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 <[email protected]> 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 + 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samtools-1.3/test/mpileup/mpileup.3.bam | Bin 31216 -> 0 bytes samtools-1.3/test/mpileup/mpileup.ref.fa | 71 - samtools-1.3/test/mpileup/mpileup.ref.fa.fai | 1 - samtools-1.3/test/mpileup/mpileup.reg | 144 - samtools-1.3/test/mpileup/overlap50.sam | 5 - 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/rsem.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
