All pull requests

Pull requests

• Decode a BAM record's fixed-length fields from one read

  #1958·tfenne opened Oct 30, 2026Member·

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  1

• Read a record's name in ProgressLogger only for a line that prints it

  #1957·tfenne opened Oct 30, 2026Member·

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  3

• Hand items to AbstractAsyncWriter's writing thread in batches

  #1956·tfenne opened Oct 30, 2026Member·

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  1

• Keep a BAM record's stored bytes when a tag it doesn't have is removed

  #1955·tfenne opened Oct 30, 2026Member·

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• Add a JMH benchmark of BAMRecordCodec

  #1954·tfenne opened Oct 30, 2026Member·

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  3

• Check the CRCs of a BAM's header blocks when VALIDATE_CRC_CHECKSUMS is on

  #1953·tfenne opened Oct 30, 2026Member·

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  1

• Reject a BAM record whose read-name length is 0 when it is decoded

  #1952·tfenne opened Oct 30, 2026Member·

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  1

• Make setReadString("*") go through setReadBases so BAMRecord sees it

  #1951·tfenne opened Oct 30, 2026Member·

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  1

• Keep a BAM record's other tags when one of its tags is repeated

  #1950·tfenne opened Oct 30, 2026Member·

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  3

• Stop AsyncBufferedIterator's thread on close even if its interrupt is swallowed

  #1945·tfenne opened Oct 29, 2026Member·

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  3

• Keep a corrupt BGZF block's failure with the block so async reads don't hang

  #1943·tfenne opened Oct 29, 2026Member·

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  3

• Support for GTF files: GtfCodec and GtfWriter

  featuretribble
  #1744·lindenb opened Apr 15, 2025Contributor·5 tasks done·

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  3

• Correct NM tag calculation

  bambugcramsam
  #1536·michaelgatzen opened Feb 8, 2021Contributor·

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  6

• Introduce local disk cache for references

  cramfeature
  #1523·jkaczynski1 opened Dec 21, 2020·4 of 5 tasks·

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  18

• Add support for the TP (topology) tag in the sequence dictionary

  bamcramfeaturesamWaiting for revisions
  #1363·nh13 opened May 2, 2019Member·

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  19

  

• Async BAM performance improvements

  bamfeatureWaiting for revisions
  #1249·d-cameron opened Jan 2, 2019Contributor·

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