[med-svn] [rsem] 05/07: Merge tag 'upstream/1.2.28+dfsg'
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sat Mar 5 12:36:09 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch 1.2.28
in repository rsem.
commit 7b2aedba7ebbec7754c41819c1f6b9b27bf65bf2
Merge: fd85219 1f68569
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Mon Feb 22 04:33:14 2016 -0800
Merge tag 'upstream/1.2.28+dfsg'
Upstream version 1.2.28+dfsg
GTFItem.h | 4 +-
Makefile | 7 +-
README.md | 4 +-
WHAT_IS_NEW | 7 +
rsem-gff3-to-gtf | 18 +-
rsem_perl_utils.pm | 2 +-
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samtools-1.3/test/dat/view.001.02.bed | 22 -
samtools-1.3/test/dat/view.001.fa | 4 -
samtools-1.3/test/dat/view.001.fa.fai | 2 -
samtools-1.3/test/dat/view.001.sam | 62 -
samtools-1.3/test/dat/view.002.01.bed | 25 -
samtools-1.3/test/dat/view.002.02.bed | 30 -
samtools-1.3/test/dat/view.002.fa | 2 -
samtools-1.3/test/dat/view.002.fa.fai | 1 -
samtools-1.3/test/dat/view.002.sam | 83 -
samtools-1.3/test/dat/view.003.expected.sam | 39 -
samtools-1.3/test/dat/view.003.sam | 39 -
samtools-1.3/test/fixmate/1_coord_sort.sam | 16 -
.../test/fixmate/1_coord_sort.sam.expected | 0
.../test/fixmate/1_coord_sort.sam.expected.err | 2 -
samtools-1.3/test/fixmate/2_isize_overflow.sam | 18 -
.../test/fixmate/2_isize_overflow.sam.expected | 18 -
samtools-1.3/test/fixmate/3_reverse_read_pp_lt.sam | 5 -
.../test/fixmate/3_reverse_read_pp_lt.sam.expected | 5 -
.../test/fixmate/4_reverse_read_pp_equal.sam | 5 -
.../fixmate/4_reverse_read_pp_equal.sam.expected | 5 -
samtools-1.3/test/fixmate/5_ct.sam | 5 -
samtools-1.3/test/fixmate/5_ct.sam.expected | 5 -
samtools-1.3/test/fixmate/6_ct_replace.sam | 5 -
.../test/fixmate/6_ct_replace.sam.expected | 5 -
.../test/idxstats/test_input_1_a.bam.expected | 5 -
.../test/idxstats/test_input_1_a.bam.expected.err | 0
samtools-1.3/test/merge/2.merge.expected.bam | Bin 1228 -> 0 bytes
samtools-1.3/test/merge/3.merge.expected.bam | Bin 1233 -> 0 bytes
samtools-1.3/test/merge/3.merge.expected.err | 1 -
samtools-1.3/test/merge/4.merge.expected.bam | Bin 689 -> 0 bytes
samtools-1.3/test/merge/5.merge.expected.bam | Bin 1115 -> 0 bytes
samtools-1.3/test/merge/5.merge.expected.sam | 61 -
samtools-1.3/test/merge/6.merge.expected.bam | Bin 899 -> 0 bytes
samtools-1.3/test/merge/7.merge.expected.bam | Bin 1056 -> 0 bytes
samtools-1.3/test/merge/test_3.fofn | 2 -
samtools-1.3/test/merge/test_bam_translate.c | 596 -
samtools-1.3/test/merge/test_header.sam | 11 -
samtools-1.3/test/merge/test_rtrans_build.c | 118 -
samtools-1.3/test/merge/test_trans_tbl_init.c | 574 -
samtools-1.3/test/mpileup/1read.bam | Bin 525 -> 0 bytes
samtools-1.3/test/mpileup/1read.sam | 1 -
samtools-1.3/test/mpileup/anomalous.sam | 6 -
samtools-1.3/test/mpileup/c1#ID.bam | Bin 293 -> 0 bytes
samtools-1.3/test/mpileup/c1#ID2.bam | Bin 377 -> 0 bytes
samtools-1.3/test/mpileup/c1#clip.bam | Bin 265 -> 0 bytes
samtools-1.3/test/mpileup/c1#pad1.bam | Bin 299 -> 0 bytes
samtools-1.3/test/mpileup/c1#pad2.bam | Bin 349 -> 0 bytes
