[med-svn] [khmer] branch master updated (f4fe8f4 -> 2a4eb71)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sat Jan 31 13:40:45 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch master
in repository khmer.
from f4fe8f4 Strings with colons need to be quoted
new b3f8d03 More cleanups
new 788794c Merge branch 'master' of git+ssh://git.debian.org/git/debian-med/khmer
new 69dfb20 install scripts to match 'khmer' frontend
new dba0044 Imported Upstream version 1.3
new ceee317 Imported Upstream version 1.3
new cc780a2 Imported Upstream version 1.3
new 5c17a1b Merge tag 'upstream/1.3'
new 2a4eb71 Build the docs
The 8 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitattributes | 1 +
.gitignore | 44 +
.landscape.yaml | 9 +
CODE_OF_CONDUCT.rst | 35 +
PKG-INFO | 94 -
bink.ipynb | 535 +
data/100k-filtered.fa | 200000 ++++++++++++++++++
data/100k-surrendered.fa | 42 +
data/16s+23s.fa | 800 +
data/16s.fa | 714 +
data/1m-bigpart.fa | 44872 ++++
data/23s.fa | 86 +
data/25k-casava1_8.fq.bz2 | Bin 0 -> 1154579 bytes
data/25k.fq.gz | Bin 0 -> 1437611 bytes
data/MSB2-part.group1.fa | 100806 +++++++++
data/MSB2-part.group10.fa | 101128 +++++++++
data/MSB2-part.group31.fa | 103446 +++++++++
data/high-sodd.fa | 384 +
data/inconsistent.fa | 17104 ++
data/mda-test.fa | 28 +
data/primers.fa | 4 +
data/sequential-shuffled.fa | 79936 +++++++
data/sequential.fa | 79936 +++++++
data/stamps-genomes.fa | 4 +
data/stamps-reads.fa.gz | Bin 0 -> 3155976 bytes
debian/control | 28 +-
debian/inject-into-alioth-git | 18 -
debian/patches/local-libs | 3 -
debian/rules | 9 +-
doc/LICENSE.txt | 36 +
doc/Makefile | 90 +
doc/README.html | 403 +
doc/_static/labibi.css | 54 +
doc/_static/labibi.js | 29 +
doc/_templates/page.html | 143 +
doc/citations.txt | 1 +
doc/conf.py | 229 +
doc/contributors.txt | 33 +
doc/dev/CODE_OF_CONDUCT.txt | 1 +
doc/dev/a-quick-guide-to-testing.txt | 102 +
doc/dev/codebase-guide.txt | 18 +
doc/dev/coding-guidelines-and-review.txt | 77 +
doc/dev/crazy-ideas.txt | 10 +
doc/dev/details.txt | 7 +
doc/dev/development.txt | 160 +
doc/dev/for-khmer-developers.txt | 26 +
doc/dev/getting-started.txt | 287 +
doc/dev/hackathon.txt | 60 +
doc/dev/index.txt | 27 +
doc/dev/release.txt | 255 +
doc/index.txt | 55 +
doc/introduction.txt | 93 +
doc/libstdc++.tag | 122336 +++++++++++
doc/release-notes/release-1.0.1.md | 52 +
doc/release-notes/release-1.0.md | 86 +
doc/release-notes/release-1.1.md | 58 +
doc/release-notes/release-1.2.md | 98 +
doc/release-notes/release-1.3.md | 57 +
doc/requirements.txt | 1 +
doc/roadmap.txt | 63 +
doc/run-corn-50m.sh | 72 +
doc/user/artifact-removal.graffle | 815 +
doc/user/artifact-removal.png | Bin 0 -> 39640 bytes
doc/user/biblio.txt | 17 +
doc/user/blog-posts.txt | 53 +
doc/user/choosing-table-sizes.txt | 149 +
doc/user/examples.txt | 28 +
doc/user/galaxy.txt | 39 +
doc/user/guide.txt | 246 +
doc/user/index.txt | 19 +
doc/user/install.txt | 73 +
doc/user/known-issues.txt | 21 +
doc/user/partitioning-big-data.txt | 146 +
doc/user/partitioning-workflow.graffle | 727 +
doc/user/partitioning-workflow.png | Bin 0 -> 33291 bytes
doc/user/scripts.txt | 133 +
examples/README.txt | 5 +
examples/stamps k-mer distributions.ipynb | 153 +
examples/stamps/do.sh | 25 +
jenkins-build.sh | 66 +
khmer/_version.py | 196 +-
lib/.gitignore | 9 +
lib/read_aligner_test.sh | 1 +
