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how to index a read in a circular sequence?

Status: Open.

#847 In samtools/hts-specs;

· yfarjoun opened on Dec 18, 2025

A molecular-annotation-spec for SAM/BAM/CRAM with new reserved tags

sam

sam-tags

Status: Open.

#846 In samtools/hts-specs;

· mrvollger opened on Nov 20, 2025

Fix explaination of BS data series in CRAM

cram

Status: Open.

#845 In samtools/hts-specs;

· jkbonfield opened on Oct 23, 2025

TLEN meaning when leftmost and rightmost are the same for a pair, or the same for a single record

cram

sam

Status: Open.

#842 In samtools/hts-specs;

· jkbonfield opened on Sep 3, 2025

htsget: using htsget server to mask regions from users (i.e clinical usecase(s))

htsget

Status: Open.

#838 In samtools/hts-specs;

· brainstorm opened on Aug 6, 2025

htsget: spec should indicate (dictate?) whether .vcf.gz is preferred (mandatory?) over plaintext .vcf?

htsget

Status: Open.

#837 In samtools/hts-specs;

· brainstorm opened on Aug 6, 2025

Incorrect encoding for haploid individual in GT example

vcf

Status: Open.

#835 In samtools/hts-specs;

· daviesrob opened on Jul 15, 2025

VCF text cut off by the edge of the page

vcf

Status: Open.

#834 In samtools/hts-specs;

· daviesrob opened on Jul 15, 2025

Percent encoding is under-defined

vcf

Status: Open.

#829 In samtools/hts-specs;

· d-cameron opened on May 28, 2025

HQ is underdefined

vcf

Status: Open.

#827 In samtools/hts-specs;

· d-cameron opened on May 14, 2025

GL genotype ordering does not account for phasing

vcf

Status: Open.

#826 In samtools/hts-specs;

· d-cameron opened on May 14, 2025

Sequence Collections in SAM headers

sam

Status: Open.

#824 In samtools/hts-specs;

· jkbonfield opened on Apr 30, 2025