {
+ } while (*++scan == *++match && *++scan == *++match &&
+ *++scan == *++match && *++scan == *++match &&
+ *++scan == *++match && *++scan == *++match &&
+ *++scan == *++match && *++scan == *++match &&
+ scan < strend);
+
+ Assert(scan <= s->window+(unsigned)(s->window_size-1), "wild scan");
+
+ len = MAX_MATCH - (int)(strend - scan);
+ scan = strend - MAX_MATCH;
+
+#endif /* UNALIGNED_OK */
+
+ if (len > best_len) {
+ s->match_start = cur_match;
+ best_len = len;
+ if (len >= nice_match) break;
+#ifdef UNALIGNED_OK
+ scan_end = *(ushf*)(scan+best_len-1);
+#else
+ scan_end1 = scan[best_len-1];
+ scan_end = scan[best_len];
+#endif
+ }
+ } while ((cur_match = prev[cur_match & wmask]) > limit
+ && --chain_length != 0);
+
+ if ((uInt)best_len <= s->lookahead) return (uInt)best_len;
+ return s->lookahead;
+}
+#endif /* ASMV */
+
+#else /* FASTEST */
+
+/* ---------------------------------------------------------------------------
+ * Optimized version for FASTEST only
+ */
+local uInt longest_match(s, cur_match)
+ deflate_state *s;
+ IPos cur_match; /* current match */
+{
+ register Bytef *scan = s->window + s->strstart; /* current string */
+ register Bytef *match; /* matched string */
+ register int len; /* length of current match */
+ register Bytef *strend = s->window + s->strstart + MAX_MATCH;
+
+ /* The code is optimized for HASH_BITS >= 8 and MAX_MATCH-2 multiple of 16.
+ * It is easy to get rid of this optimization if necessary.
+ */
+ Assert(s->hash_bits >= 8 && MAX_MATCH == 258, "Code too clever");
+
+ Assert((ulg)s->strstart <= s->window_size-MIN_LOOKAHEAD, "need lookahead");
+
+ Assert(cur_match < s->strstart, "no future");
+
+ match = s->window + cur_match;
+
+ /* Return failure if the match length is less than 2:
+ */
+ if (match[0] != scan[0] || match[1] != scan[1]) return MIN_MATCH-1;
+
+ /* The check at best_len-1 can be removed because it will be made
+ * again later. (This heuristic is not always a win.)
+ * It is not necessary to compare scan[2] and match[2] since they
+ * are always equal when the other bytes match, given that
+ * the hash keys are equal and that HASH_BITS >= 8.
+ */
+ scan += 2, match += 2;
+ Assert(*scan == *match, "match[2]?");
+
+ /* We check for insufficient lookahead only every 8th comparison;
+ * the 256th check will be made at strstart+258.
+ */
+ do {
+ } while (*++scan == *++match && *++scan == *++match &&
+ *++scan == *++match && *++scan == *++match &&
+ *++scan == *++match && *++scan == *++match &&
+ *++scan == *++match && *++scan == *++match &&
+ scan < strend);
+
+ Assert(scan <= s->window+(unsigned)(s->window_size-1), "wild scan");
+
+ len = MAX_MATCH - (int)(strend - scan);
+
+ if (len < MIN_MATCH) return MIN_MATCH - 1;
+
+ s->match_start = cur_match;
+ return (uInt)len <= s->lookahead ? (uInt)len : s->lookahead;
+}
+
+#endif /* FASTEST */
+
+#ifdef DEBUG
+/* ===========================================================================
+ * Check that the match at match_start is indeed a match.
+ */
+local void check_match(s, start, match, length)
+ deflate_state *s;
+ IPos start, match;
+ int length;
+{
+ /* check that the match is indeed a match */
+ if (zmemcmp(s->window + match,
+ s->window + start, length) != EQUAL) {
+ fprintf(stderr, " start %u, match %u, length %d\n",
+ start, match, length);
+ do {
+ fprintf(stderr, "%c%c", s->window[match++], s->window[start++]);
+ } while (--length != 0);
+ z_error("invalid match");
+ }
+ if (z_verbose > 1) {
+ fprintf(stderr,"\\[%d,%d]", start-match, length);
+ do { putc(s->window[start++], stderr); } while (--length != 0);
+ }
+}
+#else
+# define check_match(s, start, match, length)
+#endif /* DEBUG */
+
+/* ===========================================================================
+ * Fill the window when the lookahead becomes insufficient.
+ * Updates strstart and lookahead.
+ *
+ * IN assertion: lookahead < MIN_LOOKAHEAD
+ * OUT assertions: strstart <= window_size-MIN_LOOKAHEAD
+ * At least one byte has been read, or avail_in == 0; reads are
+ * performed for at least two bytes (required for the zip translate_eol
+ * option -- not supported here).
+ */
+local void fill_window(s)
+ deflate_state *s;
+{
+ register unsigned n, m;
+ register Posf *p;
+ unsigned more; /* Amount of free space at the end of the window. */
+ uInt wsize = s->w_size;
+
+ Assert(s->lookahead < MIN_LOOKAHEAD, "already enough lookahead");
+
+ do {
+ more = (unsigned)(s->window_size -(ulg)s->lookahead -(ulg)s->strstart);
+
+ /* Deal with !@#$% 64K limit: */
+ if (sizeof(int) <= 2) {
+ if (more == 0 && s->strstart == 0 && s->lookahead == 0) {
+ more = wsize;
+
+ } else if (more == (unsigned)(-1)) {
+ /* Very unlikely, but possible on 16 bit machine if
+ * strstart == 0 && lookahead == 1 (input done a byte at time)
+ */
+ more--;
+ }
+ }
+
+ /* If the window is almost full and there is insufficient lookahead,
+ * move the upper half to the lower one to make room in the upper half.
+ */
+ if (s->strstart >= wsize+MAX_DIST(s)) {
+
+ zmemcpy(s->window, s->window+wsize, (unsigned)wsize);
+ s->match_start -= wsize;
+ s->strstart -= wsize; /* we now have strstart >= MAX_DIST */
+ s->block_start -= (long) wsize;
+
+ /* Slide the hash table (could be avoided with 32 bit values
+ at the expense of memory usage). We slide even when level == 0
+ to keep the hash table consistent if we switch back to level > 0
+ later. (Using level 0 permanently is not an optimal usage of
+ zlib, so we don't care about this pathological case.)
+ */
+ n = s->hash_size;
+ p = &s->head[n];
+ do {
+ m = *--p;
+ *p = (Pos)(m >= wsize ? m-wsize : NIL);
+ } while (--n);
+
+ n = wsize;
+#ifndef FASTEST
+ p = &s->prev[n];
+ do {
+ m = *--p;
+ *p = (Pos)(m >= wsize ? m-wsize : NIL);
+ /* If n is not on any hash chain, prev[n] is garbage but
+ * its value will never be used.
+ */
+ } while (--n);
+#endif
+ more += wsize;
+ }
+ if (s->strm->avail_in == 0) break;
+
+ /* If there was no sliding:
+ * strstart <= WSIZE+MAX_DIST-1 && lookahead <= MIN_LOOKAHEAD - 1 &&
+ * more == window_size - lookahead - strstart
+ * => more >= window_size - (MIN_LOOKAHEAD-1 + WSIZE + MAX_DIST-1)
+ * => more >= window_size - 2*WSIZE + 2
+ * In the BIG_MEM or MMAP case (not yet supported),
+ * window_size == input_size + MIN_LOOKAHEAD &&
+ * strstart + s->lookahead <= input_size => more >= MIN_LOOKAHEAD.
+ * Otherwise, window_size == 2*WSIZE so more >= 2.
+ * If there was sliding, more >= WSIZE. So in all cases, more >= 2.
+ */
+ Assert(more >= 2, "more < 2");
+
+ n = read_buf(s->strm, s->window + s->strstart + s->lookahead, more);
+ s->lookahead += n;
+
+ /* Initialize the hash value now that we have some input: */
+ if (s->lookahead + s->insert >= MIN_MATCH) {
+ uInt str = s->strstart - s->insert;
+ s->ins_h = s->window[str];
+ UPDATE_HASH(s, s->ins_h, s->window[str + 1]);
+#if MIN_MATCH != 3
+ Call UPDATE_HASH() MIN_MATCH-3 more times
+#endif
+ while (s->insert) {
+ UPDATE_HASH(s, s->ins_h, s->window[str + MIN_MATCH-1]);
+#ifndef FASTEST
+ s->prev[str & s->w_mask] = s->head[s->ins_h];
+#endif
+ s->head[s->ins_h] = (Pos)str;
+ str++;
+ s->insert--;
+ if (s->lookahead + s->insert < MIN_MATCH)
+ break;
+ }
+ }
+ /* If the whole input has less than MIN_MATCH bytes, ins_h is garbage,
+ * but this is not important since only literal bytes will be emitted.
+ */
+
+ } while (s->lookahead < MIN_LOOKAHEAD && s->strm->avail_in != 0);
+
+ /* If the WIN_INIT bytes after the end of the current data have never been
+ * written, then zero those bytes in order to avoid memory check reports of
+ * the use of uninitialized (or uninitialised as Julian writes) bytes by
+ * the longest match routines. Update the high water mark for the next
+ * time through here. WIN_INIT is set to MAX_MATCH since the longest match
+ * routines allow scanning to strstart + MAX_MATCH, ignoring lookahead.
+ */
+ if (s->high_water < s->window_size) {
+ ulg curr = s->strstart + (ulg)(s->lookahead);
+ ulg init;
+
+ if (s->high_water < curr) {
+ /* Previous high water mark below current data -- zero WIN_INIT
+ * bytes or up to end of window, whichever is less.
+ */
+ init = s->window_size - curr;
+ if (init > WIN_INIT)
+ init = WIN_INIT;
+ zmemzero(s->window + curr, (unsigned)init);
+ s->high_water = curr + init;
+ }
+ else if (s->high_water < (ulg)curr + WIN_INIT) {
+ /* High water mark at or above current data, but below current data
+ * plus WIN_INIT -- zero out to current data plus WIN_INIT, or up
+ * to end of window, whichever is less.
+ */
+ init = (ulg)curr + WIN_INIT - s->high_water;
+ if (init > s->window_size - s->high_water)
+ init = s->window_size - s->high_water;
+ zmemzero(s->window + s->high_water, (unsigned)init);
+ s->high_water += init;
+ }
+ }
+
+ Assert((ulg)s->strstart <= s->window_size - MIN_LOOKAHEAD,
+ "not enough room for search");
+}
+
+/* ===========================================================================
+ * Flush the current block, with given end-of-file flag.
+ * IN assertion: strstart is set to the end of the current match.
+ */
+#define FLUSH_BLOCK_ONLY(s, last) { \
+ _tr_flush_block(s, (s->block_start >= 0L ? \
+ (charf *)&s->window[(unsigned)s->block_start] : \
+ (charf *)Z_NULL), \
+ (ulg)((long)s->strstart - s->block_start), \
+ (last)); \
+ s->block_start = s->strstart; \
+ flush_pending(s->strm); \
+ Tracev((stderr,"[FLUSH]")); \
+}
+
+/* Same but force premature exit if necessary. */
+#define FLUSH_BLOCK(s, last) { \
+ FLUSH_BLOCK_ONLY(s, last); \
+ if (s->strm->avail_out == 0) return (last) ? finish_started : need_more; \
+}
+
+/* ===========================================================================
+ * Copy without compression as much as possible from the input stream, return
+ * the current block state.
+ * This function does not insert new strings in the dictionary since
+ * uncompressible data is probably not useful. This function is used
+ * only for the level=0 compression option.
+ * NOTE: this function should be optimized to avoid extra copying from
+ * window to pending_buf.
+ */
+local block_state deflate_stored(s, flush)
+ deflate_state *s;
+ int flush;
+{
+ /* Stored blocks are limited to 0xffff bytes, pending_buf is limited
+ * to pending_buf_size, and each stored block has a 5 byte header:
+ */
+ ulg max_block_size = 0xffff;
+ ulg max_start;
+
+ if (max_block_size > s->pending_buf_size - 5) {
+ max_block_size = s->pending_buf_size - 5;
+ }
+
+ /* Copy as much as possible from input to output: */
+ for (;;) {
+ /* Fill the window as much as possible: */
+ if (s->lookahead <= 1) {
+
+ Assert(s->strstart < s->w_size+MAX_DIST(s) ||
+ s->block_start >= (long)s->w_size, "slide too late");
+
+ fill_window(s);
+ if (s->lookahead == 0 && flush == Z_NO_FLUSH) return need_more;
+
+ if (s->lookahead == 0) break; /* flush the current block */
+ }
+ Assert(s->block_start >= 0L, "block gone");
+
+ s->strstart += s->lookahead;
+ s->lookahead = 0;
+
+ /* Emit a stored block if pending_buf will be full: */
+ max_start = s->block_start + max_block_size;
+ if (s->strstart == 0 || (ulg)s->strstart >= max_start) {
+ /* strstart == 0 is possible when wraparound on 16-bit machine */
+ s->lookahead = (uInt)(s->strstart - max_start);
+ s->strstart = (uInt)max_start;
+ FLUSH_BLOCK(s, 0);
+ }
+ /* Flush if we may have to slide, otherwise block_start may become
+ * negative and the data will be gone:
+ */
+ if (s->strstart - (uInt)s->block_start >= MAX_DIST(s)) {
+ FLUSH_BLOCK(s, 0);
+ }
+ }
+ s->insert = 0;
+ if (flush == Z_FINISH) {
+ FLUSH_BLOCK(s, 1);
+ return finish_done;
+ }
+ if ((long)s->strstart > s->block_start)
+ FLUSH_BLOCK(s, 0);
+ return block_done;
+}
+
+/* ===========================================================================
+ * Compress as much as possible from the input stream, return the current
+ * block state.
+ * This function does not perform lazy evaluation of matches and inserts
+ * new strings in the dictionary only for unmatched strings or for short
+ * matches. It is used only for the fast compression options.
+ */
+local block_state deflate_fast(s, flush)
+ deflate_state *s;
+ int flush;
+{
+ IPos hash_head; /* head of the hash chain */
+ int bflush; /* set if current block must be flushed */
+
+ for (;;) {
+ /* Make sure that we always have enough lookahead, except
+ * at the end of the input file. We need MAX_MATCH bytes
+ * for the next match, plus MIN_MATCH bytes to insert the
+ * string following the next match.
+ */
+ if (s->lookahead < MIN_LOOKAHEAD) {
+ fill_window(s);
+ if (s->lookahead < MIN_LOOKAHEAD && flush == Z_NO_FLUSH) {
+ return need_more;
+ }
+ if (s->lookahead == 0) break; /* flush the current block */
+ }
+
+ /* Insert the string window[strstart .. strstart+2] in the
+ * dictionary, and set hash_head to the head of the hash chain:
+ */
+ hash_head = NIL;
+ if (s->lookahead >= MIN_MATCH) {
+ INSERT_STRING(s, s->strstart, hash_head);
+ }
+
+ /* Find the longest match, discarding those <= prev_length.
+ * At this point we have always match_length < MIN_MATCH
+ */
+ if (hash_head != NIL && s->strstart - hash_head <= MAX_DIST(s)) {
+ /* To simplify the code, we prevent matches with the string
+ * of window index 0 (in particular we have to avoid a match
+ * of the string with itself at the start of the input file).
+ */
+ s->match_length = longest_match (s, hash_head);
+ /* longest_match() sets match_start */
+ }
+ if (s->match_length >= MIN_MATCH) {
+ check_match(s, s->strstart, s->match_start, s->match_length);
+
+ _tr_tally_dist(s, s->strstart - s->match_start,
+ s->match_length - MIN_MATCH, bflush);
+
+ s->lookahead -= s->match_length;
+
+ /* Insert new strings in the hash table only if the match length
+ * is not too large. This saves time but degrades compression.
+ */
+#ifndef FASTEST
+ if (s->match_length <= s->max_insert_length &&
+ s->lookahead >= MIN_MATCH) {
+ s->match_length--; /* string at strstart already in table */
+ do {
+ s->strstart++;
+ INSERT_STRING(s, s->strstart, hash_head);
+ /* strstart never exceeds WSIZE-MAX_MATCH, so there are
+ * always MIN_MATCH bytes ahead.
+ */
+ } while (--s->match_length != 0);
+ s->strstart++;
+ } else
+#endif
+ {
+ s->strstart += s->match_length;
+ s->match_length = 0;
+ s->ins_h = s->window[s->strstart];
+ UPDATE_HASH(s, s->ins_h, s->window[s->strstart+1]);
+#if MIN_MATCH != 3
+ Call UPDATE_HASH() MIN_MATCH-3 more times
+#endif
+ /* If lookahead < MIN_MATCH, ins_h is garbage, but it does not
+ * matter since it will be recomputed at next deflate call.
+ */
+ }
+ } else {
+ /* No match, output a literal byte */
+ Tracevv((stderr,"%c", s->window[s->strstart]));
+ _tr_tally_lit (s, s->window[s->strstart], bflush);
+ s->lookahead--;
+ s->strstart++;
+ }
+ if (bflush) FLUSH_BLOCK(s, 0);
+ }
+ s->insert = s->strstart < MIN_MATCH-1 ? s->strstart : MIN_MATCH-1;
+ if (flush == Z_FINISH) {
+ FLUSH_BLOCK(s, 1);
+ return finish_done;
+ }
+ if (s->last_lit)
+ FLUSH_BLOCK(s, 0);
+ return block_done;
+}
+
+#ifndef FASTEST
+/* ===========================================================================
+ * Same as above, but achieves better compression. We use a lazy
+ * evaluation for matches: a match is finally adopted only if there is
+ * no better match at the next window position.
+ */
+local block_state deflate_slow(s, flush)
+ deflate_state *s;
+ int flush;
+{
+ IPos hash_head; /* head of hash chain */
+ int bflush; /* set if current block must be flushed */
+
+ /* Process the input block. */
+ for (;;) {
+ /* Make sure that we always have enough lookahead, except
+ * at the end of the input file. We need MAX_MATCH bytes
+ * for the next match, plus MIN_MATCH bytes to insert the
+ * string following the next match.
+ */
+ if (s->lookahead < MIN_LOOKAHEAD) {
+ fill_window(s);
+ if (s->lookahead < MIN_LOOKAHEAD && flush == Z_NO_FLUSH) {
+ return need_more;
+ }
+ if (s->lookahead == 0) break; /* flush the current block */
+ }
+
+ /* Insert the string window[strstart .. strstart+2] in the
+ * dictionary, and set hash_head to the head of the hash chain:
+ */
+ hash_head = NIL;
+ if (s->lookahead >= MIN_MATCH) {
+ INSERT_STRING(s, s->strstart, hash_head);
+ }
+
+ /* Find the longest match, discarding those <= prev_length.
+ */
+ s->prev_length = s->match_length, s->prev_match = s->match_start;
+ s->match_length = MIN_MATCH-1;
+
+ if (hash_head != NIL && s->prev_length < s->max_lazy_match &&
+ s->strstart - hash_head <= MAX_DIST(s)) {
+ /* To simplify the code, we prevent matches with the string
+ * of window index 0 (in particular we have to avoid a match
+ * of the string with itself at the start of the input file).
+ */
+ s->match_length = longest_match (s, hash_head);
+ /* longest_match() sets match_start */
+
+ if (s->match_length <= 5 && (s->strategy == Z_FILTERED
+#if TOO_FAR <= 32767
+ || (s->match_length == MIN_MATCH &&
+ s->strstart - s->match_start > TOO_FAR)
+#endif
+ )) {
+
+ /* If prev_match is also MIN_MATCH, match_start is garbage
+ * but we will ignore the current match anyway.
+ */
+ s->match_length = MIN_MATCH-1;
+ }
+ }
+ /* If there was a match at the previous step and the current
+ * match is not better, output the previous match:
+ */
+ if (s->prev_length >= MIN_MATCH && s->match_length <= s->prev_length) {
+ uInt max_insert = s->strstart + s->lookahead - MIN_MATCH;
+ /* Do not insert strings in hash table beyond this. */
+
+ check_match(s, s->strstart-1, s->prev_match, s->prev_length);
+
+ _tr_tally_dist(s, s->strstart -1 - s->prev_match,
+ s->prev_length - MIN_MATCH, bflush);
+
+ /* Insert in hash table all strings up to the end of the match.
+ * strstart-1 and strstart are already inserted. If there is not
+ * enough lookahead, the last two strings are not inserted in
+ * the hash table.
+ */
+ s->lookahead -= s->prev_length-1;
+ s->prev_length -= 2;
+ do {
+ if (++s->strstart <= max_insert) {
+ INSERT_STRING(s, s->strstart, hash_head);
+ }
+ } while (--s->prev_length != 0);
+ s->match_available = 0;
+ s->match_length = MIN_MATCH-1;
+ s->strstart++;
+
+ if (bflush) FLUSH_BLOCK(s, 0);
+
+ } else if (s->match_available) {
+ /* If there was no match at the previous position, output a
+ * single literal. If there was a match but the current match
+ * is longer, truncate the previous match to a single literal.
+ */
+ Tracevv((stderr,"%c", s->window[s->strstart-1]));
+ _tr_tally_lit(s, s->window[s->strstart-1], bflush);
+ if (bflush) {
+ FLUSH_BLOCK_ONLY(s, 0);
+ }
+ s->strstart++;
+ s->lookahead--;
+ if (s->strm->avail_out == 0) return need_more;
+ } else {
+ /* There is no previous match to compare with, wait for
+ * the next step to decide.
+ */
+ s->match_available = 1;
+ s->strstart++;
+ s->lookahead--;
+ }
+ }
+ Assert (flush != Z_NO_FLUSH, "no flush?");
+ if (s->match_available) {
+ Tracevv((stderr,"%c", s->window[s->strstart-1]));
+ _tr_tally_lit(s, s->window[s->strstart-1], bflush);
+ s->match_available = 0;
+ }
+ s->insert = s->strstart < MIN_MATCH-1 ? s->strstart : MIN_MATCH-1;
+ if (flush == Z_FINISH) {
+ FLUSH_BLOCK(s, 1);
+ return finish_done;
+ }
+ if (s->last_lit)
+ FLUSH_BLOCK(s, 0);
+ return block_done;
+}
+#endif /* FASTEST */
+
+/* ===========================================================================
+ * For Z_RLE, simply look for runs of bytes, generate matches only of distance
+ * one. Do not maintain a hash table. (It will be regenerated if this run of
+ * deflate switches away from Z_RLE.)
+ */
+local block_state deflate_rle(s, flush)
+ deflate_state *s;
+ int flush;
+{
+ int bflush; /* set if current block must be flushed */
+ uInt prev; /* byte at distance one to match */
+ Bytef *scan, *strend; /* scan goes up to strend for length of run */
+
+ for (;;) {
+ /* Make sure that we always have enough lookahead, except
+ * at the end of the input file. We need MAX_MATCH bytes
+ * for the longest run, plus one for the unrolled loop.
+ */
+ if (s->lookahead <= MAX_MATCH) {
+ fill_window(s);
+ if (s->lookahead <= MAX_MATCH && flush == Z_NO_FLUSH) {
+ return need_more;
+ }
+ if (s->lookahead == 0) break; /* flush the current block */
+ }
+
+ /* See how many times the previous byte repeats */
+ s->match_length = 0;
+ if (s->lookahead >= MIN_MATCH && s->strstart > 0) {
+ scan = s->window + s->strstart - 1;
+ prev = *scan;
+ if (prev == *++scan && prev == *++scan && prev == *++scan) {
+ strend = s->window + s->strstart + MAX_MATCH;
+ do {
+ } while (prev == *++scan && prev == *++scan &&
+ prev == *++scan && prev == *++scan &&
+ prev == *++scan && prev == *++scan &&
+ prev == *++scan && prev == *++scan &&
+ scan < strend);
+ s->match_length = MAX_MATCH - (int)(strend - scan);
+ if (s->match_length > s->lookahead)
+ s->match_length = s->lookahead;
+ }
+ Assert(scan <= s->window+(uInt)(s->window_size-1), "wild scan");
+ }
+
+ /* Emit match if have run of MIN_MATCH or longer, else emit literal */
+ if (s->match_length >= MIN_MATCH) {
+ check_match(s, s->strstart, s->strstart - 1, s->match_length);
+
+ _tr_tally_dist(s, 1, s->match_length - MIN_MATCH, bflush);
+
+ s->lookahead -= s->match_length;
+ s->strstart += s->match_length;
+ s->match_length = 0;
+ } else {
+ /* No match, output a literal byte */
+ Tracevv((stderr,"%c", s->window[s->strstart]));
+ _tr_tally_lit (s, s->window[s->strstart], bflush);
+ s->lookahead--;
+ s->strstart++;
+ }
+ if (bflush) FLUSH_BLOCK(s, 0);
+ }
+ s->insert = 0;
+ if (flush == Z_FINISH) {
+ FLUSH_BLOCK(s, 1);
+ return finish_done;
+ }
+ if (s->last_lit)
+ FLUSH_BLOCK(s, 0);
+ return block_done;
+}
+
+/* ===========================================================================
+ * For Z_HUFFMAN_ONLY, do not look for matches. Do not maintain a hash table.
+ * (It will be regenerated if this run of deflate switches away from Huffman.)
+ */
+local block_state deflate_huff(s, flush)
+ deflate_state *s;
+ int flush;
+{
+ int bflush; /* set if current block must be flushed */
+
+ for (;;) {
+ /* Make sure that we have a literal to write. */
+ if (s->lookahead == 0) {
+ fill_window(s);
+ if (s->lookahead == 0) {
+ if (flush == Z_NO_FLUSH)
+ return need_more;
+ break; /* flush the current block */
+ }
+ }
+
+ /* Output a literal byte */
+ s->match_length = 0;
+ Tracevv((stderr,"%c", s->window[s->strstart]));
+ _tr_tally_lit (s, s->window[s->strstart], bflush);
+ s->lookahead--;
+ s->strstart++;
+ if (bflush) FLUSH_BLOCK(s, 0);
+ }
+ s->insert = 0;
+ if (flush == Z_FINISH) {
+ FLUSH_BLOCK(s, 1);
+ return finish_done;
+ }
+ if (s->last_lit)
+ FLUSH_BLOCK(s, 0);
+ return block_done;
+}
diff --git a/third-party/zlib/deflate.h b/third-party/zlib/deflate.h
new file mode 100644
index 0000000..ce0299e
--- /dev/null
+++ b/third-party/zlib/deflate.h
@@ -0,0 +1,346 @@
+/* deflate.h -- internal compression state
+ * Copyright (C) 1995-2012 Jean-loup Gailly
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* WARNING: this file should *not* be used by applications. It is
+ part of the implementation of the compression library and is
+ subject to change. Applications should only use zlib.h.
+ */
+
+/* @(#) $Id$ */
+
+#ifndef DEFLATE_H
+#define DEFLATE_H
+
+#include "zutil.h"
+
+/* define NO_GZIP when compiling if you want to disable gzip header and
+ trailer creation by deflate(). NO_GZIP would be used to avoid linking in
+ the crc code when it is not needed. For shared libraries, gzip encoding
+ should be left enabled. */
+#ifndef NO_GZIP
+# define GZIP
+#endif
+
+/* ===========================================================================
+ * Internal compression state.
+ */
+
+#define LENGTH_CODES 29
+/* number of length codes, not counting the special END_BLOCK code */
+
+#define LITERALS 256
+/* number of literal bytes 0..255 */
+
+#define L_CODES (LITERALS+1+LENGTH_CODES)
+/* number of Literal or Length codes, including the END_BLOCK code */
+
+#define D_CODES 30
+/* number of distance codes */
+
+#define BL_CODES 19
+/* number of codes used to transfer the bit lengths */
+
+#define HEAP_SIZE (2*L_CODES+1)
+/* maximum heap size */
+
+#define MAX_BITS 15
+/* All codes must not exceed MAX_BITS bits */
+
+#define Buf_size 16
+/* size of bit buffer in bi_buf */
+
+#define INIT_STATE 42
+#define EXTRA_STATE 69
+#define NAME_STATE 73
+#define COMMENT_STATE 91
+#define HCRC_STATE 103
+#define BUSY_STATE 113
+#define FINISH_STATE 666
+/* Stream status */
+
+
+/* Data structure describing a single value and its code string. */
+typedef struct ct_data_s {
+ union {
+ ush freq; /* frequency count */
+ ush code; /* bit string */
+ } fc;
+ union {
+ ush dad; /* father node in Huffman tree */
+ ush len; /* length of bit string */
+ } dl;
+} FAR ct_data;
+
+#define Freq fc.freq
+#define Code fc.code
+#define Dad dl.dad
+#define Len dl.len
+
+typedef struct static_tree_desc_s static_tree_desc;
+
+typedef struct tree_desc_s {
+ ct_data *dyn_tree; /* the dynamic tree */
+ int max_code; /* largest code with non zero frequency */
+ static_tree_desc *stat_desc; /* the corresponding static tree */
+} FAR tree_desc;
+
+typedef ush Pos;
+typedef Pos FAR Posf;
+typedef unsigned IPos;
+
+/* A Pos is an index in the character window. We use short instead of int to
+ * save space in the various tables. IPos is used only for parameter passing.
+ */
+
+typedef struct internal_state {
+ z_streamp strm; /* pointer back to this zlib stream */
+ int status; /* as the name implies */
+ Bytef *pending_buf; /* output still pending */
+ ulg pending_buf_size; /* size of pending_buf */
+ Bytef *pending_out; /* next pending byte to output to the stream */
+ uInt pending; /* nb of bytes in the pending buffer */
+ int wrap; /* bit 0 true for zlib, bit 1 true for gzip */
+ gz_headerp gzhead; /* gzip header information to write */
+ uInt gzindex; /* where in extra, name, or comment */
+ Byte method; /* can only be DEFLATED */
+ int last_flush; /* value of flush param for previous deflate call */
+
+ /* used by deflate.c: */
+
+ uInt w_size; /* LZ77 window size (32K by default) */
+ uInt w_bits; /* log2(w_size) (8..16) */
+ uInt w_mask; /* w_size - 1 */
+
+ Bytef *window;
+ /* Sliding window. Input bytes are read into the second half of the window,
+ * and move to the first half later to keep a dictionary of at least wSize
+ * bytes. With this organization, matches are limited to a distance of
+ * wSize-MAX_MATCH bytes, but this ensures that IO is always
+ * performed with a length multiple of the block size. Also, it limits
+ * the window size to 64K, which is quite useful on MSDOS.
+ * To do: use the user input buffer as sliding window.
+ */
+
+ ulg window_size;
+ /* Actual size of window: 2*wSize, except when the user input buffer
+ * is directly used as sliding window.
+ */
+
+ Posf *prev;
+ /* Link to older string with same hash index. To limit the size of this
+ * array to 64K, this link is maintained only for the last 32K strings.
+ * An index in this array is thus a window index modulo 32K.
+ */
+
+ Posf *head; /* Heads of the hash chains or NIL. */
+
+ uInt ins_h; /* hash index of string to be inserted */
+ uInt hash_size; /* number of elements in hash table */
+ uInt hash_bits; /* log2(hash_size) */
+ uInt hash_mask; /* hash_size-1 */
+
+ uInt hash_shift;
+ /* Number of bits by which ins_h must be shifted at each input
+ * step. It must be such that after MIN_MATCH steps, the oldest
+ * byte no longer takes part in the hash key, that is:
+ * hash_shift * MIN_MATCH >= hash_bits
+ */
+
+ long block_start;
+ /* Window position at the beginning of the current output block. Gets
+ * negative when the window is moved backwards.
+ */
+
+ uInt match_length; /* length of best match */
+ IPos prev_match; /* previous match */
+ int match_available; /* set if previous match exists */
+ uInt strstart; /* start of string to insert */
+ uInt match_start; /* start of matching string */
+ uInt lookahead; /* number of valid bytes ahead in window */
+
+ uInt prev_length;
+ /* Length of the best match at previous step. Matches not greater than this
+ * are discarded. This is used in the lazy match evaluation.
+ */
+
+ uInt max_chain_length;
+ /* To speed up deflation, hash chains are never searched beyond this
+ * length. A higher limit improves compression ratio but degrades the
+ * speed.
+ */
+
+ uInt max_lazy_match;
+ /* Attempt to find a better match only when the current match is strictly
+ * smaller than this value. This mechanism is used only for compression
+ * levels >= 4.
+ */
+# define max_insert_length max_lazy_match
+ /* Insert new strings in the hash table only if the match length is not
+ * greater than this length. This saves time but degrades compression.
+ * max_insert_length is used only for compression levels <= 3.
+ */
+
+ int level; /* compression level (1..9) */
+ int strategy; /* favor or force Huffman coding*/
+
+ uInt good_match;
+ /* Use a faster search when the previous match is longer than this */
+
+ int nice_match; /* Stop searching when current match exceeds this */
+
+ /* used by trees.c: */
+ /* Didn't use ct_data typedef below to suppress compiler warning */
+ struct ct_data_s dyn_ltree[HEAP_SIZE]; /* literal and length tree */
+ struct ct_data_s dyn_dtree[2*D_CODES+1]; /* distance tree */
+ struct ct_data_s bl_tree[2*BL_CODES+1]; /* Huffman tree for bit lengths */
+
+ struct tree_desc_s l_desc; /* desc. for literal tree */
+ struct tree_desc_s d_desc; /* desc. for distance tree */
+ struct tree_desc_s bl_desc; /* desc. for bit length tree */
+
+ ush bl_count[MAX_BITS+1];
+ /* number of codes at each bit length for an optimal tree */
+
+ int heap[2*L_CODES+1]; /* heap used to build the Huffman trees */
+ int heap_len; /* number of elements in the heap */
+ int heap_max; /* element of largest frequency */
+ /* The sons of heap[n] are heap[2*n] and heap[2*n+1]. heap[0] is not used.
+ * The same heap array is used to build all trees.
+ */
+
+ uch depth[2*L_CODES+1];
+ /* Depth of each subtree used as tie breaker for trees of equal frequency
+ */
+
+ uchf *l_buf; /* buffer for literals or lengths */
+
+ uInt lit_bufsize;
+ /* Size of match buffer for literals/lengths. There are 4 reasons for
+ * limiting lit_bufsize to 64K:
+ * - frequencies can be kept in 16 bit counters
+ * - if compression is not successful for the first block, all input
+ * data is still in the window so we can still emit a stored block even
+ * when input comes from standard input. (This can also be done for
+ * all blocks if lit_bufsize is not greater than 32K.)
+ * - if compression is not successful for a file smaller than 64K, we can
+ * even emit a stored file instead of a stored block (saving 5 bytes).
+ * This is applicable only for zip (not gzip or zlib).
+ * - creating new Huffman trees less frequently may not provide fast
+ * adaptation to changes in the input data statistics. (Take for
+ * example a binary file with poorly compressible code followed by
+ * a highly compressible string table.) Smaller buffer sizes give
+ * fast adaptation but have of course the overhead of transmitting
+ * trees more frequently.
+ * - I can't count above 4
+ */
+
+ uInt last_lit; /* running index in l_buf */
+
+ ushf *d_buf;
+ /* Buffer for distances. To simplify the code, d_buf and l_buf have
+ * the same number of elements. To use different lengths, an extra flag
+ * array would be necessary.
+ */
+
+ ulg opt_len; /* bit length of current block with optimal trees */
+ ulg static_len; /* bit length of current block with static trees */
+ uInt matches; /* number of string matches in current block */
+ uInt insert; /* bytes at end of window left to insert */
+
+#ifdef DEBUG
+ ulg compressed_len; /* total bit length of compressed file mod 2^32 */
+ ulg bits_sent; /* bit length of compressed data sent mod 2^32 */
+#endif
+
+ ush bi_buf;
+ /* Output buffer. bits are inserted starting at the bottom (least
+ * significant bits).
+ */
+ int bi_valid;
+ /* Number of valid bits in bi_buf. All bits above the last valid bit
+ * are always zero.
+ */
+
+ ulg high_water;
+ /* High water mark offset in window for initialized bytes -- bytes above
+ * this are set to zero in order to avoid memory check warnings when
+ * longest match routines access bytes past the input. This is then
+ * updated to the new high water mark.
+ */
+
+} FAR deflate_state;
+
+/* Output a byte on the stream.
+ * IN assertion: there is enough room in pending_buf.
+ */
+#define put_byte(s, c) {s->pending_buf[s->pending++] = (c);}
+
+
+#define MIN_LOOKAHEAD (MAX_MATCH+MIN_MATCH+1)
+/* Minimum amount of lookahead, except at the end of the input file.
+ * See deflate.c for comments about the MIN_MATCH+1.
+ */
+
+#define MAX_DIST(s) ((s)->w_size-MIN_LOOKAHEAD)
+/* In order to simplify the code, particularly on 16 bit machines, match
+ * distances are limited to MAX_DIST instead of WSIZE.
+ */
+
+#define WIN_INIT MAX_MATCH
+/* Number of bytes after end of data in window to initialize in order to avoid
+ memory checker errors from longest match routines */
+
+ /* in trees.c */
+void ZLIB_INTERNAL _tr_init OF((deflate_state *s));
+int ZLIB_INTERNAL _tr_tally OF((deflate_state *s, unsigned dist, unsigned lc));
+void ZLIB_INTERNAL _tr_flush_block OF((deflate_state *s, charf *buf,
+ ulg stored_len, int last));
+void ZLIB_INTERNAL _tr_flush_bits OF((deflate_state *s));
+void ZLIB_INTERNAL _tr_align OF((deflate_state *s));
+void ZLIB_INTERNAL _tr_stored_block OF((deflate_state *s, charf *buf,
+ ulg stored_len, int last));
+
+#define d_code(dist) \
+ ((dist) < 256 ? _dist_code[dist] : _dist_code[256+((dist)>>7)])
+/* Mapping from a distance to a distance code. dist is the distance - 1 and
+ * must not have side effects. _dist_code[256] and _dist_code[257] are never
+ * used.
+ */
+
+#ifndef DEBUG
+/* Inline versions of _tr_tally for speed: */
+
+#if defined(GEN_TREES_H) || !defined(STDC)
+ extern uch ZLIB_INTERNAL _length_code[];
+ extern uch ZLIB_INTERNAL _dist_code[];
+#else
+ extern const uch ZLIB_INTERNAL _length_code[];
+ extern const uch ZLIB_INTERNAL _dist_code[];
+#endif
+
+# define _tr_tally_lit(s, c, flush) \
+ { uch cc = (c); \
+ s->d_buf[s->last_lit] = 0; \
+ s->l_buf[s->last_lit++] = cc; \
+ s->dyn_ltree[cc].Freq++; \
+ flush = (s->last_lit == s->lit_bufsize-1); \
+ }
+# define _tr_tally_dist(s, distance, length, flush) \
+ { uch len = (length); \
+ ush dist = (distance); \
+ s->d_buf[s->last_lit] = dist; \
+ s->l_buf[s->last_lit++] = len; \
+ dist--; \
+ s->dyn_ltree[_length_code[len]+LITERALS+1].Freq++; \
+ s->dyn_dtree[d_code(dist)].Freq++; \
+ flush = (s->last_lit == s->lit_bufsize-1); \
+ }
+#else
+# define _tr_tally_lit(s, c, flush) flush = _tr_tally(s, 0, c)
+# define _tr_tally_dist(s, distance, length, flush) \
+ flush = _tr_tally(s, distance, length)
+#endif
+
+#endif /* DEFLATE_H */
diff --git a/third-party/zlib/doc/algorithm.txt b/third-party/zlib/doc/algorithm.txt
new file mode 100644
index 0000000..c97f495
--- /dev/null
+++ b/third-party/zlib/doc/algorithm.txt
@@ -0,0 +1,209 @@
+1. Compression algorithm (deflate)
+
+The deflation algorithm used by gzip (also zip and zlib) is a variation of
+LZ77 (Lempel-Ziv 1977, see reference below). It finds duplicated strings in
+the input data. The second occurrence of a string is replaced by a
+pointer to the previous string, in the form of a pair (distance,
+length). Distances are limited to 32K bytes, and lengths are limited
+to 258 bytes. When a string does not occur anywhere in the previous
+32K bytes, it is emitted as a sequence of literal bytes. (In this
+description, `string' must be taken as an arbitrary sequence of bytes,
+and is not restricted to printable characters.)
+
+Literals or match lengths are compressed with one Huffman tree, and
+match distances are compressed with another tree. The trees are stored
+in a compact form at the start of each block. The blocks can have any
+size (except that the compressed data for one block must fit in
+available memory). A block is terminated when deflate() determines that
+it would be useful to start another block with fresh trees. (This is
+somewhat similar to the behavior of LZW-based _compress_.)
+
+Duplicated strings are found using a hash table. All input strings of
+length 3 are inserted in the hash table. A hash index is computed for
+the next 3 bytes. If the hash chain for this index is not empty, all
+strings in the chain are compared with the current input string, and
+the longest match is selected.
+
+The hash chains are searched starting with the most recent strings, to
+favor small distances and thus take advantage of the Huffman encoding.
+The hash chains are singly linked. There are no deletions from the
+hash chains, the algorithm simply discards matches that are too old.
+
+To avoid a worst-case situation, very long hash chains are arbitrarily
+truncated at a certain length, determined by a runtime option (level
+parameter of deflateInit). So deflate() does not always find the longest
+possible match but generally finds a match which is long enough.
+
+deflate() also defers the selection of matches with a lazy evaluation
+mechanism. After a match of length N has been found, deflate() searches for
+a longer match at the next input byte. If a longer match is found, the
+previous match is truncated to a length of one (thus producing a single
+literal byte) and the process of lazy evaluation begins again. Otherwise,
+the original match is kept, and the next match search is attempted only N
+steps later.
+
+The lazy match evaluation is also subject to a runtime parameter. If
+the current match is long enough, deflate() reduces the search for a longer
+match, thus speeding up the whole process. If compression ratio is more
+important than speed, deflate() attempts a complete second search even if
+the first match is already long enough.
+
+The lazy match evaluation is not performed for the fastest compression
+modes (level parameter 1 to 3). For these fast modes, new strings
+are inserted in the hash table only when no match was found, or
+when the match is not too long. This degrades the compression ratio
+but saves time since there are both fewer insertions and fewer searches.
+
+
+2. Decompression algorithm (inflate)
+
+2.1 Introduction
+
+The key question is how to represent a Huffman code (or any prefix code) so
+that you can decode fast. The most important characteristic is that shorter
+codes are much more common than longer codes, so pay attention to decoding the
+short codes fast, and let the long codes take longer to decode.
+
+inflate() sets up a first level table that covers some number of bits of
+input less than the length of longest code. It gets that many bits from the
+stream, and looks it up in the table. The table will tell if the next
+code is that many bits or less and how many, and if it is, it will tell
+the value, else it will point to the next level table for which inflate()
+grabs more bits and tries to decode a longer code.
+
+How many bits to make the first lookup is a tradeoff between the time it
+takes to decode and the time it takes to build the table. If building the
+table took no time (and if you had infinite memory), then there would only
+be a first level table to cover all the way to the longest code. However,
+building the table ends up taking a lot longer for more bits since short
+codes are replicated many times in such a table. What inflate() does is
+simply to make the number of bits in the first table a variable, and then
+to set that variable for the maximum speed.
+
+For inflate, which has 286 possible codes for the literal/length tree, the size
+of the first table is nine bits. Also the distance trees have 30 possible
+values, and the size of the first table is six bits. Note that for each of
+those cases, the table ended up one bit longer than the ``average'' code
+length, i.e. the code length of an approximately flat code which would be a
+little more than eight bits for 286 symbols and a little less than five bits
+for 30 symbols.
+
+
+2.2 More details on the inflate table lookup
+
+Ok, you want to know what this cleverly obfuscated inflate tree actually
+looks like. You are correct that it's not a Huffman tree. It is simply a
+lookup table for the first, let's say, nine bits of a Huffman symbol. The
+symbol could be as short as one bit or as long as 15 bits. If a particular
+symbol is shorter than nine bits, then that symbol's translation is duplicated
+in all those entries that start with that symbol's bits. For example, if the
+symbol is four bits, then it's duplicated 32 times in a nine-bit table. If a
+symbol is nine bits long, it appears in the table once.
+
+If the symbol is longer than nine bits, then that entry in the table points
+to another similar table for the remaining bits. Again, there are duplicated
+entries as needed. The idea is that most of the time the symbol will be short
+and there will only be one table look up. (That's whole idea behind data
+compression in the first place.) For the less frequent long symbols, there
+will be two lookups. If you had a compression method with really long
+symbols, you could have as many levels of lookups as is efficient. For
+inflate, two is enough.
+
+So a table entry either points to another table (in which case nine bits in
+the above example are gobbled), or it contains the translation for the symbol
+and the number of bits to gobble. Then you start again with the next
+ungobbled bit.
+
+You may wonder: why not just have one lookup table for how ever many bits the
+longest symbol is? The reason is that if you do that, you end up spending
+more time filling in duplicate symbol entries than you do actually decoding.
+At least for deflate's output that generates new trees every several 10's of
+kbytes. You can imagine that filling in a 2^15 entry table for a 15-bit code
+would take too long if you're only decoding several thousand symbols. At the
+other extreme, you could make a new table for every bit in the code. In fact,
+that's essentially a Huffman tree. But then you spend too much time
+traversing the tree while decoding, even for short symbols.
+
+So the number of bits for the first lookup table is a trade of the time to
+fill out the table vs. the time spent looking at the second level and above of
+the table.
+
+Here is an example, scaled down:
+
+The code being decoded, with 10 symbols, from 1 to 6 bits long:
+
+A: 0
+B: 10
+C: 1100
+D: 11010
+E: 11011
+F: 11100
+G: 11101
+H: 11110
+I: 111110
+J: 111111
+
+Let's make the first table three bits long (eight entries):
+
+000: A,1
+001: A,1
+010: A,1
+011: A,1
+100: B,2
+101: B,2
+110: -> table X (gobble 3 bits)
+111: -> table Y (gobble 3 bits)
+
+Each entry is what the bits decode as and how many bits that is, i.e. how
+many bits to gobble. Or the entry points to another table, with the number of
+bits to gobble implicit in the size of the table.
+
+Table X is two bits long since the longest code starting with 110 is five bits
+long:
+
+00: C,1
+01: C,1
+10: D,2
+11: E,2
+
+Table Y is three bits long since the longest code starting with 111 is six
+bits long:
+
+000: F,2
+001: F,2
+010: G,2
+011: G,2
+100: H,2
+101: H,2
+110: I,3
+111: J,3
+
+So what we have here are three tables with a total of 20 entries that had to
+be constructed. That's compared to 64 entries for a single table. Or
+compared to 16 entries for a Huffman tree (six two entry tables and one four
+entry table). Assuming that the code ideally represents the probability of
+the symbols, it takes on the average 1.25 lookups per symbol. That's compared
+to one lookup for the single table, or 1.66 lookups per symbol for the
+Huffman tree.
+
+There, I think that gives you a picture of what's going on. For inflate, the
+meaning of a particular symbol is often more than just a letter. It can be a
+byte (a "literal"), or it can be either a length or a distance which
+indicates a base value and a number of bits to fetch after the code that is
+added to the base value. Or it might be the special end-of-block code. The
+data structures created in inftrees.c try to encode all that information
+compactly in the tables.
+
+
+Jean-loup Gailly Mark Adler
+jloup at gzip.org madler at alumni.caltech.edu
+
+
+References:
+
+[LZ77] Ziv J., Lempel A., ``A Universal Algorithm for Sequential Data
+Compression,'' IEEE Transactions on Information Theory, Vol. 23, No. 3,
+pp. 337-343.
+
+``DEFLATE Compressed Data Format Specification'' available in
+http://tools.ietf.org/html/rfc1951
diff --git a/third-party/zlib/doc/rfc1950.txt b/third-party/zlib/doc/rfc1950.txt
new file mode 100644
index 0000000..ce6428a
--- /dev/null
+++ b/third-party/zlib/doc/rfc1950.txt
@@ -0,0 +1,619 @@
+
+
+
+
+
+
+Network Working Group P. Deutsch
+Request for Comments: 1950 Aladdin Enterprises
+Category: Informational J-L. Gailly
+ Info-ZIP
+ May 1996
+
+
+ ZLIB Compressed Data Format Specification version 3.3
+
+Status of This Memo
+
+ This memo provides information for the Internet community. This memo
+ does not specify an Internet standard of any kind. Distribution of
+ this memo is unlimited.
+
+IESG Note:
+
+ The IESG takes no position on the validity of any Intellectual
+ Property Rights statements contained in this document.
+
+Notices
+
+ Copyright (c) 1996 L. Peter Deutsch and Jean-Loup Gailly
+
+ Permission is granted to copy and distribute this document for any
+ purpose and without charge, including translations into other
+ languages and incorporation into compilations, provided that the
+ copyright notice and this notice are preserved, and that any
+ substantive changes or deletions from the original are clearly
+ marked.
+
+ A pointer to the latest version of this and related documentation in
+ HTML format can be found at the URL
+ <ftp://ftp.uu.net/graphics/png/documents/zlib/zdoc-index.html>.
+
+Abstract
+
+ This specification defines a lossless compressed data format. The
+ data can be produced or consumed, even for an arbitrarily long
+ sequentially presented input data stream, using only an a priori
+ bounded amount of intermediate storage. The format presently uses
+ the DEFLATE compression method but can be easily extended to use
+ other compression methods. It can be implemented readily in a manner
+ not covered by patents. This specification also defines the ADLER-32
+ checksum (an extension and improvement of the Fletcher checksum),
+ used for detection of data corruption, and provides an algorithm for
+ computing it.
+
+
+
+
+Deutsch & Gailly Informational [Page 1]
+
+RFC 1950 ZLIB Compressed Data Format Specification May 1996
+
+
+Table of Contents
+
+ 1. Introduction ................................................... 2
+ 1.1. Purpose ................................................... 2
+ 1.2. Intended audience ......................................... 3
+ 1.3. Scope ..................................................... 3
+ 1.4. Compliance ................................................ 3
+ 1.5. Definitions of terms and conventions used ................ 3
+ 1.6. Changes from previous versions ............................ 3
+ 2. Detailed specification ......................................... 3
+ 2.1. Overall conventions ....................................... 3
+ 2.2. Data format ............................................... 4
+ 2.3. Compliance ................................................ 7
+ 3. References ..................................................... 7
+ 4. Source code .................................................... 8
+ 5. Security Considerations ........................................ 8
+ 6. Acknowledgements ............................................... 8
+ 7. Authors' Addresses ............................................. 8
+ 8. Appendix: Rationale ............................................ 9
+ 9. Appendix: Sample code ..........................................10
+
+1. Introduction
+
+ 1.1. Purpose
+
+ The purpose of this specification is to define a lossless
+ compressed data format that:
+
+ * Is independent of CPU type, operating system, file system,
+ and character set, and hence can be used for interchange;
+
+ * Can be produced or consumed, even for an arbitrarily long
+ sequentially presented input data stream, using only an a
+ priori bounded amount of intermediate storage, and hence can
+ be used in data communications or similar structures such as
+ Unix filters;
+
+ * Can use a number of different compression methods;
+
+ * Can be implemented readily in a manner not covered by
+ patents, and hence can be practiced freely.
+
+ The data format defined by this specification does not attempt to
+ allow random access to compressed data.
+
+
+
+
+
+
+
+Deutsch & Gailly Informational [Page 2]
+
+RFC 1950 ZLIB Compressed Data Format Specification May 1996
+
+
+ 1.2. Intended audience
+
+ This specification is intended for use by implementors of software
+ to compress data into zlib format and/or decompress data from zlib
+ format.
+
+ The text of the specification assumes a basic background in
+ programming at the level of bits and other primitive data
+ representations.
+
+ 1.3. Scope
+
+ The specification specifies a compressed data format that can be
+ used for in-memory compression of a sequence of arbitrary bytes.
+
+ 1.4. Compliance
+
+ Unless otherwise indicated below, a compliant decompressor must be
+ able to accept and decompress any data set that conforms to all
+ the specifications presented here; a compliant compressor must
+ produce data sets that conform to all the specifications presented
+ here.
+
+ 1.5. Definitions of terms and conventions used
+
+ byte: 8 bits stored or transmitted as a unit (same as an octet).
+ (For this specification, a byte is exactly 8 bits, even on
+ machines which store a character on a number of bits different
+ from 8.) See below, for the numbering of bits within a byte.
+
+ 1.6. Changes from previous versions
+
+ Version 3.1 was the first public release of this specification.
+ In version 3.2, some terminology was changed and the Adler-32
+ sample code was rewritten for clarity. In version 3.3, the
+ support for a preset dictionary was introduced, and the
+ specification was converted to RFC style.
+
+2. Detailed specification
+
+ 2.1. Overall conventions
+
+ In the diagrams below, a box like this:
+
+ +---+
+ | | <-- the vertical bars might be missing
+ +---+
+
+
+
+
+Deutsch & Gailly Informational [Page 3]
+
+RFC 1950 ZLIB Compressed Data Format Specification May 1996
+
+
+ represents one byte; a box like this:
+
+ +==============+
+ | |
+ +==============+
+
+ represents a variable number of bytes.
+
+ Bytes stored within a computer do not have a "bit order", since
+ they are always treated as a unit. However, a byte considered as
+ an integer between 0 and 255 does have a most- and least-
+ significant bit, and since we write numbers with the most-
+ significant digit on the left, we also write bytes with the most-
+ significant bit on the left. In the diagrams below, we number the
+ bits of a byte so that bit 0 is the least-significant bit, i.e.,
+ the bits are numbered:
+
+ +--------+
+ |76543210|
+ +--------+
+
+ Within a computer, a number may occupy multiple bytes. All
+ multi-byte numbers in the format described here are stored with
+ the MOST-significant byte first (at the lower memory address).
+ For example, the decimal number 520 is stored as:
+
+ 0 1
+ +--------+--------+
+ |00000010|00001000|
+ +--------+--------+
+ ^ ^
+ | |
+ | + less significant byte = 8
+ + more significant byte = 2 x 256
+
+ 2.2. Data format
+
+ A zlib stream has the following structure:
+
+ 0 1
+ +---+---+
+ |CMF|FLG| (more-->)
+ +---+---+
+
+
+
+
+
+
+
+
+Deutsch & Gailly Informational [Page 4]
+
+RFC 1950 ZLIB Compressed Data Format Specification May 1996
+
+
+ (if FLG.FDICT set)
+
+ 0 1 2 3
+ +---+---+---+---+
+ | DICTID | (more-->)
+ +---+---+---+---+
+
+ +=====================+---+---+---+---+
+ |...compressed data...| ADLER32 |
+ +=====================+---+---+---+---+
+
+ Any data which may appear after ADLER32 are not part of the zlib
+ stream.
+
+ CMF (Compression Method and flags)
+ This byte is divided into a 4-bit compression method and a 4-
+ bit information field depending on the compression method.
+
+ bits 0 to 3 CM Compression method
+ bits 4 to 7 CINFO Compression info
+
+ CM (Compression method)
+ This identifies the compression method used in the file. CM = 8
+ denotes the "deflate" compression method with a window size up
+ to 32K. This is the method used by gzip and PNG (see
+ references [1] and [2] in Chapter 3, below, for the reference
+ documents). CM = 15 is reserved. It might be used in a future
+ version of this specification to indicate the presence of an
+ extra field before the compressed data.
+
+ CINFO (Compression info)
+ For CM = 8, CINFO is the base-2 logarithm of the LZ77 window
+ size, minus eight (CINFO=7 indicates a 32K window size). Values
+ of CINFO above 7 are not allowed in this version of the
+ specification. CINFO is not defined in this specification for
+ CM not equal to 8.
+
+ FLG (FLaGs)
+ This flag byte is divided as follows:
+
+ bits 0 to 4 FCHECK (check bits for CMF and FLG)
+ bit 5 FDICT (preset dictionary)
+ bits 6 to 7 FLEVEL (compression level)
+
+ The FCHECK value must be such that CMF and FLG, when viewed as
+ a 16-bit unsigned integer stored in MSB order (CMF*256 + FLG),
+ is a multiple of 31.
+
+
+
+
+Deutsch & Gailly Informational [Page 5]
+
+RFC 1950 ZLIB Compressed Data Format Specification May 1996
+
+
+ FDICT (Preset dictionary)
+ If FDICT is set, a DICT dictionary identifier is present
+ immediately after the FLG byte. The dictionary is a sequence of
+ bytes which are initially fed to the compressor without
+ producing any compressed output. DICT is the Adler-32 checksum
+ of this sequence of bytes (see the definition of ADLER32
+ below). The decompressor can use this identifier to determine
+ which dictionary has been used by the compressor.
+
+ FLEVEL (Compression level)
+ These flags are available for use by specific compression
+ methods. The "deflate" method (CM = 8) sets these flags as
+ follows:
+
+ 0 - compressor used fastest algorithm
+ 1 - compressor used fast algorithm
+ 2 - compressor used default algorithm
+ 3 - compressor used maximum compression, slowest algorithm
+
+ The information in FLEVEL is not needed for decompression; it
+ is there to indicate if recompression might be worthwhile.
+
+ compressed data
+ For compression method 8, the compressed data is stored in the
+ deflate compressed data format as described in the document
+ "DEFLATE Compressed Data Format Specification" by L. Peter
+ Deutsch. (See reference [3] in Chapter 3, below)
+
+ Other compressed data formats are not specified in this version
+ of the zlib specification.
+
+ ADLER32 (Adler-32 checksum)
+ This contains a checksum value of the uncompressed data
+ (excluding any dictionary data) computed according to Adler-32
+ algorithm. This algorithm is a 32-bit extension and improvement
+ of the Fletcher algorithm, used in the ITU-T X.224 / ISO 8073
+ standard. See references [4] and [5] in Chapter 3, below)
+
+ Adler-32 is composed of two sums accumulated per byte: s1 is
+ the sum of all bytes, s2 is the sum of all s1 values. Both sums
+ are done modulo 65521. s1 is initialized to 1, s2 to zero. The
+ Adler-32 checksum is stored as s2*65536 + s1 in most-
+ significant-byte first (network) order.
+
+
+
+
+
+
+
+
+Deutsch & Gailly Informational [Page 6]
+
+RFC 1950 ZLIB Compressed Data Format Specification May 1996
+
+
+ 2.3. Compliance
+
+ A compliant compressor must produce streams with correct CMF, FLG
+ and ADLER32, but need not support preset dictionaries. When the
+ zlib data format is used as part of another standard data format,
+ the compressor may use only preset dictionaries that are specified
+ by this other data format. If this other format does not use the
+ preset dictionary feature, the compressor must not set the FDICT
+ flag.
+
+ A compliant decompressor must check CMF, FLG, and ADLER32, and
+ provide an error indication if any of these have incorrect values.
+ A compliant decompressor must give an error indication if CM is
+ not one of the values defined in this specification (only the
+ value 8 is permitted in this version), since another value could
+ indicate the presence of new features that would cause subsequent
+ data to be interpreted incorrectly. A compliant decompressor must
+ give an error indication if FDICT is set and DICTID is not the
+ identifier of a known preset dictionary. A decompressor may
+ ignore FLEVEL and still be compliant. When the zlib data format
+ is being used as a part of another standard format, a compliant
+ decompressor must support all the preset dictionaries specified by
+ the other format. When the other format does not use the preset
+ dictionary feature, a compliant decompressor must reject any
+ stream in which the FDICT flag is set.
+
+3. References
+
+ [1] Deutsch, L.P.,"GZIP Compressed Data Format Specification",
+ available in ftp://ftp.uu.net/pub/archiving/zip/doc/
+
+ [2] Thomas Boutell, "PNG (Portable Network Graphics) specification",
+ available in ftp://ftp.uu.net/graphics/png/documents/
+
+ [3] Deutsch, L.P.,"DEFLATE Compressed Data Format Specification",
+ available in ftp://ftp.uu.net/pub/archiving/zip/doc/
+
+ [4] Fletcher, J. G., "An Arithmetic Checksum for Serial
+ Transmissions," IEEE Transactions on Communications, Vol. COM-30,
+ No. 1, January 1982, pp. 247-252.
+
+ [5] ITU-T Recommendation X.224, Annex D, "Checksum Algorithms,"
+ November, 1993, pp. 144, 145. (Available from
+ gopher://info.itu.ch). ITU-T X.244 is also the same as ISO 8073.
+
+
+
+
+
+
+
+Deutsch & Gailly Informational [Page 7]
+
+RFC 1950 ZLIB Compressed Data Format Specification May 1996
+
+
+4. Source code
+
+ Source code for a C language implementation of a "zlib" compliant
+ library is available at ftp://ftp.uu.net/pub/archiving/zip/zlib/.
+
+5. Security Considerations
+
+ A decoder that fails to check the ADLER32 checksum value may be
+ subject to undetected data corruption.
+
+6. Acknowledgements
+
+ Trademarks cited in this document are the property of their
+ respective owners.
+
+ Jean-Loup Gailly and Mark Adler designed the zlib format and wrote
+ the related software described in this specification. Glenn
+ Randers-Pehrson converted this document to RFC and HTML format.
+
+7. Authors' Addresses
+
+ L. Peter Deutsch
+ Aladdin Enterprises
+ 203 Santa Margarita Ave.
+ Menlo Park, CA 94025
+
+ Phone: (415) 322-0103 (AM only)
+ FAX: (415) 322-1734
+ EMail: <ghost at aladdin.com>
+
+
+ Jean-Loup Gailly
+
+ EMail: <gzip at prep.ai.mit.edu>
+
+ Questions about the technical content of this specification can be
+ sent by email to
+
+ Jean-Loup Gailly <gzip at prep.ai.mit.edu> and
+ Mark Adler <madler at alumni.caltech.edu>
+
+ Editorial comments on this specification can be sent by email to
+
+ L. Peter Deutsch <ghost at aladdin.com> and
+ Glenn Randers-Pehrson <randeg at alumni.rpi.edu>
+
+
+
+
+
+
+Deutsch & Gailly Informational [Page 8]
+
+RFC 1950 ZLIB Compressed Data Format Specification May 1996
+
+
+8. Appendix: Rationale
+
+ 8.1. Preset dictionaries
+
+ A preset dictionary is specially useful to compress short input
+ sequences. The compressor can take advantage of the dictionary
+ context to encode the input in a more compact manner. The
+ decompressor can be initialized with the appropriate context by
+ virtually decompressing a compressed version of the dictionary
+ without producing any output. However for certain compression
+ algorithms such as the deflate algorithm this operation can be
+ achieved without actually performing any decompression.
+
+ The compressor and the decompressor must use exactly the same
+ dictionary. The dictionary may be fixed or may be chosen among a
+ certain number of predefined dictionaries, according to the kind
+ of input data. The decompressor can determine which dictionary has
+ been chosen by the compressor by checking the dictionary
+ identifier. This document does not specify the contents of
+ predefined dictionaries, since the optimal dictionaries are
+ application specific. Standard data formats using this feature of
+ the zlib specification must precisely define the allowed
+ dictionaries.
+
+ 8.2. The Adler-32 algorithm
+
+ The Adler-32 algorithm is much faster than the CRC32 algorithm yet
+ still provides an extremely low probability of undetected errors.
+
+ The modulo on unsigned long accumulators can be delayed for 5552
+ bytes, so the modulo operation time is negligible. If the bytes
+ are a, b, c, the second sum is 3a + 2b + c + 3, and so is position
+ and order sensitive, unlike the first sum, which is just a
+ checksum. That 65521 is prime is important to avoid a possible
+ large class of two-byte errors that leave the check unchanged.
+ (The Fletcher checksum uses 255, which is not prime and which also
+ makes the Fletcher check insensitive to single byte changes 0 <->
+ 255.)
+
+ The sum s1 is initialized to 1 instead of zero to make the length
+ of the sequence part of s2, so that the length does not have to be
+ checked separately. (Any sequence of zeroes has a Fletcher
+ checksum of zero.)
+
+
+
+
+
+
+
+
+Deutsch & Gailly Informational [Page 9]
+
+RFC 1950 ZLIB Compressed Data Format Specification May 1996
+
+
+9. Appendix: Sample code
+
+ The following C code computes the Adler-32 checksum of a data buffer.
+ It is written for clarity, not for speed. The sample code is in the
+ ANSI C programming language. Non C users may find it easier to read
+ with these hints:
+
+ & Bitwise AND operator.
+ >> Bitwise right shift operator. When applied to an
+ unsigned quantity, as here, right shift inserts zero bit(s)
+ at the left.
+ << Bitwise left shift operator. Left shift inserts zero
+ bit(s) at the right.
+ ++ "n++" increments the variable n.
+ % modulo operator: a % b is the remainder of a divided by b.
+
+ #define BASE 65521 /* largest prime smaller than 65536 */
+
+ /*
+ Update a running Adler-32 checksum with the bytes buf[0..len-1]
+ and return the updated checksum. The Adler-32 checksum should be
+ initialized to 1.
+
+ Usage example:
+
+ unsigned long adler = 1L;
+
+ while (read_buffer(buffer, length) != EOF) {
+ adler = update_adler32(adler, buffer, length);
+ }
+ if (adler != original_adler) error();
+ */
+ unsigned long update_adler32(unsigned long adler,
+ unsigned char *buf, int len)
+ {
+ unsigned long s1 = adler & 0xffff;
+ unsigned long s2 = (adler >> 16) & 0xffff;
+ int n;
+
+ for (n = 0; n < len; n++) {
+ s1 = (s1 + buf[n]) % BASE;
+ s2 = (s2 + s1) % BASE;
+ }
+ return (s2 << 16) + s1;
+ }
+
+ /* Return the adler32 of the bytes buf[0..len-1] */
+
+
+
+
+Deutsch & Gailly Informational [Page 10]
+
+RFC 1950 ZLIB Compressed Data Format Specification May 1996
+
+
+ unsigned long adler32(unsigned char *buf, int len)
+ {
+ return update_adler32(1L, buf, len);
+ }
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Deutsch & Gailly Informational [Page 11]
+
diff --git a/third-party/zlib/doc/rfc1951.txt b/third-party/zlib/doc/rfc1951.txt
new file mode 100644
index 0000000..403c8c7
--- /dev/null
+++ b/third-party/zlib/doc/rfc1951.txt
@@ -0,0 +1,955 @@
+
+
+
+
+
+
+Network Working Group P. Deutsch
+Request for Comments: 1951 Aladdin Enterprises
+Category: Informational May 1996
+
+
+ DEFLATE Compressed Data Format Specification version 1.3
+
+Status of This Memo
+
+ This memo provides information for the Internet community. This memo
+ does not specify an Internet standard of any kind. Distribution of
+ this memo is unlimited.
+
+IESG Note:
+
+ The IESG takes no position on the validity of any Intellectual
+ Property Rights statements contained in this document.
+
+Notices
+
+ Copyright (c) 1996 L. Peter Deutsch
+
+ Permission is granted to copy and distribute this document for any
+ purpose and without charge, including translations into other
+ languages and incorporation into compilations, provided that the
+ copyright notice and this notice are preserved, and that any
+ substantive changes or deletions from the original are clearly
+ marked.
+
+ A pointer to the latest version of this and related documentation in
+ HTML format can be found at the URL
+ <ftp://ftp.uu.net/graphics/png/documents/zlib/zdoc-index.html>.
+
+Abstract
+
+ This specification defines a lossless compressed data format that
+ compresses data using a combination of the LZ77 algorithm and Huffman
+ coding, with efficiency comparable to the best currently available
+ general-purpose compression methods. The data can be produced or
+ consumed, even for an arbitrarily long sequentially presented input
+ data stream, using only an a priori bounded amount of intermediate
+ storage. The format can be implemented readily in a manner not
+ covered by patents.
+
+
+
+
+
+
+
+
+Deutsch Informational [Page 1]
+
+RFC 1951 DEFLATE Compressed Data Format Specification May 1996
+
+
+Table of Contents
+
+ 1. Introduction ................................................... 2
+ 1.1. Purpose ................................................... 2
+ 1.2. Intended audience ......................................... 3
+ 1.3. Scope ..................................................... 3
+ 1.4. Compliance ................................................ 3
+ 1.5. Definitions of terms and conventions used ................ 3
+ 1.6. Changes from previous versions ............................ 4
+ 2. Compressed representation overview ............................. 4
+ 3. Detailed specification ......................................... 5
+ 3.1. Overall conventions ....................................... 5
+ 3.1.1. Packing into bytes .................................. 5
+ 3.2. Compressed block format ................................... 6
+ 3.2.1. Synopsis of prefix and Huffman coding ............... 6
+ 3.2.2. Use of Huffman coding in the "deflate" format ....... 7
+ 3.2.3. Details of block format ............................. 9
+ 3.2.4. Non-compressed blocks (BTYPE=00) ................... 11
+ 3.2.5. Compressed blocks (length and distance codes) ...... 11
+ 3.2.6. Compression with fixed Huffman codes (BTYPE=01) .... 12
+ 3.2.7. Compression with dynamic Huffman codes (BTYPE=10) .. 13
+ 3.3. Compliance ............................................... 14
+ 4. Compression algorithm details ................................. 14
+ 5. References .................................................... 16
+ 6. Security Considerations ....................................... 16
+ 7. Source code ................................................... 16
+ 8. Acknowledgements .............................................. 16
+ 9. Author's Address .............................................. 17
+
+1. Introduction
+
+ 1.1. Purpose
+
+ The purpose of this specification is to define a lossless
+ compressed data format that:
+ * Is independent of CPU type, operating system, file system,
+ and character set, and hence can be used for interchange;
+ * Can be produced or consumed, even for an arbitrarily long
+ sequentially presented input data stream, using only an a
+ priori bounded amount of intermediate storage, and hence
+ can be used in data communications or similar structures
+ such as Unix filters;
+ * Compresses data with efficiency comparable to the best
+ currently available general-purpose compression methods,
+ and in particular considerably better than the "compress"
+ program;
+ * Can be implemented readily in a manner not covered by
+ patents, and hence can be practiced freely;
+
+
+
+Deutsch Informational [Page 2]
+
+RFC 1951 DEFLATE Compressed Data Format Specification May 1996
+
+
+ * Is compatible with the file format produced by the current
+ widely used gzip utility, in that conforming decompressors
+ will be able to read data produced by the existing gzip
+ compressor.
+
+ The data format defined by this specification does not attempt to:
+
+ * Allow random access to compressed data;
+ * Compress specialized data (e.g., raster graphics) as well
+ as the best currently available specialized algorithms.
+
+ A simple counting argument shows that no lossless compression
+ algorithm can compress every possible input data set. For the
+ format defined here, the worst case expansion is 5 bytes per 32K-
+ byte block, i.e., a size increase of 0.015% for large data sets.
+ English text usually compresses by a factor of 2.5 to 3;
+ executable files usually compress somewhat less; graphical data
+ such as raster images may compress much more.
+
+ 1.2. Intended audience
+
+ This specification is intended for use by implementors of software
+ to compress data into "deflate" format and/or decompress data from
+ "deflate" format.
+
+ The text of the specification assumes a basic background in
+ programming at the level of bits and other primitive data
+ representations. Familiarity with the technique of Huffman coding
+ is helpful but not required.
+
+ 1.3. Scope
+
+ The specification specifies a method for representing a sequence
+ of bytes as a (usually shorter) sequence of bits, and a method for
+ packing the latter bit sequence into bytes.
+
+ 1.4. Compliance
+
+ Unless otherwise indicated below, a compliant decompressor must be
+ able to accept and decompress any data set that conforms to all
+ the specifications presented here; a compliant compressor must
+ produce data sets that conform to all the specifications presented
+ here.
+
+ 1.5. Definitions of terms and conventions used
+
+ Byte: 8 bits stored or transmitted as a unit (same as an octet).
+ For this specification, a byte is exactly 8 bits, even on machines
+
+
+
+Deutsch Informational [Page 3]
+
+RFC 1951 DEFLATE Compressed Data Format Specification May 1996
+
+
+ which store a character on a number of bits different from eight.
+ See below, for the numbering of bits within a byte.
+
+ String: a sequence of arbitrary bytes.
+
+ 1.6. Changes from previous versions
+
+ There have been no technical changes to the deflate format since
+ version 1.1 of this specification. In version 1.2, some
+ terminology was changed. Version 1.3 is a conversion of the
+ specification to RFC style.
+
+2. Compressed representation overview
+
+ A compressed data set consists of a series of blocks, corresponding
+ to successive blocks of input data. The block sizes are arbitrary,
+ except that non-compressible blocks are limited to 65,535 bytes.
+
+ Each block is compressed using a combination of the LZ77 algorithm
+ and Huffman coding. The Huffman trees for each block are independent
+ of those for previous or subsequent blocks; the LZ77 algorithm may
+ use a reference to a duplicated string occurring in a previous block,
+ up to 32K input bytes before.
+
+ Each block consists of two parts: a pair of Huffman code trees that
+ describe the representation of the compressed data part, and a
+ compressed data part. (The Huffman trees themselves are compressed
+ using Huffman encoding.) The compressed data consists of a series of
+ elements of two types: literal bytes (of strings that have not been
+ detected as duplicated within the previous 32K input bytes), and
+ pointers to duplicated strings, where a pointer is represented as a
+ pair <length, backward distance>. The representation used in the
+ "deflate" format limits distances to 32K bytes and lengths to 258
+ bytes, but does not limit the size of a block, except for
+ uncompressible blocks, which are limited as noted above.
+
+ Each type of value (literals, distances, and lengths) in the
+ compressed data is represented using a Huffman code, using one code
+ tree for literals and lengths and a separate code tree for distances.
+ The code trees for each block appear in a compact form just before
+ the compressed data for that block.
+
+
+
+
+
+
+
+
+
+
+Deutsch Informational [Page 4]
+
+RFC 1951 DEFLATE Compressed Data Format Specification May 1996
+
+
+3. Detailed specification
+
+ 3.1. Overall conventions In the diagrams below, a box like this:
+
+ +---+
+ | | <-- the vertical bars might be missing
+ +---+
+
+ represents one byte; a box like this:
+
+ +==============+
+ | |
+ +==============+
+
+ represents a variable number of bytes.
+
+ Bytes stored within a computer do not have a "bit order", since
+ they are always treated as a unit. However, a byte considered as
+ an integer between 0 and 255 does have a most- and least-
+ significant bit, and since we write numbers with the most-
+ significant digit on the left, we also write bytes with the most-
+ significant bit on the left. In the diagrams below, we number the
+ bits of a byte so that bit 0 is the least-significant bit, i.e.,
+ the bits are numbered:
+
+ +--------+
+ |76543210|
+ +--------+
+
+ Within a computer, a number may occupy multiple bytes. All
+ multi-byte numbers in the format described here are stored with
+ the least-significant byte first (at the lower memory address).
+ For example, the decimal number 520 is stored as:
+
+ 0 1
+ +--------+--------+
+ |00001000|00000010|
+ +--------+--------+
+ ^ ^
+ | |
+ | + more significant byte = 2 x 256
+ + less significant byte = 8
+
+ 3.1.1. Packing into bytes
+
+ This document does not address the issue of the order in which
+ bits of a byte are transmitted on a bit-sequential medium,
+ since the final data format described here is byte- rather than
+
+
+
+Deutsch Informational [Page 5]
+
+RFC 1951 DEFLATE Compressed Data Format Specification May 1996
+
+
+ bit-oriented. However, we describe the compressed block format
+ in below, as a sequence of data elements of various bit
+ lengths, not a sequence of bytes. We must therefore specify
+ how to pack these data elements into bytes to form the final
+ compressed byte sequence:
+
+ * Data elements are packed into bytes in order of
+ increasing bit number within the byte, i.e., starting
+ with the least-significant bit of the byte.
+ * Data elements other than Huffman codes are packed
+ starting with the least-significant bit of the data
+ element.
+ * Huffman codes are packed starting with the most-
+ significant bit of the code.
+
+ In other words, if one were to print out the compressed data as
+ a sequence of bytes, starting with the first byte at the
+ *right* margin and proceeding to the *left*, with the most-
+ significant bit of each byte on the left as usual, one would be
+ able to parse the result from right to left, with fixed-width
+ elements in the correct MSB-to-LSB order and Huffman codes in
+ bit-reversed order (i.e., with the first bit of the code in the
+ relative LSB position).
+
+ 3.2. Compressed block format
+
+ 3.2.1. Synopsis of prefix and Huffman coding
+
+ Prefix coding represents symbols from an a priori known
+ alphabet by bit sequences (codes), one code for each symbol, in
+ a manner such that different symbols may be represented by bit
+ sequences of different lengths, but a parser can always parse
+ an encoded string unambiguously symbol-by-symbol.
+
+ We define a prefix code in terms of a binary tree in which the
+ two edges descending from each non-leaf node are labeled 0 and
+ 1 and in which the leaf nodes correspond one-for-one with (are
+ labeled with) the symbols of the alphabet; then the code for a
+ symbol is the sequence of 0's and 1's on the edges leading from
+ the root to the leaf labeled with that symbol. For example:
+
+
+
+
+
+
+
+
+
+
+
+Deutsch Informational [Page 6]
+
+RFC 1951 DEFLATE Compressed Data Format Specification May 1996
+
+
+ /\ Symbol Code
+ 0 1 ------ ----
+ / \ A 00
+ /\ B B 1
+ 0 1 C 011
+ / \ D 010
+ A /\
+ 0 1
+ / \
+ D C
+
+ A parser can decode the next symbol from an encoded input
+ stream by walking down the tree from the root, at each step
+ choosing the edge corresponding to the next input bit.
+
+ Given an alphabet with known symbol frequencies, the Huffman
+ algorithm allows the construction of an optimal prefix code
+ (one which represents strings with those symbol frequencies
+ using the fewest bits of any possible prefix codes for that
+ alphabet). Such a code is called a Huffman code. (See
+ reference [1] in Chapter 5, references for additional
+ information on Huffman codes.)
+
+ Note that in the "deflate" format, the Huffman codes for the
+ various alphabets must not exceed certain maximum code lengths.
+ This constraint complicates the algorithm for computing code
+ lengths from symbol frequencies. Again, see Chapter 5,
+ references for details.
+
+ 3.2.2. Use of Huffman coding in the "deflate" format
+
+ The Huffman codes used for each alphabet in the "deflate"
+ format have two additional rules:
+
+ * All codes of a given bit length have lexicographically
+ consecutive values, in the same order as the symbols
+ they represent;
+
+ * Shorter codes lexicographically precede longer codes.
+
+
+
+
+
+
+
+
+
+
+
+
+Deutsch Informational [Page 7]
+
+RFC 1951 DEFLATE Compressed Data Format Specification May 1996
+
+
+ We could recode the example above to follow this rule as
+ follows, assuming that the order of the alphabet is ABCD:
+
+ Symbol Code
+ ------ ----
+ A 10
+ B 0
+ C 110
+ D 111
+
+ I.e., 0 precedes 10 which precedes 11x, and 110 and 111 are
+ lexicographically consecutive.
+
+ Given this rule, we can define the Huffman code for an alphabet
+ just by giving the bit lengths of the codes for each symbol of
+ the alphabet in order; this is sufficient to determine the
+ actual codes. In our example, the code is completely defined
+ by the sequence of bit lengths (2, 1, 3, 3). The following
+ algorithm generates the codes as integers, intended to be read
+ from most- to least-significant bit. The code lengths are
+ initially in tree[I].Len; the codes are produced in
+ tree[I].Code.
+
+ 1) Count the number of codes for each code length. Let
+ bl_count[N] be the number of codes of length N, N >= 1.
+
+ 2) Find the numerical value of the smallest code for each
+ code length:
+
+ code = 0;
+ bl_count[0] = 0;
+ for (bits = 1; bits <= MAX_BITS; bits++) {
+ code = (code + bl_count[bits-1]) << 1;
+ next_code[bits] = code;
+ }
+
+ 3) Assign numerical values to all codes, using consecutive
+ values for all codes of the same length with the base
+ values determined at step 2. Codes that are never used
+ (which have a bit length of zero) must not be assigned a
+ value.
+
+ for (n = 0; n <= max_code; n++) {
+ len = tree[n].Len;
+ if (len != 0) {
+ tree[n].Code = next_code[len];
+ next_code[len]++;
+ }
+
+
+
+Deutsch Informational [Page 8]
+
+RFC 1951 DEFLATE Compressed Data Format Specification May 1996
+
+
+ }
+
+ Example:
+
+ Consider the alphabet ABCDEFGH, with bit lengths (3, 3, 3, 3,
+ 3, 2, 4, 4). After step 1, we have:
+
+ N bl_count[N]
+ - -----------
+ 2 1
+ 3 5
+ 4 2
+
+ Step 2 computes the following next_code values:
+
+ N next_code[N]
+ - ------------
+ 1 0
+ 2 0
+ 3 2
+ 4 14
+
+ Step 3 produces the following code values:
+
+ Symbol Length Code
+ ------ ------ ----
+ A 3 010
+ B 3 011
+ C 3 100
+ D 3 101
+ E 3 110
+ F 2 00
+ G 4 1110
+ H 4 1111
+
+ 3.2.3. Details of block format
+
+ Each block of compressed data begins with 3 header bits
+ containing the following data:
+
+ first bit BFINAL
+ next 2 bits BTYPE
+
+ Note that the header bits do not necessarily begin on a byte
+ boundary, since a block does not necessarily occupy an integral
+ number of bytes.
+
+
+
+
+
+Deutsch Informational [Page 9]
+
+RFC 1951 DEFLATE Compressed Data Format Specification May 1996
+
+
+ BFINAL is set if and only if this is the last block of the data
+ set.
+
+ BTYPE specifies how the data are compressed, as follows:
+
+ 00 - no compression
+ 01 - compressed with fixed Huffman codes
+ 10 - compressed with dynamic Huffman codes
+ 11 - reserved (error)
+
+ The only difference between the two compressed cases is how the
+ Huffman codes for the literal/length and distance alphabets are
+ defined.
+
+ In all cases, the decoding algorithm for the actual data is as
+ follows:
+
+ do
+ read block header from input stream.
+ if stored with no compression
+ skip any remaining bits in current partially
+ processed byte
+ read LEN and NLEN (see next section)
+ copy LEN bytes of data to output
+ otherwise
+ if compressed with dynamic Huffman codes
+ read representation of code trees (see
+ subsection below)
+ loop (until end of block code recognized)
+ decode literal/length value from input stream
+ if value < 256
+ copy value (literal byte) to output stream
+ otherwise
+ if value = end of block (256)
+ break from loop
+ otherwise (value = 257..285)
+ decode distance from input stream
+
+ move backwards distance bytes in the output
+ stream, and copy length bytes from this
+ position to the output stream.
+ end loop
+ while not last block
+
+ Note that a duplicated string reference may refer to a string
+ in a previous block; i.e., the backward distance may cross one
+ or more block boundaries. However a distance cannot refer past
+ the beginning of the output stream. (An application using a
+
+
+
+Deutsch Informational [Page 10]
+
+RFC 1951 DEFLATE Compressed Data Format Specification May 1996
+
+
+ preset dictionary might discard part of the output stream; a
+ distance can refer to that part of the output stream anyway)
+ Note also that the referenced string may overlap the current
+ position; for example, if the last 2 bytes decoded have values
+ X and Y, a string reference with <length = 5, distance = 2>
+ adds X,Y,X,Y,X to the output stream.
+
+ We now specify each compression method in turn.
+
+ 3.2.4. Non-compressed blocks (BTYPE=00)
+
+ Any bits of input up to the next byte boundary are ignored.
+ The rest of the block consists of the following information:
+
+ 0 1 2 3 4...
+ +---+---+---+---+================================+
+ | LEN | NLEN |... LEN bytes of literal data...|
+ +---+---+---+---+================================+
+
+ LEN is the number of data bytes in the block. NLEN is the
+ one's complement of LEN.
+
+ 3.2.5. Compressed blocks (length and distance codes)
+
+ As noted above, encoded data blocks in the "deflate" format
+ consist of sequences of symbols drawn from three conceptually
+ distinct alphabets: either literal bytes, from the alphabet of
+ byte values (0..255), or <length, backward distance> pairs,
+ where the length is drawn from (3..258) and the distance is
+ drawn from (1..32,768). In fact, the literal and length
+ alphabets are merged into a single alphabet (0..285), where
+ values 0..255 represent literal bytes, the value 256 indicates
+ end-of-block, and values 257..285 represent length codes
+ (possibly in conjunction with extra bits following the symbol
+ code) as follows:
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Deutsch Informational [Page 11]
+
+RFC 1951 DEFLATE Compressed Data Format Specification May 1996
+
+
+ Extra Extra Extra
+ Code Bits Length(s) Code Bits Lengths Code Bits Length(s)
+ ---- ---- ------ ---- ---- ------- ---- ---- -------
+ 257 0 3 267 1 15,16 277 4 67-82
+ 258 0 4 268 1 17,18 278 4 83-98
+ 259 0 5 269 2 19-22 279 4 99-114
+ 260 0 6 270 2 23-26 280 4 115-130
+ 261 0 7 271 2 27-30 281 5 131-162
+ 262 0 8 272 2 31-34 282 5 163-194
+ 263 0 9 273 3 35-42 283 5 195-226
+ 264 0 10 274 3 43-50 284 5 227-257
+ 265 1 11,12 275 3 51-58 285 0 258
+ 266 1 13,14 276 3 59-66
+
+ The extra bits should be interpreted as a machine integer
+ stored with the most-significant bit first, e.g., bits 1110
+ represent the value 14.
+
+ Extra Extra Extra
+ Code Bits Dist Code Bits Dist Code Bits Distance
+ ---- ---- ---- ---- ---- ------ ---- ---- --------
+ 0 0 1 10 4 33-48 20 9 1025-1536
+ 1 0 2 11 4 49-64 21 9 1537-2048
+ 2 0 3 12 5 65-96 22 10 2049-3072
+ 3 0 4 13 5 97-128 23 10 3073-4096
+ 4 1 5,6 14 6 129-192 24 11 4097-6144
+ 5 1 7,8 15 6 193-256 25 11 6145-8192
+ 6 2 9-12 16 7 257-384 26 12 8193-12288
+ 7 2 13-16 17 7 385-512 27 12 12289-16384
+ 8 3 17-24 18 8 513-768 28 13 16385-24576
+ 9 3 25-32 19 8 769-1024 29 13 24577-32768
+
+ 3.2.6. Compression with fixed Huffman codes (BTYPE=01)
+
+ The Huffman codes for the two alphabets are fixed, and are not
+ represented explicitly in the data. The Huffman code lengths
+ for the literal/length alphabet are:
+
+ Lit Value Bits Codes
+ --------- ---- -----
+ 0 - 143 8 00110000 through
+ 10111111
+ 144 - 255 9 110010000 through
+ 111111111
+ 256 - 279 7 0000000 through
+ 0010111
+ 280 - 287 8 11000000 through
+ 11000111
+
+
+
+Deutsch Informational [Page 12]
+
+RFC 1951 DEFLATE Compressed Data Format Specification May 1996
+
+
+ The code lengths are sufficient to generate the actual codes,
+ as described above; we show the codes in the table for added
+ clarity. Literal/length values 286-287 will never actually
+ occur in the compressed data, but participate in the code
+ construction.
+
+ Distance codes 0-31 are represented by (fixed-length) 5-bit
+ codes, with possible additional bits as shown in the table
+ shown in Paragraph 3.2.5, above. Note that distance codes 30-
+ 31 will never actually occur in the compressed data.
+
+ 3.2.7. Compression with dynamic Huffman codes (BTYPE=10)
+
+ The Huffman codes for the two alphabets appear in the block
+ immediately after the header bits and before the actual
+ compressed data, first the literal/length code and then the
+ distance code. Each code is defined by a sequence of code
+ lengths, as discussed in Paragraph 3.2.2, above. For even
+ greater compactness, the code length sequences themselves are
+ compressed using a Huffman code. The alphabet for code lengths
+ is as follows:
+
+ 0 - 15: Represent code lengths of 0 - 15
+ 16: Copy the previous code length 3 - 6 times.
+ The next 2 bits indicate repeat length
+ (0 = 3, ... , 3 = 6)
+ Example: Codes 8, 16 (+2 bits 11),
+ 16 (+2 bits 10) will expand to
+ 12 code lengths of 8 (1 + 6 + 5)
+ 17: Repeat a code length of 0 for 3 - 10 times.
+ (3 bits of length)
+ 18: Repeat a code length of 0 for 11 - 138 times
+ (7 bits of length)
+
+ A code length of 0 indicates that the corresponding symbol in
+ the literal/length or distance alphabet will not occur in the
+ block, and should not participate in the Huffman code
+ construction algorithm given earlier. If only one distance
+ code is used, it is encoded using one bit, not zero bits; in
+ this case there is a single code length of one, with one unused
+ code. One distance code of zero bits means that there are no
+ distance codes used at all (the data is all literals).
+
+ We can now define the format of the block:
+
+ 5 Bits: HLIT, # of Literal/Length codes - 257 (257 - 286)
+ 5 Bits: HDIST, # of Distance codes - 1 (1 - 32)
+ 4 Bits: HCLEN, # of Code Length codes - 4 (4 - 19)
+
+
+
+Deutsch Informational [Page 13]
+
+RFC 1951 DEFLATE Compressed Data Format Specification May 1996
+
+
+ (HCLEN + 4) x 3 bits: code lengths for the code length
+ alphabet given just above, in the order: 16, 17, 18,
+ 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15
+
+ These code lengths are interpreted as 3-bit integers
+ (0-7); as above, a code length of 0 means the
+ corresponding symbol (literal/length or distance code
+ length) is not used.
+
+ HLIT + 257 code lengths for the literal/length alphabet,
+ encoded using the code length Huffman code
+
+ HDIST + 1 code lengths for the distance alphabet,
+ encoded using the code length Huffman code
+
+ The actual compressed data of the block,
+ encoded using the literal/length and distance Huffman
+ codes
+
+ The literal/length symbol 256 (end of data),
+ encoded using the literal/length Huffman code
+
+ The code length repeat codes can cross from HLIT + 257 to the
+ HDIST + 1 code lengths. In other words, all code lengths form
+ a single sequence of HLIT + HDIST + 258 values.
+
+ 3.3. Compliance
+
+ A compressor may limit further the ranges of values specified in
+ the previous section and still be compliant; for example, it may
+ limit the range of backward pointers to some value smaller than
+ 32K. Similarly, a compressor may limit the size of blocks so that
+ a compressible block fits in memory.
+
+ A compliant decompressor must accept the full range of possible
+ values defined in the previous section, and must accept blocks of
+ arbitrary size.
+
+4. Compression algorithm details
+
+ While it is the intent of this document to define the "deflate"
+ compressed data format without reference to any particular
+ compression algorithm, the format is related to the compressed
+ formats produced by LZ77 (Lempel-Ziv 1977, see reference [2] below);
+ since many variations of LZ77 are patented, it is strongly
+ recommended that the implementor of a compressor follow the general
+ algorithm presented here, which is known not to be patented per se.
+ The material in this section is not part of the definition of the
+
+
+
+Deutsch Informational [Page 14]
+
+RFC 1951 DEFLATE Compressed Data Format Specification May 1996
+
+
+ specification per se, and a compressor need not follow it in order to
+ be compliant.
+
+ The compressor terminates a block when it determines that starting a
+ new block with fresh trees would be useful, or when the block size
+ fills up the compressor's block buffer.
+
+ The compressor uses a chained hash table to find duplicated strings,
+ using a hash function that operates on 3-byte sequences. At any
+ given point during compression, let XYZ be the next 3 input bytes to
+ be examined (not necessarily all different, of course). First, the
+ compressor examines the hash chain for XYZ. If the chain is empty,
+ the compressor simply writes out X as a literal byte and advances one
+ byte in the input. If the hash chain is not empty, indicating that
+ the sequence XYZ (or, if we are unlucky, some other 3 bytes with the
+ same hash function value) has occurred recently, the compressor
+ compares all strings on the XYZ hash chain with the actual input data
+ sequence starting at the current point, and selects the longest
+ match.
+
+ The compressor searches the hash chains starting with the most recent
+ strings, to favor small distances and thus take advantage of the
+ Huffman encoding. The hash chains are singly linked. There are no
+ deletions from the hash chains; the algorithm simply discards matches
+ that are too old. To avoid a worst-case situation, very long hash
+ chains are arbitrarily truncated at a certain length, determined by a
+ run-time parameter.
