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<code>FastaSequenceIndexCreator</code> cannot create an index for FASTA files with multiple empty lines at the end of the file

Status: Open.

#1748 In samtools/htsjdk;

· nvnieuwk opened on Jul 7, 2025

CRAM files with CSI index do not work

Status: Open.

#1747 In samtools/htsjdk;

· Bjoernsen opened on Jun 12, 2025

Lots of allocatable memory results in no buffering in SortingCollection

Status: Open.

#1741 In samtools/htsjdk;

· cmnbroad opened on Apr 7, 2025

Add peek method for SortingLongCollections

Status: Open.

#1733 In samtools/htsjdk;

· PramodRaoB opened on Dec 17, 2024

<code>Failure getting reference bases</code> inadequately describes the missing index error

cram

Status: Open.

#1732 In samtools/htsjdk;

· multimeric opened on Dec 3, 2024

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

Status: Open.

#1728 In samtools/htsjdk;

· jkbonfield opened on Oct 31, 2024

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

Status: Open.

#1724 In samtools/htsjdk;

· julesjacobsen opened on Oct 16, 2024

Duplicate ALT allele in VCF causes exception

SV

vcf

Status: Open.

#1718 In samtools/htsjdk;

· bartcharbon opened on Oct 4, 2024

Incomplete license metadata in build.gradle

Status: Open.

#1710 In samtools/htsjdk;

· tapdiego-amzn opened on May 23, 2024

Truncation issue with GZIPInputStream when reading bgzip-compressed streams

Status: Open.

#1691 In samtools/htsjdk;

· jkmatila opened on Oct 16, 2023

Resolve issues around integrating HTTP NIO provider

Status: Open.

#1689 In samtools/htsjdk;

· lbergelson opened on Oct 13, 2023

VariantContext has inconsistent behavior on getting allele type with spanning deletions

Status: Open.

#1686 In samtools/htsjdk;

· rickymagner opened on Oct 2, 2023