[med-svn] [khmer] branch upstream updated (53d51f6 -> cc780a2)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sat Jan 31 14:58:43 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch upstream
in repository khmer.
from 53d51f6 Imported Upstream version 1.3
adds dba0044 Imported Upstream version 1.3
adds ceee317 Imported Upstream version 1.3
adds cc780a2 Imported Upstream version 1.3
No new revisions were added by this update.
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
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 +
{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 +
third-party/zlib/contrib/asm686/match.S | 357 +
third-party/zlib/contrib/blast/test.pk | Bin 0 -> 8 bytes
third-party/zlib/contrib/delphi/ZLib.pas | 557 +
third-party/zlib/contrib/delphi/ZLibConst.pas | 11 +
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
third-party/zlib/contrib/dotzlib/DotZLib.sln | 21 +
.../zlib/contrib/dotzlib/DotZLib/AssemblyInfo.cs | 58 +
.../zlib/contrib/dotzlib/DotZLib/ChecksumImpl.cs | 202 +
.../zlib/contrib/dotzlib/DotZLib/CircularBuffer.cs | 83 +
.../zlib/contrib/dotzlib/DotZLib/CodecBase.cs | 198 +
.../zlib/contrib/dotzlib/DotZLib/Deflater.cs | 106 +
.../zlib/contrib/dotzlib/DotZLib/DotZLib.cs | 288 +
.../zlib/contrib/dotzlib/DotZLib/DotZLib.csproj | 141 +
.../zlib/contrib/dotzlib/DotZLib/GZipStream.cs | 301 +
.../zlib/contrib/dotzlib/DotZLib/Inflater.cs | 105 +
.../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 +
.../zlib/contrib/iostream2/zstream_test.cpp | 25 +
third-party/zlib/contrib/iostream3/TODO | 17 +
third-party/zlib/contrib/masmx64/bld_ml64.bat | 2 +
third-party/zlib/contrib/masmx64/gvmat64.asm | 553 +
third-party/zlib/contrib/masmx64/inffasx64.asm | 396 +
third-party/zlib/contrib/masmx86/bld_ml32.bat | 2 +
third-party/zlib/contrib/masmx86/inffas32.asm | 1080 +
third-party/zlib/contrib/masmx86/match686.asm | 479 +
third-party/zlib/contrib/minizip/configure.ac | 32 +
third-party/zlib/contrib/minizip/make_vms.com | 25 +
third-party/zlib/contrib/minizip/minizip.pc.in | 12 +
third-party/zlib/contrib/pascal/example.pas | 599 +
third-party/zlib/contrib/pascal/zlibd32.mak | 99 +
third-party/zlib/contrib/pascal/zlibpas.pas | 276 +
third-party/zlib/contrib/puff/zeros.raw | Bin 0 -> 2517 bytes
.../zlib/contrib/vstudio/vc10/miniunz.vcxproj | 310 +
.../contrib/vstudio/vc10/miniunz.vcxproj.filters | 22 +
.../zlib/contrib/vstudio/vc10/minizip.vcxproj | 307 +
.../contrib/vstudio/vc10/minizip.vcxproj.filters | 22 +
.../zlib/contrib/vstudio/vc10/testzlib.vcxproj | 420 +
.../contrib/vstudio/vc10/testzlib.vcxproj.filters | 58 +
.../zlib/contrib/vstudio/vc10/testzlibdll.vcxproj | 310 +
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third-party/zlib/contrib/vstudio/vc10/zlib.rc | 32 +
.../zlib/contrib/vstudio/vc10/zlibstat.vcxproj | 473 +
.../contrib/vstudio/vc10/zlibstat.vcxproj.filters | 77 +
third-party/zlib/contrib/vstudio/vc10/zlibvc.def | 143 +
third-party/zlib/contrib/vstudio/vc10/zlibvc.sln | 135 +
.../zlib/contrib/vstudio/vc10/zlibvc.vcxproj | 657 +
.../contrib/vstudio/vc10/zlibvc.vcxproj.filters | 118 +
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.../zlib/contrib/vstudio/vc11/testzlib.vcxproj | 426 +
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third-party/zlib/contrib/vstudio/vc11/zlib.rc | 32 +
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third-party/zlib/contrib/vstudio/vc11/zlibvc.def | 143 +
third-party/zlib/contrib/vstudio/vc11/zlibvc.sln | 117 +
.../zlib/contrib/vstudio/vc11/zlibvc.vcxproj | 688 +
.../zlib/contrib/vstudio/vc9/miniunz.vcproj | 565 +
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.../zlib/contrib/vstudio/vc9/testzlib.vcproj | 852 +
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third-party/zlib/contrib/vstudio/vc9/zlib.rc | 32 +
.../zlib/contrib/vstudio/vc9/zlibstat.vcproj | 835 +
third-party/zlib/contrib/vstudio/vc9/zlibvc.def | 143 +
third-party/zlib/contrib/vstudio/vc9/zlibvc.sln | 144 +
third-party/zlib/contrib/vstudio/vc9/zlibvc.vcproj | 1156 +
third-party/zlib/examples/zlib_how.html | 545 +
third-party/zlib/make_vms.com | 867 +
third-party/zlib/old/descrip.mms | 48 +
third-party/zlib/old/os2/zlib.def | 51 +
third-party/zlib/qnx/package.qpg | 141 +
third-party/zlib/treebuild.xml | 116 +
third-party/zlib/watcom/watcom_f.mak | 43 +
third-party/zlib/watcom/watcom_l.mak | 43 +
third-party/zlib/win32/zlib.def | 86 +
third-party/zlib/win32/zlib1.rc | 40 +
third-party/zlib/zconf.h.cmakein | 513 +
third-party/zlib/zlib.3 | 151 +
