[med-svn] [rsem] 04/05: Merge tag 'upstream/1.3.0+dfsg'
Andreas Tille
tille at debian.org
Fri Dec 9 14:51:00 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository rsem.
commit 1c42e3802b949eae0c0aac101f9052df89d4c197
Merge: 8441ddf 782bbe2
Author: Andreas Tille <tille at debian.org>
Date: Fri Dec 9 14:33:32 2016 +0100
Merge tag 'upstream/1.3.0+dfsg'
Upstream version 1.3.0+dfsg
.gitignore | 15 +-
GTFItem.h | 328 +-
Gibbs.cpp | 89 +-
Makefile | 8 +-
README.md | 97 +-
SamParser.h | 20 +-
Transcripts.h | 2 +-
WHAT_IS_NEW | 10 +
pRSEM/ChIPSeqExperiment.py | 257 +
pRSEM/ChIPSeqReplicate.py | 43 +
pRSEM/File.py | 47 +
pRSEM/Gene.py | 143 +
pRSEM/Makefile | 35 +
pRSEM/Param.py | 178 +
pRSEM/Prsem.py | 253 +
pRSEM/Transcript.py | 189 +
pRSEM/Util.py | 173 +
pRSEM/filterSam2Bed.c | 52 +
pRSEM/idrCode/README.txt | 146 +
pRSEM/idrCode/batch-consistency-analysis.r | 164 +
pRSEM/idrCode/batch-consistency-plot-merged2.r | 213 +
pRSEM/idrCode/batch-consistency-plot.r | 67 +
pRSEM/idrCode/functions-all-clayton-12-13.r | 3182 +++
pRSEM/idrCode/idrOverlap2npk.sh | 37 +
pRSEM/idrCode/peakCallingPipelineForIdr.txt | 11 +
pRSEM/idrCode/submit.idrmerge.lsf.sh | 72 +
pRSEM/idrCode/submit.idrpair.lsf.sh | 90 +
pRSEM/installRLib.R | 71 +
pRSEM/phantompeakqualtools/README.txt | 203 +
.../peakCallingPipelineForIdr.txt | 1 +
pRSEM/phantompeakqualtools/run_spp.R | 885 +
pRSEM/phantompeakqualtools/run_spp_nodups.R | 886 +
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.../spp_1.10.1_on_R3.3/man/spp-package.Rd | 144 +
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.../spp_1.10.1_on_R3.3/src/BamAlignment.cpp | 696 +
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pRSEM/process-chipseq.R | 61 +
pRSEM/process-rnaseq.R | 982 +
pRSEM/prsem-calculate-expression | 74 +
pRSEM/prsem-prepare-reference | 70 +
pRSEM/prsem-testing-procedure | 104 +
rsem-calculate-expression | 475 +-
rsem-gff3-to-gtf | 23 +-
rsem-prepare-reference | 108 +-
rsem-run-prsem-testing-procedure | 324 +
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samtools-1.3/htslib-1.3/test/c1#pad3.sam | 14 -
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samtools-1.3/htslib-1.3/test/ce#5b.sam | 12 -
samtools-1.3/htslib-1.3/test/ce#large_seq.sam | 3 -
samtools-1.3/htslib-1.3/test/ce#supp.sam | 6 -
samtools-1.3/htslib-1.3/test/ce#tag_depadded.sam | 11 -
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samtools-1.3/htslib-1.3/test/ce#unmap1.sam | 20 -
samtools-1.3/htslib-1.3/test/ce#unmap2.sam | 29 -
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samtools-1.3/htslib-1.3/test/compare_sam.pl | 194 -
samtools-1.3/htslib-1.3/test/cross_validate.sh | 126 -
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samtools-1.3/htslib-1.3/test/fieldarith.c | 72 -
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samtools-1.3/htslib-1.3/test/sam.c | 208 -
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samtools-1.3/htslib-1.3/test/test-vcf-api.c | 282 -
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samtools-1.3/htslib-1.3/test/xx#blank.sam | 0
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samtools-1.3/htslib-1.3/test/xx#tlen.sam | 34 -
samtools-1.3/htslib-1.3/test/xx#tlen2.sam | 36 -
samtools-1.3/htslib-1.3/test/xx#triplet.sam | 7 -
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samtools-1.3/htslib-1.3/vcf.5 | 120 -
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samtools-1.3/stats_isize.h | 83 -
samtools-1.3/test/addrprg/1_fixup.sam | 30 -
samtools-1.3/test/addrprg/1_fixup.sam.expected | 30 -
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samtools-1.3/test/addrprg/2_fixup_orphan.sam | 30 -
.../test/addrprg/2_fixup_orphan.sam.expected | 30 -
.../test/addrprg/2_fixup_orphan.sam.expected.err | 0
samtools-1.3/test/addrprg/3_fixup.sam.expected | 0
