Issues

• Single breakends not recognised by bcf_set_variant_type()

  samtools/htslib#2108 · Filter by author pd3 opened on Oct 16, 2026

• CI testing for signed-off-by commits

  samtools/htslib#2014 · Filter by author jkbonfield opened on May 20, 2026
  

• Suggestion: populate INFO name in warning "INFO tag id=146"

  samtools/htslib#1996 · Filter by author davmlaw opened on Feb 20, 2026
  4

  

• tabix performance

  samtools/htslib#1949 · Filter by author pd3 opened on Sep 2, 2025
  1

  

• hts_idx_t file query API

  samtools/htslib#1902 · Filter by author d-cameron opened on Apr 2, 2025
  4

  

• Add option to disable periodic hflush during multithreaded writes?

  samtools/htslib#1869 · Filter by author julianhess opened on Jan 2, 2025
  1

  

• bcftools consensous fails to write to GCP

  samtools/htslib#1865 · Filter by author Ieremie opened on Nov 11, 2024
  1

  

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

  samtools/htslib#1814 · Filter by author pettyalex opened on Jul 31, 2024 · wishlist
  4

  

• Linking against Intel ISAL for faster deflate operations

  samtools/htslib#1780 · Filter by author pettyalex opened on May 6, 2024
  9

  

• No warning on messed up VCF

  samtools/htslib#1778 · Filter by author pd3 opened on Apr 30, 2024

• todo: Improve --regions-overlap variant

  samtools/htslib#1746 · Filter by author pd3 opened on Feb 9, 2024

• Index file downloads when using GCS file

  samtools/htslib#1615 · Filter by author ggydush opened on May 3, 2023
  1

• bcftools view with region filter drops variants at POS=0 (telomeres)

  samtools/htslib#1571 · Filter by author colin-nolan opened on Feb 24, 2023
  5

  

• int overflow for big variant lines in vcf

  samtools/htslib#1539 · Filter by author arnaldurgylfason opened on Dec 16, 2022
  4

  

• bcf_hdr_remove leaves hash keys behind

  samtools/htslib#1533 · Filter by author pd3 opened on Dec 6, 2022
  10

  

• tabix returns row from VCF file multiple times

  samtools/htslib#1470 · Filter by author jwimberl opened on Jul 11, 2022
  4

• Extend vcf.h API to distinguish between the two indel types

  breaks-ABI
  samtools/htslib#1454 · Filter by author pd3 opened on Jun 14, 2022
  1

• Feature request: extend mpileup API

  samtools/htslib#1453 · Filter by author pd3 opened on Jun 14, 2022
  3

• Add support for bam/bai files in Azure blob storage

  samtools/htslib#1440 · Filter by author smrgit opened on May 25, 2022
  6

  

• tabix: how to retain header for arbitrary file types?

  samtools/htslib#1434 · Filter by author carbocation opened on May 11, 2022
  2

  

• Random read error on google cloud.

  samtools/htslib#1424 · Filter by author stefangroha opened on Apr 21, 2022
  4

  

• hts_log_error() extension for better error reporting

  samtools/htslib#1397 · Filter by author lczech opened on Feb 14, 2022
  5

  

• [Documentation] Short examples?

  samtools/htslib#1368 · Filter by author rubyFeedback opened on Jan 1, 2022 · wishlist
  1

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

  samtools/htslib#1338 · Filter by author ghuls opened on Oct 4, 2021 · wishlist
  12

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

  samtools/htslib#1315 · Filter by author junaruga opened on Aug 8, 2021 · wishlist
  1