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cram
htslib
test
- auxf#values.sam
- auxf.fa
- auxf.fa.fai
- c1#bounds.sam
- c1#clip.sam
- c1#pad1.sam
- c1#pad2.sam
- c1#pad3.sam
- c1.fa
- c1.fa.fai
- ce#1.sam
- ce#2.sam
- ce#5.sam
- ce#5b.sam
- ce#large_seq.sam
- ce#tag_depadded.sam
- ce#tag_padded.sam
- ce#unmap.sam
- ce#unmap1.sam
- ce#unmap2.sam
- ce.fa
- ce.fa.fai
- compare_sam.pl
- fieldarith.c
- fieldarith.sam
- hfile.c
- sam.c
- test-regidx.c
- test-vcf-api.c
- test-vcf-api.out
- test-vcf-sweep.c
- test-vcf-sweep.out
- test.pl
- test_view.c
- test_view.pl
- xx#blank.sam
- xx#large_aux.sam
- xx#large_aux2.sam
- xx#minimal.sam
- xx#pair.sam
- xx#rg.sam
- xx#triplet.sam
- xx#unsorted.sam
- xx.fa
- xx.fa.fai
.gitattributes
.gitignore
.travis.yml
INSTALL
LICENSE
Makefile
NEWS
README
README.md
bgzf.c
bgzip.c
config.mk.in
configure.ac
faidx.5
faidx.c
hfile.c
hfile_internal.h
hfile_irods.c
hfile_net.c
hts.c
htsfile.1
htsfile.c
htslib.mk
htslib.pc.in
htslib_vars.mk
kfunc.c
knetfile.c
kstring.c
regidx.c
sam.5
sam.c
synced_bcf_reader.c
tabix.1
tabix.c
tbx.c
vcf.5
vcf.c
vcf_sweep.c
vcfutils.c

test

jmarshall

Reinstate faidx_fetch_nseq() alongside faidx_nseq()

Jan 30, 2015

38d93e2 · Jan 30, 2015

History

This branch is 6 commits ahead of, 2222 commits behind samtools/htslib:develop.

Name	Name	Last commit message	Last commit date
parent directory ..
auxf#values.sam	auxf#values.sam	Avoid aux.* filenames, which are invalid on Windows	Jan 16, 2015
auxf.fa	auxf.fa	Avoid aux.* filenames, which are invalid on Windows	Jan 16, 2015
auxf.fa.fai	auxf.fa.fai	Avoid aux.* filenames, which are invalid on Windows	Jan 16, 2015
c1#bounds.sam	c1#bounds.sam	(io_lib r3439)	Sep 20, 2013
c1#clip.sam	c1#clip.sam	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
c1#pad1.sam	c1#pad1.sam	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
c1#pad2.sam	c1#pad2.sam	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
c1#pad3.sam	c1#pad3.sam	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
c1.fa	c1.fa	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
c1.fa.fai	c1.fa.fai	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
ce#1.sam	ce#1.sam	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
ce#2.sam	ce#2.sam	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
ce#5.sam	ce#5.sam	Fixed CRAM to code with the 0x800 supplementary flag.	Oct 15, 2013
ce#5b.sam	ce#5b.sam	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
ce#large_seq.sam	ce#large_seq.sam	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
ce#tag_depadded.sam	ce#tag_depadded.sam	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
ce#tag_padded.sam	ce#tag_padded.sam	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
ce#unmap.sam	ce#unmap.sam	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
ce#unmap1.sam	ce#unmap1.sam	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
ce#unmap2.sam	ce#unmap2.sam	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
ce.fa	ce.fa	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
ce.fa.fai	ce.fa.fai	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
compare_sam.pl	compare_sam.pl	Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT	Aug 1, 2014
fieldarith.c	fieldarith.c	Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT	Aug 1, 2014
fieldarith.sam	fieldarith.sam	Add bam_endpos(const bam1_t *)	Oct 2, 2013
hfile.c	hfile.c	Account for read buffering in hseek(SEEK_CUR)	Nov 28, 2014
sam.c	sam.c	Reinstate faidx_fetch_nseq() alongside faidx_nseq()	Jan 30, 2015
test-regidx.c	test-regidx.c	Added regidx API which should replace bcf_sr_regions at some point	Sep 25, 2014
test-vcf-api.c	test-vcf-api.c	Fix in bgzf's gzip reading plus added a test for this	Oct 29, 2014
test-vcf-api.out	test-vcf-api.out	vcf: bcf_hdr_get_hrec() interface made more general	Jul 3, 2014
test-vcf-sweep.c	test-vcf-sweep.c	Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT	Aug 1, 2014
test-vcf-sweep.out	test-vcf-sweep.out	kseq,hts: Enable seek() on kstreams and hts_useek(),hts_utell() on ht…	Sep 5, 2013
test.pl	test.pl	Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT	Aug 1, 2014
test_view.c	test_view.c	Minor change to allow REQUIRED_FIELDS option to be specified in hex or	Jan 8, 2015
test_view.pl	test_view.pl	Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT	Aug 1, 2014
xx#blank.sam	xx#blank.sam	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
xx#large_aux.sam	xx#large_aux.sam	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
xx#large_aux2.sam	xx#large_aux2.sam	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
xx#minimal.sam	xx#minimal.sam	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
xx#pair.sam	xx#pair.sam	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
xx#rg.sam	xx#rg.sam	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
xx#triplet.sam	xx#triplet.sam	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
xx#unsorted.sam	xx#unsorted.sam	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
xx.fa	xx.fa	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013
xx.fa.fai	xx.fa.fai	Added some synthetic SAM test data and a test perl script to trial	Jul 22, 2013

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