samtools htsjdk issues - Githubissues

samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

http://samtools.github.io/htsjdk/

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issues

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reducing memory required in IntervalMergerIterator when not concatting names

#1711 meganshand closed 6 days ago
1
Incomplete license metadata in build.gradle

#1710 tapdiego-amzn opened 1 month ago
0
SamUtils PairOrientation is confusingly ambiguous about paired reads needing to map to the same contig

#1709 yfarjoun opened 1 month ago
0
Fix CRAMReferenceRegion updating.

#1708 cmnbroad closed 1 month ago
0
Ignore version validation for BCF in VCFHeaderReader because we only need the header

#1707 lindenb opened 3 months ago
0
Upgrade to samtools 1.19.1 for interop testing.

#1706 cmnbroad closed 4 months ago
2
Add FQZComp Codec (Update CRAM Codecs to CRAM 3.1)

#1704 yash-puligundla opened 5 months ago
0
Implement VCF bundles.

#1703 cmnbroad opened 5 months ago
0
Implements collections of bundles.

#1702 cmnbroad opened 5 months ago
1
Iterator not working on vcffileReader

#1701 AlessandroBalestrucci closed 5 months ago
3
Minor updates to MemoryMappedFileBuffer

#1700 lbergelson opened 5 months ago
0
Updating our dependencies to the the newest version

#1699 lbergelson closed 6 months ago
0
Update for to use Java 21

#1698 lbergelson opened 6 months ago
0
Update to gradle 8.5

#1697 lbergelson closed 6 months ago
0
Updating tests in SAMRecordUnitTest to remove ambiguity

#1696 lbergelson closed 6 months ago
2
Ambiguous assertions in the tests

#1695 pgrt closed 6 months ago
1
Improving the somewhat slipshod change I made to HtsPath

#1694 lbergelson closed 6 months ago
0
Re-Ordering priority in SeekableStreamFactory

#1693 lbergelson closed 6 months ago
1
Truncation issue with GZIPInputStream when reading bgzip-compressed streams

#1691 jkmatila opened 8 months ago
1
Update test dependencies to newest versions

#1690 lbergelson closed 8 months ago
0
Resolve issues around integrating HTTP NIO provider

#1689 lbergelson opened 8 months ago
0
Fix IOUtil.unrollPaths for http paths with query parameters

#1688 lbergelson closed 8 months ago
0
Update snappy-java

#1687 bbimber closed 9 months ago
1
VariantContext has inconsistent behavior on getting allele type with spanning deletions

#1686 rickymagner opened 9 months ago
0
support for Azure blob storage? (specifically access to BAM/CRAM files in Azure blob storage by IGV)

#1685 smrgit opened 9 months ago
0
VCF_CSI_index_implementation

#1684 gokalpcelik opened 9 months ago
1
VCF 4.4 optimistic read switch.

#1683 cmnbroad closed 9 months ago
1
IOUtil.openFileForMd5CalculatingWriting() puts the md5 file in the wrong place.

#1682 lbergelson opened 10 months ago
0
Update some methods to accept Path input

#1681 takutosato closed 9 months ago
1
Add NamedFeature for common interface to name in bed or interval_list

#1680 rickymagner closed 11 months ago
1
two methods for Genotype: HasRefAllele HasAltAllele

#1678 lindenb closed 11 months ago
0
Update two remaining out of date dependencies

#1677 lbergelson closed 11 months ago
0
Move the EnaRefServiceTest to the externalAPI test group

#1675 lbergelson closed 11 months ago
0
Zero len array

#1674 gileshall closed 11 months ago
0
Deleted Java developers team

#1673 lbergelson opened 11 months ago
0
SAMFileWriterFactory creates .bai file when writing .cram file

#1672 rickymagner opened 11 months ago
1
htsjdk.samtools.util.IOUtil.assertFileIsWritable on certain NFS environments fails to correctly assess permissions

#1671 jd-daniels opened 1 year ago
2
Update snappy-java and migrate mjson to org.json to address CVEs

#1670 bbimber closed 11 months ago
4
Remove remaining incorrect zero-length-B-array checks and exception throwing

#1669 jmarshall closed 11 months ago
8
Error when reading a VCF 4.3 file with spaces in INFO field values

#1667 jkmatila opened 1 year ago
1
SamReaderFactory should use current defaults when makeDefault() is called

#1666 lbergelson opened 1 year ago
0
Question: How to generate FAI files and TBI files

#1665 Lys9527 opened 1 year ago
5
removed redundant code that sets the secondary alignment flag for a r…

#1664 KleinSamuel closed 11 months ago
0
Add Name Tokenization Codec (Update CRAM Codecs to CRAM 3.1)

#1663 yash-puligundla opened 1 year ago
0
proposal for a package htsjdk.tribble.gtf

#1662 lindenb opened 1 year ago
0
Escaped doublequotes in INFO descriptions result in invalid VCF file

#1661 bartcharbon opened 1 year ago
2
SamReader slower than expected on network drive

#1660 BeatWolf opened 1 year ago
1
Remove low-value progress logging message

#1659 nh13 closed 1 year ago
0
CRAM: 8-Bin Base Quality Compression

#1658 JWollnik opened 1 year ago
1
Histogram class uses unsafe methods for returning min/max

#1657 rickymagner opened 1 year ago
0