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Commits on Dec 12, 2024

• SamUtils PairOrientation is confusingly ambiguous about paired reads needing to map to the same contig (#1709)

  Show description for 9fe9042
  yfarjoun

  authored
  9fe9042

Commits on Dec 11, 2024

• Minor README format improvement(#1731)

  ArtoriaZhang

  authored
  a9aea4d

Commits on Oct 29, 2024

• Improve GFF API by adding new convenience methods

  Show description for dbebac3
  lindenb

  authored
  dbebac3

• Treat .vcf.bgz as a valid vcf extension in FileExtension (#1727)

  Show description for 4ea3285
  lindenb

  authored
  4ea3285

Commits on Oct 28, 2024

• Add ReferenceSequenceFile.getSubsequenceAt(final Locatable locatable ) (#1725)

  lindenb

  authored
  fd56496

Commits on Oct 7, 2024

• Update commons compress to a 1.26.0 (#1720)

  lbergelson

  authored
  a37ffa6

• Replace toPath().toString() with getURIString() (#1719)

  Show description for 1cb5f07
  lbergelson

  authored
  1cb5f07

Commits on Oct 2, 2024

• SamReaderFactory opens non-regular File and Path the same way (#1717)

  kshakir

  authored
  4c1c766

Commits on Sep 17, 2024

• Make Snappy technically an optional dependency (#1715)

  Show description for 966737b
  lbergelson

  authored
  966737b

Commits on Sep 3, 2024

• Implement VCF bundles. (#1703)

  Show description for 46f6f0f
  cmnbroad

  authored
  46f6f0f

Commits on Aug 13, 2024

• Implements collections of bundles. (#1702)

  cmnbroad

  authored
  204a0db

Commits on Jul 3, 2024

• reducing memory required in IntervalMergerIterator when not concatting names (#1711)

  Show description for 9e89d3c
  meganshand

  authored
  9e89d3c

Commits on Jun 4, 2024

• Fix CRAMReferenceRegion updating. (#1708)

  Show description for 127f3de
  cmnbroad

  authored
  127f3de

Commits on Mar 5, 2024

• Upgrade to samtools 1.19.1 for interop testing. (#1706)

  Show description for 222d10b
  cmnbroad

  authored
  222d10b

Commits on Dec 19, 2023

• Updating our dependencies to the the newest versions (#1699)

  Show description for b16416c
  lbergelson

  authored
  b16416c

Commits on Dec 18, 2023

• Update to gradle 8.5 (#1697)

  Show description for 2d13eb7
  lbergelson

  authored
  2d13eb7

• Updating tests in SAMRecordUnitTest to explicitly compare values as primitives (#1696)

  Show description for 1ca889d
  

  lbergelson

  and

  Pierre Gruet

  authored
  1ca889d

Commits on Dec 13, 2023

• Improving the last changes to HtsPath (#1694)

  Show description for b23c36a
  lbergelson

  authored
  b23c36a

Commits on Dec 12, 2023

• Pefer FileSystemProvider plugins for http/ftp over legacy handlers(#1693)

  Show description for 40e3a8b
  lbergelson

  authored
  40e3a8b

Commits on Oct 13, 2023

• Update test dependencies to newest versions (#1690)

  Show description for 3964abe
  lbergelson

  authored
  3964abe

• Fix IOUtil.unrollPaths for http paths with query parameters (#1688)

  Show description for 5f0d484
  lbergelson

  authored
  5f0d484

Commits on Oct 11, 2023

• Update some methods in BamFileIoUtils accept Path input (#1681)

  takutosato

  authored
  6d1a796

Commits on Oct 6, 2023

• Support lenient (optimistic) read-only VCF 4.4. (#1683)

  Show description for c6b1fe1
  cmnbroad

  authored
  c6b1fe1

• Update snappy-java (#1687)

  Show description for 85a0f0f
  bbimber

  authored
  85a0f0f

Commits on Aug 9, 2023

• Add IntervalFileFeature for common interface to name in bed or interval_list (#1680)

  Show description for 38dbd0e
  rickymagner

  authored
  38dbd0e

Commits on Aug 8, 2023

• Update two remaining out of date dependencies (#1677)

  lbergelson

  authored
  5cc90ed

• Add new Genotype methods hasRefAllele and hasAltAllele (#1678)

  lindenb

  authored
  1e5ec5a

Commits on Aug 4, 2023

• Move the EnaRefServiceTest to the externalAPI test group (#1675)

  lbergelson

  authored
  20334af

Commits on Aug 3, 2023

• add SINGULAR platform to read group (#1635)

  omicsorama

  authored
  75eac46

• Zero len array (#1674)

  Show description for d486d53
  

  gileshall

  and

  jmarshall

  authored
  d486d53

Commits on Aug 1, 2023

• Update org.json

  

  bbimber

  authored and

  lbergelson

  committed
  44817ee

• Test fix

  

  bbimber

  authored and

  lbergelson

  committed
  500cffd

• Test fix

  

  bbimber

  authored and

  lbergelson

  committed
  662c827

• Minor code cleanup

  

  bbimber

  authored and

  lbergelson

  committed
  e58f8a2

• Test fixes

  

  bbimber

  authored and

  lbergelson

  committed
  b1085da

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