+
+ To improve overall compression, the compressor optionally defers the
+ selection of matches ("lazy matching"): after a match of length N has
+ been found, the compressor searches for a longer match starting at
+ the next input byte. If it finds a longer match, it truncates the
+ previous match to a length of one (thus producing a single literal
+ byte) and then emits the longer match. Otherwise, it emits the
+ original match, and, as described above, advances N bytes before
+ continuing.
+
+ Run-time parameters also control this "lazy match" procedure. If
+ compression ratio is most important, the compressor attempts a
+ complete second search regardless of the length of the first match.
+ In the normal case, if the current match is "long enough", the
+ compressor reduces the search for a longer match, thus speeding up
+ the process. If speed is most important, the compressor inserts new
+ strings in the hash table only when no match was found, or when the
+ match is not "too long". This degrades the compression ratio but
+ saves time since there are both fewer insertions and fewer searches.
+
+
+
+
+
+Deutsch Informational [Page 15]
+
+RFC 1951 DEFLATE Compressed Data Format Specification May 1996
+
+
+5. References
+
+ [1] Huffman, D. A., "A Method for the Construction of Minimum
+ Redundancy Codes", Proceedings of the Institute of Radio
+ Engineers, September 1952, Volume 40, Number 9, pp. 1098-1101.
+
+ [2] Ziv J., Lempel A., "A Universal Algorithm for Sequential Data
+ Compression", IEEE Transactions on Information Theory, Vol. 23,
+ No. 3, pp. 337-343.
+
+ [3] Gailly, J.-L., and Adler, M., ZLIB documentation and sources,
+ available in ftp://ftp.uu.net/pub/archiving/zip/doc/
+
+ [4] Gailly, J.-L., and Adler, M., GZIP documentation and sources,
+ available as gzip-*.tar in ftp://prep.ai.mit.edu/pub/gnu/
+
+ [5] Schwartz, E. S., and Kallick, B. "Generating a canonical prefix
+ encoding." Comm. ACM, 7,3 (Mar. 1964), pp. 166-169.
+
+ [6] Hirschberg and Lelewer, "Efficient decoding of prefix codes,"
+ Comm. ACM, 33,4, April 1990, pp. 449-459.
+
+6. Security Considerations
+
+ Any data compression method involves the reduction of redundancy in
+ the data. Consequently, any corruption of the data is likely to have
+ severe effects and be difficult to correct. Uncompressed text, on
+ the other hand, will probably still be readable despite the presence
+ of some corrupted bytes.
+
+ It is recommended that systems using this data format provide some
+ means of validating the integrity of the compressed data. See
+ reference [3], for example.
+
+7. Source code
+
+ Source code for a C language implementation of a "deflate" compliant
+ compressor and decompressor is available within the zlib package at
+ ftp://ftp.uu.net/pub/archiving/zip/zlib/.
+
+8. Acknowledgements
+
+ Trademarks cited in this document are the property of their
+ respective owners.
+
+ Phil Katz designed the deflate format. Jean-Loup Gailly and Mark
+ Adler wrote the related software described in this specification.
+ Glenn Randers-Pehrson converted this document to RFC and HTML format.
+
+
+
+Deutsch Informational [Page 16]
+
+RFC 1951 DEFLATE Compressed Data Format Specification May 1996
+
+
+9. Author's Address
+
+ L. Peter Deutsch
+ Aladdin Enterprises
+ 203 Santa Margarita Ave.
+ Menlo Park, CA 94025
+
+ Phone: (415) 322-0103 (AM only)
+ FAX: (415) 322-1734
+ EMail: <ghost at aladdin.com>
+
+ Questions about the technical content of this specification can be
+ sent by email to:
+
+ Jean-Loup Gailly <gzip at prep.ai.mit.edu> and
+ Mark Adler <madler at alumni.caltech.edu>
+
+ Editorial comments on this specification can be sent by email to:
+
+ L. Peter Deutsch <ghost at aladdin.com> and
+ Glenn Randers-Pehrson <randeg at alumni.rpi.edu>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Deutsch Informational [Page 17]
+
diff --git a/third-party/zlib/doc/rfc1952.txt b/third-party/zlib/doc/rfc1952.txt
new file mode 100644
index 0000000..a8e51b4
--- /dev/null
+++ b/third-party/zlib/doc/rfc1952.txt
@@ -0,0 +1,675 @@
+
+
+
+
+
+
+Network Working Group P. Deutsch
+Request for Comments: 1952 Aladdin Enterprises
+Category: Informational May 1996
+
+
+ GZIP file format specification version 4.3
+
+Status of This Memo
+
+ This memo provides information for the Internet community. This memo
+ does not specify an Internet standard of any kind. Distribution of
+ this memo is unlimited.
+
+IESG Note:
+
+ The IESG takes no position on the validity of any Intellectual
+ Property Rights statements contained in this document.
+
+Notices
+
+ Copyright (c) 1996 L. Peter Deutsch
+
+ Permission is granted to copy and distribute this document for any
+ purpose and without charge, including translations into other
+ languages and incorporation into compilations, provided that the
+ copyright notice and this notice are preserved, and that any
+ substantive changes or deletions from the original are clearly
+ marked.
+
+ A pointer to the latest version of this and related documentation in
+ HTML format can be found at the URL
+ <ftp://ftp.uu.net/graphics/png/documents/zlib/zdoc-index.html>.
+
+Abstract
+
+ This specification defines a lossless compressed data format that is
+ compatible with the widely used GZIP utility. The format includes a
+ cyclic redundancy check value for detecting data corruption. The
+ format presently uses the DEFLATE method of compression but can be
+ easily extended to use other compression methods. The format can be
+ implemented readily in a manner not covered by patents.
+
+
+
+
+
+
+
+
+
+
+Deutsch Informational [Page 1]
+
+RFC 1952 GZIP File Format Specification May 1996
+
+
+Table of Contents
+
+ 1. Introduction ................................................... 2
+ 1.1. Purpose ................................................... 2
+ 1.2. Intended audience ......................................... 3
+ 1.3. Scope ..................................................... 3
+ 1.4. Compliance ................................................ 3
+ 1.5. Definitions of terms and conventions used ................. 3
+ 1.6. Changes from previous versions ............................ 3
+ 2. Detailed specification ......................................... 4
+ 2.1. Overall conventions ....................................... 4
+ 2.2. File format ............................................... 5
+ 2.3. Member format ............................................. 5
+ 2.3.1. Member header and trailer ........................... 6
+ 2.3.1.1. Extra field ................................... 8
+ 2.3.1.2. Compliance .................................... 9
+ 3. References .................................................. 9
+ 4. Security Considerations .................................... 10
+ 5. Acknowledgements ........................................... 10
+ 6. Author's Address ........................................... 10
+ 7. Appendix: Jean-Loup Gailly's gzip utility .................. 11
+ 8. Appendix: Sample CRC Code .................................. 11
+
+1. Introduction
+
+ 1.1. Purpose
+
+ The purpose of this specification is to define a lossless
+ compressed data format that:
+
+ * Is independent of CPU type, operating system, file system,
+ and character set, and hence can be used for interchange;
+ * Can compress or decompress a data stream (as opposed to a
+ randomly accessible file) to produce another data stream,
+ using only an a priori bounded amount of intermediate
+ storage, and hence can be used in data communications or
+ similar structures such as Unix filters;
+ * Compresses data with efficiency comparable to the best
+ currently available general-purpose compression methods,
+ and in particular considerably better than the "compress"
+ program;
+ * Can be implemented readily in a manner not covered by
+ patents, and hence can be practiced freely;
+ * Is compatible with the file format produced by the current
+ widely used gzip utility, in that conforming decompressors
+ will be able to read data produced by the existing gzip
+ compressor.
+
+
+
+
+Deutsch Informational [Page 2]
+
+RFC 1952 GZIP File Format Specification May 1996
+
+
+ The data format defined by this specification does not attempt to:
+
+ * Provide random access to compressed data;
+ * Compress specialized data (e.g., raster graphics) as well as
+ the best currently available specialized algorithms.
+
+ 1.2. Intended audience
+
+ This specification is intended for use by implementors of software
+ to compress data into gzip format and/or decompress data from gzip
+ format.
+
+ The text of the specification assumes a basic background in
+ programming at the level of bits and other primitive data
+ representations.
+
+ 1.3. Scope
+
+ The specification specifies a compression method and a file format
+ (the latter assuming only that a file can store a sequence of
+ arbitrary bytes). It does not specify any particular interface to
+ a file system or anything about character sets or encodings
+ (except for file names and comments, which are optional).
+
+ 1.4. Compliance
+
+ Unless otherwise indicated below, a compliant decompressor must be
+ able to accept and decompress any file that conforms to all the
+ specifications presented here; a compliant compressor must produce
+ files that conform to all the specifications presented here. The
+ material in the appendices is not part of the specification per se
+ and is not relevant to compliance.
+
+ 1.5. Definitions of terms and conventions used
+
+ byte: 8 bits stored or transmitted as a unit (same as an octet).
+ (For this specification, a byte is exactly 8 bits, even on
+ machines which store a character on a number of bits different
+ from 8.) See below for the numbering of bits within a byte.
+
+ 1.6. Changes from previous versions
+
+ There have been no technical changes to the gzip format since
+ version 4.1 of this specification. In version 4.2, some
+ terminology was changed, and the sample CRC code was rewritten for
+ clarity and to eliminate the requirement for the caller to do pre-
+ and post-conditioning. Version 4.3 is a conversion of the
+ specification to RFC style.
+
+
+
+Deutsch Informational [Page 3]
+
+RFC 1952 GZIP File Format Specification May 1996
+
+
+2. Detailed specification
+
+ 2.1. Overall conventions
+
+ In the diagrams below, a box like this:
+
+ +---+
+ | | <-- the vertical bars might be missing
+ +---+
+
+ represents one byte; a box like this:
+
+ +==============+
+ | |
+ +==============+
+
+ represents a variable number of bytes.
+
+ Bytes stored within a computer do not have a "bit order", since
+ they are always treated as a unit. However, a byte considered as
+ an integer between 0 and 255 does have a most- and least-
+ significant bit, and since we write numbers with the most-
+ significant digit on the left, we also write bytes with the most-
+ significant bit on the left. In the diagrams below, we number the
+ bits of a byte so that bit 0 is the least-significant bit, i.e.,
+ the bits are numbered:
+
+ +--------+
+ |76543210|
+ +--------+
+
+ This document does not address the issue of the order in which
+ bits of a byte are transmitted on a bit-sequential medium, since
+ the data format described here is byte- rather than bit-oriented.
+
+ Within a computer, a number may occupy multiple bytes. All
+ multi-byte numbers in the format described here are stored with
+ the least-significant byte first (at the lower memory address).
+ For example, the decimal number 520 is stored as:
+
+ 0 1
+ +--------+--------+
+ |00001000|00000010|
+ +--------+--------+
+ ^ ^
+ | |
+ | + more significant byte = 2 x 256
+ + less significant byte = 8
+
+
+
+Deutsch Informational [Page 4]
+
+RFC 1952 GZIP File Format Specification May 1996
+
+
+ 2.2. File format
+
+ A gzip file consists of a series of "members" (compressed data
+ sets). The format of each member is specified in the following
+ section. The members simply appear one after another in the file,
+ with no additional information before, between, or after them.
+
+ 2.3. Member format
+
+ Each member has the following structure:
+
+ +---+---+---+---+---+---+---+---+---+---+
+ |ID1|ID2|CM |FLG| MTIME |XFL|OS | (more-->)
+ +---+---+---+---+---+---+---+---+---+---+
+
+ (if FLG.FEXTRA set)
+
+ +---+---+=================================+
+ | XLEN |...XLEN bytes of "extra field"...| (more-->)
+ +---+---+=================================+
+
+ (if FLG.FNAME set)
+
+ +=========================================+
+ |...original file name, zero-terminated...| (more-->)
+ +=========================================+
+
+ (if FLG.FCOMMENT set)
+
+ +===================================+
+ |...file comment, zero-terminated...| (more-->)
+ +===================================+
+
+ (if FLG.FHCRC set)
+
+ +---+---+
+ | CRC16 |
+ +---+---+
+
+ +=======================+
+ |...compressed blocks...| (more-->)
+ +=======================+
+
+ 0 1 2 3 4 5 6 7
+ +---+---+---+---+---+---+---+---+
+ | CRC32 | ISIZE |
+ +---+---+---+---+---+---+---+---+
+
+
+
+
+Deutsch Informational [Page 5]
+
+RFC 1952 GZIP File Format Specification May 1996
+
+
+ 2.3.1. Member header and trailer
+
+ ID1 (IDentification 1)
+ ID2 (IDentification 2)
+ These have the fixed values ID1 = 31 (0x1f, \037), ID2 = 139
+ (0x8b, \213), to identify the file as being in gzip format.
+
+ CM (Compression Method)
+ This identifies the compression method used in the file. CM
+ = 0-7 are reserved. CM = 8 denotes the "deflate"
+ compression method, which is the one customarily used by
+ gzip and which is documented elsewhere.
+
+ FLG (FLaGs)
+ This flag byte is divided into individual bits as follows:
+
+ bit 0 FTEXT
+ bit 1 FHCRC
+ bit 2 FEXTRA
+ bit 3 FNAME
+ bit 4 FCOMMENT
+ bit 5 reserved
+ bit 6 reserved
+ bit 7 reserved
+
+ If FTEXT is set, the file is probably ASCII text. This is
+ an optional indication, which the compressor may set by
+ checking a small amount of the input data to see whether any
+ non-ASCII characters are present. In case of doubt, FTEXT
+ is cleared, indicating binary data. For systems which have
+ different file formats for ascii text and binary data, the
+ decompressor can use FTEXT to choose the appropriate format.
+ We deliberately do not specify the algorithm used to set
+ this bit, since a compressor always has the option of
+ leaving it cleared and a decompressor always has the option
+ of ignoring it and letting some other program handle issues
+ of data conversion.
+
+ If FHCRC is set, a CRC16 for the gzip header is present,
+ immediately before the compressed data. The CRC16 consists
+ of the two least significant bytes of the CRC32 for all
+ bytes of the gzip header up to and not including the CRC16.
+ [The FHCRC bit was never set by versions of gzip up to
+ 1.2.4, even though it was documented with a different
+ meaning in gzip 1.2.4.]
+
+ If FEXTRA is set, optional extra fields are present, as
+ described in a following section.
+
+
+
+Deutsch Informational [Page 6]
+
+RFC 1952 GZIP File Format Specification May 1996
+
+
+ If FNAME is set, an original file name is present,
+ terminated by a zero byte. The name must consist of ISO
+ 8859-1 (LATIN-1) characters; on operating systems using
+ EBCDIC or any other character set for file names, the name
+ must be translated to the ISO LATIN-1 character set. This
+ is the original name of the file being compressed, with any
+ directory components removed, and, if the file being
+ compressed is on a file system with case insensitive names,
+ forced to lower case. There is no original file name if the
+ data was compressed from a source other than a named file;
+ for example, if the source was stdin on a Unix system, there
+ is no file name.
+
+ If FCOMMENT is set, a zero-terminated file comment is
+ present. This comment is not interpreted; it is only
+ intended for human consumption. The comment must consist of
+ ISO 8859-1 (LATIN-1) characters. Line breaks should be
+ denoted by a single line feed character (10 decimal).
+
+ Reserved FLG bits must be zero.
+
+ MTIME (Modification TIME)
+ This gives the most recent modification time of the original
+ file being compressed. The time is in Unix format, i.e.,
+ seconds since 00:00:00 GMT, Jan. 1, 1970. (Note that this
+ may cause problems for MS-DOS and other systems that use
+ local rather than Universal time.) If the compressed data
+ did not come from a file, MTIME is set to the time at which
+ compression started. MTIME = 0 means no time stamp is
+ available.
+
+ XFL (eXtra FLags)
+ These flags are available for use by specific compression
+ methods. The "deflate" method (CM = 8) sets these flags as
+ follows:
+
+ XFL = 2 - compressor used maximum compression,
+ slowest algorithm
+ XFL = 4 - compressor used fastest algorithm
+
+ OS (Operating System)
+ This identifies the type of file system on which compression
+ took place. This may be useful in determining end-of-line
+ convention for text files. The currently defined values are
+ as follows:
+
+
+
+
+
+
+Deutsch Informational [Page 7]
+
+RFC 1952 GZIP File Format Specification May 1996
+
+
+ 0 - FAT filesystem (MS-DOS, OS/2, NT/Win32)
+ 1 - Amiga
+ 2 - VMS (or OpenVMS)
+ 3 - Unix
+ 4 - VM/CMS
+ 5 - Atari TOS
+ 6 - HPFS filesystem (OS/2, NT)
+ 7 - Macintosh
+ 8 - Z-System
+ 9 - CP/M
+ 10 - TOPS-20
+ 11 - NTFS filesystem (NT)
+ 12 - QDOS
+ 13 - Acorn RISCOS
+ 255 - unknown
+
+ XLEN (eXtra LENgth)
+ If FLG.FEXTRA is set, this gives the length of the optional
+ extra field. See below for details.
+
+ CRC32 (CRC-32)
+ This contains a Cyclic Redundancy Check value of the
+ uncompressed data computed according to CRC-32 algorithm
+ used in the ISO 3309 standard and in section 8.1.1.6.2 of
+ ITU-T recommendation V.42. (See http://www.iso.ch for
+ ordering ISO documents. See gopher://info.itu.ch for an
+ online version of ITU-T V.42.)
+
+ ISIZE (Input SIZE)
+ This contains the size of the original (uncompressed) input
+ data modulo 2^32.
+
+ 2.3.1.1. Extra field
+
+ If the FLG.FEXTRA bit is set, an "extra field" is present in
+ the header, with total length XLEN bytes. It consists of a
+ series of subfields, each of the form:
+
+ +---+---+---+---+==================================+
+ |SI1|SI2| LEN |... LEN bytes of subfield data ...|
+ +---+---+---+---+==================================+
+
+ SI1 and SI2 provide a subfield ID, typically two ASCII letters
+ with some mnemonic value. Jean-Loup Gailly
+ <gzip at prep.ai.mit.edu> is maintaining a registry of subfield
+ IDs; please send him any subfield ID you wish to use. Subfield
+ IDs with SI2 = 0 are reserved for future use. The following
+ IDs are currently defined:
+
+
+
+Deutsch Informational [Page 8]
+
+RFC 1952 GZIP File Format Specification May 1996
+
+
+ SI1 SI2 Data
+ ---------- ---------- ----
+ 0x41 ('A') 0x70 ('P') Apollo file type information
+
+ LEN gives the length of the subfield data, excluding the 4
+ initial bytes.
+
+ 2.3.1.2. Compliance
+
+ A compliant compressor must produce files with correct ID1,
+ ID2, CM, CRC32, and ISIZE, but may set all the other fields in
+ the fixed-length part of the header to default values (255 for
+ OS, 0 for all others). The compressor must set all reserved
+ bits to zero.
+
+ A compliant decompressor must check ID1, ID2, and CM, and
+ provide an error indication if any of these have incorrect
+ values. It must examine FEXTRA/XLEN, FNAME, FCOMMENT and FHCRC
+ at least so it can skip over the optional fields if they are
+ present. It need not examine any other part of the header or
+ trailer; in particular, a decompressor may ignore FTEXT and OS
+ and always produce binary output, and still be compliant. A
+ compliant decompressor must give an error indication if any
+ reserved bit is non-zero, since such a bit could indicate the
+ presence of a new field that would cause subsequent data to be
+ interpreted incorrectly.
+
+3. References
+
+ [1] "Information Processing - 8-bit single-byte coded graphic
+ character sets - Part 1: Latin alphabet No.1" (ISO 8859-1:1987).
+ The ISO 8859-1 (Latin-1) character set is a superset of 7-bit
+ ASCII. Files defining this character set are available as
+ iso_8859-1.* in ftp://ftp.uu.net/graphics/png/documents/
+
+ [2] ISO 3309
+
+ [3] ITU-T recommendation V.42
+
+ [4] Deutsch, L.P.,"DEFLATE Compressed Data Format Specification",
+ available in ftp://ftp.uu.net/pub/archiving/zip/doc/
+
+ [5] Gailly, J.-L., GZIP documentation, available as gzip-*.tar in
+ ftp://prep.ai.mit.edu/pub/gnu/
+
+ [6] Sarwate, D.V., "Computation of Cyclic Redundancy Checks via Table
+ Look-Up", Communications of the ACM, 31(8), pp.1008-1013.
+
+
+
+
+Deutsch Informational [Page 9]
+
+RFC 1952 GZIP File Format Specification May 1996
+
+
+ [7] Schwaderer, W.D., "CRC Calculation", April 85 PC Tech Journal,
+ pp.118-133.
+
+ [8] ftp://ftp.adelaide.edu.au/pub/rocksoft/papers/crc_v3.txt,
+ describing the CRC concept.
+
+4. Security Considerations
+
+ Any data compression method involves the reduction of redundancy in
+ the data. Consequently, any corruption of the data is likely to have
+ severe effects and be difficult to correct. Uncompressed text, on
+ the other hand, will probably still be readable despite the presence
+ of some corrupted bytes.
+
+ It is recommended that systems using this data format provide some
+ means of validating the integrity of the compressed data, such as by
+ setting and checking the CRC-32 check value.
+
+5. Acknowledgements
+
+ Trademarks cited in this document are the property of their
+ respective owners.
+
+ Jean-Loup Gailly designed the gzip format and wrote, with Mark Adler,
+ the related software described in this specification. Glenn
+ Randers-Pehrson converted this document to RFC and HTML format.
+
+6. Author's Address
+
+ L. Peter Deutsch
+ Aladdin Enterprises
+ 203 Santa Margarita Ave.
+ Menlo Park, CA 94025
+
+ Phone: (415) 322-0103 (AM only)
+ FAX: (415) 322-1734
+ EMail: <ghost at aladdin.com>
+
+ Questions about the technical content of this specification can be
+ sent by email to:
+
+ Jean-Loup Gailly <gzip at prep.ai.mit.edu> and
+ Mark Adler <madler at alumni.caltech.edu>
+
+ Editorial comments on this specification can be sent by email to:
+
+ L. Peter Deutsch <ghost at aladdin.com> and
+ Glenn Randers-Pehrson <randeg at alumni.rpi.edu>
+
+
+
+Deutsch Informational [Page 10]
+
+RFC 1952 GZIP File Format Specification May 1996
+
+
+7. Appendix: Jean-Loup Gailly's gzip utility
+
+ The most widely used implementation of gzip compression, and the
+ original documentation on which this specification is based, were
+ created by Jean-Loup Gailly <gzip at prep.ai.mit.edu>. Since this
+ implementation is a de facto standard, we mention some more of its
+ features here. Again, the material in this section is not part of
+ the specification per se, and implementations need not follow it to
+ be compliant.
+
+ When compressing or decompressing a file, gzip preserves the
+ protection, ownership, and modification time attributes on the local
+ file system, since there is no provision for representing protection
+ attributes in the gzip file format itself. Since the file format
+ includes a modification time, the gzip decompressor provides a
+ command line switch that assigns the modification time from the file,
+ rather than the local modification time of the compressed input, to
+ the decompressed output.
+
+8. Appendix: Sample CRC Code
+
+ The following sample code represents a practical implementation of
+ the CRC (Cyclic Redundancy Check). (See also ISO 3309 and ITU-T V.42
+ for a formal specification.)
+
+ The sample code is in the ANSI C programming language. Non C users
+ may find it easier to read with these hints:
+
+ & Bitwise AND operator.
+ ^ Bitwise exclusive-OR operator.
+ >> Bitwise right shift operator. When applied to an
+ unsigned quantity, as here, right shift inserts zero
+ bit(s) at the left.
+ ! Logical NOT operator.
+ ++ "n++" increments the variable n.
+ 0xNNN 0x introduces a hexadecimal (base 16) constant.
+ Suffix L indicates a long value (at least 32 bits).
+
+ /* Table of CRCs of all 8-bit messages. */
+ unsigned long crc_table[256];
+
+ /* Flag: has the table been computed? Initially false. */
+ int crc_table_computed = 0;
+
+ /* Make the table for a fast CRC. */
+ void make_crc_table(void)
+ {
+ unsigned long c;
+
+
+
+Deutsch Informational [Page 11]
+
+RFC 1952 GZIP File Format Specification May 1996
+
+
+ int n, k;
+ for (n = 0; n < 256; n++) {
+ c = (unsigned long) n;
+ for (k = 0; k < 8; k++) {
+ if (c & 1) {
+ c = 0xedb88320L ^ (c >> 1);
+ } else {
+ c = c >> 1;
+ }
+ }
+ crc_table[n] = c;
+ }
+ crc_table_computed = 1;
+ }
+
+ /*
+ Update a running crc with the bytes buf[0..len-1] and return
+ the updated crc. The crc should be initialized to zero. Pre- and
+ post-conditioning (one's complement) is performed within this
+ function so it shouldn't be done by the caller. Usage example:
+
+ unsigned long crc = 0L;
+
+ while (read_buffer(buffer, length) != EOF) {
+ crc = update_crc(crc, buffer, length);
+ }
+ if (crc != original_crc) error();
+ */
+ unsigned long update_crc(unsigned long crc,
+ unsigned char *buf, int len)
+ {
+ unsigned long c = crc ^ 0xffffffffL;
+ int n;
+
+ if (!crc_table_computed)
+ make_crc_table();
+ for (n = 0; n < len; n++) {
+ c = crc_table[(c ^ buf[n]) & 0xff] ^ (c >> 8);
+ }
+ return c ^ 0xffffffffL;
+ }
+
+ /* Return the CRC of the bytes buf[0..len-1]. */
+ unsigned long crc(unsigned char *buf, int len)
+ {
+ return update_crc(0L, buf, len);
+ }
+
+
+
+
+Deutsch Informational [Page 12]
+
diff --git a/third-party/zlib/doc/txtvsbin.txt b/third-party/zlib/doc/txtvsbin.txt
new file mode 100644
index 0000000..3d0f063
--- /dev/null
+++ b/third-party/zlib/doc/txtvsbin.txt
@@ -0,0 +1,107 @@
+A Fast Method for Identifying Plain Text Files
+==============================================
+
+
+Introduction
+------------
+
+Given a file coming from an unknown source, it is sometimes desirable
+to find out whether the format of that file is plain text. Although
+this may appear like a simple task, a fully accurate detection of the
+file type requires heavy-duty semantic analysis on the file contents.
+It is, however, possible to obtain satisfactory results by employing
+various heuristics.
+
+Previous versions of PKZip and other zip-compatible compression tools
+were using a crude detection scheme: if more than 80% (4/5) of the bytes
+found in a certain buffer are within the range [7..127], the file is
+labeled as plain text, otherwise it is labeled as binary. A prominent
+limitation of this scheme is the restriction to Latin-based alphabets.
+Other alphabets, like Greek, Cyrillic or Asian, make extensive use of
+the bytes within the range [128..255], and texts using these alphabets
+are most often misidentified by this scheme; in other words, the rate
+of false negatives is sometimes too high, which means that the recall
+is low. Another weakness of this scheme is a reduced precision, due to
+the false positives that may occur when binary files containing large
+amounts of textual characters are misidentified as plain text.
+
+In this article we propose a new, simple detection scheme that features
+a much increased precision and a near-100% recall. This scheme is
+designed to work on ASCII, Unicode and other ASCII-derived alphabets,
+and it handles single-byte encodings (ISO-8859, MacRoman, KOI8, etc.)
+and variable-sized encodings (ISO-2022, UTF-8, etc.). Wider encodings
+(UCS-2/UTF-16 and UCS-4/UTF-32) are not handled, however.
+
+
+The Algorithm
+-------------
+
+The algorithm works by dividing the set of bytecodes [0..255] into three
+categories:
+- The white list of textual bytecodes:
+ 9 (TAB), 10 (LF), 13 (CR), 32 (SPACE) to 255.
+- The gray list of tolerated bytecodes:
+ 7 (BEL), 8 (BS), 11 (VT), 12 (FF), 26 (SUB), 27 (ESC).
+- The black list of undesired, non-textual bytecodes:
+ 0 (NUL) to 6, 14 to 31.
+
+If a file contains at least one byte that belongs to the white list and
+no byte that belongs to the black list, then the file is categorized as
+plain text; otherwise, it is categorized as binary. (The boundary case,
+when the file is empty, automatically falls into the latter category.)
+
+
+Rationale
+---------
+
+The idea behind this algorithm relies on two observations.
+
+The first observation is that, although the full range of 7-bit codes
+[0..127] is properly specified by the ASCII standard, most control
+characters in the range [0..31] are not used in practice. The only
+widely-used, almost universally-portable control codes are 9 (TAB),
+10 (LF) and 13 (CR). There are a few more control codes that are
+recognized on a reduced range of platforms and text viewers/editors:
+7 (BEL), 8 (BS), 11 (VT), 12 (FF), 26 (SUB) and 27 (ESC); but these
+codes are rarely (if ever) used alone, without being accompanied by
+some printable text. Even the newer, portable text formats such as
+XML avoid using control characters outside the list mentioned here.
+
+The second observation is that most of the binary files tend to contain
+control characters, especially 0 (NUL). Even though the older text
+detection schemes observe the presence of non-ASCII codes from the range
+[128..255], the precision rarely has to suffer if this upper range is
+labeled as textual, because the files that are genuinely binary tend to
+contain both control characters and codes from the upper range. On the
+other hand, the upper range needs to be labeled as textual, because it
+is used by virtually all ASCII extensions. In particular, this range is
+used for encoding non-Latin scripts.
+
+Since there is no counting involved, other than simply observing the
+presence or the absence of some byte values, the algorithm produces
+consistent results, regardless what alphabet encoding is being used.
+(If counting were involved, it could be possible to obtain different
+results on a text encoded, say, using ISO-8859-16 versus UTF-8.)
+
+There is an extra category of plain text files that are "polluted" with
+one or more black-listed codes, either by mistake or by peculiar design
+considerations. In such cases, a scheme that tolerates a small fraction
+of black-listed codes would provide an increased recall (i.e. more true
+positives). This, however, incurs a reduced precision overall, since
+false positives are more likely to appear in binary files that contain
+large chunks of textual data. Furthermore, "polluted" plain text should
+be regarded as binary by general-purpose text detection schemes, because
+general-purpose text processing algorithms might not be applicable.
+Under this premise, it is safe to say that our detection method provides
+a near-100% recall.
+
+Experiments have been run on many files coming from various platforms
+and applications. We tried plain text files, system logs, source code,
+formatted office documents, compiled object code, etc. The results
+confirm the optimistic assumptions about the capabilities of this
+algorithm.
+
+
+--
+Cosmin Truta
+Last updated: 2006-May-28
diff --git a/third-party/zlib/gzclose.c b/third-party/zlib/gzclose.c
new file mode 100644
index 0000000..caeb99a
--- /dev/null
+++ b/third-party/zlib/gzclose.c
@@ -0,0 +1,25 @@
+/* gzclose.c -- zlib gzclose() function
+ * Copyright (C) 2004, 2010 Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+#include "gzguts.h"
+
+/* gzclose() is in a separate file so that it is linked in only if it is used.
+ That way the other gzclose functions can be used instead to avoid linking in
+ unneeded compression or decompression routines. */
+int ZEXPORT gzclose(file)
+ gzFile file;
+{
+#ifndef NO_GZCOMPRESS
+ gz_statep state;
+
+ if (file == NULL)
+ return Z_STREAM_ERROR;
+ state = (gz_statep)file;
+
+ return state->mode == GZ_READ ? gzclose_r(file) : gzclose_w(file);
+#else
+ return gzclose_r(file);
+#endif
+}
diff --git a/third-party/zlib/gzguts.h b/third-party/zlib/gzguts.h
new file mode 100644
index 0000000..d87659d
--- /dev/null
+++ b/third-party/zlib/gzguts.h
@@ -0,0 +1,209 @@
+/* gzguts.h -- zlib internal header definitions for gz* operations
+ * Copyright (C) 2004, 2005, 2010, 2011, 2012, 2013 Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+#ifdef _LARGEFILE64_SOURCE
+# ifndef _LARGEFILE_SOURCE
+# define _LARGEFILE_SOURCE 1
+# endif
+# ifdef _FILE_OFFSET_BITS
+# undef _FILE_OFFSET_BITS
+# endif
+#endif
+
+#ifdef HAVE_HIDDEN
+# define ZLIB_INTERNAL __attribute__((visibility ("hidden")))
+#else
+# define ZLIB_INTERNAL
+#endif
+
+#include <stdio.h>
+#include "zlib.h"
+#ifdef STDC
+# include <string.h>
+# include <stdlib.h>
+# include <limits.h>
+#endif
+#include <fcntl.h>
+
+#ifdef _WIN32
+# include <stddef.h>
+#endif
+
+#if defined(__TURBOC__) || defined(_MSC_VER) || defined(_WIN32)
+# include <io.h>
+#endif
+
+#ifdef WINAPI_FAMILY
+# define open _open
+# define read _read
+# define write _write
+# define close _close
+#endif
+
+#ifdef NO_DEFLATE /* for compatibility with old definition */
+# define NO_GZCOMPRESS
+#endif
+
+#if defined(STDC99) || (defined(__TURBOC__) && __TURBOC__ >= 0x550)
+# ifndef HAVE_VSNPRINTF
+# define HAVE_VSNPRINTF
+# endif
+#endif
+
+#if defined(__CYGWIN__)
+# ifndef HAVE_VSNPRINTF
+# define HAVE_VSNPRINTF
+# endif
+#endif
+
+#if defined(MSDOS) && defined(__BORLANDC__) && (BORLANDC > 0x410)
+# ifndef HAVE_VSNPRINTF
+# define HAVE_VSNPRINTF
+# endif
+#endif
+
+#ifndef HAVE_VSNPRINTF
+# ifdef MSDOS
+/* vsnprintf may exist on some MS-DOS compilers (DJGPP?),
+ but for now we just assume it doesn't. */
+# define NO_vsnprintf
+# endif
+# ifdef __TURBOC__
+# define NO_vsnprintf
+# endif
+# ifdef WIN32
+/* In Win32, vsnprintf is available as the "non-ANSI" _vsnprintf. */
+# if !defined(vsnprintf) && !defined(NO_vsnprintf)
+# if !defined(_MSC_VER) || ( defined(_MSC_VER) && _MSC_VER < 1500 )
+# define vsnprintf _vsnprintf
+# endif
+# endif
+# endif
+# ifdef __SASC
+# define NO_vsnprintf
+# endif
+# ifdef VMS
+# define NO_vsnprintf
+# endif
+# ifdef __OS400__
+# define NO_vsnprintf
+# endif
+# ifdef __MVS__
+# define NO_vsnprintf
+# endif
+#endif
+
+/* unlike snprintf (which is required in C99, yet still not supported by
+ Microsoft more than a decade later!), _snprintf does not guarantee null
+ termination of the result -- however this is only used in gzlib.c where
+ the result is assured to fit in the space provided */
+#ifdef _MSC_VER
+# define snprintf _snprintf
+#endif
+
+#ifndef local
+# define local static
+#endif
+/* compile with -Dlocal if your debugger can't find static symbols */
+
+/* gz* functions always use library allocation functions */
+#ifndef STDC
+ extern voidp malloc OF((uInt size));
+ extern void free OF((voidpf ptr));
+#endif
+
+/* get errno and strerror definition */
+#if defined UNDER_CE
+# include <windows.h>
+# define zstrerror() gz_strwinerror((DWORD)GetLastError())
+#else
+# ifndef NO_STRERROR
+# include <errno.h>
+# define zstrerror() strerror(errno)
+# else
+# define zstrerror() "stdio error (consult errno)"
+# endif
+#endif
+
+/* provide prototypes for these when building zlib without LFS */
+#if !defined(_LARGEFILE64_SOURCE) || _LFS64_LARGEFILE-0 == 0
+ ZEXTERN gzFile ZEXPORT gzopen64 OF((const char *, const char *));
+ ZEXTERN z_off64_t ZEXPORT gzseek64 OF((gzFile, z_off64_t, int));
+ ZEXTERN z_off64_t ZEXPORT gztell64 OF((gzFile));
+ ZEXTERN z_off64_t ZEXPORT gzoffset64 OF((gzFile));
+#endif
+
+/* default memLevel */
+#if MAX_MEM_LEVEL >= 8
+# define DEF_MEM_LEVEL 8
+#else
+# define DEF_MEM_LEVEL MAX_MEM_LEVEL
+#endif
+
+/* default i/o buffer size -- double this for output when reading (this and
+ twice this must be able to fit in an unsigned type) */
+#define GZBUFSIZE 8192
+
+/* gzip modes, also provide a little integrity check on the passed structure */
+#define GZ_NONE 0
+#define GZ_READ 7247
+#define GZ_WRITE 31153
+#define GZ_APPEND 1 /* mode set to GZ_WRITE after the file is opened */
+
+/* values for gz_state how */
+#define LOOK 0 /* look for a gzip header */
+#define COPY 1 /* copy input directly */
+#define GZIP 2 /* decompress a gzip stream */
+
+/* internal gzip file state data structure */
+typedef struct {
+ /* exposed contents for gzgetc() macro */
+ struct gzFile_s x; /* "x" for exposed */
+ /* x.have: number of bytes available at x.next */
+ /* x.next: next output data to deliver or write */
+ /* x.pos: current position in uncompressed data */
+ /* used for both reading and writing */
+ int mode; /* see gzip modes above */
+ int fd; /* file descriptor */
+ char *path; /* path or fd for error messages */
+ unsigned size; /* buffer size, zero if not allocated yet */
+ unsigned want; /* requested buffer size, default is GZBUFSIZE */
+ unsigned char *in; /* input buffer */
+ unsigned char *out; /* output buffer (double-sized when reading) */
+ int direct; /* 0 if processing gzip, 1 if transparent */
+ /* just for reading */
+ int how; /* 0: get header, 1: copy, 2: decompress */
+ z_off64_t start; /* where the gzip data started, for rewinding */
+ int eof; /* true if end of input file reached */
+ int past; /* true if read requested past end */
+ /* just for writing */
+ int level; /* compression level */
+ int strategy; /* compression strategy */
+ /* seek request */
+ z_off64_t skip; /* amount to skip (already rewound if backwards) */
+ int seek; /* true if seek request pending */
+ /* error information */
+ int err; /* error code */
+ char *msg; /* error message */
+ /* zlib inflate or deflate stream */
+ z_stream strm; /* stream structure in-place (not a pointer) */
+} gz_state;
+typedef gz_state FAR *gz_statep;
+
+/* shared functions */
+void ZLIB_INTERNAL gz_error OF((gz_statep, int, const char *));
+#if defined UNDER_CE
+char ZLIB_INTERNAL *gz_strwinerror OF((DWORD error));
+#endif
+
+/* GT_OFF(x), where x is an unsigned value, is true if x > maximum z_off64_t
+ value -- needed when comparing unsigned to z_off64_t, which is signed
+ (possible z_off64_t types off_t, off64_t, and long are all signed) */
+#ifdef INT_MAX
+# define GT_OFF(x) (sizeof(int) == sizeof(z_off64_t) && (x) > INT_MAX)
+#else
+unsigned ZLIB_INTERNAL gz_intmax OF((void));
+# define GT_OFF(x) (sizeof(int) == sizeof(z_off64_t) && (x) > gz_intmax())
+#endif
diff --git a/third-party/zlib/gzlib.c b/third-party/zlib/gzlib.c
new file mode 100644
index 0000000..fae202e
--- /dev/null
+++ b/third-party/zlib/gzlib.c
@@ -0,0 +1,634 @@
+/* gzlib.c -- zlib functions common to reading and writing gzip files
+ * Copyright (C) 2004, 2010, 2011, 2012, 2013 Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+#include "gzguts.h"
+
+#if defined(_WIN32) && !defined(__BORLANDC__)
+# define LSEEK _lseeki64
+#else
+#if defined(_LARGEFILE64_SOURCE) && _LFS64_LARGEFILE-0
+# define LSEEK lseek64
+#else
+# define LSEEK lseek
+#endif
+#endif
+
+/* Local functions */
+local void gz_reset OF((gz_statep));
+local gzFile gz_open OF((const void *, int, const char *));
+
+#if defined UNDER_CE
+
+/* Map the Windows error number in ERROR to a locale-dependent error message
+ string and return a pointer to it. Typically, the values for ERROR come
+ from GetLastError.
+
+ The string pointed to shall not be modified by the application, but may be
+ overwritten by a subsequent call to gz_strwinerror
+
+ The gz_strwinerror function does not change the current setting of
+ GetLastError. */
+char ZLIB_INTERNAL *gz_strwinerror (error)
+ DWORD error;
+{
+ static char buf[1024];
+
+ wchar_t *msgbuf;
+ DWORD lasterr = GetLastError();
+ DWORD chars = FormatMessage(FORMAT_MESSAGE_FROM_SYSTEM
+ | FORMAT_MESSAGE_ALLOCATE_BUFFER,
+ NULL,
+ error,
+ 0, /* Default language */
+ (LPVOID)&msgbuf,
+ 0,
+ NULL);
+ if (chars != 0) {
+ /* If there is an \r\n appended, zap it. */
+ if (chars >= 2
+ && msgbuf[chars - 2] == '\r' && msgbuf[chars - 1] == '\n') {
+ chars -= 2;
+ msgbuf[chars] = 0;
+ }
+
+ if (chars > sizeof (buf) - 1) {
+ chars = sizeof (buf) - 1;
+ msgbuf[chars] = 0;
+ }
+
+ wcstombs(buf, msgbuf, chars + 1);
+ LocalFree(msgbuf);
+ }
+ else {
+ sprintf(buf, "unknown win32 error (%ld)", error);
+ }
+
+ SetLastError(lasterr);
+ return buf;
+}
+
+#endif /* UNDER_CE */
+
+/* Reset gzip file state */
+local void gz_reset(state)
+ gz_statep state;
+{
+ state->x.have = 0; /* no output data available */
+ if (state->mode == GZ_READ) { /* for reading ... */
+ state->eof = 0; /* not at end of file */
+ state->past = 0; /* have not read past end yet */
+ state->how = LOOK; /* look for gzip header */
+ }
+ state->seek = 0; /* no seek request pending */
+ gz_error(state, Z_OK, NULL); /* clear error */
+ state->x.pos = 0; /* no uncompressed data yet */
+ state->strm.avail_in = 0; /* no input data yet */
+}
+
+/* Open a gzip file either by name or file descriptor. */
+local gzFile gz_open(path, fd, mode)
+ const void *path;
+ int fd;
+ const char *mode;
+{
+ gz_statep state;
+ size_t len;
+ int oflag;
+#ifdef O_CLOEXEC
+ int cloexec = 0;
+#endif
+#ifdef O_EXCL
+ int exclusive = 0;
+#endif
+
+ /* check input */
+ if (path == NULL)
+ return NULL;
+
+ /* allocate gzFile structure to return */
+ state = (gz_statep)malloc(sizeof(gz_state));
+ if (state == NULL)
+ return NULL;
+ state->size = 0; /* no buffers allocated yet */
+ state->want = GZBUFSIZE; /* requested buffer size */
+ state->msg = NULL; /* no error message yet */
+
+ /* interpret mode */
+ state->mode = GZ_NONE;
+ state->level = Z_DEFAULT_COMPRESSION;
+ state->strategy = Z_DEFAULT_STRATEGY;
+ state->direct = 0;
+ while (*mode) {
+ if (*mode >= '0' && *mode <= '9')
+ state->level = *mode - '0';
+ else
+ switch (*mode) {
+ case 'r':
+ state->mode = GZ_READ;
+ break;
+#ifndef NO_GZCOMPRESS
+ case 'w':
+ state->mode = GZ_WRITE;
+ break;
+ case 'a':
+ state->mode = GZ_APPEND;
+ break;
+#endif
+ case '+': /* can't read and write at the same time */
+ free(state);
+ return NULL;
+ case 'b': /* ignore -- will request binary anyway */
+ break;
+#ifdef O_CLOEXEC
+ case 'e':
+ cloexec = 1;
+ break;
+#endif
+#ifdef O_EXCL
+ case 'x':
+ exclusive = 1;
+ break;
+#endif
+ case 'f':
+ state->strategy = Z_FILTERED;
+ break;
+ case 'h':
+ state->strategy = Z_HUFFMAN_ONLY;
+ break;
+ case 'R':
+ state->strategy = Z_RLE;
+ break;
+ case 'F':
+ state->strategy = Z_FIXED;
+ break;
+ case 'T':
+ state->direct = 1;
+ break;
+ default: /* could consider as an error, but just ignore */
+ ;
+ }
+ mode++;
+ }
+
+ /* must provide an "r", "w", or "a" */
+ if (state->mode == GZ_NONE) {
+ free(state);
+ return NULL;
+ }
+
+ /* can't force transparent read */
+ if (state->mode == GZ_READ) {
+ if (state->direct) {
+ free(state);
+ return NULL;
+ }
+ state->direct = 1; /* for empty file */
+ }
+
+ /* save the path name for error messages */
+#ifdef _WIN32
+ if (fd == -2) {
+ len = wcstombs(NULL, path, 0);
+ if (len == (size_t)-1)
+ len = 0;
+ }
+ else
+#endif
+ len = strlen((const char *)path);
+ state->path = (char *)malloc(len + 1);
+ if (state->path == NULL) {
+ free(state);
+ return NULL;
+ }
+#ifdef _WIN32
+ if (fd == -2)
+ if (len)
+ wcstombs(state->path, path, len + 1);
+ else
+ *(state->path) = 0;
+ else
+#endif
+#if !defined(NO_snprintf) && !defined(NO_vsnprintf)
+ snprintf(state->path, len + 1, "%s", (const char *)path);
+#else
+ strcpy(state->path, path);
+#endif
+
+ /* compute the flags for open() */
+ oflag =
+#ifdef O_LARGEFILE
+ O_LARGEFILE |
+#endif
+#ifdef O_BINARY
+ O_BINARY |
+#endif
+#ifdef O_CLOEXEC
+ (cloexec ? O_CLOEXEC : 0) |
+#endif
+ (state->mode == GZ_READ ?
+ O_RDONLY :
+ (O_WRONLY | O_CREAT |
+#ifdef O_EXCL
+ (exclusive ? O_EXCL : 0) |
+#endif
+ (state->mode == GZ_WRITE ?
+ O_TRUNC :
+ O_APPEND)));
+
+ /* open the file with the appropriate flags (or just use fd) */
+ state->fd = fd > -1 ? fd : (
+#ifdef _WIN32
+ fd == -2 ? _wopen(path, oflag, 0666) :
+#endif
+ open((const char *)path, oflag, 0666));
+ if (state->fd == -1) {
+ free(state->path);
+ free(state);
+ return NULL;
+ }
+ if (state->mode == GZ_APPEND)
+ state->mode = GZ_WRITE; /* simplify later checks */
+
+ /* save the current position for rewinding (only if reading) */
+ if (state->mode == GZ_READ) {
+ state->start = LSEEK(state->fd, 0, SEEK_CUR);
+ if (state->start == -1) state->start = 0;
+ }
+
+ /* initialize stream */
+ gz_reset(state);
+
+ /* return stream */
+ return (gzFile)state;
+}
+
+/* -- see zlib.h -- */
+gzFile ZEXPORT gzopen(path, mode)
+ const char *path;
+ const char *mode;
+{
+ return gz_open(path, -1, mode);
+}
+
+/* -- see zlib.h -- */
+gzFile ZEXPORT gzopen64(path, mode)
+ const char *path;
+ const char *mode;
+{
+ return gz_open(path, -1, mode);
+}
+
+/* -- see zlib.h -- */
+gzFile ZEXPORT gzdopen(fd, mode)
+ int fd;
+ const char *mode;
+{
+ char *path; /* identifier for error messages */
+ gzFile gz;
+
+ if (fd == -1 || (path = (char *)malloc(7 + 3 * sizeof(int))) == NULL)
+ return NULL;
+#if !defined(NO_snprintf) && !defined(NO_vsnprintf)
+ snprintf(path, 7 + 3 * sizeof(int), "<fd:%d>", fd); /* for debugging */
+#else
+ sprintf(path, "<fd:%d>", fd); /* for debugging */
+#endif
+ gz = gz_open(path, fd, mode);
+ free(path);
+ return gz;
+}
+
+/* -- see zlib.h -- */
+#ifdef _WIN32
+gzFile ZEXPORT gzopen_w(path, mode)
+ const wchar_t *path;
+ const char *mode;
+{
+ return gz_open(path, -2, mode);
+}
+#endif
+
+/* -- see zlib.h -- */
+int ZEXPORT gzbuffer(file, size)
+ gzFile file;
+ unsigned size;
+{
+ gz_statep state;
+
+ /* get internal structure and check integrity */
+ if (file == NULL)
+ return -1;
+ state = (gz_statep)file;
+ if (state->mode != GZ_READ && state->mode != GZ_WRITE)
+ return -1;
+
+ /* make sure we haven't already allocated memory */
+ if (state->size != 0)
+ return -1;
+
+ /* check and set requested size */
+ if (size < 2)
+ size = 2; /* need two bytes to check magic header */
+ state->want = size;
+ return 0;
+}
+
+/* -- see zlib.h -- */
+int ZEXPORT gzrewind(file)
+ gzFile file;
+{
+ gz_statep state;
+
+ /* get internal structure */
+ if (file == NULL)
+ return -1;
+ state = (gz_statep)file;
+
+ /* check that we're reading and that there's no error */
+ if (state->mode != GZ_READ ||
+ (state->err != Z_OK && state->err != Z_BUF_ERROR))
+ return -1;
+
+ /* back up and start over */
+ if (LSEEK(state->fd, state->start, SEEK_SET) == -1)
+ return -1;
+ gz_reset(state);
+ return 0;
+}
+
+/* -- see zlib.h -- */
+z_off64_t ZEXPORT gzseek64(file, offset, whence)
+ gzFile file;
+ z_off64_t offset;
+ int whence;
+{
+ unsigned n;
+ z_off64_t ret;
+ gz_statep state;
+
+ /* get internal structure and check integrity */
+ if (file == NULL)
+ return -1;
+ state = (gz_statep)file;
+ if (state->mode != GZ_READ && state->mode != GZ_WRITE)
+ return -1;
+
+ /* check that there's no error */
+ if (state->err != Z_OK && state->err != Z_BUF_ERROR)
+ return -1;
+
+ /* can only seek from start or relative to current position */
+ if (whence != SEEK_SET && whence != SEEK_CUR)
+ return -1;
+
+ /* normalize offset to a SEEK_CUR specification */
+ if (whence == SEEK_SET)
+ offset -= state->x.pos;
+ else if (state->seek)
+ offset += state->skip;
+ state->seek = 0;
+
+ /* if within raw area while reading, just go there */
+ if (state->mode == GZ_READ && state->how == COPY &&
+ state->x.pos + offset >= 0) {
+ ret = LSEEK(state->fd, offset - state->x.have, SEEK_CUR);
+ if (ret == -1)
+ return -1;
+ state->x.have = 0;
+ state->eof = 0;
+ state->past = 0;
+ state->seek = 0;
+ gz_error(state, Z_OK, NULL);
+ state->strm.avail_in = 0;
+ state->x.pos += offset;
+ return state->x.pos;
+ }
+
+ /* calculate skip amount, rewinding if needed for back seek when reading */
+ if (offset < 0) {
+ if (state->mode != GZ_READ) /* writing -- can't go backwards */
+ return -1;
+ offset += state->x.pos;
+ if (offset < 0) /* before start of file! */
+ return -1;
+ if (gzrewind(file) == -1) /* rewind, then skip to offset */
+ return -1;
+ }
+
+ /* if reading, skip what's in output buffer (one less gzgetc() check) */
+ if (state->mode == GZ_READ) {
+ n = GT_OFF(state->x.have) || (z_off64_t)state->x.have > offset ?
+ (unsigned)offset : state->x.have;
+ state->x.have -= n;
+ state->x.next += n;
+ state->x.pos += n;
+ offset -= n;
+ }
+
+ /* request skip (if not zero) */
+ if (offset) {
+ state->seek = 1;
+ state->skip = offset;
+ }
+ return state->x.pos + offset;
+}
+
+/* -- see zlib.h -- */
+z_off_t ZEXPORT gzseek(file, offset, whence)
+ gzFile file;
+ z_off_t offset;
+ int whence;
+{
+ z_off64_t ret;
+
+ ret = gzseek64(file, (z_off64_t)offset, whence);
+ return ret == (z_off_t)ret ? (z_off_t)ret : -1;
+}
+
+/* -- see zlib.h -- */
+z_off64_t ZEXPORT gztell64(file)
+ gzFile file;
+{
+ gz_statep state;
+
+ /* get internal structure and check integrity */
+ if (file == NULL)
+ return -1;
+ state = (gz_statep)file;
+ if (state->mode != GZ_READ && state->mode != GZ_WRITE)
+ return -1;
+
+ /* return position */
+ return state->x.pos + (state->seek ? state->skip : 0);
+}
+
+/* -- see zlib.h -- */
+z_off_t ZEXPORT gztell(file)
+ gzFile file;
+{
+ z_off64_t ret;
+
+ ret = gztell64(file);
+ return ret == (z_off_t)ret ? (z_off_t)ret : -1;
+}
+
+/* -- see zlib.h -- */
+z_off64_t ZEXPORT gzoffset64(file)
+ gzFile file;
+{
+ z_off64_t offset;
+ gz_statep state;
+
+ /* get internal structure and check integrity */
+ if (file == NULL)
+ return -1;
+ state = (gz_statep)file;
+ if (state->mode != GZ_READ && state->mode != GZ_WRITE)
+ return -1;
+
+ /* compute and return effective offset in file */
+ offset = LSEEK(state->fd, 0, SEEK_CUR);
+ if (offset == -1)
+ return -1;
+ if (state->mode == GZ_READ) /* reading */
+ offset -= state->strm.avail_in; /* don't count buffered input */
+ return offset;
+}
+
+/* -- see zlib.h -- */
+z_off_t ZEXPORT gzoffset(file)
+ gzFile file;
+{
+ z_off64_t ret;
+
+ ret = gzoffset64(file);
+ return ret == (z_off_t)ret ? (z_off_t)ret : -1;
+}
+
+/* -- see zlib.h -- */
+int ZEXPORT gzeof(file)
+ gzFile file;
+{
+ gz_statep state;
+
+ /* get internal structure and check integrity */
+ if (file == NULL)
+ return 0;
+ state = (gz_statep)file;
+ if (state->mode != GZ_READ && state->mode != GZ_WRITE)
+ return 0;
+
+ /* return end-of-file state */
+ return state->mode == GZ_READ ? state->past : 0;
+}
+
+/* -- see zlib.h -- */
+const char * ZEXPORT gzerror(file, errnum)
+ gzFile file;
+ int *errnum;
+{
+ gz_statep state;
+
+ /* get internal structure and check integrity */
+ if (file == NULL)
+ return NULL;
+ state = (gz_statep)file;
+ if (state->mode != GZ_READ && state->mode != GZ_WRITE)
+ return NULL;
+
+ /* return error information */
+ if (errnum != NULL)
+ *errnum = state->err;
+ return state->err == Z_MEM_ERROR ? "out of memory" :
+ (state->msg == NULL ? "" : state->msg);
+}
+
+/* -- see zlib.h -- */
+void ZEXPORT gzclearerr(file)
+ gzFile file;
+{
+ gz_statep state;
+
+ /* get internal structure and check integrity */
+ if (file == NULL)
+ return;
+ state = (gz_statep)file;
+ if (state->mode != GZ_READ && state->mode != GZ_WRITE)
+ return;
+
+ /* clear error and end-of-file */
+ if (state->mode == GZ_READ) {
+ state->eof = 0;
+ state->past = 0;
+ }
+ gz_error(state, Z_OK, NULL);
+}
+
+/* Create an error message in allocated memory and set state->err and
+ state->msg accordingly. Free any previous error message already there. Do
+ not try to free or allocate space if the error is Z_MEM_ERROR (out of
+ memory). Simply save the error message as a static string. If there is an
+ allocation failure constructing the error message, then convert the error to
+ out of memory. */
+void ZLIB_INTERNAL gz_error(state, err, msg)
+ gz_statep state;
+ int err;
+ const char *msg;
+{
+ /* free previously allocated message and clear */
+ if (state->msg != NULL) {
+ if (state->err != Z_MEM_ERROR)
+ free(state->msg);
+ state->msg = NULL;
+ }
+
+ /* if fatal, set state->x.have to 0 so that the gzgetc() macro fails */
+ if (err != Z_OK && err != Z_BUF_ERROR)
+ state->x.have = 0;
+
+ /* set error code, and if no message, then done */
+ state->err = err;
+ if (msg == NULL)
+ return;
+
+ /* for an out of memory error, return literal string when requested */
+ if (err == Z_MEM_ERROR)
+ return;
+
+ /* construct error message with path */
+ if ((state->msg = (char *)malloc(strlen(state->path) + strlen(msg) + 3)) ==
+ NULL) {
+ state->err = Z_MEM_ERROR;
+ return;
+ }
+#if !defined(NO_snprintf) && !defined(NO_vsnprintf)
+ snprintf(state->msg, strlen(state->path) + strlen(msg) + 3,
+ "%s%s%s", state->path, ": ", msg);
+#else
+ strcpy(state->msg, state->path);
+ strcat(state->msg, ": ");
+ strcat(state->msg, msg);
+#endif
+ return;
+}
+
+#ifndef INT_MAX
+/* portably return maximum value for an int (when limits.h presumed not
+ available) -- we need to do this to cover cases where 2's complement not
+ used, since C standard permits 1's complement and sign-bit representations,
+ otherwise we could just use ((unsigned)-1) >> 1 */
+unsigned ZLIB_INTERNAL gz_intmax()
+{
+ unsigned p, q;
+
+ p = 1;
+ do {
+ q = p;
+ p <<= 1;
+ p++;
+ } while (p > q);
+ return q >> 1;
+}
+#endif
diff --git a/third-party/zlib/gzread.c b/third-party/zlib/gzread.c
new file mode 100644
index 0000000..bf4538e
--- /dev/null
+++ b/third-party/zlib/gzread.c
@@ -0,0 +1,594 @@
+/* gzread.c -- zlib functions for reading gzip files
+ * Copyright (C) 2004, 2005, 2010, 2011, 2012, 2013 Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+#include "gzguts.h"
+
+/* Local functions */
+local int gz_load OF((gz_statep, unsigned char *, unsigned, unsigned *));
+local int gz_avail OF((gz_statep));
+local int gz_look OF((gz_statep));
+local int gz_decomp OF((gz_statep));
+local int gz_fetch OF((gz_statep));
+local int gz_skip OF((gz_statep, z_off64_t));
+
+/* Use read() to load a buffer -- return -1 on error, otherwise 0. Read from
+ state->fd, and update state->eof, state->err, and state->msg as appropriate.
+ This function needs to loop on read(), since read() is not guaranteed to
+ read the number of bytes requested, depending on the type of descriptor. */
+local int gz_load(state, buf, len, have)
+ gz_statep state;
+ unsigned char *buf;
+ unsigned len;
+ unsigned *have;
+{
+ int ret;
+
+ *have = 0;
+ do {
+ ret = read(state->fd, buf + *have, len - *have);
+ if (ret <= 0)
+ break;
+ *have += ret;
+ } while (*have < len);
+ if (ret < 0) {
+ gz_error(state, Z_ERRNO, zstrerror());
+ return -1;
+ }
+ if (ret == 0)
+ state->eof = 1;
+ return 0;
+}
+
+/* Load up input buffer and set eof flag if last data loaded -- return -1 on
+ error, 0 otherwise. Note that the eof flag is set when the end of the input
+ file is reached, even though there may be unused data in the buffer. Once
+ that data has been used, no more attempts will be made to read the file.
+ If strm->avail_in != 0, then the current data is moved to the beginning of
+ the input buffer, and then the remainder of the buffer is loaded with the
+ available data from the input file. */
+local int gz_avail(state)
+ gz_statep state;
+{
+ unsigned got;
+ z_streamp strm = &(state->strm);
+
+ if (state->err != Z_OK && state->err != Z_BUF_ERROR)
+ return -1;
+ if (state->eof == 0) {
+ if (strm->avail_in) { /* copy what's there to the start */
+ unsigned char *p = state->in;
+ unsigned const char *q = strm->next_in;
+ unsigned n = strm->avail_in;
+ do {
+ *p++ = *q++;
+ } while (--n);
+ }
+ if (gz_load(state, state->in + strm->avail_in,
+ state->size - strm->avail_in, &got) == -1)
+ return -1;
+ strm->avail_in += got;
+ strm->next_in = state->in;
+ }
+ return 0;
+}
+
+/* Look for gzip header, set up for inflate or copy. state->x.have must be 0.
+ If this is the first time in, allocate required memory. state->how will be
+ left unchanged if there is no more input data available, will be set to COPY
+ if there is no gzip header and direct copying will be performed, or it will
+ be set to GZIP for decompression. If direct copying, then leftover input
+ data from the input buffer will be copied to the output buffer. In that
+ case, all further file reads will be directly to either the output buffer or
+ a user buffer. If decompressing, the inflate state will be initialized.
+ gz_look() will return 0 on success or -1 on failure. */
+local int gz_look(state)
+ gz_statep state;
+{
+ z_streamp strm = &(state->strm);
+
+ /* allocate read buffers and inflate memory */
+ if (state->size == 0) {
+ /* allocate buffers */
+ state->in = (unsigned char *)malloc(state->want);
+ state->out = (unsigned char *)malloc(state->want << 1);
+ if (state->in == NULL || state->out == NULL) {
+ if (state->out != NULL)
+ free(state->out);
+ if (state->in != NULL)
+ free(state->in);
+ gz_error(state, Z_MEM_ERROR, "out of memory");
+ return -1;
+ }
+ state->size = state->want;
+
+ /* allocate inflate memory */
+ state->strm.zalloc = Z_NULL;
+ state->strm.zfree = Z_NULL;
+ state->strm.opaque = Z_NULL;
+ state->strm.avail_in = 0;
+ state->strm.next_in = Z_NULL;
+ if (inflateInit2(&(state->strm), 15 + 16) != Z_OK) { /* gunzip */
+ free(state->out);
+ free(state->in);
+ state->size = 0;
+ gz_error(state, Z_MEM_ERROR, "out of memory");
+ return -1;
+ }
+ }
+
+ /* get at least the magic bytes in the input buffer */
+ if (strm->avail_in < 2) {
+ if (gz_avail(state) == -1)
+ return -1;
+ if (strm->avail_in == 0)
+ return 0;
+ }
+
+ /* look for gzip magic bytes -- if there, do gzip decoding (note: there is
+ a logical dilemma here when considering the case of a partially written
+ gzip file, to wit, if a single 31 byte is written, then we cannot tell
+ whether this is a single-byte file, or just a partially written gzip
+ file -- for here we assume that if a gzip file is being written, then
+ the header will be written in a single operation, so that reading a
+ single byte is sufficient indication that it is not a gzip file) */
+ if (strm->avail_in > 1 &&
+ strm->next_in[0] == 31 && strm->next_in[1] == 139) {
+ inflateReset(strm);
+ state->how = GZIP;
+ state->direct = 0;
+ return 0;
+ }
+
+ /* no gzip header -- if we were decoding gzip before, then this is trailing
+ garbage. Ignore the trailing garbage and finish. */
+ if (state->direct == 0) {
+ strm->avail_in = 0;
+ state->eof = 1;
+ state->x.have = 0;
+ return 0;
+ }
+
+ /* doing raw i/o, copy any leftover input to output -- this assumes that
+ the output buffer is larger than the input buffer, which also assures
+ space for gzungetc() */
+ state->x.next = state->out;
+ if (strm->avail_in) {
+ memcpy(state->x.next, strm->next_in, strm->avail_in);
+ state->x.have = strm->avail_in;
+ strm->avail_in = 0;
+ }
+ state->how = COPY;
+ state->direct = 1;
+ return 0;
+}
+
+/* Decompress from input to the provided next_out and avail_out in the state.
+ On return, state->x.have and state->x.next point to the just decompressed
+ data. If the gzip stream completes, state->how is reset to LOOK to look for
+ the next gzip stream or raw data, once state->x.have is depleted. Returns 0
+ on success, -1 on failure. */
+local int gz_decomp(state)
+ gz_statep state;
+{
+ int ret = Z_OK;
+ unsigned had;
+ z_streamp strm = &(state->strm);
+
+ /* fill output buffer up to end of deflate stream */
+ had = strm->avail_out;
+ do {
+ /* get more input for inflate() */
+ if (strm->avail_in == 0 && gz_avail(state) == -1)
+ return -1;
+ if (strm->avail_in == 0) {
+ gz_error(state, Z_BUF_ERROR, "unexpected end of file");
+ break;
+ }
+
+ /* decompress and handle errors */
+ ret = inflate(strm, Z_NO_FLUSH);
+ if (ret == Z_STREAM_ERROR || ret == Z_NEED_DICT) {
+ gz_error(state, Z_STREAM_ERROR,
+ "internal error: inflate stream corrupt");
+ return -1;
+ }
+ if (ret == Z_MEM_ERROR) {
+ gz_error(state, Z_MEM_ERROR, "out of memory");
+ return -1;
+ }
+ if (ret == Z_DATA_ERROR) { /* deflate stream invalid */
+ gz_error(state, Z_DATA_ERROR,
+ strm->msg == NULL ? "compressed data error" : strm->msg);
+ return -1;
+ }
+ } while (strm->avail_out && ret != Z_STREAM_END);
+
+ /* update available output */
+ state->x.have = had - strm->avail_out;
+ state->x.next = strm->next_out - state->x.have;
+
+ /* if the gzip stream completed successfully, look for another */
+ if (ret == Z_STREAM_END)
+ state->how = LOOK;
+
+ /* good decompression */
+ return 0;
+}
+
+/* Fetch data and put it in the output buffer. Assumes state->x.have is 0.
+ Data is either copied from the input file or decompressed from the input
+ file depending on state->how. If state->how is LOOK, then a gzip header is
+ looked for to determine whether to copy or decompress. Returns -1 on error,
+ otherwise 0. gz_fetch() will leave state->how as COPY or GZIP unless the
+ end of the input file has been reached and all data has been processed. */
+local int gz_fetch(state)
+ gz_statep state;
+{
+ z_streamp strm = &(state->strm);
+
+ do {
+ switch(state->how) {
+ case LOOK: /* -> LOOK, COPY (only if never GZIP), or GZIP */
+ if (gz_look(state) == -1)
+ return -1;
+ if (state->how == LOOK)
+ return 0;
+ break;
+ case COPY: /* -> COPY */
+ if (gz_load(state, state->out, state->size << 1, &(state->x.have))
+ == -1)
+ return -1;
+ state->x.next = state->out;
+ return 0;
+ case GZIP: /* -> GZIP or LOOK (if end of gzip stream) */
+ strm->avail_out = state->size << 1;
+ strm->next_out = state->out;
+ if (gz_decomp(state) == -1)
+ return -1;
+ }
+ } while (state->x.have == 0 && (!state->eof || strm->avail_in));
+ return 0;
+}
+
+/* Skip len uncompressed bytes of output. Return -1 on error, 0 on success. */
+local int gz_skip(state, len)
+ gz_statep state;
+ z_off64_t len;
+{
+ unsigned n;
+
+ /* skip over len bytes or reach end-of-file, whichever comes first */
+ while (len)
+ /* skip over whatever is in output buffer */
+ if (state->x.have) {
+ n = GT_OFF(state->x.have) || (z_off64_t)state->x.have > len ?
+ (unsigned)len : state->x.have;
+ state->x.have -= n;
+ state->x.next += n;
+ state->x.pos += n;
+ len -= n;
+ }
+
+ /* output buffer empty -- return if we're at the end of the input */
+ else if (state->eof && state->strm.avail_in == 0)
+ break;
+
+ /* need more data to skip -- load up output buffer */
+ else {
+ /* get more output, looking for header if required */
+ if (gz_fetch(state) == -1)
+ return -1;
+ }
+ return 0;
+}
+
+/* -- see zlib.h -- */
+int ZEXPORT gzread(file, buf, len)
+ gzFile file;
+ voidp buf;
+ unsigned len;
+{
+ unsigned got, n;
+ gz_statep state;
+ z_streamp strm;
+
+ /* get internal structure */
+ if (file == NULL)
+ return -1;
+ state = (gz_statep)file;
+ strm = &(state->strm);
+
+ /* check that we're reading and that there's no (serious) error */
+ if (state->mode != GZ_READ ||
+ (state->err != Z_OK && state->err != Z_BUF_ERROR))
+ return -1;
+
+ /* since an int is returned, make sure len fits in one, otherwise return
+ with an error (this avoids the flaw in the interface) */
+ if ((int)len < 0) {
+ gz_error(state, Z_DATA_ERROR, "requested length does not fit in int");
+ return -1;
+ }
+
+ /* if len is zero, avoid unnecessary operations */
+ if (len == 0)
+ return 0;
+
+ /* process a skip request */
+ if (state->seek) {
+ state->seek = 0;
+ if (gz_skip(state, state->skip) == -1)
+ return -1;
+ }
+
+ /* get len bytes to buf, or less than len if at the end */
+ got = 0;
+ do {
+ /* first just try copying data from the output buffer */
+ if (state->x.have) {
+ n = state->x.have > len ? len : state->x.have;
+ memcpy(buf, state->x.next, n);
+ state->x.next += n;
+ state->x.have -= n;
+ }
+
+ /* output buffer empty -- return if we're at the end of the input */
+ else if (state->eof && strm->avail_in == 0) {
+ state->past = 1; /* tried to read past end */
+ break;
+ }
+
+ /* need output data -- for small len or new stream load up our output
+ buffer */
+ else if (state->how == LOOK || len < (state->size << 1)) {
+ /* get more output, looking for header if required */
+ if (gz_fetch(state) == -1)
+ return -1;
+ continue; /* no progress yet -- go back to copy above */
+ /* the copy above assures that we will leave with space in the
+ output buffer, allowing at least one gzungetc() to succeed */
+ }
+
+ /* large len -- read directly into user buffer */
+ else if (state->how == COPY) { /* read directly */
+ if (gz_load(state, (unsigned char *)buf, len, &n) == -1)
+ return -1;
+ }
+
+ /* large len -- decompress directly into user buffer */
+ else { /* state->how == GZIP */
+ strm->avail_out = len;
+ strm->next_out = (unsigned char *)buf;
+ if (gz_decomp(state) == -1)
+ return -1;
+ n = state->x.have;
+ state->x.have = 0;
+ }
+
+ /* update progress */
+ len -= n;
+ buf = (char *)buf + n;
+ got += n;
+ state->x.pos += n;
+ } while (len);
+
+ /* return number of bytes read into user buffer (will fit in int) */
+ return (int)got;
+}
+
+/* -- see zlib.h -- */
+#ifdef Z_PREFIX_SET
+# undef z_gzgetc
+#else
+# undef gzgetc
+#endif
+int ZEXPORT gzgetc(file)
+ gzFile file;
+{
+ int ret;
+ unsigned char buf[1];
+ gz_statep state;
+
+ /* get internal structure */
+ if (file == NULL)
+ return -1;
+ state = (gz_statep)file;
+
+ /* check that we're reading and that there's no (serious) error */
+ if (state->mode != GZ_READ ||
+ (state->err != Z_OK && state->err != Z_BUF_ERROR))
+ return -1;
+
+ /* try output buffer (no need to check for skip request) */
+ if (state->x.have) {
+ state->x.have--;
+ state->x.pos++;
+ return *(state->x.next)++;
+ }
+
+ /* nothing there -- try gzread() */
+ ret = gzread(file, buf, 1);
+ return ret < 1 ? -1 : buf[0];
+}
+
+int ZEXPORT gzgetc_(file)
+gzFile file;
+{
+ return gzgetc(file);
+}
+
+/* -- see zlib.h -- */
+int ZEXPORT gzungetc(c, file)
+ int c;
+ gzFile file;
+{
+ gz_statep state;
+
+ /* get internal structure */
+ if (file == NULL)
+ return -1;
+ state = (gz_statep)file;
+
+ /* check that we're reading and that there's no (serious) error */
+ if (state->mode != GZ_READ ||
+ (state->err != Z_OK && state->err != Z_BUF_ERROR))
+ return -1;
+
+ /* process a skip request */
+ if (state->seek) {
+ state->seek = 0;
+ if (gz_skip(state, state->skip) == -1)
+ return -1;
+ }
+
+ /* can't push EOF */
+ if (c < 0)
+ return -1;
+
+ /* if output buffer empty, put byte at end (allows more pushing) */
+ if (state->x.have == 0) {
+ state->x.have = 1;
+ state->x.next = state->out + (state->size << 1) - 1;
+ state->x.next[0] = c;
+ state->x.pos--;
+ state->past = 0;
+ return c;
+ }
+
+ /* if no room, give up (must have already done a gzungetc()) */
+ if (state->x.have == (state->size << 1)) {
+ gz_error(state, Z_DATA_ERROR, "out of room to push characters");
+ return -1;
+ }
+
+ /* slide output data if needed and insert byte before existing data */
+ if (state->x.next == state->out) {
+ unsigned char *src = state->out + state->x.have;
+ unsigned char *dest = state->out + (state->size << 1);
+ while (src > state->out)
+ *--dest = *--src;
+ state->x.next = dest;
+ }
+ state->x.have++;
+ state->x.next--;
+ state->x.next[0] = c;
+ state->x.pos--;
+ state->past = 0;
+ return c;
+}
+
+/* -- see zlib.h -- */
+char * ZEXPORT gzgets(file, buf, len)
+ gzFile file;
+ char *buf;
+ int len;
+{
+ unsigned left, n;
+ char *str;
+ unsigned char *eol;
+ gz_statep state;
+
+ /* check parameters and get internal structure */
+ if (file == NULL || buf == NULL || len < 1)
+ return NULL;
+ state = (gz_statep)file;
+
+ /* check that we're reading and that there's no (serious) error */
+ if (state->mode != GZ_READ ||
+ (state->err != Z_OK && state->err != Z_BUF_ERROR))
+ return NULL;
+
+ /* process a skip request */
+ if (state->seek) {
+ state->seek = 0;
+ if (gz_skip(state, state->skip) == -1)
+ return NULL;
+ }
+
+ /* copy output bytes up to new line or len - 1, whichever comes first --
+ append a terminating zero to the string (we don't check for a zero in
+ the contents, let the user worry about that) */
+ str = buf;
+ left = (unsigned)len - 1;
+ if (left) do {
+ /* assure that something is in the output buffer */
+ if (state->x.have == 0 && gz_fetch(state) == -1)
+ return NULL; /* error */
+ if (state->x.have == 0) { /* end of file */
+ state->past = 1; /* read past end */
+ break; /* return what we have */
+ }
+
+ /* look for end-of-line in current output buffer */
+ n = state->x.have > left ? left : state->x.have;
+ eol = (unsigned char *)memchr(state->x.next, '\n', n);
+ if (eol != NULL)
+ n = (unsigned)(eol - state->x.next) + 1;
+
+ /* copy through end-of-line, or remainder if not found */
+ memcpy(buf, state->x.next, n);
+ state->x.have -= n;
+ state->x.next += n;
+ state->x.pos += n;
+ left -= n;
+ buf += n;
+ } while (left && eol == NULL);
+
+ /* return terminated string, or if nothing, end of file */
+ if (buf == str)
+ return NULL;
+ buf[0] = 0;
+ return str;
+}
+
+/* -- see zlib.h -- */
+int ZEXPORT gzdirect(file)
+ gzFile file;
+{
+ gz_statep state;
+
+ /* get internal structure */
+ if (file == NULL)
+ return 0;
+ state = (gz_statep)file;
+
+ /* if the state is not known, but we can find out, then do so (this is
+ mainly for right after a gzopen() or gzdopen()) */
+ if (state->mode == GZ_READ && state->how == LOOK && state->x.have == 0)
+ (void)gz_look(state);
+
+ /* return 1 if transparent, 0 if processing a gzip stream */
+ return state->direct;
+}
+
+/* -- see zlib.h -- */
+int ZEXPORT gzclose_r(file)
+ gzFile file;
+{
+ int ret, err;
+ gz_statep state;
+
+ /* get internal structure */
+ if (file == NULL)
+ return Z_STREAM_ERROR;
+ state = (gz_statep)file;
+
+ /* check that we're reading */
+ if (state->mode != GZ_READ)
+ return Z_STREAM_ERROR;
+
+ /* free memory and close file */
+ if (state->size) {
+ inflateEnd(&(state->strm));
+ free(state->out);
+ free(state->in);
+ }
+ err = state->err == Z_BUF_ERROR ? Z_BUF_ERROR : Z_OK;
+ gz_error(state, Z_OK, NULL);
+ free(state->path);
+ ret = close(state->fd);
+ free(state);
+ return ret ? Z_ERRNO : err;
+}
diff --git a/third-party/zlib/gzwrite.c b/third-party/zlib/gzwrite.c
new file mode 100644
index 0000000..aa767fb
--- /dev/null
+++ b/third-party/zlib/gzwrite.c
@@ -0,0 +1,577 @@
+/* gzwrite.c -- zlib functions for writing gzip files
+ * Copyright (C) 2004, 2005, 2010, 2011, 2012, 2013 Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+#include "gzguts.h"
+
+/* Local functions */
+local int gz_init OF((gz_statep));
+local int gz_comp OF((gz_statep, int));
+local int gz_zero OF((gz_statep, z_off64_t));
+
+/* Initialize state for writing a gzip file. Mark initialization by setting
+ state->size to non-zero. Return -1 on failure or 0 on success. */
+local int gz_init(state)
+ gz_statep state;
+{
+ int ret;
+ z_streamp strm = &(state->strm);
+
+ /* allocate input buffer */
+ state->in = (unsigned char *)malloc(state->want);
+ if (state->in == NULL) {
+ gz_error(state, Z_MEM_ERROR, "out of memory");
+ return -1;
+ }
+
+ /* only need output buffer and deflate state if compressing */
+ if (!state->direct) {
+ /* allocate output buffer */
+ state->out = (unsigned char *)malloc(state->want);
+ if (state->out == NULL) {
+ free(state->in);
+ gz_error(state, Z_MEM_ERROR, "out of memory");
+ return -1;
+ }
+
+ /* allocate deflate memory, set up for gzip compression */
+ strm->zalloc = Z_NULL;
+ strm->zfree = Z_NULL;
+ strm->opaque = Z_NULL;
+ ret = deflateInit2(strm, state->level, Z_DEFLATED,
+ MAX_WBITS + 16, DEF_MEM_LEVEL, state->strategy);
+ if (ret != Z_OK) {
+ free(state->out);
+ free(state->in);
+ gz_error(state, Z_MEM_ERROR, "out of memory");
+ return -1;
+ }
+ }
+
+ /* mark state as initialized */
+ state->size = state->want;
+
+ /* initialize write buffer if compressing */
+ if (!state->direct) {
+ strm->avail_out = state->size;
+ strm->next_out = state->out;
+ state->x.next = strm->next_out;
+ }
+ return 0;
+}
+
+/* Compress whatever is at avail_in and next_in and write to the output file.
+ Return -1 if there is an error writing to the output file, otherwise 0.
+ flush is assumed to be a valid deflate() flush value. If flush is Z_FINISH,
+ then the deflate() state is reset to start a new gzip stream. If gz->direct
+ is true, then simply write to the output file without compressing, and
+ ignore flush. */
+local int gz_comp(state, flush)
+ gz_statep state;
+ int flush;
+{
+ int ret, got;
+ unsigned have;
+ z_streamp strm = &(state->strm);
+
+ /* allocate memory if this is the first time through */
+ if (state->size == 0 && gz_init(state) == -1)
+ return -1;
+
+ /* write directly if requested */
+ if (state->direct) {
+ got = write(state->fd, strm->next_in, strm->avail_in);
+ if (got < 0 || (unsigned)got != strm->avail_in) {
+ gz_error(state, Z_ERRNO, zstrerror());
+ return -1;
+ }
+ strm->avail_in = 0;
+ return 0;
+ }
+
+ /* run deflate() on provided input until it produces no more output */
+ ret = Z_OK;
+ do {
+ /* write out current buffer contents if full, or if flushing, but if
+ doing Z_FINISH then don't write until we get to Z_STREAM_END */
+ if (strm->avail_out == 0 || (flush != Z_NO_FLUSH &&
+ (flush != Z_FINISH || ret == Z_STREAM_END))) {
+ have = (unsigned)(strm->next_out - state->x.next);
+ if (have && ((got = write(state->fd, state->x.next, have)) < 0 ||
+ (unsigned)got != have)) {
+ gz_error(state, Z_ERRNO, zstrerror());
+ return -1;
+ }
+ if (strm->avail_out == 0) {
+ strm->avail_out = state->size;
+ strm->next_out = state->out;
+ }
+ state->x.next = strm->next_out;
+ }
+
+ /* compress */
+ have = strm->avail_out;
+ ret = deflate(strm, flush);
+ if (ret == Z_STREAM_ERROR) {
+ gz_error(state, Z_STREAM_ERROR,
+ "internal error: deflate stream corrupt");
+ return -1;
+ }
+ have -= strm->avail_out;
+ } while (have);
+
+ /* if that completed a deflate stream, allow another to start */
+ if (flush == Z_FINISH)
+ deflateReset(strm);
+
+ /* all done, no errors */
+ return 0;
+}
+
+/* Compress len zeros to output. Return -1 on error, 0 on success. */
+local int gz_zero(state, len)
+ gz_statep state;
+ z_off64_t len;
+{
+ int first;
+ unsigned n;
+ z_streamp strm = &(state->strm);
+
+ /* consume whatever's left in the input buffer */
+ if (strm->avail_in && gz_comp(state, Z_NO_FLUSH) == -1)
+ return -1;
+
+ /* compress len zeros (len guaranteed > 0) */
+ first = 1;
+ while (len) {
+ n = GT_OFF(state->size) || (z_off64_t)state->size > len ?
+ (unsigned)len : state->size;
+ if (first) {
+ memset(state->in, 0, n);
+ first = 0;
+ }
+ strm->avail_in = n;
+ strm->next_in = state->in;
+ state->x.pos += n;
+ if (gz_comp(state, Z_NO_FLUSH) == -1)
+ return -1;
+ len -= n;
+ }
+ return 0;
+}
+
+/* -- see zlib.h -- */
+int ZEXPORT gzwrite(file, buf, len)
+ gzFile file;
+ voidpc buf;
+ unsigned len;
+{
+ unsigned put = len;
+ gz_statep state;
+ z_streamp strm;
+
+ /* get internal structure */
+ if (file == NULL)
+ return 0;
+ state = (gz_statep)file;
+ strm = &(state->strm);
+
+ /* check that we're writing and that there's no error */
+ if (state->mode != GZ_WRITE || state->err != Z_OK)
+ return 0;
+
+ /* since an int is returned, make sure len fits in one, otherwise return
+ with an error (this avoids the flaw in the interface) */
+ if ((int)len < 0) {
+ gz_error(state, Z_DATA_ERROR, "requested length does not fit in int");
+ return 0;
+ }
+
+ /* if len is zero, avoid unnecessary operations */
+ if (len == 0)
+ return 0;
+
+ /* allocate memory if this is the first time through */
+ if (state->size == 0 && gz_init(state) == -1)
+ return 0;
+
+ /* check for seek request */
+ if (state->seek) {
+ state->seek = 0;
+ if (gz_zero(state, state->skip) == -1)
+ return 0;
+ }
+
+ /* for small len, copy to input buffer, otherwise compress directly */
+ if (len < state->size) {
+ /* copy to input buffer, compress when full */
+ do {
+ unsigned have, copy;
+
+ if (strm->avail_in == 0)
+ strm->next_in = state->in;
+ have = (unsigned)((strm->next_in + strm->avail_in) - state->in);
+ copy = state->size - have;
+ if (copy > len)
+ copy = len;
+ memcpy(state->in + have, buf, copy);
+ strm->avail_in += copy;
+ state->x.pos += copy;
+ buf = (const char *)buf + copy;
+ len -= copy;
+ if (len && gz_comp(state, Z_NO_FLUSH) == -1)
+ return 0;
+ } while (len);
+ }
+ else {
+ /* consume whatever's left in the input buffer */
+ if (strm->avail_in && gz_comp(state, Z_NO_FLUSH) == -1)
+ return 0;
+
+ /* directly compress user buffer to file */
+ strm->avail_in = len;
+ strm->next_in = (z_const Bytef *)buf;
+ state->x.pos += len;
+ if (gz_comp(state, Z_NO_FLUSH) == -1)
+ return 0;
+ }
+
+ /* input was all buffered or compressed (put will fit in int) */
+ return (int)put;
+}
+
+/* -- see zlib.h -- */
+int ZEXPORT gzputc(file, c)
+ gzFile file;
+ int c;
+{
+ unsigned have;
+ unsigned char buf[1];
+ gz_statep state;
+ z_streamp strm;
+
+ /* get internal structure */
+ if (file == NULL)
+ return -1;
+ state = (gz_statep)file;
+ strm = &(state->strm);
+
+ /* check that we're writing and that there's no error */
+ if (state->mode != GZ_WRITE || state->err != Z_OK)
+ return -1;
+
+ /* check for seek request */
+ if (state->seek) {
+ state->seek = 0;
+ if (gz_zero(state, state->skip) == -1)
+ return -1;
+ }
+
+ /* try writing to input buffer for speed (state->size == 0 if buffer not
+ initialized) */
+ if (state->size) {
+ if (strm->avail_in == 0)
+ strm->next_in = state->in;
+ have = (unsigned)((strm->next_in + strm->avail_in) - state->in);
+ if (have < state->size) {
+ state->in[have] = c;
+ strm->avail_in++;
+ state->x.pos++;
+ return c & 0xff;
+ }
+ }
+
+ /* no room in buffer or not initialized, use gz_write() */
+ buf[0] = c;
+ if (gzwrite(file, buf, 1) != 1)
+ return -1;
+ return c & 0xff;
+}
+
+/* -- see zlib.h -- */
+int ZEXPORT gzputs(file, str)
+ gzFile file;
+ const char *str;
+{
+ int ret;
+ unsigned len;
+
+ /* write string */
+ len = (unsigned)strlen(str);
+ ret = gzwrite(file, str, len);
+ return ret == 0 && len != 0 ? -1 : ret;
+}
+
+#if defined(STDC) || defined(Z_HAVE_STDARG_H)
+#include <stdarg.h>
+
+/* -- see zlib.h -- */
+int ZEXPORTVA gzvprintf(gzFile file, const char *format, va_list va)
+{
+ int size, len;
+ gz_statep state;
+ z_streamp strm;
+
+ /* get internal structure */
+ if (file == NULL)
+ return -1;
+ state = (gz_statep)file;
+ strm = &(state->strm);
+
+ /* check that we're writing and that there's no error */
+ if (state->mode != GZ_WRITE || state->err != Z_OK)
+ return 0;
+
+ /* make sure we have some buffer space */
+ if (state->size == 0 && gz_init(state) == -1)
+ return 0;
+
+ /* check for seek request */
+ if (state->seek) {
+ state->seek = 0;
+ if (gz_zero(state, state->skip) == -1)
+ return 0;
+ }
+
+ /* consume whatever's left in the input buffer */
+ if (strm->avail_in && gz_comp(state, Z_NO_FLUSH) == -1)
+ return 0;
+
+ /* do the printf() into the input buffer, put length in len */
+ size = (int)(state->size);
+ state->in[size - 1] = 0;
+#ifdef NO_vsnprintf
+# ifdef HAS_vsprintf_void
+ (void)vsprintf((char *)(state->in), format, va);
+ for (len = 0; len < size; len++)
+ if (state->in[len] == 0) break;
+# else
+ len = vsprintf((char *)(state->in), format, va);
+# endif
+#else
+# ifdef HAS_vsnprintf_void
+ (void)vsnprintf((char *)(state->in), size, format, va);
+ len = strlen((char *)(state->in));
+# else
+ len = vsnprintf((char *)(state->in), size, format, va);
+# endif
+#endif
+
+ /* check that printf() results fit in buffer */
+ if (len <= 0 || len >= (int)size || state->in[size - 1] != 0)
+ return 0;
+
+ /* update buffer and position, defer compression until needed */
+ strm->avail_in = (unsigned)len;
+ strm->next_in = state->in;
+ state->x.pos += len;
+ return len;
+}
+
+int ZEXPORTVA gzprintf(gzFile file, const char *format, ...)
+{
+ va_list va;
+ int ret;
+
+ va_start(va, format);
+ ret = gzvprintf(file, format, va);
+ va_end(va);
+ return ret;
+}
+
+#else /* !STDC && !Z_HAVE_STDARG_H */
+
+/* -- see zlib.h -- */
+int ZEXPORTVA gzprintf (file, format, a1, a2, a3, a4, a5, a6, a7, a8, a9, a10,
+ a11, a12, a13, a14, a15, a16, a17, a18, a19, a20)
+ gzFile file;
+ const char *format;
+ int a1, a2, a3, a4, a5, a6, a7, a8, a9, a10,
+ a11, a12, a13, a14, a15, a16, a17, a18, a19, a20;
+{
+ int size, len;
+ gz_statep state;
+ z_streamp strm;
+
+ /* get internal structure */
+ if (file == NULL)
+ return -1;
+ state = (gz_statep)file;
+ strm = &(state->strm);
+
+ /* check that can really pass pointer in ints */
+ if (sizeof(int) != sizeof(void *))
+ return 0;
+
+ /* check that we're writing and that there's no error */
+ if (state->mode != GZ_WRITE || state->err != Z_OK)
+ return 0;
+
+ /* make sure we have some buffer space */
+ if (state->size == 0 && gz_init(state) == -1)
+ return 0;
+
+ /* check for seek request */
+ if (state->seek) {
+ state->seek = 0;
+ if (gz_zero(state, state->skip) == -1)
+ return 0;
+ }
+
+ /* consume whatever's left in the input buffer */
+ if (strm->avail_in && gz_comp(state, Z_NO_FLUSH) == -1)
+ return 0;
+
+ /* do the printf() into the input buffer, put length in len */
+ size = (int)(state->size);
+ state->in[size - 1] = 0;
+#ifdef NO_snprintf
+# ifdef HAS_sprintf_void
+ sprintf((char *)(state->in), format, a1, a2, a3, a4, a5, a6, a7, a8,
+ a9, a10, a11, a12, a13, a14, a15, a16, a17, a18, a19, a20);
+ for (len = 0; len < size; len++)
+ if (state->in[len] == 0) break;
+# else
+ len = sprintf((char *)(state->in), format, a1, a2, a3, a4, a5, a6, a7, a8,
+ a9, a10, a11, a12, a13, a14, a15, a16, a17, a18, a19, a20);
+# endif
+#else
+# ifdef HAS_snprintf_void
+ snprintf((char *)(state->in), size, format, a1, a2, a3, a4, a5, a6, a7, a8,
+ a9, a10, a11, a12, a13, a14, a15, a16, a17, a18, a19, a20);
+ len = strlen((char *)(state->in));
+# else
+ len = snprintf((char *)(state->in), size, format, a1, a2, a3, a4, a5, a6,
+ a7, a8, a9, a10, a11, a12, a13, a14, a15, a16, a17, a18,
+ a19, a20);
+# endif
+#endif
+
+ /* check that printf() results fit in buffer */
+ if (len <= 0 || len >= (int)size || state->in[size - 1] != 0)
+ return 0;
+
+ /* update buffer and position, defer compression until needed */
+ strm->avail_in = (unsigned)len;
+ strm->next_in = state->in;
+ state->x.pos += len;
+ return len;
+}
+
+#endif
+
+/* -- see zlib.h -- */
+int ZEXPORT gzflush(file, flush)
+ gzFile file;
+ int flush;
+{
+ gz_statep state;
+
+ /* get internal structure */
+ if (file == NULL)
+ return -1;
+ state = (gz_statep)file;
+
+ /* check that we're writing and that there's no error */
+ if (state->mode != GZ_WRITE || state->err != Z_OK)
+ return Z_STREAM_ERROR;
+
+ /* check flush parameter */
+ if (flush < 0 || flush > Z_FINISH)
+ return Z_STREAM_ERROR;
+
+ /* check for seek request */
+ if (state->seek) {
+ state->seek = 0;
+ if (gz_zero(state, state->skip) == -1)
+ return -1;
+ }
+
+ /* compress remaining data with requested flush */
+ gz_comp(state, flush);
+ return state->err;
+}
+
+/* -- see zlib.h -- */
+int ZEXPORT gzsetparams(file, level, strategy)
+ gzFile file;
+ int level;
+ int strategy;
+{
+ gz_statep state;
+ z_streamp strm;
+
+ /* get internal structure */
+ if (file == NULL)
+ return Z_STREAM_ERROR;
+ state = (gz_statep)file;
+ strm = &(state->strm);
+
+ /* check that we're writing and that there's no error */
+ if (state->mode != GZ_WRITE || state->err != Z_OK)
+ return Z_STREAM_ERROR;
+
+ /* if no change is requested, then do nothing */
+ if (level == state->level && strategy == state->strategy)
+ return Z_OK;
+
+ /* check for seek request */
+ if (state->seek) {
+ state->seek = 0;
+ if (gz_zero(state, state->skip) == -1)
+ return -1;
+ }
+
+ /* change compression parameters for subsequent input */
+ if (state->size) {
+ /* flush previous input with previous parameters before changing */
+ if (strm->avail_in && gz_comp(state, Z_PARTIAL_FLUSH) == -1)
+ return state->err;
+ deflateParams(strm, level, strategy);
+ }
+ state->level = level;
+ state->strategy = strategy;
+ return Z_OK;
+}
+
+/* -- see zlib.h -- */
+int ZEXPORT gzclose_w(file)
+ gzFile file;
+{
+ int ret = Z_OK;
+ gz_statep state;
+
+ /* get internal structure */
+ if (file == NULL)
+ return Z_STREAM_ERROR;
+ state = (gz_statep)file;
+
+ /* check that we're writing */
+ if (state->mode != GZ_WRITE)
+ return Z_STREAM_ERROR;
+
+ /* check for seek request */
+ if (state->seek) {
+ state->seek = 0;
+ if (gz_zero(state, state->skip) == -1)
+ ret = state->err;
+ }
+
+ /* flush, free memory, and close file */
+ if (gz_comp(state, Z_FINISH) == -1)
+ ret = state->err;
+ if (state->size) {
+ if (!state->direct) {
+ (void)deflateEnd(&(state->strm));
+ free(state->out);
+ }
+ free(state->in);
+ }
+ gz_error(state, Z_OK, NULL);
+ free(state->path);
+ if (close(state->fd) == -1)
+ ret = Z_ERRNO;
+ free(state);
+ return ret;
+}
diff --git a/third-party/zlib/infback.c b/third-party/zlib/infback.c
new file mode 100644
index 0000000..f3833c2
--- /dev/null
+++ b/third-party/zlib/infback.c
@@ -0,0 +1,640 @@
+/* infback.c -- inflate using a call-back interface
+ * Copyright (C) 1995-2011 Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/*
+ This code is largely copied from inflate.c. Normally either infback.o or
+ inflate.o would be linked into an application--not both. The interface
+ with inffast.c is retained so that optimized assembler-coded versions of
+ inflate_fast() can be used with either inflate.c or infback.c.