sandbox/README.rst | 184 +
sandbox/abundance-hist-by-position.py | 40 +
sandbox/assembly-diff-2.py | 47 +
sandbox/assembly-diff.py | 68 +
sandbox/assemstats3.py | 133 +
sandbox/bloom_count.py | 40 +
sandbox/bloom_count_intersection.py | 60 +
sandbox/build-sparse-graph.py | 72 +
sandbox/calc-best-assembly.py | 64 +
sandbox/calc-error-profile.py | 156 +
sandbox/calc-median-distribution.py | 65 +
sandbox/collect-reads.py | 149 +
sandbox/collect-variants.py | 161 +
sandbox/combine-pe.py | 66 +
sandbox/compare-partitions.py | 68 +
sandbox/correct-errors.py | 213 +
sandbox/count-within-radius.py | 60 +
sandbox/degree-by-position.py | 47 +
sandbox/dn-identify-errors.py | 147 +
sandbox/ec.py | 60 +
sandbox/error-correct-pass2.py | 85 +
sandbox/extract-single-partition.py | 34 +
sandbox/fasta-to-abundance-hist.py | 30 +
sandbox/filter-below-abund.py | 58 +
sandbox/filter-median-and-pct.py | 83 +
sandbox/filter-median.py | 72 +
sandbox/find-high-abund-kmers.py | 81 +
sandbox/find-unpart.py | 53 +
sandbox/graph-size.py | 66 +
sandbox/hi-lo-abundance-by-position.py | 36 +
sandbox/memusg | 46 +
sandbox/multi-rename.py | 25 +
sandbox/normalize-by-align.py | 150 +
sandbox/normalize-by-median-pct.py | 177 +
sandbox/print-stoptags.py | 22 +
sandbox/print-tagset.py | 23 +
sandbox/read_aligner.py | 64 +
sandbox/readstats.py | 51 +
sandbox/renumber-partitions.py | 40 +
sandbox/saturate-by-median.py | 260 +
sandbox/shuffle-fasta.py | 27 +
sandbox/shuffle-reverse-rotary.py | 42 +
sandbox/slice-reads-by-coverage.py | 69 +
sandbox/split-fasta.py | 32 +
sandbox/split-sequences-by-length.py | 59 +
sandbox/stoptag-abundance-hist.py | 51 +
sandbox/stoptags-by-position.py | 45 +
sandbox/strip-partition.py | 23 +
sandbox/subset-report.py | 37 +
sandbox/sweep-files.py | 204 +
sandbox/sweep-out-reads-with-contigs.py | 40 +
sandbox/sweep-reads.py | 402 +
sandbox/sweep-reads2.py | 86 +
sandbox/sweep-reads3.py | 98 +
sandbox/to-casava-1.8-fastq.py | 61 +
sandbox/trim-low-abund.py | 236 +
sandbox/uniqify-sequences.py | 67 +
sandbox/write-interleave.py | 29 +
sandbox/write-trimmomatic.py | 27 +
{tests => scripts}/.gitignore | 0
scripts/galaxy/abundance-dist-single.xml | 98 +
scripts/galaxy/abundance-dist.xml | 68 +
scripts/galaxy/count-median.xml | 58 +
scripts/galaxy/do-partition.xml | 107 +
scripts/galaxy/extract-partitions.xml | 77 +
scripts/galaxy/filter-below-abund.py | 1 +
scripts/galaxy/filter-below-abund.xml | 65 +
scripts/galaxy/gedlab.py | 24 +
scripts/galaxy/macros.xml | 160 +
scripts/galaxy/test-data/random-20-a.fa.part | 1 +
scripts/galaxy/test-data/test-abund-read-2.ct | Bin 0 -> 20000150 bytes
scripts/galaxy/test-data/test-abund-read-2.ct.info | 2 +
scripts/galaxy/test-data/test-abund-read-2.fa | 1 +
.../test-data/test-abund-read-2.nobigcount.ct | Bin 0 -> 20000130 bytes
.../test-data/test-abund-read-2.nobigcount.ct.info | 2 +
scripts/galaxy/test-data/test-abund-read-paired.fa | 1 +
scripts/galaxy/tool_dependencies.xml | 10 +
third-party/bzip2/.gitignore | 2 +
third-party/bzip2/bzdiff | 76 +
third-party/bzip2/bzgrep | 75 +
third-party/bzip2/bzip2.1.preformatted | 399 +
third-party/bzip2/bzmore | 61 +
third-party/seqan/LICENSE | 26 +
third-party/seqan/core/include/seqan/align/INFO | 13 +
third-party/seqan/core/include/seqan/bam_io/INFO | 12 +
third-party/seqan/core/include/seqan/basic/INFO | 14 +
