RE: https://genomic.social/@yokofakun/115740891523944578

https://github.com/samtools/htsjdk/discussions/1760#discussioncomment-16384234

> HTSJDK has not been the most actively maintained project for a long time, and with many departures from Broad in the last couple of years, it's not clear to me who still has an active interest in helping maintain the project.

#java #htsjdk #samtools

CVE Alert: CVE-2026-31973 - samtools - samtools - https://www.redpacketsecurity.com/cve-alert-cve-2026-31973-samtools-samtools/

#OSINT #ThreatIntel #CyberSecurity #cve-2026-31973 #samtools #

#samtools 1.23 released https://github.com/samtools/samtools/releases/tag/1.23

#samtools #hts #bioinformatics

My PhD student authored a rather niche piece of software written in Rust that introduces a new type of index for BAM files, allowing fast counting and filtering of reads based on their FLAG attributes:

https://www.researchgate.net/publication/396084914_bafiq_BAM_Flag_Index_Tool_for_Faster_Repeated_Queries_of_Mapped_Reads

Although we mention possible usage scenarios, we are far from sure how frequent, or useful these might be. Would be grateful for any input on this from the community, especially from people who can imagine including #bafiq in their pipelines or BAM file repositories. Negative examples might also help.
#bioinformatics #genomics #sequencing #genome #samtools

https://github.com/Dedaniya08/samtools This repository is a GPU-accelerated fork of samtools/samtools, originally developed by Genome Research Ltd. and contributors.

#samtools #bioinformatics #gpu

@kaasbaas #wikipedia (English language) is only ~22GB of #bzip2 compressed #xml (uncompressed size is ~86GB).
is it possible to access it without decompression? I guess #random #access to .xml.bz2 should be a solved problem, right?
we're routinely using gzip with random access in #bioinformatics ie via #samtools or #tabix

EDIT:
Wikipedia xml.bz2 does support random access for multistream version. does @kiwix or any other wiki reader support it? I couldn't find info on their website...

Just out: @multiqc v1.25.2 🎉

This patch release fixes a whole host of bugs, the most important one being for #bcl2fastq 🐛

There are also a host of small additions sneaking in for #ngsbits, #picard, #Nanostat, #Samtools and more - so well worth the update!

https://github.com/MultiQC/MultiQC/releases/tag/v1.25.2

gcc -g -Wall -O2 -fvisibility=hidden -I. -c -o simd.o simd.c

simd.c:126:5: warning: implicit declaration of function ‘_mm_lddqu_si128’ [-Wimplicit-function-declaration]
__m128i nuc_lookup_vec = _mm_lddqu_si128((__m128i *)seq_nt16_str);
^
simd.c:126:30: error: incompatible types when initializing type ‘__m128i’ using type ‘int’
__m128i nuc_lookup_vec = _mm_lddqu_si128((__m128i *)seq_nt16_str);

🤔 #samtools 1.21