+ */
+
+#include "zutil.h"
+#include "inftrees.h"
+#include "inflate.h"
+#include "inffast.h"
+
+/* function prototypes */
+local void fixedtables OF((struct inflate_state FAR *state));
+
+/*
+ strm provides memory allocation functions in zalloc and zfree, or
+ Z_NULL to use the library memory allocation functions.
+
+ windowBits is in the range 8..15, and window is a user-supplied
+ window and output buffer that is 2**windowBits bytes.
+ */
+int ZEXPORT inflateBackInit_(strm, windowBits, window, version, stream_size)
+z_streamp strm;
+int windowBits;
+unsigned char FAR *window;
+const char *version;
+int stream_size;
+{
+ struct inflate_state FAR *state;
+
+ if (version == Z_NULL || version[0] != ZLIB_VERSION[0] ||
+ stream_size != (int)(sizeof(z_stream)))
+ return Z_VERSION_ERROR;
+ if (strm == Z_NULL || window == Z_NULL ||
+ windowBits < 8 || windowBits > 15)
+ return Z_STREAM_ERROR;
+ strm->msg = Z_NULL; /* in case we return an error */
+ if (strm->zalloc == (alloc_func)0) {
+#ifdef Z_SOLO
+ return Z_STREAM_ERROR;
+#else
+ strm->zalloc = zcalloc;
+ strm->opaque = (voidpf)0;
+#endif
+ }
+ if (strm->zfree == (free_func)0)
+#ifdef Z_SOLO
+ return Z_STREAM_ERROR;
+#else
+ strm->zfree = zcfree;
+#endif
+ state = (struct inflate_state FAR *)ZALLOC(strm, 1,
+ sizeof(struct inflate_state));
+ if (state == Z_NULL) return Z_MEM_ERROR;
+ Tracev((stderr, "inflate: allocated\n"));
+ strm->state = (struct internal_state FAR *)state;
+ state->dmax = 32768U;
+ state->wbits = windowBits;
+ state->wsize = 1U << windowBits;
+ state->window = window;
+ state->wnext = 0;
+ state->whave = 0;
+ return Z_OK;
+}
+
+/*
+ Return state with length and distance decoding tables and index sizes set to
+ fixed code decoding. Normally this returns fixed tables from inffixed.h.
+ If BUILDFIXED is defined, then instead this routine builds the tables the
+ first time it's called, and returns those tables the first time and
+ thereafter. This reduces the size of the code by about 2K bytes, in
+ exchange for a little execution time. However, BUILDFIXED should not be
+ used for threaded applications, since the rewriting of the tables and virgin
+ may not be thread-safe.
+ */
+local void fixedtables(state)
+struct inflate_state FAR *state;
+{
+#ifdef BUILDFIXED
+ static int virgin = 1;
+ static code *lenfix, *distfix;
+ static code fixed[544];
+
+ /* build fixed huffman tables if first call (may not be thread safe) */
+ if (virgin) {
+ unsigned sym, bits;
+ static code *next;
+
+ /* literal/length table */
+ sym = 0;
+ while (sym < 144) state->lens[sym++] = 8;
+ while (sym < 256) state->lens[sym++] = 9;
+ while (sym < 280) state->lens[sym++] = 7;
+ while (sym < 288) state->lens[sym++] = 8;
+ next = fixed;
+ lenfix = next;
+ bits = 9;
+ inflate_table(LENS, state->lens, 288, &(next), &(bits), state->work);
+
+ /* distance table */
+ sym = 0;
+ while (sym < 32) state->lens[sym++] = 5;
+ distfix = next;
+ bits = 5;
+ inflate_table(DISTS, state->lens, 32, &(next), &(bits), state->work);
+
+ /* do this just once */
+ virgin = 0;
+ }
+#else /* !BUILDFIXED */
+# include "inffixed.h"
+#endif /* BUILDFIXED */
+ state->lencode = lenfix;
+ state->lenbits = 9;
+ state->distcode = distfix;
+ state->distbits = 5;
+}
+
+/* Macros for inflateBack(): */
+
+/* Load returned state from inflate_fast() */
+#define LOAD() \
+ do { \
+ put = strm->next_out; \
+ left = strm->avail_out; \
+ next = strm->next_in; \
+ have = strm->avail_in; \
+ hold = state->hold; \
+ bits = state->bits; \
+ } while (0)
+
+/* Set state from registers for inflate_fast() */
+#define RESTORE() \
+ do { \
+ strm->next_out = put; \
+ strm->avail_out = left; \
+ strm->next_in = next; \
+ strm->avail_in = have; \
+ state->hold = hold; \
+ state->bits = bits; \
+ } while (0)
+
+/* Clear the input bit accumulator */
+#define INITBITS() \
+ do { \
+ hold = 0; \
+ bits = 0; \
+ } while (0)
+
+/* Assure that some input is available. If input is requested, but denied,
+ then return a Z_BUF_ERROR from inflateBack(). */
+#define PULL() \
+ do { \
+ if (have == 0) { \
+ have = in(in_desc, &next); \
+ if (have == 0) { \
+ next = Z_NULL; \
+ ret = Z_BUF_ERROR; \
+ goto inf_leave; \
+ } \
+ } \
+ } while (0)
+
+/* Get a byte of input into the bit accumulator, or return from inflateBack()
+ with an error if there is no input available. */
+#define PULLBYTE() \
+ do { \
+ PULL(); \
+ have--; \
+ hold += (unsigned long)(*next++) << bits; \
+ bits += 8; \
+ } while (0)
+
+/* Assure that there are at least n bits in the bit accumulator. If there is
+ not enough available input to do that, then return from inflateBack() with
+ an error. */
+#define NEEDBITS(n) \
+ do { \
+ while (bits < (unsigned)(n)) \
+ PULLBYTE(); \
+ } while (0)
+
+/* Return the low n bits of the bit accumulator (n < 16) */
+#define BITS(n) \
+ ((unsigned)hold & ((1U << (n)) - 1))
+
+/* Remove n bits from the bit accumulator */
+#define DROPBITS(n) \
+ do { \
+ hold >>= (n); \
+ bits -= (unsigned)(n); \
+ } while (0)
+
+/* Remove zero to seven bits as needed to go to a byte boundary */
+#define BYTEBITS() \
+ do { \
+ hold >>= bits & 7; \
+ bits -= bits & 7; \
+ } while (0)
+
+/* Assure that some output space is available, by writing out the window
+ if it's full. If the write fails, return from inflateBack() with a
+ Z_BUF_ERROR. */
+#define ROOM() \
+ do { \
+ if (left == 0) { \
+ put = state->window; \
+ left = state->wsize; \
+ state->whave = left; \
+ if (out(out_desc, put, left)) { \
+ ret = Z_BUF_ERROR; \
+ goto inf_leave; \
+ } \
+ } \
+ } while (0)
+
+/*
+ strm provides the memory allocation functions and window buffer on input,
+ and provides information on the unused input on return. For Z_DATA_ERROR
+ returns, strm will also provide an error message.
+
+ in() and out() are the call-back input and output functions. When
+ inflateBack() needs more input, it calls in(). When inflateBack() has
+ filled the window with output, or when it completes with data in the
+ window, it calls out() to write out the data. The application must not
+ change the provided input until in() is called again or inflateBack()
+ returns. The application must not change the window/output buffer until
+ inflateBack() returns.
+
+ in() and out() are called with a descriptor parameter provided in the
+ inflateBack() call. This parameter can be a structure that provides the
+ information required to do the read or write, as well as accumulated
+ information on the input and output such as totals and check values.
+
+ in() should return zero on failure. out() should return non-zero on
+ failure. If either in() or out() fails, than inflateBack() returns a
+ Z_BUF_ERROR. strm->next_in can be checked for Z_NULL to see whether it
+ was in() or out() that caused in the error. Otherwise, inflateBack()
+ returns Z_STREAM_END on success, Z_DATA_ERROR for an deflate format
+ error, or Z_MEM_ERROR if it could not allocate memory for the state.
+ inflateBack() can also return Z_STREAM_ERROR if the input parameters
+ are not correct, i.e. strm is Z_NULL or the state was not initialized.
+ */
+int ZEXPORT inflateBack(strm, in, in_desc, out, out_desc)
+z_streamp strm;
+in_func in;
+void FAR *in_desc;
+out_func out;
+void FAR *out_desc;
+{
+ struct inflate_state FAR *state;
+ z_const unsigned char FAR *next; /* next input */
+ unsigned char FAR *put; /* next output */
+ unsigned have, left; /* available input and output */
+ unsigned long hold; /* bit buffer */
+ unsigned bits; /* bits in bit buffer */
+ unsigned copy; /* number of stored or match bytes to copy */
+ unsigned char FAR *from; /* where to copy match bytes from */
+ code here; /* current decoding table entry */
+ code last; /* parent table entry */
+ unsigned len; /* length to copy for repeats, bits to drop */
+ int ret; /* return code */
+ static const unsigned short order[19] = /* permutation of code lengths */
+ {16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15};
+
+ /* Check that the strm exists and that the state was initialized */
+ if (strm == Z_NULL || strm->state == Z_NULL)
+ return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)strm->state;
+
+ /* Reset the state */
+ strm->msg = Z_NULL;
+ state->mode = TYPE;
+ state->last = 0;
+ state->whave = 0;
+ next = strm->next_in;
+ have = next != Z_NULL ? strm->avail_in : 0;
+ hold = 0;
+ bits = 0;
+ put = state->window;
+ left = state->wsize;
+
+ /* Inflate until end of block marked as last */
+ for (;;)
+ switch (state->mode) {
+ case TYPE:
+ /* determine and dispatch block type */
+ if (state->last) {
+ BYTEBITS();
+ state->mode = DONE;
+ break;
+ }
+ NEEDBITS(3);
+ state->last = BITS(1);
+ DROPBITS(1);
+ switch (BITS(2)) {
+ case 0: /* stored block */
+ Tracev((stderr, "inflate: stored block%s\n",
+ state->last ? " (last)" : ""));
+ state->mode = STORED;
+ break;
+ case 1: /* fixed block */
+ fixedtables(state);
+ Tracev((stderr, "inflate: fixed codes block%s\n",
+ state->last ? " (last)" : ""));
+ state->mode = LEN; /* decode codes */
+ break;
+ case 2: /* dynamic block */
+ Tracev((stderr, "inflate: dynamic codes block%s\n",
+ state->last ? " (last)" : ""));
+ state->mode = TABLE;
+ break;
+ case 3:
+ strm->msg = (char *)"invalid block type";
+ state->mode = BAD;
+ }
+ DROPBITS(2);
+ break;
+
+ case STORED:
+ /* get and verify stored block length */
+ BYTEBITS(); /* go to byte boundary */
+ NEEDBITS(32);
+ if ((hold & 0xffff) != ((hold >> 16) ^ 0xffff)) {
+ strm->msg = (char *)"invalid stored block lengths";
+ state->mode = BAD;
+ break;
+ }
+ state->length = (unsigned)hold & 0xffff;
+ Tracev((stderr, "inflate: stored length %u\n",
+ state->length));
+ INITBITS();
+
+ /* copy stored block from input to output */
+ while (state->length != 0) {
+ copy = state->length;
+ PULL();
+ ROOM();
+ if (copy > have) copy = have;
+ if (copy > left) copy = left;
+ zmemcpy(put, next, copy);
+ have -= copy;
+ next += copy;
+ left -= copy;
+ put += copy;
+ state->length -= copy;
+ }
+ Tracev((stderr, "inflate: stored end\n"));
+ state->mode = TYPE;
+ break;
+
+ case TABLE:
+ /* get dynamic table entries descriptor */
+ NEEDBITS(14);
+ state->nlen = BITS(5) + 257;
+ DROPBITS(5);
+ state->ndist = BITS(5) + 1;
+ DROPBITS(5);
+ state->ncode = BITS(4) + 4;
+ DROPBITS(4);
+#ifndef PKZIP_BUG_WORKAROUND
+ if (state->nlen > 286 || state->ndist > 30) {
+ strm->msg = (char *)"too many length or distance symbols";
+ state->mode = BAD;
+ break;
+ }
+#endif
+ Tracev((stderr, "inflate: table sizes ok\n"));
+
+ /* get code length code lengths (not a typo) */
+ state->have = 0;
+ while (state->have < state->ncode) {
+ NEEDBITS(3);
+ state->lens[order[state->have++]] = (unsigned short)BITS(3);
+ DROPBITS(3);
+ }
+ while (state->have < 19)
+ state->lens[order[state->have++]] = 0;
+ state->next = state->codes;
+ state->lencode = (code const FAR *)(state->next);
+ state->lenbits = 7;
+ ret = inflate_table(CODES, state->lens, 19, &(state->next),
+ &(state->lenbits), state->work);
+ if (ret) {
+ strm->msg = (char *)"invalid code lengths set";
+ state->mode = BAD;
+ break;
+ }
+ Tracev((stderr, "inflate: code lengths ok\n"));
+
+ /* get length and distance code code lengths */
+ state->have = 0;
+ while (state->have < state->nlen + state->ndist) {
+ for (;;) {
+ here = state->lencode[BITS(state->lenbits)];
+ if ((unsigned)(here.bits) <= bits) break;
+ PULLBYTE();
+ }
+ if (here.val < 16) {
+ DROPBITS(here.bits);
+ state->lens[state->have++] = here.val;
+ }
+ else {
+ if (here.val == 16) {
+ NEEDBITS(here.bits + 2);
+ DROPBITS(here.bits);
+ if (state->have == 0) {
+ strm->msg = (char *)"invalid bit length repeat";
+ state->mode = BAD;
+ break;
+ }
+ len = (unsigned)(state->lens[state->have - 1]);
+ copy = 3 + BITS(2);
+ DROPBITS(2);
+ }
+ else if (here.val == 17) {
+ NEEDBITS(here.bits + 3);
+ DROPBITS(here.bits);
+ len = 0;
+ copy = 3 + BITS(3);
+ DROPBITS(3);
+ }
+ else {
+ NEEDBITS(here.bits + 7);
+ DROPBITS(here.bits);
+ len = 0;
+ copy = 11 + BITS(7);
+ DROPBITS(7);
+ }
+ if (state->have + copy > state->nlen + state->ndist) {
+ strm->msg = (char *)"invalid bit length repeat";
+ state->mode = BAD;
+ break;
+ }
+ while (copy--)
+ state->lens[state->have++] = (unsigned short)len;
+ }
+ }
+
+ /* handle error breaks in while */
+ if (state->mode == BAD) break;
+
+ /* check for end-of-block code (better have one) */
+ if (state->lens[256] == 0) {
+ strm->msg = (char *)"invalid code -- missing end-of-block";
+ state->mode = BAD;
+ break;
+ }
+
+ /* build code tables -- note: do not change the lenbits or distbits
+ values here (9 and 6) without reading the comments in inftrees.h
+ concerning the ENOUGH constants, which depend on those values */
+ state->next = state->codes;
+ state->lencode = (code const FAR *)(state->next);
+ state->lenbits = 9;
+ ret = inflate_table(LENS, state->lens, state->nlen, &(state->next),
+ &(state->lenbits), state->work);
+ if (ret) {
+ strm->msg = (char *)"invalid literal/lengths set";
+ state->mode = BAD;
+ break;
+ }
+ state->distcode = (code const FAR *)(state->next);
+ state->distbits = 6;
+ ret = inflate_table(DISTS, state->lens + state->nlen, state->ndist,
+ &(state->next), &(state->distbits), state->work);
+ if (ret) {
+ strm->msg = (char *)"invalid distances set";
+ state->mode = BAD;
+ break;
+ }
+ Tracev((stderr, "inflate: codes ok\n"));
+ state->mode = LEN;
+
+ case LEN:
+ /* use inflate_fast() if we have enough input and output */
+ if (have >= 6 && left >= 258) {
+ RESTORE();
+ if (state->whave < state->wsize)
+ state->whave = state->wsize - left;
+ inflate_fast(strm, state->wsize);
+ LOAD();
+ break;
+ }
+
+ /* get a literal, length, or end-of-block code */
+ for (;;) {
+ here = state->lencode[BITS(state->lenbits)];
+ if ((unsigned)(here.bits) <= bits) break;
+ PULLBYTE();
+ }
+ if (here.op && (here.op & 0xf0) == 0) {
+ last = here;
+ for (;;) {
+ here = state->lencode[last.val +
+ (BITS(last.bits + last.op) >> last.bits)];
+ if ((unsigned)(last.bits + here.bits) <= bits) break;
+ PULLBYTE();
+ }
+ DROPBITS(last.bits);
+ }
+ DROPBITS(here.bits);
+ state->length = (unsigned)here.val;
+
+ /* process literal */
+ if (here.op == 0) {
+ Tracevv((stderr, here.val >= 0x20 && here.val < 0x7f ?
+ "inflate: literal '%c'\n" :
+ "inflate: literal 0x%02x\n", here.val));
+ ROOM();
+ *put++ = (unsigned char)(state->length);
+ left--;
+ state->mode = LEN;
+ break;
+ }
+
+ /* process end of block */
+ if (here.op & 32) {
+ Tracevv((stderr, "inflate: end of block\n"));
+ state->mode = TYPE;
+ break;
+ }
+
+ /* invalid code */
+ if (here.op & 64) {
+ strm->msg = (char *)"invalid literal/length code";
+ state->mode = BAD;
+ break;
+ }
+
+ /* length code -- get extra bits, if any */
+ state->extra = (unsigned)(here.op) & 15;
+ if (state->extra != 0) {
+ NEEDBITS(state->extra);
+ state->length += BITS(state->extra);
+ DROPBITS(state->extra);
+ }
+ Tracevv((stderr, "inflate: length %u\n", state->length));
+
+ /* get distance code */
+ for (;;) {
+ here = state->distcode[BITS(state->distbits)];
+ if ((unsigned)(here.bits) <= bits) break;
+ PULLBYTE();
+ }
+ if ((here.op & 0xf0) == 0) {
+ last = here;
+ for (;;) {
+ here = state->distcode[last.val +
+ (BITS(last.bits + last.op) >> last.bits)];
+ if ((unsigned)(last.bits + here.bits) <= bits) break;
+ PULLBYTE();
+ }
+ DROPBITS(last.bits);
+ }
+ DROPBITS(here.bits);
+ if (here.op & 64) {
+ strm->msg = (char *)"invalid distance code";
+ state->mode = BAD;
+ break;
+ }
+ state->offset = (unsigned)here.val;
+
+ /* get distance extra bits, if any */
+ state->extra = (unsigned)(here.op) & 15;
+ if (state->extra != 0) {
+ NEEDBITS(state->extra);
+ state->offset += BITS(state->extra);
+ DROPBITS(state->extra);
+ }
+ if (state->offset > state->wsize - (state->whave < state->wsize ?
+ left : 0)) {
+ strm->msg = (char *)"invalid distance too far back";
+ state->mode = BAD;
+ break;
+ }
+ Tracevv((stderr, "inflate: distance %u\n", state->offset));
+
+ /* copy match from window to output */
+ do {
+ ROOM();
+ copy = state->wsize - state->offset;
+ if (copy < left) {
+ from = put + copy;
+ copy = left - copy;
+ }
+ else {
+ from = put - state->offset;
+ copy = left;
+ }
+ if (copy > state->length) copy = state->length;
+ state->length -= copy;
+ left -= copy;
+ do {
+ *put++ = *from++;
+ } while (--copy);
+ } while (state->length != 0);
+ break;
+
+ case DONE:
+ /* inflate stream terminated properly -- write leftover output */
+ ret = Z_STREAM_END;
+ if (left < state->wsize) {
+ if (out(out_desc, state->window, state->wsize - left))
+ ret = Z_BUF_ERROR;
+ }
+ goto inf_leave;
+
+ case BAD:
+ ret = Z_DATA_ERROR;
+ goto inf_leave;
+
+ default: /* can't happen, but makes compilers happy */
+ ret = Z_STREAM_ERROR;
+ goto inf_leave;
+ }
+
+ /* Return unused input */
+ inf_leave:
+ strm->next_in = next;
+ strm->avail_in = have;
+ return ret;
+}
+
+int ZEXPORT inflateBackEnd(strm)
+z_streamp strm;
+{
+ if (strm == Z_NULL || strm->state == Z_NULL || strm->zfree == (free_func)0)
+ return Z_STREAM_ERROR;
+ ZFREE(strm, strm->state);
+ strm->state = Z_NULL;
+ Tracev((stderr, "inflate: end\n"));
+ return Z_OK;
+}
diff --git a/third-party/zlib/inffast.c b/third-party/zlib/inffast.c
new file mode 100644
index 0000000..bda59ce
--- /dev/null
+++ b/third-party/zlib/inffast.c
@@ -0,0 +1,340 @@
+/* inffast.c -- fast decoding
+ * Copyright (C) 1995-2008, 2010, 2013 Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+#include "zutil.h"
+#include "inftrees.h"
+#include "inflate.h"
+#include "inffast.h"
+
+#ifndef ASMINF
+
+/* Allow machine dependent optimization for post-increment or pre-increment.
+ Based on testing to date,
+ Pre-increment preferred for:
+ - PowerPC G3 (Adler)
+ - MIPS R5000 (Randers-Pehrson)
+ Post-increment preferred for:
+ - none
+ No measurable difference:
+ - Pentium III (Anderson)
+ - M68060 (Nikl)
+ */
+#ifdef POSTINC
+# define OFF 0
+# define PUP(a) *(a)++
+#else
+# define OFF 1
+# define PUP(a) *++(a)
+#endif
+
+/*
+ Decode literal, length, and distance codes and write out the resulting
+ literal and match bytes until either not enough input or output is
+ available, an end-of-block is encountered, or a data error is encountered.
+ When large enough input and output buffers are supplied to inflate(), for
+ example, a 16K input buffer and a 64K output buffer, more than 95% of the
+ inflate execution time is spent in this routine.
+
+ Entry assumptions:
+
+ state->mode == LEN
+ strm->avail_in >= 6
+ strm->avail_out >= 258
+ start >= strm->avail_out
+ state->bits < 8
+
+ On return, state->mode is one of:
+
+ LEN -- ran out of enough output space or enough available input
+ TYPE -- reached end of block code, inflate() to interpret next block
+ BAD -- error in block data
+
+ Notes:
+
+ - The maximum input bits used by a length/distance pair is 15 bits for the
+ length code, 5 bits for the length extra, 15 bits for the distance code,
+ and 13 bits for the distance extra. This totals 48 bits, or six bytes.
+ Therefore if strm->avail_in >= 6, then there is enough input to avoid
+ checking for available input while decoding.
+
+ - The maximum bytes that a single length/distance pair can output is 258
+ bytes, which is the maximum length that can be coded. inflate_fast()
+ requires strm->avail_out >= 258 for each loop to avoid checking for
+ output space.
+ */
+void ZLIB_INTERNAL inflate_fast(strm, start)
+z_streamp strm;
+unsigned start; /* inflate()'s starting value for strm->avail_out */
+{
+ struct inflate_state FAR *state;
+ z_const unsigned char FAR *in; /* local strm->next_in */
+ z_const unsigned char FAR *last; /* have enough input while in < last */
+ unsigned char FAR *out; /* local strm->next_out */
+ unsigned char FAR *beg; /* inflate()'s initial strm->next_out */
+ unsigned char FAR *end; /* while out < end, enough space available */
+#ifdef INFLATE_STRICT
+ unsigned dmax; /* maximum distance from zlib header */
+#endif
+ unsigned wsize; /* window size or zero if not using window */
+ unsigned whave; /* valid bytes in the window */
+ unsigned wnext; /* window write index */
+ unsigned char FAR *window; /* allocated sliding window, if wsize != 0 */
+ unsigned long hold; /* local strm->hold */
+ unsigned bits; /* local strm->bits */
+ code const FAR *lcode; /* local strm->lencode */
+ code const FAR *dcode; /* local strm->distcode */
+ unsigned lmask; /* mask for first level of length codes */
+ unsigned dmask; /* mask for first level of distance codes */
+ code here; /* retrieved table entry */
+ unsigned op; /* code bits, operation, extra bits, or */
+ /* window position, window bytes to copy */
+ unsigned len; /* match length, unused bytes */
+ unsigned dist; /* match distance */
+ unsigned char FAR *from; /* where to copy match from */
+
+ /* copy state to local variables */
+ state = (struct inflate_state FAR *)strm->state;
+ in = strm->next_in - OFF;
+ last = in + (strm->avail_in - 5);
+ out = strm->next_out - OFF;
+ beg = out - (start - strm->avail_out);
+ end = out + (strm->avail_out - 257);
+#ifdef INFLATE_STRICT
+ dmax = state->dmax;
+#endif
+ wsize = state->wsize;
+ whave = state->whave;
+ wnext = state->wnext;
+ window = state->window;
+ hold = state->hold;
+ bits = state->bits;
+ lcode = state->lencode;
+ dcode = state->distcode;
+ lmask = (1U << state->lenbits) - 1;
+ dmask = (1U << state->distbits) - 1;
+
+ /* decode literals and length/distances until end-of-block or not enough
+ input data or output space */
+ do {
+ if (bits < 15) {
+ hold += (unsigned long)(PUP(in)) << bits;
+ bits += 8;
+ hold += (unsigned long)(PUP(in)) << bits;
+ bits += 8;
+ }
+ here = lcode[hold & lmask];
+ dolen:
+ op = (unsigned)(here.bits);
+ hold >>= op;
+ bits -= op;
+ op = (unsigned)(here.op);
+ if (op == 0) { /* literal */
+ Tracevv((stderr, here.val >= 0x20 && here.val < 0x7f ?
+ "inflate: literal '%c'\n" :
+ "inflate: literal 0x%02x\n", here.val));
+ PUP(out) = (unsigned char)(here.val);
+ }
+ else if (op & 16) { /* length base */
+ len = (unsigned)(here.val);
+ op &= 15; /* number of extra bits */
+ if (op) {
+ if (bits < op) {
+ hold += (unsigned long)(PUP(in)) << bits;
+ bits += 8;
+ }
+ len += (unsigned)hold & ((1U << op) - 1);
+ hold >>= op;
+ bits -= op;
+ }
+ Tracevv((stderr, "inflate: length %u\n", len));
+ if (bits < 15) {
+ hold += (unsigned long)(PUP(in)) << bits;
+ bits += 8;
+ hold += (unsigned long)(PUP(in)) << bits;
+ bits += 8;
+ }
+ here = dcode[hold & dmask];
+ dodist:
+ op = (unsigned)(here.bits);
+ hold >>= op;
+ bits -= op;
+ op = (unsigned)(here.op);
+ if (op & 16) { /* distance base */
+ dist = (unsigned)(here.val);
+ op &= 15; /* number of extra bits */
+ if (bits < op) {
+ hold += (unsigned long)(PUP(in)) << bits;
+ bits += 8;
+ if (bits < op) {
+ hold += (unsigned long)(PUP(in)) << bits;
+ bits += 8;
+ }
+ }
+ dist += (unsigned)hold & ((1U << op) - 1);
+#ifdef INFLATE_STRICT
+ if (dist > dmax) {
+ strm->msg = (char *)"invalid distance too far back";
+ state->mode = BAD;
+ break;
+ }
+#endif
+ hold >>= op;
+ bits -= op;
+ Tracevv((stderr, "inflate: distance %u\n", dist));
+ op = (unsigned)(out - beg); /* max distance in output */
+ if (dist > op) { /* see if copy from window */
+ op = dist - op; /* distance back in window */
+ if (op > whave) {
+ if (state->sane) {
+ strm->msg =
+ (char *)"invalid distance too far back";
+ state->mode = BAD;
+ break;
+ }
+#ifdef INFLATE_ALLOW_INVALID_DISTANCE_TOOFAR_ARRR
+ if (len <= op - whave) {
+ do {
+ PUP(out) = 0;
+ } while (--len);
+ continue;
+ }
+ len -= op - whave;
+ do {
+ PUP(out) = 0;
+ } while (--op > whave);
+ if (op == 0) {
+ from = out - dist;
+ do {
+ PUP(out) = PUP(from);
+ } while (--len);
+ continue;
+ }
+#endif
+ }
+ from = window - OFF;
+ if (wnext == 0) { /* very common case */
+ from += wsize - op;
+ if (op < len) { /* some from window */
+ len -= op;
+ do {
+ PUP(out) = PUP(from);
+ } while (--op);
+ from = out - dist; /* rest from output */
+ }
+ }
+ else if (wnext < op) { /* wrap around window */
+ from += wsize + wnext - op;
+ op -= wnext;
+ if (op < len) { /* some from end of window */
+ len -= op;
+ do {
+ PUP(out) = PUP(from);
+ } while (--op);
+ from = window - OFF;
+ if (wnext < len) { /* some from start of window */
+ op = wnext;
+ len -= op;
+ do {
+ PUP(out) = PUP(from);
+ } while (--op);
+ from = out - dist; /* rest from output */
+ }
+ }
+ }
+ else { /* contiguous in window */
+ from += wnext - op;
+ if (op < len) { /* some from window */
+ len -= op;
+ do {
+ PUP(out) = PUP(from);
+ } while (--op);
+ from = out - dist; /* rest from output */
+ }
+ }
+ while (len > 2) {
+ PUP(out) = PUP(from);
+ PUP(out) = PUP(from);
+ PUP(out) = PUP(from);
+ len -= 3;
+ }
+ if (len) {
+ PUP(out) = PUP(from);
+ if (len > 1)
+ PUP(out) = PUP(from);
+ }
+ }
+ else {
+ from = out - dist; /* copy direct from output */
+ do { /* minimum length is three */
+ PUP(out) = PUP(from);
+ PUP(out) = PUP(from);
+ PUP(out) = PUP(from);
+ len -= 3;
+ } while (len > 2);
+ if (len) {
+ PUP(out) = PUP(from);
+ if (len > 1)
+ PUP(out) = PUP(from);
+ }
+ }
+ }
+ else if ((op & 64) == 0) { /* 2nd level distance code */
+ here = dcode[here.val + (hold & ((1U << op) - 1))];
+ goto dodist;
+ }
+ else {
+ strm->msg = (char *)"invalid distance code";
+ state->mode = BAD;
+ break;
+ }
+ }
+ else if ((op & 64) == 0) { /* 2nd level length code */
+ here = lcode[here.val + (hold & ((1U << op) - 1))];
+ goto dolen;
+ }
+ else if (op & 32) { /* end-of-block */
+ Tracevv((stderr, "inflate: end of block\n"));
+ state->mode = TYPE;
+ break;
+ }
+ else {
+ strm->msg = (char *)"invalid literal/length code";
+ state->mode = BAD;
+ break;
+ }
+ } while (in < last && out < end);
+
+ /* return unused bytes (on entry, bits < 8, so in won't go too far back) */
+ len = bits >> 3;
+ in -= len;
+ bits -= len << 3;
+ hold &= (1U << bits) - 1;
+
+ /* update state and return */
+ strm->next_in = in + OFF;
+ strm->next_out = out + OFF;
+ strm->avail_in = (unsigned)(in < last ? 5 + (last - in) : 5 - (in - last));
+ strm->avail_out = (unsigned)(out < end ?
+ 257 + (end - out) : 257 - (out - end));
+ state->hold = hold;
+ state->bits = bits;
+ return;
+}
+
+/*
+ inflate_fast() speedups that turned out slower (on a PowerPC G3 750CXe):
+ - Using bit fields for code structure
+ - Different op definition to avoid & for extra bits (do & for table bits)
+ - Three separate decoding do-loops for direct, window, and wnext == 0
+ - Special case for distance > 1 copies to do overlapped load and store copy
+ - Explicit branch predictions (based on measured branch probabilities)
+ - Deferring match copy and interspersed it with decoding subsequent codes
+ - Swapping literal/length else
+ - Swapping window/direct else
+ - Larger unrolled copy loops (three is about right)
+ - Moving len -= 3 statement into middle of loop
+ */
+
+#endif /* !ASMINF */
diff --git a/third-party/zlib/inffast.h b/third-party/zlib/inffast.h
new file mode 100644
index 0000000..e5c1aa4
--- /dev/null
+++ b/third-party/zlib/inffast.h
@@ -0,0 +1,11 @@
+/* inffast.h -- header to use inffast.c
+ * Copyright (C) 1995-2003, 2010 Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* WARNING: this file should *not* be used by applications. It is
+ part of the implementation of the compression library and is
+ subject to change. Applications should only use zlib.h.
+ */
+
+void ZLIB_INTERNAL inflate_fast OF((z_streamp strm, unsigned start));
diff --git a/third-party/zlib/inffixed.h b/third-party/zlib/inffixed.h
new file mode 100644
index 0000000..d628327
--- /dev/null
+++ b/third-party/zlib/inffixed.h
@@ -0,0 +1,94 @@
+ /* inffixed.h -- table for decoding fixed codes
+ * Generated automatically by makefixed().
+ */
+
+ /* WARNING: this file should *not* be used by applications.
+ It is part of the implementation of this library and is
+ subject to change. Applications should only use zlib.h.
+ */
+
+ static const code lenfix[512] = {
+ {96,7,0},{0,8,80},{0,8,16},{20,8,115},{18,7,31},{0,8,112},{0,8,48},
+ {0,9,192},{16,7,10},{0,8,96},{0,8,32},{0,9,160},{0,8,0},{0,8,128},
+ {0,8,64},{0,9,224},{16,7,6},{0,8,88},{0,8,24},{0,9,144},{19,7,59},
+ {0,8,120},{0,8,56},{0,9,208},{17,7,17},{0,8,104},{0,8,40},{0,9,176},
+ {0,8,8},{0,8,136},{0,8,72},{0,9,240},{16,7,4},{0,8,84},{0,8,20},
+ {21,8,227},{19,7,43},{0,8,116},{0,8,52},{0,9,200},{17,7,13},{0,8,100},
+ {0,8,36},{0,9,168},{0,8,4},{0,8,132},{0,8,68},{0,9,232},{16,7,8},
+ {0,8,92},{0,8,28},{0,9,152},{20,7,83},{0,8,124},{0,8,60},{0,9,216},
+ {18,7,23},{0,8,108},{0,8,44},{0,9,184},{0,8,12},{0,8,140},{0,8,76},
+ {0,9,248},{16,7,3},{0,8,82},{0,8,18},{21,8,163},{19,7,35},{0,8,114},
+ {0,8,50},{0,9,196},{17,7,11},{0,8,98},{0,8,34},{0,9,164},{0,8,2},
+ {0,8,130},{0,8,66},{0,9,228},{16,7,7},{0,8,90},{0,8,26},{0,9,148},
+ {20,7,67},{0,8,122},{0,8,58},{0,9,212},{18,7,19},{0,8,106},{0,8,42},
+ {0,9,180},{0,8,10},{0,8,138},{0,8,74},{0,9,244},{16,7,5},{0,8,86},
+ {0,8,22},{64,8,0},{19,7,51},{0,8,118},{0,8,54},{0,9,204},{17,7,15},
+ {0,8,102},{0,8,38},{0,9,172},{0,8,6},{0,8,134},{0,8,70},{0,9,236},
+ {16,7,9},{0,8,94},{0,8,30},{0,9,156},{20,7,99},{0,8,126},{0,8,62},
+ {0,9,220},{18,7,27},{0,8,110},{0,8,46},{0,9,188},{0,8,14},{0,8,142},
+ {0,8,78},{0,9,252},{96,7,0},{0,8,81},{0,8,17},{21,8,131},{18,7,31},
+ {0,8,113},{0,8,49},{0,9,194},{16,7,10},{0,8,97},{0,8,33},{0,9,162},
+ {0,8,1},{0,8,129},{0,8,65},{0,9,226},{16,7,6},{0,8,89},{0,8,25},
+ {0,9,146},{19,7,59},{0,8,121},{0,8,57},{0,9,210},{17,7,17},{0,8,105},
+ {0,8,41},{0,9,178},{0,8,9},{0,8,137},{0,8,73},{0,9,242},{16,7,4},
+ {0,8,85},{0,8,21},{16,8,258},{19,7,43},{0,8,117},{0,8,53},{0,9,202},
+ {17,7,13},{0,8,101},{0,8,37},{0,9,170},{0,8,5},{0,8,133},{0,8,69},
+ {0,9,234},{16,7,8},{0,8,93},{0,8,29},{0,9,154},{20,7,83},{0,8,125},
+ {0,8,61},{0,9,218},{18,7,23},{0,8,109},{0,8,45},{0,9,186},{0,8,13},
+ {0,8,141},{0,8,77},{0,9,250},{16,7,3},{0,8,83},{0,8,19},{21,8,195},
+ {19,7,35},{0,8,115},{0,8,51},{0,9,198},{17,7,11},{0,8,99},{0,8,35},
+ {0,9,166},{0,8,3},{0,8,131},{0,8,67},{0,9,230},{16,7,7},{0,8,91},
+ {0,8,27},{0,9,150},{20,7,67},{0,8,123},{0,8,59},{0,9,214},{18,7,19},
+ {0,8,107},{0,8,43},{0,9,182},{0,8,11},{0,8,139},{0,8,75},{0,9,246},
+ {16,7,5},{0,8,87},{0,8,23},{64,8,0},{19,7,51},{0,8,119},{0,8,55},
+ {0,9,206},{17,7,15},{0,8,103},{0,8,39},{0,9,174},{0,8,7},{0,8,135},
+ {0,8,71},{0,9,238},{16,7,9},{0,8,95},{0,8,31},{0,9,158},{20,7,99},
+ {0,8,127},{0,8,63},{0,9,222},{18,7,27},{0,8,111},{0,8,47},{0,9,190},
+ {0,8,15},{0,8,143},{0,8,79},{0,9,254},{96,7,0},{0,8,80},{0,8,16},
+ {20,8,115},{18,7,31},{0,8,112},{0,8,48},{0,9,193},{16,7,10},{0,8,96},
+ {0,8,32},{0,9,161},{0,8,0},{0,8,128},{0,8,64},{0,9,225},{16,7,6},
+ {0,8,88},{0,8,24},{0,9,145},{19,7,59},{0,8,120},{0,8,56},{0,9,209},
+ {17,7,17},{0,8,104},{0,8,40},{0,9,177},{0,8,8},{0,8,136},{0,8,72},
+ {0,9,241},{16,7,4},{0,8,84},{0,8,20},{21,8,227},{19,7,43},{0,8,116},
+ {0,8,52},{0,9,201},{17,7,13},{0,8,100},{0,8,36},{0,9,169},{0,8,4},
+ {0,8,132},{0,8,68},{0,9,233},{16,7,8},{0,8,92},{0,8,28},{0,9,153},
+ {20,7,83},{0,8,124},{0,8,60},{0,9,217},{18,7,23},{0,8,108},{0,8,44},
+ {0,9,185},{0,8,12},{0,8,140},{0,8,76},{0,9,249},{16,7,3},{0,8,82},
+ {0,8,18},{21,8,163},{19,7,35},{0,8,114},{0,8,50},{0,9,197},{17,7,11},
+ {0,8,98},{0,8,34},{0,9,165},{0,8,2},{0,8,130},{0,8,66},{0,9,229},
+ {16,7,7},{0,8,90},{0,8,26},{0,9,149},{20,7,67},{0,8,122},{0,8,58},
+ {0,9,213},{18,7,19},{0,8,106},{0,8,42},{0,9,181},{0,8,10},{0,8,138},
+ {0,8,74},{0,9,245},{16,7,5},{0,8,86},{0,8,22},{64,8,0},{19,7,51},
+ {0,8,118},{0,8,54},{0,9,205},{17,7,15},{0,8,102},{0,8,38},{0,9,173},
+ {0,8,6},{0,8,134},{0,8,70},{0,9,237},{16,7,9},{0,8,94},{0,8,30},
+ {0,9,157},{20,7,99},{0,8,126},{0,8,62},{0,9,221},{18,7,27},{0,8,110},
+ {0,8,46},{0,9,189},{0,8,14},{0,8,142},{0,8,78},{0,9,253},{96,7,0},
+ {0,8,81},{0,8,17},{21,8,131},{18,7,31},{0,8,113},{0,8,49},{0,9,195},
+ {16,7,10},{0,8,97},{0,8,33},{0,9,163},{0,8,1},{0,8,129},{0,8,65},
+ {0,9,227},{16,7,6},{0,8,89},{0,8,25},{0,9,147},{19,7,59},{0,8,121},
+ {0,8,57},{0,9,211},{17,7,17},{0,8,105},{0,8,41},{0,9,179},{0,8,9},
+ {0,8,137},{0,8,73},{0,9,243},{16,7,4},{0,8,85},{0,8,21},{16,8,258},
+ {19,7,43},{0,8,117},{0,8,53},{0,9,203},{17,7,13},{0,8,101},{0,8,37},
+ {0,9,171},{0,8,5},{0,8,133},{0,8,69},{0,9,235},{16,7,8},{0,8,93},
+ {0,8,29},{0,9,155},{20,7,83},{0,8,125},{0,8,61},{0,9,219},{18,7,23},
+ {0,8,109},{0,8,45},{0,9,187},{0,8,13},{0,8,141},{0,8,77},{0,9,251},
+ {16,7,3},{0,8,83},{0,8,19},{21,8,195},{19,7,35},{0,8,115},{0,8,51},
+ {0,9,199},{17,7,11},{0,8,99},{0,8,35},{0,9,167},{0,8,3},{0,8,131},
+ {0,8,67},{0,9,231},{16,7,7},{0,8,91},{0,8,27},{0,9,151},{20,7,67},
+ {0,8,123},{0,8,59},{0,9,215},{18,7,19},{0,8,107},{0,8,43},{0,9,183},
+ {0,8,11},{0,8,139},{0,8,75},{0,9,247},{16,7,5},{0,8,87},{0,8,23},
+ {64,8,0},{19,7,51},{0,8,119},{0,8,55},{0,9,207},{17,7,15},{0,8,103},
+ {0,8,39},{0,9,175},{0,8,7},{0,8,135},{0,8,71},{0,9,239},{16,7,9},
+ {0,8,95},{0,8,31},{0,9,159},{20,7,99},{0,8,127},{0,8,63},{0,9,223},
+ {18,7,27},{0,8,111},{0,8,47},{0,9,191},{0,8,15},{0,8,143},{0,8,79},
+ {0,9,255}
+ };
+
+ static const code distfix[32] = {
+ {16,5,1},{23,5,257},{19,5,17},{27,5,4097},{17,5,5},{25,5,1025},
+ {21,5,65},{29,5,16385},{16,5,3},{24,5,513},{20,5,33},{28,5,8193},
+ {18,5,9},{26,5,2049},{22,5,129},{64,5,0},{16,5,2},{23,5,385},
+ {19,5,25},{27,5,6145},{17,5,7},{25,5,1537},{21,5,97},{29,5,24577},
+ {16,5,4},{24,5,769},{20,5,49},{28,5,12289},{18,5,13},{26,5,3073},
+ {22,5,193},{64,5,0}
+ };
diff --git a/third-party/zlib/inflate.c b/third-party/zlib/inflate.c
new file mode 100644
index 0000000..870f89b
--- /dev/null
+++ b/third-party/zlib/inflate.c
@@ -0,0 +1,1512 @@
+/* inflate.c -- zlib decompression
+ * Copyright (C) 1995-2012 Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/*
+ * Change history:
+ *
+ * 1.2.beta0 24 Nov 2002
+ * - First version -- complete rewrite of inflate to simplify code, avoid
+ * creation of window when not needed, minimize use of window when it is
+ * needed, make inffast.c even faster, implement gzip decoding, and to
+ * improve code readability and style over the previous zlib inflate code
+ *
+ * 1.2.beta1 25 Nov 2002
+ * - Use pointers for available input and output checking in inffast.c
+ * - Remove input and output counters in inffast.c
+ * - Change inffast.c entry and loop from avail_in >= 7 to >= 6
+ * - Remove unnecessary second byte pull from length extra in inffast.c
+ * - Unroll direct copy to three copies per loop in inffast.c
+ *
+ * 1.2.beta2 4 Dec 2002
+ * - Change external routine names to reduce potential conflicts
+ * - Correct filename to inffixed.h for fixed tables in inflate.c
+ * - Make hbuf[] unsigned char to match parameter type in inflate.c
+ * - Change strm->next_out[-state->offset] to *(strm->next_out - state->offset)
+ * to avoid negation problem on Alphas (64 bit) in inflate.c
+ *
+ * 1.2.beta3 22 Dec 2002
+ * - Add comments on state->bits assertion in inffast.c
+ * - Add comments on op field in inftrees.h
+ * - Fix bug in reuse of allocated window after inflateReset()
+ * - Remove bit fields--back to byte structure for speed
+ * - Remove distance extra == 0 check in inflate_fast()--only helps for lengths
+ * - Change post-increments to pre-increments in inflate_fast(), PPC biased?
+ * - Add compile time option, POSTINC, to use post-increments instead (Intel?)
+ * - Make MATCH copy in inflate() much faster for when inflate_fast() not used
+ * - Use local copies of stream next and avail values, as well as local bit
+ * buffer and bit count in inflate()--for speed when inflate_fast() not used
+ *
+ * 1.2.beta4 1 Jan 2003
+ * - Split ptr - 257 statements in inflate_table() to avoid compiler warnings
+ * - Move a comment on output buffer sizes from inffast.c to inflate.c
+ * - Add comments in inffast.c to introduce the inflate_fast() routine
+ * - Rearrange window copies in inflate_fast() for speed and simplification
+ * - Unroll last copy for window match in inflate_fast()
+ * - Use local copies of window variables in inflate_fast() for speed
+ * - Pull out common wnext == 0 case for speed in inflate_fast()
+ * - Make op and len in inflate_fast() unsigned for consistency
+ * - Add FAR to lcode and dcode declarations in inflate_fast()
+ * - Simplified bad distance check in inflate_fast()
+ * - Added inflateBackInit(), inflateBack(), and inflateBackEnd() in new
+ * source file infback.c to provide a call-back interface to inflate for
+ * programs like gzip and unzip -- uses window as output buffer to avoid
+ * window copying
+ *
+ * 1.2.beta5 1 Jan 2003
+ * - Improved inflateBack() interface to allow the caller to provide initial
+ * input in strm.
+ * - Fixed stored blocks bug in inflateBack()
+ *
+ * 1.2.beta6 4 Jan 2003
+ * - Added comments in inffast.c on effectiveness of POSTINC
+ * - Typecasting all around to reduce compiler warnings
+ * - Changed loops from while (1) or do {} while (1) to for (;;), again to
+ * make compilers happy
+ * - Changed type of window in inflateBackInit() to unsigned char *
+ *
+ * 1.2.beta7 27 Jan 2003
+ * - Changed many types to unsigned or unsigned short to avoid warnings
+ * - Added inflateCopy() function
+ *
+ * 1.2.0 9 Mar 2003
+ * - Changed inflateBack() interface to provide separate opaque descriptors
+ * for the in() and out() functions
+ * - Changed inflateBack() argument and in_func typedef to swap the length
+ * and buffer address return values for the input function
+ * - Check next_in and next_out for Z_NULL on entry to inflate()
+ *
+ * The history for versions after 1.2.0 are in ChangeLog in zlib distribution.
+ */
+
+#include "zutil.h"
+#include "inftrees.h"
+#include "inflate.h"
+#include "inffast.h"
+
+#ifdef MAKEFIXED
+# ifndef BUILDFIXED
+# define BUILDFIXED
+# endif
+#endif
+
+/* function prototypes */
+local void fixedtables OF((struct inflate_state FAR *state));
+local int updatewindow OF((z_streamp strm, const unsigned char FAR *end,
+ unsigned copy));
+#ifdef BUILDFIXED
+ void makefixed OF((void));
+#endif
+local unsigned syncsearch OF((unsigned FAR *have, const unsigned char FAR *buf,
+ unsigned len));
+
+int ZEXPORT inflateResetKeep(strm)
+z_streamp strm;
+{
+ struct inflate_state FAR *state;
+
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)strm->state;
+ strm->total_in = strm->total_out = state->total = 0;
+ strm->msg = Z_NULL;
+ if (state->wrap) /* to support ill-conceived Java test suite */
+ strm->adler = state->wrap & 1;
+ state->mode = HEAD;
+ state->last = 0;
+ state->havedict = 0;
+ state->dmax = 32768U;
+ state->head = Z_NULL;
+ state->hold = 0;
+ state->bits = 0;
+ state->lencode = state->distcode = state->next = state->codes;
+ state->sane = 1;
+ state->back = -1;
+ Tracev((stderr, "inflate: reset\n"));
+ return Z_OK;
+}
+
+int ZEXPORT inflateReset(strm)
+z_streamp strm;
+{
+ struct inflate_state FAR *state;
+
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)strm->state;
+ state->wsize = 0;
+ state->whave = 0;
+ state->wnext = 0;
+ return inflateResetKeep(strm);
+}
+
+int ZEXPORT inflateReset2(strm, windowBits)
+z_streamp strm;
+int windowBits;
+{
+ int wrap;
+ struct inflate_state FAR *state;
+
+ /* get the state */
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)strm->state;
+
+ /* extract wrap request from windowBits parameter */
+ if (windowBits < 0) {
+ wrap = 0;
+ windowBits = -windowBits;
+ }
+ else {
+ wrap = (windowBits >> 4) + 1;
+#ifdef GUNZIP
+ if (windowBits < 48)
+ windowBits &= 15;
+#endif
+ }
+
+ /* set number of window bits, free window if different */
+ if (windowBits && (windowBits < 8 || windowBits > 15))
+ return Z_STREAM_ERROR;
+ if (state->window != Z_NULL && state->wbits != (unsigned)windowBits) {
+ ZFREE(strm, state->window);
+ state->window = Z_NULL;
+ }
+
+ /* update state and reset the rest of it */
+ state->wrap = wrap;
+ state->wbits = (unsigned)windowBits;
+ return inflateReset(strm);
+}
+
+int ZEXPORT inflateInit2_(strm, windowBits, version, stream_size)
+z_streamp strm;
+int windowBits;
+const char *version;
+int stream_size;
+{
+ int ret;
+ struct inflate_state FAR *state;
+
+ if (version == Z_NULL || version[0] != ZLIB_VERSION[0] ||
+ stream_size != (int)(sizeof(z_stream)))
+ return Z_VERSION_ERROR;
+ if (strm == Z_NULL) return Z_STREAM_ERROR;
+ strm->msg = Z_NULL; /* in case we return an error */
+ if (strm->zalloc == (alloc_func)0) {
+#ifdef Z_SOLO
+ return Z_STREAM_ERROR;
+#else
+ strm->zalloc = zcalloc;
+ strm->opaque = (voidpf)0;
+#endif
+ }
+ if (strm->zfree == (free_func)0)
+#ifdef Z_SOLO
+ return Z_STREAM_ERROR;
+#else
+ strm->zfree = zcfree;
+#endif
+ state = (struct inflate_state FAR *)
+ ZALLOC(strm, 1, sizeof(struct inflate_state));
+ if (state == Z_NULL) return Z_MEM_ERROR;
+ Tracev((stderr, "inflate: allocated\n"));
+ strm->state = (struct internal_state FAR *)state;
+ state->window = Z_NULL;
+ ret = inflateReset2(strm, windowBits);
+ if (ret != Z_OK) {
+ ZFREE(strm, state);
+ strm->state = Z_NULL;
+ }
+ return ret;
+}
+
+int ZEXPORT inflateInit_(strm, version, stream_size)
+z_streamp strm;
+const char *version;
+int stream_size;
+{
+ return inflateInit2_(strm, DEF_WBITS, version, stream_size);
+}
+
+int ZEXPORT inflatePrime(strm, bits, value)
+z_streamp strm;
+int bits;
+int value;
+{
+ struct inflate_state FAR *state;
+
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)strm->state;
+ if (bits < 0) {
+ state->hold = 0;
+ state->bits = 0;
+ return Z_OK;
+ }
+ if (bits > 16 || state->bits + bits > 32) return Z_STREAM_ERROR;
+ value &= (1L << bits) - 1;
+ state->hold += value << state->bits;
+ state->bits += bits;
+ return Z_OK;
+}
+
+/*
+ Return state with length and distance decoding tables and index sizes set to
+ fixed code decoding. Normally this returns fixed tables from inffixed.h.
+ If BUILDFIXED is defined, then instead this routine builds the tables the
+ first time it's called, and returns those tables the first time and
+ thereafter. This reduces the size of the code by about 2K bytes, in
+ exchange for a little execution time. However, BUILDFIXED should not be
+ used for threaded applications, since the rewriting of the tables and virgin
+ may not be thread-safe.
+ */
+local void fixedtables(state)
+struct inflate_state FAR *state;
+{
+#ifdef BUILDFIXED
+ static int virgin = 1;
+ static code *lenfix, *distfix;
+ static code fixed[544];
+
+ /* build fixed huffman tables if first call (may not be thread safe) */
+ if (virgin) {
+ unsigned sym, bits;
+ static code *next;
+
+ /* literal/length table */
+ sym = 0;
+ while (sym < 144) state->lens[sym++] = 8;
+ while (sym < 256) state->lens[sym++] = 9;
+ while (sym < 280) state->lens[sym++] = 7;
+ while (sym < 288) state->lens[sym++] = 8;
+ next = fixed;
+ lenfix = next;
+ bits = 9;
+ inflate_table(LENS, state->lens, 288, &(next), &(bits), state->work);
+
+ /* distance table */
+ sym = 0;
+ while (sym < 32) state->lens[sym++] = 5;
+ distfix = next;
+ bits = 5;
+ inflate_table(DISTS, state->lens, 32, &(next), &(bits), state->work);
+
+ /* do this just once */
+ virgin = 0;
+ }
+#else /* !BUILDFIXED */
+# include "inffixed.h"
+#endif /* BUILDFIXED */
+ state->lencode = lenfix;
+ state->lenbits = 9;
+ state->distcode = distfix;
+ state->distbits = 5;
+}
+
+#ifdef MAKEFIXED
+#include <stdio.h>
+
+/*
+ Write out the inffixed.h that is #include'd above. Defining MAKEFIXED also
+ defines BUILDFIXED, so the tables are built on the fly. makefixed() writes
+ those tables to stdout, which would be piped to inffixed.h. A small program
+ can simply call makefixed to do this:
+
+ void makefixed(void);
+
+ int main(void)
+ {
+ makefixed();
+ return 0;
+ }
+
+ Then that can be linked with zlib built with MAKEFIXED defined and run:
+
+ a.out > inffixed.h
+ */
+void makefixed()
+{
+ unsigned low, size;
+ struct inflate_state state;
+
+ fixedtables(&state);
+ puts(" /* inffixed.h -- table for decoding fixed codes");
+ puts(" * Generated automatically by makefixed().");
+ puts(" */");
+ puts("");
+ puts(" /* WARNING: this file should *not* be used by applications.");
+ puts(" It is part of the implementation of this library and is");
+ puts(" subject to change. Applications should only use zlib.h.");
+ puts(" */");
+ puts("");
+ size = 1U << 9;
+ printf(" static const code lenfix[%u] = {", size);
+ low = 0;
+ for (;;) {
+ if ((low % 7) == 0) printf("\n ");
+ printf("{%u,%u,%d}", (low & 127) == 99 ? 64 : state.lencode[low].op,
+ state.lencode[low].bits, state.lencode[low].val);
+ if (++low == size) break;
+ putchar(',');
+ }
+ puts("\n };");
+ size = 1U << 5;
+ printf("\n static const code distfix[%u] = {", size);
+ low = 0;
+ for (;;) {
+ if ((low % 6) == 0) printf("\n ");
+ printf("{%u,%u,%d}", state.distcode[low].op, state.distcode[low].bits,
+ state.distcode[low].val);
+ if (++low == size) break;
+ putchar(',');
+ }
+ puts("\n };");
+}
+#endif /* MAKEFIXED */
+
+/*
+ Update the window with the last wsize (normally 32K) bytes written before
+ returning. If window does not exist yet, create it. This is only called
+ when a window is already in use, or when output has been written during this
+ inflate call, but the end of the deflate stream has not been reached yet.
+ It is also called to create a window for dictionary data when a dictionary
+ is loaded.
+
+ Providing output buffers larger than 32K to inflate() should provide a speed
+ advantage, since only the last 32K of output is copied to the sliding window
+ upon return from inflate(), and since all distances after the first 32K of
+ output will fall in the output data, making match copies simpler and faster.
+ The advantage may be dependent on the size of the processor's data caches.
+ */
+local int updatewindow(strm, end, copy)
+z_streamp strm;
+const Bytef *end;
+unsigned copy;
+{
+ struct inflate_state FAR *state;
+ unsigned dist;
+
+ state = (struct inflate_state FAR *)strm->state;
+
+ /* if it hasn't been done already, allocate space for the window */
+ if (state->window == Z_NULL) {
+ state->window = (unsigned char FAR *)
+ ZALLOC(strm, 1U << state->wbits,
+ sizeof(unsigned char));
+ if (state->window == Z_NULL) return 1;
+ }
+
+ /* if window not in use yet, initialize */
+ if (state->wsize == 0) {
+ state->wsize = 1U << state->wbits;
+ state->wnext = 0;
+ state->whave = 0;
+ }
+
+ /* copy state->wsize or less output bytes into the circular window */
+ if (copy >= state->wsize) {
+ zmemcpy(state->window, end - state->wsize, state->wsize);
+ state->wnext = 0;
+ state->whave = state->wsize;
+ }
+ else {
+ dist = state->wsize - state->wnext;
+ if (dist > copy) dist = copy;
+ zmemcpy(state->window + state->wnext, end - copy, dist);
+ copy -= dist;
+ if (copy) {
+ zmemcpy(state->window, end - copy, copy);
+ state->wnext = copy;
+ state->whave = state->wsize;
+ }
+ else {
+ state->wnext += dist;
+ if (state->wnext == state->wsize) state->wnext = 0;
+ if (state->whave < state->wsize) state->whave += dist;
+ }
+ }
+ return 0;
+}
+
+/* Macros for inflate(): */
+
+/* check function to use adler32() for zlib or crc32() for gzip */
+#ifdef GUNZIP
+# define UPDATE(check, buf, len) \
+ (state->flags ? crc32(check, buf, len) : adler32(check, buf, len))
+#else
+# define UPDATE(check, buf, len) adler32(check, buf, len)
+#endif
+
+/* check macros for header crc */
+#ifdef GUNZIP
+# define CRC2(check, word) \
+ do { \
+ hbuf[0] = (unsigned char)(word); \
+ hbuf[1] = (unsigned char)((word) >> 8); \
+ check = crc32(check, hbuf, 2); \
+ } while (0)
+
+# define CRC4(check, word) \
+ do { \
+ hbuf[0] = (unsigned char)(word); \
+ hbuf[1] = (unsigned char)((word) >> 8); \
+ hbuf[2] = (unsigned char)((word) >> 16); \
+ hbuf[3] = (unsigned char)((word) >> 24); \
+ check = crc32(check, hbuf, 4); \
+ } while (0)
+#endif
+
+/* Load registers with state in inflate() for speed */
+#define LOAD() \
+ do { \
+ put = strm->next_out; \
+ left = strm->avail_out; \
+ next = strm->next_in; \
+ have = strm->avail_in; \
+ hold = state->hold; \
+ bits = state->bits; \
+ } while (0)
+
+/* Restore state from registers in inflate() */
+#define RESTORE() \
+ do { \
+ strm->next_out = put; \
+ strm->avail_out = left; \
+ strm->next_in = next; \
+ strm->avail_in = have; \
+ state->hold = hold; \
+ state->bits = bits; \
+ } while (0)
+
+/* Clear the input bit accumulator */
+#define INITBITS() \
+ do { \
+ hold = 0; \
+ bits = 0; \
+ } while (0)
+
+/* Get a byte of input into the bit accumulator, or return from inflate()
+ if there is no input available. */
+#define PULLBYTE() \
+ do { \
+ if (have == 0) goto inf_leave; \
+ have--; \
+ hold += (unsigned long)(*next++) << bits; \
+ bits += 8; \
+ } while (0)
+
+/* Assure that there are at least n bits in the bit accumulator. If there is
+ not enough available input to do that, then return from inflate(). */
+#define NEEDBITS(n) \
+ do { \
+ while (bits < (unsigned)(n)) \
+ PULLBYTE(); \
+ } while (0)
+
+/* Return the low n bits of the bit accumulator (n < 16) */
+#define BITS(n) \
+ ((unsigned)hold & ((1U << (n)) - 1))
+
+/* Remove n bits from the bit accumulator */
+#define DROPBITS(n) \
+ do { \
+ hold >>= (n); \
+ bits -= (unsigned)(n); \
+ } while (0)
+
+/* Remove zero to seven bits as needed to go to a byte boundary */
+#define BYTEBITS() \
+ do { \
+ hold >>= bits & 7; \
+ bits -= bits & 7; \
+ } while (0)
+
+/*
+ inflate() uses a state machine to process as much input data and generate as
+ much output data as possible before returning. The state machine is
+ structured roughly as follows:
+
+ for (;;) switch (state) {
+ ...
+ case STATEn:
+ if (not enough input data or output space to make progress)
+ return;
+ ... make progress ...
+ state = STATEm;
+ break;
+ ...
+ }
+
+ so when inflate() is called again, the same case is attempted again, and
+ if the appropriate resources are provided, the machine proceeds to the
+ next state. The NEEDBITS() macro is usually the way the state evaluates
+ whether it can proceed or should return. NEEDBITS() does the return if
+ the requested bits are not available. The typical use of the BITS macros
+ is:
+
+ NEEDBITS(n);
+ ... do something with BITS(n) ...
+ DROPBITS(n);
+
+ where NEEDBITS(n) either returns from inflate() if there isn't enough
+ input left to load n bits into the accumulator, or it continues. BITS(n)
+ gives the low n bits in the accumulator. When done, DROPBITS(n) drops
+ the low n bits off the accumulator. INITBITS() clears the accumulator
+ and sets the number of available bits to zero. BYTEBITS() discards just
+ enough bits to put the accumulator on a byte boundary. After BYTEBITS()
+ and a NEEDBITS(8), then BITS(8) would return the next byte in the stream.
+
+ NEEDBITS(n) uses PULLBYTE() to get an available byte of input, or to return
+ if there is no input available. The decoding of variable length codes uses
+ PULLBYTE() directly in order to pull just enough bytes to decode the next
+ code, and no more.
+
+ Some states loop until they get enough input, making sure that enough
+ state information is maintained to continue the loop where it left off
+ if NEEDBITS() returns in the loop. For example, want, need, and keep
+ would all have to actually be part of the saved state in case NEEDBITS()
+ returns:
+
+ case STATEw:
+ while (want < need) {
+ NEEDBITS(n);
+ keep[want++] = BITS(n);
+ DROPBITS(n);
+ }
+ state = STATEx;
+ case STATEx:
+
+ As shown above, if the next state is also the next case, then the break
+ is omitted.
+
+ A state may also return if there is not enough output space available to
+ complete that state. Those states are copying stored data, writing a
+ literal byte, and copying a matching string.
+
+ When returning, a "goto inf_leave" is used to update the total counters,
+ update the check value, and determine whether any progress has been made
+ during that inflate() call in order to return the proper return code.
+ Progress is defined as a change in either strm->avail_in or strm->avail_out.
+ When there is a window, goto inf_leave will update the window with the last
+ output written. If a goto inf_leave occurs in the middle of decompression
+ and there is no window currently, goto inf_leave will create one and copy
+ output to the window for the next call of inflate().
+
+ In this implementation, the flush parameter of inflate() only affects the
+ return code (per zlib.h). inflate() always writes as much as possible to
+ strm->next_out, given the space available and the provided input--the effect
+ documented in zlib.h of Z_SYNC_FLUSH. Furthermore, inflate() always defers
+ the allocation of and copying into a sliding window until necessary, which
+ provides the effect documented in zlib.h for Z_FINISH when the entire input
+ stream available. So the only thing the flush parameter actually does is:
+ when flush is set to Z_FINISH, inflate() cannot return Z_OK. Instead it
+ will return Z_BUF_ERROR if it has not reached the end of the stream.
+ */
+
+int ZEXPORT inflate(strm, flush)
+z_streamp strm;
+int flush;
+{
+ struct inflate_state FAR *state;
+ z_const unsigned char FAR *next; /* next input */
+ unsigned char FAR *put; /* next output */
+ unsigned have, left; /* available input and output */
+ unsigned long hold; /* bit buffer */
+ unsigned bits; /* bits in bit buffer */
+ unsigned in, out; /* save starting available input and output */
+ unsigned copy; /* number of stored or match bytes to copy */
+ unsigned char FAR *from; /* where to copy match bytes from */
+ code here; /* current decoding table entry */
+ code last; /* parent table entry */
+ unsigned len; /* length to copy for repeats, bits to drop */
+ int ret; /* return code */
+#ifdef GUNZIP
+ unsigned char hbuf[4]; /* buffer for gzip header crc calculation */
+#endif
+ static const unsigned short order[19] = /* permutation of code lengths */
+ {16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15};
+
+ if (strm == Z_NULL || strm->state == Z_NULL || strm->next_out == Z_NULL ||
+ (strm->next_in == Z_NULL && strm->avail_in != 0))
+ return Z_STREAM_ERROR;
+
+ state = (struct inflate_state FAR *)strm->state;
+ if (state->mode == TYPE) state->mode = TYPEDO; /* skip check */
+ LOAD();
+ in = have;
+ out = left;
+ ret = Z_OK;
+ for (;;)
+ switch (state->mode) {
+ case HEAD:
+ if (state->wrap == 0) {
+ state->mode = TYPEDO;
+ break;
+ }
+ NEEDBITS(16);
+#ifdef GUNZIP
+ if ((state->wrap & 2) && hold == 0x8b1f) { /* gzip header */
+ state->check = crc32(0L, Z_NULL, 0);
+ CRC2(state->check, hold);
+ INITBITS();
+ state->mode = FLAGS;
+ break;
+ }
+ state->flags = 0; /* expect zlib header */
+ if (state->head != Z_NULL)
+ state->head->done = -1;
+ if (!(state->wrap & 1) || /* check if zlib header allowed */
+#else
+ if (
+#endif
+ ((BITS(8) << 8) + (hold >> 8)) % 31) {
+ strm->msg = (char *)"incorrect header check";
+ state->mode = BAD;
+ break;
+ }
+ if (BITS(4) != Z_DEFLATED) {
+ strm->msg = (char *)"unknown compression method";
+ state->mode = BAD;
+ break;
+ }
+ DROPBITS(4);
+ len = BITS(4) + 8;
+ if (state->wbits == 0)
+ state->wbits = len;
+ else if (len > state->wbits) {
+ strm->msg = (char *)"invalid window size";
+ state->mode = BAD;
+ break;
+ }
+ state->dmax = 1U << len;
+ Tracev((stderr, "inflate: zlib header ok\n"));
+ strm->adler = state->check = adler32(0L, Z_NULL, 0);
+ state->mode = hold & 0x200 ? DICTID : TYPE;
+ INITBITS();
+ break;
+#ifdef GUNZIP
+ case FLAGS:
+ NEEDBITS(16);
+ state->flags = (int)(hold);
+ if ((state->flags & 0xff) != Z_DEFLATED) {
+ strm->msg = (char *)"unknown compression method";
+ state->mode = BAD;
+ break;
+ }
+ if (state->flags & 0xe000) {
+ strm->msg = (char *)"unknown header flags set";
+ state->mode = BAD;
+ break;
+ }
+ if (state->head != Z_NULL)
+ state->head->text = (int)((hold >> 8) & 1);
+ if (state->flags & 0x0200) CRC2(state->check, hold);
+ INITBITS();
+ state->mode = TIME;
+ case TIME:
+ NEEDBITS(32);
+ if (state->head != Z_NULL)
+ state->head->time = hold;
+ if (state->flags & 0x0200) CRC4(state->check, hold);
+ INITBITS();
+ state->mode = OS;
+ case OS:
+ NEEDBITS(16);
+ if (state->head != Z_NULL) {
+ state->head->xflags = (int)(hold & 0xff);
+ state->head->os = (int)(hold >> 8);
+ }
+ if (state->flags & 0x0200) CRC2(state->check, hold);
+ INITBITS();
+ state->mode = EXLEN;
+ case EXLEN:
+ if (state->flags & 0x0400) {
+ NEEDBITS(16);
+ state->length = (unsigned)(hold);
+ if (state->head != Z_NULL)
+ state->head->extra_len = (unsigned)hold;
+ if (state->flags & 0x0200) CRC2(state->check, hold);
+ INITBITS();
+ }
+ else if (state->head != Z_NULL)
+ state->head->extra = Z_NULL;
+ state->mode = EXTRA;
+ case EXTRA:
+ if (state->flags & 0x0400) {
+ copy = state->length;
+ if (copy > have) copy = have;
+ if (copy) {
+ if (state->head != Z_NULL &&
+ state->head->extra != Z_NULL) {
+ len = state->head->extra_len - state->length;
+ zmemcpy(state->head->extra + len, next,
+ len + copy > state->head->extra_max ?
+ state->head->extra_max - len : copy);
+ }
+ if (state->flags & 0x0200)
+ state->check = crc32(state->check, next, copy);
+ have -= copy;
+ next += copy;
+ state->length -= copy;
+ }
+ if (state->length) goto inf_leave;
+ }
+ state->length = 0;
+ state->mode = NAME;
+ case NAME:
+ if (state->flags & 0x0800) {
+ if (have == 0) goto inf_leave;
+ copy = 0;
+ do {
+ len = (unsigned)(next[copy++]);
+ if (state->head != Z_NULL &&
+ state->head->name != Z_NULL &&
+ state->length < state->head->name_max)
+ state->head->name[state->length++] = len;
+ } while (len && copy < have);
+ if (state->flags & 0x0200)
+ state->check = crc32(state->check, next, copy);
+ have -= copy;
+ next += copy;
+ if (len) goto inf_leave;
+ }
+ else if (state->head != Z_NULL)
+ state->head->name = Z_NULL;
+ state->length = 0;
+ state->mode = COMMENT;
+ case COMMENT:
+ if (state->flags & 0x1000) {
+ if (have == 0) goto inf_leave;
+ copy = 0;
+ do {
+ len = (unsigned)(next[copy++]);
+ if (state->head != Z_NULL &&
+ state->head->comment != Z_NULL &&
+ state->length < state->head->comm_max)
+ state->head->comment[state->length++] = len;
+ } while (len && copy < have);
+ if (state->flags & 0x0200)
+ state->check = crc32(state->check, next, copy);
+ have -= copy;
+ next += copy;
+ if (len) goto inf_leave;
+ }
+ else if (state->head != Z_NULL)
+ state->head->comment = Z_NULL;
+ state->mode = HCRC;
+ case HCRC:
+ if (state->flags & 0x0200) {
+ NEEDBITS(16);
+ if (hold != (state->check & 0xffff)) {
+ strm->msg = (char *)"header crc mismatch";
+ state->mode = BAD;
+ break;
+ }
+ INITBITS();
+ }
+ if (state->head != Z_NULL) {
+ state->head->hcrc = (int)((state->flags >> 9) & 1);
+ state->head->done = 1;
+ }
+ strm->adler = state->check = crc32(0L, Z_NULL, 0);
+ state->mode = TYPE;
+ break;
+#endif
+ case DICTID:
+ NEEDBITS(32);
+ strm->adler = state->check = ZSWAP32(hold);
+ INITBITS();
+ state->mode = DICT;
+ case DICT:
+ if (state->havedict == 0) {
+ RESTORE();
+ return Z_NEED_DICT;
+ }
+ strm->adler = state->check = adler32(0L, Z_NULL, 0);
+ state->mode = TYPE;
+ case TYPE:
+ if (flush == Z_BLOCK || flush == Z_TREES) goto inf_leave;
+ case TYPEDO:
+ if (state->last) {
+ BYTEBITS();
+ state->mode = CHECK;
+ break;
+ }
+ NEEDBITS(3);
+ state->last = BITS(1);
+ DROPBITS(1);
+ switch (BITS(2)) {
+ case 0: /* stored block */
+ Tracev((stderr, "inflate: stored block%s\n",
+ state->last ? " (last)" : ""));
+ state->mode = STORED;
+ break;
+ case 1: /* fixed block */
+ fixedtables(state);
+ Tracev((stderr, "inflate: fixed codes block%s\n",
+ state->last ? " (last)" : ""));
+ state->mode = LEN_; /* decode codes */
+ if (flush == Z_TREES) {
+ DROPBITS(2);
+ goto inf_leave;
+ }
+ break;
+ case 2: /* dynamic block */
+ Tracev((stderr, "inflate: dynamic codes block%s\n",
+ state->last ? " (last)" : ""));
+ state->mode = TABLE;
+ break;
+ case 3:
+ strm->msg = (char *)"invalid block type";
+ state->mode = BAD;
+ }
+ DROPBITS(2);
+ break;
+ case STORED:
+ BYTEBITS(); /* go to byte boundary */
+ NEEDBITS(32);
+ if ((hold & 0xffff) != ((hold >> 16) ^ 0xffff)) {
+ strm->msg = (char *)"invalid stored block lengths";
+ state->mode = BAD;
+ break;
+ }
+ state->length = (unsigned)hold & 0xffff;
+ Tracev((stderr, "inflate: stored length %u\n",
+ state->length));
+ INITBITS();
+ state->mode = COPY_;
+ if (flush == Z_TREES) goto inf_leave;
+ case COPY_:
+ state->mode = COPY;
+ case COPY:
+ copy = state->length;
+ if (copy) {
+ if (copy > have) copy = have;
+ if (copy > left) copy = left;
+ if (copy == 0) goto inf_leave;
+ zmemcpy(put, next, copy);
+ have -= copy;
+ next += copy;
+ left -= copy;
+ put += copy;
+ state->length -= copy;
+ break;
+ }
+ Tracev((stderr, "inflate: stored end\n"));
+ state->mode = TYPE;
+ break;
+ case TABLE:
+ NEEDBITS(14);
+ state->nlen = BITS(5) + 257;
+ DROPBITS(5);
+ state->ndist = BITS(5) + 1;
+ DROPBITS(5);
+ state->ncode = BITS(4) + 4;
+ DROPBITS(4);
+#ifndef PKZIP_BUG_WORKAROUND
+ if (state->nlen > 286 || state->ndist > 30) {
+ strm->msg = (char *)"too many length or distance symbols";
+ state->mode = BAD;
+ break;
+ }
+#endif
+ Tracev((stderr, "inflate: table sizes ok\n"));
+ state->have = 0;
+ state->mode = LENLENS;
+ case LENLENS:
+ while (state->have < state->ncode) {
+ NEEDBITS(3);
+ state->lens[order[state->have++]] = (unsigned short)BITS(3);
+ DROPBITS(3);
+ }
+ while (state->have < 19)
+ state->lens[order[state->have++]] = 0;
+ state->next = state->codes;
+ state->lencode = (const code FAR *)(state->next);
+ state->lenbits = 7;
+ ret = inflate_table(CODES, state->lens, 19, &(state->next),
+ &(state->lenbits), state->work);
+ if (ret) {
+ strm->msg = (char *)"invalid code lengths set";
+ state->mode = BAD;
+ break;
+ }
+ Tracev((stderr, "inflate: code lengths ok\n"));
+ state->have = 0;
+ state->mode = CODELENS;
+ case CODELENS:
+ while (state->have < state->nlen + state->ndist) {
+ for (;;) {
+ here = state->lencode[BITS(state->lenbits)];
+ if ((unsigned)(here.bits) <= bits) break;
+ PULLBYTE();
+ }
+ if (here.val < 16) {
+ DROPBITS(here.bits);
+ state->lens[state->have++] = here.val;
+ }
+ else {
+ if (here.val == 16) {
+ NEEDBITS(here.bits + 2);
+ DROPBITS(here.bits);
+ if (state->have == 0) {
+ strm->msg = (char *)"invalid bit length repeat";
+ state->mode = BAD;
+ break;
+ }
+ len = state->lens[state->have - 1];
+ copy = 3 + BITS(2);
+ DROPBITS(2);
+ }
+ else if (here.val == 17) {
+ NEEDBITS(here.bits + 3);
+ DROPBITS(here.bits);
+ len = 0;
+ copy = 3 + BITS(3);
+ DROPBITS(3);
+ }
+ else {
+ NEEDBITS(here.bits + 7);
+ DROPBITS(here.bits);
+ len = 0;
+ copy = 11 + BITS(7);
+ DROPBITS(7);
+ }
+ if (state->have + copy > state->nlen + state->ndist) {
+ strm->msg = (char *)"invalid bit length repeat";
+ state->mode = BAD;
+ break;
+ }
+ while (copy--)
+ state->lens[state->have++] = (unsigned short)len;
+ }
+ }
+
+ /* handle error breaks in while */
+ if (state->mode == BAD) break;
+
+ /* check for end-of-block code (better have one) */
+ if (state->lens[256] == 0) {
+ strm->msg = (char *)"invalid code -- missing end-of-block";
+ state->mode = BAD;
+ break;
+ }
+
+ /* build code tables -- note: do not change the lenbits or distbits
+ values here (9 and 6) without reading the comments in inftrees.h
+ concerning the ENOUGH constants, which depend on those values */
+ state->next = state->codes;
+ state->lencode = (const code FAR *)(state->next);
+ state->lenbits = 9;
+ ret = inflate_table(LENS, state->lens, state->nlen, &(state->next),
+ &(state->lenbits), state->work);
+ if (ret) {
+ strm->msg = (char *)"invalid literal/lengths set";
+ state->mode = BAD;
+ break;
+ }
+ state->distcode = (const code FAR *)(state->next);
+ state->distbits = 6;
+ ret = inflate_table(DISTS, state->lens + state->nlen, state->ndist,
+ &(state->next), &(state->distbits), state->work);
+ if (ret) {
+ strm->msg = (char *)"invalid distances set";
+ state->mode = BAD;
+ break;
+ }
+ Tracev((stderr, "inflate: codes ok\n"));
+ state->mode = LEN_;
+ if (flush == Z_TREES) goto inf_leave;
+ case LEN_:
+ state->mode = LEN;
+ case LEN:
+ if (have >= 6 && left >= 258) {
+ RESTORE();
+ inflate_fast(strm, out);
+ LOAD();
+ if (state->mode == TYPE)
+ state->back = -1;
+ break;
+ }
+ state->back = 0;
+ for (;;) {
+ here = state->lencode[BITS(state->lenbits)];
+ if ((unsigned)(here.bits) <= bits) break;
+ PULLBYTE();
+ }
+ if (here.op && (here.op & 0xf0) == 0) {
+ last = here;
+ for (;;) {
+ here = state->lencode[last.val +
+ (BITS(last.bits + last.op) >> last.bits)];
+ if ((unsigned)(last.bits + here.bits) <= bits) break;
+ PULLBYTE();
+ }
+ DROPBITS(last.bits);
+ state->back += last.bits;
+ }
+ DROPBITS(here.bits);
+ state->back += here.bits;
+ state->length = (unsigned)here.val;
+ if ((int)(here.op) == 0) {
+ Tracevv((stderr, here.val >= 0x20 && here.val < 0x7f ?
+ "inflate: literal '%c'\n" :
+ "inflate: literal 0x%02x\n", here.val));
+ state->mode = LIT;
+ break;
+ }
+ if (here.op & 32) {
+ Tracevv((stderr, "inflate: end of block\n"));
+ state->back = -1;
+ state->mode = TYPE;
+ break;
+ }
+ if (here.op & 64) {
+ strm->msg = (char *)"invalid literal/length code";
+ state->mode = BAD;
+ break;
+ }
+ state->extra = (unsigned)(here.op) & 15;
+ state->mode = LENEXT;
+ case LENEXT:
+ if (state->extra) {
+ NEEDBITS(state->extra);
+ state->length += BITS(state->extra);
+ DROPBITS(state->extra);
+ state->back += state->extra;
+ }
+ Tracevv((stderr, "inflate: length %u\n", state->length));
+ state->was = state->length;
+ state->mode = DIST;
+ case DIST:
+ for (;;) {
+ here = state->distcode[BITS(state->distbits)];
+ if ((unsigned)(here.bits) <= bits) break;
+ PULLBYTE();
+ }
+ if ((here.op & 0xf0) == 0) {
+ last = here;
+ for (;;) {
+ here = state->distcode[last.val +
+ (BITS(last.bits + last.op) >> last.bits)];
+ if ((unsigned)(last.bits + here.bits) <= bits) break;
+ PULLBYTE();
+ }
+ DROPBITS(last.bits);
+ state->back += last.bits;
+ }
+ DROPBITS(here.bits);
+ state->back += here.bits;
+ if (here.op & 64) {
+ strm->msg = (char *)"invalid distance code";
+ state->mode = BAD;
+ break;
+ }
+ state->offset = (unsigned)here.val;
+ state->extra = (unsigned)(here.op) & 15;
+ state->mode = DISTEXT;
+ case DISTEXT:
+ if (state->extra) {
+ NEEDBITS(state->extra);
+ state->offset += BITS(state->extra);
+ DROPBITS(state->extra);
+ state->back += state->extra;
+ }
+#ifdef INFLATE_STRICT
+ if (state->offset > state->dmax) {
+ strm->msg = (char *)"invalid distance too far back";
+ state->mode = BAD;
+ break;
+ }
+#endif
+ Tracevv((stderr, "inflate: distance %u\n", state->offset));
+ state->mode = MATCH;
+ case MATCH:
+ if (left == 0) goto inf_leave;
+ copy = out - left;
+ if (state->offset > copy) { /* copy from window */
+ copy = state->offset - copy;
+ if (copy > state->whave) {
+ if (state->sane) {
+ strm->msg = (char *)"invalid distance too far back";
+ state->mode = BAD;
+ break;
+ }
+#ifdef INFLATE_ALLOW_INVALID_DISTANCE_TOOFAR_ARRR
+ Trace((stderr, "inflate.c too far\n"));
+ copy -= state->whave;
+ if (copy > state->length) copy = state->length;
+ if (copy > left) copy = left;
+ left -= copy;
+ state->length -= copy;
+ do {
+ *put++ = 0;
+ } while (--copy);
+ if (state->length == 0) state->mode = LEN;
+ break;
+#endif
+ }
+ if (copy > state->wnext) {
+ copy -= state->wnext;
+ from = state->window + (state->wsize - copy);
+ }
+ else
+ from = state->window + (state->wnext - copy);
+ if (copy > state->length) copy = state->length;
+ }
+ else { /* copy from output */
+ from = put - state->offset;
+ copy = state->length;
+ }
+ if (copy > left) copy = left;
+ left -= copy;
+ state->length -= copy;
+ do {
+ *put++ = *from++;
+ } while (--copy);
+ if (state->length == 0) state->mode = LEN;
+ break;
+ case LIT:
+ if (left == 0) goto inf_leave;
+ *put++ = (unsigned char)(state->length);
+ left--;
+ state->mode = LEN;
+ break;
+ case CHECK:
+ if (state->wrap) {
+ NEEDBITS(32);
+ out -= left;
+ strm->total_out += out;
+ state->total += out;
+ if (out)
+ strm->adler = state->check =
+ UPDATE(state->check, put - out, out);
+ out = left;
+ if ((
+#ifdef GUNZIP
+ state->flags ? hold :
+#endif
+ ZSWAP32(hold)) != state->check) {
+ strm->msg = (char *)"incorrect data check";
+ state->mode = BAD;
+ break;
+ }
+ INITBITS();
+ Tracev((stderr, "inflate: check matches trailer\n"));
+ }
+#ifdef GUNZIP
+ state->mode = LENGTH;
+ case LENGTH:
+ if (state->wrap && state->flags) {
+ NEEDBITS(32);
+ if (hold != (state->total & 0xffffffffUL)) {
+ strm->msg = (char *)"incorrect length check";
+ state->mode = BAD;
+ break;
+ }
+ INITBITS();
+ Tracev((stderr, "inflate: length matches trailer\n"));
+ }
+#endif
+ state->mode = DONE;
+ case DONE:
+ ret = Z_STREAM_END;
+ goto inf_leave;
+ case BAD:
+ ret = Z_DATA_ERROR;
+ goto inf_leave;
+ case MEM:
+ return Z_MEM_ERROR;
+ case SYNC:
+ default:
+ return Z_STREAM_ERROR;
+ }
+
+ /*
+ Return from inflate(), updating the total counts and the check value.
+ If there was no progress during the inflate() call, return a buffer
+ error. Call updatewindow() to create and/or update the window state.
+ Note: a memory error from inflate() is non-recoverable.
+ */
+ inf_leave:
+ RESTORE();
+ if (state->wsize || (out != strm->avail_out && state->mode < BAD &&
+ (state->mode < CHECK || flush != Z_FINISH)))
+ if (updatewindow(strm, strm->next_out, out - strm->avail_out)) {
+ state->mode = MEM;
+ return Z_MEM_ERROR;
+ }
+ in -= strm->avail_in;
+ out -= strm->avail_out;
+ strm->total_in += in;
+ strm->total_out += out;
+ state->total += out;
+ if (state->wrap && out)
+ strm->adler = state->check =
+ UPDATE(state->check, strm->next_out - out, out);
+ strm->data_type = state->bits + (state->last ? 64 : 0) +
+ (state->mode == TYPE ? 128 : 0) +
+ (state->mode == LEN_ || state->mode == COPY_ ? 256 : 0);
+ if (((in == 0 && out == 0) || flush == Z_FINISH) && ret == Z_OK)
+ ret = Z_BUF_ERROR;
+ return ret;
+}
+
+int ZEXPORT inflateEnd(strm)
+z_streamp strm;
+{
+ struct inflate_state FAR *state;
+ if (strm == Z_NULL || strm->state == Z_NULL || strm->zfree == (free_func)0)
+ return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)strm->state;
+ if (state->window != Z_NULL) ZFREE(strm, state->window);
+ ZFREE(strm, strm->state);
+ strm->state = Z_NULL;
+ Tracev((stderr, "inflate: end\n"));
+ return Z_OK;
+}
+
+int ZEXPORT inflateGetDictionary(strm, dictionary, dictLength)
+z_streamp strm;
+Bytef *dictionary;
+uInt *dictLength;
+{
+ struct inflate_state FAR *state;
+
+ /* check state */
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)strm->state;
+
+ /* copy dictionary */
+ if (state->whave && dictionary != Z_NULL) {
+ zmemcpy(dictionary, state->window + state->wnext,
+ state->whave - state->wnext);
+ zmemcpy(dictionary + state->whave - state->wnext,
+ state->window, state->wnext);
+ }
+ if (dictLength != Z_NULL)
+ *dictLength = state->whave;
+ return Z_OK;
+}
+
+int ZEXPORT inflateSetDictionary(strm, dictionary, dictLength)
+z_streamp strm;
+const Bytef *dictionary;
+uInt dictLength;
+{
+ struct inflate_state FAR *state;
+ unsigned long dictid;
+ int ret;
+
+ /* check state */
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)strm->state;
+ if (state->wrap != 0 && state->mode != DICT)
+ return Z_STREAM_ERROR;
+
+ /* check for correct dictionary identifier */
+ if (state->mode == DICT) {
+ dictid = adler32(0L, Z_NULL, 0);
+ dictid = adler32(dictid, dictionary, dictLength);
+ if (dictid != state->check)
+ return Z_DATA_ERROR;
+ }
+
+ /* copy dictionary to window using updatewindow(), which will amend the
+ existing dictionary if appropriate */
+ ret = updatewindow(strm, dictionary + dictLength, dictLength);
+ if (ret) {
+ state->mode = MEM;
+ return Z_MEM_ERROR;
+ }
+ state->havedict = 1;
+ Tracev((stderr, "inflate: dictionary set\n"));
+ return Z_OK;
+}
+
+int ZEXPORT inflateGetHeader(strm, head)
+z_streamp strm;
+gz_headerp head;
+{
+ struct inflate_state FAR *state;
+
+ /* check state */
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)strm->state;
+ if ((state->wrap & 2) == 0) return Z_STREAM_ERROR;
+
+ /* save header structure */
+ state->head = head;
+ head->done = 0;
+ return Z_OK;
+}
+
+/*
+ Search buf[0..len-1] for the pattern: 0, 0, 0xff, 0xff. Return when found
+ or when out of input. When called, *have is the number of pattern bytes
+ found in order so far, in 0..3. On return *have is updated to the new
+ state. If on return *have equals four, then the pattern was found and the
+ return value is how many bytes were read including the last byte of the
+ pattern. If *have is less than four, then the pattern has not been found
+ yet and the return value is len. In the latter case, syncsearch() can be
+ called again with more data and the *have state. *have is initialized to
+ zero for the first call.
