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Bug when reading BCF files with GT in INFO

bug

Status: Open.

#352 In chrovis/cljam;

· r6eve opened on Jun 24, 2026

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

Status: Open.

#348 In chrovis/cljam;

· alumi opened on Jun 2, 2026

Problematic behaviors around BAM index generation

Status: Open.

#316 In chrovis/cljam;

· athos opened on Jul 11, 2024

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

bug

Status: Open.

#315 In chrovis/cljam;

· athos opened on Jul 5, 2024

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

bug

Status: Open.

#314 In chrovis/cljam;

· athos opened on Jul 5, 2024

Test coverage fails sometimes on some environments

Status: Open.

#301 In chrovis/cljam;

· athos opened on Feb 27, 2024

Report position in read for reads in a pileup

enhancement

Status: Open.

#274 In chrovis/cljam;

· alumi opened on May 30, 2023

CRAM support?

enhancement

Status: Open.

#223 In chrovis/cljam;

· indraniel opened on Mar 24, 2021

mpileup loses bases of alignments starting with a insertion

Status: Open.

#139 In chrovis/cljam;

· alumi opened on Aug 10, 2018

##META meta info support for VCF/BCF

Status: Open.

#137 In chrovis/cljam;

· athos opened on Jul 4, 2018

Pileup reads with adjacent indels.

Status: Open.

#28 In chrovis/cljam;

· alumi opened on Feb 10, 2017