[med-svn] [khmer] branch upstream updated (a9e0b66 -> a119d2c)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sun Jun 25 16:46:40 UTC 2017
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch upstream
in repository khmer.
from a9e0b66 Imported Upstream version 2.0+dfsg
adds 021bb43 New upstream version 2.0~pre2.1-20170216-b2ab51575c2fa4c6bff078387ed8b67c4299df12
adds a119d2c New upstream version 2.1.1+dfsg
No new revisions were added by this update.
Summary of changes:
.dictionary | 155 +
doc/dev/details.rst => .github/CONTRIBUTING.md | 24 +-
.github/PULL_REQUEST_TEMPLATE.md | 16 +
.gitignore | 5 +-
.mailmap | 10 +-
.travis.yml | 91 +
CHANGELOG.md | 79 +
CITATION | 12 +-
CONTRIBUTING.md | 42 -
IDEAS | 18 -
MANIFEST.in | 5 +-
Makefile | 223 +-
README.rst | 117 +-
TODO | 80 -
author-skips.txt | 15 +
authors.csv | 68 +
ci_scripts/install.sh | 31 +
data/16s+23s.fa | 800 -
data/16s.fa | 714 -
data/1m-bigpart.fa | 44872 --------
data/23s.fa | 86 -
data/MSB2-part.group1.fa | 100806 -----------------
data/MSB2-part.group10.fa | 101128 -----------------
data/MSB2-part.group31.fa | 103446 ------------------
data/high-sodd.fa | 384 -
data/mda-test.fa | 28 -
data/primers.fa | 4 -
doc/conf.py | 31 +-
doc/contributors.rst | 51 +-
doc/dev/a-quick-guide-to-testing.rst | 50 +-
doc/dev/binary-file-formats.rst | 14 +-
doc/dev/codebase-guide.rst | 23 +-
doc/dev/coding-guidelines-and-review.rst | 189 -
doc/dev/development.rst | 95 +-
doc/dev/for-khmer-developers.rst | 33 +-
doc/dev/getting-started.rst | 399 +-
doc/dev/guidelines-continued-dev.rst | 269 +
doc/dev/index.rst | 16 +-
doc/dev/python-api.rst | 152 +
doc/dev/release.rst | 127 +-
doc/dev/scripts-and-sandbox.rst | 47 +-
doc/index.rst | 53 +-
doc/introduction.rst | 115 +-
doc/release-notes/release-1.2.md | 64 +-
doc/release-notes/release-1.2.rst | 25 +-
doc/release-notes/release-1.4.md | 10 +-
doc/release-notes/release-1.4.rst | 12 +-
doc/release-notes/release-2.0.md | 4 +-
doc/release-notes/release-2.0.rst | 4 +-
doc/release-notes/release-2.1.md | 47 +
doc/release-notes/release-2.1.rst | 78 +
doc/requirements.txt | 5 +-
doc/roadmap.rst | 16 +-
doc/{dev/crazy-ideas.rst => user/api-examples.rst} | 31 +-
doc/user/blog-posts.rst | 22 +-
doc/user/choosing-table-sizes.rst | 53 +-
doc/user/guide.rst | 16 +-
doc/user/index.rst | 16 +-
doc/user/install.rst | 43 +-
doc/user/known-issues.rst | 23 +-
doc/whats-new-2.0.rst | 197 -
examples/README.txt | 5 -
examples/c++-api/.gitignore | 3 +
examples/c++-api/Makefile | 20 +
examples/c++-api/bloom.cc | 38 +
examples/c++-api/consume.cc | 39 +
examples/c++-api/exact-counting.cc | 40 +
examples/c++-api/reads.fastq | 532 +
examples/python-api/bloom.py | 26 +
examples/python-api/consume.py | 20 +
examples/python-api/exact-counting.py | 39 +
examples/stamps/do.sh | 8 +-
khmer/__init__.py | 172 +-
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 | 6100 +-
khmer/_version.py | 488 +-
khmer/kfile.py | 38 +-
khmer/khmer_args.py | 368 +-
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/{.check_openmp.cc => alphabets.hh} | 23 +-
lib/assembler.cc | 533 +
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 | 1168 +-
lib/hashtable.hh | 490 +-
lib/hllcounter.cc | 39 +-
lib/hllcounter.hh | 33 +-
lib/khmer.hh | 22 +-
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 | 61 +-
lib/oxli.pc.in | 4 +-
lib/read_aligner.cc | 24 +-
lib/read_aligner.hh | 8 +-
lib/read_parsers.cc | 407 +-
lib/read_parsers.hh | 189 +-
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 | 325 +-
lib/traversal.hh | 253 +-
oxli/__init__.py | 15 +-
oxli/build_graph.py | 14 +-
oxli/functions.py | 21 +-
oxli/partition.py | 49 +
papers/paper-v2.1.md | 121 +