samtools-1.3/test/mpileup/c1#pad3.bam | Bin 382 -> 0 bytes
samtools-1.3/test/mpileup/c1.fa | 4 -
samtools-1.3/test/mpileup/c1.fa.fai | 2 -
samtools-1.3/test/mpileup/ce#5b.bam | Bin 557 -> 0 bytes
samtools-1.3/test/mpileup/ce#5b.bam.bai | Bin 416 -> 0 bytes
samtools-1.3/test/mpileup/ce#5b.cram | Bin 13183 -> 0 bytes
samtools-1.3/test/mpileup/ce#5b.cram.crai | Bin 75 -> 0 bytes
samtools-1.3/test/mpileup/ce#5b.sam | 12 -
samtools-1.3/test/mpileup/ce#large_seq.bam | Bin 345315 -> 0 bytes
samtools-1.3/test/mpileup/ce#unmap.bam | Bin 233 -> 0 bytes
samtools-1.3/test/mpileup/ce#unmap1.bam | Bin 896 -> 0 bytes
samtools-1.3/test/mpileup/ce#unmap2.bam | Bin 1344 -> 0 bytes
samtools-1.3/test/mpileup/ce.fa | 20803 -------------------
samtools-1.3/test/mpileup/ce.fa.fai | 7 -
samtools-1.3/test/mpileup/deep.sam | 9001 --------
samtools-1.3/test/mpileup/depth.reg | 39 -
samtools-1.3/test/mpileup/expected/1.out.f3-6.gz | Bin 596114 -> 0 bytes
samtools-1.3/test/mpileup/expected/10.out | 40 -
samtools-1.3/test/mpileup/expected/11.out | 9 -
samtools-1.3/test/mpileup/expected/12.out | 9 -
samtools-1.3/test/mpileup/expected/13.out | 4101 ----
samtools-1.3/test/mpileup/expected/14.out | 4101 ----
samtools-1.3/test/mpileup/expected/15.out | 4101 ----
samtools-1.3/test/mpileup/expected/16.out | 4101 ----
samtools-1.3/test/mpileup/expected/17.out | 4101 ----
samtools-1.3/test/mpileup/expected/18.out | 4101 ----
samtools-1.3/test/mpileup/expected/19.out | 4101 ----
samtools-1.3/test/mpileup/expected/2.out | 0
samtools-1.3/test/mpileup/expected/20.out | 4101 ----
samtools-1.3/test/mpileup/expected/21.out | 4101 ----
samtools-1.3/test/mpileup/expected/22.out | 4101 ----
samtools-1.3/test/mpileup/expected/23.out | 150 -
samtools-1.3/test/mpileup/expected/24.out | 150 -
samtools-1.3/test/mpileup/expected/25.out | 150 -
samtools-1.3/test/mpileup/expected/26.out | 100 -
samtools-1.3/test/mpileup/expected/27.out | 100 -
samtools-1.3/test/mpileup/expected/28.out | 4101 ----
samtools-1.3/test/mpileup/expected/29.out | 0
samtools-1.3/test/mpileup/expected/3.out | 0
samtools-1.3/test/mpileup/expected/30.out | 100 -
samtools-1.3/test/mpileup/expected/31.out | 100 -
samtools-1.3/test/mpileup/expected/32.out | 100 -
samtools-1.3/test/mpileup/expected/33.out | 12 -
samtools-1.3/test/mpileup/expected/34.out | 12 -
samtools-1.3/test/mpileup/expected/35.out | 3397 ---
samtools-1.3/test/mpileup/expected/37.out | 4101 ----
samtools-1.3/test/mpileup/expected/38.out | 102 -
samtools-1.3/test/mpileup/expected/39.out | 11 -
samtools-1.3/test/mpileup/expected/4.out | 101 -
samtools-1.3/test/mpileup/expected/40.out | 84 -
samtools-1.3/test/mpileup/expected/41.out | 21 -
samtools-1.3/test/mpileup/expected/42.out | 0
samtools-1.3/test/mpileup/expected/43.out | 3893 ----
samtools-1.3/test/mpileup/expected/44.out | 3893 ----
samtools-1.3/test/mpileup/expected/45.out | 4097 ----
samtools-1.3/test/mpileup/expected/46.out | 4097 ----
samtools-1.3/test/mpileup/expected/47.out | 1 -
