[med-svn] [rsem] branch master updated (7f434dc -> d27e227)
Andreas Tille
tille at debian.org
Fri Dec 9 14:50:54 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository rsem.
from 7f434dc new upstream release
new 94e4742 * d/watch: - version=4 - xz compression
new 8441ddf New upstream version, remove samtools 1.3 code copy
new 782bbe2 New upstream version 1.3.0+dfsg
new 1c42e38 Merge tag 'upstream/1.3.0+dfsg'
new d27e227 Use debian packaged samtools
The 5 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:
.gitignore | 15 +-
GTFItem.h | 328 +-
Gibbs.cpp | 89 +-
Makefile | 8 +-
README.md | 97 +-
SamParser.h | 20 +-
Transcripts.h | 2 +-
WHAT_IS_NEW | 10 +
debian/changelog | 10 +
debian/control | 3 +-
debian/copyright | 6 +-
debian/dirs | 1 +
debian/patches/series | 1 +
debian/patches/use_debian_packaged_samtools.patch | 70 +
debian/rules | 4 +-
debian/watch | 4 +-
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 +
.../spp_1.10.1_on_R3.2/DESCRIPTION | 12 +
.../spp_1.10.1_on_R3.2/NAMESPACE | 3 +
.../spp_1.10.1_on_R3.2/R/zroutines.R | 2501 +++
.../spp_1.10.1_on_R3.2}/configure | 3894 ++--
.../spp_1.10.1_on_R3.2/configure.ac | 7 +
.../man/add.broad.peak.regions.Rd | 27 +
.../man/find.binding.positions.Rd | 128 +
.../man/get.binding.characteristics.Rd | 55 +
.../man/get.broad.enrichment.clusters.Rd | 27 +
.../get.conservative.fold.enrichment.profile.Rd | 59 +
.../spp_1.10.1_on_R3.2/man/get.mser.Rd | 46 +
.../man/get.mser.interpolation.Rd | 56 +
.../man/get.smoothed.enrichment.mle.Rd | 35 +
.../man/get.smoothed.tag.density.Rd | 45 +
.../man/output.binding.results.Rd | 24 +
.../spp_1.10.1_on_R3.2/man/read.bam.tags.Rd | 24 +
.../spp_1.10.1_on_R3.2/man/read.bin.maqmap.tags.Rd | 23 +
.../spp_1.10.1_on_R3.2/man/read.bowtie.tags.Rd | 23 +
.../spp_1.10.1_on_R3.2/man/read.eland.tags.Rd | 30 +
.../spp_1.10.1_on_R3.2/man/read.maqmap.tags.Rd | 23 +
.../spp_1.10.1_on_R3.2/man/read.meland.tags.Rd | 29 +
.../man/remove.local.tag.anomalies.Rd | 46 +
.../man/select.informative.tags.Rd | 29 +
.../spp_1.10.1_on_R3.2/man/spp-package.Rd | 144 +
.../spp_1.10.1_on_R3.2/man/write.broadpeak.info.Rd | 16 +
.../man/write.narrowpeak.binding.Rd | 21 +
.../spp_1.10.1_on_R3.2/man/writewig.Rd | 31 +
.../spp_1.10.1_on_R3.2/src/BGZF.cpp | 398 +
.../spp_1.10.1_on_R3.2/src/BGZF.h | 322 +
.../spp_1.10.1_on_R3.2/src/BamAlignment.cpp | 696 +
.../spp_1.10.1_on_R3.2/src/BamAlignment.h | 203 +
.../spp_1.10.1_on_R3.2/src/BamAux.h | 227 +
.../spp_1.10.1_on_R3.2/src/BamIndex.cpp | 230 +
.../spp_1.10.1_on_R3.2/src/BamIndex.h | 145 +
.../spp_1.10.1_on_R3.2/src/BamMultiReader.cpp | 450 +
.../spp_1.10.1_on_R3.2/src/BamMultiReader.h | 136 +
.../spp_1.10.1_on_R3.2/src/BamReader.cpp | 66 +
.../spp_1.10.1_on_R3.2/src/BamReader.h | 130 +
.../spp_1.10.1_on_R3.2/src/BamReader_p.cpp | 729 +
.../spp_1.10.1_on_R3.2/src/BamReader_p.h | 137 +
.../spp_1.10.1_on_R3.2/src/BamStandardIndex_p.cpp | 910 +
.../spp_1.10.1_on_R3.2/src/BamStandardIndex_p.h | 213 +
.../spp_1.10.1_on_R3.2/src/BamToolsIndex_p.cpp | 577 +
.../spp_1.10.1_on_R3.2/src/BamToolsIndex_p.h | 192 +
.../spp_1.10.1_on_R3.2/src/BamWriter.cpp | 47 +