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/fasta-to-abundance-hist.py | 57 -
sandbox/find-high-abund-kmers.py | 107 -
sandbox/graph-size.py | 2 +-
sandbox/hi-lo-abundance-by-position.py | 65 -
sandbox/link-compact-dbg.py | 198 +
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 | 83 +-
scripts/abundance-dist.py | 60 +-
scripts/annotate-partitions.py | 13 +-
scripts/count-median.py | 16 +-
scripts/do-partition.py | 54 +-
scripts/extract-long-sequences.py | 11 +-
scripts/extract-paired-reads.py | 32 +-
scripts/extract-partitions.py | 308 +-
scripts/fastq-to-fasta.py | 20 +-
scripts/filter-abund-single.py | 103 +-
scripts/filter-abund.py | 100 +-
scripts/filter-stoptags.py | 19 +-
scripts/find-knots.py | 13 +-
scripts/interleave-reads.py | 46 +-
scripts/load-graph.py | 6 +-
scripts/load-into-counting.py | 63 +-
scripts/make-initial-stoptags.py | 14 +-
scripts/merge-partitions.py | 15 +-
scripts/normalize-by-median.py | 65 +-
scripts/partition-graph.py | 52 +-
scripts/readstats.py | 26 +-
scripts/sample-reads-randomly.py | 38 +-
scripts/split-paired-reads.py | 36 +-
scripts/trim-low-abund.py | 544 +-
scripts/unique-kmers.py | 35 +-
setup.cfg | 24 +-
setup.py | 88 +-
sort-authors-list.py | 22 +-
tests/__init__.py | 1 +
tests/khmer_tst_utils.py | 109 +-
tests/test-data/README.rst | 10 +
tests/test-data/goodversion-k12.ht | Bin 16 -> 28 bytes
tests/test-data/goodversion-k12.ht.gz | Bin 38 -> 56 bytes
tests/test-data/goodversion-k32.stoptags | Bin 1174 -> 1354 bytes
...ed-mixed.fa.pe => paired-mixed-witherror.fa.pe} | 2 +-
tests/test-data/{paired.fq => paired.malformat.fq} | 6 +-
.../{paired.fq.1 => paired.malformat.fq.2} | 6 +-
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-data/valid-read-testing.fq | 36 +
tests/test_assembly.py | 906 +
tests/test_countgraph.py | 357 +-
tests/test_counting_single.py | 60 +-
tests/{test_filter.py => test_counttable.py} | 85 +-
.../test_cpython_hierarchy.py | 74 +-
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 | 131 +
tests/test_nodegraph.py | 489 +-
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 | 156 +-
tests/test_sandbox_scripts.py | 128 +-
tests/test_script_arguments.py | 265 +-
tests/test_script_output.py | 184 +
tests/test_scripts.py | 1653 +-
tests/test_sequence_validation.py | 335 +
tests/test_streaming_io.py | 92 +-
tests/test_subset_graph.py | 143 +-
tests/test_tabletype.py | 448 +
tests/test_threaded_sequence_processor.py | 47 +-
tests/test_version.py | 11 +-
third-party/seqan/ChangeLog | 5 +
.../core/include/seqan/basic/debug_test_system.h | 2 +-
versioneer.py | 1905 +-
236 files changed, 25850 insertions(+), 366033 deletions(-)
create mode 100644 .dictionary
rename doc/dev/details.rst => .github/CONTRIBUTING.md (86%)
create mode 100644 .github/PULL_REQUEST_TEMPLATE.md
create mode 100644 .travis.yml
create mode 100644 CHANGELOG.md
delete mode 100644 CONTRIBUTING.md
delete mode 100644 IDEAS
delete mode 100644 TODO
create mode 100644 author-skips.txt
create mode 100644 authors.csv
create mode 100644 ci_scripts/install.sh
delete mode 100644 data/16s+23s.fa
delete mode 100644 data/16s.fa
delete mode 100644 data/1m-bigpart.fa
delete mode 100644 data/23s.fa
delete mode 100644 data/MSB2-part.group1.fa
delete mode 100644 data/MSB2-part.group10.fa
delete mode 100644 data/MSB2-part.group31.fa
delete mode 100644 data/high-sodd.fa
delete mode 100644 data/mda-test.fa
delete mode 100644 data/primers.fa
delete mode 100644 doc/dev/coding-guidelines-and-review.rst
create mode 100644 doc/dev/guidelines-continued-dev.rst
create mode 100644 doc/dev/python-api.rst
create mode 100644 doc/release-notes/release-2.1.md
create mode 100644 doc/release-notes/release-2.1.rst
rename doc/{dev/crazy-ideas.rst => user/api-examples.rst} (63%)
