Rev htslib · broadinstitute/gamgee@76a1c91 · GitHub

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jmthibault79 committed Nov 12, 2014

1 parent 49081a0 commit 76a1c91

lib/htslib

Submodule htslib updated 50 files

+2 −0		.gitignore
+38 −6		Makefile
+2 −2		README.md
+53 −19		bgzf.c
+1 −4		cram/cram.h
+149 −74		cram/cram_codecs.c
+16 −6		cram/cram_codecs.h
+901 −335		cram/cram_decode.c
+1,137 −761		cram/cram_encode.c
+64 −15		cram/cram_index.c
+879 −382		cram/cram_io.c
+46 −17		cram/cram_io.h
+4 −1		cram/cram_samtools.c
+108 −15		cram/cram_stats.c
+190 −129		cram/cram_structs.h
+27 −33		cram/open_trace_file.c
+2 −0		cram/os.h
+336 −0		cram/rANS_byte.h
+821 −0		cram/rANS_static.c
+44 −0		cram/rANS_static.h
+2 −6		cram/sam_header.c
+0 −4		cram/sam_header.h
+138 −40		cram/thread_pool.c
+14 −1		cram/thread_pool.h
+1 −1		cram/vlen.c
+16 −6		faidx.c
+271 −112		hts.c
+158 −0		htsfile.c
+5 −0		htslib.mk
+4 −3		htslib/bgzf.h
+15 −0		htslib/faidx.h
+116 −21		htslib/hts.h
+13 −2		htslib/khash_str2int.h
+140 −0		htslib/regidx.h
+13 −4		htslib/synced_bcf_reader.h
+10 −9		htslib/vcf.h
+1 −0		htslib_vars.mk
+3 −5		knetfile.c
+322 −0		regidx.c
+93 −33		sam.c
+62 −22		synced_bcf_reader.c
+17 −18		tabix.1
+27 −1		tabix.c
+5 −0		tbx.c
+29 −2		test/sam.c
+116 −0		test/test-regidx.c
+52 −5		test/test-vcf-api.c
+90 −2		test/test_view.c
+121 −93		vcf.c
+16 −16		vcfutils.c

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