Issues

• VALIDATE_CRC_CHECKSUMS doesn't check the blocks that hold a BAM's header

  samtools/htsjdk#1949 · Filter by author tfenne opened on Oct 29, 2026

• BAMRecordCodec accepts a read-name length of 0 and fails later with StringIndexOutOfBoundsException

  samtools/htsjdk#1948 · Filter by author tfenne opened on Oct 29, 2026

• SAMRecord.setReadString("*") is ignored when a BAMRecord is written

  samtools/htsjdk#1947 · Filter by author tfenne opened on Oct 29, 2026

• BinaryTagCodec.readTags drops the tags after a repeated tag

  samtools/htsjdk#1946 · Filter by author tfenne opened on Oct 29, 2026

• AsyncBufferedIterator.close() can hang when the wrapped iterator swallows the interrupt

  samtools/htsjdk#1944 · Filter by author tfenne opened on Oct 29, 2026

• AsyncBlockCompressedInputStream hangs forever on a corrupt BGZF block

  samtools/htsjdk#1942 · Filter by author tfenne opened on Oct 29, 2026

• Read FTP and HTTP(S) through NIO FileSystemProviders

  samtools/htsjdk#1897 · Filter by author tfenne opened on Oct 5, 2026

• SamPairUtil.setMateInformationOnSupplementalAlignment copies TLEN from the mate primary instead of computing it

  samtools/htsjdk#1795 · Filter by author nh13 opened on Jul 31, 2026

• HTSJDK QUAL floating-point precision error from log10PError round-trip

  bcfbugvcf
  samtools/htsjdk#1757 · Filter by author MarcoLotz opened on Mar 20, 2026

• Add peek method for SortingLongCollections

  feature
  samtools/htsjdk#1733 · Filter by author PramodRaoB opened on Dec 17, 2024
  1

  

• Add a module-info.java to enable use on the module path and build a binary with jlink

  chore
  samtools/htsjdk#1724 · Filter by author julesjacobsen opened on Oct 16, 2024

• Duplicate ALT allele in VCF causes exception

  bugvcf
  samtools/htsjdk#1718 · Filter by author bartcharbon opened on Oct 4, 2024
  3

• Resolve issues around integrating HTTP NIO provider

  bug
  samtools/htsjdk#1689 · Filter by author lbergelson opened on Oct 13, 2023

• VariantContext has inconsistent behavior on getting allele type with spanning deletions

  bcfbugvcf
  samtools/htsjdk#1686 · Filter by author rickymagner opened on Oct 2, 2023

• VCF sorting change breaks existing VCFs

  bugvcf
  samtools/htsjdk#1637 · Filter by author lbergelson opened on Nov 23, 2022
  1

  

• Give VCFEncoder an option to print float values with full precision

  featurevcf
  samtools/htsjdk#1598 · Filter by author roland-ewald opened on Mar 23, 2022
  1

• HtsGetVCFReader implementation?

  bcffeaturevcf
  samtools/htsjdk#1555 · Filter by author brainstorm opened on Jun 15, 2021
  5

• Enforce reserved fields in the header

  featurevcf
  samtools/htsjdk#1553 · Filter by author nh13 opened on May 6, 2021
  1

• Should htsjdk accept IUPAC ambiugous codes?

  bcffeaturevcf
  samtools/htsjdk#1543 · Filter by author SHuang-Broad opened on Apr 5, 2021
  2

• SAM NM tag calculation is off-spec

  bugsam
  samtools/htsjdk#1535 · Filter by author michaelgatzen opened on Feb 8, 2021

• Update the javadoc published on samtools.github.io

  chore
  samtools/htsjdk#1518 · Filter by author cmnbroad opened on Nov 9, 2020

• Extended Attributes in Genotype not parsed

  bcffeaturevcf
  samtools/htsjdk#1502 · Filter by author BoscoSuen opened on Aug 21, 2020
  1

• Partially missing AD and PL are treated as empty

  bugvcf
  samtools/htsjdk#1385 · Filter by author lbergelson opened on Jun 13, 2019
  5

• Limited API visibility issues around attributes

  featuresam
  samtools/htsjdk#1353 · Filter by author heuermh opened on Apr 18, 2019
  3

• CRAM should validate the SAM header against the reference being used

  cramfeature
  samtools/htsjdk#1244 · Filter by author cmnbroad opened on Dec 19, 2018