#htslib — Public Fediverse posts

#Duckdb #htslib #Genomics #Bioinformatics #RStats duckths: Read HTS (VCF/BCF/BAM/CRAM/FASTA/FASTQ/GTF/GFF) files in DuckDB via htslib Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension genomic.social/@bioinfhotep...

SMT (@[email protected]...

#Duckdb #htslib #Genomics #Bioinformatics #RStats duckths: Read HTS (VCF/BCF/BAM/CRAM/FASTA/FASTQ/GTF/GFF) files in DuckDB via htslib Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension genomic.social/@bioinfhotep...

SMT (@[email protected]...

#Genomics #Bioinformatics
Release of duckhts: #htslib based #Duckdb Extension for High Throughput Sequencing File Formats
https://duckdb.org/community_extensions/extensions/duckhts
Allied Self contained #Rstats package Rduckhts : https://rgenomicsetl.r-universe.dev/Rduckhts

For now the lifecycle of the APIs (Duckdb C API extension and R package) are "experimental". They are mostly targeted to some ETL use cases, but will add some some useful scalar and aggregation functions including Heng Li's C Genomic ranges

Feedback and testing welcome !

#Genomics #Bioinformatics
Release of duckhts: #htslib based #Duckdb Extension for High Throughput Sequencing File Formats
https://duckdb.org/community_extensions/extensions/duckhts
Allied Self contained #Rstats package Rduckhts : https://rgenomicsetl.r-universe.dev/Rduckhts

For now the lifecycle of the APIs (Duckdb C API extension and R package) are "experimental". They are mostly targeted to some ETL use cases, but will add some some useful scalar and aggregation functions including Heng Li's C Genomic ranges

Feedback and testing welcome !

#Genomics #Bioinformatics
Release of duckhts: #htslib based #Duckdb Extension for High Throughput Sequencing File Formats
https://duckdb.org/community_extensions/extensions/duckhts
Allied Self contained #Rstats package Rduckhts : https://rgenomicsetl.r-universe.dev/Rduckhts

For now the lifecycle of the APIs (Duckdb C API extension and R package) are "experimental". They are mostly targeted to some ETL use cases, but will add some some useful scalar and aggregation functions including Heng Li's C Genomic ranges

Feedback and testing welcome !

#Genomics #Bioinformatics
Release of duckhts: #htslib based #Duckdb Extension for High Throughput Sequencing File Formats
https://duckdb.org/community_extensions/extensions/duckhts
Allied Self contained #Rstats package Rduckhts : https://rgenomicsetl.r-universe.dev/Rduckhts

For now the lifecycle of the APIs (Duckdb C API extension and R package) are "experimental". They are mostly targeted to some ETL use cases, but will add some some useful scalar and aggregation functions including Heng Li's C Genomic ranges

Feedback and testing welcome !

#Genomics #Bioinformatics
Release of duckhts: #htslib based #Duckdb Extension for High Throughput Sequencing File Formats
https://duckdb.org/community_extensions/extensions/duckhts
Allied Self contained #Rstats package Rduckhts : https://rgenomicsetl.r-universe.dev/Rduckhts

For now the lifecycle of the APIs (Duckdb C API extension and R package) are "experimental". They are mostly targeted to some ETL use cases, but will add some some useful scalar and aggregation functions including Heng Li's C Genomic ranges

Feedback and testing welcome !

#RStats Rduckhts: 'DuckDB' 'HTS' File Reader Extension for 'R' Sitting on the shoulders of the great #htslib API and the duckdb C API Package : rgenomicsetl.r-universe.dev/Rduckhts

#RStats Rduckhts: 'DuckDB' 'HTS' File Reader Extension for 'R' Sitting on the shoulders of the great #htslib API and the duckdb C API Package : rgenomicsetl.r-universe.dev/Rduckhts

#RStats Rduckhts: 'DuckDB' 'HTS' File Reader Extension for 'R' Sitting on the shoulders of the great #htslib API and the duckdb C API Package : rgenomicsetl.r-universe.dev/Rduckhts

#RStats Rduckhts: 'DuckDB' 'HTS' File Reader Extension for 'R' Sitting on the shoulders of the great #htslib API and the duckdb C API Package : rgenomicsetl.r-universe.dev/Rduckhts

#RStats Rduckhts: 'DuckDB' 'HTS' File Reader Extension for 'R' Sitting on the shoulders of the great #htslib API and the duckdb C API Package : rgenomicsetl.r-universe.dev/Rduckhts

Maybe the fastest BCF/VCF to #RStats DataFrames using #htslib and #duckdb C API. Easily the title of fastest BCF/VCF to parquet convertors in #RStats (no other R options :D). This was motivated, among other things, by the idea of trying out #DuckLake in a familiar field github.com/RGenomicsETL...

