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samtools
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htslib
C library for high-throughput sequencing data formats
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Improve API docs for bgzf_mt
#1556
jkbonfield
closed
1 year ago
0
Feature request: add support for on the fly creation of VCF/BCF indexes
#1555
pd3
closed
1 year ago
1
Catch errors from bgzf_getline() in hts_readlist, hts_readlines
#1554
daviesrob
closed
1 year ago
0
Can we pass an input file descriptor to bgzf_mt ?
#1553
rpadmanabhan
closed
1 year ago
1
Merges neighbouring I and D ops into one op within pileup.
#1552
jkbonfield
closed
1 year ago
0
Speed up load_ref_portion.
#1551
jkbonfield
closed
1 year ago
0
Behaviour of `bam_mods_query_type()` / interface to `hts_base_mod_state`
#1550
cjw85
closed
1 year ago
11
January 2023 release copyright update
#1549
whitwham
closed
1 year ago
0
Initial test framework for #1543 (to be continued)
#1548
pd3
closed
1 year ago
8
Update copyright date in LICENSE file and version messages
#1547
daviesrob
closed
1 year ago
0
Expand CRAM API a bit to cope with new samtools cram_size command.
#1546
jkbonfield
closed
1 year ago
3
Don't error when making an iterator on a tid not in the index
#1545
daviesrob
closed
1 year ago
2
Make bcf_hdr_idinfo_exists() more robust
#1544
pd3
closed
1 year ago
0
VCF header parser has O(n^2) complexity in the number of generic header lines
#1543
freeseek
closed
1 year ago
5
Improve support for very long input lines (> 2Gbyte)
#1542
daviesrob
closed
1 year ago
2
Issue accessing S3-stored VCFs
#1541
agilly
closed
1 year ago
4
Installation on mac
#1540
akr55
closed
1 year ago
2
int overflow for big variant lines in vcf
#1539
arnaldurgylfason
opened
1 year ago
4
bcf_hdr_idinfo_exists(hdr,type,int_id) on binary VCFs with gapped BCF_DT_ID tables
#1538
freeseek
closed
1 year ago
0
Cut down the number of embed_ref=2 tests that get run
#1537
daviesrob
closed
1 year ago
1
Switch MacOS CI tests to an ARM-based image
#1536
daviesrob
closed
1 year ago
0
Fix htslib 1533
#1535
pd3
closed
1 year ago
0
hts_itr_query fails on empty BCFs with gapped tid blocks
#1534
pd3
closed
1 year ago
1
bcf_hdr_remove leaves hash keys behind
#1533
pd3
opened
1 year ago
10
Make it easier to modify shared library permissions during install
#1532
jkbonfield
closed
1 year ago
2
return value of bam_get_seq() when sequence not stored in the bam file
#1531
lmjakt
closed
1 year ago
6
Ensure strings in config_vars.h are escaped correctly
#1530
daviesrob
closed
1 year ago
1
bgzf_read_block added error return
#1529
bir3
closed
1 year ago
6
tabix on truncated file returns successfully with exit status 0
#1528
bir3
closed
1 year ago
3
Preprocessor definitions with quotation marks
#1527
lczech
closed
1 year ago
4
How to get reads depth by sam.h
#1526
leon945945
closed
1 year ago
4
Install the shared library .so file as executable
#1525
StephDC
closed
1 year ago
7
Fix build on ancient versions of gcc
#1524
daviesrob
closed
1 year ago
0
std=c99 required by gcc 4.8.5
#1523
lmjakt
closed
1 year ago
2
Add CRAM SQ/M5 header checking when specifying a fasta file.
#1522
jkbonfield
closed
1 year ago
4
Fix ref fix from c91804c
#1521
jkbonfield
closed
1 year ago
0
Fix buffer read-overrun in bam_plp_insertion_mod.
#1520
jkbonfield
closed
1 year ago
0
Add faidx_seq_len64(), fai_adjust_region() interfaces and faidx tests
#1519
daviesrob
closed
1 year ago
0
Check for invalid BC tags in fastq output.
#1518
jkbonfield
closed
1 year ago
2
Warn if ref file is given but it doesn't contain the refs we need.
#1517
jkbonfield
closed
1 year ago
0
Add an fai_line_length function.
#1516
jkbonfield
closed
1 year ago
1
Trouble converting .cram to .fq
#1515
0106WeiWeiDeng
closed
1 year ago
10
Are `bam_aux_first` and `bam_aux_next` available from the shared library?
#1514
kojix2
closed
1 year ago
2
A minor speed improvement to VCF parsing by 5-9%
#1513
jkbonfield
closed
1 year ago
3
Fix a typo in sam.h documentation
#1512
kojix2
closed
1 year ago
1
Switch to building libdeflate with cmake
#1511
daviesrob
closed
1 year ago
0
bcf_strerror method to get description of error code
#1510
vasudeva8
closed
1 year ago
2
Use POSIX `grep`
#1509
SoapGentoo
closed
1 year ago
1
tok3_decode_names() in cram/cram_io.c is undefined.
#1508
wangyugui
closed
1 year ago
2
Prevent crash when only FASTA entry has no sequence.
#1507
jkbonfield
closed
1 year ago
1
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