.../spp_1.10.1_on_R3.2/src/BamWriter.h | 50 +
.../spp_1.10.1_on_R3.2/src/BamWriter_p.cpp | 379 +
.../spp_1.10.1_on_R3.2/src/BamWriter_p.h | 63 +
.../spp_1.10.1_on_R3.2/src/Makevars.in | 4 +
.../spp_1.10.1_on_R3.2/src/api_global.h | 22 +
.../spp_1.10.1_on_R3.2/src/bamread.cpp | 222 +
.../spp_1.10.1_on_R3.2/src/bamtools_global.h | 32 +
.../spp_1.10.1_on_R3.2/src/bed2vector.cpp | 2628 +++
.../spp_1.10.1_on_R3.2/src/cdensum.c | 144 +
.../spp_1.10.1_on_R3.2/src/const.h | 18 +
.../spp_1.10.1_on_R3.2/src/maqmap.c | 164 +
.../spp_1.10.1_on_R3.2/src/maqmap.h | 70 +
.../spp_1.10.1_on_R3.2/src/maqread.cpp | 207 +
.../spp_1.10.1_on_R3.2/src/pc.h | 20 +
.../spp_1.10.1_on_R3.2/src/peaks.cpp | 804 +
.../spp_1.10.1_on_R3.2/src/wdl.cpp | 657 +
.../spp_1.10.1_on_R3.3/DESCRIPTION | 12 +
.../spp_1.10.1_on_R3.3/NAMESPACE | 3 +
.../spp_1.10.1_on_R3.3/R/zroutines.R | 2501 +++
.../spp_1.10.1_on_R3.3}/configure | 3894 ++--
.../spp_1.10.1_on_R3.3/configure.ac | 7 +
.../man/add.broad.peak.regions.Rd | 27 +
.../man/find.binding.positions.Rd | 130 +
.../man/get.binding.characteristics.Rd | 58 +
.../man/get.broad.enrichment.clusters.Rd | 27 +
.../get.conservative.fold.enrichment.profile.Rd | 59 +
.../spp_1.10.1_on_R3.3/man/get.mser.Rd | 46 +
.../man/get.mser.interpolation.Rd | 56 +
.../man/get.smoothed.enrichment.mle.Rd | 35 +
.../man/get.smoothed.tag.density.Rd | 45 +
.../man/output.binding.results.Rd | 26 +
.../spp_1.10.1_on_R3.3/man/read.bam.tags.Rd | 24 +
.../spp_1.10.1_on_R3.3/man/read.bin.maqmap.tags.Rd | 23 +
.../spp_1.10.1_on_R3.3/man/read.bowtie.tags.Rd | 23 +
.../spp_1.10.1_on_R3.3/man/read.eland.tags.Rd | 30 +
.../spp_1.10.1_on_R3.3/man/read.maqmap.tags.Rd | 23 +
.../spp_1.10.1_on_R3.3/man/read.meland.tags.Rd | 29 +
.../man/remove.local.tag.anomalies.Rd | 46 +
.../man/select.informative.tags.Rd | 29 +
.../spp_1.10.1_on_R3.3/man/spp-package.Rd | 144 +
.../spp_1.10.1_on_R3.3/man/write.broadpeak.info.Rd | 16 +
.../man/write.narrowpeak.binding.Rd | 21 +
.../spp_1.10.1_on_R3.3/man/writewig.Rd | 31 +
.../spp_1.10.1_on_R3.3/src/BGZF.cpp | 398 +
.../spp_1.10.1_on_R3.3/src/BGZF.h | 322 +
.../spp_1.10.1_on_R3.3/src/BamAlignment.cpp | 696 +
.../spp_1.10.1_on_R3.3/src/BamAlignment.h | 203 +
.../spp_1.10.1_on_R3.3/src/BamAux.h | 227 +
.../spp_1.10.1_on_R3.3/src/BamIndex.cpp | 230 +
.../spp_1.10.1_on_R3.3/src/BamIndex.h | 145 +
.../spp_1.10.1_on_R3.3/src/BamMultiReader.cpp | 450 +
.../spp_1.10.1_on_R3.3/src/BamMultiReader.h | 136 +
.../spp_1.10.1_on_R3.3/src/BamReader.cpp | 66 +
.../spp_1.10.1_on_R3.3/src/BamReader.h | 130 +
.../spp_1.10.1_on_R3.3/src/BamReader_p.cpp | 729 +
.../spp_1.10.1_on_R3.3/src/BamReader_p.h | 137 +
.../spp_1.10.1_on_R3.3/src/BamStandardIndex_p.cpp | 910 +
.../spp_1.10.1_on_R3.3/src/BamStandardIndex_p.h | 213 +
.../spp_1.10.1_on_R3.3/src/BamToolsIndex_p.cpp | 577 +
.../spp_1.10.1_on_R3.3/src/BamToolsIndex_p.h | 192 +
.../spp_1.10.1_on_R3.3/src/BamWriter.cpp | 47 +
.../spp_1.10.1_on_R3.3/src/BamWriter.h | 50 +
.../spp_1.10.1_on_R3.3/src/BamWriter_p.cpp | 379 +
.../spp_1.10.1_on_R3.3/src/BamWriter_p.h | 63 +
.../spp_1.10.1_on_R3.3/src/Makevars.in | 4 +