+ */
+local unsigned syncsearch(have, buf, len)
+unsigned FAR *have;
+const unsigned char FAR *buf;
+unsigned len;
+{
+ unsigned got;
+ unsigned next;
+
+ got = *have;
+ next = 0;
+ while (next < len && got < 4) {
+ if ((int)(buf[next]) == (got < 2 ? 0 : 0xff))
+ got++;
+ else if (buf[next])
+ got = 0;
+ else
+ got = 4 - got;
+ next++;
+ }
+ *have = got;
+ return next;
+}
+
+int ZEXPORT inflateSync(strm)
+z_streamp strm;
+{
+ unsigned len; /* number of bytes to look at or looked at */
+ unsigned long in, out; /* temporary to save total_in and total_out */
+ unsigned char buf[4]; /* to restore bit buffer to byte string */
+ struct inflate_state FAR *state;
+
+ /* check parameters */
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)strm->state;
+ if (strm->avail_in == 0 && state->bits < 8) return Z_BUF_ERROR;
+
+ /* if first time, start search in bit buffer */
+ if (state->mode != SYNC) {
+ state->mode = SYNC;
+ state->hold <<= state->bits & 7;
+ state->bits -= state->bits & 7;
+ len = 0;
+ while (state->bits >= 8) {
+ buf[len++] = (unsigned char)(state->hold);
+ state->hold >>= 8;
+ state->bits -= 8;
+ }
+ state->have = 0;
+ syncsearch(&(state->have), buf, len);
+ }
+
+ /* search available input */
+ len = syncsearch(&(state->have), strm->next_in, strm->avail_in);
+ strm->avail_in -= len;
+ strm->next_in += len;
+ strm->total_in += len;
+
+ /* return no joy or set up to restart inflate() on a new block */
+ if (state->have != 4) return Z_DATA_ERROR;
+ in = strm->total_in; out = strm->total_out;
+ inflateReset(strm);
+ strm->total_in = in; strm->total_out = out;
+ state->mode = TYPE;
+ return Z_OK;
+}
+
+/*
+ Returns true if inflate is currently at the end of a block generated by
+ Z_SYNC_FLUSH or Z_FULL_FLUSH. This function is used by one PPP
+ implementation to provide an additional safety check. PPP uses
+ Z_SYNC_FLUSH but removes the length bytes of the resulting empty stored
+ block. When decompressing, PPP checks that at the end of input packet,
+ inflate is waiting for these length bytes.
+ */
+int ZEXPORT inflateSyncPoint(strm)
+z_streamp strm;
+{
+ struct inflate_state FAR *state;
+
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)strm->state;
+ return state->mode == STORED && state->bits == 0;
+}
+
+int ZEXPORT inflateCopy(dest, source)
+z_streamp dest;
+z_streamp source;
+{
+ struct inflate_state FAR *state;
+ struct inflate_state FAR *copy;
+ unsigned char FAR *window;
+ unsigned wsize;
+
+ /* check input */
+ if (dest == Z_NULL || source == Z_NULL || source->state == Z_NULL ||
+ source->zalloc == (alloc_func)0 || source->zfree == (free_func)0)
+ return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)source->state;
+
+ /* allocate space */
+ copy = (struct inflate_state FAR *)
+ ZALLOC(source, 1, sizeof(struct inflate_state));
+ if (copy == Z_NULL) return Z_MEM_ERROR;
+ window = Z_NULL;
+ if (state->window != Z_NULL) {
+ window = (unsigned char FAR *)
+ ZALLOC(source, 1U << state->wbits, sizeof(unsigned char));
+ if (window == Z_NULL) {
+ ZFREE(source, copy);
+ return Z_MEM_ERROR;
+ }
+ }
+
+ /* copy state */
+ zmemcpy((voidpf)dest, (voidpf)source, sizeof(z_stream));
+ zmemcpy((voidpf)copy, (voidpf)state, sizeof(struct inflate_state));
+ if (state->lencode >= state->codes &&
+ state->lencode <= state->codes + ENOUGH - 1) {
+ copy->lencode = copy->codes + (state->lencode - state->codes);
+ copy->distcode = copy->codes + (state->distcode - state->codes);
+ }
+ copy->next = copy->codes + (state->next - state->codes);
+ if (window != Z_NULL) {
+ wsize = 1U << state->wbits;
+ zmemcpy(window, state->window, wsize);
+ }
+ copy->window = window;
+ dest->state = (struct internal_state FAR *)copy;
+ return Z_OK;
+}
+
+int ZEXPORT inflateUndermine(strm, subvert)
+z_streamp strm;
+int subvert;
+{
+ struct inflate_state FAR *state;
+
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)strm->state;
+ state->sane = !subvert;
+#ifdef INFLATE_ALLOW_INVALID_DISTANCE_TOOFAR_ARRR
+ return Z_OK;
+#else
+ state->sane = 1;
+ return Z_DATA_ERROR;
+#endif
+}
+
+long ZEXPORT inflateMark(strm)
+z_streamp strm;
+{
+ struct inflate_state FAR *state;
+
+ if (strm == Z_NULL || strm->state == Z_NULL) return -1L << 16;
+ state = (struct inflate_state FAR *)strm->state;
+ return ((long)(state->back) << 16) +
+ (state->mode == COPY ? state->length :
+ (state->mode == MATCH ? state->was - state->length : 0));
+}
diff --git a/third-party/zlib/inflate.h b/third-party/zlib/inflate.h
new file mode 100644
index 0000000..95f4986
--- /dev/null
+++ b/third-party/zlib/inflate.h
@@ -0,0 +1,122 @@
+/* inflate.h -- internal inflate state definition
+ * Copyright (C) 1995-2009 Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* WARNING: this file should *not* be used by applications. It is
+ part of the implementation of the compression library and is
+ subject to change. Applications should only use zlib.h.
+ */
+
+/* define NO_GZIP when compiling if you want to disable gzip header and
+ trailer decoding by inflate(). NO_GZIP would be used to avoid linking in
+ the crc code when it is not needed. For shared libraries, gzip decoding
+ should be left enabled. */
+#ifndef NO_GZIP
+# define GUNZIP
+#endif
+
+/* Possible inflate modes between inflate() calls */
+typedef enum {
+ HEAD, /* i: waiting for magic header */
+ FLAGS, /* i: waiting for method and flags (gzip) */
+ TIME, /* i: waiting for modification time (gzip) */
+ OS, /* i: waiting for extra flags and operating system (gzip) */
+ EXLEN, /* i: waiting for extra length (gzip) */
+ EXTRA, /* i: waiting for extra bytes (gzip) */
+ NAME, /* i: waiting for end of file name (gzip) */
+ COMMENT, /* i: waiting for end of comment (gzip) */
+ HCRC, /* i: waiting for header crc (gzip) */
+ DICTID, /* i: waiting for dictionary check value */
+ DICT, /* waiting for inflateSetDictionary() call */
+ TYPE, /* i: waiting for type bits, including last-flag bit */
+ TYPEDO, /* i: same, but skip check to exit inflate on new block */
+ STORED, /* i: waiting for stored size (length and complement) */
+ COPY_, /* i/o: same as COPY below, but only first time in */
+ COPY, /* i/o: waiting for input or output to copy stored block */
+ TABLE, /* i: waiting for dynamic block table lengths */
+ LENLENS, /* i: waiting for code length code lengths */
+ CODELENS, /* i: waiting for length/lit and distance code lengths */
+ LEN_, /* i: same as LEN below, but only first time in */
+ LEN, /* i: waiting for length/lit/eob code */
+ LENEXT, /* i: waiting for length extra bits */
+ DIST, /* i: waiting for distance code */
+ DISTEXT, /* i: waiting for distance extra bits */
+ MATCH, /* o: waiting for output space to copy string */
+ LIT, /* o: waiting for output space to write literal */
+ CHECK, /* i: waiting for 32-bit check value */
+ LENGTH, /* i: waiting for 32-bit length (gzip) */
+ DONE, /* finished check, done -- remain here until reset */
+ BAD, /* got a data error -- remain here until reset */
+ MEM, /* got an inflate() memory error -- remain here until reset */
+ SYNC /* looking for synchronization bytes to restart inflate() */
+} inflate_mode;
+
+/*
+ State transitions between above modes -
+
+ (most modes can go to BAD or MEM on error -- not shown for clarity)
+
+ Process header:
+ HEAD -> (gzip) or (zlib) or (raw)
+ (gzip) -> FLAGS -> TIME -> OS -> EXLEN -> EXTRA -> NAME -> COMMENT ->
+ HCRC -> TYPE
+ (zlib) -> DICTID or TYPE
+ DICTID -> DICT -> TYPE
+ (raw) -> TYPEDO
+ Read deflate blocks:
+ TYPE -> TYPEDO -> STORED or TABLE or LEN_ or CHECK
+ STORED -> COPY_ -> COPY -> TYPE
+ TABLE -> LENLENS -> CODELENS -> LEN_
+ LEN_ -> LEN
+ Read deflate codes in fixed or dynamic block:
+ LEN -> LENEXT or LIT or TYPE
+ LENEXT -> DIST -> DISTEXT -> MATCH -> LEN
+ LIT -> LEN
+ Process trailer:
+ CHECK -> LENGTH -> DONE
+ */
+
+/* state maintained between inflate() calls. Approximately 10K bytes. */
+struct inflate_state {
+ inflate_mode mode; /* current inflate mode */
+ int last; /* true if processing last block */
+ int wrap; /* bit 0 true for zlib, bit 1 true for gzip */
+ int havedict; /* true if dictionary provided */
+ int flags; /* gzip header method and flags (0 if zlib) */
+ unsigned dmax; /* zlib header max distance (INFLATE_STRICT) */
+ unsigned long check; /* protected copy of check value */
+ unsigned long total; /* protected copy of output count */
+ gz_headerp head; /* where to save gzip header information */
+ /* sliding window */
+ unsigned wbits; /* log base 2 of requested window size */
+ unsigned wsize; /* window size or zero if not using window */
+ unsigned whave; /* valid bytes in the window */
+ unsigned wnext; /* window write index */
+ unsigned char FAR *window; /* allocated sliding window, if needed */
+ /* bit accumulator */
+ unsigned long hold; /* input bit accumulator */
+ unsigned bits; /* number of bits in "in" */
+ /* for string and stored block copying */
+ unsigned length; /* literal or length of data to copy */
+ unsigned offset; /* distance back to copy string from */
+ /* for table and code decoding */
+ unsigned extra; /* extra bits needed */
+ /* fixed and dynamic code tables */
+ code const FAR *lencode; /* starting table for length/literal codes */
+ code const FAR *distcode; /* starting table for distance codes */
+ unsigned lenbits; /* index bits for lencode */
+ unsigned distbits; /* index bits for distcode */
+ /* dynamic table building */
+ unsigned ncode; /* number of code length code lengths */
+ unsigned nlen; /* number of length code lengths */
+ unsigned ndist; /* number of distance code lengths */
+ unsigned have; /* number of code lengths in lens[] */
+ code FAR *next; /* next available space in codes[] */
+ unsigned short lens[320]; /* temporary storage for code lengths */
+ unsigned short work[288]; /* work area for code table building */
+ code codes[ENOUGH]; /* space for code tables */
+ int sane; /* if false, allow invalid distance too far */
+ int back; /* bits back of last unprocessed length/lit */
+ unsigned was; /* initial length of match */
+};
diff --git a/third-party/zlib/inftrees.c b/third-party/zlib/inftrees.c
new file mode 100644
index 0000000..44d89cf
--- /dev/null
+++ b/third-party/zlib/inftrees.c
@@ -0,0 +1,306 @@
+/* inftrees.c -- generate Huffman trees for efficient decoding
+ * Copyright (C) 1995-2013 Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+#include "zutil.h"
+#include "inftrees.h"
+
+#define MAXBITS 15
+
+const char inflate_copyright[] =
+ " inflate 1.2.8 Copyright 1995-2013 Mark Adler ";
+/*
+ If you use the zlib library in a product, an acknowledgment is welcome
+ in the documentation of your product. If for some reason you cannot
+ include such an acknowledgment, I would appreciate that you keep this
+ copyright string in the executable of your product.
+ */
+
+/*
+ Build a set of tables to decode the provided canonical Huffman code.
+ The code lengths are lens[0..codes-1]. The result starts at *table,
+ whose indices are 0..2^bits-1. work is a writable array of at least
+ lens shorts, which is used as a work area. type is the type of code
+ to be generated, CODES, LENS, or DISTS. On return, zero is success,
+ -1 is an invalid code, and +1 means that ENOUGH isn't enough. table
+ on return points to the next available entry's address. bits is the
+ requested root table index bits, and on return it is the actual root
+ table index bits. It will differ if the request is greater than the
+ longest code or if it is less than the shortest code.
+ */
+int ZLIB_INTERNAL inflate_table(type, lens, codes, table, bits, work)
+codetype type;
+unsigned short FAR *lens;
+unsigned codes;
+code FAR * FAR *table;
+unsigned FAR *bits;
+unsigned short FAR *work;
+{
+ unsigned len; /* a code's length in bits */
+ unsigned sym; /* index of code symbols */
+ unsigned min, max; /* minimum and maximum code lengths */
+ unsigned root; /* number of index bits for root table */
+ unsigned curr; /* number of index bits for current table */
+ unsigned drop; /* code bits to drop for sub-table */
+ int left; /* number of prefix codes available */
+ unsigned used; /* code entries in table used */
+ unsigned huff; /* Huffman code */
+ unsigned incr; /* for incrementing code, index */
+ unsigned fill; /* index for replicating entries */
+ unsigned low; /* low bits for current root entry */
+ unsigned mask; /* mask for low root bits */
+ code here; /* table entry for duplication */
+ code FAR *next; /* next available space in table */
+ const unsigned short FAR *base; /* base value table to use */
+ const unsigned short FAR *extra; /* extra bits table to use */
+ int end; /* use base and extra for symbol > end */
+ unsigned short count[MAXBITS+1]; /* number of codes of each length */
+ unsigned short offs[MAXBITS+1]; /* offsets in table for each length */
+ static const unsigned short lbase[31] = { /* Length codes 257..285 base */
+ 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 15, 17, 19, 23, 27, 31,
+ 35, 43, 51, 59, 67, 83, 99, 115, 131, 163, 195, 227, 258, 0, 0};
+ static const unsigned short lext[31] = { /* Length codes 257..285 extra */
+ 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 18, 18, 18, 18,
+ 19, 19, 19, 19, 20, 20, 20, 20, 21, 21, 21, 21, 16, 72, 78};
+ static const unsigned short dbase[32] = { /* Distance codes 0..29 base */
+ 1, 2, 3, 4, 5, 7, 9, 13, 17, 25, 33, 49, 65, 97, 129, 193,
+ 257, 385, 513, 769, 1025, 1537, 2049, 3073, 4097, 6145,
+ 8193, 12289, 16385, 24577, 0, 0};
+ static const unsigned short dext[32] = { /* Distance codes 0..29 extra */
+ 16, 16, 16, 16, 17, 17, 18, 18, 19, 19, 20, 20, 21, 21, 22, 22,
+ 23, 23, 24, 24, 25, 25, 26, 26, 27, 27,
+ 28, 28, 29, 29, 64, 64};
+
+ /*
+ Process a set of code lengths to create a canonical Huffman code. The
+ code lengths are lens[0..codes-1]. Each length corresponds to the
+ symbols 0..codes-1. The Huffman code is generated by first sorting the
+ symbols by length from short to long, and retaining the symbol order
+ for codes with equal lengths. Then the code starts with all zero bits
+ for the first code of the shortest length, and the codes are integer
+ increments for the same length, and zeros are appended as the length
+ increases. For the deflate format, these bits are stored backwards
+ from their more natural integer increment ordering, and so when the
+ decoding tables are built in the large loop below, the integer codes
+ are incremented backwards.
+
+ This routine assumes, but does not check, that all of the entries in
+ lens[] are in the range 0..MAXBITS. The caller must assure this.
+ 1..MAXBITS is interpreted as that code length. zero means that that
+ symbol does not occur in this code.
+
+ The codes are sorted by computing a count of codes for each length,
+ creating from that a table of starting indices for each length in the
+ sorted table, and then entering the symbols in order in the sorted
+ table. The sorted table is work[], with that space being provided by
+ the caller.
+
+ The length counts are used for other purposes as well, i.e. finding
+ the minimum and maximum length codes, determining if there are any
+ codes at all, checking for a valid set of lengths, and looking ahead
+ at length counts to determine sub-table sizes when building the
+ decoding tables.
+ */
+
+ /* accumulate lengths for codes (assumes lens[] all in 0..MAXBITS) */
+ for (len = 0; len <= MAXBITS; len++)
+ count[len] = 0;
+ for (sym = 0; sym < codes; sym++)
+ count[lens[sym]]++;
+
+ /* bound code lengths, force root to be within code lengths */
+ root = *bits;
+ for (max = MAXBITS; max >= 1; max--)
+ if (count[max] != 0) break;
+ if (root > max) root = max;
+ if (max == 0) { /* no symbols to code at all */
+ here.op = (unsigned char)64; /* invalid code marker */
+ here.bits = (unsigned char)1;
+ here.val = (unsigned short)0;
+ *(*table)++ = here; /* make a table to force an error */
+ *(*table)++ = here;
+ *bits = 1;
+ return 0; /* no symbols, but wait for decoding to report error */
+ }
+ for (min = 1; min < max; min++)
+ if (count[min] != 0) break;
+ if (root < min) root = min;
+
+ /* check for an over-subscribed or incomplete set of lengths */
+ left = 1;
+ for (len = 1; len <= MAXBITS; len++) {
+ left <<= 1;
+ left -= count[len];
+ if (left < 0) return -1; /* over-subscribed */
+ }
+ if (left > 0 && (type == CODES || max != 1))
+ return -1; /* incomplete set */
+
+ /* generate offsets into symbol table for each length for sorting */
+ offs[1] = 0;
+ for (len = 1; len < MAXBITS; len++)
+ offs[len + 1] = offs[len] + count[len];
+
+ /* sort symbols by length, by symbol order within each length */
+ for (sym = 0; sym < codes; sym++)
+ if (lens[sym] != 0) work[offs[lens[sym]]++] = (unsigned short)sym;
+
+ /*
+ Create and fill in decoding tables. In this loop, the table being
+ filled is at next and has curr index bits. The code being used is huff
+ with length len. That code is converted to an index by dropping drop
+ bits off of the bottom. For codes where len is less than drop + curr,
+ those top drop + curr - len bits are incremented through all values to
+ fill the table with replicated entries.
+
+ root is the number of index bits for the root table. When len exceeds
+ root, sub-tables are created pointed to by the root entry with an index
+ of the low root bits of huff. This is saved in low to check for when a
+ new sub-table should be started. drop is zero when the root table is
+ being filled, and drop is root when sub-tables are being filled.
+
+ When a new sub-table is needed, it is necessary to look ahead in the
+ code lengths to determine what size sub-table is needed. The length
+ counts are used for this, and so count[] is decremented as codes are
+ entered in the tables.
+
+ used keeps track of how many table entries have been allocated from the
+ provided *table space. It is checked for LENS and DIST tables against
+ the constants ENOUGH_LENS and ENOUGH_DISTS to guard against changes in
+ the initial root table size constants. See the comments in inftrees.h
+ for more information.
+
+ sym increments through all symbols, and the loop terminates when
+ all codes of length max, i.e. all codes, have been processed. This
+ routine permits incomplete codes, so another loop after this one fills
+ in the rest of the decoding tables with invalid code markers.
+ */
+
+ /* set up for code type */
+ switch (type) {
+ case CODES:
+ base = extra = work; /* dummy value--not used */
+ end = 19;
+ break;
+ case LENS:
+ base = lbase;
+ base -= 257;
+ extra = lext;
+ extra -= 257;
+ end = 256;
+ break;
+ default: /* DISTS */
+ base = dbase;
+ extra = dext;
+ end = -1;
+ }
+
+ /* initialize state for loop */
+ huff = 0; /* starting code */
+ sym = 0; /* starting code symbol */
+ len = min; /* starting code length */
+ next = *table; /* current table to fill in */
+ curr = root; /* current table index bits */
+ drop = 0; /* current bits to drop from code for index */
+ low = (unsigned)(-1); /* trigger new sub-table when len > root */
+ used = 1U << root; /* use root table entries */
+ mask = used - 1; /* mask for comparing low */
+
+ /* check available table space */
+ if ((type == LENS && used > ENOUGH_LENS) ||
+ (type == DISTS && used > ENOUGH_DISTS))
+ return 1;
+
+ /* process all codes and make table entries */
+ for (;;) {
+ /* create table entry */
+ here.bits = (unsigned char)(len - drop);
+ if ((int)(work[sym]) < end) {
+ here.op = (unsigned char)0;
+ here.val = work[sym];
+ }
+ else if ((int)(work[sym]) > end) {
+ here.op = (unsigned char)(extra[work[sym]]);
+ here.val = base[work[sym]];
+ }
+ else {
+ here.op = (unsigned char)(32 + 64); /* end of block */
+ here.val = 0;
+ }
+
+ /* replicate for those indices with low len bits equal to huff */
+ incr = 1U << (len - drop);
+ fill = 1U << curr;
+ min = fill; /* save offset to next table */
+ do {
+ fill -= incr;
+ next[(huff >> drop) + fill] = here;
+ } while (fill != 0);
+
+ /* backwards increment the len-bit code huff */
+ incr = 1U << (len - 1);
+ while (huff & incr)
+ incr >>= 1;
+ if (incr != 0) {
+ huff &= incr - 1;
+ huff += incr;
+ }
+ else
+ huff = 0;
+
+ /* go to next symbol, update count, len */
+ sym++;
+ if (--(count[len]) == 0) {
+ if (len == max) break;
+ len = lens[work[sym]];
+ }
+
+ /* create new sub-table if needed */
+ if (len > root && (huff & mask) != low) {
+ /* if first time, transition to sub-tables */
+ if (drop == 0)
+ drop = root;
+
+ /* increment past last table */
+ next += min; /* here min is 1 << curr */
+
+ /* determine length of next table */
+ curr = len - drop;
+ left = (int)(1 << curr);
+ while (curr + drop < max) {
+ left -= count[curr + drop];
+ if (left <= 0) break;
+ curr++;
+ left <<= 1;
+ }
+
+ /* check for enough space */
+ used += 1U << curr;
+ if ((type == LENS && used > ENOUGH_LENS) ||
+ (type == DISTS && used > ENOUGH_DISTS))
+ return 1;
+
+ /* point entry in root table to sub-table */
+ low = huff & mask;
+ (*table)[low].op = (unsigned char)curr;
+ (*table)[low].bits = (unsigned char)root;
+ (*table)[low].val = (unsigned short)(next - *table);
+ }
+ }
+
+ /* fill in remaining table entry if code is incomplete (guaranteed to have
+ at most one remaining entry, since if the code is incomplete, the
+ maximum code length that was allowed to get this far is one bit) */
+ if (huff != 0) {
+ here.op = (unsigned char)64; /* invalid code marker */
+ here.bits = (unsigned char)(len - drop);
+ here.val = (unsigned short)0;
+ next[huff] = here;
+ }
+
+ /* set return parameters */
+ *table += used;
+ *bits = root;
+ return 0;
+}
diff --git a/third-party/zlib/inftrees.h b/third-party/zlib/inftrees.h
new file mode 100644
index 0000000..baa53a0
--- /dev/null
+++ b/third-party/zlib/inftrees.h
@@ -0,0 +1,62 @@
+/* inftrees.h -- header to use inftrees.c
+ * Copyright (C) 1995-2005, 2010 Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* WARNING: this file should *not* be used by applications. It is
+ part of the implementation of the compression library and is
+ subject to change. Applications should only use zlib.h.
+ */
+
+/* Structure for decoding tables. Each entry provides either the
+ information needed to do the operation requested by the code that
+ indexed that table entry, or it provides a pointer to another
+ table that indexes more bits of the code. op indicates whether
+ the entry is a pointer to another table, a literal, a length or
+ distance, an end-of-block, or an invalid code. For a table
+ pointer, the low four bits of op is the number of index bits of
+ that table. For a length or distance, the low four bits of op
+ is the number of extra bits to get after the code. bits is
+ the number of bits in this code or part of the code to drop off
+ of the bit buffer. val is the actual byte to output in the case
+ of a literal, the base length or distance, or the offset from
+ the current table to the next table. Each entry is four bytes. */
+typedef struct {
+ unsigned char op; /* operation, extra bits, table bits */
+ unsigned char bits; /* bits in this part of the code */
+ unsigned short val; /* offset in table or code value */
+} code;
+
+/* op values as set by inflate_table():
+ 00000000 - literal
+ 0000tttt - table link, tttt != 0 is the number of table index bits
+ 0001eeee - length or distance, eeee is the number of extra bits
+ 01100000 - end of block
+ 01000000 - invalid code
+ */
+
+/* Maximum size of the dynamic table. The maximum number of code structures is
+ 1444, which is the sum of 852 for literal/length codes and 592 for distance
+ codes. These values were found by exhaustive searches using the program
+ examples/enough.c found in the zlib distribtution. The arguments to that
+ program are the number of symbols, the initial root table size, and the
+ maximum bit length of a code. "enough 286 9 15" for literal/length codes
+ returns returns 852, and "enough 30 6 15" for distance codes returns 592.
+ The initial root table size (9 or 6) is found in the fifth argument of the
+ inflate_table() calls in inflate.c and infback.c. If the root table size is
+ changed, then these maximum sizes would be need to be recalculated and
+ updated. */
+#define ENOUGH_LENS 852
+#define ENOUGH_DISTS 592
+#define ENOUGH (ENOUGH_LENS+ENOUGH_DISTS)
+
+/* Type of code to build for inflate_table() */
+typedef enum {
+ CODES,
+ LENS,
+ DISTS
+} codetype;
+
+int ZLIB_INTERNAL inflate_table OF((codetype type, unsigned short FAR *lens,
+ unsigned codes, code FAR * FAR *table,
+ unsigned FAR *bits, unsigned short FAR *work));
diff --git a/third-party/zlib/make_vms.com b/third-party/zlib/make_vms.com
new file mode 100644
index 0000000..65e9d0c
--- /dev/null
+++ b/third-party/zlib/make_vms.com
@@ -0,0 +1,867 @@
+$! make libz under VMS written by
+$! Martin P.J. Zinser
+$!
+$! In case of problems with the install you might contact me at
+$! zinser at zinser.no-ip.info(preferred) or
+$! martin.zinser at eurexchange.com (work)
+$!
+$! Make procedure history for Zlib
+$!
+$!------------------------------------------------------------------------------
+$! Version history
+$! 0.01 20060120 First version to receive a number
+$! 0.02 20061008 Adapt to new Makefile.in
+$! 0.03 20091224 Add support for large file check
+$! 0.04 20100110 Add new gzclose, gzlib, gzread, gzwrite
+$! 0.05 20100221 Exchange zlibdefs.h by zconf.h.in
+$! 0.06 20120111 Fix missing amiss_err, update zconf_h.in, fix new exmples
+$! subdir path, update module search in makefile.in
+$! 0.07 20120115 Triggered by work done by Alexey Chupahin completly redesigned
+$! shared image creation
+$! 0.08 20120219 Make it work on VAX again, pre-load missing symbols to shared
+$! image
+$! 0.09 20120305 SMS. P1 sets builder ("MMK", "MMS", " " (built-in)).
+$! "" -> automatic, preference: MMK, MMS, built-in.
+$!
+$ on error then goto err_exit
+$!
+$ true = 1
+$ false = 0
+$ tmpnam = "temp_" + f$getjpi("","pid")
+$ tt = tmpnam + ".txt"
+$ tc = tmpnam + ".c"
+$ th = tmpnam + ".h"
+$ define/nolog tconfig 'th'
+$ its_decc = false
+$ its_vaxc = false
+$ its_gnuc = false
+$ s_case = False
+$!
+$! Setup variables holding "config" information
+$!
+$ Make = "''p1'"
+$ name = "Zlib"
+$ version = "?.?.?"
+$ v_string = "ZLIB_VERSION"
+$ v_file = "zlib.h"
+$ ccopt = "/include = []"
+$ lopts = ""
+$ dnsrl = ""
+$ aconf_in_file = "zconf.h.in#zconf.h_in#zconf_h.in"
+$ conf_check_string = ""
+$ linkonly = false
+$ optfile = name + ".opt"
+$ mapfile = name + ".map"
+$ libdefs = ""
+$ vax = f$getsyi("HW_MODEL").lt.1024
+$ axp = f$getsyi("HW_MODEL").ge.1024 .and. f$getsyi("HW_MODEL").lt.4096
+$ ia64 = f$getsyi("HW_MODEL").ge.4096
+$!
+$! 2012-03-05 SMS.
+$! Why is this needed? And if it is needed, why not simply ".not. vax"?
+$!
+$!!! if axp .or. ia64 then set proc/parse=extended
+$!
+$ whoami = f$parse(f$environment("Procedure"),,,,"NO_CONCEAL")
+$ mydef = F$parse(whoami,,,"DEVICE")
+$ mydir = f$parse(whoami,,,"DIRECTORY") - "]["
+$ myproc = f$parse(whoami,,,"Name") + f$parse(whoami,,,"type")
+$!
+$! Check for MMK/MMS
+$!
+$ if (Make .eqs. "")
+$ then
+$ If F$Search ("Sys$System:MMS.EXE") .nes. "" Then Make = "MMS"
+$ If F$Type (MMK) .eqs. "STRING" Then Make = "MMK"
+$ else
+$ Make = f$edit( Make, "trim")
+$ endif
+$!
+$ gosub find_version
+$!
+$ open/write topt tmp.opt
+$ open/write optf 'optfile'
+$!
+$ gosub check_opts
+$!
+$! Look for the compiler used
+$!
+$ gosub check_compiler
+$ close topt
+$ close optf
+$!
+$ if its_decc
+$ then
+$ ccopt = "/prefix=all" + ccopt
+$ if f$trnlnm("SYS") .eqs. ""
+$ then
+$ if axp
+$ then
+$ define sys sys$library:
+$ else
+$ ccopt = "/decc" + ccopt
+$ define sys decc$library_include:
+$ endif
+$ endif
+$!
+$! 2012-03-05 SMS.
+$! Why /NAMES = AS_IS? Why not simply ".not. vax"? And why not on VAX?
+$!
+$ if axp .or. ia64
+$ then
+$ ccopt = ccopt + "/name=as_is/opt=(inline=speed)"
+$ s_case = true
+$ endif
+$ endif
+$ if its_vaxc .or. its_gnuc
+$ then
+$ if f$trnlnm("SYS").eqs."" then define sys sys$library:
+$ endif
+$!
+$! Build a fake configure input header
+$!
+$ open/write conf_hin config.hin
+$ write conf_hin "#undef _LARGEFILE64_SOURCE"
+$ close conf_hin
+$!
+$!
+$ i = 0
+$FIND_ACONF:
+$ fname = f$element(i,"#",aconf_in_file)
+$ if fname .eqs. "#" then goto AMISS_ERR
+$ if f$search(fname) .eqs. ""
+$ then
+$ i = i + 1
+$ goto find_aconf
+$ endif
+$ open/read/err=aconf_err aconf_in 'fname'
+$ open/write aconf zconf.h
+$ACONF_LOOP:
+$ read/end_of_file=aconf_exit aconf_in line
+$ work = f$edit(line, "compress,trim")
+$ if f$extract(0,6,work) .nes. "#undef"
+$ then
+$ if f$extract(0,12,work) .nes. "#cmakedefine"
+$ then
+$ write aconf line
+$ endif
+$ else
+$ cdef = f$element(1," ",work)
+$ gosub check_config
+$ endif
+$ goto aconf_loop
+$ACONF_EXIT:
+$ write aconf ""
+$ write aconf "/* VMS specifics added by make_vms.com: */"
+$ write aconf "#define VMS 1"
+$ write aconf "#include <unistd.h>"
+$ write aconf "#include <unixio.h>"
+$ write aconf "#ifdef _LARGEFILE"
+$ write aconf "# define off64_t __off64_t"
+$ write aconf "# define fopen64 fopen"
+$ write aconf "# define fseeko64 fseeko"
+$ write aconf "# define lseek64 lseek"
+$ write aconf "# define ftello64 ftell"
+$ write aconf "#endif"
+$ write aconf "#if !defined( __VAX) && (__CRTL_VER >= 70312000)"
+$ write aconf "# define HAVE_VSNPRINTF"
+$ write aconf "#endif"
+$ close aconf_in
+$ close aconf
+$ if f$search("''th'") .nes. "" then delete 'th';*
+$! Build the thing plain or with mms
+$!
+$ write sys$output "Compiling Zlib sources ..."
+$ if make.eqs.""
+$ then
+$ if (f$search( "example.obj;*") .nes. "") then delete example.obj;*
+$ if (f$search( "minigzip.obj;*") .nes. "") then delete minigzip.obj;*
+$ CALL MAKE adler32.OBJ "CC ''CCOPT' adler32" -
+ adler32.c zlib.h zconf.h
+$ CALL MAKE compress.OBJ "CC ''CCOPT' compress" -
+ compress.c zlib.h zconf.h
+$ CALL MAKE crc32.OBJ "CC ''CCOPT' crc32" -
+ crc32.c zlib.h zconf.h
+$ CALL MAKE deflate.OBJ "CC ''CCOPT' deflate" -
+ deflate.c deflate.h zutil.h zlib.h zconf.h
+$ CALL MAKE gzclose.OBJ "CC ''CCOPT' gzclose" -
+ gzclose.c zutil.h zlib.h zconf.h
+$ CALL MAKE gzlib.OBJ "CC ''CCOPT' gzlib" -
+ gzlib.c zutil.h zlib.h zconf.h
+$ CALL MAKE gzread.OBJ "CC ''CCOPT' gzread" -
+ gzread.c zutil.h zlib.h zconf.h
+$ CALL MAKE gzwrite.OBJ "CC ''CCOPT' gzwrite" -
+ gzwrite.c zutil.h zlib.h zconf.h
+$ CALL MAKE infback.OBJ "CC ''CCOPT' infback" -
+ infback.c zutil.h inftrees.h inflate.h inffast.h inffixed.h
+$ CALL MAKE inffast.OBJ "CC ''CCOPT' inffast" -
+ inffast.c zutil.h zlib.h zconf.h inffast.h
+$ CALL MAKE inflate.OBJ "CC ''CCOPT' inflate" -
+ inflate.c zutil.h zlib.h zconf.h infblock.h
+$ CALL MAKE inftrees.OBJ "CC ''CCOPT' inftrees" -
+ inftrees.c zutil.h zlib.h zconf.h inftrees.h
+$ CALL MAKE trees.OBJ "CC ''CCOPT' trees" -
+ trees.c deflate.h zutil.h zlib.h zconf.h
+$ CALL MAKE uncompr.OBJ "CC ''CCOPT' uncompr" -
+ uncompr.c zlib.h zconf.h
+$ CALL MAKE zutil.OBJ "CC ''CCOPT' zutil" -
+ zutil.c zutil.h zlib.h zconf.h
+$ write sys$output "Building Zlib ..."
+$ CALL MAKE libz.OLB "lib/crea libz.olb *.obj" *.OBJ
+$ write sys$output "Building example..."
+$ CALL MAKE example.OBJ "CC ''CCOPT' [.test]example" -
+ [.test]example.c zlib.h zconf.h
+$ call make example.exe "LINK example,libz.olb/lib" example.obj libz.olb
+$ write sys$output "Building minigzip..."
+$ CALL MAKE minigzip.OBJ "CC ''CCOPT' [.test]minigzip" -
+ [.test]minigzip.c zlib.h zconf.h
+$ call make minigzip.exe -
+ "LINK minigzip,libz.olb/lib" -
+ minigzip.obj libz.olb
+$ else
+$ gosub crea_mms
+$ write sys$output "Make ''name' ''version' with ''Make' "
+$ 'make'
+$ endif
+$!
+$! Create shareable image
+$!
+$ gosub crea_olist
+$ write sys$output "Creating libzshr.exe"
+$ call map_2_shopt 'mapfile' 'optfile'
+$ LINK_'lopts'/SHARE=libzshr.exe modules.opt/opt,'optfile'/opt
+$ write sys$output "Zlib build completed"
+$ delete/nolog tmp.opt;*
+$ exit
+$AMISS_ERR:
+$ write sys$output "No source for config.hin found."
+$ write sys$output "Tried any of ''aconf_in_file'"
+$ goto err_exit
+$CC_ERR:
+$ write sys$output "C compiler required to build ''name'"
+$ goto err_exit
+$ERR_EXIT:
+$ set message/facil/ident/sever/text
+$ close/nolog optf
+$ close/nolog topt
+$ close/nolog aconf_in
+$ close/nolog aconf
+$ close/nolog out
+$ close/nolog min
+$ close/nolog mod
+$ close/nolog h_in
+$ write sys$output "Exiting..."
+$ exit 2
+$!
+$!
+$MAKE: SUBROUTINE !SUBROUTINE TO CHECK DEPENDENCIES
+$ V = 'F$Verify(0)
+$! P1 = What we are trying to make
+$! P2 = Command to make it
+$! P3 - P8 What it depends on
+$
+$ If F$Search(P1) .Eqs. "" Then Goto Makeit
+$ Time = F$CvTime(F$File(P1,"RDT"))
+$arg=3
+$Loop:
+$ Argument = P'arg
+$ If Argument .Eqs. "" Then Goto Exit
+$ El=0
+$Loop2:
+$ File = F$Element(El," ",Argument)
+$ If File .Eqs. " " Then Goto Endl
+$ AFile = ""
+$Loop3:
+$ OFile = AFile
+$ AFile = F$Search(File)
+$ If AFile .Eqs. "" .Or. AFile .Eqs. OFile Then Goto NextEl
+$ If F$CvTime(F$File(AFile,"RDT")) .Ges. Time Then Goto Makeit
+$ Goto Loop3
+$NextEL:
+$ El = El + 1
+$ Goto Loop2
+$EndL:
+$ arg=arg+1
+$ If arg .Le. 8 Then Goto Loop
+$ Goto Exit
+$
+$Makeit:
+$ VV=F$VERIFY(0)
+$ write sys$output P2
+$ 'P2
+$ VV='F$Verify(VV)
+$Exit:
+$ If V Then Set Verify
+$ENDSUBROUTINE
+$!------------------------------------------------------------------------------
+$!
+$! Check command line options and set symbols accordingly
+$!
+$!------------------------------------------------------------------------------
+$! Version history
+$! 0.01 20041206 First version to receive a number
+$! 0.02 20060126 Add new "HELP" target
+$ CHECK_OPTS:
+$ i = 1
+$ OPT_LOOP:
+$ if i .lt. 9
+$ then
+$ cparm = f$edit(p'i',"upcase")
+$!
+$! Check if parameter actually contains something
+$!
+$ if f$edit(cparm,"trim") .nes. ""
+$ then
+$ if cparm .eqs. "DEBUG"
+$ then
+$ ccopt = ccopt + "/noopt/deb"
+$ lopts = lopts + "/deb"
+$ endif
+$ if f$locate("CCOPT=",cparm) .lt. f$length(cparm)
+$ then
+$ start = f$locate("=",cparm) + 1
+$ len = f$length(cparm) - start
+$ ccopt = ccopt + f$extract(start,len,cparm)
+$ if f$locate("AS_IS",f$edit(ccopt,"UPCASE")) .lt. f$length(ccopt) -
+ then s_case = true
+$ endif
+$ if cparm .eqs. "LINK" then linkonly = true
+$ if f$locate("LOPTS=",cparm) .lt. f$length(cparm)
+$ then
+$ start = f$locate("=",cparm) + 1
+$ len = f$length(cparm) - start
+$ lopts = lopts + f$extract(start,len,cparm)
+$ endif
+$ if f$locate("CC=",cparm) .lt. f$length(cparm)
+$ then
+$ start = f$locate("=",cparm) + 1
+$ len = f$length(cparm) - start
+$ cc_com = f$extract(start,len,cparm)
+ if (cc_com .nes. "DECC") .and. -
+ (cc_com .nes. "VAXC") .and. -
+ (cc_com .nes. "GNUC")
+$ then
+$ write sys$output "Unsupported compiler choice ''cc_com' ignored"
+$ write sys$output "Use DECC, VAXC, or GNUC instead"
+$ else
+$ if cc_com .eqs. "DECC" then its_decc = true
+$ if cc_com .eqs. "VAXC" then its_vaxc = true
+$ if cc_com .eqs. "GNUC" then its_gnuc = true
+$ endif
+$ endif
+$ if f$locate("MAKE=",cparm) .lt. f$length(cparm)
+$ then
+$ start = f$locate("=",cparm) + 1
+$ len = f$length(cparm) - start
+$ mmks = f$extract(start,len,cparm)
+$ if (mmks .eqs. "MMK") .or. (mmks .eqs. "MMS")
+$ then
+$ make = mmks
+$ else
+$ write sys$output "Unsupported make choice ''mmks' ignored"
+$ write sys$output "Use MMK or MMS instead"
+$ endif
+$ endif
+$ if cparm .eqs. "HELP" then gosub bhelp
+$ endif
+$ i = i + 1
+$ goto opt_loop
+$ endif
+$ return
+$!------------------------------------------------------------------------------
+$!
+$! Look for the compiler used
+$!
+$! Version history
+$! 0.01 20040223 First version to receive a number
+$! 0.02 20040229 Save/set value of decc$no_rooted_search_lists
+$! 0.03 20060202 Extend handling of GNU C
+$! 0.04 20090402 Compaq -> hp
+$CHECK_COMPILER:
+$ if (.not. (its_decc .or. its_vaxc .or. its_gnuc))
+$ then
+$ its_decc = (f$search("SYS$SYSTEM:DECC$COMPILER.EXE") .nes. "")
+$ its_vaxc = .not. its_decc .and. (F$Search("SYS$System:VAXC.Exe") .nes. "")
+$ its_gnuc = .not. (its_decc .or. its_vaxc) .and. (f$trnlnm("gnu_cc") .nes. "")
+$ endif
+$!
+$! Exit if no compiler available
+$!
+$ if (.not. (its_decc .or. its_vaxc .or. its_gnuc))
+$ then goto CC_ERR
+$ else
+$ if its_decc
+$ then
+$ write sys$output "CC compiler check ... hp C"
+$ if f$trnlnm("decc$no_rooted_search_lists") .nes. ""
+$ then
+$ dnrsl = f$trnlnm("decc$no_rooted_search_lists")
+$ endif
+$ define/nolog decc$no_rooted_search_lists 1
+$ else
+$ if its_vaxc then write sys$output "CC compiler check ... VAX C"
+$ if its_gnuc
+$ then
+$ write sys$output "CC compiler check ... GNU C"
+$ if f$trnlnm(topt) then write topt "gnu_cc:[000000]gcclib.olb/lib"
+$ if f$trnlnm(optf) then write optf "gnu_cc:[000000]gcclib.olb/lib"
+$ cc = "gcc"
+$ endif
+$ if f$trnlnm(topt) then write topt "sys$share:vaxcrtl.exe/share"
+$ if f$trnlnm(optf) then write optf "sys$share:vaxcrtl.exe/share"
+$ endif
+$ endif
+$ return
+$!------------------------------------------------------------------------------
+$!
+$! If MMS/MMK are available dump out the descrip.mms if required
+$!
+$CREA_MMS:
+$ write sys$output "Creating descrip.mms..."
+$ create descrip.mms
+$ open/append out descrip.mms
+$ copy sys$input: out
+$ deck
+# descrip.mms: MMS description file for building zlib on VMS
+# written by Martin P.J. Zinser
+# <zinser at zinser.no-ip.info or martin.zinser at eurexchange.com>
+
+OBJS = adler32.obj, compress.obj, crc32.obj, gzclose.obj, gzlib.obj\
+ gzread.obj, gzwrite.obj, uncompr.obj, infback.obj\
+ deflate.obj, trees.obj, zutil.obj, inflate.obj, \
+ inftrees.obj, inffast.obj
+
+$ eod
+$ write out "CFLAGS=", ccopt
+$ write out "LOPTS=", lopts
+$ write out "all : example.exe minigzip.exe libz.olb"
+$ copy sys$input: out
+$ deck
+ @ write sys$output " Example applications available"
+
+libz.olb : libz.olb($(OBJS))
+ @ write sys$output " libz available"
+
+example.exe : example.obj libz.olb
+ link $(LOPTS) example,libz.olb/lib
+
+minigzip.exe : minigzip.obj libz.olb
+ link $(LOPTS) minigzip,libz.olb/lib
+
+clean :
+ delete *.obj;*,libz.olb;*,*.opt;*,*.exe;*
+
+
+# Other dependencies.
+adler32.obj : adler32.c zutil.h zlib.h zconf.h
+compress.obj : compress.c zlib.h zconf.h
+crc32.obj : crc32.c zutil.h zlib.h zconf.h
+deflate.obj : deflate.c deflate.h zutil.h zlib.h zconf.h
+example.obj : [.test]example.c zlib.h zconf.h
+gzclose.obj : gzclose.c zutil.h zlib.h zconf.h
+gzlib.obj : gzlib.c zutil.h zlib.h zconf.h
+gzread.obj : gzread.c zutil.h zlib.h zconf.h
+gzwrite.obj : gzwrite.c zutil.h zlib.h zconf.h
+inffast.obj : inffast.c zutil.h zlib.h zconf.h inftrees.h inffast.h
+inflate.obj : inflate.c zutil.h zlib.h zconf.h
+inftrees.obj : inftrees.c zutil.h zlib.h zconf.h inftrees.h
+minigzip.obj : [.test]minigzip.c zlib.h zconf.h
+trees.obj : trees.c deflate.h zutil.h zlib.h zconf.h
+uncompr.obj : uncompr.c zlib.h zconf.h
+zutil.obj : zutil.c zutil.h zlib.h zconf.h
+infback.obj : infback.c zutil.h inftrees.h inflate.h inffast.h inffixed.h
+$ eod
+$ close out
+$ return
+$!------------------------------------------------------------------------------
+$!
+$! Read list of core library sources from makefile.in and create options
+$! needed to build shareable image
+$!
+$CREA_OLIST:
+$ open/read min makefile.in
+$ open/write mod modules.opt
+$ src_check_list = "OBJZ =#OBJG ="
+$MRLOOP:
+$ read/end=mrdone min rec
+$ i = 0
+$SRC_CHECK_LOOP:
+$ src_check = f$element(i, "#", src_check_list)
+$ i = i+1
+$ if src_check .eqs. "#" then goto mrloop
+$ if (f$extract(0,6,rec) .nes. src_check) then goto src_check_loop
+$ rec = rec - src_check
+$ gosub extra_filnam
+$ if (f$element(1,"\",rec) .eqs. "\") then goto mrloop
+$MRSLOOP:
+$ read/end=mrdone min rec
+$ gosub extra_filnam
+$ if (f$element(1,"\",rec) .nes. "\") then goto mrsloop
+$MRDONE:
+$ close min
+$ close mod
+$ return
+$!------------------------------------------------------------------------------
+$!
+$! Take record extracted in crea_olist and split it into single filenames
+$!
+$EXTRA_FILNAM:
+$ myrec = f$edit(rec - "\", "trim,compress")
+$ i = 0
+$FELOOP:
+$ srcfil = f$element(i," ", myrec)
+$ if (srcfil .nes. " ")
+$ then
+$ write mod f$parse(srcfil,,,"NAME"), ".obj"
+$ i = i + 1
+$ goto feloop
+$ endif
+$ return
+$!------------------------------------------------------------------------------
+$!
+$! Find current Zlib version number
+$!
+$FIND_VERSION:
+$ open/read h_in 'v_file'
+$hloop:
+$ read/end=hdone h_in rec
+$ rec = f$edit(rec,"TRIM")
+$ if (f$extract(0,1,rec) .nes. "#") then goto hloop
+$ rec = f$edit(rec - "#", "TRIM")
+$ if f$element(0," ",rec) .nes. "define" then goto hloop
+$ if f$element(1," ",rec) .eqs. v_string
+$ then
+$ version = 'f$element(2," ",rec)'
+$ goto hdone
+$ endif
+$ goto hloop
+$hdone:
+$ close h_in
+$ return
+$!------------------------------------------------------------------------------
+$!
+$CHECK_CONFIG:
+$!
+$ in_ldef = f$locate(cdef,libdefs)
+$ if (in_ldef .lt. f$length(libdefs))
+$ then
+$ write aconf "#define ''cdef' 1"
+$ libdefs = f$extract(0,in_ldef,libdefs) + -
+ f$extract(in_ldef + f$length(cdef) + 1, -
+ f$length(libdefs) - in_ldef - f$length(cdef) - 1, -
+ libdefs)
+$ else
+$ if (f$type('cdef') .eqs. "INTEGER")
+$ then
+$ write aconf "#define ''cdef' ", 'cdef'
+$ else
+$ if (f$type('cdef') .eqs. "STRING")
+$ then
+$ write aconf "#define ''cdef' ", """", '''cdef'', """"
+$ else
+$ gosub check_cc_def
+$ endif
+$ endif
+$ endif
+$ return
+$!------------------------------------------------------------------------------
+$!
+$! Check if this is a define relating to the properties of the C/C++
+$! compiler
+$!
+$ CHECK_CC_DEF:
+$ if (cdef .eqs. "_LARGEFILE64_SOURCE")
+$ then
+$ copy sys$input: 'tc'
+$ deck
+#include "tconfig"
+#define _LARGEFILE
+#include <stdio.h>
+
+int main(){
+FILE *fp;
+ fp = fopen("temp.txt","r");
+ fseeko(fp,1,SEEK_SET);
+ fclose(fp);
+}
+
+$ eod
+$ test_inv = false
+$ comm_h = false
+$ gosub cc_prop_check
+$ return
+$ endif
+$ write aconf "/* ", line, " */"
+$ return
+$!------------------------------------------------------------------------------
+$!
+$! Check for properties of C/C++ compiler
+$!
+$! Version history
+$! 0.01 20031020 First version to receive a number
+$! 0.02 20031022 Added logic for defines with value
+$! 0.03 20040309 Make sure local config file gets not deleted
+$! 0.04 20041230 Also write include for configure run
+$! 0.05 20050103 Add processing of "comment defines"
+$CC_PROP_CHECK:
+$ cc_prop = true
+$ is_need = false
+$ is_need = (f$extract(0,4,cdef) .eqs. "NEED") .or. (test_inv .eq. true)
+$ if f$search(th) .eqs. "" then create 'th'
+$ set message/nofac/noident/nosever/notext
+$ on error then continue
+$ cc 'tmpnam'
+$ if .not. ($status) then cc_prop = false
+$ on error then continue
+$! The headers might lie about the capabilities of the RTL
+$ link 'tmpnam',tmp.opt/opt
+$ if .not. ($status) then cc_prop = false
+$ set message/fac/ident/sever/text
+$ on error then goto err_exit
+$ delete/nolog 'tmpnam'.*;*/exclude='th'
+$ if (cc_prop .and. .not. is_need) .or. -
+ (.not. cc_prop .and. is_need)
+$ then
+$ write sys$output "Checking for ''cdef'... yes"
+$ if f$type('cdef_val'_yes) .nes. ""
+$ then
+$ if f$type('cdef_val'_yes) .eqs. "INTEGER" -
+ then call write_config f$fao("#define !AS !UL",cdef,'cdef_val'_yes)
+$ if f$type('cdef_val'_yes) .eqs. "STRING" -
+ then call write_config f$fao("#define !AS !AS",cdef,'cdef_val'_yes)
+$ else
+$ call write_config f$fao("#define !AS 1",cdef)
+$ endif
+$ if (cdef .eqs. "HAVE_FSEEKO") .or. (cdef .eqs. "_LARGE_FILES") .or. -
+ (cdef .eqs. "_LARGEFILE64_SOURCE") then -
+ call write_config f$string("#define _LARGEFILE 1")
+$ else
+$ write sys$output "Checking for ''cdef'... no"
+$ if (comm_h)
+$ then
+ call write_config f$fao("/* !AS */",line)
+$ else
+$ if f$type('cdef_val'_no) .nes. ""
+$ then
+$ if f$type('cdef_val'_no) .eqs. "INTEGER" -
+ then call write_config f$fao("#define !AS !UL",cdef,'cdef_val'_no)
+$ if f$type('cdef_val'_no) .eqs. "STRING" -
+ then call write_config f$fao("#define !AS !AS",cdef,'cdef_val'_no)
+$ else
+$ call write_config f$fao("#undef !AS",cdef)
+$ endif
+$ endif
+$ endif
+$ return
+$!------------------------------------------------------------------------------
+$!
+$! Check for properties of C/C++ compiler with multiple result values
+$!
+$! Version history
+$! 0.01 20040127 First version
+$! 0.02 20050103 Reconcile changes from cc_prop up to version 0.05
+$CC_MPROP_CHECK:
+$ cc_prop = true
+$ i = 1
+$ idel = 1
+$ MT_LOOP:
+$ if f$type(result_'i') .eqs. "STRING"
+$ then
+$ set message/nofac/noident/nosever/notext
+$ on error then continue
+$ cc 'tmpnam'_'i'
+$ if .not. ($status) then cc_prop = false
+$ on error then continue
+$! The headers might lie about the capabilities of the RTL
+$ link 'tmpnam'_'i',tmp.opt/opt
+$ if .not. ($status) then cc_prop = false
+$ set message/fac/ident/sever/text
+$ on error then goto err_exit
+$ delete/nolog 'tmpnam'_'i'.*;*
+$ if (cc_prop)
+$ then
+$ write sys$output "Checking for ''cdef'... ", mdef_'i'
+$ if f$type(mdef_'i') .eqs. "INTEGER" -
+ then call write_config f$fao("#define !AS !UL",cdef,mdef_'i')
+$ if f$type('cdef_val'_yes) .eqs. "STRING" -
+ then call write_config f$fao("#define !AS !AS",cdef,mdef_'i')
+$ goto msym_clean
+$ else
+$ i = i + 1
+$ goto mt_loop
+$ endif
+$ endif
+$ write sys$output "Checking for ''cdef'... no"
+$ call write_config f$fao("#undef !AS",cdef)
+$ MSYM_CLEAN:
+$ if (idel .le. msym_max)
+$ then
+$ delete/sym mdef_'idel'
+$ idel = idel + 1
+$ goto msym_clean
+$ endif
+$ return
+$!------------------------------------------------------------------------------
+$!
+$! Write configuration to both permanent and temporary config file
+$!
+$! Version history
+$! 0.01 20031029 First version to receive a number
+$!
+$WRITE_CONFIG: SUBROUTINE
+$ write aconf 'p1'
+$ open/append confh 'th'
+$ write confh 'p1'
+$ close confh
+$ENDSUBROUTINE
+$!------------------------------------------------------------------------------
+$!
+$! Analyze the project map file and create the symbol vector for a shareable
+$! image from it
+$!
+$! Version history
+$! 0.01 20120128 First version
+$! 0.02 20120226 Add pre-load logic
+$!
+$ MAP_2_SHOPT: Subroutine
+$!
+$ SAY := "WRITE_ SYS$OUTPUT"
+$!
+$ IF F$SEARCH("''P1'") .EQS. ""
+$ THEN
+$ SAY "MAP_2_SHOPT-E-NOSUCHFILE: Error, inputfile ''p1' not available"
+$ goto exit_m2s
+$ ENDIF
+$ IF "''P2'" .EQS. ""
+$ THEN
+$ SAY "MAP_2_SHOPT: Error, no output file provided"
+$ goto exit_m2s
+$ ENDIF
+$!
+$ module1 = "deflate#deflateEnd#deflateInit_#deflateParams#deflateSetDictionary"
+$ module2 = "gzclose#gzerror#gzgetc#gzgets#gzopen#gzprintf#gzputc#gzputs#gzread"
+$ module3 = "gzseek#gztell#inflate#inflateEnd#inflateInit_#inflateSetDictionary"
+$ module4 = "inflateSync#uncompress#zlibVersion#compress"
+$ open/read map 'p1
+$ if axp .or. ia64
+$ then
+$ open/write aopt a.opt
+$ open/write bopt b.opt
+$ write aopt " CASE_SENSITIVE=YES"
+$ write bopt "SYMBOL_VECTOR= (-"
+$ mod_sym_num = 1
+$ MOD_SYM_LOOP:
+$ if f$type(module'mod_sym_num') .nes. ""
+$ then
+$ mod_in = 0
+$ MOD_SYM_IN:
+$ shared_proc = f$element(mod_in, "#", module'mod_sym_num')
+$ if shared_proc .nes. "#"
+$ then
+$ write aopt f$fao(" symbol_vector=(!AS/!AS=PROCEDURE)",-
+ f$edit(shared_proc,"upcase"),shared_proc)
+$ write bopt f$fao("!AS=PROCEDURE,-",shared_proc)
+$ mod_in = mod_in + 1
+$ goto mod_sym_in
+$ endif
+$ mod_sym_num = mod_sym_num + 1
+$ goto mod_sym_loop
+$ endif
+$MAP_LOOP:
+$ read/end=map_end map line
+$ if (f$locate("{",line).lt. f$length(line)) .or. -
+ (f$locate("global:", line) .lt. f$length(line))
+$ then
+$ proc = true
+$ goto map_loop
+$ endif
+$ if f$locate("}",line).lt. f$length(line) then proc = false
+$ if f$locate("local:", line) .lt. f$length(line) then proc = false
+$ if proc
+$ then
+$ shared_proc = f$edit(line,"collapse")
+$ chop_semi = f$locate(";", shared_proc)
+$ if chop_semi .lt. f$length(shared_proc) then -
+ shared_proc = f$extract(0, chop_semi, shared_proc)
+$ write aopt f$fao(" symbol_vector=(!AS/!AS=PROCEDURE)",-
+ f$edit(shared_proc,"upcase"),shared_proc)
+$ write bopt f$fao("!AS=PROCEDURE,-",shared_proc)
+$ endif
+$ goto map_loop
+$MAP_END:
+$ close/nolog aopt
+$ close/nolog bopt
+$ open/append libopt 'p2'
+$ open/read aopt a.opt
+$ open/read bopt b.opt
+$ALOOP:
+$ read/end=aloop_end aopt line
+$ write libopt line
+$ goto aloop
+$ALOOP_END:
+$ close/nolog aopt
+$ sv = ""
+$BLOOP:
+$ read/end=bloop_end bopt svn
+$ if (svn.nes."")
+$ then
+$ if (sv.nes."") then write libopt sv
+$ sv = svn
+$ endif
+$ goto bloop
+$BLOOP_END:
+$ write libopt f$extract(0,f$length(sv)-2,sv), "-"
+$ write libopt ")"
+$ close/nolog bopt
+$ delete/nolog/noconf a.opt;*,b.opt;*
+$ else
+$ if vax
+$ then
+$ open/append libopt 'p2'
+$ mod_sym_num = 1
+$ VMOD_SYM_LOOP:
+$ if f$type(module'mod_sym_num') .nes. ""
+$ then
+$ mod_in = 0
+$ VMOD_SYM_IN:
+$ shared_proc = f$element(mod_in, "#", module'mod_sym_num')
+$ if shared_proc .nes. "#"
+$ then
+$ write libopt f$fao("UNIVERSAL=!AS",-
+ f$edit(shared_proc,"upcase"))
+$ mod_in = mod_in + 1
+$ goto vmod_sym_in
+$ endif
+$ mod_sym_num = mod_sym_num + 1
+$ goto vmod_sym_loop
+$ endif
+$VMAP_LOOP:
+$ read/end=vmap_end map line
+$ if (f$locate("{",line).lt. f$length(line)) .or. -
+ (f$locate("global:", line) .lt. f$length(line))
+$ then
+$ proc = true
+$ goto vmap_loop
+$ endif
+$ if f$locate("}",line).lt. f$length(line) then proc = false
+$ if f$locate("local:", line) .lt. f$length(line) then proc = false
+$ if proc
+$ then
+$ shared_proc = f$edit(line,"collapse")
+$ chop_semi = f$locate(";", shared_proc)
+$ if chop_semi .lt. f$length(shared_proc) then -
+ shared_proc = f$extract(0, chop_semi, shared_proc)
+$ write libopt f$fao("UNIVERSAL=!AS",-
+ f$edit(shared_proc,"upcase"))
+$ endif
+$ goto vmap_loop
+$VMAP_END:
+$ else
+$ write sys$output "Unknown Architecture (Not VAX, AXP, or IA64)"
+$ write sys$output "No options file created"
+$ endif
+$ endif
+$ EXIT_M2S:
+$ close/nolog map
+$ close/nolog libopt
+$ endsubroutine
diff --git a/third-party/zlib/test/example.c b/third-party/zlib/test/example.c
new file mode 100644
index 0000000..138a699
--- /dev/null
+++ b/third-party/zlib/test/example.c
@@ -0,0 +1,601 @@
+/* example.c -- usage example of the zlib compression library
+ * Copyright (C) 1995-2006, 2011 Jean-loup Gailly.
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* @(#) $Id$ */
+
+#include "zlib.h"
+#include <stdio.h>
+
+#ifdef STDC
+# include <string.h>
+# include <stdlib.h>
+#endif
+
+#if defined(VMS) || defined(RISCOS)
+# define TESTFILE "foo-gz"
+#else
+# define TESTFILE "foo.gz"
+#endif
+
+#define CHECK_ERR(err, msg) { \
+ if (err != Z_OK) { \
+ fprintf(stderr, "%s error: %d\n", msg, err); \
+ exit(1); \
+ } \
+}
+
+z_const char hello[] = "hello, hello!";
+/* "hello world" would be more standard, but the repeated "hello"
+ * stresses the compression code better, sorry...
+ */
+
+const char dictionary[] = "hello";
+uLong dictId; /* Adler32 value of the dictionary */
+
+void test_deflate OF((Byte *compr, uLong comprLen));
+void test_inflate OF((Byte *compr, uLong comprLen,
+ Byte *uncompr, uLong uncomprLen));
+void test_large_deflate OF((Byte *compr, uLong comprLen,
+ Byte *uncompr, uLong uncomprLen));
+void test_large_inflate OF((Byte *compr, uLong comprLen,
+ Byte *uncompr, uLong uncomprLen));
+void test_flush OF((Byte *compr, uLong *comprLen));
+void test_sync OF((Byte *compr, uLong comprLen,
+ Byte *uncompr, uLong uncomprLen));
+void test_dict_deflate OF((Byte *compr, uLong comprLen));
+void test_dict_inflate OF((Byte *compr, uLong comprLen,
+ Byte *uncompr, uLong uncomprLen));
+int main OF((int argc, char *argv[]));
+
+
+#ifdef Z_SOLO
+
+void *myalloc OF((void *, unsigned, unsigned));
+void myfree OF((void *, void *));
+
+void *myalloc(q, n, m)
+ void *q;
+ unsigned n, m;
+{
+ q = Z_NULL;
+ return calloc(n, m);
+}
+
+void myfree(void *q, void *p)
+{
+ q = Z_NULL;
+ free(p);
+}
+
+static alloc_func zalloc = myalloc;
+static free_func zfree = myfree;
+
+#else /* !Z_SOLO */
+
+static alloc_func zalloc = (alloc_func)0;
+static free_func zfree = (free_func)0;
+
+void test_compress OF((Byte *compr, uLong comprLen,
+ Byte *uncompr, uLong uncomprLen));
+void test_gzio OF((const char *fname,
+ Byte *uncompr, uLong uncomprLen));
+
+/* ===========================================================================
+ * Test compress() and uncompress()
+ */
+void test_compress(compr, comprLen, uncompr, uncomprLen)
+ Byte *compr, *uncompr;
+ uLong comprLen, uncomprLen;
+{
+ int err;
+ uLong len = (uLong)strlen(hello)+1;
+
+ err = compress(compr, &comprLen, (const Bytef*)hello, len);
+ CHECK_ERR(err, "compress");
+
+ strcpy((char*)uncompr, "garbage");
+
+ err = uncompress(uncompr, &uncomprLen, compr, comprLen);
+ CHECK_ERR(err, "uncompress");
+
+ if (strcmp((char*)uncompr, hello)) {
+ fprintf(stderr, "bad uncompress\n");
+ exit(1);
+ } else {
+ printf("uncompress(): %s\n", (char *)uncompr);
+ }
+}
+
+/* ===========================================================================
+ * Test read/write of .gz files
+ */
+void test_gzio(fname, uncompr, uncomprLen)
+ const char *fname; /* compressed file name */
+ Byte *uncompr;
+ uLong uncomprLen;
+{
+#ifdef NO_GZCOMPRESS
+ fprintf(stderr, "NO_GZCOMPRESS -- gz* functions cannot compress\n");
+#else
+ int err;
+ int len = (int)strlen(hello)+1;
+ gzFile file;
+ z_off_t pos;
+
+ file = gzopen(fname, "wb");
+ if (file == NULL) {
+ fprintf(stderr, "gzopen error\n");
+ exit(1);
+ }
+ gzputc(file, 'h');
+ if (gzputs(file, "ello") != 4) {
+ fprintf(stderr, "gzputs err: %s\n", gzerror(file, &err));
+ exit(1);
+ }
+ if (gzprintf(file, ", %s!", "hello") != 8) {
+ fprintf(stderr, "gzprintf err: %s\n", gzerror(file, &err));
+ exit(1);
+ }
+ gzseek(file, 1L, SEEK_CUR); /* add one zero byte */
+ gzclose(file);
+
+ file = gzopen(fname, "rb");
+ if (file == NULL) {
+ fprintf(stderr, "gzopen error\n");
+ exit(1);
+ }
+ strcpy((char*)uncompr, "garbage");
+
+ if (gzread(file, uncompr, (unsigned)uncomprLen) != len) {
+ fprintf(stderr, "gzread err: %s\n", gzerror(file, &err));
+ exit(1);
+ }
+ if (strcmp((char*)uncompr, hello)) {
+ fprintf(stderr, "bad gzread: %s\n", (char*)uncompr);
+ exit(1);
+ } else {
+ printf("gzread(): %s\n", (char*)uncompr);
+ }
+
+ pos = gzseek(file, -8L, SEEK_CUR);
+ if (pos != 6 || gztell(file) != pos) {
+ fprintf(stderr, "gzseek error, pos=%ld, gztell=%ld\n",
+ (long)pos, (long)gztell(file));
+ exit(1);
+ }
+
+ if (gzgetc(file) != ' ') {
+ fprintf(stderr, "gzgetc error\n");
+ exit(1);
+ }
+
+ if (gzungetc(' ', file) != ' ') {
+ fprintf(stderr, "gzungetc error\n");
+ exit(1);
+ }
+
+ gzgets(file, (char*)uncompr, (int)uncomprLen);
+ if (strlen((char*)uncompr) != 7) { /* " hello!" */
+ fprintf(stderr, "gzgets err after gzseek: %s\n", gzerror(file, &err));
+ exit(1);
+ }
+ if (strcmp((char*)uncompr, hello + 6)) {
+ fprintf(stderr, "bad gzgets after gzseek\n");
+ exit(1);
+ } else {
+ printf("gzgets() after gzseek: %s\n", (char*)uncompr);
+ }
+
+ gzclose(file);
+#endif
+}
+
+#endif /* Z_SOLO */
+
+/* ===========================================================================
+ * Test deflate() with small buffers
+ */
+void test_deflate(compr, comprLen)
+ Byte *compr;
+ uLong comprLen;
+{
+ z_stream c_stream; /* compression stream */
+ int err;
+ uLong len = (uLong)strlen(hello)+1;
+
+ c_stream.zalloc = zalloc;
+ c_stream.zfree = zfree;
+ c_stream.opaque = (voidpf)0;
+
+ err = deflateInit(&c_stream, Z_DEFAULT_COMPRESSION);
+ CHECK_ERR(err, "deflateInit");
+
+ c_stream.next_in = (z_const unsigned char *)hello;
+ c_stream.next_out = compr;
+
+ while (c_stream.total_in != len && c_stream.total_out < comprLen) {
+ c_stream.avail_in = c_stream.avail_out = 1; /* force small buffers */
+ err = deflate(&c_stream, Z_NO_FLUSH);
+ CHECK_ERR(err, "deflate");
+ }
+ /* Finish the stream, still forcing small buffers: */
+ for (;;) {
+ c_stream.avail_out = 1;
+ err = deflate(&c_stream, Z_FINISH);
+ if (err == Z_STREAM_END) break;
+ CHECK_ERR(err, "deflate");
+ }
+
+ err = deflateEnd(&c_stream);
+ CHECK_ERR(err, "deflateEnd");
+}
+
+/* ===========================================================================
+ * Test inflate() with small buffers
+ */
+void test_inflate(compr, comprLen, uncompr, uncomprLen)
+ Byte *compr, *uncompr;
+ uLong comprLen, uncomprLen;
+{
+ int err;
+ z_stream d_stream; /* decompression stream */
+
+ strcpy((char*)uncompr, "garbage");
+
+ d_stream.zalloc = zalloc;
+ d_stream.zfree = zfree;
+ d_stream.opaque = (voidpf)0;
+
+ d_stream.next_in = compr;
+ d_stream.avail_in = 0;
+ d_stream.next_out = uncompr;
+
+ err = inflateInit(&d_stream);
+ CHECK_ERR(err, "inflateInit");
+
+ while (d_stream.total_out < uncomprLen && d_stream.total_in < comprLen) {
+ d_stream.avail_in = d_stream.avail_out = 1; /* force small buffers */
+ err = inflate(&d_stream, Z_NO_FLUSH);
+ if (err == Z_STREAM_END) break;
+ CHECK_ERR(err, "inflate");
+ }
+
+ err = inflateEnd(&d_stream);
+ CHECK_ERR(err, "inflateEnd");
+
+ if (strcmp((char*)uncompr, hello)) {
+ fprintf(stderr, "bad inflate\n");
+ exit(1);
+ } else {
+ printf("inflate(): %s\n", (char *)uncompr);
+ }
+}
+
+/* ===========================================================================
+ * Test deflate() with large buffers and dynamic change of compression level
+ */
+void test_large_deflate(compr, comprLen, uncompr, uncomprLen)
+ Byte *compr, *uncompr;
+ uLong comprLen, uncomprLen;
+{
+ z_stream c_stream; /* compression stream */
+ int err;
+
+ c_stream.zalloc = zalloc;
+ c_stream.zfree = zfree;
+ c_stream.opaque = (voidpf)0;
+
+ err = deflateInit(&c_stream, Z_BEST_SPEED);
+ CHECK_ERR(err, "deflateInit");
+
+ c_stream.next_out = compr;
+ c_stream.avail_out = (uInt)comprLen;
+
+ /* At this point, uncompr is still mostly zeroes, so it should compress
+ * very well:
+ */
+ c_stream.next_in = uncompr;
+ c_stream.avail_in = (uInt)uncomprLen;
+ err = deflate(&c_stream, Z_NO_FLUSH);
+ CHECK_ERR(err, "deflate");
+ if (c_stream.avail_in != 0) {
+ fprintf(stderr, "deflate not greedy\n");
+ exit(1);
+ }
+
+ /* Feed in already compressed data and switch to no compression: */
+ deflateParams(&c_stream, Z_NO_COMPRESSION, Z_DEFAULT_STRATEGY);
+ c_stream.next_in = compr;
+ c_stream.avail_in = (uInt)comprLen/2;
+ err = deflate(&c_stream, Z_NO_FLUSH);
+ CHECK_ERR(err, "deflate");
+
+ /* Switch back to compressing mode: */
+ deflateParams(&c_stream, Z_BEST_COMPRESSION, Z_FILTERED);
+ c_stream.next_in = uncompr;
+ c_stream.avail_in = (uInt)uncomprLen;
+ err = deflate(&c_stream, Z_NO_FLUSH);
+ CHECK_ERR(err, "deflate");
+
+ err = deflate(&c_stream, Z_FINISH);
+ if (err != Z_STREAM_END) {
+ fprintf(stderr, "deflate should report Z_STREAM_END\n");
+ exit(1);
+ }
+ err = deflateEnd(&c_stream);
+ CHECK_ERR(err, "deflateEnd");
+}
+
+/* ===========================================================================
+ * Test inflate() with large buffers
+ */
+void test_large_inflate(compr, comprLen, uncompr, uncomprLen)
+ Byte *compr, *uncompr;
+ uLong comprLen, uncomprLen;
+{
+ int err;
+ z_stream d_stream; /* decompression stream */
+
+ strcpy((char*)uncompr, "garbage");
+
+ d_stream.zalloc = zalloc;
+ d_stream.zfree = zfree;
+ d_stream.opaque = (voidpf)0;
+
+ d_stream.next_in = compr;
+ d_stream.avail_in = (uInt)comprLen;
+
+ err = inflateInit(&d_stream);
+ CHECK_ERR(err, "inflateInit");
+
+ for (;;) {
+ d_stream.next_out = uncompr; /* discard the output */
+ d_stream.avail_out = (uInt)uncomprLen;
+ err = inflate(&d_stream, Z_NO_FLUSH);
+ if (err == Z_STREAM_END) break;
+ CHECK_ERR(err, "large inflate");
+ }
+
+ err = inflateEnd(&d_stream);
+ CHECK_ERR(err, "inflateEnd");
+
+ if (d_stream.total_out != 2*uncomprLen + comprLen/2) {
+ fprintf(stderr, "bad large inflate: %ld\n", d_stream.total_out);
+ exit(1);
+ } else {
+ printf("large_inflate(): OK\n");
+ }
+}
+
+/* ===========================================================================
+ * Test deflate() with full flush
+ */
+void test_flush(compr, comprLen)
+ Byte *compr;
+ uLong *comprLen;
+{
+ z_stream c_stream; /* compression stream */
+ int err;
+ uInt len = (uInt)strlen(hello)+1;
+
+ c_stream.zalloc = zalloc;
+ c_stream.zfree = zfree;
+ c_stream.opaque = (voidpf)0;
+
+ err = deflateInit(&c_stream, Z_DEFAULT_COMPRESSION);
+ CHECK_ERR(err, "deflateInit");
+
+ c_stream.next_in = (z_const unsigned char *)hello;
+ c_stream.next_out = compr;
+ c_stream.avail_in = 3;
+ c_stream.avail_out = (uInt)*comprLen;
+ err = deflate(&c_stream, Z_FULL_FLUSH);
+ CHECK_ERR(err, "deflate");
+
+ compr[3]++; /* force an error in first compressed block */
+ c_stream.avail_in = len - 3;
+
+ err = deflate(&c_stream, Z_FINISH);
+ if (err != Z_STREAM_END) {
+ CHECK_ERR(err, "deflate");
+ }
+ err = deflateEnd(&c_stream);
+ CHECK_ERR(err, "deflateEnd");
+
+ *comprLen = c_stream.total_out;
+}
+
+/* ===========================================================================
+ * Test inflateSync()
+ */
+void test_sync(compr, comprLen, uncompr, uncomprLen)
+ Byte *compr, *uncompr;
+ uLong comprLen, uncomprLen;
+{
+ int err;
+ z_stream d_stream; /* decompression stream */
+
+ strcpy((char*)uncompr, "garbage");
+
+ d_stream.zalloc = zalloc;
+ d_stream.zfree = zfree;
+ d_stream.opaque = (voidpf)0;
+
+ d_stream.next_in = compr;
+ d_stream.avail_in = 2; /* just read the zlib header */
+
+ err = inflateInit(&d_stream);
+ CHECK_ERR(err, "inflateInit");
+
+ d_stream.next_out = uncompr;
+ d_stream.avail_out = (uInt)uncomprLen;
+
+ inflate(&d_stream, Z_NO_FLUSH);
+ CHECK_ERR(err, "inflate");
+
+ d_stream.avail_in = (uInt)comprLen-2; /* read all compressed data */
+ err = inflateSync(&d_stream); /* but skip the damaged part */
+ CHECK_ERR(err, "inflateSync");
+
+ err = inflate(&d_stream, Z_FINISH);
+ if (err != Z_DATA_ERROR) {
+ fprintf(stderr, "inflate should report DATA_ERROR\n");
+ /* Because of incorrect adler32 */
+ exit(1);
+ }
+ err = inflateEnd(&d_stream);
+ CHECK_ERR(err, "inflateEnd");
+
+ printf("after inflateSync(): hel%s\n", (char *)uncompr);
+}
+
+/* ===========================================================================
+ * Test deflate() with preset dictionary
+ */
+void test_dict_deflate(compr, comprLen)
+ Byte *compr;
+ uLong comprLen;
+{
+ z_stream c_stream; /* compression stream */
+ int err;
+
+ c_stream.zalloc = zalloc;
+ c_stream.zfree = zfree;
+ c_stream.opaque = (voidpf)0;
+
+ err = deflateInit(&c_stream, Z_BEST_COMPRESSION);
+ CHECK_ERR(err, "deflateInit");
+
+ err = deflateSetDictionary(&c_stream,
+ (const Bytef*)dictionary, (int)sizeof(dictionary));
+ CHECK_ERR(err, "deflateSetDictionary");
+
+ dictId = c_stream.adler;
+ c_stream.next_out = compr;
+ c_stream.avail_out = (uInt)comprLen;
+
+ c_stream.next_in = (z_const unsigned char *)hello;
+ c_stream.avail_in = (uInt)strlen(hello)+1;
+
+ err = deflate(&c_stream, Z_FINISH);
+ if (err != Z_STREAM_END) {
+ fprintf(stderr, "deflate should report Z_STREAM_END\n");
+ exit(1);
+ }
+ err = deflateEnd(&c_stream);
+ CHECK_ERR(err, "deflateEnd");
+}
+
+/* ===========================================================================
+ * Test inflate() with a preset dictionary
+ */
+void test_dict_inflate(compr, comprLen, uncompr, uncomprLen)
+ Byte *compr, *uncompr;
+ uLong comprLen, uncomprLen;
+{
+ int err;
+ z_stream d_stream; /* decompression stream */
+
+ strcpy((char*)uncompr, "garbage");
+
+ d_stream.zalloc = zalloc;
+ d_stream.zfree = zfree;
+ d_stream.opaque = (voidpf)0;
+
+ d_stream.next_in = compr;
+ d_stream.avail_in = (uInt)comprLen;
+
+ err = inflateInit(&d_stream);
+ CHECK_ERR(err, "inflateInit");
+
+ d_stream.next_out = uncompr;
+ d_stream.avail_out = (uInt)uncomprLen;
+
+ for (;;) {
+ err = inflate(&d_stream, Z_NO_FLUSH);
+ if (err == Z_STREAM_END) break;
+ if (err == Z_NEED_DICT) {
+ if (d_stream.adler != dictId) {
+ fprintf(stderr, "unexpected dictionary");
+ exit(1);
+ }
+ err = inflateSetDictionary(&d_stream, (const Bytef*)dictionary,
+ (int)sizeof(dictionary));
+ }
+ CHECK_ERR(err, "inflate with dict");
+ }
+
+ err = inflateEnd(&d_stream);
+ CHECK_ERR(err, "inflateEnd");
+
+ if (strcmp((char*)uncompr, hello)) {
+ fprintf(stderr, "bad inflate with dict\n");
+ exit(1);
+ } else {
+ printf("inflate with dictionary: %s\n", (char *)uncompr);
+ }
+}
+
+/* ===========================================================================
+ * Usage: example [output.gz [input.gz]]
+ */
+
+int main(argc, argv)
+ int argc;
+ char *argv[];
+{
+ Byte *compr, *uncompr;
+ uLong comprLen = 10000*sizeof(int); /* don't overflow on MSDOS */
+ uLong uncomprLen = comprLen;
+ static const char* myVersion = ZLIB_VERSION;
+
+ if (zlibVersion()[0] != myVersion[0]) {
+ fprintf(stderr, "incompatible zlib version\n");
+ exit(1);
+
+ } else if (strcmp(zlibVersion(), ZLIB_VERSION) != 0) {
+ fprintf(stderr, "warning: different zlib version\n");
+ }
+
+ printf("zlib version %s = 0x%04x, compile flags = 0x%lx\n",
+ ZLIB_VERSION, ZLIB_VERNUM, zlibCompileFlags());
+
+ compr = (Byte*)calloc((uInt)comprLen, 1);
+ uncompr = (Byte*)calloc((uInt)uncomprLen, 1);
+ /* compr and uncompr are cleared to avoid reading uninitialized
+ * data and to ensure that uncompr compresses well.
+ */
+ if (compr == Z_NULL || uncompr == Z_NULL) {
+ printf("out of memory\n");
+ exit(1);
+ }
+
+#ifdef Z_SOLO
+ argc = strlen(argv[0]);
+#else
+ test_compress(compr, comprLen, uncompr, uncomprLen);
+
+ test_gzio((argc > 1 ? argv[1] : TESTFILE),
+ uncompr, uncomprLen);
+#endif
+
+ test_deflate(compr, comprLen);
+ test_inflate(compr, comprLen, uncompr, uncomprLen);
+
+ test_large_deflate(compr, comprLen, uncompr, uncomprLen);
+ test_large_inflate(compr, comprLen, uncompr, uncomprLen);
+
+ test_flush(compr, &comprLen);
+ test_sync(compr, comprLen, uncompr, uncomprLen);
+ comprLen = uncomprLen;
+
+ test_dict_deflate(compr, comprLen);
+ test_dict_inflate(compr, comprLen, uncompr, uncomprLen);
+
+ free(compr);
+ free(uncompr);
+
+ return 0;
+}
diff --git a/third-party/zlib/test/infcover.c b/third-party/zlib/test/infcover.c
new file mode 100644
index 0000000..fe3d920
--- /dev/null
+++ b/third-party/zlib/test/infcover.c
@@ -0,0 +1,671 @@
+/* infcover.c -- test zlib's inflate routines with full code coverage
+ * Copyright (C) 2011 Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* to use, do: ./configure --cover && make cover */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#include "zlib.h"
+
+/* get definition of internal structure so we can mess with it (see pull()),
+ and so we can call inflate_trees() (see cover5()) */
+#define ZLIB_INTERNAL
+#include "inftrees.h"
+#include "inflate.h"
+
+#define local static
+
+/* -- memory tracking routines -- */
+
+/*
+ These memory tracking routines are provided to zlib and track all of zlib's
+ allocations and deallocations, check for LIFO operations, keep a current
+ and high water mark of total bytes requested, optionally set a limit on the
+ total memory that can be allocated, and when done check for memory leaks.
+
+ They are used as follows:
+
+ z_stream strm;
+ mem_setup(&strm) initializes the memory tracking and sets the
+ zalloc, zfree, and opaque members of strm to use
+ memory tracking for all zlib operations on strm
+ mem_limit(&strm, limit) sets a limit on the total bytes requested -- a
+ request that exceeds this limit will result in an
+ allocation failure (returns NULL) -- setting the
+ limit to zero means no limit, which is the default
+ after mem_setup()
+ mem_used(&strm, "msg") prints to stderr "msg" and the total bytes used
+ mem_high(&strm, "msg") prints to stderr "msg" and the high water mark
+ mem_done(&strm, "msg") ends memory tracking, releases all allocations
+ for the tracking as well as leaked zlib blocks, if
+ any. If there was anything unusual, such as leaked
+ blocks, non-FIFO frees, or frees of addresses not
+ allocated, then "msg" and information about the
+ problem is printed to stderr. If everything is
+ normal, nothing is printed. mem_done resets the
+ strm members to Z_NULL to use the default memory
+ allocation routines on the next zlib initialization
+ using strm.
+ */
+
+/* these items are strung together in a linked list, one for each allocation */
+struct mem_item {
+ void *ptr; /* pointer to allocated memory */
+ size_t size; /* requested size of allocation */
+ struct mem_item *next; /* pointer to next item in list, or NULL */
+};
+
+/* this structure is at the root of the linked list, and tracks statistics */
+struct mem_zone {
+ struct mem_item *first; /* pointer to first item in list, or NULL */
+ size_t total, highwater; /* total allocations, and largest total */
+ size_t limit; /* memory allocation limit, or 0 if no limit */
+ int notlifo, rogue; /* counts of non-LIFO frees and rogue frees */
+};
+
+/* memory allocation routine to pass to zlib */
+local void *mem_alloc(void *mem, unsigned count, unsigned size)
+{
+ void *ptr;
+ struct mem_item *item;
+ struct mem_zone *zone = mem;
+ size_t len = count * (size_t)size;
+
+ /* induced allocation failure */
+ if (zone == NULL || (zone->limit && zone->total + len > zone->limit))
+ return NULL;
+
+ /* perform allocation using the standard library, fill memory with a
+ non-zero value to make sure that the code isn't depending on zeros */
+ ptr = malloc(len);
+ if (ptr == NULL)
+ return NULL;
+ memset(ptr, 0xa5, len);
+
+ /* create a new item for the list */
+ item = malloc(sizeof(struct mem_item));
+ if (item == NULL) {
+ free(ptr);
+ return NULL;
+ }
+ item->ptr = ptr;
+ item->size = len;
+
+ /* insert item at the beginning of the list */
+ item->next = zone->first;
+ zone->first = item;
+
+ /* update the statistics */
+ zone->total += item->size;
+ if (zone->total > zone->highwater)
+ zone->highwater = zone->total;
+
+ /* return the allocated memory */
+ return ptr;
+}
+
+/* memory free routine to pass to zlib */
+local void mem_free(void *mem, void *ptr)
+{
+ struct mem_item *item, *next;
+ struct mem_zone *zone = mem;
+
+ /* if no zone, just do a free */
+ if (zone == NULL) {
+ free(ptr);
+ return;
+ }
+
+ /* point next to the item that matches ptr, or NULL if not found -- remove
+ the item from the linked list if found */
+ next = zone->first;
+ if (next) {
+ if (next->ptr == ptr)
+ zone->first = next->next; /* first one is it, remove from list */
+ else {
+ do { /* search the linked list */
+ item = next;
+ next = item->next;
+ } while (next != NULL && next->ptr != ptr);
+ if (next) { /* if found, remove from linked list */
+ item->next = next->next;
+ zone->notlifo++; /* not a LIFO free */
+ }
+
+ }
+ }
+
+ /* if found, update the statistics and free the item */
+ if (next) {
+ zone->total -= next->size;
+ free(next);
+ }
+
+ /* if not found, update the rogue count */
+ else
+ zone->rogue++;
+
+ /* in any case, do the requested free with the standard library function */
+ free(ptr);
+}
+
+/* set up a controlled memory allocation space for monitoring, set the stream
+ parameters to the controlled routines, with opaque pointing to the space */
+local void mem_setup(z_stream *strm)
+{
+ struct mem_zone *zone;
+
+ zone = malloc(sizeof(struct mem_zone));
+ assert(zone != NULL);
+ zone->first = NULL;
+ zone->total = 0;
+ zone->highwater = 0;
+ zone->limit = 0;
+ zone->notlifo = 0;
+ zone->rogue = 0;
+ strm->opaque = zone;
+ strm->zalloc = mem_alloc;
+ strm->zfree = mem_free;
+}
+
+/* set a limit on the total memory allocation, or 0 to remove the limit */
+local void mem_limit(z_stream *strm, size_t limit)
+{
+ struct mem_zone *zone = strm->opaque;
+
+ zone->limit = limit;
+}
+
+/* show the current total requested allocations in bytes */
+local void mem_used(z_stream *strm, char *prefix)
+{
+ struct mem_zone *zone = strm->opaque;
+
+ fprintf(stderr, "%s: %lu allocated\n", prefix, zone->total);
+}
+
+/* show the high water allocation in bytes */
+local void mem_high(z_stream *strm, char *prefix)
+{
+ struct mem_zone *zone = strm->opaque;
+
+ fprintf(stderr, "%s: %lu high water mark\n", prefix, zone->highwater);
+}
+
+/* release the memory allocation zone -- if there are any surprises, notify */
+local void mem_done(z_stream *strm, char *prefix)
+{
+ int count = 0;
+ struct mem_item *item, *next;
+ struct mem_zone *zone = strm->opaque;
+
+ /* show high water mark */
+ mem_high(strm, prefix);
+
+ /* free leftover allocations and item structures, if any */
+ item = zone->first;
+ while (item != NULL) {
+ free(item->ptr);
+ next = item->next;
+ free(item);
+ item = next;
+ count++;
+ }
+
+ /* issue alerts about anything unexpected */
+ if (count || zone->total)
+ fprintf(stderr, "** %s: %lu bytes in %d blocks not freed\n",
+ prefix, zone->total, count);
+ if (zone->notlifo)
+ fprintf(stderr, "** %s: %d frees not LIFO\n", prefix, zone->notlifo);
+ if (zone->rogue)
+ fprintf(stderr, "** %s: %d frees not recognized\n",
+ prefix, zone->rogue);
+
+ /* free the zone and delete from the stream */
+ free(zone);
+ strm->opaque = Z_NULL;
+ strm->zalloc = Z_NULL;
+ strm->zfree = Z_NULL;
+}
+
+/* -- inflate test routines -- */
+
+/* Decode a hexadecimal string, set *len to length, in[] to the bytes. This
+ decodes liberally, in that hex digits can be adjacent, in which case two in
+ a row writes a byte. Or they can delimited by any non-hex character, where
+ the delimiters are ignored except when a single hex digit is followed by a
+ delimiter in which case that single digit writes a byte. The returned
+ data is allocated and must eventually be freed. NULL is returned if out of
+ memory. If the length is not needed, then len can be NULL. */
+local unsigned char *h2b(const char *hex, unsigned *len)
+{
+ unsigned char *in;
+ unsigned next, val;
+
+ in = malloc((strlen(hex) + 1) >> 1);
+ if (in == NULL)
+ return NULL;
+ next = 0;
+ val = 1;
+ do {
+ if (*hex >= '0' && *hex <= '9')
+ val = (val << 4) + *hex - '0';
+ else if (*hex >= 'A' && *hex <= 'F')
+ val = (val << 4) + *hex - 'A' + 10;
+ else if (*hex >= 'a' && *hex <= 'f')
+ val = (val << 4) + *hex - 'a' + 10;
+ else if (val != 1 && val < 32) /* one digit followed by delimiter */
+ val += 240; /* make it look like two digits */
+ if (val > 255) { /* have two digits */
+ in[next++] = val & 0xff; /* save the decoded byte */
+ val = 1; /* start over */
+ }
+ } while (*hex++); /* go through the loop with the terminating null */
+ if (len != NULL)
+ *len = next;
+ in = reallocf(in, next);
+ return in;
+}
+
+/* generic inflate() run, where hex is the hexadecimal input data, what is the
+ text to include in an error message, step is how much input data to feed
+ inflate() on each call, or zero to feed it all, win is the window bits
+ parameter to inflateInit2(), len is the size of the output buffer, and err
+ is the error code expected from the first inflate() call (the second
+ inflate() call is expected to return Z_STREAM_END). If win is 47, then
+ header information is collected with inflateGetHeader(). If a zlib stream
+ is looking for a dictionary, then an empty dictionary is provided.