third-party/seqan/core/include/seqan/file/INFO | 13 +
third-party/seqan/core/include/seqan/gff_io/INFO | 10 +
.../seqan/core/include/seqan/graph_algorithms/INFO | 11 +
.../seqan/core/include/seqan/graph_align/INFO | 9 +
.../seqan/core/include/seqan/graph_types/INFO | 9 +
third-party/seqan/core/include/seqan/modifier/INFO | 11 +
third-party/seqan/core/include/seqan/parallel/INFO | 12 +
third-party/seqan/core/include/seqan/platform/INFO | 11 +
third-party/seqan/core/include/seqan/random/INFO | 8 +
third-party/seqan/core/include/seqan/score/INFO | 11 +
third-party/seqan/core/include/seqan/seq_io/INFO | 12 +
third-party/seqan/core/include/seqan/sequence/INFO | 15 +
third-party/seqan/core/include/seqan/store/INFO | 12 +
third-party/seqan/core/include/seqan/stream/INFO | 32 +
third-party/seqan/core/include/seqan/system/INFO | 9 +
third-party/zlib/.gitignore | 5 +
third-party/zlib/as400/bndsrc | 215 +
third-party/zlib/as400/compile.clp | 110 +
third-party/zlib/as400/zlib.inc | 451 +
third-party/zlib/contrib/ada/buffer_demo.adb | 106 +
third-party/zlib/contrib/ada/mtest.adb | 156 +
third-party/zlib/contrib/ada/read.adb | 156 +
third-party/zlib/contrib/ada/test.adb | 463 +
third-party/zlib/contrib/ada/zlib-streams.adb | 225 +
third-party/zlib/contrib/ada/zlib-streams.ads | 114 +
third-party/zlib/contrib/ada/zlib-thin.adb | 141 +
third-party/zlib/contrib/ada/zlib-thin.ads | 450 +
third-party/zlib/contrib/ada/zlib.adb | 701 +
third-party/zlib/contrib/ada/zlib.ads | 328 +
third-party/zlib/contrib/ada/zlib.gpr | 20 +
third-party/zlib/contrib/amd64/amd64-match.S | 452 +
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third-party/zlib/contrib/blast/test.pk | Bin 0 -> 8 bytes
third-party/zlib/contrib/delphi/ZLib.pas | 557 +
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third-party/zlib/contrib/delphi/zlibd32.mak | 99 +
third-party/zlib/contrib/dotzlib/DotZLib.build | 33 +
third-party/zlib/contrib/dotzlib/DotZLib.chm | Bin 0 -> 72726 bytes
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.../zlib/contrib/dotzlib/DotZLib/UnitTests.cs | 274 +
third-party/zlib/contrib/gcc_gvmat64/gvmat64.S | 574 +
third-party/zlib/contrib/inflate86/inffast.S | 1368 +
third-party/zlib/contrib/iostream/test.cpp | 24 +
third-party/zlib/contrib/iostream/zfstream.cpp | 329 +
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third-party/zlib/contrib/masmx64/gvmat64.asm | 553 +
third-party/zlib/contrib/masmx64/inffasx64.asm | 396 +
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third-party/zlib/contrib/puff/zeros.raw | Bin 0 -> 2517 bytes
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third-party/zlib/contrib/vstudio/vc9/zlibvc.sln | 144 +
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third-party/zlib/make_vms.com | 867 +
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third-party/zlib/zconf.h.cmakein | 513 +
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third-party/zlib/zlib.map | 83 +
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third-party/zlib/zlib2ansi | 152 +
286 files changed, 890883 insertions(+), 132 deletions(-)
create mode 100644 .gitattributes
create mode 100644 .gitignore
create mode 100644 .landscape.yaml
create mode 100644 CODE_OF_CONDUCT.rst
delete mode 100644 PKG-INFO
create mode 100644 bink.ipynb
create mode 100644 data/100k-filtered.fa