samtools-1.3/test/mpileup/expected/48.out | 4104 ----
samtools-1.3/test/mpileup/expected/49.out | 4104 ----
samtools-1.3/test/mpileup/expected/5.out | 10 -
samtools-1.3/test/mpileup/expected/50.out | 4104 ----
samtools-1.3/test/mpileup/expected/51.out | 4104 ----
samtools-1.3/test/mpileup/expected/52.out | 4208 ----
samtools-1.3/test/mpileup/expected/53.out | 1 -
samtools-1.3/test/mpileup/expected/54.out | 1 -
samtools-1.3/test/mpileup/expected/55.out | 1 -
samtools-1.3/test/mpileup/expected/56.out | 1 -
samtools-1.3/test/mpileup/expected/57.out | 1 -
samtools-1.3/test/mpileup/expected/58.out | 1 -
samtools-1.3/test/mpileup/expected/59.out | 1 -
samtools-1.3/test/mpileup/expected/6.out | 10 -
samtools-1.3/test/mpileup/expected/60.out | 0
samtools-1.3/test/mpileup/expected/61.out | 1 -
samtools-1.3/test/mpileup/expected/62.out | 0
samtools-1.3/test/mpileup/expected/63.out | 1 -
samtools-1.3/test/mpileup/expected/64.out | 0
samtools-1.3/test/mpileup/expected/65.out | 1 -
samtools-1.3/test/mpileup/expected/66.out | 0
samtools-1.3/test/mpileup/expected/67.out | 1 -
samtools-1.3/test/mpileup/expected/68.out | 0
samtools-1.3/test/mpileup/expected/69.out | 0
samtools-1.3/test/mpileup/expected/7.out | 10 -
samtools-1.3/test/mpileup/expected/70.out | 1 -
samtools-1.3/test/mpileup/expected/71.out | 1 -
samtools-1.3/test/mpileup/expected/72.out | 0
samtools-1.3/test/mpileup/expected/73.out | 1 -
samtools-1.3/test/mpileup/expected/74.out | 0
samtools-1.3/test/mpileup/expected/75.out | 1 -
samtools-1.3/test/mpileup/expected/76.out | 4101 ----
samtools-1.3/test/mpileup/expected/77.out | 4101 ----
samtools-1.3/test/mpileup/expected/8.out | 5 -
samtools-1.3/test/mpileup/expected/9.out | 10 -
samtools-1.3/test/mpileup/expected/d1_1.out | 6 -
samtools-1.3/test/mpileup/expected/d1_12.out | 9 -
samtools-1.3/test/mpileup/expected/d1_2.out | 6 -
samtools-1.3/test/mpileup/expected/d2_12r.out | 5 -
samtools-1.3/test/mpileup/expected/d3_12.out | 20 -
samtools-1.3/test/mpileup/expected/d3_12r1a.out | 12 -
samtools-1.3/test/mpileup/expected/d3_12r2a.out | 6 -
samtools-1.3/test/mpileup/expected/d4_12.out | 60 -
samtools-1.3/test/mpileup/expected/d4_12b.out | 17 -
samtools-1.3/test/mpileup/expected/d4_12r.out | 12 -
samtools-1.3/test/mpileup/indels.sam | 9 -
.../mpileup/md5/02099b2aad2cfe707759353724fb40ae | 1 -
.../mpileup/md5/0d4dfc45807d6a11439e858605cb364d | 1 -
.../mpileup/md5/351f64d4f4f9ddd45b35336ad97aa6de | 1 -
.../mpileup/md5/6ec590eb82c361a61e6baabce20109bc | 1 -
.../mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1 | 1 -
.../mpileup/md5/73d180d5cb3860a2713927b6812eab0e | 1 -
samtools-1.3/test/mpileup/mpileup-E.bam | Bin 280 -> 0 bytes
samtools-1.3/test/mpileup/mpileup.1.bam | Bin 71637 -> 0 bytes
samtools-1.3/test/mpileup/mpileup.1.bam.bai | Bin 776 -> 0 bytes
samtools-1.3/test/mpileup/mpileup.2.bam | Bin 31556 -> 0 bytes
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 --
557 files changed, 26 insertions(+), 262935 deletions(-)
--
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