+ inflate() is run until all of the input data is consumed. */
+local void inf(char *hex, char *what, unsigned step, int win, unsigned len,
+ int err)
+{
+ int ret;
+ unsigned have;
+ unsigned char *in, *out;
+ z_stream strm, copy;
+ gz_header head;
+
+ mem_setup(&strm);
+ strm.avail_in = 0;
+ strm.next_in = Z_NULL;
+ ret = inflateInit2(&strm, win);
+ if (ret != Z_OK) {
+ mem_done(&strm, what);
+ return;
+ }
+ out = malloc(len); assert(out != NULL);
+ if (win == 47) {
+ head.extra = out;
+ head.extra_max = len;
+ head.name = out;
+ head.name_max = len;
+ head.comment = out;
+ head.comm_max = len;
+ ret = inflateGetHeader(&strm, &head); assert(ret == Z_OK);
+ }
+ in = h2b(hex, &have); assert(in != NULL);
+ if (step == 0 || step > have)
+ step = have;
+ strm.avail_in = step;
+ have -= step;
+ strm.next_in = in;
+ do {
+ strm.avail_out = len;
+ strm.next_out = out;
+ ret = inflate(&strm, Z_NO_FLUSH); assert(err == 9 || ret == err);
+ if (ret != Z_OK && ret != Z_BUF_ERROR && ret != Z_NEED_DICT)
+ break;
+ if (ret == Z_NEED_DICT) {
+ ret = inflateSetDictionary(&strm, in, 1);
+ assert(ret == Z_DATA_ERROR);
+ mem_limit(&strm, 1);
+ ret = inflateSetDictionary(&strm, out, 0);
+ assert(ret == Z_MEM_ERROR);
+ mem_limit(&strm, 0);
+ ((struct inflate_state *)strm.state)->mode = DICT;
+ ret = inflateSetDictionary(&strm, out, 0);
+ assert(ret == Z_OK);
+ ret = inflate(&strm, Z_NO_FLUSH); assert(ret == Z_BUF_ERROR);
+ }
+ ret = inflateCopy(©, &strm); assert(ret == Z_OK);
+ ret = inflateEnd(©); assert(ret == Z_OK);
+ err = 9; /* don't care next time around */
+ have += strm.avail_in;
+ strm.avail_in = step > have ? have : step;
+ have -= strm.avail_in;
+ } while (strm.avail_in);
+ free(in);
+ free(out);
+ ret = inflateReset2(&strm, -8); assert(ret == Z_OK);
+ ret = inflateEnd(&strm); assert(ret == Z_OK);
+ mem_done(&strm, what);
+}
+
+/* cover all of the lines in inflate.c up to inflate() */
+local void cover_support(void)
+{
+ int ret;
+ z_stream strm;
+
+ mem_setup(&strm);
+ strm.avail_in = 0;
+ strm.next_in = Z_NULL;
+ ret = inflateInit(&strm); assert(ret == Z_OK);
+ mem_used(&strm, "inflate init");
+ ret = inflatePrime(&strm, 5, 31); assert(ret == Z_OK);
+ ret = inflatePrime(&strm, -1, 0); assert(ret == Z_OK);
+ ret = inflateSetDictionary(&strm, Z_NULL, 0);
+ assert(ret == Z_STREAM_ERROR);
+ ret = inflateEnd(&strm); assert(ret == Z_OK);
+ mem_done(&strm, "prime");
+
+ inf("63 0", "force window allocation", 0, -15, 1, Z_OK);
+ inf("63 18 5", "force window replacement", 0, -8, 259, Z_OK);
+ inf("63 18 68 30 d0 0 0", "force split window update", 4, -8, 259, Z_OK);
+ inf("3 0", "use fixed blocks", 0, -15, 1, Z_STREAM_END);
+ inf("", "bad window size", 0, 1, 0, Z_STREAM_ERROR);
+
+ mem_setup(&strm);
+ strm.avail_in = 0;
+ strm.next_in = Z_NULL;
+ ret = inflateInit_(&strm, ZLIB_VERSION - 1, (int)sizeof(z_stream));
+ assert(ret == Z_VERSION_ERROR);
+ mem_done(&strm, "wrong version");
+
+ strm.avail_in = 0;
+ strm.next_in = Z_NULL;
+ ret = inflateInit(&strm); assert(ret == Z_OK);
+ ret = inflateEnd(&strm); assert(ret == Z_OK);
+ fputs("inflate built-in memory routines\n", stderr);
+}
+
+/* cover all inflate() header and trailer cases and code after inflate() */
+local void cover_wrap(void)
+{
+ int ret;
+ z_stream strm, copy;
+ unsigned char dict[257];
+
+ ret = inflate(Z_NULL, 0); assert(ret == Z_STREAM_ERROR);
+ ret = inflateEnd(Z_NULL); assert(ret == Z_STREAM_ERROR);
+ ret = inflateCopy(Z_NULL, Z_NULL); assert(ret == Z_STREAM_ERROR);
+ fputs("inflate bad parameters\n", stderr);
+
+ inf("1f 8b 0 0", "bad gzip method", 0, 31, 0, Z_DATA_ERROR);
+ inf("1f 8b 8 80", "bad gzip flags", 0, 31, 0, Z_DATA_ERROR);
+ inf("77 85", "bad zlib method", 0, 15, 0, Z_DATA_ERROR);
+ inf("8 99", "set window size from header", 0, 0, 0, Z_OK);
+ inf("78 9c", "bad zlib window size", 0, 8, 0, Z_DATA_ERROR);
+ inf("78 9c 63 0 0 0 1 0 1", "check adler32", 0, 15, 1, Z_STREAM_END);
+ inf("1f 8b 8 1e 0 0 0 0 0 0 1 0 0 0 0 0 0", "bad header crc", 0, 47, 1,
+ Z_DATA_ERROR);
+ inf("1f 8b 8 2 0 0 0 0 0 0 1d 26 3 0 0 0 0 0 0 0 0 0", "check gzip length",
+ 0, 47, 0, Z_STREAM_END);
+ inf("78 90", "bad zlib header check", 0, 47, 0, Z_DATA_ERROR);
+ inf("8 b8 0 0 0 1", "need dictionary", 0, 8, 0, Z_NEED_DICT);
+ inf("78 9c 63 0", "compute adler32", 0, 15, 1, Z_OK);
+
+ mem_setup(&strm);
+ strm.avail_in = 0;
+ strm.next_in = Z_NULL;
+ ret = inflateInit2(&strm, -8);
+ strm.avail_in = 2;
+ strm.next_in = (void *)"\x63";
+ strm.avail_out = 1;
+ strm.next_out = (void *)&ret;
+ mem_limit(&strm, 1);
+ ret = inflate(&strm, Z_NO_FLUSH); assert(ret == Z_MEM_ERROR);
+ ret = inflate(&strm, Z_NO_FLUSH); assert(ret == Z_MEM_ERROR);
+ mem_limit(&strm, 0);
+ memset(dict, 0, 257);
+ ret = inflateSetDictionary(&strm, dict, 257);
+ assert(ret == Z_OK);
+ mem_limit(&strm, (sizeof(struct inflate_state) << 1) + 256);
+ ret = inflatePrime(&strm, 16, 0); assert(ret == Z_OK);
+ strm.avail_in = 2;
+ strm.next_in = (void *)"\x80";
+ ret = inflateSync(&strm); assert(ret == Z_DATA_ERROR);
+ ret = inflate(&strm, Z_NO_FLUSH); assert(ret == Z_STREAM_ERROR);
+ strm.avail_in = 4;
+ strm.next_in = (void *)"\0\0\xff\xff";
+ ret = inflateSync(&strm); assert(ret == Z_OK);
+ (void)inflateSyncPoint(&strm);
+ ret = inflateCopy(©, &strm); assert(ret == Z_MEM_ERROR);
+ mem_limit(&strm, 0);
+ ret = inflateUndermine(&strm, 1); assert(ret == Z_DATA_ERROR);
+ (void)inflateMark(&strm);
+ ret = inflateEnd(&strm); assert(ret == Z_OK);
+ mem_done(&strm, "miscellaneous, force memory errors");
+}
+
+/* input and output functions for inflateBack() */
+local unsigned pull(void *desc, unsigned char **buf)
+{
+ static unsigned int next = 0;
+ static unsigned char dat[] = {0x63, 0, 2, 0};
+ struct inflate_state *state;
+
+ if (desc == Z_NULL) {
+ next = 0;
+ return 0; /* no input (already provided at next_in) */
+ }
+ state = (void *)((z_stream *)desc)->state;
+ if (state != Z_NULL)
+ state->mode = SYNC; /* force an otherwise impossible situation */
+ return next < sizeof(dat) ? (*buf = dat + next++, 1) : 0;
+}
+
+local int push(void *desc, unsigned char *buf, unsigned len)
+{
+ buf += len;
+ return desc != Z_NULL; /* force error if desc not null */
+}
+
+/* cover inflateBack() up to common deflate data cases and after those */
+local void cover_back(void)
+{
+ int ret;
+ z_stream strm;
+ unsigned char win[32768];
+
+ ret = inflateBackInit_(Z_NULL, 0, win, 0, 0);
+ assert(ret == Z_VERSION_ERROR);
+ ret = inflateBackInit(Z_NULL, 0, win); assert(ret == Z_STREAM_ERROR);
+ ret = inflateBack(Z_NULL, Z_NULL, Z_NULL, Z_NULL, Z_NULL);
+ assert(ret == Z_STREAM_ERROR);
+ ret = inflateBackEnd(Z_NULL); assert(ret == Z_STREAM_ERROR);
+ fputs("inflateBack bad parameters\n", stderr);
+
+ mem_setup(&strm);
+ ret = inflateBackInit(&strm, 15, win); assert(ret == Z_OK);
+ strm.avail_in = 2;
+ strm.next_in = (void *)"\x03";
+ ret = inflateBack(&strm, pull, Z_NULL, push, Z_NULL);
+ assert(ret == Z_STREAM_END);
+ /* force output error */
+ strm.avail_in = 3;
+ strm.next_in = (void *)"\x63\x00";
+ ret = inflateBack(&strm, pull, Z_NULL, push, &strm);
+ assert(ret == Z_BUF_ERROR);
+ /* force mode error by mucking with state */
+ ret = inflateBack(&strm, pull, &strm, push, Z_NULL);
+ assert(ret == Z_STREAM_ERROR);
+ ret = inflateBackEnd(&strm); assert(ret == Z_OK);
+ mem_done(&strm, "inflateBack bad state");
+
+ ret = inflateBackInit(&strm, 15, win); assert(ret == Z_OK);
+ ret = inflateBackEnd(&strm); assert(ret == Z_OK);
+ fputs("inflateBack built-in memory routines\n", stderr);
+}
+
+/* do a raw inflate of data in hexadecimal with both inflate and inflateBack */
+local int try(char *hex, char *id, int err)
+{
+ int ret;
+ unsigned len, size;
+ unsigned char *in, *out, *win;
+ char *prefix;
+ z_stream strm;
+
+ /* convert to hex */
+ in = h2b(hex, &len);
+ assert(in != NULL);
+
+ /* allocate work areas */
+ size = len << 3;
+ out = malloc(size);
+ assert(out != NULL);
+ win = malloc(32768);
+ assert(win != NULL);
+ prefix = malloc(strlen(id) + 6);
+ assert(prefix != NULL);
+
+ /* first with inflate */
+ strcpy(prefix, id);
+ strcat(prefix, "-late");
+ mem_setup(&strm);
+ strm.avail_in = 0;
+ strm.next_in = Z_NULL;
+ ret = inflateInit2(&strm, err < 0 ? 47 : -15);
+ assert(ret == Z_OK);
+ strm.avail_in = len;
+ strm.next_in = in;
+ do {
+ strm.avail_out = size;
+ strm.next_out = out;
+ ret = inflate(&strm, Z_TREES);
+ assert(ret != Z_STREAM_ERROR && ret != Z_MEM_ERROR);
+ if (ret == Z_DATA_ERROR || ret == Z_NEED_DICT)
+ break;
+ } while (strm.avail_in || strm.avail_out == 0);
+ if (err) {
+ assert(ret == Z_DATA_ERROR);
+ assert(strcmp(id, strm.msg) == 0);
+ }
+ inflateEnd(&strm);
+ mem_done(&strm, prefix);
+
+ /* then with inflateBack */
+ if (err >= 0) {
+ strcpy(prefix, id);
+ strcat(prefix, "-back");
+ mem_setup(&strm);
+ ret = inflateBackInit(&strm, 15, win);
+ assert(ret == Z_OK);
+ strm.avail_in = len;
+ strm.next_in = in;
+ ret = inflateBack(&strm, pull, Z_NULL, push, Z_NULL);
+ assert(ret != Z_STREAM_ERROR);
+ if (err) {
+ assert(ret == Z_DATA_ERROR);
+ assert(strcmp(id, strm.msg) == 0);
+ }
+ inflateBackEnd(&strm);
+ mem_done(&strm, prefix);
+ }
+
+ /* clean up */
+ free(prefix);
+ free(win);
+ free(out);
+ free(in);
+ return ret;
+}
+
+/* cover deflate data cases in both inflate() and inflateBack() */
+local void cover_inflate(void)
+{
+ try("0 0 0 0 0", "invalid stored block lengths", 1);
+ try("3 0", "fixed", 0);
+ try("6", "invalid block type", 1);
+ try("1 1 0 fe ff 0", "stored", 0);
+ try("fc 0 0", "too many length or distance symbols", 1);
+ try("4 0 fe ff", "invalid code lengths set", 1);
+ try("4 0 24 49 0", "invalid bit length repeat", 1);
+ try("4 0 24 e9 ff ff", "invalid bit length repeat", 1);
+ try("4 0 24 e9 ff 6d", "invalid code -- missing end-of-block", 1);
+ try("4 80 49 92 24 49 92 24 71 ff ff 93 11 0",
+ "invalid literal/lengths set", 1);
+ try("4 80 49 92 24 49 92 24 f b4 ff ff c3 84", "invalid distances set", 1);
+ try("4 c0 81 8 0 0 0 0 20 7f eb b 0 0", "invalid literal/length code", 1);
+ try("2 7e ff ff", "invalid distance code", 1);
+ try("c c0 81 0 0 0 0 0 90 ff 6b 4 0", "invalid distance too far back", 1);
+
+ /* also trailer mismatch just in inflate() */
+ try("1f 8b 8 0 0 0 0 0 0 0 3 0 0 0 0 1", "incorrect data check", -1);
+ try("1f 8b 8 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 1",
+ "incorrect length check", -1);
+ try("5 c0 21 d 0 0 0 80 b0 fe 6d 2f 91 6c", "pull 17", 0);
+ try("5 e0 81 91 24 cb b2 2c 49 e2 f 2e 8b 9a 47 56 9f fb fe ec d2 ff 1f",
+ "long code", 0);
+ try("ed c0 1 1 0 0 0 40 20 ff 57 1b 42 2c 4f", "length extra", 0);
+ try("ed cf c1 b1 2c 47 10 c4 30 fa 6f 35 1d 1 82 59 3d fb be 2e 2a fc f c",
+ "long distance and extra", 0);
+ try("ed c0 81 0 0 0 0 80 a0 fd a9 17 a9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 "
+ "0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6", "window end", 0);
+ inf("2 8 20 80 0 3 0", "inflate_fast TYPE return", 0, -15, 258,
+ Z_STREAM_END);
+ inf("63 18 5 40 c 0", "window wrap", 3, -8, 300, Z_OK);
+}
+
+/* cover remaining lines in inftrees.c */
+local void cover_trees(void)
+{
+ int ret;
+ unsigned bits;
+ unsigned short lens[16], work[16];
+ code *next, table[ENOUGH_DISTS];
+
+ /* we need to call inflate_table() directly in order to manifest not-
+ enough errors, since zlib insures that enough is always enough */
+ for (bits = 0; bits < 15; bits++)
+ lens[bits] = (unsigned short)(bits + 1);
+ lens[15] = 15;
+ next = table;
+ bits = 15;
+ ret = inflate_table(DISTS, lens, 16, &next, &bits, work);
+ assert(ret == 1);
+ next = table;
+ bits = 1;
+ ret = inflate_table(DISTS, lens, 16, &next, &bits, work);
+ assert(ret == 1);
+ fputs("inflate_table not enough errors\n", stderr);
+}
+
+/* cover remaining inffast.c decoding and window copying */
+local void cover_fast(void)
+{
+ inf("e5 e0 81 ad 6d cb b2 2c c9 01 1e 59 63 ae 7d ee fb 4d fd b5 35 41 68"
+ " ff 7f 0f 0 0 0", "fast length extra bits", 0, -8, 258, Z_DATA_ERROR);
+ inf("25 fd 81 b5 6d 59 b6 6a 49 ea af 35 6 34 eb 8c b9 f6 b9 1e ef 67 49"
+ " 50 fe ff ff 3f 0 0", "fast distance extra bits", 0, -8, 258,
+ Z_DATA_ERROR);
+ inf("3 7e 0 0 0 0 0", "fast invalid distance code", 0, -8, 258,
+ Z_DATA_ERROR);
+ inf("1b 7 0 0 0 0 0", "fast invalid literal/length code", 0, -8, 258,
+ Z_DATA_ERROR);
+ inf("d c7 1 ae eb 38 c 4 41 a0 87 72 de df fb 1f b8 36 b1 38 5d ff ff 0",
+ "fast 2nd level codes and too far back", 0, -8, 258, Z_DATA_ERROR);
+ inf("63 18 5 8c 10 8 0 0 0 0", "very common case", 0, -8, 259, Z_OK);
+ inf("63 60 60 18 c9 0 8 18 18 18 26 c0 28 0 29 0 0 0",
+ "contiguous and wrap around window", 6, -8, 259, Z_OK);
+ inf("63 0 3 0 0 0 0 0", "copy direct from output", 0, -8, 259,
+ Z_STREAM_END);
+}
+
+int main(void)
+{
+ fprintf(stderr, "%s\n", zlibVersion());
+ cover_support();
+ cover_wrap();
+ cover_back();
+ cover_inflate();
+ cover_trees();
+ cover_fast();
+ return 0;
+}
diff --git a/third-party/zlib/test/minigzip.c b/third-party/zlib/test/minigzip.c
new file mode 100644
index 0000000..b3025a4
--- /dev/null
+++ b/third-party/zlib/test/minigzip.c
@@ -0,0 +1,651 @@
+/* minigzip.c -- simulate gzip using the zlib compression library
+ * Copyright (C) 1995-2006, 2010, 2011 Jean-loup Gailly.
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/*
+ * minigzip is a minimal implementation of the gzip utility. This is
+ * only an example of using zlib and isn't meant to replace the
+ * full-featured gzip. No attempt is made to deal with file systems
+ * limiting names to 14 or 8+3 characters, etc... Error checking is
+ * very limited. So use minigzip only for testing; use gzip for the
+ * real thing. On MSDOS, use only on file names without extension
+ * or in pipe mode.
+ */
+
+/* @(#) $Id$ */
+
+#include "zlib.h"
+#include <stdio.h>
+
+#ifdef STDC
+# include <string.h>
+# include <stdlib.h>
+#endif
+
+#ifdef USE_MMAP
+# include <sys/types.h>
+# include <sys/mman.h>
+# include <sys/stat.h>
+#endif
+
+#if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__)
+# include <fcntl.h>
+# include <io.h>
+# ifdef UNDER_CE
+# include <stdlib.h>
+# endif
+# define SET_BINARY_MODE(file) setmode(fileno(file), O_BINARY)
+#else
+# define SET_BINARY_MODE(file)
+#endif
+
+#ifdef _MSC_VER
+# define snprintf _snprintf
+#endif
+
+#ifdef VMS
+# define unlink delete
+# define GZ_SUFFIX "-gz"
+#endif
+#ifdef RISCOS
+# define unlink remove
+# define GZ_SUFFIX "-gz"
+# define fileno(file) file->__file
+#endif
+#if defined(__MWERKS__) && __dest_os != __be_os && __dest_os != __win32_os
+# include <unix.h> /* for fileno */
+#endif
+
+#if !defined(Z_HAVE_UNISTD_H) && !defined(_LARGEFILE64_SOURCE)
+#ifndef WIN32 /* unlink already in stdio.h for WIN32 */
+ extern int unlink OF((const char *));
+#endif
+#endif
+
+#if defined(UNDER_CE)
+# include <windows.h>
+# define perror(s) pwinerror(s)
+
+/* Map the Windows error number in ERROR to a locale-dependent error
+ message string and return a pointer to it. Typically, the values
+ for ERROR come from GetLastError.
+
+ The string pointed to shall not be modified by the application,
+ but may be overwritten by a subsequent call to strwinerror
+
+ The strwinerror function does not change the current setting
+ of GetLastError. */
+
+static char *strwinerror (error)
+ DWORD error;
+{
+ static char buf[1024];
+
+ wchar_t *msgbuf;
+ DWORD lasterr = GetLastError();
+ DWORD chars = FormatMessage(FORMAT_MESSAGE_FROM_SYSTEM
+ | FORMAT_MESSAGE_ALLOCATE_BUFFER,
+ NULL,
+ error,
+ 0, /* Default language */
+ (LPVOID)&msgbuf,
+ 0,
+ NULL);
+ if (chars != 0) {
+ /* If there is an \r\n appended, zap it. */
+ if (chars >= 2
+ && msgbuf[chars - 2] == '\r' && msgbuf[chars - 1] == '\n') {
+ chars -= 2;
+ msgbuf[chars] = 0;
+ }
+
+ if (chars > sizeof (buf) - 1) {
+ chars = sizeof (buf) - 1;
+ msgbuf[chars] = 0;
+ }
+
+ wcstombs(buf, msgbuf, chars + 1);
+ LocalFree(msgbuf);
+ }
+ else {
+ sprintf(buf, "unknown win32 error (%ld)", error);
+ }
+
+ SetLastError(lasterr);
+ return buf;
+}
+
+static void pwinerror (s)
+ const char *s;
+{
+ if (s && *s)
+ fprintf(stderr, "%s: %s\n", s, strwinerror(GetLastError ()));
+ else
+ fprintf(stderr, "%s\n", strwinerror(GetLastError ()));
+}
+
+#endif /* UNDER_CE */
+
+#ifndef GZ_SUFFIX
+# define GZ_SUFFIX ".gz"
+#endif
+#define SUFFIX_LEN (sizeof(GZ_SUFFIX)-1)
+
+#define BUFLEN 16384
+#define MAX_NAME_LEN 1024
+
+#ifdef MAXSEG_64K
+# define local static
+ /* Needed for systems with limitation on stack size. */
+#else
+# define local
+#endif
+
+#ifdef Z_SOLO
+/* for Z_SOLO, create simplified gz* functions using deflate and inflate */
+
+#if defined(Z_HAVE_UNISTD_H) || defined(Z_LARGE)
+# include <unistd.h> /* for unlink() */
+#endif
+
+void *myalloc OF((void *, unsigned, unsigned));
+void myfree OF((void *, void *));
+
+void *myalloc(q, n, m)
+ void *q;
+ unsigned n, m;
+{
+ q = Z_NULL;
+ return calloc(n, m);
+}
+
+void myfree(q, p)
+ void *q, *p;
+{
+ q = Z_NULL;
+ free(p);
+}
+
+typedef struct gzFile_s {
+ FILE *file;
+ int write;
+ int err;
+ char *msg;
+ z_stream strm;
+} *gzFile;
+
+gzFile gzopen OF((const char *, const char *));
+gzFile gzdopen OF((int, const char *));
+gzFile gz_open OF((const char *, int, const char *));
+
+gzFile gzopen(path, mode)
+const char *path;
+const char *mode;
+{
+ return gz_open(path, -1, mode);
+}
+
+gzFile gzdopen(fd, mode)
+int fd;
+const char *mode;
+{
+ return gz_open(NULL, fd, mode);
+}
+
+gzFile gz_open(path, fd, mode)
+ const char *path;
+ int fd;
+ const char *mode;
+{
+ gzFile gz;
+ int ret;
+
+ gz = malloc(sizeof(struct gzFile_s));
+ if (gz == NULL)
+ return NULL;
+ gz->write = strchr(mode, 'w') != NULL;
+ gz->strm.zalloc = myalloc;
+ gz->strm.zfree = myfree;
+ gz->strm.opaque = Z_NULL;
+ if (gz->write)
+ ret = deflateInit2(&(gz->strm), -1, 8, 15 + 16, 8, 0);
+ else {
+ gz->strm.next_in = 0;
+ gz->strm.avail_in = Z_NULL;
+ ret = inflateInit2(&(gz->strm), 15 + 16);
+ }
+ if (ret != Z_OK) {
+ free(gz);
+ return NULL;
+ }
+ gz->file = path == NULL ? fdopen(fd, gz->write ? "wb" : "rb") :
+ fopen(path, gz->write ? "wb" : "rb");
+ if (gz->file == NULL) {
+ gz->write ? deflateEnd(&(gz->strm)) : inflateEnd(&(gz->strm));
+ free(gz);
+ return NULL;
+ }
+ gz->err = 0;
+ gz->msg = "";
+ return gz;
+}
+
+int gzwrite OF((gzFile, const void *, unsigned));
+
+int gzwrite(gz, buf, len)
+ gzFile gz;
+ const void *buf;
+ unsigned len;
+{
+ z_stream *strm;
+ unsigned char out[BUFLEN];
+
+ if (gz == NULL || !gz->write)
+ return 0;
+ strm = &(gz->strm);
+ strm->next_in = (void *)buf;
+ strm->avail_in = len;
+ do {
+ strm->next_out = out;
+ strm->avail_out = BUFLEN;
+ (void)deflate(strm, Z_NO_FLUSH);
+ fwrite(out, 1, BUFLEN - strm->avail_out, gz->file);
+ } while (strm->avail_out == 0);
+ return len;
+}
+
+int gzread OF((gzFile, void *, unsigned));
+
+int gzread(gz, buf, len)
+ gzFile gz;
+ void *buf;
+ unsigned len;
+{
+ int ret;
+ unsigned got;
+ unsigned char in[1];
+ z_stream *strm;
+
+ if (gz == NULL || gz->write)
+ return 0;
+ if (gz->err)
+ return 0;
+ strm = &(gz->strm);
+ strm->next_out = (void *)buf;
+ strm->avail_out = len;
+ do {
+ got = fread(in, 1, 1, gz->file);
+ if (got == 0)
+ break;
+ strm->next_in = in;
+ strm->avail_in = 1;
+ ret = inflate(strm, Z_NO_FLUSH);
+ if (ret == Z_DATA_ERROR) {
+ gz->err = Z_DATA_ERROR;
+ gz->msg = strm->msg;
+ return 0;
+ }
+ if (ret == Z_STREAM_END)
+ inflateReset(strm);
+ } while (strm->avail_out);
+ return len - strm->avail_out;
+}
+
+int gzclose OF((gzFile));
+
+int gzclose(gz)
+ gzFile gz;
+{
+ z_stream *strm;
+ unsigned char out[BUFLEN];
+
+ if (gz == NULL)
+ return Z_STREAM_ERROR;
+ strm = &(gz->strm);
+ if (gz->write) {
+ strm->next_in = Z_NULL;
+ strm->avail_in = 0;
+ do {
+ strm->next_out = out;
+ strm->avail_out = BUFLEN;
+ (void)deflate(strm, Z_FINISH);
+ fwrite(out, 1, BUFLEN - strm->avail_out, gz->file);
+ } while (strm->avail_out == 0);
+ deflateEnd(strm);
+ }
+ else
+ inflateEnd(strm);
+ fclose(gz->file);
+ free(gz);
+ return Z_OK;
+}
+
+const char *gzerror OF((gzFile, int *));
+
+const char *gzerror(gz, err)
+ gzFile gz;
+ int *err;
+{
+ *err = gz->err;
+ return gz->msg;
+}
+
+#endif
+
+char *prog;
+
+void error OF((const char *msg));
+void gz_compress OF((FILE *in, gzFile out));
+#ifdef USE_MMAP
+int gz_compress_mmap OF((FILE *in, gzFile out));
+#endif
+void gz_uncompress OF((gzFile in, FILE *out));
+void file_compress OF((char *file, char *mode));
+void file_uncompress OF((char *file));
+int main OF((int argc, char *argv[]));
+
+/* ===========================================================================
+ * Display error message and exit
+ */
+void error(msg)
+ const char *msg;
+{
+ fprintf(stderr, "%s: %s\n", prog, msg);
+ exit(1);
+}
+
+/* ===========================================================================
+ * Compress input to output then close both files.
+ */
+
+void gz_compress(in, out)
+ FILE *in;
+ gzFile out;
+{
+ local char buf[BUFLEN];
+ int len;
+ int err;
+
+#ifdef USE_MMAP
+ /* Try first compressing with mmap. If mmap fails (minigzip used in a
+ * pipe), use the normal fread loop.
+ */
+ if (gz_compress_mmap(in, out) == Z_OK) return;
+#endif
+ for (;;) {
+ len = (int)fread(buf, 1, sizeof(buf), in);
+ if (ferror(in)) {
+ perror("fread");
+ exit(1);
+ }
+ if (len == 0) break;
+
+ if (gzwrite(out, buf, (unsigned)len) != len) error(gzerror(out, &err));
+ }
+ fclose(in);
+ if (gzclose(out) != Z_OK) error("failed gzclose");
+}
+
+#ifdef USE_MMAP /* MMAP version, Miguel Albrecht <malbrech at eso.org> */
+
+/* Try compressing the input file at once using mmap. Return Z_OK if
+ * if success, Z_ERRNO otherwise.
+ */
+int gz_compress_mmap(in, out)
+ FILE *in;
+ gzFile out;
+{
+ int len;
+ int err;
+ int ifd = fileno(in);
+ caddr_t buf; /* mmap'ed buffer for the entire input file */
+ off_t buf_len; /* length of the input file */
+ struct stat sb;
+
+ /* Determine the size of the file, needed for mmap: */
+ if (fstat(ifd, &sb) < 0) return Z_ERRNO;
+ buf_len = sb.st_size;
+ if (buf_len <= 0) return Z_ERRNO;
+
+ /* Now do the actual mmap: */
+ buf = mmap((caddr_t) 0, buf_len, PROT_READ, MAP_SHARED, ifd, (off_t)0);
+ if (buf == (caddr_t)(-1)) return Z_ERRNO;
+
+ /* Compress the whole file at once: */
+ len = gzwrite(out, (char *)buf, (unsigned)buf_len);
+
+ if (len != (int)buf_len) error(gzerror(out, &err));
+
+ munmap(buf, buf_len);
+ fclose(in);
+ if (gzclose(out) != Z_OK) error("failed gzclose");
+ return Z_OK;
+}
+#endif /* USE_MMAP */
+
+/* ===========================================================================
+ * Uncompress input to output then close both files.
+ */
+void gz_uncompress(in, out)
+ gzFile in;
+ FILE *out;
+{
+ local char buf[BUFLEN];
+ int len;
+ int err;
+
+ for (;;) {
+ len = gzread(in, buf, sizeof(buf));
+ if (len < 0) error (gzerror(in, &err));
+ if (len == 0) break;
+
+ if ((int)fwrite(buf, 1, (unsigned)len, out) != len) {
+ error("failed fwrite");
+ }
+ }
+ if (fclose(out)) error("failed fclose");
+
+ if (gzclose(in) != Z_OK) error("failed gzclose");
+}
+
+
+/* ===========================================================================
+ * Compress the given file: create a corresponding .gz file and remove the
+ * original.
+ */
+void file_compress(file, mode)
+ char *file;
+ char *mode;
+{
+ local char outfile[MAX_NAME_LEN];
+ FILE *in;
+ gzFile out;
+
+ if (strlen(file) + strlen(GZ_SUFFIX) >= sizeof(outfile)) {
+ fprintf(stderr, "%s: filename too long\n", prog);
+ exit(1);
+ }
+
+#if !defined(NO_snprintf) && !defined(NO_vsnprintf)
+ snprintf(outfile, sizeof(outfile), "%s%s", file, GZ_SUFFIX);
+#else
+ strcpy(outfile, file);
+ strcat(outfile, GZ_SUFFIX);
+#endif
+
+ in = fopen(file, "rb");
+ if (in == NULL) {
+ perror(file);
+ exit(1);
+ }
+ out = gzopen(outfile, mode);
+ if (out == NULL) {
+ fprintf(stderr, "%s: can't gzopen %s\n", prog, outfile);
+ exit(1);
+ }
+ gz_compress(in, out);
+
+ unlink(file);
+}
+
+
+/* ===========================================================================
+ * Uncompress the given file and remove the original.
+ */
+void file_uncompress(file)
+ char *file;
+{
+ local char buf[MAX_NAME_LEN];
+ char *infile, *outfile;
+ FILE *out;
+ gzFile in;
+ size_t len = strlen(file);
+
+ if (len + strlen(GZ_SUFFIX) >= sizeof(buf)) {
+ fprintf(stderr, "%s: filename too long\n", prog);
+ exit(1);
+ }
+
+#if !defined(NO_snprintf) && !defined(NO_vsnprintf)
+ snprintf(buf, sizeof(buf), "%s", file);
+#else
+ strcpy(buf, file);
+#endif
+
+ if (len > SUFFIX_LEN && strcmp(file+len-SUFFIX_LEN, GZ_SUFFIX) == 0) {
+ infile = file;
+ outfile = buf;
+ outfile[len-3] = '\0';
+ } else {
+ outfile = file;
+ infile = buf;
+#if !defined(NO_snprintf) && !defined(NO_vsnprintf)
+ snprintf(buf + len, sizeof(buf) - len, "%s", GZ_SUFFIX);
+#else
+ strcat(infile, GZ_SUFFIX);
+#endif
+ }
+ in = gzopen(infile, "rb");
+ if (in == NULL) {
+ fprintf(stderr, "%s: can't gzopen %s\n", prog, infile);
+ exit(1);
+ }
+ out = fopen(outfile, "wb");
+ if (out == NULL) {
+ perror(file);
+ exit(1);
+ }
+
+ gz_uncompress(in, out);
+
+ unlink(infile);
+}
+
+
+/* ===========================================================================
+ * Usage: minigzip [-c] [-d] [-f] [-h] [-r] [-1 to -9] [files...]
+ * -c : write to standard output
+ * -d : decompress
+ * -f : compress with Z_FILTERED
+ * -h : compress with Z_HUFFMAN_ONLY
+ * -r : compress with Z_RLE
+ * -1 to -9 : compression level
+ */
+
+int main(argc, argv)
+ int argc;
+ char *argv[];
+{
+ int copyout = 0;
+ int uncompr = 0;
+ gzFile file;
+ char *bname, outmode[20];
+
+#if !defined(NO_snprintf) && !defined(NO_vsnprintf)
+ snprintf(outmode, sizeof(outmode), "%s", "wb6 ");
+#else
+ strcpy(outmode, "wb6 ");
+#endif
+
+ prog = argv[0];
+ bname = strrchr(argv[0], '/');
+ if (bname)
+ bname++;
+ else
+ bname = argv[0];
+ argc--, argv++;
+
+ if (!strcmp(bname, "gunzip"))
+ uncompr = 1;
+ else if (!strcmp(bname, "zcat"))
+ copyout = uncompr = 1;
+
+ while (argc > 0) {
+ if (strcmp(*argv, "-c") == 0)
+ copyout = 1;
+ else if (strcmp(*argv, "-d") == 0)
+ uncompr = 1;
+ else if (strcmp(*argv, "-f") == 0)
+ outmode[3] = 'f';
+ else if (strcmp(*argv, "-h") == 0)
+ outmode[3] = 'h';
+ else if (strcmp(*argv, "-r") == 0)
+ outmode[3] = 'R';
+ else if ((*argv)[0] == '-' && (*argv)[1] >= '1' && (*argv)[1] <= '9' &&
+ (*argv)[2] == 0)
+ outmode[2] = (*argv)[1];
+ else
+ break;
+ argc--, argv++;
+ }
+ if (outmode[3] == ' ')
+ outmode[3] = 0;
+ if (argc == 0) {
+ SET_BINARY_MODE(stdin);
+ SET_BINARY_MODE(stdout);
+ if (uncompr) {
+ file = gzdopen(fileno(stdin), "rb");
+ if (file == NULL) error("can't gzdopen stdin");
+ gz_uncompress(file, stdout);
+ } else {
+ file = gzdopen(fileno(stdout), outmode);
+ if (file == NULL) error("can't gzdopen stdout");
+ gz_compress(stdin, file);
+ }
+ } else {
+ if (copyout) {
+ SET_BINARY_MODE(stdout);
+ }
+ do {
+ if (uncompr) {
+ if (copyout) {
+ file = gzopen(*argv, "rb");
+ if (file == NULL)
+ fprintf(stderr, "%s: can't gzopen %s\n", prog, *argv);
+ else
+ gz_uncompress(file, stdout);
+ } else {
+ file_uncompress(*argv);
+ }
+ } else {
+ if (copyout) {
+ FILE * in = fopen(*argv, "rb");
+
+ if (in == NULL) {
+ perror(*argv);
+ } else {
+ file = gzdopen(fileno(stdout), outmode);
+ if (file == NULL) error("can't gzdopen stdout");
+
+ gz_compress(in, file);
+ }
+
+ } else {
+ file_compress(*argv, outmode);
+ }
+ }
+ } while (argv++, --argc);
+ }
+ return 0;
+}
diff --git a/third-party/zlib/treebuild.xml b/third-party/zlib/treebuild.xml
new file mode 100644
index 0000000..38d29d7
--- /dev/null
+++ b/third-party/zlib/treebuild.xml
@@ -0,0 +1,116 @@
+<?xml version="1.0" ?>
+<package name="zlib" version="1.2.8">
+ <library name="zlib" dlversion="1.2.8" dlname="z">
+ <property name="description"> zip compression library </property>
+ <property name="include-target-dir" value="$(@PACKAGE/install-includedir)" />
+
+ <!-- fixme: not implemented yet -->
+ <property name="compiler/c/inline" value="yes" />
+
+ <include-file name="zlib.h" scope="public" mode="644" />
+ <include-file name="zconf.h" scope="public" mode="644" />
+
+ <source name="adler32.c">
+ <depend name="zlib.h" />
+ <depend name="zconf.h" />
+ </source>
+ <source name="compress.c">
+ <depend name="zlib.h" />
+ <depend name="zconf.h" />
+ </source>
+ <source name="crc32.c">
+ <depend name="zlib.h" />
+ <depend name="zconf.h" />
+ <depend name="crc32.h" />
+ </source>
+ <source name="gzclose.c">
+ <depend name="zlib.h" />
+ <depend name="zconf.h" />
+ <depend name="gzguts.h" />
+ </source>
+ <source name="gzlib.c">
+ <depend name="zlib.h" />
+ <depend name="zconf.h" />
+ <depend name="gzguts.h" />
+ </source>
+ <source name="gzread.c">
+ <depend name="zlib.h" />
+ <depend name="zconf.h" />
+ <depend name="gzguts.h" />
+ </source>
+ <source name="gzwrite.c">
+ <depend name="zlib.h" />
+ <depend name="zconf.h" />
+ <depend name="gzguts.h" />
+ </source>
+ <source name="uncompr.c">
+ <depend name="zlib.h" />
+ <depend name="zconf.h" />
+ </source>
+ <source name="deflate.c">
+ <depend name="zlib.h" />
+ <depend name="zconf.h" />
+ <depend name="zutil.h" />
+ <depend name="deflate.h" />
+ </source>
+ <source name="trees.c">
+ <depend name="zlib.h" />
+ <depend name="zconf.h" />
+ <depend name="zutil.h" />
+ <depend name="deflate.h" />
+ <depend name="trees.h" />
+ </source>
+ <source name="zutil.c">
+ <depend name="zlib.h" />
+ <depend name="zconf.h" />
+ <depend name="zutil.h" />
+ </source>
+ <source name="inflate.c">
+ <depend name="zlib.h" />
+ <depend name="zconf.h" />
+ <depend name="zutil.h" />
+ <depend name="inftrees.h" />
+ <depend name="inflate.h" />
+ <depend name="inffast.h" />
+ </source>
+ <source name="infback.c">
+ <depend name="zlib.h" />
+ <depend name="zconf.h" />
+ <depend name="zutil.h" />
+ <depend name="inftrees.h" />
+ <depend name="inflate.h" />
+ <depend name="inffast.h" />
+ </source>
+ <source name="inftrees.c">
+ <depend name="zlib.h" />
+ <depend name="zconf.h" />
+ <depend name="zutil.h" />
+ <depend name="inftrees.h" />
+ </source>
+ <source name="inffast.c">
+ <depend name="zlib.h" />
+ <depend name="zconf.h" />
+ <depend name="zutil.h" />
+ <depend name="inftrees.h" />
+ <depend name="inflate.h" />
+ <depend name="inffast.h" />
+ </source>
+ </library>
+</package>
+
+<!--
+CFLAGS=-O
+#CFLAGS=-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7
+#CFLAGS=-g -DDEBUG
+#CFLAGS=-O3 -Wall -Wwrite-strings -Wpointer-arith -Wconversion \
+# -Wstrict-prototypes -Wmissing-prototypes
+
+# OBJA =
+# to use the asm code: make OBJA=match.o
+#
+match.o: match.S
+ $(CPP) match.S > _match.s
+ $(CC) -c _match.s
+ mv _match.o match.o
+ rm -f _match.s
+-->
diff --git a/third-party/zlib/trees.c b/third-party/zlib/trees.c
new file mode 100644
index 0000000..1fd7759
--- /dev/null
+++ b/third-party/zlib/trees.c
@@ -0,0 +1,1226 @@
+/* trees.c -- output deflated data using Huffman coding
+ * Copyright (C) 1995-2012 Jean-loup Gailly
+ * detect_data_type() function provided freely by Cosmin Truta, 2006
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/*
+ * ALGORITHM
+ *
+ * The "deflation" process uses several Huffman trees. The more
+ * common source values are represented by shorter bit sequences.
+ *
+ * Each code tree is stored in a compressed form which is itself
+ * a Huffman encoding of the lengths of all the code strings (in
+ * ascending order by source values). The actual code strings are
+ * reconstructed from the lengths in the inflate process, as described
+ * in the deflate specification.
+ *
+ * REFERENCES
+ *
+ * Deutsch, L.P.,"'Deflate' Compressed Data Format Specification".
+ * Available in ftp.uu.net:/pub/archiving/zip/doc/deflate-1.1.doc
+ *
+ * Storer, James A.
+ * Data Compression: Methods and Theory, pp. 49-50.
+ * Computer Science Press, 1988. ISBN 0-7167-8156-5.
+ *
+ * Sedgewick, R.
+ * Algorithms, p290.
+ * Addison-Wesley, 1983. ISBN 0-201-06672-6.
+ */
+
+/* @(#) $Id$ */
+
+/* #define GEN_TREES_H */
+
+#include "deflate.h"
+
+#ifdef DEBUG
+# include <ctype.h>
+#endif
+
+/* ===========================================================================
+ * Constants
+ */
+
+#define MAX_BL_BITS 7
+/* Bit length codes must not exceed MAX_BL_BITS bits */
+
+#define END_BLOCK 256
+/* end of block literal code */
+
+#define REP_3_6 16
+/* repeat previous bit length 3-6 times (2 bits of repeat count) */
+
+#define REPZ_3_10 17
+/* repeat a zero length 3-10 times (3 bits of repeat count) */
+
+#define REPZ_11_138 18
+/* repeat a zero length 11-138 times (7 bits of repeat count) */
+
+local const int extra_lbits[LENGTH_CODES] /* extra bits for each length code */
+ = {0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0};
+
+local const int extra_dbits[D_CODES] /* extra bits for each distance code */
+ = {0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13};
+
+local const int extra_blbits[BL_CODES]/* extra bits for each bit length code */
+ = {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,3,7};
+
+local const uch bl_order[BL_CODES]
+ = {16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15};
+/* The lengths of the bit length codes are sent in order of decreasing
+ * probability, to avoid transmitting the lengths for unused bit length codes.
+ */
+
+/* ===========================================================================
+ * Local data. These are initialized only once.
+ */
+
+#define DIST_CODE_LEN 512 /* see definition of array dist_code below */
+
+#if defined(GEN_TREES_H) || !defined(STDC)
+/* non ANSI compilers may not accept trees.h */
+
+local ct_data static_ltree[L_CODES+2];
+/* The static literal tree. Since the bit lengths are imposed, there is no
+ * need for the L_CODES extra codes used during heap construction. However
+ * The codes 286 and 287 are needed to build a canonical tree (see _tr_init
+ * below).
+ */
+
+local ct_data static_dtree[D_CODES];
+/* The static distance tree. (Actually a trivial tree since all codes use
+ * 5 bits.)
+ */
+
+uch _dist_code[DIST_CODE_LEN];
+/* Distance codes. The first 256 values correspond to the distances
+ * 3 .. 258, the last 256 values correspond to the top 8 bits of
+ * the 15 bit distances.
+ */
+
+uch _length_code[MAX_MATCH-MIN_MATCH+1];
+/* length code for each normalized match length (0 == MIN_MATCH) */
+
+local int base_length[LENGTH_CODES];
+/* First normalized length for each code (0 = MIN_MATCH) */
+
+local int base_dist[D_CODES];
+/* First normalized distance for each code (0 = distance of 1) */
+
+#else
+# include "trees.h"
+#endif /* GEN_TREES_H */
+
+struct static_tree_desc_s {
+ const ct_data *static_tree; /* static tree or NULL */
+ const intf *extra_bits; /* extra bits for each code or NULL */
+ int extra_base; /* base index for extra_bits */
+ int elems; /* max number of elements in the tree */
+ int max_length; /* max bit length for the codes */
+};
+
+local static_tree_desc static_l_desc =
+{static_ltree, extra_lbits, LITERALS+1, L_CODES, MAX_BITS};
+
+local static_tree_desc static_d_desc =
+{static_dtree, extra_dbits, 0, D_CODES, MAX_BITS};
+
+local static_tree_desc static_bl_desc =
+{(const ct_data *)0, extra_blbits, 0, BL_CODES, MAX_BL_BITS};
+
+/* ===========================================================================
+ * Local (static) routines in this file.
+ */
+
+local void tr_static_init OF((void));
+local void init_block OF((deflate_state *s));
+local void pqdownheap OF((deflate_state *s, ct_data *tree, int k));
+local void gen_bitlen OF((deflate_state *s, tree_desc *desc));
+local void gen_codes OF((ct_data *tree, int max_code, ushf *bl_count));
+local void build_tree OF((deflate_state *s, tree_desc *desc));
+local void scan_tree OF((deflate_state *s, ct_data *tree, int max_code));
+local void send_tree OF((deflate_state *s, ct_data *tree, int max_code));
+local int build_bl_tree OF((deflate_state *s));
+local void send_all_trees OF((deflate_state *s, int lcodes, int dcodes,
+ int blcodes));
+local void compress_block OF((deflate_state *s, const ct_data *ltree,
+ const ct_data *dtree));
+local int detect_data_type OF((deflate_state *s));
+local unsigned bi_reverse OF((unsigned value, int length));
+local void bi_windup OF((deflate_state *s));
+local void bi_flush OF((deflate_state *s));
+local void copy_block OF((deflate_state *s, charf *buf, unsigned len,
+ int header));
+
+#ifdef GEN_TREES_H
+local void gen_trees_header OF((void));
+#endif
+
+#ifndef DEBUG
+# define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
+ /* Send a code of the given tree. c and tree must not have side effects */
+
+#else /* DEBUG */
+# define send_code(s, c, tree) \
+ { if (z_verbose>2) fprintf(stderr,"\ncd %3d ",(c)); \
+ send_bits(s, tree[c].Code, tree[c].Len); }
+#endif
+
+/* ===========================================================================
+ * Output a short LSB first on the stream.
+ * IN assertion: there is enough room in pendingBuf.
+ */
+#define put_short(s, w) { \
+ put_byte(s, (uch)((w) & 0xff)); \
+ put_byte(s, (uch)((ush)(w) >> 8)); \
+}
+
+/* ===========================================================================
+ * Send a value on a given number of bits.
+ * IN assertion: length <= 16 and value fits in length bits.
+ */
+#ifdef DEBUG
+local void send_bits OF((deflate_state *s, int value, int length));
+
+local void send_bits(s, value, length)
+ deflate_state *s;
+ int value; /* value to send */
+ int length; /* number of bits */
+{
+ Tracevv((stderr," l %2d v %4x ", length, value));
+ Assert(length > 0 && length <= 15, "invalid length");
+ s->bits_sent += (ulg)length;
+
+ /* If not enough room in bi_buf, use (valid) bits from bi_buf and
+ * (16 - bi_valid) bits from value, leaving (width - (16-bi_valid))
+ * unused bits in value.
+ */
+ if (s->bi_valid > (int)Buf_size - length) {
+ s->bi_buf |= (ush)value << s->bi_valid;
+ put_short(s, s->bi_buf);
+ s->bi_buf = (ush)value >> (Buf_size - s->bi_valid);
+ s->bi_valid += length - Buf_size;
+ } else {
+ s->bi_buf |= (ush)value << s->bi_valid;
+ s->bi_valid += length;
+ }
+}
+#else /* !DEBUG */
+
+#define send_bits(s, value, length) \
+{ int len = length;\
+ if (s->bi_valid > (int)Buf_size - len) {\
+ int val = value;\
+ s->bi_buf |= (ush)val << s->bi_valid;\
+ put_short(s, s->bi_buf);\
+ s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
+ s->bi_valid += len - Buf_size;\
+ } else {\
+ s->bi_buf |= (ush)(value) << s->bi_valid;\
+ s->bi_valid += len;\
+ }\
+}
+#endif /* DEBUG */
+
+
+/* the arguments must not have side effects */
+
+/* ===========================================================================
+ * Initialize the various 'constant' tables.
+ */
+local void tr_static_init()
+{
+#if defined(GEN_TREES_H) || !defined(STDC)
+ static int static_init_done = 0;
+ int n; /* iterates over tree elements */
+ int bits; /* bit counter */
+ int length; /* length value */
+ int code; /* code value */
+ int dist; /* distance index */
+ ush bl_count[MAX_BITS+1];
+ /* number of codes at each bit length for an optimal tree */
+
+ if (static_init_done) return;
+
+ /* For some embedded targets, global variables are not initialized: */
+#ifdef NO_INIT_GLOBAL_POINTERS
+ static_l_desc.static_tree = static_ltree;
+ static_l_desc.extra_bits = extra_lbits;
+ static_d_desc.static_tree = static_dtree;
+ static_d_desc.extra_bits = extra_dbits;
+ static_bl_desc.extra_bits = extra_blbits;
+#endif
+
+ /* Initialize the mapping length (0..255) -> length code (0..28) */
+ length = 0;
+ for (code = 0; code < LENGTH_CODES-1; code++) {
+ base_length[code] = length;
+ for (n = 0; n < (1<<extra_lbits[code]); n++) {
+ _length_code[length++] = (uch)code;
+ }
+ }
+ Assert (length == 256, "tr_static_init: length != 256");
+ /* Note that the length 255 (match length 258) can be represented
+ * in two different ways: code 284 + 5 bits or code 285, so we
+ * overwrite length_code[255] to use the best encoding:
+ */
+ _length_code[length-1] = (uch)code;
+
+ /* Initialize the mapping dist (0..32K) -> dist code (0..29) */
+ dist = 0;
+ for (code = 0 ; code < 16; code++) {
+ base_dist[code] = dist;
+ for (n = 0; n < (1<<extra_dbits[code]); n++) {
+ _dist_code[dist++] = (uch)code;
+ }
+ }
+ Assert (dist == 256, "tr_static_init: dist != 256");
+ dist >>= 7; /* from now on, all distances are divided by 128 */
+ for ( ; code < D_CODES; code++) {
+ base_dist[code] = dist << 7;
+ for (n = 0; n < (1<<(extra_dbits[code]-7)); n++) {
+ _dist_code[256 + dist++] = (uch)code;
+ }
+ }
+ Assert (dist == 256, "tr_static_init: 256+dist != 512");
+
+ /* Construct the codes of the static literal tree */
+ for (bits = 0; bits <= MAX_BITS; bits++) bl_count[bits] = 0;
+ n = 0;
+ while (n <= 143) static_ltree[n++].Len = 8, bl_count[8]++;
+ while (n <= 255) static_ltree[n++].Len = 9, bl_count[9]++;
+ while (n <= 279) static_ltree[n++].Len = 7, bl_count[7]++;
+ while (n <= 287) static_ltree[n++].Len = 8, bl_count[8]++;
+ /* Codes 286 and 287 do not exist, but we must include them in the
+ * tree construction to get a canonical Huffman tree (longest code
+ * all ones)
+ */
+ gen_codes((ct_data *)static_ltree, L_CODES+1, bl_count);
+
+ /* The static distance tree is trivial: */
+ for (n = 0; n < D_CODES; n++) {
+ static_dtree[n].Len = 5;
+ static_dtree[n].Code = bi_reverse((unsigned)n, 5);
+ }
+ static_init_done = 1;
+
+# ifdef GEN_TREES_H
+ gen_trees_header();
+# endif
+#endif /* defined(GEN_TREES_H) || !defined(STDC) */
+}
+
+/* ===========================================================================
+ * Genererate the file trees.h describing the static trees.
+ */
+#ifdef GEN_TREES_H
+# ifndef DEBUG
+# include <stdio.h>
+# endif
+
+# define SEPARATOR(i, last, width) \
+ ((i) == (last)? "\n};\n\n" : \
+ ((i) % (width) == (width)-1 ? ",\n" : ", "))
+
+void gen_trees_header()
+{
+ FILE *header = fopen("trees.h", "w");
+ int i;
+
+ Assert (header != NULL, "Can't open trees.h");
+ fprintf(header,
+ "/* header created automatically with -DGEN_TREES_H */\n\n");
+
+ fprintf(header, "local const ct_data static_ltree[L_CODES+2] = {\n");
+ for (i = 0; i < L_CODES+2; i++) {
+ fprintf(header, "{{%3u},{%3u}}%s", static_ltree[i].Code,
+ static_ltree[i].Len, SEPARATOR(i, L_CODES+1, 5));
+ }
+
+ fprintf(header, "local const ct_data static_dtree[D_CODES] = {\n");
+ for (i = 0; i < D_CODES; i++) {
+ fprintf(header, "{{%2u},{%2u}}%s", static_dtree[i].Code,
+ static_dtree[i].Len, SEPARATOR(i, D_CODES-1, 5));
+ }
+
+ fprintf(header, "const uch ZLIB_INTERNAL _dist_code[DIST_CODE_LEN] = {\n");
+ for (i = 0; i < DIST_CODE_LEN; i++) {
+ fprintf(header, "%2u%s", _dist_code[i],
+ SEPARATOR(i, DIST_CODE_LEN-1, 20));
+ }
+
+ fprintf(header,
+ "const uch ZLIB_INTERNAL _length_code[MAX_MATCH-MIN_MATCH+1]= {\n");
+ for (i = 0; i < MAX_MATCH-MIN_MATCH+1; i++) {
+ fprintf(header, "%2u%s", _length_code[i],
+ SEPARATOR(i, MAX_MATCH-MIN_MATCH, 20));
+ }
+
+ fprintf(header, "local const int base_length[LENGTH_CODES] = {\n");
+ for (i = 0; i < LENGTH_CODES; i++) {
+ fprintf(header, "%1u%s", base_length[i],
+ SEPARATOR(i, LENGTH_CODES-1, 20));
+ }
+
+ fprintf(header, "local const int base_dist[D_CODES] = {\n");
+ for (i = 0; i < D_CODES; i++) {
+ fprintf(header, "%5u%s", base_dist[i],
+ SEPARATOR(i, D_CODES-1, 10));
+ }
+
+ fclose(header);
+}
+#endif /* GEN_TREES_H */
+
+/* ===========================================================================
+ * Initialize the tree data structures for a new zlib stream.
+ */
+void ZLIB_INTERNAL _tr_init(s)
+ deflate_state *s;
+{
+ tr_static_init();
+
+ s->l_desc.dyn_tree = s->dyn_ltree;
+ s->l_desc.stat_desc = &static_l_desc;
+
+ s->d_desc.dyn_tree = s->dyn_dtree;
+ s->d_desc.stat_desc = &static_d_desc;
+
+ s->bl_desc.dyn_tree = s->bl_tree;
+ s->bl_desc.stat_desc = &static_bl_desc;
+
+ s->bi_buf = 0;
+ s->bi_valid = 0;
+#ifdef DEBUG
+ s->compressed_len = 0L;
+ s->bits_sent = 0L;
+#endif
+
+ /* Initialize the first block of the first file: */
+ init_block(s);
+}
+
+/* ===========================================================================
+ * Initialize a new block.
+ */
+local void init_block(s)
+ deflate_state *s;
+{
+ int n; /* iterates over tree elements */
+
+ /* Initialize the trees. */
+ for (n = 0; n < L_CODES; n++) s->dyn_ltree[n].Freq = 0;
+ for (n = 0; n < D_CODES; n++) s->dyn_dtree[n].Freq = 0;
+ for (n = 0; n < BL_CODES; n++) s->bl_tree[n].Freq = 0;
+
+ s->dyn_ltree[END_BLOCK].Freq = 1;
+ s->opt_len = s->static_len = 0L;
+ s->last_lit = s->matches = 0;
+}
+
+#define SMALLEST 1
+/* Index within the heap array of least frequent node in the Huffman tree */
+
+
+/* ===========================================================================
+ * Remove the smallest element from the heap and recreate the heap with
+ * one less element. Updates heap and heap_len.
+ */
+#define pqremove(s, tree, top) \
+{\
+ top = s->heap[SMALLEST]; \
+ s->heap[SMALLEST] = s->heap[s->heap_len--]; \
+ pqdownheap(s, tree, SMALLEST); \
+}
+
+/* ===========================================================================
+ * Compares to subtrees, using the tree depth as tie breaker when
+ * the subtrees have equal frequency. This minimizes the worst case length.
+ */
+#define smaller(tree, n, m, depth) \
+ (tree[n].Freq < tree[m].Freq || \
+ (tree[n].Freq == tree[m].Freq && depth[n] <= depth[m]))
+
+/* ===========================================================================
+ * Restore the heap property by moving down the tree starting at node k,
+ * exchanging a node with the smallest of its two sons if necessary, stopping
+ * when the heap property is re-established (each father smaller than its
+ * two sons).
+ */
+local void pqdownheap(s, tree, k)
+ deflate_state *s;
+ ct_data *tree; /* the tree to restore */
+ int k; /* node to move down */
+{
+ int v = s->heap[k];
+ int j = k << 1; /* left son of k */
+ while (j <= s->heap_len) {
+ /* Set j to the smallest of the two sons: */
+ if (j < s->heap_len &&
+ smaller(tree, s->heap[j+1], s->heap[j], s->depth)) {
+ j++;
+ }
+ /* Exit if v is smaller than both sons */
+ if (smaller(tree, v, s->heap[j], s->depth)) break;
+
+ /* Exchange v with the smallest son */
+ s->heap[k] = s->heap[j]; k = j;
+
+ /* And continue down the tree, setting j to the left son of k */
+ j <<= 1;
+ }
+ s->heap[k] = v;
+}
+
+/* ===========================================================================
+ * Compute the optimal bit lengths for a tree and update the total bit length
+ * for the current block.
+ * IN assertion: the fields freq and dad are set, heap[heap_max] and
+ * above are the tree nodes sorted by increasing frequency.
+ * OUT assertions: the field len is set to the optimal bit length, the
+ * array bl_count contains the frequencies for each bit length.
+ * The length opt_len is updated; static_len is also updated if stree is
+ * not null.
+ */
+local void gen_bitlen(s, desc)
+ deflate_state *s;
+ tree_desc *desc; /* the tree descriptor */
+{
+ ct_data *tree = desc->dyn_tree;
+ int max_code = desc->max_code;
+ const ct_data *stree = desc->stat_desc->static_tree;
+ const intf *extra = desc->stat_desc->extra_bits;
+ int base = desc->stat_desc->extra_base;
+ int max_length = desc->stat_desc->max_length;
+ int h; /* heap index */
+ int n, m; /* iterate over the tree elements */
+ int bits; /* bit length */
+ int xbits; /* extra bits */
+ ush f; /* frequency */
+ int overflow = 0; /* number of elements with bit length too large */
+
+ for (bits = 0; bits <= MAX_BITS; bits++) s->bl_count[bits] = 0;
+
+ /* In a first pass, compute the optimal bit lengths (which may
+ * overflow in the case of the bit length tree).
+ */
+ tree[s->heap[s->heap_max]].Len = 0; /* root of the heap */
+
+ for (h = s->heap_max+1; h < HEAP_SIZE; h++) {
+ n = s->heap[h];
+ bits = tree[tree[n].Dad].Len + 1;
+ if (bits > max_length) bits = max_length, overflow++;
+ tree[n].Len = (ush)bits;
+ /* We overwrite tree[n].Dad which is no longer needed */
+
+ if (n > max_code) continue; /* not a leaf node */
+
+ s->bl_count[bits]++;
+ xbits = 0;
+ if (n >= base) xbits = extra[n-base];
+ f = tree[n].Freq;
+ s->opt_len += (ulg)f * (bits + xbits);
+ if (stree) s->static_len += (ulg)f * (stree[n].Len + xbits);
+ }
+ if (overflow == 0) return;
+
+ Trace((stderr,"\nbit length overflow\n"));
+ /* This happens for example on obj2 and pic of the Calgary corpus */
+
+ /* Find the first bit length which could increase: */
+ do {
+ bits = max_length-1;
+ while (s->bl_count[bits] == 0) bits--;
+ s->bl_count[bits]--; /* move one leaf down the tree */
+ s->bl_count[bits+1] += 2; /* move one overflow item as its brother */
+ s->bl_count[max_length]--;
+ /* The brother of the overflow item also moves one step up,
+ * but this does not affect bl_count[max_length]
+ */
+ overflow -= 2;
+ } while (overflow > 0);
+
+ /* Now recompute all bit lengths, scanning in increasing frequency.
+ * h is still equal to HEAP_SIZE. (It is simpler to reconstruct all
+ * lengths instead of fixing only the wrong ones. This idea is taken
+ * from 'ar' written by Haruhiko Okumura.)
+ */
+ for (bits = max_length; bits != 0; bits--) {
+ n = s->bl_count[bits];
+ while (n != 0) {
+ m = s->heap[--h];
+ if (m > max_code) continue;
+ if ((unsigned) tree[m].Len != (unsigned) bits) {
+ Trace((stderr,"code %d bits %d->%d\n", m, tree[m].Len, bits));
+ s->opt_len += ((long)bits - (long)tree[m].Len)
+ *(long)tree[m].Freq;
+ tree[m].Len = (ush)bits;
+ }
+ n--;
+ }
+ }
+}
+
+/* ===========================================================================
+ * Generate the codes for a given tree and bit counts (which need not be
+ * optimal).
+ * IN assertion: the array bl_count contains the bit length statistics for
+ * the given tree and the field len is set for all tree elements.
+ * OUT assertion: the field code is set for all tree elements of non
+ * zero code length.
+ */
+local void gen_codes (tree, max_code, bl_count)
+ ct_data *tree; /* the tree to decorate */
+ int max_code; /* largest code with non zero frequency */
+ ushf *bl_count; /* number of codes at each bit length */
+{
+ ush next_code[MAX_BITS+1]; /* next code value for each bit length */
+ ush code = 0; /* running code value */
+ int bits; /* bit index */
+ int n; /* code index */
+
+ /* The distribution counts are first used to generate the code values
+ * without bit reversal.
+ */
+ for (bits = 1; bits <= MAX_BITS; bits++) {
+ next_code[bits] = code = (code + bl_count[bits-1]) << 1;
+ }
+ /* Check that the bit counts in bl_count are consistent. The last code
+ * must be all ones.
+ */
+ Assert (code + bl_count[MAX_BITS]-1 == (1<<MAX_BITS)-1,
+ "inconsistent bit counts");
+ Tracev((stderr,"\ngen_codes: max_code %d ", max_code));
+
+ for (n = 0; n <= max_code; n++) {
+ int len = tree[n].Len;
+ if (len == 0) continue;
+ /* Now reverse the bits */
+ tree[n].Code = bi_reverse(next_code[len]++, len);
+
+ Tracecv(tree != static_ltree, (stderr,"\nn %3d %c l %2d c %4x (%x) ",
+ n, (isgraph(n) ? n : ' '), len, tree[n].Code, next_code[len]-1));
+ }
+}
+
+/* ===========================================================================
+ * Construct one Huffman tree and assigns the code bit strings and lengths.
+ * Update the total bit length for the current block.
+ * IN assertion: the field freq is set for all tree elements.
+ * OUT assertions: the fields len and code are set to the optimal bit length
+ * and corresponding code. The length opt_len is updated; static_len is
+ * also updated if stree is not null. The field max_code is set.
+ */
+local void build_tree(s, desc)
+ deflate_state *s;
+ tree_desc *desc; /* the tree descriptor */
+{
+ ct_data *tree = desc->dyn_tree;
+ const ct_data *stree = desc->stat_desc->static_tree;
+ int elems = desc->stat_desc->elems;
+ int n, m; /* iterate over heap elements */
+ int max_code = -1; /* largest code with non zero frequency */
+ int node; /* new node being created */
+
+ /* Construct the initial heap, with least frequent element in
+ * heap[SMALLEST]. The sons of heap[n] are heap[2*n] and heap[2*n+1].
+ * heap[0] is not used.
+ */
+ s->heap_len = 0, s->heap_max = HEAP_SIZE;
+
+ for (n = 0; n < elems; n++) {
+ if (tree[n].Freq != 0) {
+ s->heap[++(s->heap_len)] = max_code = n;
+ s->depth[n] = 0;
+ } else {
+ tree[n].Len = 0;
+ }
+ }
+
+ /* The pkzip format requires that at least one distance code exists,
+ * and that at least one bit should be sent even if there is only one
+ * possible code. So to avoid special checks later on we force at least
+ * two codes of non zero frequency.
+ */
+ while (s->heap_len < 2) {
+ node = s->heap[++(s->heap_len)] = (max_code < 2 ? ++max_code : 0);
+ tree[node].Freq = 1;
+ s->depth[node] = 0;
+ s->opt_len--; if (stree) s->static_len -= stree[node].Len;
+ /* node is 0 or 1 so it does not have extra bits */
+ }
+ desc->max_code = max_code;
+
+ /* The elements heap[heap_len/2+1 .. heap_len] are leaves of the tree,
+ * establish sub-heaps of increasing lengths:
+ */
+ for (n = s->heap_len/2; n >= 1; n--) pqdownheap(s, tree, n);
+
+ /* Construct the Huffman tree by repeatedly combining the least two
+ * frequent nodes.
+ */
+ node = elems; /* next internal node of the tree */
+ do {
+ pqremove(s, tree, n); /* n = node of least frequency */
+ m = s->heap[SMALLEST]; /* m = node of next least frequency */
+
+ s->heap[--(s->heap_max)] = n; /* keep the nodes sorted by frequency */
+ s->heap[--(s->heap_max)] = m;
+
+ /* Create a new node father of n and m */
+ tree[node].Freq = tree[n].Freq + tree[m].Freq;
+ s->depth[node] = (uch)((s->depth[n] >= s->depth[m] ?
+ s->depth[n] : s->depth[m]) + 1);
+ tree[n].Dad = tree[m].Dad = (ush)node;
+#ifdef DUMP_BL_TREE
+ if (tree == s->bl_tree) {
+ fprintf(stderr,"\nnode %d(%d), sons %d(%d) %d(%d)",
+ node, tree[node].Freq, n, tree[n].Freq, m, tree[m].Freq);
+ }
+#endif
+ /* and insert the new node in the heap */
+ s->heap[SMALLEST] = node++;
+ pqdownheap(s, tree, SMALLEST);
+
+ } while (s->heap_len >= 2);
+
+ s->heap[--(s->heap_max)] = s->heap[SMALLEST];
+
+ /* At this point, the fields freq and dad are set. We can now
+ * generate the bit lengths.
+ */
+ gen_bitlen(s, (tree_desc *)desc);
+
+ /* The field len is now set, we can generate the bit codes */
+ gen_codes ((ct_data *)tree, max_code, s->bl_count);
+}
+
+/* ===========================================================================
+ * Scan a literal or distance tree to determine the frequencies of the codes
+ * in the bit length tree.
+ */
+local void scan_tree (s, tree, max_code)
+ deflate_state *s;
+ ct_data *tree; /* the tree to be scanned */
+ int max_code; /* and its largest code of non zero frequency */
+{
+ int n; /* iterates over all tree elements */
+ int prevlen = -1; /* last emitted length */
+ int curlen; /* length of current code */
+ int nextlen = tree[0].Len; /* length of next code */
+ int count = 0; /* repeat count of the current code */
+ int max_count = 7; /* max repeat count */
+ int min_count = 4; /* min repeat count */
+
+ if (nextlen == 0) max_count = 138, min_count = 3;
+ tree[max_code+1].Len = (ush)0xffff; /* guard */
+
+ for (n = 0; n <= max_code; n++) {
+ curlen = nextlen; nextlen = tree[n+1].Len;
+ if (++count < max_count && curlen == nextlen) {
+ continue;
+ } else if (count < min_count) {
+ s->bl_tree[curlen].Freq += count;
+ } else if (curlen != 0) {
+ if (curlen != prevlen) s->bl_tree[curlen].Freq++;
+ s->bl_tree[REP_3_6].Freq++;
+ } else if (count <= 10) {
+ s->bl_tree[REPZ_3_10].Freq++;
+ } else {
+ s->bl_tree[REPZ_11_138].Freq++;
+ }
+ count = 0; prevlen = curlen;
+ if (nextlen == 0) {
+ max_count = 138, min_count = 3;
+ } else if (curlen == nextlen) {
+ max_count = 6, min_count = 3;
+ } else {
+ max_count = 7, min_count = 4;
+ }
+ }
+}
+
+/* ===========================================================================
+ * Send a literal or distance tree in compressed form, using the codes in
+ * bl_tree.
+ */
+local void send_tree (s, tree, max_code)
+ deflate_state *s;
+ ct_data *tree; /* the tree to be scanned */
+ int max_code; /* and its largest code of non zero frequency */
+{
+ int n; /* iterates over all tree elements */
+ int prevlen = -1; /* last emitted length */
+ int curlen; /* length of current code */
+ int nextlen = tree[0].Len; /* length of next code */
+ int count = 0; /* repeat count of the current code */
+ int max_count = 7; /* max repeat count */
+ int min_count = 4; /* min repeat count */
+
+ /* tree[max_code+1].Len = -1; */ /* guard already set */
+ if (nextlen == 0) max_count = 138, min_count = 3;
+
+ for (n = 0; n <= max_code; n++) {
+ curlen = nextlen; nextlen = tree[n+1].Len;
+ if (++count < max_count && curlen == nextlen) {
+ continue;
+ } else if (count < min_count) {
+ do { send_code(s, curlen, s->bl_tree); } while (--count != 0);
+
+ } else if (curlen != 0) {
+ if (curlen != prevlen) {
+ send_code(s, curlen, s->bl_tree); count--;
+ }
+ Assert(count >= 3 && count <= 6, " 3_6?");
+ send_code(s, REP_3_6, s->bl_tree); send_bits(s, count-3, 2);
+
+ } else if (count <= 10) {
+ send_code(s, REPZ_3_10, s->bl_tree); send_bits(s, count-3, 3);
+
+ } else {
+ send_code(s, REPZ_11_138, s->bl_tree); send_bits(s, count-11, 7);
+ }
+ count = 0; prevlen = curlen;
+ if (nextlen == 0) {
+ max_count = 138, min_count = 3;
+ } else if (curlen == nextlen) {
+ max_count = 6, min_count = 3;
+ } else {
+ max_count = 7, min_count = 4;
+ }
+ }
+}
+
+/* ===========================================================================
+ * Construct the Huffman tree for the bit lengths and return the index in
+ * bl_order of the last bit length code to send.
+ */
+local int build_bl_tree(s)
+ deflate_state *s;
+{
+ int max_blindex; /* index of last bit length code of non zero freq */
+
+ /* Determine the bit length frequencies for literal and distance trees */
+ scan_tree(s, (ct_data *)s->dyn_ltree, s->l_desc.max_code);
+ scan_tree(s, (ct_data *)s->dyn_dtree, s->d_desc.max_code);
+
+ /* Build the bit length tree: */
+ build_tree(s, (tree_desc *)(&(s->bl_desc)));
+ /* opt_len now includes the length of the tree representations, except
+ * the lengths of the bit lengths codes and the 5+5+4 bits for the counts.
+ */
+
+ /* Determine the number of bit length codes to send. The pkzip format
+ * requires that at least 4 bit length codes be sent. (appnote.txt says
+ * 3 but the actual value used is 4.)
+ */
+ for (max_blindex = BL_CODES-1; max_blindex >= 3; max_blindex--) {
+ if (s->bl_tree[bl_order[max_blindex]].Len != 0) break;
+ }
+ /* Update opt_len to include the bit length tree and counts */
+ s->opt_len += 3*(max_blindex+1) + 5+5+4;
+ Tracev((stderr, "\ndyn trees: dyn %ld, stat %ld",
+ s->opt_len, s->static_len));
+
+ return max_blindex;
+}
+
+/* ===========================================================================
+ * Send the header for a block using dynamic Huffman trees: the counts, the
+ * lengths of the bit length codes, the literal tree and the distance tree.
+ * IN assertion: lcodes >= 257, dcodes >= 1, blcodes >= 4.
+ */
+local void send_all_trees(s, lcodes, dcodes, blcodes)
+ deflate_state *s;
+ int lcodes, dcodes, blcodes; /* number of codes for each tree */
+{
+ int rank; /* index in bl_order */
+
+ Assert (lcodes >= 257 && dcodes >= 1 && blcodes >= 4, "not enough codes");
+ Assert (lcodes <= L_CODES && dcodes <= D_CODES && blcodes <= BL_CODES,
+ "too many codes");
+ Tracev((stderr, "\nbl counts: "));
+ send_bits(s, lcodes-257, 5); /* not +255 as stated in appnote.txt */
+ send_bits(s, dcodes-1, 5);
+ send_bits(s, blcodes-4, 4); /* not -3 as stated in appnote.txt */
+ for (rank = 0; rank < blcodes; rank++) {
+ Tracev((stderr, "\nbl code %2d ", bl_order[rank]));
+ send_bits(s, s->bl_tree[bl_order[rank]].Len, 3);
+ }
+ Tracev((stderr, "\nbl tree: sent %ld", s->bits_sent));
+
+ send_tree(s, (ct_data *)s->dyn_ltree, lcodes-1); /* literal tree */
+ Tracev((stderr, "\nlit tree: sent %ld", s->bits_sent));
+
+ send_tree(s, (ct_data *)s->dyn_dtree, dcodes-1); /* distance tree */
+ Tracev((stderr, "\ndist tree: sent %ld", s->bits_sent));
+}
+
+/* ===========================================================================
+ * Send a stored block
+ */
+void ZLIB_INTERNAL _tr_stored_block(s, buf, stored_len, last)
+ deflate_state *s;
+ charf *buf; /* input block */
+ ulg stored_len; /* length of input block */
+ int last; /* one if this is the last block for a file */
+{
+ send_bits(s, (STORED_BLOCK<<1)+last, 3); /* send block type */
+#ifdef DEBUG
+ s->compressed_len = (s->compressed_len + 3 + 7) & (ulg)~7L;
+ s->compressed_len += (stored_len + 4) << 3;
+#endif
+ copy_block(s, buf, (unsigned)stored_len, 1); /* with header */
+}
+
+/* ===========================================================================
+ * Flush the bits in the bit buffer to pending output (leaves at most 7 bits)
+ */
+void ZLIB_INTERNAL _tr_flush_bits(s)
+ deflate_state *s;
+{
+ bi_flush(s);
+}
+
+/* ===========================================================================
+ * Send one empty static block to give enough lookahead for inflate.
+ * This takes 10 bits, of which 7 may remain in the bit buffer.
+ */
+void ZLIB_INTERNAL _tr_align(s)
+ deflate_state *s;
+{
+ send_bits(s, STATIC_TREES<<1, 3);
+ send_code(s, END_BLOCK, static_ltree);
+#ifdef DEBUG
+ s->compressed_len += 10L; /* 3 for block type, 7 for EOB */
+#endif
+ bi_flush(s);
+}
+
+/* ===========================================================================
+ * Determine the best encoding for the current block: dynamic trees, static
+ * trees or store, and output the encoded block to the zip file.
+ */
+void ZLIB_INTERNAL _tr_flush_block(s, buf, stored_len, last)
+ deflate_state *s;
+ charf *buf; /* input block, or NULL if too old */
+ ulg stored_len; /* length of input block */
+ int last; /* one if this is the last block for a file */
+{
+ ulg opt_lenb, static_lenb; /* opt_len and static_len in bytes */
+ int max_blindex = 0; /* index of last bit length code of non zero freq */
+
+ /* Build the Huffman trees unless a stored block is forced */
+ if (s->level > 0) {
+
+ /* Check if the file is binary or text */
+ if (s->strm->data_type == Z_UNKNOWN)
+ s->strm->data_type = detect_data_type(s);
+
+ /* Construct the literal and distance trees */
+ build_tree(s, (tree_desc *)(&(s->l_desc)));
+ Tracev((stderr, "\nlit data: dyn %ld, stat %ld", s->opt_len,
+ s->static_len));
+
+ build_tree(s, (tree_desc *)(&(s->d_desc)));
+ Tracev((stderr, "\ndist data: dyn %ld, stat %ld", s->opt_len,
+ s->static_len));
+ /* At this point, opt_len and static_len are the total bit lengths of
+ * the compressed block data, excluding the tree representations.
+ */
+
+ /* Build the bit length tree for the above two trees, and get the index
+ * in bl_order of the last bit length code to send.
+ */
+ max_blindex = build_bl_tree(s);
+
+ /* Determine the best encoding. Compute the block lengths in bytes. */
+ opt_lenb = (s->opt_len+3+7)>>3;
+ static_lenb = (s->static_len+3+7)>>3;
+
+ Tracev((stderr, "\nopt %lu(%lu) stat %lu(%lu) stored %lu lit %u ",
+ opt_lenb, s->opt_len, static_lenb, s->static_len, stored_len,
+ s->last_lit));
+
+ if (static_lenb <= opt_lenb) opt_lenb = static_lenb;
+
+ } else {
+ Assert(buf != (char*)0, "lost buf");
+ opt_lenb = static_lenb = stored_len + 5; /* force a stored block */
+ }
+
+#ifdef FORCE_STORED
+ if (buf != (char*)0) { /* force stored block */
+#else
+ if (stored_len+4 <= opt_lenb && buf != (char*)0) {
+ /* 4: two words for the lengths */
+#endif
+ /* The test buf != NULL is only necessary if LIT_BUFSIZE > WSIZE.
+ * Otherwise we can't have processed more than WSIZE input bytes since
+ * the last block flush, because compression would have been
+ * successful. If LIT_BUFSIZE <= WSIZE, it is never too late to
+ * transform a block into a stored block.
+ */
+ _tr_stored_block(s, buf, stored_len, last);
+
+#ifdef FORCE_STATIC
+ } else if (static_lenb >= 0) { /* force static trees */
+#else
+ } else if (s->strategy == Z_FIXED || static_lenb == opt_lenb) {
+#endif
+ send_bits(s, (STATIC_TREES<<1)+last, 3);
+ compress_block(s, (const ct_data *)static_ltree,
+ (const ct_data *)static_dtree);
+#ifdef DEBUG
+ s->compressed_len += 3 + s->static_len;
+#endif
+ } else {
+ send_bits(s, (DYN_TREES<<1)+last, 3);
+ send_all_trees(s, s->l_desc.max_code+1, s->d_desc.max_code+1,
+ max_blindex+1);
+ compress_block(s, (const ct_data *)s->dyn_ltree,
+ (const ct_data *)s->dyn_dtree);
+#ifdef DEBUG
+ s->compressed_len += 3 + s->opt_len;
+#endif
+ }
+ Assert (s->compressed_len == s->bits_sent, "bad compressed size");
+ /* The above check is made mod 2^32, for files larger than 512 MB
+ * and uLong implemented on 32 bits.
+ */
+ init_block(s);
+
+ if (last) {
+ bi_windup(s);
+#ifdef DEBUG
+ s->compressed_len += 7; /* align on byte boundary */
+#endif
+ }
+ Tracev((stderr,"\ncomprlen %lu(%lu) ", s->compressed_len>>3,
+ s->compressed_len-7*last));
+}
+
+/* ===========================================================================
+ * Save the match info and tally the frequency counts. Return true if
+ * the current block must be flushed.
+ */
+int ZLIB_INTERNAL _tr_tally (s, dist, lc)
+ deflate_state *s;
+ unsigned dist; /* distance of matched string */
+ unsigned lc; /* match length-MIN_MATCH or unmatched char (if dist==0) */
+{
+ s->d_buf[s->last_lit] = (ush)dist;
+ s->l_buf[s->last_lit++] = (uch)lc;
+ if (dist == 0) {
+ /* lc is the unmatched char */
+ s->dyn_ltree[lc].Freq++;
+ } else {
+ s->matches++;
+ /* Here, lc is the match length - MIN_MATCH */
+ dist--; /* dist = match distance - 1 */
+ Assert((ush)dist < (ush)MAX_DIST(s) &&
+ (ush)lc <= (ush)(MAX_MATCH-MIN_MATCH) &&
+ (ush)d_code(dist) < (ush)D_CODES, "_tr_tally: bad match");
+
+ s->dyn_ltree[_length_code[lc]+LITERALS+1].Freq++;
+ s->dyn_dtree[d_code(dist)].Freq++;
+ }
+
+#ifdef TRUNCATE_BLOCK
+ /* Try to guess if it is profitable to stop the current block here */
+ if ((s->last_lit & 0x1fff) == 0 && s->level > 2) {
+ /* Compute an upper bound for the compressed length */
+ ulg out_length = (ulg)s->last_lit*8L;
+ ulg in_length = (ulg)((long)s->strstart - s->block_start);
+ int dcode;
+ for (dcode = 0; dcode < D_CODES; dcode++) {
+ out_length += (ulg)s->dyn_dtree[dcode].Freq *
+ (5L+extra_dbits[dcode]);
+ }
+ out_length >>= 3;
+ Tracev((stderr,"\nlast_lit %u, in %ld, out ~%ld(%ld%%) ",
+ s->last_lit, in_length, out_length,
+ 100L - out_length*100L/in_length));
+ if (s->matches < s->last_lit/2 && out_length < in_length/2) return 1;
+ }
+#endif
+ return (s->last_lit == s->lit_bufsize-1);
+ /* We avoid equality with lit_bufsize because of wraparound at 64K
+ * on 16 bit machines and because stored blocks are restricted to
+ * 64K-1 bytes.
+ */
+}
+
+/* ===========================================================================
+ * Send the block data compressed using the given Huffman trees
+ */
+local void compress_block(s, ltree, dtree)
+ deflate_state *s;
+ const ct_data *ltree; /* literal tree */
+ const ct_data *dtree; /* distance tree */
+{
+ unsigned dist; /* distance of matched string */
+ int lc; /* match length or unmatched char (if dist == 0) */
+ unsigned lx = 0; /* running index in l_buf */
+ unsigned code; /* the code to send */
+ int extra; /* number of extra bits to send */
+
+ if (s->last_lit != 0) do {
+ dist = s->d_buf[lx];
+ lc = s->l_buf[lx++];
+ if (dist == 0) {
+ send_code(s, lc, ltree); /* send a literal byte */
+ Tracecv(isgraph(lc), (stderr," '%c' ", lc));
+ } else {
+ /* Here, lc is the match length - MIN_MATCH */
+ code = _length_code[lc];
+ send_code(s, code+LITERALS+1, ltree); /* send the length code */
+ extra = extra_lbits[code];
+ if (extra != 0) {
+ lc -= base_length[code];
+ send_bits(s, lc, extra); /* send the extra length bits */
+ }
+ dist--; /* dist is now the match distance - 1 */
+ code = d_code(dist);
+ Assert (code < D_CODES, "bad d_code");
+
+ send_code(s, code, dtree); /* send the distance code */
+ extra = extra_dbits[code];
+ if (extra != 0) {
+ dist -= base_dist[code];
+ send_bits(s, dist, extra); /* send the extra distance bits */
+ }
+ } /* literal or match pair ? */
+
+ /* Check that the overlay between pending_buf and d_buf+l_buf is ok: */
+ Assert((uInt)(s->pending) < s->lit_bufsize + 2*lx,
+ "pendingBuf overflow");
+
+ } while (lx < s->last_lit);
+
+ send_code(s, END_BLOCK, ltree);
+}
+
+/* ===========================================================================
+ * Check if the data type is TEXT or BINARY, using the following algorithm:
+ * - TEXT if the two conditions below are satisfied:
+ * a) There are no non-portable control characters belonging to the
+ * "black list" (0..6, 14..25, 28..31).
+ * b) There is at least one printable character belonging to the
+ * "white list" (9 {TAB}, 10 {LF}, 13 {CR}, 32..255).
+ * - BINARY otherwise.
+ * - The following partially-portable control characters form a
+ * "gray list" that is ignored in this detection algorithm:
+ * (7 {BEL}, 8 {BS}, 11 {VT}, 12 {FF}, 26 {SUB}, 27 {ESC}).
+ * IN assertion: the fields Freq of dyn_ltree are set.
+ */
+local int detect_data_type(s)
+ deflate_state *s;
+{
+ /* black_mask is the bit mask of black-listed bytes
+ * set bits 0..6, 14..25, and 28..31
+ * 0xf3ffc07f = binary 11110011111111111100000001111111
+ */
+ unsigned long black_mask = 0xf3ffc07fUL;
+ int n;
+
+ /* Check for non-textual ("black-listed") bytes. */
+ for (n = 0; n <= 31; n++, black_mask >>= 1)
+ if ((black_mask & 1) && (s->dyn_ltree[n].Freq != 0))
+ return Z_BINARY;
+
+ /* Check for textual ("white-listed") bytes. */
+ if (s->dyn_ltree[9].Freq != 0 || s->dyn_ltree[10].Freq != 0
+ || s->dyn_ltree[13].Freq != 0)
+ return Z_TEXT;
+ for (n = 32; n < LITERALS; n++)
+ if (s->dyn_ltree[n].Freq != 0)
+ return Z_TEXT;
+
+ /* There are no "black-listed" or "white-listed" bytes:
+ * this stream either is empty or has tolerated ("gray-listed") bytes only.
+ */
+ return Z_BINARY;
+}
+
+/* ===========================================================================
+ * Reverse the first len bits of a code, using straightforward code (a faster
+ * method would use a table)
+ * IN assertion: 1 <= len <= 15
+ */
+local unsigned bi_reverse(code, len)
+ unsigned code; /* the value to invert */
+ int len; /* its bit length */
+{
+ register unsigned res = 0;
+ do {
+ res |= code & 1;
+ code >>= 1, res <<= 1;
+ } while (--len > 0);
+ return res >> 1;
+}
+
+/* ===========================================================================
+ * Flush the bit buffer, keeping at most 7 bits in it.
+ */
+local void bi_flush(s)
+ deflate_state *s;
+{
+ if (s->bi_valid == 16) {
+ put_short(s, s->bi_buf);
+ s->bi_buf = 0;
+ s->bi_valid = 0;
+ } else if (s->bi_valid >= 8) {
+ put_byte(s, (Byte)s->bi_buf);
+ s->bi_buf >>= 8;
+ s->bi_valid -= 8;
+ }
+}
+
+/* ===========================================================================
+ * Flush the bit buffer and align the output on a byte boundary
+ */
+local void bi_windup(s)
+ deflate_state *s;
+{
+ if (s->bi_valid > 8) {
+ put_short(s, s->bi_buf);
+ } else if (s->bi_valid > 0) {
+ put_byte(s, (Byte)s->bi_buf);
+ }
+ s->bi_buf = 0;
+ s->bi_valid = 0;
+#ifdef DEBUG
+ s->bits_sent = (s->bits_sent+7) & ~7;
+#endif
+}
+
+/* ===========================================================================
+ * Copy a stored block, storing first the length and its
+ * one's complement if requested.
+ */
+local void copy_block(s, buf, len, header)
+ deflate_state *s;
+ charf *buf; /* the input data */
+ unsigned len; /* its length */
+ int header; /* true if block header must be written */
+{
+ bi_windup(s); /* align on byte boundary */
+
+ if (header) {
+ put_short(s, (ush)len);
+ put_short(s, (ush)~len);
+#ifdef DEBUG
+ s->bits_sent += 2*16;
+#endif
+ }
+#ifdef DEBUG
+ s->bits_sent += (ulg)len<<3;
+#endif
+ while (len--) {
+ put_byte(s, *buf++);
+ }
+}
diff --git a/third-party/zlib/trees.h b/third-party/zlib/trees.h
new file mode 100644
index 0000000..d35639d
--- /dev/null
+++ b/third-party/zlib/trees.h
@@ -0,0 +1,128 @@
+/* header created automatically with -DGEN_TREES_H */
+
+local const ct_data static_ltree[L_CODES+2] = {
+{{ 12},{ 8}}, {{140},{ 8}}, {{ 76},{ 8}}, {{204},{ 8}}, {{ 44},{ 8}},
+{{172},{ 8}}, {{108},{ 8}}, {{236},{ 8}}, {{ 28},{ 8}}, {{156},{ 8}},
+{{ 92},{ 8}}, {{220},{ 8}}, {{ 60},{ 8}}, {{188},{ 8}}, {{124},{ 8}},
+{{252},{ 8}}, {{ 2},{ 8}}, {{130},{ 8}}, {{ 66},{ 8}}, {{194},{ 8}},
+{{ 34},{ 8}}, {{162},{ 8}}, {{ 98},{ 8}}, {{226},{ 8}}, {{ 18},{ 8}},
+{{146},{ 8}}, {{ 82},{ 8}}, {{210},{ 8}}, {{ 50},{ 8}}, {{178},{ 8}},
+{{114},{ 8}}, {{242},{ 8}}, {{ 10},{ 8}}, {{138},{ 8}}, {{ 74},{ 8}},
+{{202},{ 8}}, {{ 42},{ 8}}, {{170},{ 8}}, {{106},{ 8}}, {{234},{ 8}},
+{{ 26},{ 8}}, {{154},{ 8}}, {{ 90},{ 8}}, {{218},{ 8}}, {{ 58},{ 8}},
+{{186},{ 8}}, {{122},{ 8}}, {{250},{ 8}}, {{ 6},{ 8}}, {{134},{ 8}},
+{{ 70},{ 8}}, {{198},{ 8}}, {{ 38},{ 8}}, {{166},{ 8}}, {{102},{ 8}},
+{{230},{ 8}}, {{ 22},{ 8}}, {{150},{ 8}}, {{ 86},{ 8}}, {{214},{ 8}},
+{{ 54},{ 8}}, {{182},{ 8}}, {{118},{ 8}}, {{246},{ 8}}, {{ 14},{ 8}},
+{{142},{ 8}}, {{ 78},{ 8}}, {{206},{ 8}}, {{ 46},{ 8}}, {{174},{ 8}},
+{{110},{ 8}}, {{238},{ 8}}, {{ 30},{ 8}}, {{158},{ 8}}, {{ 94},{ 8}},
+{{222},{ 8}}, {{ 62},{ 8}}, {{190},{ 8}}, {{126},{ 8}}, {{254},{ 8}},
+{{ 1},{ 8}}, {{129},{ 8}}, {{ 65},{ 8}}, {{193},{ 8}}, {{ 33},{ 8}},
+{{161},{ 8}}, {{ 97},{ 8}}, {{225},{ 8}}, {{ 17},{ 8}}, {{145},{ 8}},
+{{ 81},{ 8}}, {{209},{ 8}}, {{ 49},{ 8}}, {{177},{ 8}}, {{113},{ 8}},
+{{241},{ 8}}, {{ 9},{ 8}}, {{137},{ 8}}, {{ 73},{ 8}}, {{201},{ 8}},
+{{ 41},{ 8}}, {{169},{ 8}}, {{105},{ 8}}, {{233},{ 8}}, {{ 25},{ 8}},
+{{153},{ 8}}, {{ 89},{ 8}}, {{217},{ 8}}, {{ 57},{ 8}}, {{185},{ 8}},
+{{121},{ 8}}, {{249},{ 8}}, {{ 5},{ 8}}, {{133},{ 8}}, {{ 69},{ 8}},
+{{197},{ 8}}, {{ 37},{ 8}}, {{165},{ 8}}, {{101},{ 8}}, {{229},{ 8}},
+{{ 21},{ 8}}, {{149},{ 8}}, {{ 85},{ 8}}, {{213},{ 8}}, {{ 53},{ 8}},
+{{181},{ 8}}, {{117},{ 8}}, {{245},{ 8}}, {{ 13},{ 8}}, {{141},{ 8}},
+{{ 77},{ 8}}, {{205},{ 8}}, {{ 45},{ 8}}, {{173},{ 8}}, {{109},{ 8}},
+{{237},{ 8}}, {{ 29},{ 8}}, {{157},{ 8}}, {{ 93},{ 8}}, {{221},{ 8}},
+{{ 61},{ 8}}, {{189},{ 8}}, {{125},{ 8}}, {{253},{ 8}}, {{ 19},{ 9}},
+{{275},{ 9}}, {{147},{ 9}}, {{403},{ 9}}, {{ 83},{ 9}}, {{339},{ 9}},
+{{211},{ 9}}, {{467},{ 9}}, {{ 51},{ 9}}, {{307},{ 9}}, {{179},{ 9}},
+{{435},{ 9}}, {{115},{ 9}}, {{371},{ 9}}, {{243},{ 9}}, {{499},{ 9}},
+{{ 11},{ 9}}, {{267},{ 9}}, {{139},{ 9}}, {{395},{ 9}}, {{ 75},{ 9}},
+{{331},{ 9}}, {{203},{ 9}}, {{459},{ 9}}, {{ 43},{ 9}}, {{299},{ 9}},
+{{171},{ 9}}, {{427},{ 9}}, {{107},{ 9}}, {{363},{ 9}}, {{235},{ 9}},
+{{491},{ 9}}, {{ 27},{ 9}}, {{283},{ 9}}, {{155},{ 9}}, {{411},{ 9}},
+{{ 91},{ 9}}, {{347},{ 9}}, {{219},{ 9}}, {{475},{ 9}}, {{ 59},{ 9}},
+{{315},{ 9}}, {{187},{ 9}}, {{443},{ 9}}, {{123},{ 9}}, {{379},{ 9}},
+{{251},{ 9}}, {{507},{ 9}}, {{ 7},{ 9}}, {{263},{ 9}}, {{135},{ 9}},
+{{391},{ 9}}, {{ 71},{ 9}}, {{327},{ 9}}, {{199},{ 9}}, {{455},{ 9}},
+{{ 39},{ 9}}, {{295},{ 9}}, {{167},{ 9}}, {{423},{ 9}}, {{103},{ 9}},
+{{359},{ 9}}, {{231},{ 9}}, {{487},{ 9}}, {{ 23},{ 9}}, {{279},{ 9}},
+{{151},{ 9}}, {{407},{ 9}}, {{ 87},{ 9}}, {{343},{ 9}}, {{215},{ 9}},
+{{471},{ 9}}, {{ 55},{ 9}}, {{311},{ 9}}, {{183},{ 9}}, {{439},{ 9}},
+{{119},{ 9}}, {{375},{ 9}}, {{247},{ 9}}, {{503},{ 9}}, {{ 15},{ 9}},
+{{271},{ 9}}, {{143},{ 9}}, {{399},{ 9}}, {{ 79},{ 9}}, {{335},{ 9}},
+{{207},{ 9}}, {{463},{ 9}}, {{ 47},{ 9}}, {{303},{ 9}}, {{175},{ 9}},
+{{431},{ 9}}, {{111},{ 9}}, {{367},{ 9}}, {{239},{ 9}}, {{495},{ 9}},
+{{ 31},{ 9}}, {{287},{ 9}}, {{159},{ 9}}, {{415},{ 9}}, {{ 95},{ 9}},
+{{351},{ 9}}, {{223},{ 9}}, {{479},{ 9}}, {{ 63},{ 9}}, {{319},{ 9}},
+{{191},{ 9}}, {{447},{ 9}}, {{127},{ 9}}, {{383},{ 9}}, {{255},{ 9}},
+{{511},{ 9}}, {{ 0},{ 7}}, {{ 64},{ 7}}, {{ 32},{ 7}}, {{ 96},{ 7}},
+{{ 16},{ 7}}, {{ 80},{ 7}}, {{ 48},{ 7}}, {{112},{ 7}}, {{ 8},{ 7}},
+{{ 72},{ 7}}, {{ 40},{ 7}}, {{104},{ 7}}, {{ 24},{ 7}}, {{ 88},{ 7}},
+{{ 56},{ 7}}, {{120},{ 7}}, {{ 4},{ 7}}, {{ 68},{ 7}}, {{ 36},{ 7}},
+{{100},{ 7}}, {{ 20},{ 7}}, {{ 84},{ 7}}, {{ 52},{ 7}}, {{116},{ 7}},
+{{ 3},{ 8}}, {{131},{ 8}}, {{ 67},{ 8}}, {{195},{ 8}}, {{ 35},{ 8}},
+{{163},{ 8}}, {{ 99},{ 8}}, {{227},{ 8}}
+};
+
+local const ct_data static_dtree[D_CODES] = {
+{{ 0},{ 5}}, {{16},{ 5}}, {{ 8},{ 5}}, {{24},{ 5}}, {{ 4},{ 5}},
+{{20},{ 5}}, {{12},{ 5}}, {{28},{ 5}}, {{ 2},{ 5}}, {{18},{ 5}},
+{{10},{ 5}}, {{26},{ 5}}, {{ 6},{ 5}}, {{22},{ 5}}, {{14},{ 5}},
+{{30},{ 5}}, {{ 1},{ 5}}, {{17},{ 5}}, {{ 9},{ 5}}, {{25},{ 5}},
+{{ 5},{ 5}}, {{21},{ 5}}, {{13},{ 5}}, {{29},{ 5}}, {{ 3},{ 5}},
+{{19},{ 5}}, {{11},{ 5}}, {{27},{ 5}}, {{ 7},{ 5}}, {{23},{ 5}}
+};
+
+const uch ZLIB_INTERNAL _dist_code[DIST_CODE_LEN] = {
+ 0, 1, 2, 3, 4, 4, 5, 5, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8,
+ 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10,
+10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11,
+11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12,
+12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13,
+13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+13, 13, 13, 13, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15,
+15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 0, 0, 16, 17,
+18, 18, 19, 19, 20, 20, 20, 20, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 22, 22,
+23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24,
+24, 24, 24, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25,
+26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26,
+26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27,
+27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27,
+27, 27, 27, 27, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28,
+28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28,
+28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28,
+28, 28, 28, 28, 28, 28, 28, 28, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29,
+29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29,
+29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29,
+29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29
+};
+
+const uch ZLIB_INTERNAL _length_code[MAX_MATCH-MIN_MATCH+1]= {
+ 0, 1, 2, 3, 4, 5, 6, 7, 8, 8, 9, 9, 10, 10, 11, 11, 12, 12, 12, 12,
+13, 13, 13, 13, 14, 14, 14, 14, 15, 15, 15, 15, 16, 16, 16, 16, 16, 16, 16, 16,
+17, 17, 17, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18, 19, 19, 19, 19,
+19, 19, 19, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 22, 22, 22, 22,
+22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23,
+23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24,
+24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24,
+25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25,
+25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 26,
+26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26,
+26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27,
+27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 28
+};
+
+local const int base_length[LENGTH_CODES] = {
+0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 12, 14, 16, 20, 24, 28, 32, 40, 48, 56,
+64, 80, 96, 112, 128, 160, 192, 224, 0
+};
+
+local const int base_dist[D_CODES] = {
+ 0, 1, 2, 3, 4, 6, 8, 12, 16, 24,
+ 32, 48, 64, 96, 128, 192, 256, 384, 512, 768,
+ 1024, 1536, 2048, 3072, 4096, 6144, 8192, 12288, 16384, 24576
+};
+
diff --git a/third-party/zlib/uncompr.c b/third-party/zlib/uncompr.c
new file mode 100644
index 0000000..242e949
--- /dev/null
+++ b/third-party/zlib/uncompr.c
@@ -0,0 +1,59 @@
+/* uncompr.c -- decompress a memory buffer
+ * Copyright (C) 1995-2003, 2010 Jean-loup Gailly.
