tools biological sequences: bam-filter, count-reads, vcf-check


This package provides several tools that (at least at the time of their creation) provide functionalities beyond the routine provided by samtools and other reverse dependencies of the htslib.

These new tools are
 • bam-filter : filter BAM/CRAM/SAM files with a simple expression language
 • count-reads: count BAM/CRAM reads in regions given in a BED file
 • vcf-check : check regions of a VCF against a background for missing chunks

and yes, as the name suggests, these tools are all implemented in nim, using the nim-hts (upstream: hts-nim) wrapper for the htslib.

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