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samtools-1.3/test/addrprg/4_fixup_norg.sam | 29 -
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samtools-1.3/test/bam2fq/1.2.fq.expected | 72 -
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samtools-1.3/test/bam2fq/2.1.fq.expected | 72 -
samtools-1.3/test/bam2fq/2.2.fq.expected | 72 -
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samtools-1.3/test/bam2fq/3.1.fq.expected | 72 -
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.../dat/cram_md5/08c04d512d4797d9ba2a156c1daba468 | 1 -
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samtools-1.3/test/dat/depad.001.fa | 2 -
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samtools-1.3/test/dat/view.002.fa.fai | 1 -
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samtools-1.3/test/mpileup/overlapIllumina.bam | Bin 583 -> 0 bytes
samtools-1.3/test/mpileup/regions | 10 -
samtools-1.3/test/mpileup/regression.sh | 158 -
samtools-1.3/test/mpileup/xx#depth1.sam | 6 -
samtools-1.3/test/mpileup/xx#depth2.sam | 6 -
samtools-1.3/test/mpileup/xx#minimal.bam | Bin 215 -> 0 bytes
samtools-1.3/test/mpileup/xx#triplet.bam | Bin 247 -> 0 bytes
samtools-1.3/test/mpileup/xx.bed | 2 -
samtools-1.3/test/mpileup/xx.bed2 | 1 -
samtools-1.3/test/mpileup/xx.fa | 5 -
samtools-1.3/test/mpileup/xx.fa.fai | 2 -
.../test/quickcheck/1.quickcheck.badeof.bam | Bin 1228 -> 0 bytes
.../test/quickcheck/2.quickcheck.badheader.bam | Bin 1233 -> 0 bytes
samtools-1.3/test/quickcheck/3.quickcheck.ok.bam | Bin 1228 -> 0 bytes
samtools-1.3/test/quickcheck/4.quickcheck.ok.bam | Bin 1233 -> 0 bytes
samtools-1.3/test/quickcheck/all.expected | 2 -
samtools-1.3/test/reheader/1_view1.sam.expected | 63 -
.../test/reheader/1_view1.sam.expected.err | 0
samtools-1.3/test/reheader/2_view1.sam.expected | 63 -
.../test/reheader/2_view1.sam.expected.err | 0
samtools-1.3/test/reheader/3_view1.sam.expected | 63 -
.../test/reheader/3_view1.sam.expected.err | 0
samtools-1.3/test/reheader/hdr.sam | 28 -
samtools-1.3/test/split/test_count_rg.c | 123 -
.../test/split/test_expand_format_string.c | 123 -
samtools-1.3/test/split/test_filter_header_rg.c | 192 -
samtools-1.3/test/split/test_parse_args.c | 215 -
samtools-1.3/test/stat/1.stats.expected | 302 -
samtools-1.3/test/stat/10.stats.expected | 302 -
samtools-1.3/test/stat/10_map_cigar.sam | 8 -
.../stat/10_map_cigar.sam_s1_a_1.expected.bamstat | 302 -
.../stat/10_map_cigar.sam_s1_b_1.expected.bamstat | 302 -
samtools-1.3/test/stat/1_map_cigar.sam | 5 -
.../stat/1_map_cigar.sam_s1_a_1.expected.bamstat | 302 -
samtools-1.3/test/stat/2.stats.expected | 302 -
samtools-1.3/test/stat/2_equal_cigar_full_seq.sam | 5 -
samtools-1.3/test/stat/3.stats.expected | 265 -
samtools-1.3/test/stat/3_map_cigar_equal_seq.sam | 5 -
samtools-1.3/test/stat/4.stats.expected | 302 -
samtools-1.3/test/stat/4_X_cigar_full_seq.sam | 5 -
samtools-1.3/test/stat/5.stats.expected | 304 -
samtools-1.3/test/stat/5_insert_cigar.sam | 5 -
samtools-1.3/test/stat/6.stats.expected | 304 -
samtools-1.3/test/stat/7.stats.expected | 305 -
samtools-1.3/test/stat/7_supp.sam | 6 -
samtools-1.3/test/stat/8.stats.expected | 304 -
samtools-1.3/test/stat/8_secondary.sam | 6 -
samtools-1.3/test/stat/9.stats.expected | 302 -
samtools-1.3/test/stat/test.fa | 3 -
samtools-1.3/test/stat/test.fa.fai | 1 -
samtools-1.3/test/test.c | 53 -
samtools-1.3/test/test.h | 35 -
samtools-1.3/test/test.pl | 2448 ---
samtools-1.3/test/tview/test_get_rg_sample.c | 81 -
samtools-1.3/test/vcf-miniview.c | 115 -
samtools-1.3/win32/xcurses.h | 1377 --
samtools-1.3/win32/zconf.h | 332 -
samtools-1.3/win32/zlib.h | 1357 --
utils.h | 2 +-
712 files changed, 42291 insertions(+), 263518 deletions(-)
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