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commit b2cf913fab1d67e9773c9d58b53c2ccfd961cc17 Merge: 494f56a 3cbc6e0 Author: Afif Elghraoui <[email protected]> Date: Wed Jun 24 19:27:39 2015 -0700 Merge tag 'upstream/0.8.3+ds1' Upstream version 0.8.3+ds1 htslib/INSTALL | 79 - htslib/LICENSE | 69 - htslib/Makefile | 386 - htslib/NEWS | 50 - htslib/README | 5 - htslib/bgzf.c | 1124 -- htslib/bgzip.c | 284 - htslib/config.h | 3 - htslib/config.mk | 72 - htslib/config.mk.in | 72 - htslib/configure | 4012 ------- htslib/configure.ac | 93 - htslib/cram/cram.h | 63 - htslib/cram/cram_codecs.c | 1846 ---- htslib/cram/cram_codecs.h | 165 - htslib/cram/cram_decode.c | 2775 ----- htslib/cram/cram_decode.h | 112 - htslib/cram/cram_encode.c | 3068 ------ htslib/cram/cram_encode.h | 105 - htslib/cram/cram_index.c | 557 - htslib/cram/cram_index.h | 98 - htslib/cram/cram_io.c | 4202 -------- htslib/cram/cram_io.h | 596 -- htslib/cram/cram_samtools.c | 147 - htslib/cram/cram_samtools.h | 97 - htslib/cram/cram_stats.c | 450 - htslib/cram/cram_stats.h | 59 - htslib/cram/cram_structs.h | 809 -- htslib/cram/files.c | 76 - htslib/cram/mFILE.c | 634 -- htslib/cram/mFILE.h | 88 - htslib/cram/md5.c | 295 - htslib/cram/md5.h | 54 - htslib/cram/misc.h | 110 - htslib/cram/open_trace_file.c | 351 - htslib/cram/open_trace_file.h | 115 - htslib/cram/os.h | 308 - htslib/cram/pooled_alloc.c | 170 - htslib/cram/pooled_alloc.h | 56 - htslib/cram/rANS_byte.h | 336 - htslib/cram/rANS_static.c | 841 -- htslib/cram/rANS_static.h | 44 - htslib/cram/sam_header.c | 1218 --- htslib/cram/sam_header.h | 444 - htslib/cram/string_alloc.c | 153 - htslib/cram/string_alloc.h | 69 - htslib/cram/thread_pool.c | 811 -- htslib/cram/thread_pool.h | 210 - htslib/cram/vlen.c | 432 - htslib/cram/vlen.h | 48 - htslib/cram/zfio.c | 185 - htslib/cram/zfio.h | 54 - htslib/faidx.5 | 147 - htslib/faidx.c | 475 - htslib/hfile.c | 547 - htslib/hfile_internal.h | 76 - htslib/hfile_irods.c | 243 - htslib/hfile_net.c | 99 - htslib/hts.c | 1665 --- htslib/htsfile.1 | 71 - htslib/htsfile.c | 168 - htslib/htslib.mk | 150 - htslib/htslib.pc.in | 10 - htslib/htslib/bgzf.h | 315 - htslib/htslib/faidx.h | 135 - htslib/htslib/hfile.h | 212 - htslib/htslib/hts.h | 456 - htslib/htslib/hts_defs.h | 47 - htslib/htslib/kfunc.h | 75 - htslib/htslib/khash.h | 619 -- htslib/htslib/khash_str2int.h | 133 - htslib/htslib/klist.h | 121 - htslib/htslib/knetfile.h | 101 - htslib/htslib/kseq.h | 253 - htslib/htslib/ksort.h | 285 - htslib/htslib/kstring.h | 270 - htslib/htslib/regidx.h | 147 - htslib/htslib/sam.h | 426 - htslib/htslib/synced_bcf_reader.h | 301 - htslib/htslib/tbx.h | 77 - htslib/htslib/vcf.h | 883 -- htslib/htslib/vcf_sweep.h | 39 - htslib/htslib/vcfutils.h | 112 - htslib/htslib_vars.mk | 39 - htslib/kfunc.c | 280 - htslib/knetfile.c | 632 -- htslib/kstring.c | 254 - htslib/regidx.c | 338 - htslib/sam.5 | 68 - htslib/sam.c | 1882 ---- htslib/synced_bcf_reader.c | 1257 --- htslib/tabix.1 | 180 - htslib/tabix.c | 519 - htslib/tbx.c | 320 - htslib/test/auxf#values.sam | 5 - htslib/test/auxf.fa | 2 - htslib/test/auxf.fa.fai | 1 - htslib/test/c1#bounds.sam | 4 - htslib/test/c1#clip.sam | 8 - htslib/test/c1#pad1.sam | 10 - htslib/test/c1#pad2.sam | 14 - htslib/test/c1#pad3.sam | 14 - htslib/test/c1.fa | 2 - htslib/test/c1.fa.fai | 1 - htslib/test/ce#1.sam | 2 - htslib/test/ce#2.sam | 3 - htslib/test/ce#5.sam | 11 - htslib/test/ce#5b.sam | 12 - htslib/test/ce#large_seq.sam | 3 - htslib/test/ce#tag_depadded.sam | 11 - htslib/test/ce#tag_padded.sam | 11 - htslib/test/ce#unmap.sam | 6 - htslib/test/ce#unmap1.sam | 20 - htslib/test/ce#unmap2.sam | 29 - htslib/test/ce.fa | 20803 ------------------------------------ htslib/test/ce.fa.fai | 7 - htslib/test/compare_sam.pl | 172 - htslib/test/fieldarith.c | 72 - htslib/test/fieldarith.sam | 15 - htslib/test/hfile.c | 204 - htslib/test/sam.c | 187 - htslib/test/test-regidx.c | 116 - htslib/test/test-vcf-api.c | 282 - htslib/test/test-vcf-api.out | 28 - htslib/test/test-vcf-sweep.c | 112 - htslib/test/test-vcf-sweep.out | 4 - htslib/test/test.pl | 202 - htslib/test/test_view.c | 239 - htslib/test/test_view.pl | 71 - htslib/test/xx#blank.sam | 0 htslib/test/xx#large_aux.sam | 4 - htslib/test/xx#large_aux2.sam | 11 - htslib/test/xx#minimal.sam | 10 - htslib/test/xx#pair.sam | 7 - htslib/test/xx#rg.sam | 13 - htslib/test/xx#triplet.sam | 7 - htslib/test/xx#unsorted.sam | 8 - htslib/test/xx.fa | 5 - htslib/test/xx.fa.fai | 2 - htslib/vcf.5 | 120 - htslib/vcf.c | 3212 ------ htslib/vcf_sweep.c | 182 - htslib/vcfutils.c | 675 -- htslib/version.h | 1 - 144 files changed, 69867 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pysam.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
