#samtools — Public Fediverse posts

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

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

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

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

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 #

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 #

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 #

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 #

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

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

#samtools #hts #bioinformatics

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

#samtools #hts #bioinformatics

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

#samtools #hts #bioinformatics

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

#samtools #hts #bioinformatics

#kmers #Bioinformatics #Ancestry #lowpass Dependencies: #RStats #Perl #samtools #GenomeTester4

RE: https://bsky.app/profile/did:plc:ppvxhapnptcy5v6cih3ynmzg/post/3lwenu5d2pb2d

#kmers #Bioinformatics #Ancestry #lowpass Dependencies: #RStats #Perl #samtools #GenomeTester4

RE: https://bsky.app/profile/did:plc:ppvxhapnptcy5v6cih3ynmzg/post/3lwenu5d2pb2d

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

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

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

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

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...

@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...

@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...

@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...

@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

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

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

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

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

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

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

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

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

The PR for samtools (visualize CNVs in the #terminal ) was merged today ! #samtools #cnv #sv #structuralvariant #ascii https://github.com/samtools/samtools/pull/1910

asked #biostars "htslib/c what is the correct way to use bgzf_thread_pool ?" #C #samtools #htskib #fastq https://www.biostars.org/p/9551841/

asked #biostars "htslib/c what is the correct way to use bgzf_thread_pool ?" #C #samtools #htskib #fastq https://www.biostars.org/p/9551841/

asked #biostars "htslib/c what is the correct way to use bgzf_thread_pool ?" #C #samtools #htskib #fastq https://www.biostars.org/p/9551841/

asked #biostars "htslib/c what is the correct way to use bgzf_thread_pool ?" #C #samtools #htskib #fastq https://www.biostars.org/p/9551841/

asked #biostars "htslib/c what is the correct way to use bgzf_thread_pool ?" #C #samtools #htskib #fastq https://www.biostars.org/p/9551841/

#samtools 1.21 released : https://github.com/samtools/samtools/releases/tag/1.21

I was reminded of this helpful tool the other day to identify SAM/BAM/CRAM flag values.
Great when you are hacking away with #samtools view commands and need to know the flag number to filter based on read properties, such as read unmapped and mate unmapped.
#genomics #bioinformatics
https://broadinstitute.github.io/picard/explain-flags.html

I just wrote a new PR for `samtools coverage` to plot the depth instead of the '% of covered bases' . Useful to validate #CNV in the terminal. #samtools #bioinformatics #sv #variant #bam

https://github.com/samtools/samtools/pull/1910

https://github.com/samtools/samtools/releases/tag/1.18 #samtools release 1.18 #bioinformatics

plot depth of #coverage in the #terminal using #samtools #depth and gnuplot:

```
$ samtools depth -a -r "chr1:234-456" in.bam | cut -f 2,3 | gnuplot -e 'set terminal dumb size 120,28; plot "-" smooth csplines with lines notitle'
```

#linux #bioinformatics

#samtools 1.21 released : https://github.com/samtools/samtools/releases/tag/1.21

#samtools 1.21 released : https://github.com/samtools/samtools/releases/tag/1.21