#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 !

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

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

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

#bioinformatics #genomics #htslib