Issues

• Bug when reading BCF files with GT in INFO

  bug
  chrovis/cljam#352 · Filter by author r6eve opened on Jun 24, 2026

• Docstring of cljam.io.vcf/read-variants lists options not supported for VCF

  chrovis/cljam#348 · Filter by author alumi opened on Jun 2, 2026

• Problematic behaviors around BAM index generation

  chrovis/cljam#316 · Filter by author athos opened on Jul 11, 2024
  

• SAM/BAM/CRAM readers don't support @CO header

  bug
  chrovis/cljam#315 · Filter by author athos opened on Jul 5, 2024
  

• Read/write invariance breaks with integer tags in BAM/CRAM

  bug
  chrovis/cljam#314 · Filter by author athos opened on Jul 5, 2024
  

• Test coverage fails sometimes on some environments

  chrovis/cljam#301 · Filter by author athos opened on Feb 27, 2024

• Report position in read for reads in a pileup

  enhancement
  chrovis/cljam#274 · Filter by author alumi opened on May 30, 2023

• CRAM support?

  enhancement
  chrovis/cljam#223 · Filter by author indraniel opened on Mar 24, 2021
  1

  

• mpileup loses bases of alignments starting with a insertion

  chrovis/cljam#139 · Filter by author alumi opened on Aug 10, 2018

• ##META meta info support for VCF/BCF

  chrovis/cljam#137 · Filter by author athos opened on Jul 4, 2018

• Pileup reads with adjacent indels.

  chrovis/cljam#28 · Filter by author alumi opened on Feb 10, 2017
  1