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* @(#) $Id$ */
+
+#define ZLIB_INTERNAL
+#include "zlib.h"
+
+/* ===========================================================================
+ Decompresses the source buffer into the destination buffer. sourceLen is
+ the byte length of the source buffer. Upon entry, destLen is the total
+ size of the destination buffer, which must be large enough to hold the
+ entire uncompressed data. (The size of the uncompressed data must have
+ been saved previously by the compressor and transmitted to the decompressor
+ by some mechanism outside the scope of this compression library.)
+ Upon exit, destLen is the actual size of the compressed buffer.
+
+ uncompress returns Z_OK if success, Z_MEM_ERROR if there was not
+ enough memory, Z_BUF_ERROR if there was not enough room in the output
+ buffer, or Z_DATA_ERROR if the input data was corrupted.
+*/
+int ZEXPORT uncompress (dest, destLen, source, sourceLen)
+ Bytef *dest;
+ uLongf *destLen;
+ const Bytef *source;
+ uLong sourceLen;
+{
+ z_stream stream;
+ int err;
+
+ stream.next_in = (z_const Bytef *)source;
+ stream.avail_in = (uInt)sourceLen;
+ /* Check for source > 64K on 16-bit machine: */
+ if ((uLong)stream.avail_in != sourceLen) return Z_BUF_ERROR;
+
+ stream.next_out = dest;
+ stream.avail_out = (uInt)*destLen;
+ if ((uLong)stream.avail_out != *destLen) return Z_BUF_ERROR;
+
+ stream.zalloc = (alloc_func)0;
+ stream.zfree = (free_func)0;
+
+ err = inflateInit(&stream);
+ if (err != Z_OK) return err;
+
+ err = inflate(&stream, Z_FINISH);
+ if (err != Z_STREAM_END) {
+ inflateEnd(&stream);
+ if (err == Z_NEED_DICT || (err == Z_BUF_ERROR && stream.avail_in == 0))
+ return Z_DATA_ERROR;
+ return err;
+ }
+ *destLen = stream.total_out;
+
+ err = inflateEnd(&stream);
+ return err;
+}
diff --git a/third-party/zlib/win32/DLL_FAQ.txt b/third-party/zlib/win32/DLL_FAQ.txt
new file mode 100644
index 0000000..12c0090
--- /dev/null
+++ b/third-party/zlib/win32/DLL_FAQ.txt
@@ -0,0 +1,397 @@
+
+ Frequently Asked Questions about ZLIB1.DLL
+
+
+This document describes the design, the rationale, and the usage
+of the official DLL build of zlib, named ZLIB1.DLL. If you have
+general questions about zlib, you should see the file "FAQ" found
+in the zlib distribution, or at the following location:
+ http://www.gzip.org/zlib/zlib_faq.html
+
+
+ 1. What is ZLIB1.DLL, and how can I get it?
+
+ - ZLIB1.DLL is the official build of zlib as a DLL.
+ (Please remark the character '1' in the name.)
+
+ Pointers to a precompiled ZLIB1.DLL can be found in the zlib
+ web site at:
+ http://www.zlib.net/
+
+ Applications that link to ZLIB1.DLL can rely on the following
+ specification:
+
+ * The exported symbols are exclusively defined in the source
+ files "zlib.h" and "zlib.def", found in an official zlib
+ source distribution.
+ * The symbols are exported by name, not by ordinal.
+ * The exported names are undecorated.
+ * The calling convention of functions is "C" (CDECL).
+ * The ZLIB1.DLL binary is linked to MSVCRT.DLL.
+
+ The archive in which ZLIB1.DLL is bundled contains compiled
+ test programs that must run with a valid build of ZLIB1.DLL.
+ It is recommended to download the prebuilt DLL from the zlib
+ web site, instead of building it yourself, to avoid potential
+ incompatibilities that could be introduced by your compiler
+ and build settings. If you do build the DLL yourself, please
+ make sure that it complies with all the above requirements,
+ and it runs with the precompiled test programs, bundled with
+ the original ZLIB1.DLL distribution.
+
+ If, for any reason, you need to build an incompatible DLL,
+ please use a different file name.
+
+
+ 2. Why did you change the name of the DLL to ZLIB1.DLL?
+ What happened to the old ZLIB.DLL?
+
+ - The old ZLIB.DLL, built from zlib-1.1.4 or earlier, required
+ compilation settings that were incompatible to those used by
+ a static build. The DLL settings were supposed to be enabled
+ by defining the macro ZLIB_DLL, before including "zlib.h".
+ Incorrect handling of this macro was silently accepted at
+ build time, resulting in two major problems:
+
+ * ZLIB_DLL was missing from the old makefile. When building
+ the DLL, not all people added it to the build options. In
+ consequence, incompatible incarnations of ZLIB.DLL started
+ to circulate around the net.
+
+ * When switching from using the static library to using the
+ DLL, applications had to define the ZLIB_DLL macro and
+ to recompile all the sources that contained calls to zlib
+ functions. Failure to do so resulted in creating binaries
+ that were unable to run with the official ZLIB.DLL build.
+
+ The only possible solution that we could foresee was to make
+ a binary-incompatible change in the DLL interface, in order to
+ remove the dependency on the ZLIB_DLL macro, and to release
+ the new DLL under a different name.
+
+ We chose the name ZLIB1.DLL, where '1' indicates the major
+ zlib version number. We hope that we will not have to break
+ the binary compatibility again, at least not as long as the
+ zlib-1.x series will last.
+
+ There is still a ZLIB_DLL macro, that can trigger a more
+ efficient build and use of the DLL, but compatibility no
+ longer dependents on it.
+
+
+ 3. Can I build ZLIB.DLL from the new zlib sources, and replace
+ an old ZLIB.DLL, that was built from zlib-1.1.4 or earlier?
+
+ - In principle, you can do it by assigning calling convention
+ keywords to the macros ZEXPORT and ZEXPORTVA. In practice,
+ it depends on what you mean by "an old ZLIB.DLL", because the
+ old DLL exists in several mutually-incompatible versions.
+ You have to find out first what kind of calling convention is
+ being used in your particular ZLIB.DLL build, and to use the
+ same one in the new build. If you don't know what this is all
+ about, you might be better off if you would just leave the old
+ DLL intact.
+
+
+ 4. Can I compile my application using the new zlib interface, and
+ link it to an old ZLIB.DLL, that was built from zlib-1.1.4 or
+ earlier?
+
+ - The official answer is "no"; the real answer depends again on
+ what kind of ZLIB.DLL you have. Even if you are lucky, this
+ course of action is unreliable.
+
+ If you rebuild your application and you intend to use a newer
+ version of zlib (post- 1.1.4), it is strongly recommended to
+ link it to the new ZLIB1.DLL.
+
+
+ 5. Why are the zlib symbols exported by name, and not by ordinal?
+
+ - Although exporting symbols by ordinal is a little faster, it
+ is risky. Any single glitch in the maintenance or use of the
+ DEF file that contains the ordinals can result in incompatible
+ builds and frustrating crashes. Simply put, the benefits of
+ exporting symbols by ordinal do not justify the risks.
+
+ Technically, it should be possible to maintain ordinals in
+ the DEF file, and still export the symbols by name. Ordinals
+ exist in every DLL, and even if the dynamic linking performed
+ at the DLL startup is searching for names, ordinals serve as
+ hints, for a faster name lookup. However, if the DEF file
+ contains ordinals, the Microsoft linker automatically builds
+ an implib that will cause the executables linked to it to use
+ those ordinals, and not the names. It is interesting to
+ notice that the GNU linker for Win32 does not suffer from this
+ problem.
+
+ It is possible to avoid the DEF file if the exported symbols
+ are accompanied by a "__declspec(dllexport)" attribute in the
+ source files. You can do this in zlib by predefining the
+ ZLIB_DLL macro.
+
+
+ 6. I see that the ZLIB1.DLL functions use the "C" (CDECL) calling
+ convention. Why not use the STDCALL convention?
+ STDCALL is the standard convention in Win32, and I need it in
+ my Visual Basic project!
+
+ (For readability, we use CDECL to refer to the convention
+ triggered by the "__cdecl" keyword, STDCALL to refer to
+ the convention triggered by "__stdcall", and FASTCALL to
+ refer to the convention triggered by "__fastcall".)
+
+ - Most of the native Windows API functions (without varargs) use
+ indeed the WINAPI convention (which translates to STDCALL in
+ Win32), but the standard C functions use CDECL. If a user
+ application is intrinsically tied to the Windows API (e.g.
+ it calls native Windows API functions such as CreateFile()),
+ sometimes it makes sense to decorate its own functions with
+ WINAPI. But if ANSI C or POSIX portability is a goal (e.g.
+ it calls standard C functions such as fopen()), it is not a
+ sound decision to request the inclusion of <windows.h>, or to
+ use non-ANSI constructs, for the sole purpose to make the user
+ functions STDCALL-able.
+
+ The functionality offered by zlib is not in the category of
+ "Windows functionality", but is more like "C functionality".
+
+ Technically, STDCALL is not bad; in fact, it is slightly
+ faster than CDECL, and it works with variable-argument
+ functions, just like CDECL. It is unfortunate that, in spite
+ of using STDCALL in the Windows API, it is not the default
+ convention used by the C compilers that run under Windows.
+ The roots of the problem reside deep inside the unsafety of
+ the K&R-style function prototypes, where the argument types
+ are not specified; but that is another story for another day.
+
+ The remaining fact is that CDECL is the default convention.
+ Even if an explicit convention is hard-coded into the function
+ prototypes inside C headers, problems may appear. The
+ necessity to expose the convention in users' callbacks is one
+ of these problems.
+
+ The calling convention issues are also important when using
+ zlib in other programming languages. Some of them, like Ada
+ (GNAT) and Fortran (GNU G77), have C bindings implemented
+ initially on Unix, and relying on the C calling convention.
+ On the other hand, the pre- .NET versions of Microsoft Visual
+ Basic require STDCALL, while Borland Delphi prefers, although
+ it does not require, FASTCALL.
+
+ In fairness to all possible uses of zlib outside the C
+ programming language, we choose the default "C" convention.
+ Anyone interested in different bindings or conventions is
+ encouraged to maintain specialized projects. The "contrib/"
+ directory from the zlib distribution already holds a couple
+ of foreign bindings, such as Ada, C++, and Delphi.
+
+
+ 7. I need a DLL for my Visual Basic project. What can I do?
+
+ - Define the ZLIB_WINAPI macro before including "zlib.h", when
+ building both the DLL and the user application (except that
+ you don't need to define anything when using the DLL in Visual
+ Basic). The ZLIB_WINAPI macro will switch on the WINAPI
+ (STDCALL) convention. The name of this DLL must be different
+ than the official ZLIB1.DLL.
+
+ Gilles Vollant has contributed a build named ZLIBWAPI.DLL,
+ with the ZLIB_WINAPI macro turned on, and with the minizip
+ functionality built in. For more information, please read
+ the notes inside "contrib/vstudio/readme.txt", found in the
+ zlib distribution.
+
+
+ 8. I need to use zlib in my Microsoft .NET project. What can I
+ do?
+
+ - Henrik Ravn has contributed a .NET wrapper around zlib. Look
+ into contrib/dotzlib/, inside the zlib distribution.
+
+
+ 9. If my application uses ZLIB1.DLL, should I link it to
+ MSVCRT.DLL? Why?
+
+ - It is not required, but it is recommended to link your
+ application to MSVCRT.DLL, if it uses ZLIB1.DLL.
+
+ The executables (.EXE, .DLL, etc.) that are involved in the
+ same process and are using the C run-time library (i.e. they
+ are calling standard C functions), must link to the same
+ library. There are several libraries in the Win32 system:
+ CRTDLL.DLL, MSVCRT.DLL, the static C libraries, etc.
+ Since ZLIB1.DLL is linked to MSVCRT.DLL, the executables that
+ depend on it should also be linked to MSVCRT.DLL.
+
+
+10. Why are you saying that ZLIB1.DLL and my application should
+ be linked to the same C run-time (CRT) library? I linked my
+ application and my DLLs to different C libraries (e.g. my
+ application to a static library, and my DLLs to MSVCRT.DLL),
+ and everything works fine.
+
+ - If a user library invokes only pure Win32 API (accessible via
+ <windows.h> and the related headers), its DLL build will work
+ in any context. But if this library invokes standard C API,
+ things get more complicated.
+
+ There is a single Win32 library in a Win32 system. Every
+ function in this library resides in a single DLL module, that
+ is safe to call from anywhere. On the other hand, there are
+ multiple versions of the C library, and each of them has its
+ own separate internal state. Standalone executables and user
+ DLLs that call standard C functions must link to a C run-time
+ (CRT) library, be it static or shared (DLL). Intermixing
+ occurs when an executable (not necessarily standalone) and a
+ DLL are linked to different CRTs, and both are running in the
+ same process.
+
+ Intermixing multiple CRTs is possible, as long as their
+ internal states are kept intact. The Microsoft Knowledge Base
+ articles KB94248 "HOWTO: Use the C Run-Time" and KB140584
+ "HOWTO: Link with the Correct C Run-Time (CRT) Library"
+ mention the potential problems raised by intermixing.
+
+ If intermixing works for you, it's because your application
+ and DLLs are avoiding the corruption of each of the CRTs'
+ internal states, maybe by careful design, or maybe by fortune.
+
+ Also note that linking ZLIB1.DLL to non-Microsoft CRTs, such
+ as those provided by Borland, raises similar problems.
+
+
+11. Why are you linking ZLIB1.DLL to MSVCRT.DLL?
+
+ - MSVCRT.DLL exists on every Windows 95 with a new service pack
+ installed, or with Microsoft Internet Explorer 4 or later, and
+ on all other Windows 4.x or later (Windows 98, Windows NT 4,
+ or later). It is freely distributable; if not present in the
+ system, it can be downloaded from Microsoft or from other
+ software provider for free.
+
+ The fact that MSVCRT.DLL does not exist on a virgin Windows 95
+ is not so problematic. Windows 95 is scarcely found nowadays,
+ Microsoft ended its support a long time ago, and many recent
+ applications from various vendors, including Microsoft, do not
+ even run on it. Furthermore, no serious user should run
+ Windows 95 without a proper update installed.
+
+
+12. Why are you not linking ZLIB1.DLL to
+ <<my favorite C run-time library>> ?
+
+ - We considered and abandoned the following alternatives:
+
+ * Linking ZLIB1.DLL to a static C library (LIBC.LIB, or
+ LIBCMT.LIB) is not a good option. People are using the DLL
+ mainly to save disk space. If you are linking your program
+ to a static C library, you may as well consider linking zlib
+ in statically, too.
+
+ * Linking ZLIB1.DLL to CRTDLL.DLL looks appealing, because
+ CRTDLL.DLL is present on every Win32 installation.
+ Unfortunately, it has a series of problems: it does not
+ work properly with Microsoft's C++ libraries, it does not
+ provide support for 64-bit file offsets, (and so on...),
+ and Microsoft discontinued its support a long time ago.
+
+ * Linking ZLIB1.DLL to MSVCR70.DLL or MSVCR71.DLL, supplied
+ with the Microsoft .NET platform, and Visual C++ 7.0/7.1,
+ raises problems related to the status of ZLIB1.DLL as a
+ system component. According to the Microsoft Knowledge Base
+ article KB326922 "INFO: Redistribution of the Shared C
+ Runtime Component in Visual C++ .NET", MSVCR70.DLL and
+ MSVCR71.DLL are not supposed to function as system DLLs,
+ because they may clash with MSVCRT.DLL. Instead, the
+ application's installer is supposed to put these DLLs
+ (if needed) in the application's private directory.
+ If ZLIB1.DLL depends on a non-system runtime, it cannot
+ function as a redistributable system component.
+
+ * Linking ZLIB1.DLL to non-Microsoft runtimes, such as
+ Borland's, or Cygwin's, raises problems related to the
+ reliable presence of these runtimes on Win32 systems.
+ It's easier to let the DLL build of zlib up to the people
+ who distribute these runtimes, and who may proceed as
+ explained in the answer to Question 14.
+
+
+13. If ZLIB1.DLL cannot be linked to MSVCR70.DLL or MSVCR71.DLL,
+ how can I build/use ZLIB1.DLL in Microsoft Visual C++ 7.0
+ (Visual Studio .NET) or newer?
+
+ - Due to the problems explained in the Microsoft Knowledge Base
+ article KB326922 (see the previous answer), the C runtime that
+ comes with the VC7 environment is no longer considered a
+ system component. That is, it should not be assumed that this
+ runtime exists, or may be installed in a system directory.
+ Since ZLIB1.DLL is supposed to be a system component, it may
+ not depend on a non-system component.
+
+ In order to link ZLIB1.DLL and your application to MSVCRT.DLL
+ in VC7, you need the library of Visual C++ 6.0 or older. If
+ you don't have this library at hand, it's probably best not to
+ use ZLIB1.DLL.
+
+ We are hoping that, in the future, Microsoft will provide a
+ way to build applications linked to a proper system runtime,
+ from the Visual C++ environment. Until then, you have a
+ couple of alternatives, such as linking zlib in statically.
+ If your application requires dynamic linking, you may proceed
+ as explained in the answer to Question 14.
+
+
+14. I need to link my own DLL build to a CRT different than
+ MSVCRT.DLL. What can I do?
+
+ - Feel free to rebuild the DLL from the zlib sources, and link
+ it the way you want. You should, however, clearly state that
+ your build is unofficial. You should give it a different file
+ name, and/or install it in a private directory that can be
+ accessed by your application only, and is not visible to the
+ others (i.e. it's neither in the PATH, nor in the SYSTEM or
+ SYSTEM32 directories). Otherwise, your build may clash with
+ applications that link to the official build.
+
+ For example, in Cygwin, zlib is linked to the Cygwin runtime
+ CYGWIN1.DLL, and it is distributed under the name CYGZ.DLL.
+
+
+15. May I include additional pieces of code that I find useful,
+ link them in ZLIB1.DLL, and export them?
+
+ - No. A legitimate build of ZLIB1.DLL must not include code
+ that does not originate from the official zlib source code.
+ But you can make your own private DLL build, under a different
+ file name, as suggested in the previous answer.
+
+ For example, zlib is a part of the VCL library, distributed
+ with Borland Delphi and C++ Builder. The DLL build of VCL
+ is a redistributable file, named VCLxx.DLL.
+
+
+16. May I remove some functionality out of ZLIB1.DLL, by enabling
+ macros like NO_GZCOMPRESS or NO_GZIP at compile time?
+
+ - No. A legitimate build of ZLIB1.DLL must provide the complete
+ zlib functionality, as implemented in the official zlib source
+ code. But you can make your own private DLL build, under a
+ different file name, as suggested in the previous answer.
+
+
+17. I made my own ZLIB1.DLL build. Can I test it for compliance?
+
+ - We prefer that you download the official DLL from the zlib
+ web site. If you need something peculiar from this DLL, you
+ can send your suggestion to the zlib mailing list.
+
+ However, in case you do rebuild the DLL yourself, you can run
+ it with the test programs found in the DLL distribution.
+ Running these test programs is not a guarantee of compliance,
+ but a failure can imply a detected problem.
+
+**
+
+This document is written and maintained by
+Cosmin Truta <cosmint at cs.ubbcluj.ro>
diff --git a/third-party/zlib/win32/Makefile.bor b/third-party/zlib/win32/Makefile.bor
new file mode 100644
index 0000000..d152bbb
--- /dev/null
+++ b/third-party/zlib/win32/Makefile.bor
@@ -0,0 +1,110 @@
+# Makefile for zlib
+# Borland C++ for Win32
+#
+# Usage:
+# make -f win32/Makefile.bor
+# make -f win32/Makefile.bor LOCAL_ZLIB=-DASMV OBJA=match.obj OBJPA=+match.obj
+
+# ------------ Borland C++ ------------
+
+# Optional nonstandard preprocessor flags (e.g. -DMAX_MEM_LEVEL=7)
+# should be added to the environment via "set LOCAL_ZLIB=-DFOO" or
+# added to the declaration of LOC here:
+LOC = $(LOCAL_ZLIB)
+
+CC = bcc32
+AS = bcc32
+LD = bcc32
+AR = tlib
+CFLAGS = -a -d -k- -O2 $(LOC)
+ASFLAGS = $(LOC)
+LDFLAGS = $(LOC)
+
+
+# variables
+ZLIB_LIB = zlib.lib
+
+OBJ1 = adler32.obj compress.obj crc32.obj deflate.obj gzclose.obj gzlib.obj gzread.obj
+OBJ2 = gzwrite.obj infback.obj inffast.obj inflate.obj inftrees.obj trees.obj uncompr.obj zutil.obj
+#OBJA =
+OBJP1 = +adler32.obj+compress.obj+crc32.obj+deflate.obj+gzclose.obj+gzlib.obj+gzread.obj
+OBJP2 = +gzwrite.obj+infback.obj+inffast.obj+inflate.obj+inftrees.obj+trees.obj+uncompr.obj+zutil.obj
+#OBJPA=
+
+
+# targets
+all: $(ZLIB_LIB) example.exe minigzip.exe
+
+.c.obj:
+ $(CC) -c $(CFLAGS) $<
+
+.asm.obj:
+ $(AS) -c $(ASFLAGS) $<
+
+adler32.obj: adler32.c zlib.h zconf.h
+
+compress.obj: compress.c zlib.h zconf.h
+
+crc32.obj: crc32.c zlib.h zconf.h crc32.h
+
+deflate.obj: deflate.c deflate.h zutil.h zlib.h zconf.h
+
+gzclose.obj: gzclose.c zlib.h zconf.h gzguts.h
+
+gzlib.obj: gzlib.c zlib.h zconf.h gzguts.h
+
+gzread.obj: gzread.c zlib.h zconf.h gzguts.h
+
+gzwrite.obj: gzwrite.c zlib.h zconf.h gzguts.h
+
+infback.obj: infback.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
+ inffast.h inffixed.h
+
+inffast.obj: inffast.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
+ inffast.h
+
+inflate.obj: inflate.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
+ inffast.h inffixed.h
+
+inftrees.obj: inftrees.c zutil.h zlib.h zconf.h inftrees.h
+
+trees.obj: trees.c zutil.h zlib.h zconf.h deflate.h trees.h
+
+uncompr.obj: uncompr.c zlib.h zconf.h
+
+zutil.obj: zutil.c zutil.h zlib.h zconf.h
+
+example.obj: test/example.c zlib.h zconf.h
+
+minigzip.obj: test/minigzip.c zlib.h zconf.h
+
+
+# For the sake of the old Borland make,
+# the command line is cut to fit in the MS-DOS 128 byte limit:
+$(ZLIB_LIB): $(OBJ1) $(OBJ2) $(OBJA)
+ -del $(ZLIB_LIB)
+ $(AR) $(ZLIB_LIB) $(OBJP1)
+ $(AR) $(ZLIB_LIB) $(OBJP2)
+ $(AR) $(ZLIB_LIB) $(OBJPA)
+
+
+# testing
+test: example.exe minigzip.exe
+ example
+ echo hello world | minigzip | minigzip -d
+
+example.exe: example.obj $(ZLIB_LIB)
+ $(LD) $(LDFLAGS) example.obj $(ZLIB_LIB)
+
+minigzip.exe: minigzip.obj $(ZLIB_LIB)
+ $(LD) $(LDFLAGS) minigzip.obj $(ZLIB_LIB)
+
+
+# cleanup
+clean:
+ -del $(ZLIB_LIB)
+ -del *.obj
+ -del *.exe
+ -del *.tds
+ -del zlib.bak
+ -del foo.gz
diff --git a/third-party/zlib/win32/Makefile.gcc b/third-party/zlib/win32/Makefile.gcc
new file mode 100644
index 0000000..6d1ded6
--- /dev/null
+++ b/third-party/zlib/win32/Makefile.gcc
@@ -0,0 +1,182 @@
+# Makefile for zlib, derived from Makefile.dj2.
+# Modified for mingw32 by C. Spieler, 6/16/98.
+# Updated for zlib 1.2.x by Christian Spieler and Cosmin Truta, Mar-2003.
+# Last updated: Mar 2012.
+# Tested under Cygwin and MinGW.
+
+# Copyright (C) 1995-2003 Jean-loup Gailly.
+# For conditions of distribution and use, see copyright notice in zlib.h
+
+# To compile, or to compile and test, type from the top level zlib directory:
+#
+# make -fwin32/Makefile.gcc; make test testdll -fwin32/Makefile.gcc
+#
+# To use the asm code, type:
+# cp contrib/asm?86/match.S ./match.S
+# make LOC=-DASMV OBJA=match.o -fwin32/Makefile.gcc
+#
+# To install libz.a, zconf.h and zlib.h in the system directories, type:
+#
+# make install -fwin32/Makefile.gcc
+#
+# BINARY_PATH, INCLUDE_PATH and LIBRARY_PATH must be set.
+#
+# To install the shared lib, append SHARED_MODE=1 to the make command :
+#
+# make install -fwin32/Makefile.gcc SHARED_MODE=1
+
+# Note:
+# If the platform is *not* MinGW (e.g. it is Cygwin or UWIN),
+# the DLL name should be changed from "zlib1.dll".
+
+STATICLIB = libz.a
+SHAREDLIB = zlib1.dll
+IMPLIB = libz.dll.a
+
+#
+# Set to 1 if shared object needs to be installed
+#
+SHARED_MODE=0
+
+#LOC = -DASMV
+#LOC = -DDEBUG -g
+
+PREFIX =
+CC = $(PREFIX)gcc
+CFLAGS = $(LOC) -O3 -Wall
+
+AS = $(CC)
+ASFLAGS = $(LOC) -Wall
+
+LD = $(CC)
+LDFLAGS = $(LOC)
+
+AR = $(PREFIX)ar
+ARFLAGS = rcs
+
+RC = $(PREFIX)windres
+RCFLAGS = --define GCC_WINDRES
+
+STRIP = $(PREFIX)strip
+
+CP = cp -fp
+# If GNU install is available, replace $(CP) with install.
+INSTALL = $(CP)
+RM = rm -f
+
+prefix ?= /usr/local
+exec_prefix = $(prefix)
+
+OBJS = adler32.o compress.o crc32.o deflate.o gzclose.o gzlib.o gzread.o \
+ gzwrite.o infback.o inffast.o inflate.o inftrees.o trees.o uncompr.o zutil.o
+OBJA =
+
+all: $(STATICLIB) $(SHAREDLIB) $(IMPLIB) example.exe minigzip.exe example_d.exe minigzip_d.exe
+
+test: example.exe minigzip.exe
+ ./example
+ echo hello world | ./minigzip | ./minigzip -d
+
+testdll: example_d.exe minigzip_d.exe
+ ./example_d
+ echo hello world | ./minigzip_d | ./minigzip_d -d
+
+.c.o:
+ $(CC) $(CFLAGS) -c -o $@ $<
+
+.S.o:
+ $(AS) $(ASFLAGS) -c -o $@ $<
+
+$(STATICLIB): $(OBJS) $(OBJA)
+ $(AR) $(ARFLAGS) $@ $(OBJS) $(OBJA)
+
+$(IMPLIB): $(SHAREDLIB)
+
+$(SHAREDLIB): win32/zlib.def $(OBJS) $(OBJA) zlibrc.o
+ $(CC) -shared -Wl,--out-implib,$(IMPLIB) $(LDFLAGS) \
+ -o $@ win32/zlib.def $(OBJS) $(OBJA) zlibrc.o
+ $(STRIP) $@
+
+example.exe: example.o $(STATICLIB)
+ $(LD) $(LDFLAGS) -o $@ example.o $(STATICLIB)
+ $(STRIP) $@
+
+minigzip.exe: minigzip.o $(STATICLIB)
+ $(LD) $(LDFLAGS) -o $@ minigzip.o $(STATICLIB)
+ $(STRIP) $@
+
+example_d.exe: example.o $(IMPLIB)
+ $(LD) $(LDFLAGS) -o $@ example.o $(IMPLIB)
+ $(STRIP) $@
+
+minigzip_d.exe: minigzip.o $(IMPLIB)
+ $(LD) $(LDFLAGS) -o $@ minigzip.o $(IMPLIB)
+ $(STRIP) $@
+
+example.o: test/example.c zlib.h zconf.h
+ $(CC) $(CFLAGS) -I. -c -o $@ test/example.c
+
+minigzip.o: test/minigzip.c zlib.h zconf.h
+ $(CC) $(CFLAGS) -I. -c -o $@ test/minigzip.c
+
+zlibrc.o: win32/zlib1.rc
+ $(RC) $(RCFLAGS) -o $@ win32/zlib1.rc
+
+.PHONY: install uninstall clean
+
+install: zlib.h zconf.h $(STATICLIB) $(IMPLIB)
+ @if test -z "$(DESTDIR)$(INCLUDE_PATH)" -o -z "$(DESTDIR)$(LIBRARY_PATH)" -o -z "$(DESTDIR)$(BINARY_PATH)"; then \
+ echo INCLUDE_PATH, LIBRARY_PATH, and BINARY_PATH must be specified; \
+ exit 1; \
+ fi
+ - at mkdir -p '$(DESTDIR)$(INCLUDE_PATH)'
+ - at mkdir -p '$(DESTDIR)$(LIBRARY_PATH)' '$(DESTDIR)$(LIBRARY_PATH)'/pkgconfig
+ -if [ "$(SHARED_MODE)" = "1" ]; then \
+ mkdir -p '$(DESTDIR)$(BINARY_PATH)'; \
+ $(INSTALL) $(SHAREDLIB) '$(DESTDIR)$(BINARY_PATH)'; \
+ $(INSTALL) $(IMPLIB) '$(DESTDIR)$(LIBRARY_PATH)'; \
+ fi
+ -$(INSTALL) zlib.h '$(DESTDIR)$(INCLUDE_PATH)'
+ -$(INSTALL) zconf.h '$(DESTDIR)$(INCLUDE_PATH)'
+ -$(INSTALL) $(STATICLIB) '$(DESTDIR)$(LIBRARY_PATH)'
+ sed \
+ -e 's|@prefix@|${prefix}|g' \
+ -e 's|@exec_prefix@|${exec_prefix}|g' \
+ -e 's|@libdir@|$(LIBRARY_PATH)|g' \
+ -e 's|@sharedlibdir@|$(LIBRARY_PATH)|g' \
+ -e 's|@includedir@|$(INCLUDE_PATH)|g' \
+ -e 's|@VERSION@|'`sed -n -e '/VERSION "/s/.*"\(.*\)".*/\1/p' zlib.h`'|g' \
+ zlib.pc.in > '$(DESTDIR)$(LIBRARY_PATH)'/pkgconfig/zlib.pc
+
+uninstall:
+ -if [ "$(SHARED_MODE)" = "1" ]; then \
+ $(RM) '$(DESTDIR)$(BINARY_PATH)'/$(SHAREDLIB); \
+ $(RM) '$(DESTDIR)$(LIBRARY_PATH)'/$(IMPLIB); \
+ fi
+ -$(RM) '$(DESTDIR)$(INCLUDE_PATH)'/zlib.h
+ -$(RM) '$(DESTDIR)$(INCLUDE_PATH)'/zconf.h
+ -$(RM) '$(DESTDIR)$(LIBRARY_PATH)'/$(STATICLIB)
+
+clean:
+ -$(RM) $(STATICLIB)
+ -$(RM) $(SHAREDLIB)
+ -$(RM) $(IMPLIB)
+ -$(RM) *.o
+ -$(RM) *.exe
+ -$(RM) foo.gz
+
+adler32.o: zlib.h zconf.h
+compress.o: zlib.h zconf.h
+crc32.o: crc32.h zlib.h zconf.h
+deflate.o: deflate.h zutil.h zlib.h zconf.h
+gzclose.o: zlib.h zconf.h gzguts.h
+gzlib.o: zlib.h zconf.h gzguts.h
+gzread.o: zlib.h zconf.h gzguts.h
+gzwrite.o: zlib.h zconf.h gzguts.h
+inffast.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
+inflate.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
+infback.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
+inftrees.o: zutil.h zlib.h zconf.h inftrees.h
+trees.o: deflate.h zutil.h zlib.h zconf.h trees.h
+uncompr.o: zlib.h zconf.h
+zutil.o: zutil.h zlib.h zconf.h
diff --git a/third-party/zlib/win32/Makefile.msc b/third-party/zlib/win32/Makefile.msc
new file mode 100644
index 0000000..67b7731
--- /dev/null
+++ b/third-party/zlib/win32/Makefile.msc
@@ -0,0 +1,163 @@
+# Makefile for zlib using Microsoft (Visual) C
+# zlib is copyright (C) 1995-2006 Jean-loup Gailly and Mark Adler
+#
+# Usage:
+# nmake -f win32/Makefile.msc (standard build)
+# nmake -f win32/Makefile.msc LOC=-DFOO (nonstandard build)
+# nmake -f win32/Makefile.msc LOC="-DASMV -DASMINF" \
+# OBJA="inffas32.obj match686.obj" (use ASM code, x86)
+# nmake -f win32/Makefile.msc AS=ml64 LOC="-DASMV -DASMINF -I." \
+# OBJA="inffasx64.obj gvmat64.obj inffas8664.obj" (use ASM code, x64)
+
+# The toplevel directory of the source tree.
+#
+TOP = .
+
+# optional build flags
+LOC =
+
+# variables
+STATICLIB = zlib.lib
+SHAREDLIB = zlib1.dll
+IMPLIB = zdll.lib
+
+CC = cl
+AS = ml
+LD = link
+AR = lib
+RC = rc
+CFLAGS = -nologo -MD -W3 -O2 -Oy- -Zi -Fd"zlib" $(LOC)
+WFLAGS = -D_CRT_SECURE_NO_DEPRECATE -D_CRT_NONSTDC_NO_DEPRECATE
+ASFLAGS = -coff -Zi $(LOC)
+LDFLAGS = -nologo -debug -incremental:no -opt:ref
+ARFLAGS = -nologo
+RCFLAGS = /dWIN32 /r
+
+OBJS = adler32.obj compress.obj crc32.obj deflate.obj gzclose.obj gzlib.obj gzread.obj \
+ gzwrite.obj infback.obj inflate.obj inftrees.obj inffast.obj trees.obj uncompr.obj zutil.obj
+OBJA =
+
+
+# targets
+all: $(STATICLIB) $(SHAREDLIB) $(IMPLIB) \
+ example.exe minigzip.exe example_d.exe minigzip_d.exe
+
+$(STATICLIB): $(OBJS) $(OBJA)
+ $(AR) $(ARFLAGS) -out:$@ $(OBJS) $(OBJA)
+
+$(IMPLIB): $(SHAREDLIB)
+
+$(SHAREDLIB): $(TOP)/win32/zlib.def $(OBJS) $(OBJA) zlib1.res
+ $(LD) $(LDFLAGS) -def:$(TOP)/win32/zlib.def -dll -implib:$(IMPLIB) \
+ -out:$@ -base:0x5A4C0000 $(OBJS) $(OBJA) zlib1.res
+ if exist $@.manifest \
+ mt -nologo -manifest $@.manifest -outputresource:$@;2
+
+example.exe: example.obj $(STATICLIB)
+ $(LD) $(LDFLAGS) example.obj $(STATICLIB)
+ if exist $@.manifest \
+ mt -nologo -manifest $@.manifest -outputresource:$@;1
+
+minigzip.exe: minigzip.obj $(STATICLIB)
+ $(LD) $(LDFLAGS) minigzip.obj $(STATICLIB)
+ if exist $@.manifest \
+ mt -nologo -manifest $@.manifest -outputresource:$@;1
+
+example_d.exe: example.obj $(IMPLIB)
+ $(LD) $(LDFLAGS) -out:$@ example.obj $(IMPLIB)
+ if exist $@.manifest \
+ mt -nologo -manifest $@.manifest -outputresource:$@;1
+
+minigzip_d.exe: minigzip.obj $(IMPLIB)
+ $(LD) $(LDFLAGS) -out:$@ minigzip.obj $(IMPLIB)
+ if exist $@.manifest \
+ mt -nologo -manifest $@.manifest -outputresource:$@;1
+
+{$(TOP)}.c.obj:
+ $(CC) -c $(WFLAGS) $(CFLAGS) $<
+
+{$(TOP)/test}.c.obj:
+ $(CC) -c -I$(TOP) $(WFLAGS) $(CFLAGS) $<
+
+{$(TOP)/contrib/masmx64}.c.obj:
+ $(CC) -c $(WFLAGS) $(CFLAGS) $<
+
+{$(TOP)/contrib/masmx64}.asm.obj:
+ $(AS) -c $(ASFLAGS) $<
+
+{$(TOP)/contrib/masmx86}.asm.obj:
+ $(AS) -c $(ASFLAGS) $<
+
+adler32.obj: $(TOP)/adler32.c $(TOP)/zlib.h $(TOP)/zconf.h
+
+compress.obj: $(TOP)/compress.c $(TOP)/zlib.h $(TOP)/zconf.h
+
+crc32.obj: $(TOP)/crc32.c $(TOP)/zlib.h $(TOP)/zconf.h $(TOP)/crc32.h
+
+deflate.obj: $(TOP)/deflate.c $(TOP)/deflate.h $(TOP)/zutil.h $(TOP)/zlib.h $(TOP)/zconf.h
+
+gzclose.obj: $(TOP)/gzclose.c $(TOP)/zlib.h $(TOP)/zconf.h $(TOP)/gzguts.h
+
+gzlib.obj: $(TOP)/gzlib.c $(TOP)/zlib.h $(TOP)/zconf.h $(TOP)/gzguts.h
+
+gzread.obj: $(TOP)/gzread.c $(TOP)/zlib.h $(TOP)/zconf.h $(TOP)/gzguts.h
+
+gzwrite.obj: $(TOP)/gzwrite.c $(TOP)/zlib.h $(TOP)/zconf.h $(TOP)/gzguts.h
+
+infback.obj: $(TOP)/infback.c $(TOP)/zutil.h $(TOP)/zlib.h $(TOP)/zconf.h $(TOP)/inftrees.h $(TOP)/inflate.h \
+ $(TOP)/inffast.h $(TOP)/inffixed.h
+
+inffast.obj: $(TOP)/inffast.c $(TOP)/zutil.h $(TOP)/zlib.h $(TOP)/zconf.h $(TOP)/inftrees.h $(TOP)/inflate.h \
+ $(TOP)/inffast.h
+
+inflate.obj: $(TOP)/inflate.c $(TOP)/zutil.h $(TOP)/zlib.h $(TOP)/zconf.h $(TOP)/inftrees.h $(TOP)/inflate.h \
+ $(TOP)/inffast.h $(TOP)/inffixed.h
+
+inftrees.obj: $(TOP)/inftrees.c $(TOP)/zutil.h $(TOP)/zlib.h $(TOP)/zconf.h $(TOP)/inftrees.h
+
+trees.obj: $(TOP)/trees.c $(TOP)/zutil.h $(TOP)/zlib.h $(TOP)/zconf.h $(TOP)/deflate.h $(TOP)/trees.h
+
+uncompr.obj: $(TOP)/uncompr.c $(TOP)/zlib.h $(TOP)/zconf.h
+
+zutil.obj: $(TOP)/zutil.c $(TOP)/zutil.h $(TOP)/zlib.h $(TOP)/zconf.h
+
+gvmat64.obj: $(TOP)/contrib\masmx64\gvmat64.asm
+
+inffasx64.obj: $(TOP)/contrib\masmx64\inffasx64.asm
+
+inffas8664.obj: $(TOP)/contrib\masmx64\inffas8664.c $(TOP)/zutil.h $(TOP)/zlib.h $(TOP)/zconf.h \
+ $(TOP)/inftrees.h $(TOP)/inflate.h $(TOP)/inffast.h
+
+inffas32.obj: $(TOP)/contrib\masmx86\inffas32.asm
+
+match686.obj: $(TOP)/contrib\masmx86\match686.asm
+
+example.obj: $(TOP)/test/example.c $(TOP)/zlib.h $(TOP)/zconf.h
+
+minigzip.obj: $(TOP)/test/minigzip.c $(TOP)/zlib.h $(TOP)/zconf.h
+
+zlib1.res: $(TOP)/win32/zlib1.rc
+ $(RC) $(RCFLAGS) /fo$@ $(TOP)/win32/zlib1.rc
+
+# testing
+test: example.exe minigzip.exe
+ example
+ echo hello world | minigzip | minigzip -d
+
+testdll: example_d.exe minigzip_d.exe
+ example_d
+ echo hello world | minigzip_d | minigzip_d -d
+
+
+# cleanup
+clean:
+ -del $(STATICLIB)
+ -del $(SHAREDLIB)
+ -del $(IMPLIB)
+ -del *.obj
+ -del *.res
+ -del *.exp
+ -del *.exe
+ -del *.pdb
+ -del *.manifest
+ -del foo.gz
diff --git a/third-party/zlib/win32/README-WIN32.txt b/third-party/zlib/win32/README-WIN32.txt
new file mode 100644
index 0000000..3d77d52
--- /dev/null
+++ b/third-party/zlib/win32/README-WIN32.txt
@@ -0,0 +1,103 @@
+ZLIB DATA COMPRESSION LIBRARY
+
+zlib 1.2.8 is a general purpose data compression library. All the code is
+thread safe. The data format used by the zlib library is described by RFCs
+(Request for Comments) 1950 to 1952 in the files
+http://www.ietf.org/rfc/rfc1950.txt (zlib format), rfc1951.txt (deflate format)
+and rfc1952.txt (gzip format).
+
+All functions of the compression library are documented in the file zlib.h
+(volunteer to write man pages welcome, contact zlib at gzip.org). Two compiled
+examples are distributed in this package, example and minigzip. The example_d
+and minigzip_d flavors validate that the zlib1.dll file is working correctly.
+
+Questions about zlib should be sent to <zlib at gzip.org>. The zlib home page
+is http://zlib.net/ . Before reporting a problem, please check this site to
+verify that you have the latest version of zlib; otherwise get the latest
+version and check whether the problem still exists or not.
+
+PLEASE read DLL_FAQ.txt, and the the zlib FAQ http://zlib.net/zlib_faq.html
+before asking for help.
+
+
+Manifest:
+
+The package zlib-1.2.8-win32-x86.zip will contain the following files:
+
+ README-WIN32.txt This document
+ ChangeLog Changes since previous zlib packages
+ DLL_FAQ.txt Frequently asked questions about zlib1.dll
+ zlib.3.pdf Documentation of this library in Adobe Acrobat format
+
+ example.exe A statically-bound example (using zlib.lib, not the dll)
+ example.pdb Symbolic information for debugging example.exe
+
+ example_d.exe A zlib1.dll bound example (using zdll.lib)
+ example_d.pdb Symbolic information for debugging example_d.exe
+
+ minigzip.exe A statically-bound test program (using zlib.lib, not the dll)
+ minigzip.pdb Symbolic information for debugging minigzip.exe
+
+ minigzip_d.exe A zlib1.dll bound test program (using zdll.lib)
+ minigzip_d.pdb Symbolic information for debugging minigzip_d.exe
+
+ zlib.h Install these files into the compilers' INCLUDE path to
+ zconf.h compile programs which use zlib.lib or zdll.lib
+
+ zdll.lib Install these files into the compilers' LIB path if linking
+ zdll.exp a compiled program to the zlib1.dll binary
+
+ zlib.lib Install these files into the compilers' LIB path to link zlib
+ zlib.pdb into compiled programs, without zlib1.dll runtime dependency
+ (zlib.pdb provides debugging info to the compile time linker)
+
+ zlib1.dll Install this binary shared library into the system PATH, or
+ the program's runtime directory (where the .exe resides)
+ zlib1.pdb Install in the same directory as zlib1.dll, in order to debug
+ an application crash using WinDbg or similar tools.
+
+All .pdb files above are entirely optional, but are very useful to a developer
+attempting to diagnose program misbehavior or a crash. Many additional
+important files for developers can be found in the zlib127.zip source package
+available from http://zlib.net/ - review that package's README file for details.
+
+
+Acknowledgments:
+
+The deflate format used by zlib was defined by Phil Katz. The deflate and
+zlib specifications were written by L. Peter Deutsch. Thanks to all the
+people who reported problems and suggested various improvements in zlib; they
+are too numerous to cite here.
+
+
+Copyright notice:
+
+ (C) 1995-2012 Jean-loup Gailly and Mark Adler
+
+ This software is provided 'as-is', without any express or implied
+ warranty. In no event will the authors be held liable for any damages
+ arising from the use of this software.
+
+ Permission is granted to anyone to use this software for any purpose,
+ including commercial applications, and to alter it and redistribute it
+ freely, subject to the following restrictions:
+
+ 1. The origin of this software must not be misrepresented; you must not
+ claim that you wrote the original software. If you use this software
+ in a product, an acknowledgment in the product documentation would be
+ appreciated but is not required.
+ 2. Altered source versions must be plainly marked as such, and must not be
+ misrepresented as being the original software.
+ 3. This notice may not be removed or altered from any source distribution.
+
+ Jean-loup Gailly Mark Adler
+ jloup at gzip.org madler at alumni.caltech.edu
+
+If you use the zlib library in a product, we would appreciate *not* receiving
+lengthy legal documents to sign. The sources are provided for free but without
+warranty of any kind. The library has been entirely written by Jean-loup
+Gailly and Mark Adler; it does not include third-party code.
+
+If you redistribute modified sources, we would appreciate that you include in
+the file ChangeLog history information documenting your changes. Please read
+the FAQ for more information on the distribution of modified source versions.
diff --git a/third-party/zlib/win32/VisualC.txt b/third-party/zlib/win32/VisualC.txt
new file mode 100644
index 0000000..579a5fc
--- /dev/null
+++ b/third-party/zlib/win32/VisualC.txt
@@ -0,0 +1,3 @@
+
+To build zlib using the Microsoft Visual C++ environment,
+use the appropriate project from the projects/ directory.
diff --git a/third-party/zlib/win32/zlib.def b/third-party/zlib/win32/zlib.def
new file mode 100644
index 0000000..face655
--- /dev/null
+++ b/third-party/zlib/win32/zlib.def
@@ -0,0 +1,86 @@
+; zlib data compression library
+EXPORTS
+; basic functions
+ zlibVersion
+ deflate
+ deflateEnd
+ inflate
+ inflateEnd
+; advanced functions
+ deflateSetDictionary
+ deflateCopy
+ deflateReset
+ deflateParams
+ deflateTune
+ deflateBound
+ deflatePending
+ deflatePrime
+ deflateSetHeader
+ inflateSetDictionary
+ inflateGetDictionary
+ inflateSync
+ inflateCopy
+ inflateReset
+ inflateReset2
+ inflatePrime
+ inflateMark
+ inflateGetHeader
+ inflateBack
+ inflateBackEnd
+ zlibCompileFlags
+; utility functions
+ compress
+ compress2
+ compressBound
+ uncompress
+ gzopen
+ gzdopen
+ gzbuffer
+ gzsetparams
+ gzread
+ gzwrite
+ gzprintf
+ gzvprintf
+ gzputs
+ gzgets
+ gzputc
+ gzgetc
+ gzungetc
+ gzflush
+ gzseek
+ gzrewind
+ gztell
+ gzoffset
+ gzeof
+ gzdirect
+ gzclose
+ gzclose_r
+ gzclose_w
+ gzerror
+ gzclearerr
+; large file functions
+ gzopen64
+ gzseek64
+ gztell64
+ gzoffset64
+ adler32_combine64
+ crc32_combine64
+; checksum functions
+ adler32
+ crc32
+ adler32_combine
+ crc32_combine
+; various hacks, don't look :)
+ deflateInit_
+ deflateInit2_
+ inflateInit_
+ inflateInit2_
+ inflateBackInit_
+ gzgetc_
+ zError
+ inflateSyncPoint
+ get_crc_table
+ inflateUndermine
+ inflateResetKeep
+ deflateResetKeep
+ gzopen_w
diff --git a/third-party/zlib/win32/zlib1.rc b/third-party/zlib/win32/zlib1.rc
new file mode 100644
index 0000000..5c0feed
--- /dev/null
+++ b/third-party/zlib/win32/zlib1.rc
@@ -0,0 +1,40 @@
+#include <winver.h>
+#include "../zlib.h"
+
+#ifdef GCC_WINDRES
+VS_VERSION_INFO VERSIONINFO
+#else
+VS_VERSION_INFO VERSIONINFO MOVEABLE IMPURE LOADONCALL DISCARDABLE
+#endif
+ FILEVERSION ZLIB_VER_MAJOR,ZLIB_VER_MINOR,ZLIB_VER_REVISION,0
+ PRODUCTVERSION ZLIB_VER_MAJOR,ZLIB_VER_MINOR,ZLIB_VER_REVISION,0
+ FILEFLAGSMASK VS_FFI_FILEFLAGSMASK
+#ifdef _DEBUG
+ FILEFLAGS 1
+#else
+ FILEFLAGS 0
+#endif
+ FILEOS VOS__WINDOWS32
+ FILETYPE VFT_DLL
+ FILESUBTYPE 0 // not used
+BEGIN
+ BLOCK "StringFileInfo"
+ BEGIN
+ BLOCK "040904E4"
+ //language ID = U.S. English, char set = Windows, Multilingual
+ BEGIN
+ VALUE "FileDescription", "zlib data compression library\0"
+ VALUE "FileVersion", ZLIB_VERSION "\0"
+ VALUE "InternalName", "zlib1.dll\0"
+ VALUE "LegalCopyright", "(C) 1995-2013 Jean-loup Gailly & Mark Adler\0"
+ VALUE "OriginalFilename", "zlib1.dll\0"
+ VALUE "ProductName", "zlib\0"
+ VALUE "ProductVersion", ZLIB_VERSION "\0"
+ VALUE "Comments", "For more information visit http://www.zlib.net/\0"
+ END
+ END
+ BLOCK "VarFileInfo"
+ BEGIN
+ VALUE "Translation", 0x0409, 1252
+ END
+END
diff --git a/third-party/zlib/zconf.h.cmakein b/third-party/zlib/zconf.h.cmakein
new file mode 100644
index 0000000..043019c
--- /dev/null
+++ b/third-party/zlib/zconf.h.cmakein
@@ -0,0 +1,513 @@
+/* zconf.h -- configuration of the zlib compression library
+ * Copyright (C) 1995-2013 Jean-loup Gailly.
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* @(#) $Id$ */
+
+#ifndef ZCONF_H
+#define ZCONF_H
+#cmakedefine Z_PREFIX
+#cmakedefine Z_HAVE_UNISTD_H
+
+/*
+ * If you *really* need a unique prefix for all types and library functions,
+ * compile with -DZ_PREFIX. The "standard" zlib should be compiled without it.
+ * Even better than compiling with -DZ_PREFIX would be to use configure to set
+ * this permanently in zconf.h using "./configure --zprefix".
+ */
+#ifdef Z_PREFIX /* may be set to #if 1 by ./configure */
+# define Z_PREFIX_SET
+
+/* all linked symbols */
+# define _dist_code z__dist_code
+# define _length_code z__length_code
+# define _tr_align z__tr_align
+# define _tr_flush_bits z__tr_flush_bits
+# define _tr_flush_block z__tr_flush_block
+# define _tr_init z__tr_init
+# define _tr_stored_block z__tr_stored_block
+# define _tr_tally z__tr_tally
+# define adler32 z_adler32
+# define adler32_combine z_adler32_combine
+# define adler32_combine64 z_adler32_combine64
+# ifndef Z_SOLO
+# define compress z_compress
+# define compress2 z_compress2
+# define compressBound z_compressBound
+# endif
+# define crc32 z_crc32
+# define crc32_combine z_crc32_combine
+# define crc32_combine64 z_crc32_combine64
+# define deflate z_deflate
+# define deflateBound z_deflateBound
+# define deflateCopy z_deflateCopy
+# define deflateEnd z_deflateEnd
+# define deflateInit2_ z_deflateInit2_
+# define deflateInit_ z_deflateInit_
+# define deflateParams z_deflateParams
+# define deflatePending z_deflatePending
+# define deflatePrime z_deflatePrime
+# define deflateReset z_deflateReset
+# define deflateResetKeep z_deflateResetKeep
+# define deflateSetDictionary z_deflateSetDictionary
+# define deflateSetHeader z_deflateSetHeader
+# define deflateTune z_deflateTune
+# define deflate_copyright z_deflate_copyright
+# define get_crc_table z_get_crc_table
+# ifndef Z_SOLO
+# define gz_error z_gz_error
+# define gz_intmax z_gz_intmax
+# define gz_strwinerror z_gz_strwinerror
+# define gzbuffer z_gzbuffer
+# define gzclearerr z_gzclearerr
+# define gzclose z_gzclose
+# define gzclose_r z_gzclose_r
+# define gzclose_w z_gzclose_w
+# define gzdirect z_gzdirect
+# define gzdopen z_gzdopen
+# define gzeof z_gzeof
+# define gzerror z_gzerror
+# define gzflush z_gzflush
+# define gzgetc z_gzgetc
+# define gzgetc_ z_gzgetc_
+# define gzgets z_gzgets
+# define gzoffset z_gzoffset
+# define gzoffset64 z_gzoffset64
+# define gzopen z_gzopen
+# define gzopen64 z_gzopen64
+# ifdef _WIN32
+# define gzopen_w z_gzopen_w
+# endif
+# define gzprintf z_gzprintf
+# define gzvprintf z_gzvprintf
+# define gzputc z_gzputc
+# define gzputs z_gzputs
+# define gzread z_gzread
+# define gzrewind z_gzrewind
+# define gzseek z_gzseek
+# define gzseek64 z_gzseek64
+# define gzsetparams z_gzsetparams
+# define gztell z_gztell
+# define gztell64 z_gztell64
+# define gzungetc z_gzungetc
+# define gzwrite z_gzwrite
+# endif
+# define inflate z_inflate
+# define inflateBack z_inflateBack
+# define inflateBackEnd z_inflateBackEnd
+# define inflateBackInit_ z_inflateBackInit_
+# define inflateCopy z_inflateCopy
+# define inflateEnd z_inflateEnd
+# define inflateGetHeader z_inflateGetHeader
+# define inflateInit2_ z_inflateInit2_
+# define inflateInit_ z_inflateInit_
+# define inflateMark z_inflateMark
+# define inflatePrime z_inflatePrime
+# define inflateReset z_inflateReset
+# define inflateReset2 z_inflateReset2
+# define inflateSetDictionary z_inflateSetDictionary
+# define inflateGetDictionary z_inflateGetDictionary
+# define inflateSync z_inflateSync
+# define inflateSyncPoint z_inflateSyncPoint
+# define inflateUndermine z_inflateUndermine
+# define inflateResetKeep z_inflateResetKeep
+# define inflate_copyright z_inflate_copyright
+# define inflate_fast z_inflate_fast
+# define inflate_table z_inflate_table
+# ifndef Z_SOLO
+# define uncompress z_uncompress
+# endif
+# define zError z_zError
+# ifndef Z_SOLO
+# define zcalloc z_zcalloc
+# define zcfree z_zcfree
+# endif
+# define zlibCompileFlags z_zlibCompileFlags
+# define zlibVersion z_zlibVersion
+
+/* all zlib typedefs in zlib.h and zconf.h */
+# define Byte z_Byte
+# define Bytef z_Bytef
+# define alloc_func z_alloc_func
+# define charf z_charf
+# define free_func z_free_func
+# ifndef Z_SOLO
+# define gzFile z_gzFile
+# endif
+# define gz_header z_gz_header
+# define gz_headerp z_gz_headerp
+# define in_func z_in_func
+# define intf z_intf
+# define out_func z_out_func
+# define uInt z_uInt
+# define uIntf z_uIntf
+# define uLong z_uLong
+# define uLongf z_uLongf
+# define voidp z_voidp
+# define voidpc z_voidpc
+# define voidpf z_voidpf
+
+/* all zlib structs in zlib.h and zconf.h */
+# define gz_header_s z_gz_header_s
+# define internal_state z_internal_state
+
+#endif
+
+#if defined(__MSDOS__) && !defined(MSDOS)
+# define MSDOS
+#endif
+#if (defined(OS_2) || defined(__OS2__)) && !defined(OS2)
+# define OS2
+#endif
+#if defined(_WINDOWS) && !defined(WINDOWS)
+# define WINDOWS
+#endif
+#if defined(_WIN32) || defined(_WIN32_WCE) || defined(__WIN32__)
+# ifndef WIN32
+# define WIN32
+# endif
+#endif
+#if (defined(MSDOS) || defined(OS2) || defined(WINDOWS)) && !defined(WIN32)
+# if !defined(__GNUC__) && !defined(__FLAT__) && !defined(__386__)
+# ifndef SYS16BIT
+# define SYS16BIT
+# endif
+# endif
+#endif
+
+/*
+ * Compile with -DMAXSEG_64K if the alloc function cannot allocate more
+ * than 64k bytes at a time (needed on systems with 16-bit int).
+ */
+#ifdef SYS16BIT
+# define MAXSEG_64K
+#endif
+#ifdef MSDOS
+# define UNALIGNED_OK
+#endif
+
+#ifdef __STDC_VERSION__
+# ifndef STDC
+# define STDC
+# endif
+# if __STDC_VERSION__ >= 199901L
+# ifndef STDC99
+# define STDC99
+# endif
+# endif
+#endif
+#if !defined(STDC) && (defined(__STDC__) || defined(__cplusplus))
+# define STDC
+#endif
+#if !defined(STDC) && (defined(__GNUC__) || defined(__BORLANDC__))
+# define STDC
+#endif
+#if !defined(STDC) && (defined(MSDOS) || defined(WINDOWS) || defined(WIN32))
+# define STDC
+#endif
+#if !defined(STDC) && (defined(OS2) || defined(__HOS_AIX__))
+# define STDC
+#endif
+
+#if defined(__OS400__) && !defined(STDC) /* iSeries (formerly AS/400). */
+# define STDC
+#endif
+
+#ifndef STDC
+# ifndef const /* cannot use !defined(STDC) && !defined(const) on Mac */
+# define const /* note: need a more gentle solution here */
+# endif
+#endif
+
+#if defined(ZLIB_CONST) && !defined(z_const)
+# define z_const const
+#else
+# define z_const
+#endif
+
+/* Some Mac compilers merge all .h files incorrectly: */
+#if defined(__MWERKS__)||defined(applec)||defined(THINK_C)||defined(__SC__)
+# define NO_DUMMY_DECL
+#endif
+
+/* Maximum value for memLevel in deflateInit2 */
+#ifndef MAX_MEM_LEVEL
+# ifdef MAXSEG_64K
+# define MAX_MEM_LEVEL 8
+# else
+# define MAX_MEM_LEVEL 9
+# endif
+#endif
+
+/* Maximum value for windowBits in deflateInit2 and inflateInit2.
+ * WARNING: reducing MAX_WBITS makes minigzip unable to extract .gz files
+ * created by gzip. (Files created by minigzip can still be extracted by
+ * gzip.)
+ */
+#ifndef MAX_WBITS
+# define MAX_WBITS 15 /* 32K LZ77 window */
+#endif
+
+/* The memory requirements for deflate are (in bytes):
+ (1 << (windowBits+2)) + (1 << (memLevel+9))
+ that is: 128K for windowBits=15 + 128K for memLevel = 8 (default values)
+ plus a few kilobytes for small objects. For example, if you want to reduce
+ the default memory requirements from 256K to 128K, compile with
+ make CFLAGS="-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7"
+ Of course this will generally degrade compression (there's no free lunch).
+
+ The memory requirements for inflate are (in bytes) 1 << windowBits
+ that is, 32K for windowBits=15 (default value) plus a few kilobytes
+ for small objects.
+*/
+
+ /* Type declarations */
+
+#ifndef OF /* function prototypes */
+# ifdef STDC
+# define OF(args) args
+# else
+# define OF(args) ()
+# endif
+#endif
+
+#ifndef Z_ARG /* function prototypes for stdarg */
+# if defined(STDC) || defined(Z_HAVE_STDARG_H)
+# define Z_ARG(args) args
+# else
+# define Z_ARG(args) ()
+# endif
+#endif
+
+/* The following definitions for FAR are needed only for MSDOS mixed
+ * model programming (small or medium model with some far allocations).
+ * This was tested only with MSC; for other MSDOS compilers you may have
+ * to define NO_MEMCPY in zutil.h. If you don't need the mixed model,
+ * just define FAR to be empty.
+ */
+#ifdef SYS16BIT
+# if defined(M_I86SM) || defined(M_I86MM)
+ /* MSC small or medium model */
+# define SMALL_MEDIUM
+# ifdef _MSC_VER
+# define FAR _far
+# else
+# define FAR far
+# endif
+# endif
+# if (defined(__SMALL__) || defined(__MEDIUM__))
+ /* Turbo C small or medium model */
+# define SMALL_MEDIUM
+# ifdef __BORLANDC__
+# define FAR _far
+# else
+# define FAR far
+# endif
+# endif
+#endif
+
+#if defined(WINDOWS) || defined(WIN32)
+ /* If building or using zlib as a DLL, define ZLIB_DLL.
+ * This is not mandatory, but it offers a little performance increase.
+ */
+# ifdef ZLIB_DLL
+# if defined(WIN32) && (!defined(__BORLANDC__) || (__BORLANDC__ >= 0x500))
+# ifdef ZLIB_INTERNAL
+# define ZEXTERN extern __declspec(dllexport)
+# else
+# define ZEXTERN extern __declspec(dllimport)
+# endif
+# endif
+# endif /* ZLIB_DLL */
+ /* If building or using zlib with the WINAPI/WINAPIV calling convention,
+ * define ZLIB_WINAPI.
+ * Caution: the standard ZLIB1.DLL is NOT compiled using ZLIB_WINAPI.
+ */
+# ifdef ZLIB_WINAPI
+# ifdef FAR
+# undef FAR
+# endif
+# include <windows.h>
+ /* No need for _export, use ZLIB.DEF instead. */
+ /* For complete Windows compatibility, use WINAPI, not __stdcall. */
+# define ZEXPORT WINAPI
+# ifdef WIN32
+# define ZEXPORTVA WINAPIV
+# else
+# define ZEXPORTVA FAR CDECL
+# endif
+# endif
+#endif
+
+#if defined (__BEOS__)
+# ifdef ZLIB_DLL
+# ifdef ZLIB_INTERNAL
+# define ZEXPORT __declspec(dllexport)
+# define ZEXPORTVA __declspec(dllexport)
+# else
+# define ZEXPORT __declspec(dllimport)
+# define ZEXPORTVA __declspec(dllimport)
+# endif
+# endif
+#endif
+
+#ifndef ZEXTERN
+# define ZEXTERN extern
+#endif
+#ifndef ZEXPORT
+# define ZEXPORT
+#endif
+#ifndef ZEXPORTVA
+# define ZEXPORTVA
+#endif
+
+#ifndef FAR
+# define FAR
+#endif
+
+#if !defined(__MACTYPES__)
+typedef unsigned char Byte; /* 8 bits */
+#endif
+typedef unsigned int uInt; /* 16 bits or more */
+typedef unsigned long uLong; /* 32 bits or more */
+
+#ifdef SMALL_MEDIUM
+ /* Borland C/C++ and some old MSC versions ignore FAR inside typedef */
+# define Bytef Byte FAR
+#else
+ typedef Byte FAR Bytef;
+#endif
+typedef char FAR charf;
+typedef int FAR intf;
+typedef uInt FAR uIntf;
+typedef uLong FAR uLongf;
+
+#ifdef STDC
+ typedef void const *voidpc;
+ typedef void FAR *voidpf;
+ typedef void *voidp;
+#else
+ typedef Byte const *voidpc;
+ typedef Byte FAR *voidpf;
+ typedef Byte *voidp;
+#endif
+
+#if !defined(Z_U4) && !defined(Z_SOLO) && defined(STDC)
+# include <limits.h>
+# if (UINT_MAX == 0xffffffffUL)
+# define Z_U4 unsigned
+# elif (ULONG_MAX == 0xffffffffUL)
+# define Z_U4 unsigned long
+# elif (USHRT_MAX == 0xffffffffUL)
+# define Z_U4 unsigned short
+# endif
+#endif
+
+#ifdef Z_U4
+ typedef Z_U4 z_crc_t;
+#else
+ typedef unsigned long z_crc_t;
+#endif
+
+#ifdef HAVE_UNISTD_H /* may be set to #if 1 by ./configure */
+# define Z_HAVE_UNISTD_H
+#endif
+
+#ifdef HAVE_STDARG_H /* may be set to #if 1 by ./configure */
+# define Z_HAVE_STDARG_H
+#endif
+
+#ifdef STDC
+# ifndef Z_SOLO
+# include <sys/types.h> /* for off_t */
+# endif
+#endif
+
+#if defined(STDC) || defined(Z_HAVE_STDARG_H)
+# ifndef Z_SOLO
+# include <stdarg.h> /* for va_list */
+# endif
+#endif
+
+#ifdef _WIN32
+# ifndef Z_SOLO
+# include <stddef.h> /* for wchar_t */
+# endif
+#endif
+
+/* a little trick to accommodate both "#define _LARGEFILE64_SOURCE" and
+ * "#define _LARGEFILE64_SOURCE 1" as requesting 64-bit operations, (even
+ * though the former does not conform to the LFS document), but considering
+ * both "#undef _LARGEFILE64_SOURCE" and "#define _LARGEFILE64_SOURCE 0" as
+ * equivalently requesting no 64-bit operations
+ */
+#if defined(_LARGEFILE64_SOURCE) && -_LARGEFILE64_SOURCE - -1 == 1
+# undef _LARGEFILE64_SOURCE
+#endif
+
+#if defined(__WATCOMC__) && !defined(Z_HAVE_UNISTD_H)
+# define Z_HAVE_UNISTD_H
+#endif
+#ifndef Z_SOLO
+# if defined(Z_HAVE_UNISTD_H) || defined(_LARGEFILE64_SOURCE)
+# include <unistd.h> /* for SEEK_*, off_t, and _LFS64_LARGEFILE */
+# ifdef VMS
+# include <unixio.h> /* for off_t */
+# endif
+# ifndef z_off_t
+# define z_off_t off_t
+# endif
+# endif
+#endif
+
+#if defined(_LFS64_LARGEFILE) && _LFS64_LARGEFILE-0
+# define Z_LFS64
+#endif
+
+#if defined(_LARGEFILE64_SOURCE) && defined(Z_LFS64)
+# define Z_LARGE64
+#endif
+
+#if defined(_FILE_OFFSET_BITS) && _FILE_OFFSET_BITS-0 == 64 && defined(Z_LFS64)
+# define Z_WANT64
+#endif
+
+#if !defined(SEEK_SET) && !defined(Z_SOLO)
+# define SEEK_SET 0 /* Seek from beginning of file. */
+# define SEEK_CUR 1 /* Seek from current position. */
+# define SEEK_END 2 /* Set file pointer to EOF plus "offset" */
+#endif
+
+#ifndef z_off_t
+# define z_off_t long
+#endif
+
+#if !defined(_WIN32) && defined(Z_LARGE64)
+# define z_off64_t off64_t
+#else
+# if defined(_WIN32) && !defined(__GNUC__) && !defined(Z_SOLO)
+# define z_off64_t __int64
+# else
+# define z_off64_t z_off_t
+# endif
+#endif
+
+/* MVS linker does not support external names larger than 8 bytes */
+#if defined(__MVS__)
+ #pragma map(deflateInit_,"DEIN")
+ #pragma map(deflateInit2_,"DEIN2")
+ #pragma map(deflateEnd,"DEEND")
+ #pragma map(deflateBound,"DEBND")
+ #pragma map(inflateInit_,"ININ")
+ #pragma map(inflateInit2_,"ININ2")
+ #pragma map(inflateEnd,"INEND")
+ #pragma map(inflateSync,"INSY")
+ #pragma map(inflateSetDictionary,"INSEDI")
+ #pragma map(compressBound,"CMBND")
+ #pragma map(inflate_table,"INTABL")
+ #pragma map(inflate_fast,"INFA")
+ #pragma map(inflate_copyright,"INCOPY")
+#endif
+
+#endif /* ZCONF_H */
diff --git a/third-party/zlib/zconf.h.in b/third-party/zlib/zconf.h.in
new file mode 100644
index 0000000..9987a77
--- /dev/null
+++ b/third-party/zlib/zconf.h.in
@@ -0,0 +1,511 @@
+/* zconf.h -- configuration of the zlib compression library
+ * Copyright (C) 1995-2013 Jean-loup Gailly.
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* @(#) $Id$ */
+
+#ifndef ZCONF_H
+#define ZCONF_H
+
+/*
+ * If you *really* need a unique prefix for all types and library functions,
+ * compile with -DZ_PREFIX. The "standard" zlib should be compiled without it.
+ * Even better than compiling with -DZ_PREFIX would be to use configure to set
+ * this permanently in zconf.h using "./configure --zprefix".
+ */
+#ifdef Z_PREFIX /* may be set to #if 1 by ./configure */
+# define Z_PREFIX_SET
+
+/* all linked symbols */
+# define _dist_code z__dist_code
+# define _length_code z__length_code
+# define _tr_align z__tr_align
+# define _tr_flush_bits z__tr_flush_bits
+# define _tr_flush_block z__tr_flush_block
+# define _tr_init z__tr_init
+# define _tr_stored_block z__tr_stored_block
+# define _tr_tally z__tr_tally
+# define adler32 z_adler32
+# define adler32_combine z_adler32_combine
+# define adler32_combine64 z_adler32_combine64
+# ifndef Z_SOLO
+# define compress z_compress
+# define compress2 z_compress2
+# define compressBound z_compressBound
+# endif
+# define crc32 z_crc32
+# define crc32_combine z_crc32_combine
+# define crc32_combine64 z_crc32_combine64
+# define deflate z_deflate
+# define deflateBound z_deflateBound
+# define deflateCopy z_deflateCopy
+# define deflateEnd z_deflateEnd
+# define deflateInit2_ z_deflateInit2_
+# define deflateInit_ z_deflateInit_
+# define deflateParams z_deflateParams
+# define deflatePending z_deflatePending
+# define deflatePrime z_deflatePrime
+# define deflateReset z_deflateReset
+# define deflateResetKeep z_deflateResetKeep
+# define deflateSetDictionary z_deflateSetDictionary
+# define deflateSetHeader z_deflateSetHeader
+# define deflateTune z_deflateTune
+# define deflate_copyright z_deflate_copyright
+# define get_crc_table z_get_crc_table
+# ifndef Z_SOLO
+# define gz_error z_gz_error
+# define gz_intmax z_gz_intmax
+# define gz_strwinerror z_gz_strwinerror
+# define gzbuffer z_gzbuffer
+# define gzclearerr z_gzclearerr
+# define gzclose z_gzclose
+# define gzclose_r z_gzclose_r
+# define gzclose_w z_gzclose_w
+# define gzdirect z_gzdirect
+# define gzdopen z_gzdopen
+# define gzeof z_gzeof
+# define gzerror z_gzerror
+# define gzflush z_gzflush
+# define gzgetc z_gzgetc
+# define gzgetc_ z_gzgetc_
+# define gzgets z_gzgets
+# define gzoffset z_gzoffset
+# define gzoffset64 z_gzoffset64
+# define gzopen z_gzopen
+# define gzopen64 z_gzopen64
+# ifdef _WIN32
+# define gzopen_w z_gzopen_w
+# endif
+# define gzprintf z_gzprintf
+# define gzvprintf z_gzvprintf
+# define gzputc z_gzputc
+# define gzputs z_gzputs
+# define gzread z_gzread
+# define gzrewind z_gzrewind
+# define gzseek z_gzseek
+# define gzseek64 z_gzseek64
+# define gzsetparams z_gzsetparams
+# define gztell z_gztell
+# define gztell64 z_gztell64
+# define gzungetc z_gzungetc
+# define gzwrite z_gzwrite
+# endif
+# define inflate z_inflate
+# define inflateBack z_inflateBack
+# define inflateBackEnd z_inflateBackEnd
+# define inflateBackInit_ z_inflateBackInit_
+# define inflateCopy z_inflateCopy
+# define inflateEnd z_inflateEnd
+# define inflateGetHeader z_inflateGetHeader
+# define inflateInit2_ z_inflateInit2_
+# define inflateInit_ z_inflateInit_
+# define inflateMark z_inflateMark
+# define inflatePrime z_inflatePrime
+# define inflateReset z_inflateReset
+# define inflateReset2 z_inflateReset2
+# define inflateSetDictionary z_inflateSetDictionary
+# define inflateGetDictionary z_inflateGetDictionary
+# define inflateSync z_inflateSync
+# define inflateSyncPoint z_inflateSyncPoint
+# define inflateUndermine z_inflateUndermine
+# define inflateResetKeep z_inflateResetKeep
+# define inflate_copyright z_inflate_copyright
+# define inflate_fast z_inflate_fast
+# define inflate_table z_inflate_table
+# ifndef Z_SOLO
+# define uncompress z_uncompress
+# endif
+# define zError z_zError
+# ifndef Z_SOLO
+# define zcalloc z_zcalloc
+# define zcfree z_zcfree
+# endif
+# define zlibCompileFlags z_zlibCompileFlags
+# define zlibVersion z_zlibVersion
+
+/* all zlib typedefs in zlib.h and zconf.h */
+# define Byte z_Byte
+# define Bytef z_Bytef
+# define alloc_func z_alloc_func
+# define charf z_charf
+# define free_func z_free_func
+# ifndef Z_SOLO
+# define gzFile z_gzFile
+# endif
+# define gz_header z_gz_header
+# define gz_headerp z_gz_headerp
+# define in_func z_in_func
+# define intf z_intf
+# define out_func z_out_func
+# define uInt z_uInt
+# define uIntf z_uIntf
+# define uLong z_uLong
+# define uLongf z_uLongf
+# define voidp z_voidp
+# define voidpc z_voidpc
+# define voidpf z_voidpf
+
+/* all zlib structs in zlib.h and zconf.h */
+# define gz_header_s z_gz_header_s
+# define internal_state z_internal_state
+
+#endif
+
+#if defined(__MSDOS__) && !defined(MSDOS)
+# define MSDOS
+#endif
+#if (defined(OS_2) || defined(__OS2__)) && !defined(OS2)
+# define OS2
+#endif
+#if defined(_WINDOWS) && !defined(WINDOWS)
+# define WINDOWS
+#endif
+#if defined(_WIN32) || defined(_WIN32_WCE) || defined(__WIN32__)
+# ifndef WIN32
+# define WIN32
+# endif
+#endif
+#if (defined(MSDOS) || defined(OS2) || defined(WINDOWS)) && !defined(WIN32)
+# if !defined(__GNUC__) && !defined(__FLAT__) && !defined(__386__)
+# ifndef SYS16BIT
+# define SYS16BIT
+# endif
+# endif
+#endif
+
+/*
+ * Compile with -DMAXSEG_64K if the alloc function cannot allocate more
+ * than 64k bytes at a time (needed on systems with 16-bit int).
+ */
+#ifdef SYS16BIT
+# define MAXSEG_64K
+#endif
+#ifdef MSDOS
+# define UNALIGNED_OK
+#endif
+
+#ifdef __STDC_VERSION__
+# ifndef STDC
+# define STDC
+# endif
+# if __STDC_VERSION__ >= 199901L
+# ifndef STDC99
+# define STDC99
+# endif
+# endif
+#endif
+#if !defined(STDC) && (defined(__STDC__) || defined(__cplusplus))
+# define STDC
+#endif
+#if !defined(STDC) && (defined(__GNUC__) || defined(__BORLANDC__))
+# define STDC
+#endif
+#if !defined(STDC) && (defined(MSDOS) || defined(WINDOWS) || defined(WIN32))
+# define STDC
+#endif
+#if !defined(STDC) && (defined(OS2) || defined(__HOS_AIX__))
+# define STDC
+#endif
+
+#if defined(__OS400__) && !defined(STDC) /* iSeries (formerly AS/400). */
+# define STDC
+#endif
+
+#ifndef STDC
+# ifndef const /* cannot use !defined(STDC) && !defined(const) on Mac */
+# define const /* note: need a more gentle solution here */
+# endif
+#endif
+
+#if defined(ZLIB_CONST) && !defined(z_const)
+# define z_const const
+#else
+# define z_const
+#endif
+
+/* Some Mac compilers merge all .h files incorrectly: */
+#if defined(__MWERKS__)||defined(applec)||defined(THINK_C)||defined(__SC__)
+# define NO_DUMMY_DECL
+#endif
+
+/* Maximum value for memLevel in deflateInit2 */
+#ifndef MAX_MEM_LEVEL
+# ifdef MAXSEG_64K
+# define MAX_MEM_LEVEL 8
+# else
+# define MAX_MEM_LEVEL 9
+# endif
+#endif
+
+/* Maximum value for windowBits in deflateInit2 and inflateInit2.
+ * WARNING: reducing MAX_WBITS makes minigzip unable to extract .gz files
+ * created by gzip. (Files created by minigzip can still be extracted by
+ * gzip.)
+ */
+#ifndef MAX_WBITS
+# define MAX_WBITS 15 /* 32K LZ77 window */
+#endif
+
+/* The memory requirements for deflate are (in bytes):
+ (1 << (windowBits+2)) + (1 << (memLevel+9))
+ that is: 128K for windowBits=15 + 128K for memLevel = 8 (default values)
+ plus a few kilobytes for small objects. For example, if you want to reduce
+ the default memory requirements from 256K to 128K, compile with
+ make CFLAGS="-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7"
+ Of course this will generally degrade compression (there's no free lunch).
+
+ The memory requirements for inflate are (in bytes) 1 << windowBits
+ that is, 32K for windowBits=15 (default value) plus a few kilobytes
+ for small objects.
+*/
+
+ /* Type declarations */
+
+#ifndef OF /* function prototypes */
+# ifdef STDC
+# define OF(args) args
+# else
+# define OF(args) ()
+# endif
+#endif
+
+#ifndef Z_ARG /* function prototypes for stdarg */
+# if defined(STDC) || defined(Z_HAVE_STDARG_H)
+# define Z_ARG(args) args
+# else
+# define Z_ARG(args) ()
+# endif
+#endif
+
+/* The following definitions for FAR are needed only for MSDOS mixed
+ * model programming (small or medium model with some far allocations).
+ * This was tested only with MSC; for other MSDOS compilers you may have
+ * to define NO_MEMCPY in zutil.h. If you don't need the mixed model,
+ * just define FAR to be empty.
+ */
+#ifdef SYS16BIT
+# if defined(M_I86SM) || defined(M_I86MM)
+ /* MSC small or medium model */
+# define SMALL_MEDIUM
+# ifdef _MSC_VER
+# define FAR _far
+# else
+# define FAR far
+# endif
+# endif
+# if (defined(__SMALL__) || defined(__MEDIUM__))
+ /* Turbo C small or medium model */
+# define SMALL_MEDIUM
+# ifdef __BORLANDC__
+# define FAR _far
+# else
+# define FAR far
+# endif
+# endif
+#endif
+
+#if defined(WINDOWS) || defined(WIN32)
+ /* If building or using zlib as a DLL, define ZLIB_DLL.
+ * This is not mandatory, but it offers a little performance increase.
+ */
+# ifdef ZLIB_DLL
+# if defined(WIN32) && (!defined(__BORLANDC__) || (__BORLANDC__ >= 0x500))
+# ifdef ZLIB_INTERNAL
+# define ZEXTERN extern __declspec(dllexport)
+# else
+# define ZEXTERN extern __declspec(dllimport)
+# endif
+# endif
+# endif /* ZLIB_DLL */
+ /* If building or using zlib with the WINAPI/WINAPIV calling convention,
+ * define ZLIB_WINAPI.
+ * Caution: the standard ZLIB1.DLL is NOT compiled using ZLIB_WINAPI.
+ */
+# ifdef ZLIB_WINAPI
+# ifdef FAR
+# undef FAR
+# endif
+# include <windows.h>
+ /* No need for _export, use ZLIB.DEF instead. */
+ /* For complete Windows compatibility, use WINAPI, not __stdcall. */
+# define ZEXPORT WINAPI
+# ifdef WIN32
+# define ZEXPORTVA WINAPIV
+# else
+# define ZEXPORTVA FAR CDECL
+# endif
+# endif
+#endif
+
+#if defined (__BEOS__)
+# ifdef ZLIB_DLL
+# ifdef ZLIB_INTERNAL
+# define ZEXPORT __declspec(dllexport)
+# define ZEXPORTVA __declspec(dllexport)
+# else
+# define ZEXPORT __declspec(dllimport)
+# define ZEXPORTVA __declspec(dllimport)
+# endif
+# endif
+#endif
+
+#ifndef ZEXTERN
+# define ZEXTERN extern
+#endif
+#ifndef ZEXPORT
+# define ZEXPORT
+#endif
+#ifndef ZEXPORTVA
+# define ZEXPORTVA
+#endif
+
+#ifndef FAR
+# define FAR
+#endif
+
+#if !defined(__MACTYPES__)
+typedef unsigned char Byte; /* 8 bits */
+#endif
+typedef unsigned int uInt; /* 16 bits or more */
+typedef unsigned long uLong; /* 32 bits or more */
+
+#ifdef SMALL_MEDIUM
+ /* Borland C/C++ and some old MSC versions ignore FAR inside typedef */
+# define Bytef Byte FAR
+#else
+ typedef Byte FAR Bytef;
+#endif
+typedef char FAR charf;
+typedef int FAR intf;
+typedef uInt FAR uIntf;
+typedef uLong FAR uLongf;
+
+#ifdef STDC
+ typedef void const *voidpc;
+ typedef void FAR *voidpf;
+ typedef void *voidp;
+#else
+ typedef Byte const *voidpc;
+ typedef Byte FAR *voidpf;
+ typedef Byte *voidp;
+#endif
+
+#if !defined(Z_U4) && !defined(Z_SOLO) && defined(STDC)
+# include <limits.h>
+# if (UINT_MAX == 0xffffffffUL)
+# define Z_U4 unsigned
+# elif (ULONG_MAX == 0xffffffffUL)
+# define Z_U4 unsigned long
+# elif (USHRT_MAX == 0xffffffffUL)
+# define Z_U4 unsigned short
+# endif
+#endif
+
+#ifdef Z_U4
+ typedef Z_U4 z_crc_t;
+#else
+ typedef unsigned long z_crc_t;
+#endif
+
+#ifdef HAVE_UNISTD_H /* may be set to #if 1 by ./configure */
+# define Z_HAVE_UNISTD_H
+#endif
+
+#ifdef HAVE_STDARG_H /* may be set to #if 1 by ./configure */
+# define Z_HAVE_STDARG_H
+#endif
+
+#ifdef STDC
+# ifndef Z_SOLO
+# include <sys/types.h> /* for off_t */
+# endif
+#endif
+
+#if defined(STDC) || defined(Z_HAVE_STDARG_H)
+# ifndef Z_SOLO
+# include <stdarg.h> /* for va_list */
+# endif
+#endif
+
+#ifdef _WIN32
+# ifndef Z_SOLO
+# include <stddef.h> /* for wchar_t */
+# endif
+#endif
+
+/* a little trick to accommodate both "#define _LARGEFILE64_SOURCE" and
+ * "#define _LARGEFILE64_SOURCE 1" as requesting 64-bit operations, (even
+ * though the former does not conform to the LFS document), but considering
+ * both "#undef _LARGEFILE64_SOURCE" and "#define _LARGEFILE64_SOURCE 0" as
+ * equivalently requesting no 64-bit operations
+ */
+#if defined(_LARGEFILE64_SOURCE) && -_LARGEFILE64_SOURCE - -1 == 1
+# undef _LARGEFILE64_SOURCE
+#endif
+
+#if defined(__WATCOMC__) && !defined(Z_HAVE_UNISTD_H)
+# define Z_HAVE_UNISTD_H
+#endif
+#ifndef Z_SOLO
+# if defined(Z_HAVE_UNISTD_H) || defined(_LARGEFILE64_SOURCE)
+# include <unistd.h> /* for SEEK_*, off_t, and _LFS64_LARGEFILE */
+# ifdef VMS
+# include <unixio.h> /* for off_t */
+# endif
+# ifndef z_off_t
+# define z_off_t off_t
+# endif
+# endif
+#endif
+
+#if defined(_LFS64_LARGEFILE) && _LFS64_LARGEFILE-0
+# define Z_LFS64
+#endif
+
+#if defined(_LARGEFILE64_SOURCE) && defined(Z_LFS64)
+# define Z_LARGE64
+#endif
+
+#if defined(_FILE_OFFSET_BITS) && _FILE_OFFSET_BITS-0 == 64 && defined(Z_LFS64)
+# define Z_WANT64
+#endif
+
+#if !defined(SEEK_SET) && !defined(Z_SOLO)
+# define SEEK_SET 0 /* Seek from beginning of file. */
+# define SEEK_CUR 1 /* Seek from current position. */
+# define SEEK_END 2 /* Set file pointer to EOF plus "offset" */
+#endif
+
+#ifndef z_off_t
+# define z_off_t long
+#endif
+
+#if !defined(_WIN32) && defined(Z_LARGE64)
+# define z_off64_t off64_t
+#else
+# if defined(_WIN32) && !defined(__GNUC__) && !defined(Z_SOLO)
+# define z_off64_t __int64
+# else
+# define z_off64_t z_off_t
+# endif
+#endif
+
+/* MVS linker does not support external names larger than 8 bytes */
+#if defined(__MVS__)
+ #pragma map(deflateInit_,"DEIN")
+ #pragma map(deflateInit2_,"DEIN2")
+ #pragma map(deflateEnd,"DEEND")
+ #pragma map(deflateBound,"DEBND")
+ #pragma map(inflateInit_,"ININ")
+ #pragma map(inflateInit2_,"ININ2")
+ #pragma map(inflateEnd,"INEND")
+ #pragma map(inflateSync,"INSY")
+ #pragma map(inflateSetDictionary,"INSEDI")
+ #pragma map(compressBound,"CMBND")
+ #pragma map(inflate_table,"INTABL")
+ #pragma map(inflate_fast,"INFA")
+ #pragma map(inflate_copyright,"INCOPY")
+#endif
+
+#endif /* ZCONF_H */
diff --git a/third-party/zlib/zlib.3 b/third-party/zlib/zlib.3
new file mode 100644
index 0000000..0160e62
--- /dev/null
+++ b/third-party/zlib/zlib.3
@@ -0,0 +1,151 @@
+.TH ZLIB 3 "28 Apr 2013"
+.SH NAME
+zlib \- compression/decompression library
+.SH SYNOPSIS
+[see
+.I zlib.h
+for full description]
+.SH DESCRIPTION
+The
+.I zlib
+library is a general purpose data compression library.
+The code is thread safe, assuming that the standard library functions
+used are thread safe, such as memory allocation routines.
+It provides in-memory compression and decompression functions,
+including integrity checks of the uncompressed data.
+This version of the library supports only one compression method (deflation)
+but other algorithms may be added later
+with the same stream interface.
+.LP
+Compression can be done in a single step if the buffers are large enough
+or can be done by repeated calls of the compression function.
