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samtools
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htslib
C library for high-throughput sequencing data formats
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NEWS updates for pending release
#1649
daviesrob
closed
11 months ago
0
Base mod test harness bug fixes / improvements
#1648
daviesrob
closed
11 months ago
0
Ensure number of modifications is always set in bam_parse_basemod2()
#1647
daviesrob
closed
11 months ago
1
Fix to 2e672f33 decompress_peek_gz change.
#1646
jkbonfield
closed
11 months ago
1
Add fai_thread_pool interface.
#1645
jkbonfield
closed
11 months ago
0
Speed up the VCF parser
#1644
jkbonfield
closed
10 months ago
2
Fix decompress_peek_gz to cope with files starting on empty gzip blocks.
#1643
jkbonfield
closed
11 months ago
1
Request to support multiple input files. Currently, bgzip <file1> <file2> only compresses <file1>.
#1642
bw2
closed
8 months ago
2
Fix a containment bug in cram_index_last.
#1640
jkbonfield
closed
12 months ago
0
Inconsistency in samtools stats output - cram index issue?
#1639
jts
closed
12 months ago
3
Decompression threads for `bgzip`ped FASTA files
#1638
oleksii-nikolaienko
closed
11 months ago
2
Fix possible double frees in bcf_hdr_add_hrec() error handling
#1637
daviesrob
closed
11 months ago
5
Base mod API improvements
#1636
jkbonfield
closed
12 months ago
0
base mod API clarification
#1635
jts
closed
1 year ago
2
htslib-s3-plugin.7: fix whatis entry
#1634
emollier
closed
1 year ago
3
cram/cram_external.c: fix external htscodecs include
#1633
emollier
closed
1 year ago
1
changes to avoid segfault with uncompressed bam
#1632
vasudeva8
closed
1 year ago
0
fixes and comment update
#1631
vasudeva8
closed
1 year ago
0
Add support for non-standard chromosome names containing [:-] characters
#1630
pd3
closed
1 year ago
4
extract reads by read name
#1629
leon945945
closed
1 year ago
2
Pull in latest htscodecs and improve portability
#1628
daviesrob
closed
1 year ago
0
Failed to populate reference for id
#1627
egnarora
closed
1 year ago
9
Stop the overwriting of the end value.
#1626
whitwham
closed
1 year ago
0
Calling tabix on S3 files via jupyter notebook fails
#1625
agilly
closed
3 months ago
5
Allow repeated calls of bcf_sr_set_regions
#1624
pd3
closed
1 year ago
11
`bcf_sr_seek` behaves differently for VCF.gz and BCF
#1623
pd3
closed
1 year ago
2
Tabix does not return the correct regions
#1622
hiruna72
closed
1 year ago
2
markdup `[E::cram_flush_thread] Call to cram_encode_container failed` error
#1621
dennishendriksen
closed
12 months ago
13
Synced reader does not support regions with contigs including colons
#1620
brenochoa
closed
1 year ago
4
Add new annot-tsv program
#1619
pd3
closed
8 months ago
14
Fix example in docs for sam_hdr_add_line
#1618
kojix2
closed
1 year ago
1
Segfault when writing uncompressed BAM
#1617
tijyojwad
closed
1 year ago
2
Change bounds checking in probaln_glocal
#1616
jkbonfield
closed
1 year ago
5
Index file downloads when using GCS file
#1615
ggydush
opened
1 year ago
1
Add a missing break statement in cram_codec_to_id.
#1614
jkbonfield
closed
1 year ago
0
Protection against over sized aux tags in CRAM
#1613
jkbonfield
closed
1 year ago
0
Rename aux tag MZ to MN.
#1612
jkbonfield
closed
1 year ago
0
Mention in INSTALL that using plugins may need -rdynamic
#1611
jmarshall
closed
1 year ago
0
Can't make install on OSX (apple sillicon), permission denied
#1610
etowahadams
closed
1 year ago
1
Switched back to openssl for Alpine.
#1609
whitwham
closed
1 year ago
0
Switch to defining _XOPEN_SOURCE=600 for htscodecs tests
#1608
daviesrob
closed
1 year ago
4
Amalgamate multiple CIGAR ops into single entry.
#1607
whitwham
closed
1 year ago
3
probaln_glocal returns suboptimal alignment when bandwidth is too large
#1605
jts
closed
1 year ago
2
undeclared: gettimeofday
#1606
clausecker
closed
1 year ago
12
Enable subreading of bam file for htsget
#1602
nanjiangshu
closed
1 year ago
1
Avoid bgzf EOF check on modern MinGW releases.
#1601
jkbonfield
closed
1 year ago
7
"Couldn't register scheme handler" errors for tool linking (likely incorrectly?) to htslib
#1600
jwimberl
closed
1 year ago
12
Fix typo in kh_int_hash_func2 macro.
#1599
jkbonfield
closed
1 year ago
0
typo in kh_int_hash_func2 definition
#1598
fanxinping
closed
1 year ago
1
bcftools mpileup behaves differently for cigar M vs =/X
#1597
marcelm
closed
1 year ago
1
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