[med-svn] [khmer] 07/08: Merge tag 'upstream/1.3'
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sat Jan 31 13:40:58 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository khmer.
commit 5c17a1b138a3030968f9c5eede358db68ee8a95e
Merge: 69dfb20 cc780a2
Author: Michael R. Crusoe <mcrusoe at msu.edu>
Date: Sat Jan 31 05:12:55 2015 -0500
Merge tag 'upstream/1.3'
Upstream version 1.3
.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
doc/LICENSE.txt | 36 +
doc/Makefile | 90 +
doc/Makefile.bak | 4 +
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 +
scripts/.gitignore | 1 +
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 +
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third-party/zlib/contrib/ada/zlib-thin.adb | 141 +
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third-party/zlib/contrib/ada/zlib.gpr | 20 +
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third-party/zlib/contrib/delphi/ZLib.pas | 557 +
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third-party/zlib/contrib/gcc_gvmat64/gvmat64.S | 574 +
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third-party/zlib/contrib/iostream3/TODO | 17 +
third-party/zlib/contrib/masmx64/bld_ml64.bat | 2 +
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third-party/zlib/contrib/vstudio/vc9/zlibvc.sln | 144 +
third-party/zlib/contrib/vstudio/vc9/zlibvc.vcproj | 1156 +
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283 files changed, 890860 insertions(+), 102 deletions(-)
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