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Commits on Sep 17, 2024

• Make Snappy technically an optional dependency (samtools#1715)

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  lbergelson

  authored
  966737b

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Commits on Sep 3, 2024

• Implement VCF bundles. (samtools#1703)

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  cmnbroad

  authored
  46f6f0f

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Commits on Aug 13, 2024

• Implements collections of bundles. (samtools#1702)

  cmnbroad

  authored
  204a0db

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Commits on Jul 3, 2024

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

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  meganshand

  authored
  9e89d3c

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Commits on Jun 4, 2024

• Fix CRAMReferenceRegion updating. (samtools#1708)

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  cmnbroad

  authored
  127f3de

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Commits on Mar 5, 2024

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

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  cmnbroad

  authored
  222d10b

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Commits on Dec 19, 2023

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

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  lbergelson

  authored
  b16416c

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Commits on Dec 18, 2023

• Update to gradle 8.5 (samtools#1697)

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  lbergelson

  authored
  2d13eb7

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

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  lbergelson

  and

  Pierre Gruet

  authored
  1ca889d

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Commits on Dec 13, 2023

• Improving the last changes to HtsPath (samtools#1694)

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  lbergelson

  authored
  b23c36a

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Commits on Dec 12, 2023

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

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  lbergelson

  authored
  40e3a8b

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Commits on Oct 13, 2023

• Update test dependencies to newest versions (samtools#1690)

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  lbergelson

  authored
  3964abe

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

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  lbergelson

  authored
  5f0d484

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Commits on Oct 11, 2023

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

  takutosato

  authored
  6d1a796

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Commits on Oct 6, 2023

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

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  cmnbroad

  authored
  c6b1fe1

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• Update snappy-java (samtools#1687)

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  bbimber

  authored
  85a0f0f

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Commits on Aug 9, 2023

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

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  rickymagner

  authored
  38dbd0e

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Commits on Aug 8, 2023

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

  lbergelson

  authored
  5cc90ed

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

  lindenb

  authored
  1e5ec5a

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Commits on Aug 4, 2023

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

  lbergelson

  authored
  20334af

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Commits on Aug 3, 2023

• add SINGULAR platform to read group (samtools#1635)

  omicsorama

  authored
  75eac46

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• Zero len array (samtools#1674)

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  gileshall

  and

  jmarshall

  authored
  d486d53

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Commits on Aug 1, 2023

• Update org.json

  

  bbimber

  authored and

  lbergelson

  committed
  44817ee

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• Test fix

  

  bbimber

  authored and

  lbergelson

  committed
  500cffd

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• Test fix

  

  bbimber

  authored and

  lbergelson

  committed
  662c827

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• Minor code cleanup

  

  bbimber

  authored and

  lbergelson

  committed
  e58f8a2

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• Test fixes

  

  bbimber

  authored and

  lbergelson

  committed
  b1085da

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• Update snappy-java and migrate mjson to org.json to address CVEs

  

  bbimber

  authored and

  lbergelson

  committed
  d982871

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Commits on Jul 28, 2023

• removed redundant code that sets the secondary alignment flag for a readpair

  

  kleins95

  authored and

  lbergelson

  committed
  5404ca2

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Commits on Mar 10, 2023

• Remove low-value progress logging message (samtools#1659)

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  nh13

  authored
  6d3fc7b

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Commits on Feb 21, 2023

• Migrate to Java 17 (samtools#1649)

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  lbergelson

  authored
  670f500

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• Fix an NPE in CRAMRecordReadFeatures.restoreReadBases (samtools#1655)

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  lbergelson

  authored
  8f8d567

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Commits on Feb 17, 2023

• fix typos in the README (samtools#1654)

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  Manice18

  authored
  b0a5165

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Commits on Jan 31, 2023

• Expose the ability to encode a Genotoype into a GT field (samtools#1648)

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  lbergelson

  authored
  8108d56

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Commits on Jan 30, 2023

• Updating gradle to 7.6 (samtools#1650)

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  lbergelson

  authored
  1024da5

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