.../spp_1.10.1_on_R3.3/src/api_global.h | 22 +
.../spp_1.10.1_on_R3.3/src/bamread.cpp | 224 +
.../spp_1.10.1_on_R3.3/src/bamtools_global.h | 32 +
.../spp_1.10.1_on_R3.3/src/bed2vector.cpp | 2630 +++
.../spp_1.10.1_on_R3.3/src/cdensum.c | 144 +
.../spp_1.10.1_on_R3.3/src/const.h | 18 +
.../spp_1.10.1_on_R3.3/src/maqmap.c | 164 +
.../spp_1.10.1_on_R3.3/src/maqmap.h | 70 +
.../spp_1.10.1_on_R3.3/src/maqread.cpp | 209 +
.../spp_1.10.1_on_R3.3/src/pc.h | 20 +
.../spp_1.10.1_on_R3.3/src/peaks.cpp | 808 +
.../spp_1.10.1_on_R3.3/src/wdl.cpp | 660 +
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 +
samValidator.cpp | 258 +-
samtools-1.3/AUTHORS | 18 -
samtools-1.3/ChangeLog.old | 3875 ----
samtools-1.3/INSTALL | 123 -
samtools-1.3/LICENSE | 33 -
samtools-1.3/Makefile | 314 -
samtools-1.3/Makefile.cygwin | 314 -
samtools-1.3/Makefile.mingw | 63 -
samtools-1.3/NEWS | 979 -
samtools-1.3/README | 55 -
samtools-1.3/aclocal.m4 | 674 -
samtools-1.3/bam.c | 235 -
samtools-1.3/bam.h | 577 -
samtools-1.3/bam2bcf.c | 841 -
samtools-1.3/bam2bcf.h | 139 -
samtools-1.3/bam2bcf_indel.c | 531 -
samtools-1.3/bam2depth.c | 301 -
samtools-1.3/bam_addrprg.c | 476 -
samtools-1.3/bam_aux.c | 79 -
samtools-1.3/bam_cat.c | 558 -
samtools-1.3/bam_color.c | 169 -
samtools-1.3/bam_endian.h | 66 -
samtools-1.3/bam_flags.c | 68 -
samtools-1.3/bam_import.c | 63 -
samtools-1.3/bam_index.c | 121 -
samtools-1.3/bam_lpileup.c | 223 -
samtools-1.3/bam_lpileup.h | 57 -
samtools-1.3/bam_mate.c | 362 -
samtools-1.3/bam_md.c | 441 -
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samtools-1.3/bam_sort.c | 1839 --
samtools-1.3/bam_split.c | 567 -
samtools-1.3/bam_stat.c | 177 -
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samtools-1.3/config.h.in | 39 -
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samtools-1.3/errmod.c | 192 -
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samtools-1.3/examples/00README.txt | 41 -
samtools-1.3/examples/ex1.fa | 56 -
samtools-1.3/examples/ex1.sam.gz | Bin 114565 -> 0 bytes
samtools-1.3/examples/toy.fa | 4 -
samtools-1.3/examples/toy.sam | 14 -
samtools-1.3/faidx.c | 95 -
samtools-1.3/htslib-1.3/INSTALL | 102 -
samtools-1.3/htslib-1.3/LICENSE | 69 -
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samtools-1.3/htslib-1.3/NEWS | 74 -
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samtools-1.3/htslib-1.3/test/c1#bounds.sam | 4 -
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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#large_seq.sam | 3 -
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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/fieldarith.c | 72 -
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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/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 -
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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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samtools-1.3/test/merge/test_rtrans_build.c | 118 -
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