All issues

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

#1757

· MarcoLotz opened

on Mar 20, 2026

Extremly high random I/O in query overlaping API for CRAM

#1756

· karlestira opened

on Mar 9, 2026

Query bed file indexed with csi

#1754

· dariober opened

on Jan 24, 2026

Fast way to get number of aligned reads in indexed CRAM file.

#1752

· dariober opened

on Jan 11, 2026

Incorrect error message for out of order SAM file alignments

#1750

· Lenbok opened

on Nov 17, 2025

ReferenceSequenceFile is thread-safe for uncompressed FASTA but decidedly non-threadsafe for bgzipped FASTA files

#1749

· tfenne opened

on Oct 24, 2025

`FastaSequenceIndexCreator` cannot create an index for FASTA files with multiple empty lines at the end of the file

#1748

· nvnieuwk opened

on Jul 7, 2025

CRAM files with CSI index do not work

#1747

· Bjoernsen opened

on Jun 12, 2025

Lots of allocatable memory results in no buffering in SortingCollection

#1741

· cmnbroad opened

on Apr 7, 2025

Add peek method for SortingLongCollections

#1733

· PramodRaoB opened

on Dec 17, 2024

`Failure getting reference bases` inadequately describes the missing index error

#1732

· multimeric opened

on Dec 3, 2024

Accept U as a valid base type and convert to T for BAM.

#1728

· jkbonfield opened

on Oct 31, 2024