Maybe the fastest BCF/VCF to #RStats DataFrames using #htslib and #duckdb C API. Easily the title of fastest BCF/VCF to parquet convertors in #RStats (no other R options :D). This was motivated, among other things, by the idea of trying out #DuckLake in a familiar field github.com/RGenomicsETL...

Maybe the fastest BCF/VCF to #RStats DataFrames using #htslib and #duckdb C API. Easily the title of fastest BCF/VCF to parquet convertors in #RStats (no other R options :D). This was motivated, among other things, by the idea of trying out #DuckLake in a familiar field github.com/RGenomicsETL...

Maybe the fastest BCF/VCF to #RStats DataFrames using #htslib and #duckdb C API. Easily the title of fastest BCF/VCF to parquet convertors in #RStats (no other R options :D). This was motivated, among other things, by the idea of trying out #DuckLake in a familiar field github.com/RGenomicsETL...

Maybe the fastest BCF/VCF to #RStats DataFrames using #htslib and #duckdb C API. Easily the title of fastest BCF/VCF to parquet convertors in #RStats (no other R options :D). This was motivated, among other things, by the idea of trying out #DuckLake in a familiar field github.com/RGenomicsETL...

playing with GNU #guile and #htslib.

(define with_vcf (lambda (f action) (begin
(define header (bcf_hdr_read f))
(define b (bcf_init1))
(while (>= (bcf_read fp header b) 0) (action header b))
(bcf_hdr_destroy header)
(bcf_destroy b)
(hts_close f)
)))

#bioinformatics #guile #scheme #vcf #lisp

playing with GNU #guile and #htslib.

(define with_vcf (lambda (f action) (begin
(define header (bcf_hdr_read f))
(define b (bcf_init1))
(while (>= (bcf_read fp header b) 0) (action header b))
(bcf_hdr_destroy header)
(bcf_destroy b)
(hts_close f)
)))

#bioinformatics #guile #scheme #vcf #lisp

playing with GNU #guile and #htslib.

(define with_vcf (lambda (f action) (begin
(define header (bcf_hdr_read f))
(define b (bcf_init1))
(while (>= (bcf_read fp header b) 0) (action header b))
(bcf_hdr_destroy header)
(bcf_destroy b)
(hts_close f)
)))

#bioinformatics #guile #scheme #vcf #lisp

playing with GNU #guile and #htslib.

(define with_vcf (lambda (f action) (begin
(define header (bcf_hdr_read f))
(define b (bcf_init1))
(while (>= (bcf_read fp header b) 0) (action header b))
(bcf_hdr_destroy header)
(bcf_destroy b)
(hts_close f)
)))

#bioinformatics #guile #scheme #vcf #lisp

playing with GNU #guile and #htslib.

(define with_vcf (lambda (f action) (begin
(define header (bcf_hdr_read f))
(define b (bcf_init1))
(while (>= (bcf_read fp header b) 0) (action header b))
(bcf_hdr_destroy header)
(bcf_destroy b)
(hts_close f)
)))

#bioinformatics #guile #scheme #vcf #lisp

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

#bioinformatics #htslib

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

#bioinformatics #htslib

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

#bioinformatics #htslib

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

#bioinformatics #htslib

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

#bioinformatics #htslib

#htslib #Bioinformatics #GenomicsIO
@yokofakun any idea what is the fastest method to get the nth bcf record using htslib or bcftools.h without explicit loops? (trying out something similar to your project https://github.com/lindenb/rbcf but with ALTREP)
I guess it is possible to guess which block to (lazy) parse if one know the blocks offsets and number of records per block

#htslib #Bioinformatics #GenomicsIO
@yokofakun any idea what is the fastest method to get the nth bcf record using htslib or bcftools.h without explicit loops? (trying out something similar to your project https://github.com/lindenb/rbcf but with ALTREP)
I guess it is possible to guess which block to (lazy) parse if one know the blocks offsets and number of records per block

#htslib #Bioinformatics #GenomicsIO
@yokofakun any idea what is the fastest method to get the nth bcf record using htslib or bcftools.h without explicit loops? (trying out something similar to your project https://github.com/lindenb/rbcf but with ALTREP)
I guess it is possible to guess which block to (lazy) parse if one know the blocks offsets and number of records per block