+In the latter case,
+the application must provide more input and/or consume the output
+(providing more output space) before each call.
+.LP
+The library also supports reading and writing files in
+.IR gzip (1)
+(.gz) format
+with an interface similar to that of stdio.
+.LP
+The library does not install any signal handler.
+The decoder checks the consistency of the compressed data,
+so the library should never crash even in the case of corrupted input.
+.LP
+All functions of the compression library are documented in the file
+.IR zlib.h .
+The distribution source includes examples of use of the library
+in the files
+.I test/example.c
+and
+.IR test/minigzip.c,
+as well as other examples in the
+.IR examples/
+directory.
+.LP
+Changes to this version are documented in the file
+.I ChangeLog
+that accompanies the source.
+.LP
+.I zlib
+is available in Java using the java.util.zip package:
+.IP
+http://java.sun.com/developer/technicalArticles/Programming/compression/
+.LP
+A Perl interface to
+.IR zlib ,
+written by Paul Marquess (pmqs at cpan.org),
+is available at CPAN (Comprehensive Perl Archive Network) sites,
+including:
+.IP
+http://search.cpan.org/~pmqs/IO-Compress-Zlib/
+.LP
+A Python interface to
+.IR zlib ,
+written by A.M. Kuchling (amk at magnet.com),
+is available in Python 1.5 and later versions:
+.IP
+http://docs.python.org/library/zlib.html
+.LP
+.I zlib
+is built into
+.IR tcl:
+.IP
+http://wiki.tcl.tk/4610
+.LP
+An experimental package to read and write files in .zip format,
+written on top of
+.I zlib
+by Gilles Vollant (info at winimage.com),
+is available at:
+.IP
+http://www.winimage.com/zLibDll/minizip.html
+and also in the
+.I contrib/minizip
+directory of the main
+.I zlib
+source distribution.
+.SH "SEE ALSO"
+The
+.I zlib
+web site can be found at:
+.IP
+http://zlib.net/
+.LP
+The data format used by the zlib library is described by RFC
+(Request for Comments) 1950 to 1952 in the files:
+.IP
+http://tools.ietf.org/html/rfc1950 (for the zlib header and trailer format)
+.br
+http://tools.ietf.org/html/rfc1951 (for the deflate compressed data format)
+.br
+http://tools.ietf.org/html/rfc1952 (for the gzip header and trailer format)
+.LP
+Mark Nelson wrote an article about
+.I zlib
+for the Jan. 1997 issue of Dr. Dobb's Journal;
+a copy of the article is available at:
+.IP
+http://marknelson.us/1997/01/01/zlib-engine/
+.SH "REPORTING PROBLEMS"
+Before reporting a problem,
+please check the
+.I zlib
+web site to verify that you have the latest version of
+.IR zlib ;
+otherwise,
+obtain the latest version and see if the problem still exists.
+Please read the
+.I zlib
+FAQ at:
+.IP
+http://zlib.net/zlib_faq.html
+.LP
+before asking for help.
+Send questions and/or comments to zlib at gzip.org,
+or (for the Windows DLL version) to Gilles Vollant (info at winimage.com).
+.SH AUTHORS
+Version 1.2.8
+Copyright (C) 1995-2013 Jean-loup Gailly (jloup at gzip.org)
+and Mark Adler (madler at alumni.caltech.edu).
+.LP
+This software is provided "as-is,"
+without any express or implied warranty.
+In no event will the authors be held liable for any damages
+arising from the use of this software.
+See the distribution directory with respect to requirements
+governing redistribution.
+The deflate format used by
+.I zlib
+was defined by Phil Katz.
+The deflate and
+.I zlib
+specifications were written by L. Peter Deutsch.
+Thanks to all the people who reported problems and suggested various
+improvements in
+.IR zlib ;
+who are too numerous to cite here.
+.LP
+UNIX manual page by R. P. C. Rodgers,
+U.S. National Library of Medicine (rodgers at nlm.nih.gov).
+.\" end of man page
diff --git a/third-party/zlib/zlib.3.pdf b/third-party/zlib/zlib.3.pdf
new file mode 100644
index 0000000..a346b5d
Binary files /dev/null and b/third-party/zlib/zlib.3.pdf differ
diff --git a/third-party/zlib/zlib.h b/third-party/zlib/zlib.h
new file mode 100644
index 0000000..3e0c767
--- /dev/null
+++ b/third-party/zlib/zlib.h
@@ -0,0 +1,1768 @@
+/* zlib.h -- interface of the 'zlib' general purpose compression library
+ version 1.2.8, April 28th, 2013
+
+ Copyright (C) 1995-2013 Jean-loup Gailly and Mark Adler
+
+ This software is provided 'as-is', without any express or implied
+ warranty. In no event will the authors be held liable for any damages
+ arising from the use of this software.
+
+ Permission is granted to anyone to use this software for any purpose,
+ including commercial applications, and to alter it and redistribute it
+ freely, subject to the following restrictions:
+
+ 1. The origin of this software must not be misrepresented; you must not
+ claim that you wrote the original software. If you use this software
+ in a product, an acknowledgment in the product documentation would be
+ appreciated but is not required.
+ 2. Altered source versions must be plainly marked as such, and must not be
+ misrepresented as being the original software.
+ 3. This notice may not be removed or altered from any source distribution.
+
+ Jean-loup Gailly Mark Adler
+ jloup at gzip.org madler at alumni.caltech.edu
+
+
+ The data format used by the zlib library is described by RFCs (Request for
+ Comments) 1950 to 1952 in the files http://tools.ietf.org/html/rfc1950
+ (zlib format), rfc1951 (deflate format) and rfc1952 (gzip format).
+*/
+
+#ifndef ZLIB_H
+#define ZLIB_H
+
+#include "zconf.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#define ZLIB_VERSION "1.2.8"
+#define ZLIB_VERNUM 0x1280
+#define ZLIB_VER_MAJOR 1
+#define ZLIB_VER_MINOR 2
+#define ZLIB_VER_REVISION 8
+#define ZLIB_VER_SUBREVISION 0
+
+/*
+ The 'zlib' compression library provides in-memory compression and
+ decompression functions, including integrity checks of the uncompressed data.
+ This version of the library supports only one compression method (deflation)
+ but other algorithms will be added later and will have the same stream
+ interface.
+
+ Compression can be done in a single step if the buffers are large enough,
+ or can be done by repeated calls of the compression function. In the latter
+ case, the application must provide more input and/or consume the output
+ (providing more output space) before each call.
+
+ The compressed data format used by default by the in-memory functions is
+ the zlib format, which is a zlib wrapper documented in RFC 1950, wrapped
+ around a deflate stream, which is itself documented in RFC 1951.
+
+ The library also supports reading and writing files in gzip (.gz) format
+ with an interface similar to that of stdio using the functions that start
+ with "gz". The gzip format is different from the zlib format. gzip is a
+ gzip wrapper, documented in RFC 1952, wrapped around a deflate stream.
+
+ This library can optionally read and write gzip streams in memory as well.
+
+ The zlib format was designed to be compact and fast for use in memory
+ and on communications channels. The gzip format was designed for single-
+ file compression on file systems, has a larger header than zlib to maintain
+ directory information, and uses a different, slower check method than zlib.
+
+ The library does not install any signal handler. The decoder checks
+ the consistency of the compressed data, so the library should never crash
+ even in case of corrupted input.
+*/
+
+typedef voidpf (*alloc_func) OF((voidpf opaque, uInt items, uInt size));
+typedef void (*free_func) OF((voidpf opaque, voidpf address));
+
+struct internal_state;
+
+typedef struct z_stream_s {
+ z_const Bytef *next_in; /* next input byte */
+ uInt avail_in; /* number of bytes available at next_in */
+ uLong total_in; /* total number of input bytes read so far */
+
+ Bytef *next_out; /* next output byte should be put there */
+ uInt avail_out; /* remaining free space at next_out */
+ uLong total_out; /* total number of bytes output so far */
+
+ z_const char *msg; /* last error message, NULL if no error */
+ struct internal_state FAR *state; /* not visible by applications */
+
+ alloc_func zalloc; /* used to allocate the internal state */
+ free_func zfree; /* used to free the internal state */
+ voidpf opaque; /* private data object passed to zalloc and zfree */
+
+ int data_type; /* best guess about the data type: binary or text */
+ uLong adler; /* adler32 value of the uncompressed data */
+ uLong reserved; /* reserved for future use */
+} z_stream;
+
+typedef z_stream FAR *z_streamp;
+
+/*
+ gzip header information passed to and from zlib routines. See RFC 1952
+ for more details on the meanings of these fields.
+*/
+typedef struct gz_header_s {
+ int text; /* true if compressed data believed to be text */
+ uLong time; /* modification time */
+ int xflags; /* extra flags (not used when writing a gzip file) */
+ int os; /* operating system */
+ Bytef *extra; /* pointer to extra field or Z_NULL if none */
+ uInt extra_len; /* extra field length (valid if extra != Z_NULL) */
+ uInt extra_max; /* space at extra (only when reading header) */
+ Bytef *name; /* pointer to zero-terminated file name or Z_NULL */
+ uInt name_max; /* space at name (only when reading header) */
+ Bytef *comment; /* pointer to zero-terminated comment or Z_NULL */
+ uInt comm_max; /* space at comment (only when reading header) */
+ int hcrc; /* true if there was or will be a header crc */
+ int done; /* true when done reading gzip header (not used
+ when writing a gzip file) */
+} gz_header;
+
+typedef gz_header FAR *gz_headerp;
+
+/*
+ The application must update next_in and avail_in when avail_in has dropped
+ to zero. It must update next_out and avail_out when avail_out has dropped
+ to zero. The application must initialize zalloc, zfree and opaque before
+ calling the init function. All other fields are set by the compression
+ library and must not be updated by the application.
+
+ The opaque value provided by the application will be passed as the first
+ parameter for calls of zalloc and zfree. This can be useful for custom
+ memory management. The compression library attaches no meaning to the
+ opaque value.
+
+ zalloc must return Z_NULL if there is not enough memory for the object.
+ If zlib is used in a multi-threaded application, zalloc and zfree must be
+ thread safe.
+
+ On 16-bit systems, the functions zalloc and zfree must be able to allocate
+ exactly 65536 bytes, but will not be required to allocate more than this if
+ the symbol MAXSEG_64K is defined (see zconf.h). WARNING: On MSDOS, pointers
+ returned by zalloc for objects of exactly 65536 bytes *must* have their
+ offset normalized to zero. The default allocation function provided by this
+ library ensures this (see zutil.c). To reduce memory requirements and avoid
+ any allocation of 64K objects, at the expense of compression ratio, compile
+ the library with -DMAX_WBITS=14 (see zconf.h).
+
+ The fields total_in and total_out can be used for statistics or progress
+ reports. After compression, total_in holds the total size of the
+ uncompressed data and may be saved for use in the decompressor (particularly
+ if the decompressor wants to decompress everything in a single step).
+*/
+
+ /* constants */
+
+#define Z_NO_FLUSH 0
+#define Z_PARTIAL_FLUSH 1
+#define Z_SYNC_FLUSH 2
+#define Z_FULL_FLUSH 3
+#define Z_FINISH 4
+#define Z_BLOCK 5
+#define Z_TREES 6
+/* Allowed flush values; see deflate() and inflate() below for details */
+
+#define Z_OK 0
+#define Z_STREAM_END 1
+#define Z_NEED_DICT 2
+#define Z_ERRNO (-1)
+#define Z_STREAM_ERROR (-2)
+#define Z_DATA_ERROR (-3)
+#define Z_MEM_ERROR (-4)
+#define Z_BUF_ERROR (-5)
+#define Z_VERSION_ERROR (-6)
+/* Return codes for the compression/decompression functions. Negative values
+ * are errors, positive values are used for special but normal events.
+ */
+
+#define Z_NO_COMPRESSION 0
+#define Z_BEST_SPEED 1
+#define Z_BEST_COMPRESSION 9
+#define Z_DEFAULT_COMPRESSION (-1)
+/* compression levels */
+
+#define Z_FILTERED 1
+#define Z_HUFFMAN_ONLY 2
+#define Z_RLE 3
+#define Z_FIXED 4
+#define Z_DEFAULT_STRATEGY 0
+/* compression strategy; see deflateInit2() below for details */
+
+#define Z_BINARY 0
+#define Z_TEXT 1
+#define Z_ASCII Z_TEXT /* for compatibility with 1.2.2 and earlier */
+#define Z_UNKNOWN 2
+/* Possible values of the data_type field (though see inflate()) */
+
+#define Z_DEFLATED 8
+/* The deflate compression method (the only one supported in this version) */
+
+#define Z_NULL 0 /* for initializing zalloc, zfree, opaque */
+
+#define zlib_version zlibVersion()
+/* for compatibility with versions < 1.0.2 */
+
+
+ /* basic functions */
+
+ZEXTERN const char * ZEXPORT zlibVersion OF((void));
+/* The application can compare zlibVersion and ZLIB_VERSION for consistency.
+ If the first character differs, the library code actually used is not
+ compatible with the zlib.h header file used by the application. This check
+ is automatically made by deflateInit and inflateInit.
+ */
+
+/*
+ZEXTERN int ZEXPORT deflateInit OF((z_streamp strm, int level));
+
+ Initializes the internal stream state for compression. The fields
+ zalloc, zfree and opaque must be initialized before by the caller. If
+ zalloc and zfree are set to Z_NULL, deflateInit updates them to use default
+ allocation functions.
+
+ The compression level must be Z_DEFAULT_COMPRESSION, or between 0 and 9:
+ 1 gives best speed, 9 gives best compression, 0 gives no compression at all
+ (the input data is simply copied a block at a time). Z_DEFAULT_COMPRESSION
+ requests a default compromise between speed and compression (currently
+ equivalent to level 6).
+
+ deflateInit returns Z_OK if success, Z_MEM_ERROR if there was not enough
+ memory, Z_STREAM_ERROR if level is not a valid compression level, or
+ Z_VERSION_ERROR if the zlib library version (zlib_version) is incompatible
+ with the version assumed by the caller (ZLIB_VERSION). msg is set to null
+ if there is no error message. deflateInit does not perform any compression:
+ this will be done by deflate().
+*/
+
+
+ZEXTERN int ZEXPORT deflate OF((z_streamp strm, int flush));
+/*
+ deflate compresses as much data as possible, and stops when the input
+ buffer becomes empty or the output buffer becomes full. It may introduce
+ some output latency (reading input without producing any output) except when
+ forced to flush.
+
+ The detailed semantics are as follows. deflate performs one or both of the
+ following actions:
+
+ - Compress more input starting at next_in and update next_in and avail_in
+ accordingly. If not all input can be processed (because there is not
+ enough room in the output buffer), next_in and avail_in are updated and
+ processing will resume at this point for the next call of deflate().
+
+ - Provide more output starting at next_out and update next_out and avail_out
+ accordingly. This action is forced if the parameter flush is non zero.
+ Forcing flush frequently degrades the compression ratio, so this parameter
+ should be set only when necessary (in interactive applications). Some
+ output may be provided even if flush is not set.
+
+ Before the call of deflate(), the application should ensure that at least
+ one of the actions is possible, by providing more input and/or consuming more
+ output, and updating avail_in or avail_out accordingly; avail_out should
+ never be zero before the call. The application can consume the compressed
+ output when it wants, for example when the output buffer is full (avail_out
+ == 0), or after each call of deflate(). If deflate returns Z_OK and with
+ zero avail_out, it must be called again after making room in the output
+ buffer because there might be more output pending.
+
+ Normally the parameter flush is set to Z_NO_FLUSH, which allows deflate to
+ decide how much data to accumulate before producing output, in order to
+ maximize compression.
+
+ If the parameter flush is set to Z_SYNC_FLUSH, all pending output is
+ flushed to the output buffer and the output is aligned on a byte boundary, so
+ that the decompressor can get all input data available so far. (In
+ particular avail_in is zero after the call if enough output space has been
+ provided before the call.) Flushing may degrade compression for some
+ compression algorithms and so it should be used only when necessary. This
+ completes the current deflate block and follows it with an empty stored block
+ that is three bits plus filler bits to the next byte, followed by four bytes
+ (00 00 ff ff).
+
+ If flush is set to Z_PARTIAL_FLUSH, all pending output is flushed to the
+ output buffer, but the output is not aligned to a byte boundary. All of the
+ input data so far will be available to the decompressor, as for Z_SYNC_FLUSH.
+ This completes the current deflate block and follows it with an empty fixed
+ codes block that is 10 bits long. This assures that enough bytes are output
+ in order for the decompressor to finish the block before the empty fixed code
+ block.
+
+ If flush is set to Z_BLOCK, a deflate block is completed and emitted, as
+ for Z_SYNC_FLUSH, but the output is not aligned on a byte boundary, and up to
+ seven bits of the current block are held to be written as the next byte after
+ the next deflate block is completed. In this case, the decompressor may not
+ be provided enough bits at this point in order to complete decompression of
+ the data provided so far to the compressor. It may need to wait for the next
+ block to be emitted. This is for advanced applications that need to control
+ the emission of deflate blocks.
+
+ If flush is set to Z_FULL_FLUSH, all output is flushed as with
+ Z_SYNC_FLUSH, and the compression state is reset so that decompression can
+ restart from this point if previous compressed data has been damaged or if
+ random access is desired. Using Z_FULL_FLUSH too often can seriously degrade
+ compression.
+
+ If deflate returns with avail_out == 0, this function must be called again
+ with the same value of the flush parameter and more output space (updated
+ avail_out), until the flush is complete (deflate returns with non-zero
+ avail_out). In the case of a Z_FULL_FLUSH or Z_SYNC_FLUSH, make sure that
+ avail_out is greater than six to avoid repeated flush markers due to
+ avail_out == 0 on return.
+
+ If the parameter flush is set to Z_FINISH, pending input is processed,
+ pending output is flushed and deflate returns with Z_STREAM_END if there was
+ enough output space; if deflate returns with Z_OK, this function must be
+ called again with Z_FINISH and more output space (updated avail_out) but no
+ more input data, until it returns with Z_STREAM_END or an error. After
+ deflate has returned Z_STREAM_END, the only possible operations on the stream
+ are deflateReset or deflateEnd.
+
+ Z_FINISH can be used immediately after deflateInit if all the compression
+ is to be done in a single step. In this case, avail_out must be at least the
+ value returned by deflateBound (see below). Then deflate is guaranteed to
+ return Z_STREAM_END. If not enough output space is provided, deflate will
+ not return Z_STREAM_END, and it must be called again as described above.
+
+ deflate() sets strm->adler to the adler32 checksum of all input read
+ so far (that is, total_in bytes).
+
+ deflate() may update strm->data_type if it can make a good guess about
+ the input data type (Z_BINARY or Z_TEXT). In doubt, the data is considered
+ binary. This field is only for information purposes and does not affect the
+ compression algorithm in any manner.
+
+ deflate() returns Z_OK if some progress has been made (more input
+ processed or more output produced), Z_STREAM_END if all input has been
+ consumed and all output has been produced (only when flush is set to
+ Z_FINISH), Z_STREAM_ERROR if the stream state was inconsistent (for example
+ if next_in or next_out was Z_NULL), Z_BUF_ERROR if no progress is possible
+ (for example avail_in or avail_out was zero). Note that Z_BUF_ERROR is not
+ fatal, and deflate() can be called again with more input and more output
+ space to continue compressing.
+*/
+
+
+ZEXTERN int ZEXPORT deflateEnd OF((z_streamp strm));
+/*
+ All dynamically allocated data structures for this stream are freed.
+ This function discards any unprocessed input and does not flush any pending
+ output.
+
+ deflateEnd returns Z_OK if success, Z_STREAM_ERROR if the
+ stream state was inconsistent, Z_DATA_ERROR if the stream was freed
+ prematurely (some input or output was discarded). In the error case, msg
+ may be set but then points to a static string (which must not be
+ deallocated).
+*/
+
+
+/*
+ZEXTERN int ZEXPORT inflateInit OF((z_streamp strm));
+
+ Initializes the internal stream state for decompression. The fields
+ next_in, avail_in, zalloc, zfree and opaque must be initialized before by
+ the caller. If next_in is not Z_NULL and avail_in is large enough (the
+ exact value depends on the compression method), inflateInit determines the
+ compression method from the zlib header and allocates all data structures
+ accordingly; otherwise the allocation will be deferred to the first call of
+ inflate. If zalloc and zfree are set to Z_NULL, inflateInit updates them to
+ use default allocation functions.
+
+ inflateInit returns Z_OK if success, Z_MEM_ERROR if there was not enough
+ memory, Z_VERSION_ERROR if the zlib library version is incompatible with the
+ version assumed by the caller, or Z_STREAM_ERROR if the parameters are
+ invalid, such as a null pointer to the structure. msg is set to null if
+ there is no error message. inflateInit does not perform any decompression
+ apart from possibly reading the zlib header if present: actual decompression
+ will be done by inflate(). (So next_in and avail_in may be modified, but
+ next_out and avail_out are unused and unchanged.) The current implementation
+ of inflateInit() does not process any header information -- that is deferred
+ until inflate() is called.
+*/
+
+
+ZEXTERN int ZEXPORT inflate OF((z_streamp strm, int flush));
+/*
+ inflate decompresses as much data as possible, and stops when the input
+ buffer becomes empty or the output buffer becomes full. It may introduce
+ some output latency (reading input without producing any output) except when
+ forced to flush.
+
+ The detailed semantics are as follows. inflate performs one or both of the
+ following actions:
+
+ - Decompress more input starting at next_in and update next_in and avail_in
+ accordingly. If not all input can be processed (because there is not
+ enough room in the output buffer), next_in is updated and processing will
+ resume at this point for the next call of inflate().
+
+ - Provide more output starting at next_out and update next_out and avail_out
+ accordingly. inflate() provides as much output as possible, until there is
+ no more input data or no more space in the output buffer (see below about
+ the flush parameter).
+
+ Before the call of inflate(), the application should ensure that at least
+ one of the actions is possible, by providing more input and/or consuming more
+ output, and updating the next_* and avail_* values accordingly. The
+ application can consume the uncompressed output when it wants, for example
+ when the output buffer is full (avail_out == 0), or after each call of
+ inflate(). If inflate returns Z_OK and with zero avail_out, it must be
+ called again after making room in the output buffer because there might be
+ more output pending.
+
+ The flush parameter of inflate() can be Z_NO_FLUSH, Z_SYNC_FLUSH, Z_FINISH,
+ Z_BLOCK, or Z_TREES. Z_SYNC_FLUSH requests that inflate() flush as much
+ output as possible to the output buffer. Z_BLOCK requests that inflate()
+ stop if and when it gets to the next deflate block boundary. When decoding
+ the zlib or gzip format, this will cause inflate() to return immediately
+ after the header and before the first block. When doing a raw inflate,
+ inflate() will go ahead and process the first block, and will return when it
+ gets to the end of that block, or when it runs out of data.
+
+ The Z_BLOCK option assists in appending to or combining deflate streams.
+ Also to assist in this, on return inflate() will set strm->data_type to the
+ number of unused bits in the last byte taken from strm->next_in, plus 64 if
+ inflate() is currently decoding the last block in the deflate stream, plus
+ 128 if inflate() returned immediately after decoding an end-of-block code or
+ decoding the complete header up to just before the first byte of the deflate
+ stream. The end-of-block will not be indicated until all of the uncompressed
+ data from that block has been written to strm->next_out. The number of
+ unused bits may in general be greater than seven, except when bit 7 of
+ data_type is set, in which case the number of unused bits will be less than
+ eight. data_type is set as noted here every time inflate() returns for all
+ flush options, and so can be used to determine the amount of currently
+ consumed input in bits.
+
+ The Z_TREES option behaves as Z_BLOCK does, but it also returns when the
+ end of each deflate block header is reached, before any actual data in that
+ block is decoded. This allows the caller to determine the length of the
+ deflate block header for later use in random access within a deflate block.
+ 256 is added to the value of strm->data_type when inflate() returns
+ immediately after reaching the end of the deflate block header.
+
+ inflate() should normally be called until it returns Z_STREAM_END or an
+ error. However if all decompression is to be performed in a single step (a
+ single call of inflate), the parameter flush should be set to Z_FINISH. In
+ this case all pending input is processed and all pending output is flushed;
+ avail_out must be large enough to hold all of the uncompressed data for the
+ operation to complete. (The size of the uncompressed data may have been
+ saved by the compressor for this purpose.) The use of Z_FINISH is not
+ required to perform an inflation in one step. However it may be used to
+ inform inflate that a faster approach can be used for the single inflate()
+ call. Z_FINISH also informs inflate to not maintain a sliding window if the
+ stream completes, which reduces inflate's memory footprint. If the stream
+ does not complete, either because not all of the stream is provided or not
+ enough output space is provided, then a sliding window will be allocated and
+ inflate() can be called again to continue the operation as if Z_NO_FLUSH had
+ been used.
+
+ In this implementation, inflate() always flushes as much output as
+ possible to the output buffer, and always uses the faster approach on the
+ first call. So the effects of the flush parameter in this implementation are
+ on the return value of inflate() as noted below, when inflate() returns early
+ when Z_BLOCK or Z_TREES is used, and when inflate() avoids the allocation of
+ memory for a sliding window when Z_FINISH is used.
+
+ If a preset dictionary is needed after this call (see inflateSetDictionary
+ below), inflate sets strm->adler to the Adler-32 checksum of the dictionary
+ chosen by the compressor and returns Z_NEED_DICT; otherwise it sets
+ strm->adler to the Adler-32 checksum of all output produced so far (that is,
+ total_out bytes) and returns Z_OK, Z_STREAM_END or an error code as described
+ below. At the end of the stream, inflate() checks that its computed adler32
+ checksum is equal to that saved by the compressor and returns Z_STREAM_END
+ only if the checksum is correct.
+
+ inflate() can decompress and check either zlib-wrapped or gzip-wrapped
+ deflate data. The header type is detected automatically, if requested when
+ initializing with inflateInit2(). Any information contained in the gzip
+ header is not retained, so applications that need that information should
+ instead use raw inflate, see inflateInit2() below, or inflateBack() and
+ perform their own processing of the gzip header and trailer. When processing
+ gzip-wrapped deflate data, strm->adler32 is set to the CRC-32 of the output
+ producted so far. The CRC-32 is checked against the gzip trailer.
+
+ inflate() returns Z_OK if some progress has been made (more input processed
+ or more output produced), Z_STREAM_END if the end of the compressed data has
+ been reached and all uncompressed output has been produced, Z_NEED_DICT if a
+ preset dictionary is needed at this point, Z_DATA_ERROR if the input data was
+ corrupted (input stream not conforming to the zlib format or incorrect check
+ value), Z_STREAM_ERROR if the stream structure was inconsistent (for example
+ next_in or next_out was Z_NULL), Z_MEM_ERROR if there was not enough memory,
+ Z_BUF_ERROR if no progress is possible or if there was not enough room in the
+ output buffer when Z_FINISH is used. Note that Z_BUF_ERROR is not fatal, and
+ inflate() can be called again with more input and more output space to
+ continue decompressing. If Z_DATA_ERROR is returned, the application may
+ then call inflateSync() to look for a good compression block if a partial
+ recovery of the data is desired.
+*/
+
+
+ZEXTERN int ZEXPORT inflateEnd OF((z_streamp strm));
+/*
+ All dynamically allocated data structures for this stream are freed.
+ This function discards any unprocessed input and does not flush any pending
+ output.
+
+ inflateEnd returns Z_OK if success, Z_STREAM_ERROR if the stream state
+ was inconsistent. In the error case, msg may be set but then points to a
+ static string (which must not be deallocated).
+*/
+
+
+ /* Advanced functions */
+
+/*
+ The following functions are needed only in some special applications.
+*/
+
+/*
+ZEXTERN int ZEXPORT deflateInit2 OF((z_streamp strm,
+ int level,
+ int method,
+ int windowBits,
+ int memLevel,
+ int strategy));
+
+ This is another version of deflateInit with more compression options. The
+ fields next_in, zalloc, zfree and opaque must be initialized before by the
+ caller.
+
+ The method parameter is the compression method. It must be Z_DEFLATED in
+ this version of the library.
+
+ The windowBits parameter is the base two logarithm of the window size
+ (the size of the history buffer). It should be in the range 8..15 for this
+ version of the library. Larger values of this parameter result in better
+ compression at the expense of memory usage. The default value is 15 if
+ deflateInit is used instead.
+
+ windowBits can also be -8..-15 for raw deflate. In this case, -windowBits
+ determines the window size. deflate() will then generate raw deflate data
+ with no zlib header or trailer, and will not compute an adler32 check value.
+
+ windowBits can also be greater than 15 for optional gzip encoding. Add
+ 16 to windowBits to write a simple gzip header and trailer around the
+ compressed data instead of a zlib wrapper. The gzip header will have no
+ file name, no extra data, no comment, no modification time (set to zero), no
+ header crc, and the operating system will be set to 255 (unknown). If a
+ gzip stream is being written, strm->adler is a crc32 instead of an adler32.
+
+ The memLevel parameter specifies how much memory should be allocated
+ for the internal compression state. memLevel=1 uses minimum memory but is
+ slow and reduces compression ratio; memLevel=9 uses maximum memory for
+ optimal speed. The default value is 8. See zconf.h for total memory usage
+ as a function of windowBits and memLevel.
+
+ The strategy parameter is used to tune the compression algorithm. Use the
+ value Z_DEFAULT_STRATEGY for normal data, Z_FILTERED for data produced by a
+ filter (or predictor), Z_HUFFMAN_ONLY to force Huffman encoding only (no
+ string match), or Z_RLE to limit match distances to one (run-length
+ encoding). Filtered data consists mostly of small values with a somewhat
+ random distribution. In this case, the compression algorithm is tuned to
+ compress them better. The effect of Z_FILTERED is to force more Huffman
+ coding and less string matching; it is somewhat intermediate between
+ Z_DEFAULT_STRATEGY and Z_HUFFMAN_ONLY. Z_RLE is designed to be almost as
+ fast as Z_HUFFMAN_ONLY, but give better compression for PNG image data. The
+ strategy parameter only affects the compression ratio but not the
+ correctness of the compressed output even if it is not set appropriately.
+ Z_FIXED prevents the use of dynamic Huffman codes, allowing for a simpler
+ decoder for special applications.
+
+ deflateInit2 returns Z_OK if success, Z_MEM_ERROR if there was not enough
+ memory, Z_STREAM_ERROR if any parameter is invalid (such as an invalid
+ method), or Z_VERSION_ERROR if the zlib library version (zlib_version) is
+ incompatible with the version assumed by the caller (ZLIB_VERSION). msg is
+ set to null if there is no error message. deflateInit2 does not perform any
+ compression: this will be done by deflate().
+*/
+
+ZEXTERN int ZEXPORT deflateSetDictionary OF((z_streamp strm,
+ const Bytef *dictionary,
+ uInt dictLength));
+/*
+ Initializes the compression dictionary from the given byte sequence
+ without producing any compressed output. When using the zlib format, this
+ function must be called immediately after deflateInit, deflateInit2 or
+ deflateReset, and before any call of deflate. When doing raw deflate, this
+ function must be called either before any call of deflate, or immediately
+ after the completion of a deflate block, i.e. after all input has been
+ consumed and all output has been delivered when using any of the flush
+ options Z_BLOCK, Z_PARTIAL_FLUSH, Z_SYNC_FLUSH, or Z_FULL_FLUSH. The
+ compressor and decompressor must use exactly the same dictionary (see
+ inflateSetDictionary).
+
+ The dictionary should consist of strings (byte sequences) that are likely
+ to be encountered later in the data to be compressed, with the most commonly
+ used strings preferably put towards the end of the dictionary. Using a
+ dictionary is most useful when the data to be compressed is short and can be
+ predicted with good accuracy; the data can then be compressed better than
+ with the default empty dictionary.
+
+ Depending on the size of the compression data structures selected by
+ deflateInit or deflateInit2, a part of the dictionary may in effect be
+ discarded, for example if the dictionary is larger than the window size
+ provided in deflateInit or deflateInit2. Thus the strings most likely to be
+ useful should be put at the end of the dictionary, not at the front. In
+ addition, the current implementation of deflate will use at most the window
+ size minus 262 bytes of the provided dictionary.
+
+ Upon return of this function, strm->adler is set to the adler32 value
+ of the dictionary; the decompressor may later use this value to determine
+ which dictionary has been used by the compressor. (The adler32 value
+ applies to the whole dictionary even if only a subset of the dictionary is
+ actually used by the compressor.) If a raw deflate was requested, then the
+ adler32 value is not computed and strm->adler is not set.
+
+ deflateSetDictionary returns Z_OK if success, or Z_STREAM_ERROR if a
+ parameter is invalid (e.g. dictionary being Z_NULL) or the stream state is
+ inconsistent (for example if deflate has already been called for this stream
+ or if not at a block boundary for raw deflate). deflateSetDictionary does
+ not perform any compression: this will be done by deflate().
+*/
+
+ZEXTERN int ZEXPORT deflateCopy OF((z_streamp dest,
+ z_streamp source));
+/*
+ Sets the destination stream as a complete copy of the source stream.
+
+ This function can be useful when several compression strategies will be
+ tried, for example when there are several ways of pre-processing the input
+ data with a filter. The streams that will be discarded should then be freed
+ by calling deflateEnd. Note that deflateCopy duplicates the internal
+ compression state which can be quite large, so this strategy is slow and can
+ consume lots of memory.
+
+ deflateCopy returns Z_OK if success, Z_MEM_ERROR if there was not
+ enough memory, Z_STREAM_ERROR if the source stream state was inconsistent
+ (such as zalloc being Z_NULL). msg is left unchanged in both source and
+ destination.
+*/
+
+ZEXTERN int ZEXPORT deflateReset OF((z_streamp strm));
+/*
+ This function is equivalent to deflateEnd followed by deflateInit,
+ but does not free and reallocate all the internal compression state. The
+ stream will keep the same compression level and any other attributes that
+ may have been set by deflateInit2.
+
+ deflateReset returns Z_OK if success, or Z_STREAM_ERROR if the source
+ stream state was inconsistent (such as zalloc or state being Z_NULL).
+*/
+
+ZEXTERN int ZEXPORT deflateParams OF((z_streamp strm,
+ int level,
+ int strategy));
+/*
+ Dynamically update the compression level and compression strategy. The
+ interpretation of level and strategy is as in deflateInit2. This can be
+ used to switch between compression and straight copy of the input data, or
+ to switch to a different kind of input data requiring a different strategy.
+ If the compression level is changed, the input available so far is
+ compressed with the old level (and may be flushed); the new level will take
+ effect only at the next call of deflate().
+
+ Before the call of deflateParams, the stream state must be set as for
+ a call of deflate(), since the currently available input may have to be
+ compressed and flushed. In particular, strm->avail_out must be non-zero.
+
+ deflateParams returns Z_OK if success, Z_STREAM_ERROR if the source
+ stream state was inconsistent or if a parameter was invalid, Z_BUF_ERROR if
+ strm->avail_out was zero.
+*/
+
+ZEXTERN int ZEXPORT deflateTune OF((z_streamp strm,
+ int good_length,
+ int max_lazy,
+ int nice_length,
+ int max_chain));
+/*
+ Fine tune deflate's internal compression parameters. This should only be
+ used by someone who understands the algorithm used by zlib's deflate for
+ searching for the best matching string, and even then only by the most
+ fanatic optimizer trying to squeeze out the last compressed bit for their
+ specific input data. Read the deflate.c source code for the meaning of the
+ max_lazy, good_length, nice_length, and max_chain parameters.
+
+ deflateTune() can be called after deflateInit() or deflateInit2(), and
+ returns Z_OK on success, or Z_STREAM_ERROR for an invalid deflate stream.
+ */
+
+ZEXTERN uLong ZEXPORT deflateBound OF((z_streamp strm,
+ uLong sourceLen));
+/*
+ deflateBound() returns an upper bound on the compressed size after
+ deflation of sourceLen bytes. It must be called after deflateInit() or
+ deflateInit2(), and after deflateSetHeader(), if used. This would be used
+ to allocate an output buffer for deflation in a single pass, and so would be
+ called before deflate(). If that first deflate() call is provided the
+ sourceLen input bytes, an output buffer allocated to the size returned by
+ deflateBound(), and the flush value Z_FINISH, then deflate() is guaranteed
+ to return Z_STREAM_END. Note that it is possible for the compressed size to
+ be larger than the value returned by deflateBound() if flush options other
+ than Z_FINISH or Z_NO_FLUSH are used.
+*/
+
+ZEXTERN int ZEXPORT deflatePending OF((z_streamp strm,
+ unsigned *pending,
+ int *bits));
+/*
+ deflatePending() returns the number of bytes and bits of output that have
+ been generated, but not yet provided in the available output. The bytes not
+ provided would be due to the available output space having being consumed.
+ The number of bits of output not provided are between 0 and 7, where they
+ await more bits to join them in order to fill out a full byte. If pending
+ or bits are Z_NULL, then those values are not set.
+
+ deflatePending returns Z_OK if success, or Z_STREAM_ERROR if the source
+ stream state was inconsistent.
+ */
+
+ZEXTERN int ZEXPORT deflatePrime OF((z_streamp strm,
+ int bits,
+ int value));
+/*
+ deflatePrime() inserts bits in the deflate output stream. The intent
+ is that this function is used to start off the deflate output with the bits
+ leftover from a previous deflate stream when appending to it. As such, this
+ function can only be used for raw deflate, and must be used before the first
+ deflate() call after a deflateInit2() or deflateReset(). bits must be less
+ than or equal to 16, and that many of the least significant bits of value
+ will be inserted in the output.
+
+ deflatePrime returns Z_OK if success, Z_BUF_ERROR if there was not enough
+ room in the internal buffer to insert the bits, or Z_STREAM_ERROR if the
+ source stream state was inconsistent.
+*/
+
+ZEXTERN int ZEXPORT deflateSetHeader OF((z_streamp strm,
+ gz_headerp head));
+/*
+ deflateSetHeader() provides gzip header information for when a gzip
+ stream is requested by deflateInit2(). deflateSetHeader() may be called
+ after deflateInit2() or deflateReset() and before the first call of
+ deflate(). The text, time, os, extra field, name, and comment information
+ in the provided gz_header structure are written to the gzip header (xflag is
+ ignored -- the extra flags are set according to the compression level). The
+ caller must assure that, if not Z_NULL, name and comment are terminated with
+ a zero byte, and that if extra is not Z_NULL, that extra_len bytes are
+ available there. If hcrc is true, a gzip header crc is included. Note that
+ the current versions of the command-line version of gzip (up through version
+ 1.3.x) do not support header crc's, and will report that it is a "multi-part
+ gzip file" and give up.
+
+ If deflateSetHeader is not used, the default gzip header has text false,
+ the time set to zero, and os set to 255, with no extra, name, or comment
+ fields. The gzip header is returned to the default state by deflateReset().
+
+ deflateSetHeader returns Z_OK if success, or Z_STREAM_ERROR if the source
+ stream state was inconsistent.
+*/
+
+/*
+ZEXTERN int ZEXPORT inflateInit2 OF((z_streamp strm,
+ int windowBits));
+
+ This is another version of inflateInit with an extra parameter. The
+ fields next_in, avail_in, zalloc, zfree and opaque must be initialized
+ before by the caller.
+
+ The windowBits parameter is the base two logarithm of the maximum window
+ size (the size of the history buffer). It should be in the range 8..15 for
+ this version of the library. The default value is 15 if inflateInit is used
+ instead. windowBits must be greater than or equal to the windowBits value
+ provided to deflateInit2() while compressing, or it must be equal to 15 if
+ deflateInit2() was not used. If a compressed stream with a larger window
+ size is given as input, inflate() will return with the error code
+ Z_DATA_ERROR instead of trying to allocate a larger window.
+
+ windowBits can also be zero to request that inflate use the window size in
+ the zlib header of the compressed stream.
+
+ windowBits can also be -8..-15 for raw inflate. In this case, -windowBits
+ determines the window size. inflate() will then process raw deflate data,
+ not looking for a zlib or gzip header, not generating a check value, and not
+ looking for any check values for comparison at the end of the stream. This
+ is for use with other formats that use the deflate compressed data format
+ such as zip. Those formats provide their own check values. If a custom
+ format is developed using the raw deflate format for compressed data, it is
+ recommended that a check value such as an adler32 or a crc32 be applied to
+ the uncompressed data as is done in the zlib, gzip, and zip formats. For
+ most applications, the zlib format should be used as is. Note that comments
+ above on the use in deflateInit2() applies to the magnitude of windowBits.
+
+ windowBits can also be greater than 15 for optional gzip decoding. Add
+ 32 to windowBits to enable zlib and gzip decoding with automatic header
+ detection, or add 16 to decode only the gzip format (the zlib format will
+ return a Z_DATA_ERROR). If a gzip stream is being decoded, strm->adler is a
+ crc32 instead of an adler32.
+
+ inflateInit2 returns Z_OK if success, Z_MEM_ERROR if there was not enough
+ memory, Z_VERSION_ERROR if the zlib library version is incompatible with the
+ version assumed by the caller, or Z_STREAM_ERROR if the parameters are
+ invalid, such as a null pointer to the structure. msg is set to null if
+ there is no error message. inflateInit2 does not perform any decompression
+ apart from possibly reading the zlib header if present: actual decompression
+ will be done by inflate(). (So next_in and avail_in may be modified, but
+ next_out and avail_out are unused and unchanged.) The current implementation
+ of inflateInit2() does not process any header information -- that is
+ deferred until inflate() is called.
+*/
+
+ZEXTERN int ZEXPORT inflateSetDictionary OF((z_streamp strm,
+ const Bytef *dictionary,
+ uInt dictLength));
+/*
+ Initializes the decompression dictionary from the given uncompressed byte
+ sequence. This function must be called immediately after a call of inflate,
+ if that call returned Z_NEED_DICT. The dictionary chosen by the compressor
+ can be determined from the adler32 value returned by that call of inflate.
+ The compressor and decompressor must use exactly the same dictionary (see
+ deflateSetDictionary). For raw inflate, this function can be called at any
+ time to set the dictionary. If the provided dictionary is smaller than the
+ window and there is already data in the window, then the provided dictionary
+ will amend what's there. The application must insure that the dictionary
+ that was used for compression is provided.
+
+ inflateSetDictionary returns Z_OK if success, Z_STREAM_ERROR if a
+ parameter is invalid (e.g. dictionary being Z_NULL) or the stream state is
+ inconsistent, Z_DATA_ERROR if the given dictionary doesn't match the
+ expected one (incorrect adler32 value). inflateSetDictionary does not
+ perform any decompression: this will be done by subsequent calls of
+ inflate().
+*/
+
+ZEXTERN int ZEXPORT inflateGetDictionary OF((z_streamp strm,
+ Bytef *dictionary,
+ uInt *dictLength));
+/*
+ Returns the sliding dictionary being maintained by inflate. dictLength is
+ set to the number of bytes in the dictionary, and that many bytes are copied
+ to dictionary. dictionary must have enough space, where 32768 bytes is
+ always enough. If inflateGetDictionary() is called with dictionary equal to
+ Z_NULL, then only the dictionary length is returned, and nothing is copied.
+ Similary, if dictLength is Z_NULL, then it is not set.
+
+ inflateGetDictionary returns Z_OK on success, or Z_STREAM_ERROR if the
+ stream state is inconsistent.
+*/
+
+ZEXTERN int ZEXPORT inflateSync OF((z_streamp strm));
+/*
+ Skips invalid compressed data until a possible full flush point (see above
+ for the description of deflate with Z_FULL_FLUSH) can be found, or until all
+ available input is skipped. No output is provided.
+
+ inflateSync searches for a 00 00 FF FF pattern in the compressed data.
+ All full flush points have this pattern, but not all occurrences of this
+ pattern are full flush points.
+
+ inflateSync returns Z_OK if a possible full flush point has been found,
+ Z_BUF_ERROR if no more input was provided, Z_DATA_ERROR if no flush point
+ has been found, or Z_STREAM_ERROR if the stream structure was inconsistent.
+ In the success case, the application may save the current current value of
+ total_in which indicates where valid compressed data was found. In the
+ error case, the application may repeatedly call inflateSync, providing more
+ input each time, until success or end of the input data.
+*/
+
+ZEXTERN int ZEXPORT inflateCopy OF((z_streamp dest,
+ z_streamp source));
+/*
+ Sets the destination stream as a complete copy of the source stream.
+
+ This function can be useful when randomly accessing a large stream. The
+ first pass through the stream can periodically record the inflate state,
+ allowing restarting inflate at those points when randomly accessing the
+ stream.
+
+ inflateCopy returns Z_OK if success, Z_MEM_ERROR if there was not
+ enough memory, Z_STREAM_ERROR if the source stream state was inconsistent
+ (such as zalloc being Z_NULL). msg is left unchanged in both source and
+ destination.
+*/
+
+ZEXTERN int ZEXPORT inflateReset OF((z_streamp strm));
+/*
+ This function is equivalent to inflateEnd followed by inflateInit,
+ but does not free and reallocate all the internal decompression state. The
+ stream will keep attributes that may have been set by inflateInit2.
+
+ inflateReset returns Z_OK if success, or Z_STREAM_ERROR if the source
+ stream state was inconsistent (such as zalloc or state being Z_NULL).
+*/
+
+ZEXTERN int ZEXPORT inflateReset2 OF((z_streamp strm,
+ int windowBits));
+/*
+ This function is the same as inflateReset, but it also permits changing
+ the wrap and window size requests. The windowBits parameter is interpreted
+ the same as it is for inflateInit2.
+
+ inflateReset2 returns Z_OK if success, or Z_STREAM_ERROR if the source
+ stream state was inconsistent (such as zalloc or state being Z_NULL), or if
+ the windowBits parameter is invalid.
+*/
+
+ZEXTERN int ZEXPORT inflatePrime OF((z_streamp strm,
+ int bits,
+ int value));
+/*
+ This function inserts bits in the inflate input stream. The intent is
+ that this function is used to start inflating at a bit position in the
+ middle of a byte. The provided bits will be used before any bytes are used
+ from next_in. This function should only be used with raw inflate, and
+ should be used before the first inflate() call after inflateInit2() or
+ inflateReset(). bits must be less than or equal to 16, and that many of the
+ least significant bits of value will be inserted in the input.
+
+ If bits is negative, then the input stream bit buffer is emptied. Then
+ inflatePrime() can be called again to put bits in the buffer. This is used
+ to clear out bits leftover after feeding inflate a block description prior
+ to feeding inflate codes.
+
+ inflatePrime returns Z_OK if success, or Z_STREAM_ERROR if the source
+ stream state was inconsistent.
+*/
+
+ZEXTERN long ZEXPORT inflateMark OF((z_streamp strm));
+/*
+ This function returns two values, one in the lower 16 bits of the return
+ value, and the other in the remaining upper bits, obtained by shifting the
+ return value down 16 bits. If the upper value is -1 and the lower value is
+ zero, then inflate() is currently decoding information outside of a block.
+ If the upper value is -1 and the lower value is non-zero, then inflate is in
+ the middle of a stored block, with the lower value equaling the number of
+ bytes from the input remaining to copy. If the upper value is not -1, then
+ it is the number of bits back from the current bit position in the input of
+ the code (literal or length/distance pair) currently being processed. In
+ that case the lower value is the number of bytes already emitted for that
+ code.
+
+ A code is being processed if inflate is waiting for more input to complete
+ decoding of the code, or if it has completed decoding but is waiting for
+ more output space to write the literal or match data.
+
+ inflateMark() is used to mark locations in the input data for random
+ access, which may be at bit positions, and to note those cases where the
+ output of a code may span boundaries of random access blocks. The current
+ location in the input stream can be determined from avail_in and data_type
+ as noted in the description for the Z_BLOCK flush parameter for inflate.
+
+ inflateMark returns the value noted above or -1 << 16 if the provided
+ source stream state was inconsistent.
+*/
+
+ZEXTERN int ZEXPORT inflateGetHeader OF((z_streamp strm,
+ gz_headerp head));
+/*
+ inflateGetHeader() requests that gzip header information be stored in the
+ provided gz_header structure. inflateGetHeader() may be called after
+ inflateInit2() or inflateReset(), and before the first call of inflate().
+ As inflate() processes the gzip stream, head->done is zero until the header
+ is completed, at which time head->done is set to one. If a zlib stream is
+ being decoded, then head->done is set to -1 to indicate that there will be
+ no gzip header information forthcoming. Note that Z_BLOCK or Z_TREES can be
+ used to force inflate() to return immediately after header processing is
+ complete and before any actual data is decompressed.
+
+ The text, time, xflags, and os fields are filled in with the gzip header
+ contents. hcrc is set to true if there is a header CRC. (The header CRC
+ was valid if done is set to one.) If extra is not Z_NULL, then extra_max
+ contains the maximum number of bytes to write to extra. Once done is true,
+ extra_len contains the actual extra field length, and extra contains the
+ extra field, or that field truncated if extra_max is less than extra_len.
+ If name is not Z_NULL, then up to name_max characters are written there,
+ terminated with a zero unless the length is greater than name_max. If
+ comment is not Z_NULL, then up to comm_max characters are written there,
+ terminated with a zero unless the length is greater than comm_max. When any
+ of extra, name, or comment are not Z_NULL and the respective field is not
+ present in the header, then that field is set to Z_NULL to signal its
+ absence. This allows the use of deflateSetHeader() with the returned
+ structure to duplicate the header. However if those fields are set to
+ allocated memory, then the application will need to save those pointers
+ elsewhere so that they can be eventually freed.
+
+ If inflateGetHeader is not used, then the header information is simply
+ discarded. The header is always checked for validity, including the header
+ CRC if present. inflateReset() will reset the process to discard the header
+ information. The application would need to call inflateGetHeader() again to
+ retrieve the header from the next gzip stream.
+
+ inflateGetHeader returns Z_OK if success, or Z_STREAM_ERROR if the source
+ stream state was inconsistent.
+*/
+
+/*
+ZEXTERN int ZEXPORT inflateBackInit OF((z_streamp strm, int windowBits,
+ unsigned char FAR *window));
+
+ Initialize the internal stream state for decompression using inflateBack()
+ calls. The fields zalloc, zfree and opaque in strm must be initialized
+ before the call. If zalloc and zfree are Z_NULL, then the default library-
+ derived memory allocation routines are used. windowBits is the base two
+ logarithm of the window size, in the range 8..15. window is a caller
+ supplied buffer of that size. Except for special applications where it is
+ assured that deflate was used with small window sizes, windowBits must be 15
+ and a 32K byte window must be supplied to be able to decompress general
+ deflate streams.
+
+ See inflateBack() for the usage of these routines.
+
+ inflateBackInit will return Z_OK on success, Z_STREAM_ERROR if any of
+ the parameters are invalid, Z_MEM_ERROR if the internal state could not be
+ allocated, or Z_VERSION_ERROR if the version of the library does not match
+ the version of the header file.
+*/
+
+typedef unsigned (*in_func) OF((void FAR *,
+ z_const unsigned char FAR * FAR *));
+typedef int (*out_func) OF((void FAR *, unsigned char FAR *, unsigned));
+
+ZEXTERN int ZEXPORT inflateBack OF((z_streamp strm,
+ in_func in, void FAR *in_desc,
+ out_func out, void FAR *out_desc));
+/*
+ inflateBack() does a raw inflate with a single call using a call-back
+ interface for input and output. This is potentially more efficient than
+ inflate() for file i/o applications, in that it avoids copying between the
+ output and the sliding window by simply making the window itself the output
+ buffer. inflate() can be faster on modern CPUs when used with large
+ buffers. inflateBack() trusts the application to not change the output
+ buffer passed by the output function, at least until inflateBack() returns.
+
+ inflateBackInit() must be called first to allocate the internal state
+ and to initialize the state with the user-provided window buffer.
+ inflateBack() may then be used multiple times to inflate a complete, raw
+ deflate stream with each call. inflateBackEnd() is then called to free the
+ allocated state.
+
+ A raw deflate stream is one with no zlib or gzip header or trailer.
+ This routine would normally be used in a utility that reads zip or gzip
+ files and writes out uncompressed files. The utility would decode the
+ header and process the trailer on its own, hence this routine expects only
+ the raw deflate stream to decompress. This is different from the normal
+ behavior of inflate(), which expects either a zlib or gzip header and
+ trailer around the deflate stream.
+
+ inflateBack() uses two subroutines supplied by the caller that are then
+ called by inflateBack() for input and output. inflateBack() calls those
+ routines until it reads a complete deflate stream and writes out all of the
+ uncompressed data, or until it encounters an error. The function's
+ parameters and return types are defined above in the in_func and out_func
+ typedefs. inflateBack() will call in(in_desc, &buf) which should return the
+ number of bytes of provided input, and a pointer to that input in buf. If
+ there is no input available, in() must return zero--buf is ignored in that
+ case--and inflateBack() will return a buffer error. inflateBack() will call
+ out(out_desc, buf, len) to write the uncompressed data buf[0..len-1]. out()
+ should return zero on success, or non-zero on failure. If out() returns
+ non-zero, inflateBack() will return with an error. Neither in() nor out()
+ are permitted to change the contents of the window provided to
+ inflateBackInit(), which is also the buffer that out() uses to write from.
+ The length written by out() will be at most the window size. Any non-zero
+ amount of input may be provided by in().
+
+ For convenience, inflateBack() can be provided input on the first call by
+ setting strm->next_in and strm->avail_in. If that input is exhausted, then
+ in() will be called. Therefore strm->next_in must be initialized before
+ calling inflateBack(). If strm->next_in is Z_NULL, then in() will be called
+ immediately for input. If strm->next_in is not Z_NULL, then strm->avail_in
+ must also be initialized, and then if strm->avail_in is not zero, input will
+ initially be taken from strm->next_in[0 .. strm->avail_in - 1].
+
+ The in_desc and out_desc parameters of inflateBack() is passed as the
+ first parameter of in() and out() respectively when they are called. These
+ descriptors can be optionally used to pass any information that the caller-
+ supplied in() and out() functions need to do their job.
+
+ On return, inflateBack() will set strm->next_in and strm->avail_in to
+ pass back any unused input that was provided by the last in() call. The
+ return values of inflateBack() can be Z_STREAM_END on success, Z_BUF_ERROR
+ if in() or out() returned an error, Z_DATA_ERROR if there was a format error
+ in the deflate stream (in which case strm->msg is set to indicate the nature
+ of the error), or Z_STREAM_ERROR if the stream was not properly initialized.
+ In the case of Z_BUF_ERROR, an input or output error can be distinguished
+ using strm->next_in which will be Z_NULL only if in() returned an error. If
+ strm->next_in is not Z_NULL, then the Z_BUF_ERROR was due to out() returning
+ non-zero. (in() will always be called before out(), so strm->next_in is
+ assured to be defined if out() returns non-zero.) Note that inflateBack()
+ cannot return Z_OK.
+*/
+
+ZEXTERN int ZEXPORT inflateBackEnd OF((z_streamp strm));
+/*
+ All memory allocated by inflateBackInit() is freed.
+
+ inflateBackEnd() returns Z_OK on success, or Z_STREAM_ERROR if the stream
+ state was inconsistent.
+*/
+
+ZEXTERN uLong ZEXPORT zlibCompileFlags OF((void));
+/* Return flags indicating compile-time options.
+
+ Type sizes, two bits each, 00 = 16 bits, 01 = 32, 10 = 64, 11 = other:
+ 1.0: size of uInt
+ 3.2: size of uLong
+ 5.4: size of voidpf (pointer)
+ 7.6: size of z_off_t
+
+ Compiler, assembler, and debug options:
+ 8: DEBUG
+ 9: ASMV or ASMINF -- use ASM code
+ 10: ZLIB_WINAPI -- exported functions use the WINAPI calling convention
+ 11: 0 (reserved)
+
+ One-time table building (smaller code, but not thread-safe if true):
+ 12: BUILDFIXED -- build static block decoding tables when needed
+ 13: DYNAMIC_CRC_TABLE -- build CRC calculation tables when needed
+ 14,15: 0 (reserved)
+
+ Library content (indicates missing functionality):
+ 16: NO_GZCOMPRESS -- gz* functions cannot compress (to avoid linking
+ deflate code when not needed)
+ 17: NO_GZIP -- deflate can't write gzip streams, and inflate can't detect
+ and decode gzip streams (to avoid linking crc code)
+ 18-19: 0 (reserved)
+
+ Operation variations (changes in library functionality):
+ 20: PKZIP_BUG_WORKAROUND -- slightly more permissive inflate
+ 21: FASTEST -- deflate algorithm with only one, lowest compression level
+ 22,23: 0 (reserved)
+
+ The sprintf variant used by gzprintf (zero is best):
+ 24: 0 = vs*, 1 = s* -- 1 means limited to 20 arguments after the format
+ 25: 0 = *nprintf, 1 = *printf -- 1 means gzprintf() not secure!
+ 26: 0 = returns value, 1 = void -- 1 means inferred string length returned
+
+ Remainder:
+ 27-31: 0 (reserved)
+ */
+
+#ifndef Z_SOLO
+
+ /* utility functions */
+
+/*
+ The following utility functions are implemented on top of the basic
+ stream-oriented functions. To simplify the interface, some default options
+ are assumed (compression level and memory usage, standard memory allocation
+ functions). The source code of these utility functions can be modified if
+ you need special options.
+*/
+
+ZEXTERN int ZEXPORT compress OF((Bytef *dest, uLongf *destLen,
+ const Bytef *source, uLong sourceLen));
+/*
+ Compresses the source buffer into the destination buffer. sourceLen is
+ the byte length of the source buffer. Upon entry, destLen is the total size
+ of the destination buffer, which must be at least the value returned by
+ compressBound(sourceLen). Upon exit, destLen is the actual size of the
+ compressed buffer.
+
+ compress returns Z_OK if success, Z_MEM_ERROR if there was not
+ enough memory, Z_BUF_ERROR if there was not enough room in the output
+ buffer.
+*/
+
+ZEXTERN int ZEXPORT compress2 OF((Bytef *dest, uLongf *destLen,
+ const Bytef *source, uLong sourceLen,
+ int level));
+/*
+ Compresses the source buffer into the destination buffer. The level
+ parameter has the same meaning as in deflateInit. sourceLen is the byte
+ length of the source buffer. Upon entry, destLen is the total size of the
+ destination buffer, which must be at least the value returned by
+ compressBound(sourceLen). Upon exit, destLen is the actual size of the
+ compressed buffer.
+
+ compress2 returns Z_OK if success, Z_MEM_ERROR if there was not enough
+ memory, Z_BUF_ERROR if there was not enough room in the output buffer,
+ Z_STREAM_ERROR if the level parameter is invalid.
+*/
+
+ZEXTERN uLong ZEXPORT compressBound OF((uLong sourceLen));
+/*
+ compressBound() returns an upper bound on the compressed size after
+ compress() or compress2() on sourceLen bytes. It would be used before a
+ compress() or compress2() call to allocate the destination buffer.
+*/
+
+ZEXTERN int ZEXPORT uncompress OF((Bytef *dest, uLongf *destLen,
+ const Bytef *source, uLong sourceLen));
+/*
+ Decompresses the source buffer into the destination buffer. sourceLen is
+ the byte length of the source buffer. Upon entry, destLen is the total size
+ of the destination buffer, which must be large enough to hold the entire
+ uncompressed data. (The size of the uncompressed data must have been saved
+ previously by the compressor and transmitted to the decompressor by some
+ mechanism outside the scope of this compression library.) Upon exit, destLen
+ is the actual size of the uncompressed buffer.
+
+ uncompress returns Z_OK if success, Z_MEM_ERROR if there was not
+ enough memory, Z_BUF_ERROR if there was not enough room in the output
+ buffer, or Z_DATA_ERROR if the input data was corrupted or incomplete. In
+ the case where there is not enough room, uncompress() will fill the output
+ buffer with the uncompressed data up to that point.
+*/
+
+ /* gzip file access functions */
+
+/*
+ This library supports reading and writing files in gzip (.gz) format with
+ an interface similar to that of stdio, using the functions that start with
+ "gz". The gzip format is different from the zlib format. gzip is a gzip
+ wrapper, documented in RFC 1952, wrapped around a deflate stream.
+*/
+
+typedef struct gzFile_s *gzFile; /* semi-opaque gzip file descriptor */
+
+/*
+ZEXTERN gzFile ZEXPORT gzopen OF((const char *path, const char *mode));
+
+ Opens a gzip (.gz) file for reading or writing. The mode parameter is as
+ in fopen ("rb" or "wb") but can also include a compression level ("wb9") or
+ a strategy: 'f' for filtered data as in "wb6f", 'h' for Huffman-only
+ compression as in "wb1h", 'R' for run-length encoding as in "wb1R", or 'F'
+ for fixed code compression as in "wb9F". (See the description of
+ deflateInit2 for more information about the strategy parameter.) 'T' will
+ request transparent writing or appending with no compression and not using
+ the gzip format.
+
+ "a" can be used instead of "w" to request that the gzip stream that will
+ be written be appended to the file. "+" will result in an error, since
+ reading and writing to the same gzip file is not supported. The addition of
+ "x" when writing will create the file exclusively, which fails if the file
+ already exists. On systems that support it, the addition of "e" when
+ reading or writing will set the flag to close the file on an execve() call.
+
+ These functions, as well as gzip, will read and decode a sequence of gzip
+ streams in a file. The append function of gzopen() can be used to create
+ such a file. (Also see gzflush() for another way to do this.) When
+ appending, gzopen does not test whether the file begins with a gzip stream,
+ nor does it look for the end of the gzip streams to begin appending. gzopen
+ will simply append a gzip stream to the existing file.
+
+ gzopen can be used to read a file which is not in gzip format; in this
+ case gzread will directly read from the file without decompression. When
+ reading, this will be detected automatically by looking for the magic two-
+ byte gzip header.
+
+ gzopen returns NULL if the file could not be opened, if there was
+ insufficient memory to allocate the gzFile state, or if an invalid mode was
+ specified (an 'r', 'w', or 'a' was not provided, or '+' was provided).
+ errno can be checked to determine if the reason gzopen failed was that the
+ file could not be opened.
+*/
+
+ZEXTERN gzFile ZEXPORT gzdopen OF((int fd, const char *mode));
+/*
+ gzdopen associates a gzFile with the file descriptor fd. File descriptors
+ are obtained from calls like open, dup, creat, pipe or fileno (if the file
+ has been previously opened with fopen). The mode parameter is as in gzopen.
+
+ The next call of gzclose on the returned gzFile will also close the file
+ descriptor fd, just like fclose(fdopen(fd, mode)) closes the file descriptor
+ fd. If you want to keep fd open, use fd = dup(fd_keep); gz = gzdopen(fd,
+ mode);. The duplicated descriptor should be saved to avoid a leak, since
+ gzdopen does not close fd if it fails. If you are using fileno() to get the
+ file descriptor from a FILE *, then you will have to use dup() to avoid
+ double-close()ing the file descriptor. Both gzclose() and fclose() will
+ close the associated file descriptor, so they need to have different file
+ descriptors.
+
+ gzdopen returns NULL if there was insufficient memory to allocate the
+ gzFile state, if an invalid mode was specified (an 'r', 'w', or 'a' was not
+ provided, or '+' was provided), or if fd is -1. The file descriptor is not
+ used until the next gz* read, write, seek, or close operation, so gzdopen
+ will not detect if fd is invalid (unless fd is -1).
+*/
+
+ZEXTERN int ZEXPORT gzbuffer OF((gzFile file, unsigned size));
+/*
+ Set the internal buffer size used by this library's functions. The
+ default buffer size is 8192 bytes. This function must be called after
+ gzopen() or gzdopen(), and before any other calls that read or write the
+ file. The buffer memory allocation is always deferred to the first read or
+ write. Two buffers are allocated, either both of the specified size when
+ writing, or one of the specified size and the other twice that size when
+ reading. A larger buffer size of, for example, 64K or 128K bytes will
+ noticeably increase the speed of decompression (reading).
+
+ The new buffer size also affects the maximum length for gzprintf().
+
+ gzbuffer() returns 0 on success, or -1 on failure, such as being called
+ too late.
+*/
+
+ZEXTERN int ZEXPORT gzsetparams OF((gzFile file, int level, int strategy));
+/*
+ Dynamically update the compression level or strategy. See the description
+ of deflateInit2 for the meaning of these parameters.
+
+ gzsetparams returns Z_OK if success, or Z_STREAM_ERROR if the file was not
+ opened for writing.
+*/
+
+ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
+/*
+ Reads the given number of uncompressed bytes from the compressed file. If
+ the input file is not in gzip format, gzread copies the given number of
+ bytes into the buffer directly from the file.
+
+ After reaching the end of a gzip stream in the input, gzread will continue
+ to read, looking for another gzip stream. Any number of gzip streams may be
+ concatenated in the input file, and will all be decompressed by gzread().
+ If something other than a gzip stream is encountered after a gzip stream,
+ that remaining trailing garbage is ignored (and no error is returned).
+
+ gzread can be used to read a gzip file that is being concurrently written.
+ Upon reaching the end of the input, gzread will return with the available
+ data. If the error code returned by gzerror is Z_OK or Z_BUF_ERROR, then
+ gzclearerr can be used to clear the end of file indicator in order to permit
+ gzread to be tried again. Z_OK indicates that a gzip stream was completed
+ on the last gzread. Z_BUF_ERROR indicates that the input file ended in the
+ middle of a gzip stream. Note that gzread does not return -1 in the event
+ of an incomplete gzip stream. This error is deferred until gzclose(), which
+ will return Z_BUF_ERROR if the last gzread ended in the middle of a gzip
+ stream. Alternatively, gzerror can be used before gzclose to detect this
+ case.
+
+ gzread returns the number of uncompressed bytes actually read, less than
+ len for end of file, or -1 for error.
+*/
+
+ZEXTERN int ZEXPORT gzwrite OF((gzFile file,
+ voidpc buf, unsigned len));
+/*
+ Writes the given number of uncompressed bytes into the compressed file.
+ gzwrite returns the number of uncompressed bytes written or 0 in case of
+ error.
+*/
+
+ZEXTERN int ZEXPORTVA gzprintf Z_ARG((gzFile file, const char *format, ...));
+/*
+ Converts, formats, and writes the arguments to the compressed file under
+ control of the format string, as in fprintf. gzprintf returns the number of
+ uncompressed bytes actually written, or 0 in case of error. The number of
+ uncompressed bytes written is limited to 8191, or one less than the buffer
+ size given to gzbuffer(). The caller should assure that this limit is not
+ exceeded. If it is exceeded, then gzprintf() will return an error (0) with
+ nothing written. In this case, there may also be a buffer overflow with
+ unpredictable consequences, which is possible only if zlib was compiled with
+ the insecure functions sprintf() or vsprintf() because the secure snprintf()
+ or vsnprintf() functions were not available. This can be determined using
+ zlibCompileFlags().
+*/
+
+ZEXTERN int ZEXPORT gzputs OF((gzFile file, const char *s));
+/*
+ Writes the given null-terminated string to the compressed file, excluding
+ the terminating null character.
+
+ gzputs returns the number of characters written, or -1 in case of error.
+*/
+
+ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
+/*
+ Reads bytes from the compressed file until len-1 characters are read, or a
+ newline character is read and transferred to buf, or an end-of-file
+ condition is encountered. If any characters are read or if len == 1, the
+ string is terminated with a null character. If no characters are read due
+ to an end-of-file or len < 1, then the buffer is left untouched.
+
+ gzgets returns buf which is a null-terminated string, or it returns NULL
+ for end-of-file or in case of error. If there was an error, the contents at
+ buf are indeterminate.
+*/
+
+ZEXTERN int ZEXPORT gzputc OF((gzFile file, int c));
+/*
+ Writes c, converted to an unsigned char, into the compressed file. gzputc
+ returns the value that was written, or -1 in case of error.
+*/
+
+ZEXTERN int ZEXPORT gzgetc OF((gzFile file));
+/*
+ Reads one byte from the compressed file. gzgetc returns this byte or -1
+ in case of end of file or error. This is implemented as a macro for speed.
+ As such, it does not do all of the checking the other functions do. I.e.
+ it does not check to see if file is NULL, nor whether the structure file
+ points to has been clobbered or not.
+*/
+
+ZEXTERN int ZEXPORT gzungetc OF((int c, gzFile file));
+/*
+ Push one character back onto the stream to be read as the first character
+ on the next read. At least one character of push-back is allowed.
+ gzungetc() returns the character pushed, or -1 on failure. gzungetc() will
+ fail if c is -1, and may fail if a character has been pushed but not read
+ yet. If gzungetc is used immediately after gzopen or gzdopen, at least the
+ output buffer size of pushed characters is allowed. (See gzbuffer above.)
+ The pushed character will be discarded if the stream is repositioned with
+ gzseek() or gzrewind().
+*/
+
+ZEXTERN int ZEXPORT gzflush OF((gzFile file, int flush));
+/*
+ Flushes all pending output into the compressed file. The parameter flush
+ is as in the deflate() function. The return value is the zlib error number
+ (see function gzerror below). gzflush is only permitted when writing.
+
+ If the flush parameter is Z_FINISH, the remaining data is written and the
+ gzip stream is completed in the output. If gzwrite() is called again, a new
+ gzip stream will be started in the output. gzread() is able to read such
+ concatented gzip streams.
+
+ gzflush should be called only when strictly necessary because it will
+ degrade compression if called too often.
+*/
+
+/*
+ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile file,
+ z_off_t offset, int whence));
+
+ Sets the starting position for the next gzread or gzwrite on the given
+ compressed file. The offset represents a number of bytes in the
+ uncompressed data stream. The whence parameter is defined as in lseek(2);
+ the value SEEK_END is not supported.
+
+ If the file is opened for reading, this function is emulated but can be
+ extremely slow. If the file is opened for writing, only forward seeks are
+ supported; gzseek then compresses a sequence of zeroes up to the new
+ starting position.
+
+ gzseek returns the resulting offset location as measured in bytes from
+ the beginning of the uncompressed stream, or -1 in case of error, in
+ particular if the file is opened for writing and the new starting position
+ would be before the current position.
+*/
+
+ZEXTERN int ZEXPORT gzrewind OF((gzFile file));
+/*
+ Rewinds the given file. This function is supported only for reading.
+
+ gzrewind(file) is equivalent to (int)gzseek(file, 0L, SEEK_SET)
+*/
+
+/*
+ZEXTERN z_off_t ZEXPORT gztell OF((gzFile file));
+
+ Returns the starting position for the next gzread or gzwrite on the given
+ compressed file. This position represents a number of bytes in the
+ uncompressed data stream, and is zero when starting, even if appending or
+ reading a gzip stream from the middle of a file using gzdopen().
+
+ gztell(file) is equivalent to gzseek(file, 0L, SEEK_CUR)
+*/
+
+/*
+ZEXTERN z_off_t ZEXPORT gzoffset OF((gzFile file));
+
+ Returns the current offset in the file being read or written. This offset
+ includes the count of bytes that precede the gzip stream, for example when
+ appending or when using gzdopen() for reading. When reading, the offset
+ does not include as yet unused buffered input. This information can be used
+ for a progress indicator. On error, gzoffset() returns -1.
+*/
+
+ZEXTERN int ZEXPORT gzeof OF((gzFile file));
+/*
+ Returns true (1) if the end-of-file indicator has been set while reading,
+ false (0) otherwise. Note that the end-of-file indicator is set only if the
+ read tried to go past the end of the input, but came up short. Therefore,
+ just like feof(), gzeof() may return false even if there is no more data to
+ read, in the event that the last read request was for the exact number of
+ bytes remaining in the input file. This will happen if the input file size
+ is an exact multiple of the buffer size.
+
+ If gzeof() returns true, then the read functions will return no more data,
+ unless the end-of-file indicator is reset by gzclearerr() and the input file
+ has grown since the previous end of file was detected.
+*/
+
+ZEXTERN int ZEXPORT gzdirect OF((gzFile file));
+/*
+ Returns true (1) if file is being copied directly while reading, or false
+ (0) if file is a gzip stream being decompressed.
+
+ If the input file is empty, gzdirect() will return true, since the input
+ does not contain a gzip stream.
+
+ If gzdirect() is used immediately after gzopen() or gzdopen() it will
+ cause buffers to be allocated to allow reading the file to determine if it
+ is a gzip file. Therefore if gzbuffer() is used, it should be called before
+ gzdirect().
+
+ When writing, gzdirect() returns true (1) if transparent writing was
+ requested ("wT" for the gzopen() mode), or false (0) otherwise. (Note:
+ gzdirect() is not needed when writing. Transparent writing must be
+ explicitly requested, so the application already knows the answer. When
+ linking statically, using gzdirect() will include all of the zlib code for
+ gzip file reading and decompression, which may not be desired.)
+*/
+
+ZEXTERN int ZEXPORT gzclose OF((gzFile file));
+/*
+ Flushes all pending output if necessary, closes the compressed file and
+ deallocates the (de)compression state. Note that once file is closed, you
+ cannot call gzerror with file, since its structures have been deallocated.
+ gzclose must not be called more than once on the same file, just as free
+ must not be called more than once on the same allocation.
+
+ gzclose will return Z_STREAM_ERROR if file is not valid, Z_ERRNO on a
+ file operation error, Z_MEM_ERROR if out of memory, Z_BUF_ERROR if the
+ last read ended in the middle of a gzip stream, or Z_OK on success.
+*/
+
+ZEXTERN int ZEXPORT gzclose_r OF((gzFile file));
+ZEXTERN int ZEXPORT gzclose_w OF((gzFile file));
+/*
+ Same as gzclose(), but gzclose_r() is only for use when reading, and
+ gzclose_w() is only for use when writing or appending. The advantage to
+ using these instead of gzclose() is that they avoid linking in zlib
+ compression or decompression code that is not used when only reading or only
+ writing respectively. If gzclose() is used, then both compression and
+ decompression code will be included the application when linking to a static
+ zlib library.
+*/
+
+ZEXTERN const char * ZEXPORT gzerror OF((gzFile file, int *errnum));
+/*
+ Returns the error message for the last error which occurred on the given
+ compressed file. errnum is set to zlib error number. If an error occurred
+ in the file system and not in the compression library, errnum is set to
+ Z_ERRNO and the application may consult errno to get the exact error code.
+
+ The application must not modify the returned string. Future calls to
+ this function may invalidate the previously returned string. If file is
+ closed, then the string previously returned by gzerror will no longer be
+ available.
+
+ gzerror() should be used to distinguish errors from end-of-file for those
+ functions above that do not distinguish those cases in their return values.
+*/
+
+ZEXTERN void ZEXPORT gzclearerr OF((gzFile file));
+/*
+ Clears the error and end-of-file flags for file. This is analogous to the
+ clearerr() function in stdio. This is useful for continuing to read a gzip
+ file that is being written concurrently.
+*/
+
+#endif /* !Z_SOLO */
+
+ /* checksum functions */
+
+/*
+ These functions are not related to compression but are exported
+ anyway because they might be useful in applications using the compression
+ library.
+*/
+
+ZEXTERN uLong ZEXPORT adler32 OF((uLong adler, const Bytef *buf, uInt len));
+/*
+ Update a running Adler-32 checksum with the bytes buf[0..len-1] and
+ return the updated checksum. If buf is Z_NULL, this function returns the
+ required initial value for the checksum.
+
+ An Adler-32 checksum is almost as reliable as a CRC32 but can be computed
+ much faster.
+
+ Usage example:
+
+ uLong adler = adler32(0L, Z_NULL, 0);
+
+ while (read_buffer(buffer, length) != EOF) {
+ adler = adler32(adler, buffer, length);
+ }
+ if (adler != original_adler) error();
+*/
+
+/*
+ZEXTERN uLong ZEXPORT adler32_combine OF((uLong adler1, uLong adler2,
+ z_off_t len2));
+
+ Combine two Adler-32 checksums into one. For two sequences of bytes, seq1
+ and seq2 with lengths len1 and len2, Adler-32 checksums were calculated for
+ each, adler1 and adler2. adler32_combine() returns the Adler-32 checksum of
+ seq1 and seq2 concatenated, requiring only adler1, adler2, and len2. Note
+ that the z_off_t type (like off_t) is a signed integer. If len2 is
+ negative, the result has no meaning or utility.
+*/
+
+ZEXTERN uLong ZEXPORT crc32 OF((uLong crc, const Bytef *buf, uInt len));
+/*
+ Update a running CRC-32 with the bytes buf[0..len-1] and return the
+ updated CRC-32. If buf is Z_NULL, this function returns the required
+ initial value for the crc. Pre- and post-conditioning (one's complement) is
+ performed within this function so it shouldn't be done by the application.
+
+ Usage example:
+
+ uLong crc = crc32(0L, Z_NULL, 0);
+
+ while (read_buffer(buffer, length) != EOF) {
+ crc = crc32(crc, buffer, length);
+ }
+ if (crc != original_crc) error();
+*/
+
+/*
+ZEXTERN uLong ZEXPORT crc32_combine OF((uLong crc1, uLong crc2, z_off_t len2));
+
+ Combine two CRC-32 check values into one. For two sequences of bytes,
+ seq1 and seq2 with lengths len1 and len2, CRC-32 check values were
+ calculated for each, crc1 and crc2. crc32_combine() returns the CRC-32
+ check value of seq1 and seq2 concatenated, requiring only crc1, crc2, and
+ len2.
+*/
+
+
+ /* various hacks, don't look :) */
+
+/* deflateInit and inflateInit are macros to allow checking the zlib version
+ * and the compiler's view of z_stream:
+ */
+ZEXTERN int ZEXPORT deflateInit_ OF((z_streamp strm, int level,
+ const char *version, int stream_size));
+ZEXTERN int ZEXPORT inflateInit_ OF((z_streamp strm,
+ const char *version, int stream_size));
+ZEXTERN int ZEXPORT deflateInit2_ OF((z_streamp strm, int level, int method,
+ int windowBits, int memLevel,
+ int strategy, const char *version,
+ int stream_size));
+ZEXTERN int ZEXPORT inflateInit2_ OF((z_streamp strm, int windowBits,
+ const char *version, int stream_size));
+ZEXTERN int ZEXPORT inflateBackInit_ OF((z_streamp strm, int windowBits,
+ unsigned char FAR *window,
+ const char *version,
+ int stream_size));
+#define deflateInit(strm, level) \
+ deflateInit_((strm), (level), ZLIB_VERSION, (int)sizeof(z_stream))
+#define inflateInit(strm) \
+ inflateInit_((strm), ZLIB_VERSION, (int)sizeof(z_stream))
+#define deflateInit2(strm, level, method, windowBits, memLevel, strategy) \
+ deflateInit2_((strm),(level),(method),(windowBits),(memLevel),\
+ (strategy), ZLIB_VERSION, (int)sizeof(z_stream))
+#define inflateInit2(strm, windowBits) \
+ inflateInit2_((strm), (windowBits), ZLIB_VERSION, \
+ (int)sizeof(z_stream))
+#define inflateBackInit(strm, windowBits, window) \
+ inflateBackInit_((strm), (windowBits), (window), \
+ ZLIB_VERSION, (int)sizeof(z_stream))
+
+#ifndef Z_SOLO
+
+/* gzgetc() macro and its supporting function and exposed data structure. Note
+ * that the real internal state is much larger than the exposed structure.
+ * This abbreviated structure exposes just enough for the gzgetc() macro. The
+ * user should not mess with these exposed elements, since their names or
+ * behavior could change in the future, perhaps even capriciously. They can
+ * only be used by the gzgetc() macro. You have been warned.
+ */
+struct gzFile_s {
+ unsigned have;
+ unsigned char *next;
+ z_off64_t pos;
+};
+ZEXTERN int ZEXPORT gzgetc_ OF((gzFile file)); /* backward compatibility */
+#ifdef Z_PREFIX_SET
+# undef z_gzgetc
+# define z_gzgetc(g) \
+ ((g)->have ? ((g)->have--, (g)->pos++, *((g)->next)++) : gzgetc(g))
+#else
+# define gzgetc(g) \
+ ((g)->have ? ((g)->have--, (g)->pos++, *((g)->next)++) : gzgetc(g))
+#endif
+
+/* provide 64-bit offset functions if _LARGEFILE64_SOURCE defined, and/or
+ * change the regular functions to 64 bits if _FILE_OFFSET_BITS is 64 (if
+ * both are true, the application gets the *64 functions, and the regular
+ * functions are changed to 64 bits) -- in case these are set on systems
+ * without large file support, _LFS64_LARGEFILE must also be true
+ */
+#ifdef Z_LARGE64
+ ZEXTERN gzFile ZEXPORT gzopen64 OF((const char *, const char *));
+ ZEXTERN z_off64_t ZEXPORT gzseek64 OF((gzFile, z_off64_t, int));
+ ZEXTERN z_off64_t ZEXPORT gztell64 OF((gzFile));
+ ZEXTERN z_off64_t ZEXPORT gzoffset64 OF((gzFile));
+ ZEXTERN uLong ZEXPORT adler32_combine64 OF((uLong, uLong, z_off64_t));
+ ZEXTERN uLong ZEXPORT crc32_combine64 OF((uLong, uLong, z_off64_t));
+#endif
+
+#if !defined(ZLIB_INTERNAL) && defined(Z_WANT64)
+# ifdef Z_PREFIX_SET
+# define z_gzopen z_gzopen64
+# define z_gzseek z_gzseek64
+# define z_gztell z_gztell64
+# define z_gzoffset z_gzoffset64
+# define z_adler32_combine z_adler32_combine64
+# define z_crc32_combine z_crc32_combine64
+# else
+# define gzopen gzopen64
+# define gzseek gzseek64
+# define gztell gztell64
+# define gzoffset gzoffset64
+# define adler32_combine adler32_combine64
+# define crc32_combine crc32_combine64
+# endif
+# ifndef Z_LARGE64
+ ZEXTERN gzFile ZEXPORT gzopen64 OF((const char *, const char *));
+ ZEXTERN z_off_t ZEXPORT gzseek64 OF((gzFile, z_off_t, int));
+ ZEXTERN z_off_t ZEXPORT gztell64 OF((gzFile));
+ ZEXTERN z_off_t ZEXPORT gzoffset64 OF((gzFile));
+ ZEXTERN uLong ZEXPORT adler32_combine64 OF((uLong, uLong, z_off_t));
+ ZEXTERN uLong ZEXPORT crc32_combine64 OF((uLong, uLong, z_off_t));
+# endif
+#else
+ ZEXTERN gzFile ZEXPORT gzopen OF((const char *, const char *));
+ ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
+ ZEXTERN z_off_t ZEXPORT gztell OF((gzFile));
+ ZEXTERN z_off_t ZEXPORT gzoffset OF((gzFile));
+ ZEXTERN uLong ZEXPORT adler32_combine OF((uLong, uLong, z_off_t));
+ ZEXTERN uLong ZEXPORT crc32_combine OF((uLong, uLong, z_off_t));
+#endif
+
+#else /* Z_SOLO */
+
+ ZEXTERN uLong ZEXPORT adler32_combine OF((uLong, uLong, z_off_t));
+ ZEXTERN uLong ZEXPORT crc32_combine OF((uLong, uLong, z_off_t));
+
+#endif /* !Z_SOLO */
+
+/* hack for buggy compilers */
+#if !defined(ZUTIL_H) && !defined(NO_DUMMY_DECL)
+ struct internal_state {int dummy;};
+#endif
+
+/* undocumented functions */
+ZEXTERN const char * ZEXPORT zError OF((int));
+ZEXTERN int ZEXPORT inflateSyncPoint OF((z_streamp));
+ZEXTERN const z_crc_t FAR * ZEXPORT get_crc_table OF((void));
+ZEXTERN int ZEXPORT inflateUndermine OF((z_streamp, int));
+ZEXTERN int ZEXPORT inflateResetKeep OF((z_streamp));
+ZEXTERN int ZEXPORT deflateResetKeep OF((z_streamp));
+#if defined(_WIN32) && !defined(Z_SOLO)
+ZEXTERN gzFile ZEXPORT gzopen_w OF((const wchar_t *path,
+ const char *mode));
+#endif
+#if defined(STDC) || defined(Z_HAVE_STDARG_H)
+# ifndef Z_SOLO
+ZEXTERN int ZEXPORTVA gzvprintf Z_ARG((gzFile file,
+ const char *format,
+ va_list va));
+# endif
+#endif
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* ZLIB_H */
diff --git a/third-party/zlib/zlib.map b/third-party/zlib/zlib.map
new file mode 100644
index 0000000..55c6647
--- /dev/null
+++ b/third-party/zlib/zlib.map
@@ -0,0 +1,83 @@
+ZLIB_1.2.0 {
+ global:
+ compressBound;
+ deflateBound;
+ inflateBack;
+ inflateBackEnd;
+ inflateBackInit_;
+ inflateCopy;
+ local:
+ deflate_copyright;
+ inflate_copyright;
+ inflate_fast;
+ inflate_table;
+ zcalloc;
+ zcfree;
+ z_errmsg;
+ gz_error;
+ gz_intmax;
+ _*;
+};
+
+ZLIB_1.2.0.2 {
+ gzclearerr;
+ gzungetc;
+ zlibCompileFlags;
+} ZLIB_1.2.0;
+
+ZLIB_1.2.0.8 {
+ deflatePrime;
+} ZLIB_1.2.0.2;
+
+ZLIB_1.2.2 {
+ adler32_combine;
+ crc32_combine;
+ deflateSetHeader;
+ inflateGetHeader;
+} ZLIB_1.2.0.8;
+
+ZLIB_1.2.2.3 {
+ deflateTune;
+ gzdirect;
+} ZLIB_1.2.2;
+
+ZLIB_1.2.2.4 {
+ inflatePrime;
+} ZLIB_1.2.2.3;
+
+ZLIB_1.2.3.3 {
+ adler32_combine64;
+ crc32_combine64;
+ gzopen64;
+ gzseek64;
+ gztell64;
+ inflateUndermine;
+} ZLIB_1.2.2.4;
+
+ZLIB_1.2.3.4 {
+ inflateReset2;
+ inflateMark;
+} ZLIB_1.2.3.3;
+
+ZLIB_1.2.3.5 {
+ gzbuffer;
+ gzoffset;
+ gzoffset64;
+ gzclose_r;
+ gzclose_w;
+} ZLIB_1.2.3.4;
+
+ZLIB_1.2.5.1 {
+ deflatePending;
+} ZLIB_1.2.3.5;
+
+ZLIB_1.2.5.2 {
+ deflateResetKeep;
+ gzgetc_;
+ inflateResetKeep;
+} ZLIB_1.2.5.1;
+
+ZLIB_1.2.7.1 {
+ inflateGetDictionary;
+ gzvprintf;
+} ZLIB_1.2.5.2;
diff --git a/third-party/zlib/zlib.pc.cmakein b/third-party/zlib/zlib.pc.cmakein
new file mode 100644
index 0000000..a5e6429
--- /dev/null
+++ b/third-party/zlib/zlib.pc.cmakein
@@ -0,0 +1,13 @@
+prefix=@CMAKE_INSTALL_PREFIX@
+exec_prefix=@CMAKE_INSTALL_PREFIX@
+libdir=@INSTALL_LIB_DIR@
+sharedlibdir=@INSTALL_LIB_DIR@
+includedir=@INSTALL_INC_DIR@
+
+Name: zlib
+Description: zlib compression library
+Version: @VERSION@
+
+Requires:
+Libs: -L${libdir} -L${sharedlibdir} -lz
+Cflags: -I${includedir}
diff --git a/third-party/zlib/zlib.pc.in b/third-party/zlib/zlib.pc.in
new file mode 100644
index 0000000..7e5acf9
--- /dev/null
+++ b/third-party/zlib/zlib.pc.in
@@ -0,0 +1,13 @@
+prefix=@prefix@
+exec_prefix=@exec_prefix@
+libdir=@libdir@
+sharedlibdir=@sharedlibdir@
+includedir=@includedir@
+
+Name: zlib
+Description: zlib compression library
+Version: @VERSION@
+
+Requires:
+Libs: -L${libdir} -L${sharedlibdir} -lz
+Cflags: -I${includedir}
diff --git a/third-party/zlib/zlib2ansi b/third-party/zlib/zlib2ansi
new file mode 100755
index 0000000..15e3e16
--- /dev/null
+++ b/third-party/zlib/zlib2ansi
@@ -0,0 +1,152 @@
+#!/usr/bin/perl
+
+# Transform K&R C function definitions into ANSI equivalent.
+#
+# Author: Paul Marquess
+# Version: 1.0
+# Date: 3 October 2006
+
+# TODO
+#
+# Asumes no function pointer parameters. unless they are typedefed.
+# Assumes no literal strings that look like function definitions
+# Assumes functions start at the beginning of a line
+
+use strict;
+use warnings;
+
+local $/;
+$_ = <>;
+
+my $sp = qr{ \s* (?: /\* .*? \*/ )? \s* }x; # assume no nested comments
+
+my $d1 = qr{ $sp (?: [\w\*\s]+ $sp)* $sp \w+ $sp [\[\]\s]* $sp }x ;
+my $decl = qr{ $sp (?: \w+ $sp )+ $d1 }xo ;
+my $dList = qr{ $sp $decl (?: $sp , $d1 )* $sp ; $sp }xo ;
+
+
+while (s/^
+ ( # Start $1
+ ( # Start $2
+ .*? # Minimal eat content
+ ( ^ \w [\w\s\*]+ ) # $3 -- function name
+ \s* # optional whitespace
+ ) # $2 - Matched up to before parameter list
+
+ \( \s* # Literal "(" + optional whitespace
+ ( [^\)]+ ) # $4 - one or more anythings except ")"
+ \s* \) # optional whitespace surrounding a Literal ")"
+
+ ( (?: $dList )+ ) # $5
+
+ $sp ^ { # literal "{" at start of line
+ ) # Remember to $1
+ //xsom
+ )
+{
+ my $all = $1 ;
+ my $prefix = $2;
+ my $param_list = $4 ;
+ my $params = $5;
+
+ StripComments($params);
+ StripComments($param_list);
+ $param_list =~ s/^\s+//;
+ $param_list =~ s/\s+$//;
+
+ my $i = 0 ;
+ my %pList = map { $_ => $i++ }
+ split /\s*,\s*/, $param_list;
+ my $pMatch = '(\b' . join('|', keys %pList) . '\b)\W*$' ;
+
+ my @params = split /\s*;\s*/, $params;
+ my @outParams = ();
+ foreach my $p (@params)
+ {
+ if ($p =~ /,/)
+ {
+ my @bits = split /\s*,\s*/, $p;
+ my $first = shift @bits;
+ $first =~ s/^\s*//;
+ push @outParams, $first;
+ $first =~ /^(\w+\s*)/;
+ my $type = $1 ;
+ push @outParams, map { $type . $_ } @bits;
+ }
+ else
+ {
+ $p =~ s/^\s+//;
+ push @outParams, $p;
+ }
+ }
+
+
+ my %tmp = map { /$pMatch/; $_ => $pList{$1} }
+ @outParams ;
+
+ @outParams = map { " $_" }
+ sort { $tmp{$a} <=> $tmp{$b} }
+ @outParams ;
+
+ print $prefix ;
+ print "(\n" . join(",\n", @outParams) . ")\n";
+ print "{" ;
+
+}
+
+# Output any trailing code.
+print ;
+exit 0;
+
+
+sub StripComments
+{
+
+ no warnings;
+
+ # Strip C & C++ coments
+ # From the perlfaq
+ $_[0] =~
+
+ s{
+ /\* ## Start of /* ... */ comment
+ [^*]*\*+ ## Non-* followed by 1-or-more *'s
+ (
+ [^/*][^*]*\*+
+ )* ## 0-or-more things which don't start with /
+ ## but do end with '*'
+ / ## End of /* ... */ comment
+
+ | ## OR C++ Comment
+ // ## Start of C++ comment //
+ [^\n]* ## followed by 0-or-more non end of line characters
+
+ | ## OR various things which aren't comments:
+
+ (
+ " ## Start of " ... " string
+ (
+ \\. ## Escaped char
+ | ## OR
+ [^"\\] ## Non "\
+ )*
+ " ## End of " ... " string
+
+ | ## OR
+
+ ' ## Start of ' ... ' string
+ (
+ \\. ## Escaped char
+ | ## OR
+ [^'\\] ## Non '\
+ )*
+ ' ## End of ' ... ' string
+
+ | ## OR
+
+ . ## Anything other char
+ [^/"'\\]* ## Chars which doesn't start a comment, string or escape
+ )
+ }{$2}gxs;
+
+}
diff --git a/third-party/zlib/zutil.c b/third-party/zlib/zutil.c
new file mode 100644
index 0000000..23d2ebe
--- /dev/null
+++ b/third-party/zlib/zutil.c
@@ -0,0 +1,324 @@
+/* zutil.c -- target dependent utility functions for the compression library
+ * Copyright (C) 1995-2005, 2010, 2011, 2012 Jean-loup Gailly.
