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samtools
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htslib
C library for high-throughput sequencing data formats
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"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
Make reg2bins, reg2intervals faster on whole-chromosome queries
#1596
daviesrob
closed
1 year ago
0
Fix bug where bin number could overflow when looking for max_off
#1595
daviesrob
closed
1 year ago
0
Remove use of sprintf() from HTSlib source
#1594
daviesrob
closed
1 year ago
1
Trivial fix to expr, removing "^".
#1593
jkbonfield
closed
1 year ago
0
One invocation of `expr` incorrectly uses `/^…/`
#1592
jmarshall
closed
1 year ago
3
Instructions in INSTALL outdated for Alpine 3.17
#1591
jmarshall
closed
1 year ago
0
Add MZ:i tag as a check for base modification validity.
#1590
jkbonfield
closed
1 year ago
0
Demo
#1589
vasudeva8
closed
11 months ago
1
Extract auxiliary tags from BAM file
#1588
sagnikbanerjee15
closed
1 year ago
2
Make SIMD configure tests work for MacOS multiarch builds
#1587
daviesrob
closed
1 year ago
1
snprintf instead of unsafe sprintf
#1586
oleksii-nikolaienko
closed
1 year ago
25
Explanation of construction of binning and linear indexes
#1585
marianogabitto
closed
1 year ago
1
Counting ALT allele instances
#1584
7PintsOfCherryGarcia
closed
1 year ago
1
Remove CRAM 3.1 warning.
#1583
jkbonfield
closed
1 year ago
0
Backport attractivechaos/klib#78 to htslib.
#1582
jkbonfield
closed
1 year ago
0
Fix a couple small VCF auto-indexing bugs.
#1581
jkbonfield
closed
1 year ago
0
Slightly speed up various cram decoding functions
#1580
jkbonfield
closed
1 year ago
2
truncated gzip (not bgzf) leads to infinite loop when parsign a fastq files
#1579
goranvinterhalter
closed
1 year ago
3
Cannot install htslib in Python 3.10 conda environment because of OpenSSL
#1578
sjdv1982
closed
1 year ago
6
Fix crypt4gh redirection
#1577
daviesrob
closed
1 year ago
0
Permit fastq output to create empty FASTQ records for seq "*".
#1576
jkbonfield
closed
1 year ago
1
Check if VCF POS column could be fully parsed
#1575
pd3
closed
1 year ago
3
Fix cram_index_query_last function
#1574
jkbonfield
closed
1 year ago
3
Add VCF/BCF support for POS=0 coordinate
#1573
pd3
opened
1 year ago
5
Switch to CURLINFO_CONTENT_LENGTH_DOWNLOAD_T for newer libcurl
#1572
daviesrob
closed
1 year ago
1
`bcftools view` with region filter drops variants at POS=0 (telomeres)
#1571
colin-nolan
opened
1 year ago
5
Unexpected handling of invalid (non-integer) `POS` values
#1570
colin-nolan
closed
1 year ago
1
sam_itr_regarray not reporting reads
#1569
Mesh89
closed
1 year ago
1
Minor NEWS adjustment and additonal item
#1568
daviesrob
closed
1 year ago
0
Fix issue 1566 - basemod API and hardclips
#1567
jts
closed
1 year ago
7
basemod API and hardclipped alignments
#1566
jts
closed
1 year ago
2
Prevent spurious and random system errors from test_bgzf.c
#1565
jkbonfield
closed
1 year ago
0
disable libcurl
#1564
grenaud
closed
1 year ago
4
Update to htscodecs v1.4.0
#1563
daviesrob
closed
1 year ago
0
Fix Cram compression container substitution matrix generation.
#1562
jkbonfield
closed
1 year ago
6
htslib make install error on 3 production servers
#1561
comatosejones
closed
1 year ago
3
Add symbol versions to libhts.so
#1560
daviesrob
closed
1 year ago
13
FIx a bug in the codec learning algorithm for TOKA
#1559
jkbonfield
closed
1 year ago
1
Embed ref2 unsorted
#1558
jkbonfield
closed
1 year ago
5
January 2023 NEWS Update.
#1557
whitwham
closed
1 year ago
1
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
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