delete mode 100644 doc/whats-new-2.0.rst
delete mode 100644 examples/README.txt
create mode 100644 examples/c++-api/.gitignore
create mode 100644 examples/c++-api/Makefile
create mode 100644 examples/c++-api/bloom.cc
create mode 100644 examples/c++-api/consume.cc
create mode 100644 examples/c++-api/exact-counting.cc
create mode 100644 examples/c++-api/reads.fastq
create mode 100755 examples/python-api/bloom.py
create mode 100755 examples/python-api/consume.py
create mode 100755 examples/python-api/exact-counting.py
create mode 100644 khmer/_cpy_counttable.hh
create mode 100644 khmer/_cpy_hashgraph.hh
create mode 100644 khmer/_cpy_nodetable.hh
create mode 100644 khmer/_cpy_smallcountgraph.hh
create mode 100644 khmer/_cpy_smallcounttable.hh
copy khmer/{khmer_logger.py => trimming.py} (61%)
rename ChangeLog => legacy/ChangeLog (83%)
rename jenkins-build.sh => legacy/jenkins-build.sh (91%)
copy lib/{test-compile.cc => alphabets.cc} (84%)
copy lib/{.check_openmp.cc => alphabets.hh} (85%)
create mode 100644 lib/assembler.cc
create mode 100644 lib/assembler.hh
delete mode 100644 lib/counting.cc
delete mode 100644 lib/counting.hh
delete mode 100755 lib/get_version.py
delete mode 100644 lib/hashbits.cc
delete mode 100644 lib/hashbits.hh
copy lib/{hashtable.cc => hashgraph.cc} (55%)
create mode 100644 lib/hashgraph.hh
create mode 100644 lib/kmer_filters.cc
copy lib/{test-Colors.cc => kmer_filters.hh} (67%)
create mode 100644 lib/storage.cc
create mode 100644 lib/storage.hh
mode change 100644 => 100755 oxli/build_graph.py
mode change 100644 => 100755 oxli/functions.py
create mode 100755 oxli/partition.py
create mode 100644 papers/paper-v2.1.md
create mode 100644 pylintrc
create mode 100644 pytest.ini
delete mode 100755 sandbox/abundance-hist-by-position.py
create mode 100755 sandbox/assemble-and-track.py
create mode 100755 sandbox/assemble-on-the-go.py
mode change 100644 => 100755 sandbox/count-kmers.py
create mode 100755 sandbox/extract-compact-dbg.py
create mode 100755 sandbox/extract-unassembled-reads-2.py
create mode 100755 sandbox/extract-unassembled-reads.py
delete mode 100755 sandbox/fasta-to-abundance-hist.py
delete mode 100755 sandbox/find-high-abund-kmers.py
delete mode 100755 sandbox/hi-lo-abundance-by-position.py
create mode 100755 sandbox/link-compact-dbg.py
mode change 100644 => 100755 sandbox/optimal_args_hashbits.py
mode change 100644 => 100755 sandbox/readaligner_pairhmm_train.py
create mode 100755 sandbox/reassemble-contigs.py
create mode 100755 sandbox/streaming-assembly-simple.py
create mode 100644 tests/test-data/README.rst
copy tests/test-data/{paired-mixed.fa.pe => paired-mixed-witherror.fa.pe} (92%)
copy tests/test-data/{paired.fq => paired.malformat.fq} (95%)
copy tests/test-data/{paired.fq.1 => paired.malformat.fq.2} (90%)
create mode 100644 tests/test-data/simple-genome-reads.fa
create mode 100644 tests/test-data/simple-genome.fa
create mode 100644 tests/test-data/single-read.fa
create mode 100644 tests/test-data/unclean-reads.fastq
create mode 100644 tests/test-data/valid-read-testing.fq
create mode 100644 tests/test_assembly.py
rename tests/{test_filter.py => test_counttable.py} (53%)
copy sandbox/stoptag-abundance-hist.py => tests/test_cpython_hierarchy.py (58%)
mode change 100755 => 100644
create mode 100644 tests/test_filter_abund.py
create mode 100644 tests/test_hashset.py
create mode 100644 tests/test_nibblestorage.py
create mode 100644 tests/test_read_handling.py
create mode 100644 tests/test_script_output.py
create mode 100644 tests/test_sequence_validation.py
create mode 100644 tests/test_tabletype.py
mode change 100755 => 100644 versioneer.py
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