create mode 100644 data/100k-surrendered.fa
create mode 100644 data/16s+23s.fa
create mode 100644 data/16s.fa
create mode 100644 data/1m-bigpart.fa
create mode 100644 data/23s.fa
create mode 100644 data/25k-casava1_8.fq.bz2
create mode 100644 data/25k.fq.gz
create mode 100644 data/MSB2-part.group1.fa
create mode 100644 data/MSB2-part.group10.fa
create mode 100644 data/MSB2-part.group31.fa
create mode 100644 data/high-sodd.fa
create mode 100644 data/inconsistent.fa
create mode 100644 data/mda-test.fa
create mode 100644 data/primers.fa
create mode 100644 data/sequential-shuffled.fa
create mode 100644 data/sequential.fa
create mode 100644 data/stamps-genomes.fa
create mode 100644 data/stamps-reads.fa.gz
delete mode 100755 debian/inject-into-alioth-git
create mode 100644 doc/LICENSE.txt
create mode 100644 doc/Makefile
create mode 100644 doc/README.html
create mode 100644 doc/_static/labibi.css
create mode 100644 doc/_static/labibi.js
create mode 100644 doc/_templates/page.html
create mode 120000 doc/citations.txt
create mode 100644 doc/conf.py
create mode 100644 doc/contributors.txt
create mode 120000 doc/dev/CODE_OF_CONDUCT.txt
create mode 100644 doc/dev/a-quick-guide-to-testing.txt
create mode 100644 doc/dev/codebase-guide.txt
create mode 100644 doc/dev/coding-guidelines-and-review.txt
create mode 100644 doc/dev/crazy-ideas.txt
create mode 100644 doc/dev/details.txt
create mode 100644 doc/dev/development.txt
create mode 100644 doc/dev/for-khmer-developers.txt
create mode 100644 doc/dev/getting-started.txt
create mode 100644 doc/dev/hackathon.txt
create mode 100644 doc/dev/index.txt
create mode 100644 doc/dev/release.txt
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create mode 100644 doc/introduction.txt
create mode 100644 doc/libstdc++.tag
create mode 100644 doc/release-notes/release-1.0.1.md
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create mode 100644 doc/user/examples.txt
create mode 100644 doc/user/galaxy.txt
create mode 100644 doc/user/guide.txt
create mode 100644 doc/user/index.txt
create mode 100644 doc/user/install.txt
create mode 100644 doc/user/known-issues.txt
create mode 100644 doc/user/partitioning-big-data.txt
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create mode 100755 sandbox/normalize-by-median-pct.py
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create mode 100755 sandbox/read_aligner.py
create mode 100755 sandbox/readstats.py
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create mode 100755 sandbox/saturate-by-median.py
create mode 100755 sandbox/shuffle-fasta.py
create mode 100755 sandbox/shuffle-reverse-rotary.py
create mode 100755 sandbox/slice-reads-by-coverage.py
create mode 100755 sandbox/split-fasta.py
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create mode 100755 sandbox/stoptag-abundance-hist.py
create mode 100755 sandbox/stoptags-by-position.py
create mode 100755 sandbox/strip-partition.py
create mode 100755 sandbox/subset-report.py
create mode 100755 sandbox/sweep-files.py
create mode 100755 sandbox/sweep-out-reads-with-contigs.py
create mode 100755 sandbox/sweep-reads.py
create mode 100755 sandbox/sweep-reads2.py
create mode 100755 sandbox/sweep-reads3.py
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create mode 100755 sandbox/trim-low-abund.py
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