#htslib #Bioinformatics #GenomicsIO
@yokofakun any idea what is the fastest method to get the nth bcf record using htslib or bcftools.h without explicit loops? (trying out something similar to your project https://github.com/lindenb/rbcf but with ALTREP)
I guess it is possible to guess which block to (lazy) parse if one know the blocks offsets and number of records per block

#htslib #Bioinformatics #GenomicsIO
@yokofakun any idea what is the fastest method to get the nth bcf record using htslib or bcftools.h without explicit loops? (trying out something similar to your project https://github.com/lindenb/rbcf but with ALTREP)
I guess it is possible to guess which block to (lazy) parse if one know the blocks offsets and number of records per block

via Stephen Turner on X : "Everyone's giving NotebookLM their papers, theses, marketing materials, etc. to generate these "Podcasts".

I gave it the full text of kseq.h from seqtk. "

https://notebooklm.google.com/notebook/39e3670a-dfa5-4808-aa11-06ab8c0cfb9d/audio?original_referer=https:%2F%2Ft.co%23&pli=1

#IA #podcast #htslib #bioinformatics

via Stephen Turner on X : "Everyone's giving NotebookLM their papers, theses, marketing materials, etc. to generate these "Podcasts".

I gave it the full text of kseq.h from seqtk. "

https://notebooklm.google.com/notebook/39e3670a-dfa5-4808-aa11-06ab8c0cfb9d/audio?original_referer=https:%2F%2Ft.co%23&pli=1

#IA #podcast #htslib #bioinformatics

via Stephen Turner on X : "Everyone's giving NotebookLM their papers, theses, marketing materials, etc. to generate these "Podcasts".

I gave it the full text of kseq.h from seqtk. "

https://notebooklm.google.com/notebook/39e3670a-dfa5-4808-aa11-06ab8c0cfb9d/audio?original_referer=https:%2F%2Ft.co%23&pli=1

#IA #podcast #htslib #bioinformatics

via Stephen Turner on X : "Everyone's giving NotebookLM their papers, theses, marketing materials, etc. to generate these "Podcasts".

I gave it the full text of kseq.h from seqtk. "

https://notebooklm.google.com/notebook/39e3670a-dfa5-4808-aa11-06ab8c0cfb9d/audio?original_referer=https:%2F%2Ft.co%23&pli=1

#IA #podcast #htslib #bioinformatics

via Stephen Turner on X : "Everyone's giving NotebookLM their papers, theses, marketing materials, etc. to generate these "Podcasts".

I gave it the full text of kseq.h from seqtk. "

https://notebooklm.google.com/notebook/39e3670a-dfa5-4808-aa11-06ab8c0cfb9d/audio?original_referer=https:%2F%2Ft.co%23&pli=1

#IA #podcast #htslib #bioinformatics

new program in #htslib "annot-regs" https://raw.githubusercontent.com/pd3/utils/master/annot-regs/doc.annot-regs.pdf

new program in #htslib "annot-regs" https://raw.githubusercontent.com/pd3/utils/master/annot-regs/doc.annot-regs.pdf

new program in #htslib "annot-regs" https://raw.githubusercontent.com/pd3/utils/master/annot-regs/doc.annot-regs.pdf

new program in #htslib "annot-regs" https://raw.githubusercontent.com/pd3/utils/master/annot-regs/doc.annot-regs.pdf

new program in #htslib "annot-regs" https://raw.githubusercontent.com/pd3/utils/master/annot-regs/doc.annot-regs.pdf

PR accepted ! option "--drop-genotypes" in #bcftools concat https://github.com/samtools/bcftools/pull/1911 🥳🥳

#bioinformatics #genomics #htslib

PR accepted ! option "--drop-genotypes" in #bcftools concat https://github.com/samtools/bcftools/pull/1911 🥳🥳

#bioinformatics #genomics #htslib

PR accepted ! option "--drop-genotypes" in #bcftools concat https://github.com/samtools/bcftools/pull/1911 🥳🥳

#bioinformatics #genomics #htslib

PR accepted ! option "--drop-genotypes" in #bcftools concat https://github.com/samtools/bcftools/pull/1911 🥳🥳

#bioinformatics #genomics #htslib

PR accepted ! option "--drop-genotypes" in #bcftools concat https://github.com/samtools/bcftools/pull/1911 🥳🥳

#bioinformatics #genomics #htslib