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.