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* @(#) $Id$ */
+
+#include "zutil.h"
+#ifndef Z_SOLO
+# include "gzguts.h"
+#endif
+
+#ifndef NO_DUMMY_DECL
+struct internal_state {int dummy;}; /* for buggy compilers */
+#endif
+
+z_const char * const z_errmsg[10] = {
+"need dictionary", /* Z_NEED_DICT 2 */
+"stream end", /* Z_STREAM_END 1 */
+"", /* Z_OK 0 */
+"file error", /* Z_ERRNO (-1) */
+"stream error", /* Z_STREAM_ERROR (-2) */
+"data error", /* Z_DATA_ERROR (-3) */
+"insufficient memory", /* Z_MEM_ERROR (-4) */
+"buffer error", /* Z_BUF_ERROR (-5) */
+"incompatible version",/* Z_VERSION_ERROR (-6) */
+""};
+
+
+const char * ZEXPORT zlibVersion()
+{
+ return ZLIB_VERSION;
+}
+
+uLong ZEXPORT zlibCompileFlags()
+{
+ uLong flags;
+
+ flags = 0;
+ switch ((int)(sizeof(uInt))) {
+ case 2: break;
+ case 4: flags += 1; break;
+ case 8: flags += 2; break;
+ default: flags += 3;
+ }
+ switch ((int)(sizeof(uLong))) {
+ case 2: break;
+ case 4: flags += 1 << 2; break;
+ case 8: flags += 2 << 2; break;
+ default: flags += 3 << 2;
+ }
+ switch ((int)(sizeof(voidpf))) {
+ case 2: break;
+ case 4: flags += 1 << 4; break;
+ case 8: flags += 2 << 4; break;
+ default: flags += 3 << 4;
+ }
+ switch ((int)(sizeof(z_off_t))) {
+ case 2: break;
+ case 4: flags += 1 << 6; break;
+ case 8: flags += 2 << 6; break;
+ default: flags += 3 << 6;
+ }
+#ifdef DEBUG
+ flags += 1 << 8;
+#endif
+#if defined(ASMV) || defined(ASMINF)
+ flags += 1 << 9;
+#endif
+#ifdef ZLIB_WINAPI
+ flags += 1 << 10;
+#endif
+#ifdef BUILDFIXED
+ flags += 1 << 12;
+#endif
+#ifdef DYNAMIC_CRC_TABLE
+ flags += 1 << 13;
+#endif
+#ifdef NO_GZCOMPRESS
+ flags += 1L << 16;
+#endif
+#ifdef NO_GZIP
+ flags += 1L << 17;
+#endif
+#ifdef PKZIP_BUG_WORKAROUND
+ flags += 1L << 20;
+#endif
+#ifdef FASTEST
+ flags += 1L << 21;
+#endif
+#if defined(STDC) || defined(Z_HAVE_STDARG_H)
+# ifdef NO_vsnprintf
+ flags += 1L << 25;
+# ifdef HAS_vsprintf_void
+ flags += 1L << 26;
+# endif
+# else
+# ifdef HAS_vsnprintf_void
+ flags += 1L << 26;
+# endif
+# endif
+#else
+ flags += 1L << 24;
+# ifdef NO_snprintf
+ flags += 1L << 25;
+# ifdef HAS_sprintf_void
+ flags += 1L << 26;
+# endif
+# else
+# ifdef HAS_snprintf_void
+ flags += 1L << 26;
+# endif
+# endif
+#endif
+ return flags;
+}
+
+#ifdef DEBUG
+
+# ifndef verbose
+# define verbose 0
+# endif
+int ZLIB_INTERNAL z_verbose = verbose;
+
+void ZLIB_INTERNAL z_error (m)
+ char *m;
+{
+ fprintf(stderr, "%s\n", m);
+ exit(1);
+}
+#endif
+
+/* exported to allow conversion of error code to string for compress() and
+ * uncompress()
+ */
+const char * ZEXPORT zError(err)
+ int err;
+{
+ return ERR_MSG(err);
+}
+
+#if defined(_WIN32_WCE)
+ /* The Microsoft C Run-Time Library for Windows CE doesn't have
+ * errno. We define it as a global variable to simplify porting.
+ * Its value is always 0 and should not be used.
+ */
+ int errno = 0;
+#endif
+
+#ifndef HAVE_MEMCPY
+
+void ZLIB_INTERNAL zmemcpy(dest, source, len)
+ Bytef* dest;
+ const Bytef* source;
+ uInt len;
+{
+ if (len == 0) return;
+ do {
+ *dest++ = *source++; /* ??? to be unrolled */
+ } while (--len != 0);
+}
+
+int ZLIB_INTERNAL zmemcmp(s1, s2, len)
+ const Bytef* s1;
+ const Bytef* s2;
+ uInt len;
+{
+ uInt j;
+
+ for (j = 0; j < len; j++) {
+ if (s1[j] != s2[j]) return 2*(s1[j] > s2[j])-1;
+ }
+ return 0;
+}
+
+void ZLIB_INTERNAL zmemzero(dest, len)
+ Bytef* dest;
+ uInt len;
+{
+ if (len == 0) return;
+ do {
+ *dest++ = 0; /* ??? to be unrolled */
+ } while (--len != 0);
+}
+#endif
+
+#ifndef Z_SOLO
+
+#ifdef SYS16BIT
+
+#ifdef __TURBOC__
+/* Turbo C in 16-bit mode */
+
+# define MY_ZCALLOC
+
+/* Turbo C malloc() does not allow dynamic allocation of 64K bytes
+ * and farmalloc(64K) returns a pointer with an offset of 8, so we
+ * must fix the pointer. Warning: the pointer must be put back to its
+ * original form in order to free it, use zcfree().
+ */
+
+#define MAX_PTR 10
+/* 10*64K = 640K */
+
+local int next_ptr = 0;
+
+typedef struct ptr_table_s {
+ voidpf org_ptr;
+ voidpf new_ptr;
+} ptr_table;
+
+local ptr_table table[MAX_PTR];
+/* This table is used to remember the original form of pointers
+ * to large buffers (64K). Such pointers are normalized with a zero offset.
+ * Since MSDOS is not a preemptive multitasking OS, this table is not
+ * protected from concurrent access. This hack doesn't work anyway on
+ * a protected system like OS/2. Use Microsoft C instead.
+ */
+
+voidpf ZLIB_INTERNAL zcalloc (voidpf opaque, unsigned items, unsigned size)
+{
+ voidpf buf = opaque; /* just to make some compilers happy */
+ ulg bsize = (ulg)items*size;
+
+ /* If we allocate less than 65520 bytes, we assume that farmalloc
+ * will return a usable pointer which doesn't have to be normalized.
+ */
+ if (bsize < 65520L) {
+ buf = farmalloc(bsize);
+ if (*(ush*)&buf != 0) return buf;
+ } else {
+ buf = farmalloc(bsize + 16L);
+ }
+ if (buf == NULL || next_ptr >= MAX_PTR) return NULL;
+ table[next_ptr].org_ptr = buf;
+
+ /* Normalize the pointer to seg:0 */
+ *((ush*)&buf+1) += ((ush)((uch*)buf-0) + 15) >> 4;
+ *(ush*)&buf = 0;
+ table[next_ptr++].new_ptr = buf;
+ return buf;
+}
+
+void ZLIB_INTERNAL zcfree (voidpf opaque, voidpf ptr)
+{
+ int n;
+ if (*(ush*)&ptr != 0) { /* object < 64K */
+ farfree(ptr);
+ return;
+ }
+ /* Find the original pointer */
+ for (n = 0; n < next_ptr; n++) {
+ if (ptr != table[n].new_ptr) continue;
+
+ farfree(table[n].org_ptr);
+ while (++n < next_ptr) {
+ table[n-1] = table[n];
+ }
+ next_ptr--;
+ return;
+ }
+ ptr = opaque; /* just to make some compilers happy */
+ Assert(0, "zcfree: ptr not found");
+}
+
+#endif /* __TURBOC__ */
+
+
+#ifdef M_I86
+/* Microsoft C in 16-bit mode */
+
+# define MY_ZCALLOC
+
+#if (!defined(_MSC_VER) || (_MSC_VER <= 600))
+# define _halloc halloc
+# define _hfree hfree
+#endif
+
+voidpf ZLIB_INTERNAL zcalloc (voidpf opaque, uInt items, uInt size)
+{
+ if (opaque) opaque = 0; /* to make compiler happy */
+ return _halloc((long)items, size);
+}
+
+void ZLIB_INTERNAL zcfree (voidpf opaque, voidpf ptr)
+{
+ if (opaque) opaque = 0; /* to make compiler happy */
+ _hfree(ptr);
+}
+
+#endif /* M_I86 */
+
+#endif /* SYS16BIT */
+
+
+#ifndef MY_ZCALLOC /* Any system without a special alloc function */
+
+#ifndef STDC
+extern voidp malloc OF((uInt size));
+extern voidp calloc OF((uInt items, uInt size));
+extern void free OF((voidpf ptr));
+#endif
+
+voidpf ZLIB_INTERNAL zcalloc (opaque, items, size)
+ voidpf opaque;
+ unsigned items;
+ unsigned size;
+{
+ if (opaque) items += size - size; /* make compiler happy */
+ return sizeof(uInt) > 2 ? (voidpf)malloc(items * size) :
+ (voidpf)calloc(items, size);
+}
+
+void ZLIB_INTERNAL zcfree (opaque, ptr)
+ voidpf opaque;
+ voidpf ptr;
+{
+ free(ptr);
+ if (opaque) return; /* make compiler happy */
+}
+
+#endif /* MY_ZCALLOC */
+
+#endif /* !Z_SOLO */
diff --git a/third-party/zlib/zutil.h b/third-party/zlib/zutil.h
new file mode 100644
index 0000000..24ab06b
--- /dev/null
+++ b/third-party/zlib/zutil.h
@@ -0,0 +1,253 @@
+/* zutil.h -- internal interface and configuration of the compression library
+ * Copyright (C) 1995-2013 Jean-loup Gailly.
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* WARNING: this file should *not* be used by applications. It is
+ part of the implementation of the compression library and is
+ subject to change. Applications should only use zlib.h.
+ */
+
+/* @(#) $Id$ */
+
+#ifndef ZUTIL_H
+#define ZUTIL_H
+
+#ifdef HAVE_HIDDEN
+# define ZLIB_INTERNAL __attribute__((visibility ("hidden")))
+#else
+# define ZLIB_INTERNAL
+#endif
+
+#include "zlib.h"
+
+#if defined(STDC) && !defined(Z_SOLO)
+# if !(defined(_WIN32_WCE) && defined(_MSC_VER))
+# include <stddef.h>
+# endif
+# include <string.h>
+# include <stdlib.h>
+#endif
+
+#ifdef Z_SOLO
+ typedef long ptrdiff_t; /* guess -- will be caught if guess is wrong */
+#endif
+
+#ifndef local
+# define local static
+#endif
+/* compile with -Dlocal if your debugger can't find static symbols */
+
+typedef unsigned char uch;
+typedef uch FAR uchf;
+typedef unsigned short ush;
+typedef ush FAR ushf;
+typedef unsigned long ulg;
+
+extern z_const char * const z_errmsg[10]; /* indexed by 2-zlib_error */
+/* (size given to avoid silly warnings with Visual C++) */
+
+#define ERR_MSG(err) z_errmsg[Z_NEED_DICT-(err)]
+
+#define ERR_RETURN(strm,err) \
+ return (strm->msg = ERR_MSG(err), (err))
+/* To be used only when the state is known to be valid */
+
+ /* common constants */
+
+#ifndef DEF_WBITS
+# define DEF_WBITS MAX_WBITS
+#endif
+/* default windowBits for decompression. MAX_WBITS is for compression only */
+
+#if MAX_MEM_LEVEL >= 8
+# define DEF_MEM_LEVEL 8
+#else
+# define DEF_MEM_LEVEL MAX_MEM_LEVEL
+#endif
+/* default memLevel */
+
+#define STORED_BLOCK 0
+#define STATIC_TREES 1
+#define DYN_TREES 2
+/* The three kinds of block type */
+
+#define MIN_MATCH 3
+#define MAX_MATCH 258
+/* The minimum and maximum match lengths */
+
+#define PRESET_DICT 0x20 /* preset dictionary flag in zlib header */
+
+ /* target dependencies */
+
+#if defined(MSDOS) || (defined(WINDOWS) && !defined(WIN32))
+# define OS_CODE 0x00
+# ifndef Z_SOLO
+# if defined(__TURBOC__) || defined(__BORLANDC__)
+# if (__STDC__ == 1) && (defined(__LARGE__) || defined(__COMPACT__))
+ /* Allow compilation with ANSI keywords only enabled */
+ void _Cdecl farfree( void *block );
+ void *_Cdecl farmalloc( unsigned long nbytes );
+# else
+# include <alloc.h>
+# endif
+# else /* MSC or DJGPP */
+# include <malloc.h>
+# endif
+# endif
+#endif
+
+#ifdef AMIGA
+# define OS_CODE 0x01
+#endif
+
+#if defined(VAXC) || defined(VMS)
+# define OS_CODE 0x02
+# define F_OPEN(name, mode) \
+ fopen((name), (mode), "mbc=60", "ctx=stm", "rfm=fix", "mrs=512")
+#endif
+
+#if defined(ATARI) || defined(atarist)
+# define OS_CODE 0x05
+#endif
+
+#ifdef OS2
+# define OS_CODE 0x06
+# if defined(M_I86) && !defined(Z_SOLO)
+# include <malloc.h>
+# endif
+#endif
+
+#if defined(MACOS) || defined(TARGET_OS_MAC)
+# define OS_CODE 0x07
+# ifndef Z_SOLO
+# if defined(__MWERKS__) && __dest_os != __be_os && __dest_os != __win32_os
+# include <unix.h> /* for fdopen */
+# else
+# ifndef fdopen
+# define fdopen(fd,mode) NULL /* No fdopen() */
+# endif
+# endif
+# endif
+#endif
+
+#ifdef TOPS20
+# define OS_CODE 0x0a
+#endif
+
+#ifdef WIN32
+# ifndef __CYGWIN__ /* Cygwin is Unix, not Win32 */
+# define OS_CODE 0x0b
+# endif
+#endif
+
+#ifdef __50SERIES /* Prime/PRIMOS */
+# define OS_CODE 0x0f
+#endif
+
+#if defined(_BEOS_) || defined(RISCOS)
+# define fdopen(fd,mode) NULL /* No fdopen() */
+#endif
+
+#if (defined(_MSC_VER) && (_MSC_VER > 600)) && !defined __INTERIX
+# if defined(_WIN32_WCE)
+# define fdopen(fd,mode) NULL /* No fdopen() */
+# ifndef _PTRDIFF_T_DEFINED
+ typedef int ptrdiff_t;
+# define _PTRDIFF_T_DEFINED
+# endif
+# else
+# define fdopen(fd,type) _fdopen(fd,type)
+# endif
+#endif
+
+#if defined(__BORLANDC__) && !defined(MSDOS)
+ #pragma warn -8004
+ #pragma warn -8008
+ #pragma warn -8066
+#endif
+
+/* provide prototypes for these when building zlib without LFS */
+#if !defined(_WIN32) && \
+ (!defined(_LARGEFILE64_SOURCE) || _LFS64_LARGEFILE-0 == 0)
+ ZEXTERN uLong ZEXPORT adler32_combine64 OF((uLong, uLong, z_off_t));
+ ZEXTERN uLong ZEXPORT crc32_combine64 OF((uLong, uLong, z_off_t));
+#endif
+
+ /* common defaults */
+
+#ifndef OS_CODE
+# define OS_CODE 0x03 /* assume Unix */
+#endif
+
+#ifndef F_OPEN
+# define F_OPEN(name, mode) fopen((name), (mode))
+#endif
+
+ /* functions */
+
+#if defined(pyr) || defined(Z_SOLO)
+# define NO_MEMCPY
+#endif
+#if defined(SMALL_MEDIUM) && !defined(_MSC_VER) && !defined(__SC__)
+ /* Use our own functions for small and medium model with MSC <= 5.0.
+ * You may have to use the same strategy for Borland C (untested).
+ * The __SC__ check is for Symantec.
+ */
+# define NO_MEMCPY
+#endif
+#if defined(STDC) && !defined(HAVE_MEMCPY) && !defined(NO_MEMCPY)
+# define HAVE_MEMCPY
+#endif
+#ifdef HAVE_MEMCPY
+# ifdef SMALL_MEDIUM /* MSDOS small or medium model */
+# define zmemcpy _fmemcpy
+# define zmemcmp _fmemcmp
+# define zmemzero(dest, len) _fmemset(dest, 0, len)
+# else
+# define zmemcpy memcpy
+# define zmemcmp memcmp
+# define zmemzero(dest, len) memset(dest, 0, len)
+# endif
+#else
+ void ZLIB_INTERNAL zmemcpy OF((Bytef* dest, const Bytef* source, uInt len));
+ int ZLIB_INTERNAL zmemcmp OF((const Bytef* s1, const Bytef* s2, uInt len));
+ void ZLIB_INTERNAL zmemzero OF((Bytef* dest, uInt len));
+#endif
+
+/* Diagnostic functions */
+#ifdef DEBUG
+# include <stdio.h>
+ extern int ZLIB_INTERNAL z_verbose;
+ extern void ZLIB_INTERNAL z_error OF((char *m));
+# define Assert(cond,msg) {if(!(cond)) z_error(msg);}
+# define Trace(x) {if (z_verbose>=0) fprintf x ;}
+# define Tracev(x) {if (z_verbose>0) fprintf x ;}
+# define Tracevv(x) {if (z_verbose>1) fprintf x ;}
+# define Tracec(c,x) {if (z_verbose>0 && (c)) fprintf x ;}
+# define Tracecv(c,x) {if (z_verbose>1 && (c)) fprintf x ;}
+#else
+# define Assert(cond,msg)
+# define Trace(x)
+# define Tracev(x)
+# define Tracevv(x)
+# define Tracec(c,x)
+# define Tracecv(c,x)
+#endif
+
+#ifndef Z_SOLO
+ voidpf ZLIB_INTERNAL zcalloc OF((voidpf opaque, unsigned items,
+ unsigned size));
+ void ZLIB_INTERNAL zcfree OF((voidpf opaque, voidpf ptr));
+#endif
+
+#define ZALLOC(strm, items, size) \
+ (*((strm)->zalloc))((strm)->opaque, (items), (size))
+#define ZFREE(strm, addr) (*((strm)->zfree))((strm)->opaque, (voidpf)(addr))
+#define TRY_FREE(s, p) {if (p) ZFREE(s, p);}
+
+/* Reverse the bytes in a 32-bit value */
+#define ZSWAP32(q) ((((q) >> 24) & 0xff) + (((q) >> 8) & 0xff00) + \
+ (((q) & 0xff00) << 8) + (((q) & 0xff) << 24))
+
+#endif /* ZUTIL_H */
diff --git a/versioneer.py b/versioneer.py
old mode 100755
new mode 100644
index f624309..57509b3
--- a/versioneer.py
+++ b/versioneer.py
@@ -1,7 +1,8 @@
-# Version: 0.14
+# Version: 0.15+dev
+
+"""The Versioneer - like a rocketeer, but for versions.
-"""
The Versioneer
==============
@@ -27,8 +28,8 @@ system, and maybe making new tarballs.
## Quick Install
* `pip install versioneer` to somewhere to your $PATH
-* run `versioneer-installer` in your source tree: this installs `versioneer.py`
-* follow the instructions below (also in the `versioneer.py` docstring)
+* add a `[versioneer]` section to your setup.cfg (see below)
+* run `versioneer install` in your source tree, commit the results
## Version Identifiers
@@ -57,7 +58,7 @@ unreleased software (between tags), the version identifier should provide
enough information to help developers recreate the same tree, while also
giving them an idea of roughly how old the tree is (after version 1.2, before
version 1.3). Many VCS systems can report a description that captures this,
-for example 'git describe --tags --dirty --always' reports things like
+for example `git describe --tags --dirty --always` reports things like
"0.7-1-g574ab98-dirty" to indicate that the checkout is one revision past the
0.7 tag, has a unique revision id of "574ab98", and is "dirty" (it has
uncommitted changes.
@@ -71,16 +72,19 @@ The version identifier is used for multiple purposes:
Versioneer works by adding a special `_version.py` file into your source
tree, where your `__init__.py` can import it. This `_version.py` knows how to
-dynamically ask the VCS tool for version information at import time. However,
-when you use "setup.py build" or "setup.py sdist", `_version.py` in the new
-copy is replaced by a small static file that contains just the generated
-version data.
+dynamically ask the VCS tool for version information at import time.
`_version.py` also contains `$Revision$` markers, and the installation
process marks `_version.py` to have this marker rewritten with a tag name
-during the "git archive" command. As a result, generated tarballs will
+during the `git archive` command. As a result, generated tarballs will
contain enough information to get the proper version.
+To allow `setup.py` to compute a version too, a `versioneer.py` is added to
+the top level of your source tree, next to `setup.py` and the `setup.cfg`
+that configures it. This overrides several distutils/setuptools commands to
+compute the version when invoked, and changes `setup.py build` and `setup.py
+sdist` to replace `_version.py` with a small static file that contains just
+the generated version data.
## Installation
@@ -88,6 +92,10 @@ First, decide on values for the following configuration variables:
* `VCS`: the version control system you use. Currently accepts "git".
+* `style`: the style of version string to be produced. See "Styles" below for
+ details. Defaults to "pep440", which looks like
+ `TAG[+DISTANCE.gSHORTHASH[.dirty]]`.
+
* `versionfile_source`:
A project-relative pathname into which the generated version strings should
@@ -95,7 +103,7 @@ First, decide on values for the following configuration variables:
`__init__.py` file, so it can be imported at runtime. If your project uses
`src/myproject/__init__.py`, this should be `src/myproject/_version.py`.
This file should be checked in to your VCS as usual: the copy created below
- by `setup.py versioneer` will include code that parses expanded VCS
+ by `setup.py setup_versioneer` will include code that parses expanded VCS
keywords in generated tarballs. The 'build' and 'sdist' commands will
replace it with a copy that has just the calculated version string.
@@ -103,8 +111,8 @@ First, decide on values for the following configuration variables:
therefore never import `_version.py`), since "setup.py sdist" -based trees
still need somewhere to record the pre-calculated version strings. Anywhere
in the source tree should do. If there is a `__init__.py` next to your
- `_version.py`, the `setup.py versioneer` command (described below) will
- append some `__version__`-setting assignments, if they aren't already
+ `_version.py`, the `setup.py setup_versioneer` command (described below)
+ will append some `__version__`-setting assignments, if they aren't already
present.
* `versionfile_build`:
@@ -127,47 +135,57 @@ First, decide on values for the following configuration variables:
a string, like 'PROJECTNAME-', which appears at the start of all VCS tags.
If your tags look like 'myproject-1.2.0', then you should use
tag_prefix='myproject-'. If you use unprefixed tags like '1.2.0', this
- should be an empty string.
+ should be an empty string, using either `tag_prefix=` or `tag_prefix=''`.
* `parentdir_prefix`:
- a string, frequently the same as tag_prefix, which appears at the start of
- all unpacked tarball filenames. If your tarball unpacks into
- 'myproject-1.2.0', this should be 'myproject-'.
+ a optional string, frequently the same as tag_prefix, which appears at the
+ start of all unpacked tarball filenames. If your tarball unpacks into
+ 'myproject-1.2.0', this should be 'myproject-'. To disable this feature,
+ just omit the field from your `setup.cfg`.
-This tool provides one script, named `versioneer-installer`. That script does
-one thing: write a copy of `versioneer.py` into the current directory.
+This tool provides one script, named `versioneer`. That script has one mode,
+"install", which writes a copy of `versioneer.py` into the current directory
+and runs `versioneer.py setup` to finish the installation.
To versioneer-enable your project:
-* 1: Run `versioneer-installer` to copy `versioneer.py` into the top of your
- source tree.
-
-* 2: add the following lines to the top of your `setup.py`, with the
- configuration values you decided earlier:
+* 1: Modify your `setup.cfg`, adding a section named `[versioneer]` and
+ populating it with the configuration values you decided earlier (note that
+ the option names are not case-sensitive):
````
- import versioneer
- versioneer.VCS = 'git'
- versioneer.versionfile_source = 'src/myproject/_version.py'
- versioneer.versionfile_build = 'myproject/_version.py'
- versioneer.tag_prefix = '' # tags are like 1.2.0
- versioneer.parentdir_prefix = 'myproject-' # dirname like 'myproject-1.2.0'
+ [versioneer]
+ VCS = git
+ style = pep440
+ versionfile_source = src/myproject/_version.py
+ versionfile_build = myproject/_version.py
+ tag_prefix =
+ parentdir_prefix = myproject-
````
-* 3: add the following arguments to the setup() call in your setup.py:
+* 2: Run `versioneer install`. This will do the following:
+
+ * copy `versioneer.py` into the top of your source tree
+ * create `_version.py` in the right place (`versionfile_source`)
+ * modify your `__init__.py` (if one exists next to `_version.py`) to define
+ `__version__` (by calling a function from `_version.py`)
+ * modify your `MANIFEST.in` to include both `versioneer.py` and the
+ generated `_version.py` in sdist tarballs
+
+ `versioneer install` will complain about any problems it finds with your
+ `setup.py` or `setup.cfg`. Run it multiple times until you have fixed all
+ the problems.
+
+* 3: add a `import versioneer` to your setup.py, and add the following
+ arguments to the setup() call:
version=versioneer.get_version(),
cmdclass=versioneer.get_cmdclass(),
-* 4: now run `setup.py versioneer`, which will create `_version.py`, and will
- modify your `__init__.py` (if one exists next to `_version.py`) to define
- `__version__` (by calling a function from `_version.py`). It will also
- modify your `MANIFEST.in` to include both `versioneer.py` and the generated
- `_version.py` in sdist tarballs.
-
-* 5: commit these changes to your VCS. To make sure you won't forget,
- `setup.py versioneer` will mark everything it touched for addition.
+* 4: commit these changes to your VCS. To make sure you won't forget,
+ `versioneer install` will mark everything it touched for addition using
+ `git add`. Don't forget to add `setup.py` and `setup.cfg` too.
## Post-Installation Usage
@@ -187,9 +205,8 @@ tarballs with `git archive`), the process is:
* 1: git tag 1.0
* 2: git push; git push --tags
-Currently, all version strings must be based upon a tag. Versioneer will
-report "unknown" until your tree has at least one tag in its history. This
-restriction will be fixed eventually (see issue #12).
+Versioneer will report "0+untagged.NUMCOMMITS.gHASH" until your tree has at
+least one tag in its history.
## Version-String Flavors
@@ -198,60 +215,92 @@ importing `_version` from your main `__init__.py` file and running the
`get_versions()` function. From the "outside" (e.g. in `setup.py`), you can
import the top-level `versioneer.py` and run `get_versions()`.
-Both functions return a dictionary with different keys for different flavors
-of the version string:
-
-* `['version']`: A condensed PEP440-compliant string, equal to the
- un-prefixed tag name for actual releases, and containing an additional
- "local version" section with more detail for in-between builds. For Git,
- this is TAG[+DISTANCE.gHEX[.dirty]] , using information from `git describe
- --tags --dirty --always`. For example "0.11+2.g1076c97.dirty" indicates
- that the tree is like the "1076c97" commit but has uncommitted changes
- (".dirty"), and that this commit is two revisions ("+2") beyond the "0.11"
- tag. For released software (exactly equal to a known tag), the identifier
- will only contain the stripped tag, e.g. "0.11".
-
-* `['full']`: detailed revision identifier. For Git, this is the full SHA1
- commit id, followed by ".dirty" if the tree contains uncommitted changes,
- e.g. "1076c978a8d3cfc70f408fe5974aa6c092c949ac.dirty".
-
-Some variants are more useful than others. Including `full` in a bug report
-should allow developers to reconstruct the exact code being tested (or
-indicate the presence of local changes that should be shared with the
+Both functions return a dictionary with different flavors of version
+information:
+
+* `['version']`: A condensed version string, rendered using the selected
+ style. This is the most commonly used value for the project's version
+ string. The default "pep440" style yields strings like `0.11`,
+ `0.11+2.g1076c97`, or `0.11+2.g1076c97.dirty`. See the "Styles" section
+ below for alternative styles.
+
+* `['full-revisionid']`: detailed revision identifier. For Git, this is the
+ full SHA1 commit id, e.g. "1076c978a8d3cfc70f408fe5974aa6c092c949ac".
+
+* `['dirty']`: a boolean, True if the tree has uncommitted changes. Note that
+ this is only accurate if run in a VCS checkout, otherwise it is likely to
+ be False or None
+
+* `['error']`: if the version string could not be computed, this will be set
+ to a string describing the problem, otherwise it will be None. It may be
+ useful to throw an exception in setup.py if this is set, to avoid e.g.
+ creating tarballs with a version string of "unknown".
+
+Some variants are more useful than others. Including `full-revisionid` in a
+bug report should allow developers to reconstruct the exact code being tested
+(or indicate the presence of local changes that should be shared with the
developers). `version` is suitable for display in an "about" box or a CLI
`--version` output: it can be easily compared against release notes and lists
of bugs fixed in various releases.
-The `setup.py versioneer` command adds the following text to your
-`__init__.py` to place a basic version in `YOURPROJECT.__version__`:
+The installer adds the following text to your `__init__.py` to place a basic
+version in `YOURPROJECT.__version__`:
from ._version import get_versions
__version__ = get_versions()['version']
del get_versions
+## Styles
+
+The setup.cfg `style=` configuration controls how the VCS information is
+rendered into a version string.
+
+The default style, "pep440", produces a PEP440-compliant string, equal to the
+un-prefixed tag name for actual releases, and containing an additional "local
+version" section with more detail for in-between builds. For Git, this is
+TAG[+DISTANCE.gHEX[.dirty]] , using information from `git describe --tags
+--dirty --always`. For example "0.11+2.g1076c97.dirty" indicates that the
+tree is like the "1076c97" commit but has uncommitted changes (".dirty"), and
+that this commit is two revisions ("+2") beyond the "0.11" tag. For released
+software (exactly equal to a known tag), the identifier will only contain the
+stripped tag, e.g. "0.11".
+
+Other styles are available. See details.md in the Versioneer source tree for
+descriptions.
+
+## Debugging
+
+Versioneer tries to avoid fatal errors: if something goes wrong, it will tend
+to return a version of "0+unknown". To investigate the problem, run `setup.py
+version`, which will run the version-lookup code in a verbose mode, and will
+display the full contents of `get_versions()` (including the `error` string,
+which may help identify what went wrong).
+
## Updating Versioneer
To upgrade your project to a new release of Versioneer, do the following:
* install the new Versioneer (`pip install -U versioneer` or equivalent)
-* re-run `versioneer-installer` in your source tree to replace your copy of
- `versioneer.py`
-* edit `setup.py`, if necessary, to include any new configuration settings
+* edit `setup.cfg`, if necessary, to include any new configuration settings
indicated by the release notes
-* re-run `setup.py versioneer` to replace `SRC/_version.py`
+* re-run `versioneer install` in your source tree, to replace
+ `SRC/_version.py`
* commit any changed files
-### Upgrading from 0.10 to 0.11
-
-You must add a `versioneer.VCS = "git"` to your `setup.py` before re-running
-`setup.py versioneer`. This will enable the use of additional version-control
-systems (SVN, etc) in the future.
+### Upgrading to 0.15
-### Upgrading from 0.11 to 0.12
+Starting with this version, Versioneer is configured with a `[versioneer]`
+section in your `setup.cfg` file. Earlier versions required the `setup.py` to
+set attributes on the `versioneer` module immediately after import. The new
+version will refuse to run (raising an exception during import) until you
+have provided the necessary `setup.cfg` section.
-Nothing special.
+In addition, the Versioneer package provides an executable named
+`versioneer`, and the installation process is driven by running `versioneer
+install`. In 0.14 and earlier, the executable was named
+`versioneer-installer` and was run without an argument.
-## Upgrading to 0.14
+### Upgrading to 0.14
0.14 changes the format of the version string. 0.13 and earlier used
hyphen-separated strings like "0.11-2-g1076c97-dirty". 0.14 and beyond use a
@@ -259,6 +308,16 @@ plus-separated "local version" section strings, with dot-separated
components, like "0.11+2.g1076c97". PEP440-strict tools did not like the old
format, but should be ok with the new one.
+### Upgrading from 0.11 to 0.12
+
+Nothing special.
+
+### Upgrading from 0.10 to 0.11
+
+You must add a `versioneer.VCS = "git"` to your `setup.py` before re-running
+`setup.py setup_versioneer`. This will enable the use of additional
+version-control systems (SVN, etc) in the future.
+
## Future Directions
This tool is designed to make it easily extended to other version-control
@@ -275,39 +334,125 @@ number of intermediate scripts.
## License
-To make Versioneer easier to embed, all its code is hereby released into the
-public domain. The `_version.py` that it creates is also in the public
-domain.
+To make Versioneer easier to embed, all its code is dedicated to the public
+domain. The `_version.py` that it creates is also in the public domain.
+Specifically, both are released under the Creative Commons "Public Domain
+Dedication" license (CC0-1.0), as described in
+https://creativecommons.org/publicdomain/zero/1.0/ .
"""
-from __future__ import print_function
+from __future__ import print_function
+try:
+ import configparser
+except ImportError:
+ import ConfigParser as configparser
import errno
+import json
import os
import re
import subprocess
import sys
-from distutils.command.build import build as _build
-from distutils.command.sdist import sdist as _sdist
-from distutils.core import Command
-
-# these configuration settings will be overridden by setup.py after it
-# imports us
-versionfile_source = None
-versionfile_build = None
-tag_prefix = None
-parentdir_prefix = None
-VCS = None
+
+
+class VersioneerConfig:
+
+ """Container for Versioneer configuration parameters."""
+
+
+def get_root():
+ """Get the project root directory.
+
+ We require that all commands are run from the project root, i.e. the
+ directory that contains setup.py, setup.cfg, and versioneer.py .
+ """
+ root = os.path.realpath(os.path.abspath(os.getcwd()))
+ setup_py = os.path.join(root, "setup.py")
+ versioneer_py = os.path.join(root, "versioneer.py")
+ if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)):
+ # allow 'python path/to/setup.py COMMAND'
+ root = os.path.dirname(os.path.realpath(os.path.abspath(sys.argv[0])))
+ setup_py = os.path.join(root, "setup.py")
+ versioneer_py = os.path.join(root, "versioneer.py")
+ if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)):
+ err = ("Versioneer was unable to run the project root directory. "
+ "Versioneer requires setup.py to be executed from "
+ "its immediate directory (like 'python setup.py COMMAND'), "
+ "or in a way that lets it use sys.argv[0] to find the root "
+ "(like 'python path/to/setup.py COMMAND').")
+ raise VersioneerBadRootError(err)
+ try:
+ # Certain runtime workflows (setup.py install/develop in a setuptools
+ # tree) execute all dependencies in a single python process, so
+ # "versioneer" may be imported multiple times, and python's shared
+ # module-import table will cache the first one. So we can't use
+ # os.path.dirname(__file__), as that will find whichever
+ # versioneer.py was first imported, even in later projects.
+ me = os.path.realpath(os.path.abspath(__file__))
+ if os.path.splitext(me)[0] != os.path.splitext(versioneer_py)[0]:
+ print("Warning: build in %s is using versioneer.py from %s"
+ % (os.path.dirname(me), versioneer_py))
+ except NameError:
+ pass
+ return root
+
+
+def get_config_from_root(root):
+ """Read the project setup.cfg file to determine Versioneer config."""
+ # This might raise EnvironmentError (if setup.cfg is missing), or
+ # configparser.NoSectionError (if it lacks a [versioneer] section), or
+ # configparser.NoOptionError (if it lacks "VCS="). See the docstring at
+ # the top of versioneer.py for instructions on writing your setup.cfg .
+ setup_cfg = os.path.join(root, "setup.cfg")
+ parser = configparser.SafeConfigParser()
+ with open(setup_cfg, "r") as f:
+ parser.readfp(f)
+ VCS = parser.get("versioneer", "VCS") # mandatory
+
+ def get(parser, name):
+ if parser.has_option("versioneer", name):
+ return parser.get("versioneer", name)
+ return None
+ cfg = VersioneerConfig()
+ cfg.VCS = VCS
+ cfg.style = get(parser, "style") or ""
+ cfg.versionfile_source = get(parser, "versionfile_source")
+ cfg.versionfile_build = get(parser, "versionfile_build")
+ cfg.tag_prefix = get(parser, "tag_prefix")
+ if cfg.tag_prefix in ("''", '""'):
+ cfg.tag_prefix = ""
+ cfg.parentdir_prefix = get(parser, "parentdir_prefix")
+ cfg.verbose = get(parser, "verbose")
+ return cfg
+
+
+class NotThisMethod(Exception):
+
+ """Exception raised if a method is not valid for the current scenario."""
# these dictionaries contain VCS-specific tools
LONG_VERSION_PY = {}
+HANDLERS = {}
+
+
+def register_vcs_handler(vcs, method): # decorator
+ """Decorator to mark a method as the handler for a particular VCS."""
+ def decorate(f):
+ """Store f in HANDLERS[vcs][method]."""
+ if vcs not in HANDLERS:
+ HANDLERS[vcs] = {}
+ HANDLERS[vcs][method] = f
+ return f
+ return decorate
def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False):
+ """Call the given command(s)."""
assert isinstance(commands, list)
p = None
for c in commands:
try:
+ dispcmd = str([c] + args)
# remember shell=False, so use git.cmd on windows, not just git
p = subprocess.Popen([c] + args, cwd=cwd, stdout=subprocess.PIPE,
stderr=(subprocess.PIPE if hide_stderr
@@ -318,7 +463,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False):
if e.errno == errno.ENOENT:
continue
if verbose:
- print("unable to run %s" % args[0])
+ print("unable to run %s" % dispcmd)
print(e)
return None
else:
@@ -330,7 +475,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False):
stdout = stdout.decode()
if p.returncode != 0:
if verbose:
- print("unable to run %s (error)" % args[0])
+ print("unable to run %s (error)" % dispcmd)
return None
return stdout
LONG_VERSION_PY['git'] = '''
@@ -341,7 +486,9 @@ LONG_VERSION_PY['git'] = '''
# that just contains the computed version number.
# This file is released into the public domain. Generated by
-# versioneer-0.14 (https://github.com/warner/python-versioneer)
+# versioneer-0.15+dev (https://github.com/warner/python-versioneer)
+
+"""Git implementation of _version.py."""
import errno
import os
@@ -349,21 +496,65 @@ import re
import subprocess
import sys
-# these strings will be replaced by git during git-archive
-git_refnames = "%(DOLLAR)sFormat:%%d%(DOLLAR)s"
-git_full = "%(DOLLAR)sFormat:%%H%(DOLLAR)s"
-# these strings are filled in when 'setup.py versioneer' creates _version.py
-tag_prefix = "%(TAG_PREFIX)s"
-parentdir_prefix = "%(PARENTDIR_PREFIX)s"
-versionfile_source = "%(VERSIONFILE_SOURCE)s"
+def get_keywords():
+ """Get the keywords needed to look up the version information."""
+ # these strings will be replaced by git during git-archive.
+ # setup.py/versioneer.py will grep for the variable names, so they must
+ # each be defined on a line of their own. _version.py will just call
+ # get_keywords().
+ git_refnames = "%(DOLLAR)sFormat:%%d%(DOLLAR)s"
+ git_full = "%(DOLLAR)sFormat:%%H%(DOLLAR)s"
+ keywords = {"refnames": git_refnames, "full": git_full}
+ return keywords
+
+
+class VersioneerConfig:
+
+ """Container for Versioneer configuration parameters."""
+
+
+def get_config():
+ """Create, populate and return the VersioneerConfig() object."""
+ # these strings are filled in when 'setup.py versioneer' creates
+ # _version.py
+ cfg = VersioneerConfig()
+ cfg.VCS = "git"
+ cfg.style = "%(STYLE)s"
+ cfg.tag_prefix = "%(TAG_PREFIX)s"
+ cfg.parentdir_prefix = "%(PARENTDIR_PREFIX)s"
+ cfg.versionfile_source = "%(VERSIONFILE_SOURCE)s"
+ cfg.verbose = False
+ return cfg
+
+
+class NotThisMethod(Exception):
+
+ """Exception raised if a method is not valid for the current scenario."""
+
+
+LONG_VERSION_PY = {}
+HANDLERS = {}
+
+
+def register_vcs_handler(vcs, method): # decorator
+ """Decorator to mark a method as the handler for a particular VCS."""
+ def decorate(f):
+ """Store f in HANDLERS[vcs][method]."""
+ if vcs not in HANDLERS:
+ HANDLERS[vcs] = {}
+ HANDLERS[vcs][method] = f
+ return f
+ return decorate
def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False):
+ """Call the given command(s)."""
assert isinstance(commands, list)
p = None
for c in commands:
try:
+ dispcmd = str([c] + args)
# remember shell=False, so use git.cmd on windows, not just git
p = subprocess.Popen([c] + args, cwd=cwd, stdout=subprocess.PIPE,
stderr=(subprocess.PIPE if hide_stderr
@@ -374,7 +565,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False):
if e.errno == errno.ENOENT:
continue
if verbose:
- print("unable to run %%s" %% args[0])
+ print("unable to run %%s" %% dispcmd)
print(e)
return None
else:
@@ -386,24 +577,31 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False):
stdout = stdout.decode()
if p.returncode != 0:
if verbose:
- print("unable to run %%s (error)" %% args[0])
+ print("unable to run %%s (error)" %% dispcmd)
return None
return stdout
-def versions_from_parentdir(parentdir_prefix, root, verbose=False):
- # Source tarballs conventionally unpack into a directory that includes
- # both the project name and a version string.
+def versions_from_parentdir(parentdir_prefix, root, verbose):
+ """Try to determine the version from the parent directory name.
+
+ Source tarballs conventionally unpack into a directory that includes
+ both the project name and a version string.
+ """
dirname = os.path.basename(root)
if not dirname.startswith(parentdir_prefix):
if verbose:
print("guessing rootdir is '%%s', but '%%s' doesn't start with "
"prefix '%%s'" %% (root, dirname, parentdir_prefix))
- return None
- return {"version": dirname[len(parentdir_prefix):], "full": ""}
+ raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
+ return {"version": dirname[len(parentdir_prefix):],
+ "full-revisionid": None,
+ "dirty": False, "error": None}
+ at register_vcs_handler("git", "get_keywords")
def git_get_keywords(versionfile_abs):
+ """Extract version information from the given file."""
# the code embedded in _version.py can just fetch the value of these
# keywords. When used from setup.py, we don't want to import _version.py,
# so we do it with a regexp instead. This function is not used from
@@ -426,14 +624,16 @@ def git_get_keywords(versionfile_abs):
return keywords
-def git_versions_from_keywords(keywords, tag_prefix, verbose=False):
+ at register_vcs_handler("git", "keywords")
+def git_versions_from_keywords(keywords, tag_prefix, verbose):
+ """Get version information from git keywords."""
if not keywords:
- return {} # keyword-finding function failed to find keywords
+ raise NotThisMethod("no keywords at all, weird")
refnames = keywords["refnames"].strip()
if refnames.startswith("$Format"):
if verbose:
print("keywords are unexpanded, not using")
- return {} # unexpanded, so not in an unpacked git-archive tarball
+ raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
refs = set([r.strip() for r in refnames.strip("()").split(",")])
# starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
# just "foo-1.0". If we see a "tag: " prefix, prefer those.
@@ -459,123 +659,317 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose=False):
if verbose:
print("picking %%s" %% r)
return {"version": r,
- "full": keywords["full"].strip()}
+ "full-revisionid": keywords["full"].strip(),
+ "dirty": False, "error": None
+ }
# no suitable tags, so version is "0+unknown", but full hex is still there
if verbose:
print("no suitable tags, using unknown + full revision id")
return {"version": "0+unknown",
- "full": keywords["full"].strip()}
+ "full-revisionid": keywords["full"].strip(),
+ "dirty": False, "error": "no suitable tags"}
-def git_parse_vcs_describe(git_describe, tag_prefix, verbose=False):
- # TAG-NUM-gHEX[-dirty] or HEX[-dirty] . TAG might have hyphens.
+ at register_vcs_handler("git", "pieces_from_vcs")
+def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
+ """Get version from 'git describe' in the root of the source tree.
- # dirty
+ This only gets called if the git-archive 'subst' keywords were *not*
+ expanded, and _version.py hasn't already been rewritten with a short
+ version string, meaning we're inside a checked out source tree.
+ """
+ if not os.path.exists(os.path.join(root, ".git")):
+ if verbose:
+ print("no .git in %%s" %% root)
+ raise NotThisMethod("no .git directory")
+
+ GITS = ["git"]
+ if sys.platform == "win32":
+ GITS = ["git.cmd", "git.exe"]
+ # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
+ # if there isn't one, this yields HEX[-dirty] (no NUM)
+ describe_out = run_command(GITS, ["describe", "--tags", "--dirty",
+ "--always", "--long",
+ "--match", "%%s*" %% tag_prefix],
+ cwd=root)
+ # --long was added in git-1.5.5
+ if describe_out is None:
+ raise NotThisMethod("'git describe' failed")
+ describe_out = describe_out.strip()
+ full_out = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
+ if full_out is None:
+ raise NotThisMethod("'git rev-parse' failed")
+ full_out = full_out.strip()
+
+ pieces = {}
+ pieces["long"] = full_out
+ pieces["short"] = full_out[:7] # maybe improved later
+ pieces["error"] = None
+
+ # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
+ # TAG might have hyphens.
+ git_describe = describe_out
+
+ # look for -dirty suffix
dirty = git_describe.endswith("-dirty")
+ pieces["dirty"] = dirty
if dirty:
git_describe = git_describe[:git_describe.rindex("-dirty")]
- dirty_suffix = ".dirty" if dirty else ""
# now we have TAG-NUM-gHEX or HEX
- if "-" not in git_describe: # just HEX
- return "0+untagged.g"+git_describe+dirty_suffix, dirty
+ if "-" in git_describe:
+ # TAG-NUM-gHEX
+ mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
+ if not mo:
+ # unparseable. Maybe git-describe is misbehaving?
+ pieces["error"] = ("unable to parse git-describe output: '%%s'"
+ %% describe_out)
+ return pieces
+
+ # tag
+ full_tag = mo.group(1)
+ if not full_tag.startswith(tag_prefix):
+ if verbose:
+ fmt = "tag '%%s' doesn't start with prefix '%%s'"
+ print(fmt %% (full_tag, tag_prefix))
+ pieces["error"] = ("tag '%%s' doesn't start with prefix '%%s'"
+ %% (full_tag, tag_prefix))
+ return pieces
+ pieces["closest-tag"] = full_tag[len(tag_prefix):]
- # just TAG-NUM-gHEX
- mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
- if not mo:
- # unparseable. Maybe git-describe is misbehaving?
- return "0+unparseable"+dirty_suffix, dirty
+ # distance: number of commits since tag
+ pieces["distance"] = int(mo.group(2))
- # tag
- full_tag = mo.group(1)
- if not full_tag.startswith(tag_prefix):
- if verbose:
- fmt = "tag '%%s' doesn't start with prefix '%%s'"
- print(fmt %% (full_tag, tag_prefix))
- return None, dirty
- tag = full_tag[len(tag_prefix):]
+ # commit: short hex revision ID
+ pieces["short"] = mo.group(3)
- # distance: number of commits since tag
- distance = int(mo.group(2))
+ else:
+ # HEX: no tags
+ pieces["closest-tag"] = None
+ count_out = run_command(GITS, ["rev-list", "HEAD", "--count"],
+ cwd=root)
+ pieces["distance"] = int(count_out) # total number of commits
+
+ return pieces
+
+
+def plus_or_dot(pieces):
+ """Return a + if we don't already have one, else return a ."""
+ if "+" in pieces.get("closest-tag", ""):
+ return "."
+ return "+"
+
+
+def render_pep440(pieces):
+ """Build up version string, with post-release "local version identifier".
+
+ Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
+ get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty
+
+ Exceptions:
+ 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty]
+ """
+ if pieces["closest-tag"]:
+ rendered = pieces["closest-tag"]
+ if pieces["distance"] or pieces["dirty"]:
+ rendered += plus_or_dot(pieces)
+ rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"])
+ if pieces["dirty"]:
+ rendered += ".dirty"
+ else:
+ # exception #1
+ rendered = "0+untagged.%%d.g%%s" %% (pieces["distance"],
+ pieces["short"])
+ if pieces["dirty"]:
+ rendered += ".dirty"
+ return rendered
+
+
+def render_pep440_pre(pieces):
+ """TAG[.post.devDISTANCE] -- No -dirty.
+
+ Exceptions:
+ 1: no tags. 0.post.devDISTANCE
+ """
+ if pieces["closest-tag"]:
+ rendered = pieces["closest-tag"]
+ if pieces["distance"]:
+ rendered += ".post.dev%%d" %% pieces["distance"]
+ else:
+ # exception #1
+ rendered = "0.post.dev%%d" %% pieces["distance"]
+ return rendered
+
+
+def render_pep440_post(pieces):
+ """TAG[.postDISTANCE[.dev0]+gHEX] .
+
+ The ".dev0" means dirty. Note that .dev0 sorts backwards
+ (a dirty tree will appear "older" than the corresponding clean one),
+ but you shouldn't be releasing software with -dirty anyways.
+
+ Exceptions:
+ 1: no tags. 0.postDISTANCE[.dev0]
+ """
+ if pieces["closest-tag"]:
+ rendered = pieces["closest-tag"]
+ if pieces["distance"] or pieces["dirty"]:
+ rendered += ".post%%d" %% pieces["distance"]
+ if pieces["dirty"]:
+ rendered += ".dev0"
+ rendered += plus_or_dot(pieces)
+ rendered += "g%%s" %% pieces["short"]
+ else:
+ # exception #1
+ rendered = "0.post%%d" %% pieces["distance"]
+ if pieces["dirty"]:
+ rendered += ".dev0"
+ rendered += "+g%%s" %% pieces["short"]
+ return rendered
+
+
+def render_pep440_old(pieces):
+ """TAG[.postDISTANCE[.dev0]] .
+
+ The ".dev0" means dirty.
+
+ Eexceptions:
+ 1: no tags. 0.postDISTANCE[.dev0]
+ """
+ if pieces["closest-tag"]:
+ rendered = pieces["closest-tag"]
+ if pieces["distance"] or pieces["dirty"]:
+ rendered += ".post%%d" %% pieces["distance"]
+ if pieces["dirty"]:
+ rendered += ".dev0"
+ else:
+ # exception #1
+ rendered = "0.post%%d" %% pieces["distance"]
+ if pieces["dirty"]:
+ rendered += ".dev0"
+ return rendered
- # commit: short hex revision ID
- commit = mo.group(3)
- # now build up version string, with post-release "local version
- # identifier". Our goal: TAG[+NUM.gHEX[.dirty]] . Note that if you get a
- # tagged build and then dirty it, you'll get TAG+0.gHEX.dirty . So you
- # can always test version.endswith(".dirty").
- version = tag
- if distance or dirty:
- version += "+%%d.g%%s" %% (distance, commit) + dirty_suffix
+def render_git_describe(pieces):
+ """TAG[-DISTANCE-gHEX][-dirty].
- return version, dirty
+ Like 'git describe --tags --dirty --always'.
+ Exceptions:
+ 1: no tags. HEX[-dirty] (note: no 'g' prefix)
+ """
+ if pieces["closest-tag"]:
+ rendered = pieces["closest-tag"]
+ if pieces["distance"]:
+ rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"])
+ else:
+ # exception #1
+ rendered = pieces["short"]
+ if pieces["dirty"]:
+ rendered += "-dirty"
+ return rendered
-def git_versions_from_vcs(tag_prefix, root, verbose=False):
- # this runs 'git' from the root of the source tree. This only gets called
- # if the git-archive 'subst' keywords were *not* expanded, and
- # _version.py hasn't already been rewritten with a short version string,
- # meaning we're inside a checked out source tree.
- if not os.path.exists(os.path.join(root, ".git")):
- if verbose:
- print("no .git in %%s" %% root)
- return {} # get_versions() will try next method
+def render_git_describe_long(pieces):
+ """TAG-DISTANCE-gHEX[-dirty].
- GITS = ["git"]
- if sys.platform == "win32":
- GITS = ["git.cmd", "git.exe"]
- # if there is a tag, this yields TAG-NUM-gHEX[-dirty]
- # if there are no tags, this yields HEX[-dirty] (no NUM)
- stdout = run_command(GITS, ["describe", "--tags", "--dirty",
- "--always", "--long"],
- cwd=root)
- # --long was added in git-1.5.5
- if stdout is None:
- return {} # try next method
- version, dirty = git_parse_vcs_describe(stdout, tag_prefix, verbose)
-
- # build "full", which is FULLHEX[.dirty]
- stdout = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
- if stdout is None:
- return {}
- full = stdout.strip()
- if dirty:
- full += ".dirty"
+ Like 'git describe --tags --dirty --always -long'.
+ The distance/hash is unconditional.
+
+ Exceptions:
+ 1: no tags. HEX[-dirty] (note: no 'g' prefix)
+ """
+ if pieces["closest-tag"]:
+ rendered = pieces["closest-tag"]
+ rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"])
+ else:
+ # exception #1
+ rendered = pieces["short"]
+ if pieces["dirty"]:
+ rendered += "-dirty"
+ return rendered
+
+
+def render(pieces, style):
+ """Render the given version pieces into the requested style."""
+ if pieces["error"]:
+ return {"version": "unknown",
+ "full-revisionid": pieces.get("long"),
+ "dirty": None,
+ "error": pieces["error"]}
+
+ if not style or style == "default":
+ style = "pep440" # the default
+
+ if style == "pep440":
+ rendered = render_pep440(pieces)
+ elif style == "pep440-pre":
+ rendered = render_pep440_pre(pieces)
+ elif style == "pep440-post":
+ rendered = render_pep440_post(pieces)
+ elif style == "pep440-old":
+ rendered = render_pep440_old(pieces)
+ elif style == "git-describe":
+ rendered = render_git_describe(pieces)
+ elif style == "git-describe-long":
+ rendered = render_git_describe_long(pieces)
+ else:
+ raise ValueError("unknown style '%%s'" %% style)
- return {"version": version, "full": full}
+ return {"version": rendered, "full-revisionid": pieces["long"],
+ "dirty": pieces["dirty"], "error": None}
-def get_versions(default={"version": "0+unknown", "full": ""}, verbose=False):
+def get_versions():
+ """Get version information or return default if unable to do so."""
# I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have
# __file__, we can work backwards from there to the root. Some
# py2exe/bbfreeze/non-CPython implementations don't do __file__, in which
# case we can only use expanded keywords.
- keywords = {"refnames": git_refnames, "full": git_full}
- ver = git_versions_from_keywords(keywords, tag_prefix, verbose)
- if ver:
- return ver
+ cfg = get_config()
+ verbose = cfg.verbose
+
+ try:
+ return git_versions_from_keywords(get_keywords(), cfg.tag_prefix,
+ verbose)
+ except NotThisMethod:
+ pass
try:
root = os.path.realpath(__file__)
# versionfile_source is the relative path from the top of the source
# tree (where the .git directory might live) to this file. Invert
# this to find the root from __file__.
- for i in versionfile_source.split('/'):
+ for i in cfg.versionfile_source.split('/'):
root = os.path.dirname(root)
except NameError:
- return default
+ return {"version": "0+unknown", "full-revisionid": None,
+ "dirty": None,
+ "error": "unable to find root of source tree"}
+
+ try:
+ pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
+ return render(pieces, cfg.style)
+ except NotThisMethod:
+ pass
- return (git_versions_from_vcs(tag_prefix, root, verbose)
- or versions_from_parentdir(parentdir_prefix, root, verbose)
- or default)
+ try:
+ if cfg.parentdir_prefix:
+ return versions_from_parentdir(cfg.parentdir_prefix, root, verbose)
+ except NotThisMethod:
+ pass
+
+ return {"version": "0+unknown", "full-revisionid": None,
+ "dirty": None,
+ "error": "unable to compute version"}
'''
+ at register_vcs_handler("git", "get_keywords")
def git_get_keywords(versionfile_abs):
+ """Extract version information from the given file."""
# the code embedded in _version.py can just fetch the value of these
# keywords. When used from setup.py, we don't want to import _version.py,
# so we do it with a regexp instead. This function is not used from
@@ -598,14 +992,16 @@ def git_get_keywords(versionfile_abs):
return keywords
-def git_versions_from_keywords(keywords, tag_prefix, verbose=False):
+ at register_vcs_handler("git", "keywords")
+def git_versions_from_keywords(keywords, tag_prefix, verbose):
+ """Get version information from git keywords."""
if not keywords:
- return {} # keyword-finding function failed to find keywords
+ raise NotThisMethod("no keywords at all, weird")
refnames = keywords["refnames"].strip()
if refnames.startswith("$Format"):
if verbose:
print("keywords are unexpanded, not using")
- return {} # unexpanded, so not in an unpacked git-archive tarball
+ raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
refs = set([r.strip() for r in refnames.strip("()").split(",")])
# starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
# just "foo-1.0". If we see a "tag: " prefix, prefer those.
@@ -631,96 +1027,107 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose=False):
if verbose:
print("picking %s" % r)
return {"version": r,
- "full": keywords["full"].strip()}
+ "full-revisionid": keywords["full"].strip(),
+ "dirty": False, "error": None
+ }
# no suitable tags, so version is "0+unknown", but full hex is still there
if verbose:
print("no suitable tags, using unknown + full revision id")
return {"version": "0+unknown",
- "full": keywords["full"].strip()}
-
-
-def git_parse_vcs_describe(git_describe, tag_prefix, verbose=False):
- # TAG-NUM-gHEX[-dirty] or HEX[-dirty] . TAG might have hyphens.
+ "full-revisionid": keywords["full"].strip(),
+ "dirty": False, "error": "no suitable tags"}
- # dirty
- dirty = git_describe.endswith("-dirty")
- if dirty:
- git_describe = git_describe[:git_describe.rindex("-dirty")]
- dirty_suffix = ".dirty" if dirty else ""
- # now we have TAG-NUM-gHEX or HEX
-
- if "-" not in git_describe: # just HEX
- return "0+untagged.g"+git_describe+dirty_suffix, dirty
-
- # just TAG-NUM-gHEX
- mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
- if not mo:
- # unparseable. Maybe git-describe is misbehaving?
- return "0+unparseable"+dirty_suffix, dirty
-
- # tag
- full_tag = mo.group(1)
- if not full_tag.startswith(tag_prefix):
- if verbose:
- fmt = "tag '%s' doesn't start with prefix '%s'"
- print(fmt % (full_tag, tag_prefix))
- return None, dirty
- tag = full_tag[len(tag_prefix):]
-
- # distance: number of commits since tag
- distance = int(mo.group(2))
-
- # commit: short hex revision ID
- commit = mo.group(3)
-
- # now build up version string, with post-release "local version
- # identifier". Our goal: TAG[+NUM.gHEX[.dirty]] . Note that if you get a
- # tagged build and then dirty it, you'll get TAG+0.gHEX.dirty . So you
- # can always test version.endswith(".dirty").
- version = tag
- if distance or dirty:
- version += "+%d.g%s" % (distance, commit) + dirty_suffix
-
- return version, dirty
-
-
-def git_versions_from_vcs(tag_prefix, root, verbose=False):
- # this runs 'git' from the root of the source tree. This only gets called
- # if the git-archive 'subst' keywords were *not* expanded, and
- # _version.py hasn't already been rewritten with a short version string,
- # meaning we're inside a checked out source tree.
+ at register_vcs_handler("git", "pieces_from_vcs")
+def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
+ """Get version from 'git describe' in the root of the source tree.
+ This only gets called if the git-archive 'subst' keywords were *not*
+ expanded, and _version.py hasn't already been rewritten with a short
+ version string, meaning we're inside a checked out source tree.
+ """
if not os.path.exists(os.path.join(root, ".git")):
if verbose:
print("no .git in %s" % root)
- return {} # get_versions() will try next method
+ raise NotThisMethod("no .git directory")
GITS = ["git"]
if sys.platform == "win32":
GITS = ["git.cmd", "git.exe"]
- # if there is a tag, this yields TAG-NUM-gHEX[-dirty]
- # if there are no tags, this yields HEX[-dirty] (no NUM)
- stdout = run_command(GITS, ["describe", "--tags", "--dirty",
- "--always", "--long"],
- cwd=root)
+ # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
+ # if there isn't one, this yields HEX[-dirty] (no NUM)
+ describe_out = run_command(GITS, ["describe", "--tags", "--dirty",
+ "--always", "--long",
+ "--match", "%s*" % tag_prefix],
+ cwd=root)
# --long was added in git-1.5.5
- if stdout is None:
- return {} # try next method
- version, dirty = git_parse_vcs_describe(stdout, tag_prefix, verbose)
-
- # build "full", which is FULLHEX[.dirty]
- stdout = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
- if stdout is None:
- return {}
- full = stdout.strip()
+ if describe_out is None:
+ raise NotThisMethod("'git describe' failed")
+ describe_out = describe_out.strip()
+ full_out = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
+ if full_out is None:
+ raise NotThisMethod("'git rev-parse' failed")
+ full_out = full_out.strip()
+
+ pieces = {}
+ pieces["long"] = full_out
+ pieces["short"] = full_out[:7] # maybe improved later
+ pieces["error"] = None
+
+ # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
+ # TAG might have hyphens.
+ git_describe = describe_out
+
+ # look for -dirty suffix
+ dirty = git_describe.endswith("-dirty")
+ pieces["dirty"] = dirty
if dirty:
- full += ".dirty"
+ git_describe = git_describe[:git_describe.rindex("-dirty")]
- return {"version": version, "full": full}
+ # now we have TAG-NUM-gHEX or HEX
+
+ if "-" in git_describe:
+ # TAG-NUM-gHEX
+ mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
+ if not mo:
+ # unparseable. Maybe git-describe is misbehaving?
+ pieces["error"] = ("unable to parse git-describe output: '%s'"
+ % describe_out)
+ return pieces
+
+ # tag
+ full_tag = mo.group(1)
+ if not full_tag.startswith(tag_prefix):
+ if verbose:
+ fmt = "tag '%s' doesn't start with prefix '%s'"
+ print(fmt % (full_tag, tag_prefix))
+ pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
+ % (full_tag, tag_prefix))
+ return pieces
+ pieces["closest-tag"] = full_tag[len(tag_prefix):]
+
+ # distance: number of commits since tag
+ pieces["distance"] = int(mo.group(2))
+
+ # commit: short hex revision ID
+ pieces["short"] = mo.group(3)
+
+ else:
+ # HEX: no tags
+ pieces["closest-tag"] = None
+ count_out = run_command(GITS, ["rev-list", "HEAD", "--count"],
+ cwd=root)
+ pieces["distance"] = int(count_out) # total number of commits
+
+ return pieces
def do_vcs_install(manifest_in, versionfile_source, ipy):
+ """Git-specific installation logic for Versioneer.
+
+ For Git, this means creating/changing .gitattributes to mark _version.py
+ for export-time keyword substitution.
+ """
GITS = ["git"]
if sys.platform == "win32":
GITS = ["git.cmd", "git.exe"]
@@ -753,201 +1160,484 @@ def do_vcs_install(manifest_in, versionfile_source, ipy):
run_command(GITS, ["add", "--"] + files)
-def versions_from_parentdir(parentdir_prefix, root, verbose=False):
- # Source tarballs conventionally unpack into a directory that includes
- # both the project name and a version string.
+def versions_from_parentdir(parentdir_prefix, root, verbose):
+ """Try to determine the version from the parent directory name.
+
+ Source tarballs conventionally unpack into a directory that includes
+ both the project name and a version string.
+ """
dirname = os.path.basename(root)
if not dirname.startswith(parentdir_prefix):
if verbose:
print("guessing rootdir is '%s', but '%s' doesn't start with "
"prefix '%s'" % (root, dirname, parentdir_prefix))
- return None
- return {"version": dirname[len(parentdir_prefix):], "full": ""}
+ raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
+ return {"version": dirname[len(parentdir_prefix):],
+ "full-revisionid": None,
+ "dirty": False, "error": None}
SHORT_VERSION_PY = """
-# This file was generated by 'versioneer.py' (0.14) from
+# This file was generated by 'versioneer.py' (0.15+dev) from
# revision-control system data, or from the parent directory name of an
# unpacked source archive. Distribution tarballs contain a pre-generated copy
# of this file.
-version_version = '%(version)s'
-version_full = '%(full)s'
-def get_versions(default={}, verbose=False):
- return {'version': version_version, 'full': version_full}
+import json
+import sys
+
+version_json = '''
+%s
+''' # END VERSION_JSON
-"""
-DEFAULT = {"version": "0+unknown", "full": "unknown"}
+def get_versions():
+ return json.loads(version_json)
+"""
def versions_from_file(filename):
- versions = {}
+ """Try to determine the version from _version.py if present."""
try:
with open(filename) as f:
- for line in f.readlines():
- mo = re.match("version_version = '([^']+)'", line)
- if mo:
- versions["version"] = mo.group(1)
- mo = re.match("version_full = '([^']+)'", line)
- if mo:
- versions["full"] = mo.group(1)
+ contents = f.read()
except EnvironmentError:
- return {}
-
- return versions
+ raise NotThisMethod("unable to read _version.py")
+ mo = re.search(r"version_json = '''\n(.*)''' # END VERSION_JSON",
+ contents, re.M | re.S)
+ if not mo:
+ raise NotThisMethod("no version_json in _version.py")
+ return json.loads(mo.group(1))
def write_to_version_file(filename, versions):
+ """Write the given version number to the given _version.py file."""
+ os.unlink(filename)
+ contents = json.dumps(versions, sort_keys=True,
+ indent=1, separators=(",", ": "))
with open(filename, "w") as f:
- f.write(SHORT_VERSION_PY % versions)
+ f.write(SHORT_VERSION_PY % contents)
print("set %s to '%s'" % (filename, versions["version"]))
-def get_root():
- try:
- return os.path.dirname(os.path.abspath(__file__))
- except NameError:
- return os.path.dirname(os.path.abspath(sys.argv[0]))
+def plus_or_dot(pieces):
+ """Return a + if we don't already have one, else return a ."""
+ if "+" in pieces.get("closest-tag", ""):
+ return "."
+ return "+"
-def vcs_function(vcs, suffix):
- return getattr(sys.modules[__name__], '%s_%s' % (vcs, suffix), None)
+def render_pep440(pieces):
+ """Build up version string, with post-release "local version identifier".
+ Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
+ get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty
+
+ Exceptions:
+ 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty]
+ """
+ if pieces["closest-tag"]:
+ rendered = pieces["closest-tag"]
+ if pieces["distance"] or pieces["dirty"]:
+ rendered += plus_or_dot(pieces)
+ rendered += "%d.g%s" % (pieces["distance"], pieces["short"])
+ if pieces["dirty"]:
+ rendered += ".dirty"
+ else:
+ # exception #1
+ rendered = "0+untagged.%d.g%s" % (pieces["distance"],
+ pieces["short"])
+ if pieces["dirty"]:
+ rendered += ".dirty"
+ return rendered
+
+
+def render_pep440_pre(pieces):
+ """TAG[.post.devDISTANCE] -- No -dirty.
+
+ Exceptions:
+ 1: no tags. 0.post.devDISTANCE
+ """
+ if pieces["closest-tag"]:
+ rendered = pieces["closest-tag"]
+ if pieces["distance"]:
+ rendered += ".post.dev%d" % pieces["distance"]
+ else:
+ # exception #1
+ rendered = "0.post.dev%d" % pieces["distance"]
+ return rendered
+
+
+def render_pep440_post(pieces):
+ """TAG[.postDISTANCE[.dev0]+gHEX] .
+
+ The ".dev0" means dirty. Note that .dev0 sorts backwards
+ (a dirty tree will appear "older" than the corresponding clean one),
+ but you shouldn't be releasing software with -dirty anyways.
+
+ Exceptions:
+ 1: no tags. 0.postDISTANCE[.dev0]
+ """
+ if pieces["closest-tag"]:
+ rendered = pieces["closest-tag"]
+ if pieces["distance"] or pieces["dirty"]:
+ rendered += ".post%d" % pieces["distance"]
+ if pieces["dirty"]:
+ rendered += ".dev0"
+ rendered += plus_or_dot(pieces)
+ rendered += "g%s" % pieces["short"]
+ else:
+ # exception #1
+ rendered = "0.post%d" % pieces["distance"]
+ if pieces["dirty"]:
+ rendered += ".dev0"
+ rendered += "+g%s" % pieces["short"]
+ return rendered
+
+
+def render_pep440_old(pieces):
+ """TAG[.postDISTANCE[.dev0]] .
+
+ The ".dev0" means dirty.
+
+ Eexceptions:
+ 1: no tags. 0.postDISTANCE[.dev0]
+ """
+ if pieces["closest-tag"]:
+ rendered = pieces["closest-tag"]
+ if pieces["distance"] or pieces["dirty"]:
+ rendered += ".post%d" % pieces["distance"]
+ if pieces["dirty"]:
+ rendered += ".dev0"
+ else:
+ # exception #1
+ rendered = "0.post%d" % pieces["distance"]
+ if pieces["dirty"]:
+ rendered += ".dev0"
+ return rendered
+
+
+def render_git_describe(pieces):
+ """TAG[-DISTANCE-gHEX][-dirty].
+
+ Like 'git describe --tags --dirty --always'.
+
+ Exceptions:
+ 1: no tags. HEX[-dirty] (note: no 'g' prefix)
+ """
+ if pieces["closest-tag"]:
+ rendered = pieces["closest-tag"]
+ if pieces["distance"]:
+ rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
+ else:
+ # exception #1
+ rendered = pieces["short"]
+ if pieces["dirty"]:
+ rendered += "-dirty"
+ return rendered
+
+
+def render_git_describe_long(pieces):
+ """TAG-DISTANCE-gHEX[-dirty].
+
+ Like 'git describe --tags --dirty --always -long'.
+ The distance/hash is unconditional.
+
+ Exceptions:
+ 1: no tags. HEX[-dirty] (note: no 'g' prefix)
+ """
+ if pieces["closest-tag"]:
+ rendered = pieces["closest-tag"]
+ rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
+ else:
+ # exception #1
+ rendered = pieces["short"]
+ if pieces["dirty"]:
+ rendered += "-dirty"
+ return rendered
+
+
+def render(pieces, style):
+ """Render the given version pieces into the requested style."""
+ if pieces["error"]:
+ return {"version": "unknown",
+ "full-revisionid": pieces.get("long"),
+ "dirty": None,
+ "error": pieces["error"]}
+
+ if not style or style == "default":
+ style = "pep440" # the default
+
+ if style == "pep440":
+ rendered = render_pep440(pieces)
+ elif style == "pep440-pre":
+ rendered = render_pep440_pre(pieces)
+ elif style == "pep440-post":
+ rendered = render_pep440_post(pieces)
+ elif style == "pep440-old":
+ rendered = render_pep440_old(pieces)
+ elif style == "git-describe":
+ rendered = render_git_describe(pieces)
+ elif style == "git-describe-long":
+ rendered = render_git_describe_long(pieces)
+ else:
+ raise ValueError("unknown style '%s'" % style)
+
+ return {"version": rendered, "full-revisionid": pieces["long"],
+ "dirty": pieces["dirty"], "error": None}
+
+
+class VersioneerBadRootError(Exception):
+
+ """The project root directory is unknown or missing key files."""
+
+
+def get_versions(verbose=False):
+ """Get the project version from whatever source is available.
+
+ Returns dict with two keys: 'version' and 'full'.
+ """
+ if "versioneer" in sys.modules:
+ # see the discussion in cmdclass.py:get_cmdclass()
+ del sys.modules["versioneer"]
-def get_versions(default=DEFAULT, verbose=False):
- # returns dict with two keys: 'version' and 'full'
- assert versionfile_source is not None, \
- "please set versioneer.versionfile_source"
- assert tag_prefix is not None, "please set versioneer.tag_prefix"
- assert parentdir_prefix is not None, \
- "please set versioneer.parentdir_prefix"
- assert VCS is not None, "please set versioneer.VCS"
-
- # I am in versioneer.py, which must live at the top of the source tree,
- # which we use to compute the root directory. py2exe/bbfreeze/non-CPython
- # don't have __file__, in which case we fall back to sys.argv[0] (which
- # ought to be the setup.py script). We prefer __file__ since that's more
- # robust in cases where setup.py was invoked in some weird way (e.g. pip)
root = get_root()
- versionfile_abs = os.path.join(root, versionfile_source)
+ cfg = get_config_from_root(root)
+
+ assert cfg.VCS is not None, "please set [versioneer]VCS= in setup.cfg"
+ handlers = HANDLERS.get(cfg.VCS)
+ assert handlers, "unrecognized VCS '%s'" % cfg.VCS
+ verbose = verbose or cfg.verbose
+ assert cfg.versionfile_source is not None, \
+ "please set versioneer.versionfile_source"
+ assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix"
+
+ versionfile_abs = os.path.join(root, cfg.versionfile_source)
- # extract version from first of _version.py, VCS command (e.g. 'git
+ # extract version from first of: _version.py, VCS command (e.g. 'git
# describe'), parentdir. This is meant to work for developers using a
# source checkout, for users of a tarball created by 'setup.py sdist',
# and for users of a tarball/zipball created by 'git archive' or github's
# download-from-tag feature or the equivalent in other VCSes.
- get_keywords_f = vcs_function(VCS, "get_keywords")
- versions_from_keywords_f = vcs_function(VCS, "versions_from_keywords")
- if get_keywords_f and versions_from_keywords_f:
- vcs_keywords = get_keywords_f(versionfile_abs)
- ver = versions_from_keywords_f(vcs_keywords, tag_prefix)
- if ver:
+ get_keywords_f = handlers.get("get_keywords")
+ from_keywords_f = handlers.get("keywords")
+ if get_keywords_f and from_keywords_f:
+ try:
+ keywords = get_keywords_f(versionfile_abs)
+ ver = from_keywords_f(keywords, cfg.tag_prefix, verbose)
if verbose:
print("got version from expanded keyword %s" % ver)
return ver
+ except NotThisMethod:
+ pass
- ver = versions_from_file(versionfile_abs)
- if ver:
+ try:
+ ver = versions_from_file(versionfile_abs)
if verbose:
print("got version from file %s %s" % (versionfile_abs, ver))
return ver
+ except NotThisMethod:
+ pass
- versions_from_vcs_f = vcs_function(VCS, "versions_from_vcs")
- if versions_from_vcs_f:
- ver = versions_from_vcs_f(tag_prefix, root, verbose)
- if ver:
+ from_vcs_f = handlers.get("pieces_from_vcs")
+ if from_vcs_f:
+ try:
+ pieces = from_vcs_f(cfg.tag_prefix, root, verbose)
+ ver = render(pieces, cfg.style)
if verbose:
print("got version from VCS %s" % ver)
return ver
+ except NotThisMethod:
+ pass
- ver = versions_from_parentdir(parentdir_prefix, root, verbose)
- if ver:
- if verbose:
- print("got version from parentdir %s" % ver)
- return ver
+ try:
+ if cfg.parentdir_prefix:
+ ver = versions_from_parentdir(cfg.parentdir_prefix, root, verbose)
+ if verbose:
+ print("got version from parentdir %s" % ver)
+ return ver
+ except NotThisMethod:
+ pass
if verbose:
- print("got version from default %s" % default)
- return default
+ print("unable to compute version")
+ return {"version": "0+unknown", "full-revisionid": None,
+ "dirty": None, "error": "unable to compute version"}
-def get_version(verbose=False):
- return get_versions(verbose=verbose)["version"]
+def get_version():
+ """Get the short version string for this project."""
+ return get_versions()["version"]
-class cmd_version(Command):
- description = "report generated version string"
- user_options = []
- boolean_options = []
- def initialize_options(self):
- pass
+def get_cmdclass():
+ """Get the custom setuptools/distutils subclasses used by Versioneer."""
+ if "versioneer" in sys.modules:
+ del sys.modules["versioneer"]
+ # this fixes the "python setup.py develop" case (also 'install' and
+ # 'easy_install .'), in which subdependencies of the main project are
+ # built (using setup.py bdist_egg) in the same python process. Assume
+ # a main project A and a dependency B, which use different versions
+ # of Versioneer. A's setup.py imports A's Versioneer, leaving it in
+ # sys.modules by the time B's setup.py is executed, causing B to run
+ # with the wrong versioneer. Setuptools wraps the sub-dep builds in a
+ # sandbox that restores sys.modules to it's pre-build state, so the
+ # parent is protected against the child's "import versioneer". By
+ # removing ourselves from sys.modules here, before the child build
+ # happens, we protect the child from the parent's versioneer too.
+ # Also see https://github.com/warner/python-versioneer/issues/52
+
+ cmds = {}
+
+ # we add "version" to both distutils and setuptools
+ from distutils.core import Command
+
+ class cmd_version(Command):
+ description = "report generated version string"
+ user_options = []
+ boolean_options = []
+
+ def initialize_options(self):
+ pass
- def finalize_options(self):
- pass
+ def finalize_options(self):
+ pass
- def run(self):
- ver = get_version(verbose=True)
- print("Version is currently: %s" % ver)
+ def run(self):
+ vers = get_versions(verbose=True)
+ print("Version: %s" % vers["version"])
+ print(" full-revisionid: %s" % vers.get("full-revisionid"))
+ print(" dirty: %s" % vers.get("dirty"))
+ if vers["error"]:
+ print(" error: %s" % vers["error"])
+ cmds["version"] = cmd_version
+
+ # we override "build_py" in both distutils and setuptools
+ #
+ # most invocation pathways end up running build_py:
+ # distutils/build -> build_py
+ # distutils/install -> distutils/build ->..
+ # setuptools/bdist_wheel -> distutils/install ->..
+ # setuptools/bdist_egg -> distutils/install_lib -> build_py
+ # setuptools/install -> bdist_egg ->..
+ # setuptools/develop -> ?
+
+ # we override different "build_py" commands for both environments
+ if "setuptools" in sys.modules:
+ from setuptools.command.build_py import build_py as _build_py
+ else:
+ from distutils.command.build_py import build_py as _build_py
+ class cmd_build_py(_build_py):
+ def run(self):
+ root = get_root()
+ cfg = get_config_from_root(root)
+ versions = get_versions()
+ _build_py.run(self)
+ # now locate _version.py in the new build/ directory and replace
+ # it with an updated value
+ if cfg.versionfile_build:
+ target_versionfile = os.path.join(self.build_lib,
+ cfg.versionfile_build)
+ print("UPDATING %s" % target_versionfile)
+ write_to_version_file(target_versionfile, versions)
+ cmds["build_py"] = cmd_build_py
+
+ if "cx_Freeze" in sys.modules: # cx_freeze enabled?
+ from cx_Freeze.dist import build_exe as _build_exe
+
+ class cmd_build_exe(_build_exe):
+ def run(self):
+ root = get_root()
+ cfg = get_config_from_root(root)
+ versions = get_versions()
+ target_versionfile = cfg.versionfile_source
+ print("UPDATING %s" % target_versionfile)
+ write_to_version_file(target_versionfile, versions)
+
+ _build_exe.run(self)
+ os.unlink(target_versionfile)
+ with open(cfg.versionfile_source, "w") as f:
+ LONG = LONG_VERSION_PY[cfg.VCS]
+ f.write(LONG %
+ {"DOLLAR": "$",
+ "STYLE": cfg.style,
+ "TAG_PREFIX": cfg.tag_prefix,
+ "PARENTDIR_PREFIX": cfg.parentdir_prefix,
+ "VERSIONFILE_SOURCE": cfg.versionfile_source,
+ })
+ cmds["build_exe"] = cmd_build_exe
+ del cmds["build_py"]
+
+ # we override different "sdist" commands for both environments
+ if "setuptools" in sys.modules:
+ from setuptools.command.sdist import sdist as _sdist
+ else:
+ from distutils.command.sdist import sdist as _sdist
-class cmd_build(_build):
- def run(self):
- versions = get_versions(verbose=True)
- _build.run(self)
- # now locate _version.py in the new build/ directory and replace it
- # with an updated value
- if versionfile_build:
- target_versionfile = os.path.join(self.build_lib,
- versionfile_build)
+ class cmd_sdist(_sdist):
+ def run(self):
+ versions = get_versions()
+ self._versioneer_generated_versions = versions
+ # unless we update this, the command will keep using the old
+ # version
+ self.distribution.metadata.version = versions["version"]
+ return _sdist.run(self)
+
+ def make_release_tree(self, base_dir, files):
+ root = get_root()
+ cfg = get_config_from_root(root)
+ _sdist.make_release_tree(self, base_dir, files)
+ # now locate _version.py in the new base_dir directory
+ # (remembering that it may be a hardlink) and replace it with an
+ # updated value
+ target_versionfile = os.path.join(base_dir, cfg.versionfile_source)
print("UPDATING %s" % target_versionfile)
- os.unlink(target_versionfile)
- with open(target_versionfile, "w") as f:
- f.write(SHORT_VERSION_PY % versions)
+ write_to_version_file(target_versionfile,
+ self._versioneer_generated_versions)
+ cmds["sdist"] = cmd_sdist
-if 'cx_Freeze' in sys.modules: # cx_freeze enabled?
- from cx_Freeze.dist import build_exe as _build_exe
+ return cmds
- class cmd_build_exe(_build_exe):
- def run(self):
- versions = get_versions(verbose=True)
- target_versionfile = versionfile_source
- print("UPDATING %s" % target_versionfile)
- os.unlink(target_versionfile)
- with open(target_versionfile, "w") as f:
- f.write(SHORT_VERSION_PY % versions)
-
- _build_exe.run(self)
- os.unlink(target_versionfile)
- with open(versionfile_source, "w") as f:
- assert VCS is not None, "please set versioneer.VCS"
- LONG = LONG_VERSION_PY[VCS]
- f.write(LONG % {"DOLLAR": "$",
- "TAG_PREFIX": tag_prefix,
- "PARENTDIR_PREFIX": parentdir_prefix,
- "VERSIONFILE_SOURCE": versionfile_source,
- })
-
-
-class cmd_sdist(_sdist):
- def run(self):
- versions = get_versions(verbose=True)
- self._versioneer_generated_versions = versions
- # unless we update this, the command will keep using the old version
- self.distribution.metadata.version = versions["version"]
- return _sdist.run(self)
-
- def make_release_tree(self, base_dir, files):
- _sdist.make_release_tree(self, base_dir, files)
- # now locate _version.py in the new base_dir directory (remembering
- # that it may be a hardlink) and replace it with an updated value
- target_versionfile = os.path.join(base_dir, versionfile_source)
- print("UPDATING %s" % target_versionfile)
- os.unlink(target_versionfile)
- with open(target_versionfile, "w") as f:
- f.write(SHORT_VERSION_PY % self._versioneer_generated_versions)
+
+CONFIG_ERROR = """
+setup.cfg is missing the necessary Versioneer configuration. You need
+a section like:
+
+ [versioneer]
+ VCS = git
+ style = pep440
+ versionfile_source = src/myproject/_version.py
+ versionfile_build = myproject/_version.py
+ tag_prefix =
+ parentdir_prefix = myproject-
+
+You will also need to edit your setup.py to use the results:
+
+ import versioneer
+ setup(version=versioneer.get_version(),
+ cmdclass=versioneer.get_cmdclass(), ...)
+
+Please read the docstring in ./versioneer.py for configuration instructions,
+edit setup.cfg, and re-run the installer or 'python versioneer.py setup'.
+"""
+
+SAMPLE_CONFIG = """
+# See the docstring in versioneer.py for instructions. Note that you must
+# re-run 'versioneer.py setup' after changing this section, and commit the
+# resulting files.
+
+[versioneer]
+#VCS = git
+#style = pep440
+#versionfile_source =
+#versionfile_build =
+#tag_prefix =
+#parentdir_prefix =
+
+"""
INIT_PY_SNIPPET = """
from ._version import get_versions
@@ -956,92 +1646,128 @@ del get_versions
"""
-class cmd_update_files(Command):
- description = ("install/upgrade Versioneer files: "
- "__init__.py SRC/_version.py")
- user_options = []
- boolean_options = []
-
- def initialize_options(self):
- pass
-
- def finalize_options(self):
- pass
-
- def run(self):
- print(" creating %s" % versionfile_source)
- with open(versionfile_source, "w") as f:
- assert VCS is not None, "please set versioneer.VCS"
- LONG = LONG_VERSION_PY[VCS]
- f.write(LONG % {"DOLLAR": "$",
- "TAG_PREFIX": tag_prefix,
- "PARENTDIR_PREFIX": parentdir_prefix,
- "VERSIONFILE_SOURCE": versionfile_source,
- })
-
- ipy = os.path.join(os.path.dirname(versionfile_source), "__init__.py")
- if os.path.exists(ipy):
- try:
- with open(ipy, "r") as f:
- old = f.read()
- except EnvironmentError:
- old = ""
- if INIT_PY_SNIPPET not in old:
- print(" appending to %s" % ipy)
- with open(ipy, "a") as f:
- f.write(INIT_PY_SNIPPET)
- else:
- print(" %s unmodified" % ipy)
- else:
- print(" %s doesn't exist, ok" % ipy)
- ipy = None
-
- # Make sure both the top-level "versioneer.py" and versionfile_source
- # (PKG/_version.py, used by runtime code) are in MANIFEST.in, so
- # they'll be copied into source distributions. Pip won't be able to
- # install the package without this.
- manifest_in = os.path.join(get_root(), "MANIFEST.in")
- simple_includes = set()
+def do_setup():
+ """Main VCS-independent setup function for installing Versioneer."""
+ root = get_root()
+ try:
+ cfg = get_config_from_root(root)
+ except (EnvironmentError, configparser.NoSectionError,
+ configparser.NoOptionError) as e:
+ if isinstance(e, (EnvironmentError, configparser.NoSectionError)):
+ print("Adding sample versioneer config to setup.cfg",
+ file=sys.stderr)
+ with open(os.path.join(root, "setup.cfg"), "a") as f:
+ f.write(SAMPLE_CONFIG)
+ print(CONFIG_ERROR, file=sys.stderr)
+ return 1
+
+ print(" creating %s" % cfg.versionfile_source)
+ with open(cfg.versionfile_source, "w") as f:
+ LONG = LONG_VERSION_PY[cfg.VCS]
+ f.write(LONG % {"DOLLAR": "$",
+ "STYLE": cfg.style,
+ "TAG_PREFIX": cfg.tag_prefix,
+ "PARENTDIR_PREFIX": cfg.parentdir_prefix,
+ "VERSIONFILE_SOURCE": cfg.versionfile_source,
+ })
+
+ ipy = os.path.join(os.path.dirname(cfg.versionfile_source),
+ "__init__.py")
+ if os.path.exists(ipy):
try:
- with open(manifest_in, "r") as f:
- for line in f:
- if line.startswith("include "):
- for include in line.split()[1:]:
- simple_includes.add(include)
+ with open(ipy, "r") as f:
+ old = f.read()
except EnvironmentError:
- pass
- # That doesn't cover everything MANIFEST.in can do
- # (http://docs.python.org/2/distutils/sourcedist.html#commands), so
- # it might give some false negatives. Appending redundant 'include'
- # lines is safe, though.
- if "versioneer.py" not in simple_includes:
- print(" appending 'versioneer.py' to MANIFEST.in")
- with open(manifest_in, "a") as f:
- f.write("include versioneer.py\n")
- else:
- print(" 'versioneer.py' already in MANIFEST.in")
- if versionfile_source not in simple_includes:
- print(" appending versionfile_source ('%s') to MANIFEST.in" %
- versionfile_source)
- with open(manifest_in, "a") as f:
- f.write("include %s\n" % versionfile_source)
+ old = ""
+ if INIT_PY_SNIPPET not in old:
+ print(" appending to %s" % ipy)
+ with open(ipy, "a") as f:
+ f.write(INIT_PY_SNIPPET)
else:
- print(" versionfile_source already in MANIFEST.in")
-
- # Make VCS-specific changes. For git, this means creating/changing
- # .gitattributes to mark _version.py for export-time keyword
- # substitution.
- do_vcs_install(manifest_in, versionfile_source, ipy)
+ print(" %s unmodified" % ipy)
+ else:
+ print(" %s doesn't exist, ok" % ipy)
+ ipy = None
+
+ # Make sure both the top-level "versioneer.py" and versionfile_source
+ # (PKG/_version.py, used by runtime code) are in MANIFEST.in, so
+ # they'll be copied into source distributions. Pip won't be able to
+ # install the package without this.
+ manifest_in = os.path.join(root, "MANIFEST.in")
+ simple_includes = set()
+ try:
+ with open(manifest_in, "r") as f:
+ for line in f:
+ if line.startswith("include "):
+ for include in line.split()[1:]:
+ simple_includes.add(include)
+ except EnvironmentError:
+ pass
+ # That doesn't cover everything MANIFEST.in can do
+ # (http://docs.python.org/2/distutils/sourcedist.html#commands), so
+ # it might give some false negatives. Appending redundant 'include'
+ # lines is safe, though.
+ if "versioneer.py" not in simple_includes:
+ print(" appending 'versioneer.py' to MANIFEST.in")
+ with open(manifest_in, "a") as f:
+ f.write("include versioneer.py\n")
+ else:
+ print(" 'versioneer.py' already in MANIFEST.in")
+ if cfg.versionfile_source not in simple_includes:
+ print(" appending versionfile_source ('%s') to MANIFEST.in" %
+ cfg.versionfile_source)
+ with open(manifest_in, "a") as f:
+ f.write("include %s\n" % cfg.versionfile_source)
+ else:
+ print(" versionfile_source already in MANIFEST.in")
+ # Make VCS-specific changes. For git, this means creating/changing
+ # .gitattributes to mark _version.py for export-time keyword
+ # substitution.
+ do_vcs_install(manifest_in, cfg.versionfile_source, ipy)
+ return 0
-def get_cmdclass():
- cmds = {'version': cmd_version,
- 'versioneer': cmd_update_files,
- 'build': cmd_build,
- 'sdist': cmd_sdist,
- }
- if 'cx_Freeze' in sys.modules: # cx_freeze enabled?
- cmds['build_exe'] = cmd_build_exe
- del cmds['build']
- return cmds
+def scan_setup_py():
+ """Validate the contents of setup.py against Versioneer's expectations."""
+ found = set()
+ setters = False
+ errors = 0
+ with open("setup.py", "r") as f:
+ for line in f.readlines():
+ if "import versioneer" in line:
+ found.add("import")
+ if "versioneer.get_cmdclass()" in line:
+ found.add("cmdclass")
+ if "versioneer.get_version()" in line:
+ found.add("get_version")
+ if "versioneer.VCS" in line:
+ setters = True
+ if "versioneer.versionfile_source" in line:
+ setters = True
+ if len(found) != 3:
+ print("")
+ print("Your setup.py appears to be missing some important items")
+ print("(but I might be wrong). Please make sure it has something")
+ print("roughly like the following:")
+ print("")
+ print(" import versioneer")
+ print(" setup( version=versioneer.get_version(),")
+ print(" cmdclass=versioneer.get_cmdclass(), ...)")
+ print("")
+ errors += 1
+ if setters:
+ print("You should remove lines like 'versioneer.VCS = ' and")
+ print("'versioneer.versionfile_source = ' . This configuration")
+ print("now lives in setup.cfg, and should be removed from setup.py")
+ print("")
+ errors += 1
+ return errors
+
+if __name__ == "__main__":
+ cmd = sys.argv[1]
+ if cmd == "setup":
+ errors = do_setup()
+ errors += scan_setup_py()
+ if errors:
+ sys.exit(1)
--
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