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Potential for lzma dependency avoidance.

enhancement

Status: Open.

#937 In samtools/htslib;

· jkbonfield opened on Sep 25, 2019

bam1_t build function

Status: Open.

#789 In samtools/htslib;

· jkbonfield opened on Oct 30, 2018

CRAM in name-sorted order & reference

Status: Open.

#508 In samtools/htslib;

· jkbonfield opened on Apr 10, 2017

samtools mpileup fails if .bam are differently ordered / headers are different

bug

Status: Open.

#464 In samtools/htslib;

· lpryszcz opened on Feb 6, 2017

CRAM lossy name compression and tag white/black list

Status: Open.

#314 In samtools/htslib;

· jkbonfield opened on Jan 14, 2016

TODO: CRAM split aux tags

Status: Open.

#313 In samtools/htslib;

· jkbonfield opened on Jan 14, 2016

bgzf index - last offset?

P3: Low priority

Status: Open.

#262 In samtools/htslib;

· jvolkening opened on Aug 27, 2015

[DISCUSS] Add HTS_PARSE_* parsing flags

Status: Open (in progress).

samtools/htslibnumber 260

#260 In samtools/htslib;

· jmarshall opened on Aug 26, 2015

htslib should implement a more complete URI scheme for <code>irods:</code>

D2: Moderate

P2: Desirable

Status: Open.

#229 In samtools/htslib;

· jrandall opened on Jun 25, 2015

for creating indexing file in samtools merge

D2: Moderate

P2: Desirable

Status: Open (in progress).

samtools/htslibnumber 193

#193 In samtools/htslib;

· ionzhangj8 opened on Mar 25, 2015

CSIv2

Status: Open.

#148 In samtools/htslib;

· pd3 opened on Nov 13, 2014

Enforcing filter criteria on _all_ samples.

enhancement

Status: Open.

#126 In samtools/htslib;

· arq5x opened on Aug 28, 2014

hts_readlines() should check that the lines are textual

enhancement

Status: Open.

#66 In samtools/htslib;

· jmarshall opened on Feb 21, 2014

Interoperability with other BCF implementations

Status: Open.

#38 In samtools/htslib;

· jmarshall opened on Nov 25, 2013

Wish list - automatic merging and/or concatenation.

Status: Open.

#1174 In samtools/htslib;

· jkbonfield opened on Nov 3, 2020

Warning: shared-lib-calls-exit detected by a lint tool

Status: Open.

#1315 In samtools/htslib;

· junaruga opened on Aug 8, 2021

Feature request: Add option to tabix to interleave multiple bgzipped indexed files, without the need for external resorting.

Status: Open.

#1338 In samtools/htslib;

· ghuls opened on Oct 4, 2021

[Documentation] Short examples?

Status: Open.

#1368 In samtools/htslib;

· rubyFeedback opened on Jan 1, 2022

Google Cloud Storage hFILE not using multipart / resumable uploads or downloads for reliability

Status: Open.

#1814 In samtools/htslib;

· pettyalex opened on Jul 31, 2024