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Issues list

Accept U as a valid base type and convert to T for BAM.
#1728 opened Oct 31, 2024 by jkbonfield
3
Add a module-info.java to enable use on the module path and build a binary with jlink
#1724 opened Oct 16, 2024 by julesjacobsen
Duplicate ALT allele in VCF causes exception SV vcf
#1718 opened Oct 4, 2024 by bartcharbon
3
Incomplete license metadata in build.gradle
#1710 opened May 23, 2024 by tapdiego-amzn
Truncation issue with GZIPInputStream when reading bgzip-compressed streams
#1691 opened Oct 16, 2023 by jkmatila
2
Resolve issues around integrating HTTP NIO provider
#1689 opened Oct 13, 2023 by lbergelson
VariantContext has inconsistent behavior on getting allele type with spanning deletions
#1686 opened Oct 2, 2023 by rickymagner
support for Azure blob storage? (specifically access to BAM/CRAM files in Azure blob storage by IGV)
#1685 opened Sep 29, 2023 by smrgit
Deleted Java developers team
#1673 opened Aug 2, 2023 by lbergelson
SAMFileWriterFactory creates .bai file when writing .cram file
#1672 opened Jul 18, 2023 by rickymagner
1
htsjdk.samtools.util.IOUtil.assertFileIsWritable on certain NFS environments fails to correctly assess permissions
#1671 opened Jun 28, 2023 by jd-daniels
4
Error when reading a VCF 4.3 file with spaces in INFO field values
#1667 opened May 26, 2023 by jkmatila
1
SamReaderFactory should use current defaults when makeDefault() is called
#1666 opened May 24, 2023 by lbergelson
Question: How to generate FAI files and TBI files
#1665 opened Apr 6, 2023 by Lys9527
5
Escaped doublequotes in INFO descriptions result in invalid VCF file
#1661 opened Mar 13, 2023 by bartcharbon
2
SamReader slower than expected on network drive
#1660 opened Mar 11, 2023 by BeatWolf
1
CRAM: 8-Bin Base Quality Compression cram
#1658 opened Mar 8, 2023 by JWollnik
1
Histogram class uses unsafe methods for returning min/max
#1657 opened Feb 23, 2023 by rickymagner
Question: Tabix index to find min(POS) and max(POS) in each contig
#1652 opened Feb 14, 2023 by lindenb
Add a better error message when the reference is too long for indexing long reference Bugs and issues related to long reference sequences.
#1651 opened Feb 13, 2023 by lbergelson
5
Race conditions accessing CRAM's reference data through ReferenceSource bug
#1643 opened Jan 9, 2023 by vruano
1
@vruano
VCF sorting change breaks existing VCFs bug vcf
#1637 opened Nov 23, 2022 by lbergelson
@lbergelson
1
CRAM files have zero-length blocks with a compression method associated with them (so cannot be decompressed). bug cram
#1633 opened Nov 8, 2022 by jkbonfield
1
LittleEndianInputStream EOF test is incorrect bug
#1614 opened Jun 14, 2022 by cmnbroad
9
Remove validation of VCF Header line field order?
#1610 opened May 27, 2022 by tfenne
1
ProTip! What’s not been updated in a month: updated:<2024-09-30.