third-party/zlib/zlib.3.pdf | Bin 0 -> 8734 bytes
third-party/zlib/zlib.map | 83 +
third-party/zlib/zlib.pc.cmakein | 13 +
third-party/zlib/zlib2ansi | 152 +
283 files changed, 890859 insertions(+), 102 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
create mode 100644 doc/LICENSE.txt
create mode 100644 doc/Makefile
create mode 100644 doc/Makefile.bak
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
create mode 100644 doc/index.txt
create mode 100644 doc/introduction.txt
create mode 100644 doc/libstdc++.tag
create mode 100644 doc/release-notes/release-1.0.1.md
create mode 100644 doc/release-notes/release-1.0.md
create mode 100644 doc/release-notes/release-1.1.md
create mode 100644 doc/release-notes/release-1.2.md
create mode 100644 doc/release-notes/release-1.3.md
create mode 100644 doc/requirements.txt
create mode 100644 doc/roadmap.txt
create mode 100644 doc/run-corn-50m.sh
create mode 100644 doc/user/artifact-removal.graffle
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create mode 100644 doc/user/biblio.txt
create mode 100644 doc/user/blog-posts.txt
create mode 100644 doc/user/choosing-table-sizes.txt
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
create mode 100644 doc/user/partitioning-workflow.graffle
create mode 100644 doc/user/partitioning-workflow.png
create mode 100644 doc/user/scripts.txt
create mode 100644 examples/README.txt
create mode 100644 examples/stamps k-mer distributions.ipynb
create mode 100644 examples/stamps/do.sh
create mode 100755 jenkins-build.sh
create mode 100644 lib/.gitignore
create mode 100755 lib/read_aligner_test.sh
create mode 100644 sandbox/README.rst
create mode 100755 sandbox/abundance-hist-by-position.py
create mode 100755 sandbox/assembly-diff-2.py
create mode 100755 sandbox/assembly-diff.py
create mode 100755 sandbox/assemstats3.py
create mode 100755 sandbox/bloom_count.py
create mode 100755 sandbox/bloom_count_intersection.py
create mode 100755 sandbox/build-sparse-graph.py
create mode 100644 sandbox/calc-best-assembly.py
create mode 100755 sandbox/calc-error-profile.py
create mode 100755 sandbox/calc-median-distribution.py
create mode 100755 sandbox/collect-reads.py
create mode 100644 sandbox/collect-variants.py
create mode 100755 sandbox/combine-pe.py
create mode 100755 sandbox/compare-partitions.py
create mode 100755 sandbox/correct-errors.py
create mode 100755 sandbox/count-within-radius.py
create mode 100755 sandbox/degree-by-position.py
create mode 100755 sandbox/dn-identify-errors.py
create mode 100755 sandbox/ec.py
create mode 100755 sandbox/error-correct-pass2.py
create mode 100755 sandbox/extract-single-partition.py
create mode 100755 sandbox/fasta-to-abundance-hist.py
create mode 100755 sandbox/filter-below-abund.py
create mode 100755 sandbox/filter-median-and-pct.py
create mode 100755 sandbox/filter-median.py
create mode 100755 sandbox/find-high-abund-kmers.py
create mode 100755 sandbox/find-unpart.py
create mode 100644 sandbox/graph-size.py
create mode 100755 sandbox/hi-lo-abundance-by-position.py
create mode 100755 sandbox/memusg
create mode 100755 sandbox/multi-rename.py
create mode 100755 sandbox/normalize-by-align.py
create mode 100755 sandbox/normalize-by-median-pct.py
create mode 100755 sandbox/print-stoptags.py
create mode 100755 sandbox/print-tagset.py
create mode 100755 sandbox/read_aligner.py
create mode 100755 sandbox/readstats.py
create mode 100755 sandbox/renumber-partitions.py
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
create mode 100755 sandbox/split-sequences-by-length.py
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
create mode 100755 sandbox/to-casava-1.8-fastq.py
create mode 100755 sandbox/trim-low-abund.py
create mode 100755 sandbox/uniqify-sequences.py
create mode 100755 sandbox/write-interleave.py
create mode 100755 sandbox/write-trimmomatic.py
copy {tests => scripts}/.gitignore (100%)
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create mode 100644 scripts/galaxy/extract-partitions.xml
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create mode 100644 scripts/galaxy/gedlab.py
create mode 100644 scripts/galaxy/macros.xml
create mode 120000 scripts/galaxy/test-data/random-20-a.fa.part
create mode 100644 scripts/galaxy/test-data/test-abund-read-2.ct
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create mode 100644 third-party/seqan/LICENSE
create mode 100644 third-party/seqan/core/include/seqan/align/INFO
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