htslib
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samtools
C library for high-throughput sequencing data formats
Currently, the SOVERSION is only bumped when there are ABI changes which are not backwards compatible. This is typically insufficient for several reasons: 1. Many distributions do not track individual...
## 1. Memory leaks caused by failed `realloc` function. `bcf_get_format_values` uses `realloc` internally to resize as needed the memory block pointed to by `*dst`. E.g. ```C if ( *ndst <...
This is a follow-up to a question I asked in the samtools-devel mailinglist found [here](https://sourceforge.net/p/samtools/mailman/samtools-devel/thread/alpine.DEB.2.10.1705021150090.3055%40deskpro109045.internal.sanger.ac.uk/#msg35817501). The problem in question arises if one wants to use an identical instance of a...
To-do when dropping CRAM v1.x support. Realistically it should have been ditched ages ago as I don't believe C and Java implementations were particularly interchangeable due to spec problems. I...
Hi, We've noticed that samtools/htslib seems to have a small time penalty when making an initial connection to any s3 resource (local s3 or amazonaws s3). e.g. 1-2 second delay...
Related issue: https://github.com/samtools/samtools/issues/1984 The two main changes are: * In `s3_open_v4` an additional `hopen` is called if a redirect (status code between 300 and 399) is detected. * In `redirect_endpoint_callback`...
Fixes #1735. Added option to provide number threads to use, disabled by default. Uses the thread pool in operations except listing of sequence names (-l).
This is to ensure the timestamp on the index file is later than the one on the file being indexed, preventing spurious "The index file is older than the data...
The removal of large tags introduced by https://github.com/samtools/htslib/commit/b49eea478114759efe19e718c38e7deb00614b21 and https://github.com/samtools/htslib/commit/9db565de3d89235f625de07363f1cd726c43f8f2 could not work correctly, the memmove pointers were wrong! Resolves https://github.com/samtools/htslib/issues/1733 This is a fix of the botched pull request...
I want to adjust the genotype of some large sample size vcf file by using global ancestry results. I have ancestry results for x origins so I want to recreate...
