samtools htslib issues - Githubissues

samtools / htslib

C library for high-throughput sequencing data formats

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Using `bgzf_read_small()` breaks subsequent `bgzf_useek()` calls

#1798 jmarshall opened 1 day ago
1
Speed up faidx.

#1797 jkbonfield opened 2 days ago
0
Windows builds via GitHub Actions

#1796 jkbonfield opened 3 days ago
2
Refactor SIMD code and add ARM Neon nibble2base() implementation

#1795 jmarshall opened 5 days ago
3
Fix two occurrences of undefined behaviour in sam.c

#1794 kloetzl closed 1 day ago
4
fatal error: curl/curl.h: No such file or directory

#1793 sawma-k closed 2 days ago
1
Replace assert(0) with abort()

#1792 mp15 closed 1 week ago
2
assert(0) is bad practice

#1791 mp15 closed 1 week ago
1
How to control the version of htslib？

#1790 xmy1990 closed 2 weeks ago
3
bam_cigar_opchr - minor issue

#1789 kullrich closed 2 weeks ago
11
Fix possible out-of-bounds read in hts_itr_multi_next() (CRAM only)

#1788 daviesrob closed 3 weeks ago
0
Make BAM zero-length intervals work like CRAM

#1787 whitwham closed 3 weeks ago
1
Avoid possible race when selecting nibble2base implementation

#1786 daviesrob closed 4 weeks ago
0
Fix various cpu detection issues

#1785 daviesrob closed 1 month ago
1
Inconsistent truncation of floating-point tag values during conversion with sam_parse1 function from htslib

#1784 zhaobu closed 1 month ago
1
High memory usage with faidx API

#1783 tijyojwad closed 1 month ago
1
Filter line always added to the VCF header when opening a file for writing

#1782 nh13 closed 1 month ago
3
Use only _regions_add() in synced_bcf_reader.c when adding the list of contig names

#1781 jmarshall closed 1 month ago
1
Linking against Intel ISAL for faster deflate operations

#1780 pettyalex opened 1 month ago
3
Extend annot-tsv, adding several new options

#1779 pd3 closed 1 month ago
2
No warning on messed up VCF

#1778 pd3 opened 2 months ago
0
Compiler pedantry

#1777 jkbonfield closed 2 months ago
3
Snyk Security Scan Failure: Vulnerabilities Detected in samtools/htslib@1.20

#1776 superbsky closed 2 months ago
1
fix fuzz integer overflow in cram encoder.

#1775 jkbonfield closed 1 month ago
1
Check interval start to avoid overflowing bin numbers

#1774 jmarshall closed 1 month ago
1
Better detection for avx512f functionality

#1773 ryandesign closed 1 month ago
1
Add an inline version of bgzf_read for small reads.

#1772 jkbonfield closed 3 weeks ago
2
Extra low-level CRAM manipulation functions.

#1771 jkbonfield closed 1 month ago
0
Add support for CRAM Zstd compression

#1770 matty234 closed 2 months ago
2
Further recommend use of libdeflate and list OS packages

#1769 jkbonfield closed 2 months ago
2
Increase the input block size for bgzip.

#1768 jkbonfield opened 2 months ago
2
bgzip performance drop from v1.16

#1767 koriege opened 2 months ago
7
Add NEWS ready for 1.20 release

#1765 daviesrob closed 2 months ago
0
Make nibble2base faster using x86-64 pshufb instruction (SSSE3) and using dynamic dispatch.

#1764 rhpvorderman closed 1 month ago
14
Allow tabix indexing of GAF graph alignment files

#1763 adamnovak closed 3 months ago
3
Ensure S3 redirects use TLS

#1762 daviesrob closed 3 months ago
1
Fix duplicated but missing FORMAT bug

#1761 daviesrob closed 3 months ago
0
S3 plugin does not correctly handle 307 redirects for newly created buckets

#1760 andaca closed 3 months ago
4
Allow tabix indexing of GAF graph alignment files

#1759 adamnovak closed 3 months ago
1
[minor] Change error to warning.

#1758 whitwham closed 3 months ago
0
Check that handler->isremote has been set before calling it.

#1757 daviesrob closed 3 months ago
2
Allowing S3 virtual paths and S3 aliases as data source

#1756 mapk-amazon closed 3 months ago
1
added thread pool to tabix operations

#1755 vasudeva8 closed 3 months ago
2
Bug fix the recent bam_plp_destroy memory leak removal

#1754 jkbonfield closed 4 months ago
0
Delay closing the index file when indexing on-the-fly

#1753 daviesrob closed 3 months ago
0
Drop duplicate FORMAT tags and fix an error with dropping large tags

#1752 pd3 closed 3 months ago
2
Improve mpileup overlap removal

#1751 jkbonfield closed 4 months ago
0
Support building with htscodecs not in a submodule.

#1750 teo-tsirpanis closed 4 months ago
2
Base mod tweaks to improve validity checking.

#1749 jkbonfield closed 4 months ago
6