All pull requests

Pull requests

• Count every inserted base in CRAM NM, and store bases past the reference end as htslib does

  #1850·tfenne opened Sep 26, 2026Member·

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  7

• Read missing values, write negative doubles, report an empty VCF, and leave lazy genotypes undecoded by toString

  #1849·tfenne opened Sep 26, 2026Member·

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  4

  1

• Index FASTAs with blank lines as samtools does, read sequences past 2^30 bases, and don't treat plain gzip as indexable

  #1848·tfenne opened Sep 26, 2026Member·

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  5

• Port the orphaned Scala tests to TestNG and list all three licences in the POM

  #1847·tfenne opened Sep 26, 2026Member·

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  1

• Keep repeated VCF header lines and carry contig md5, URL and species

  #1846·tfenne opened Sep 26, 2026Member·

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  5

• Refuse unsorted records when indexing on the fly, and make closing twice harmless

  #1845·tfenne opened Sep 26, 2026Member·

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  12

• Build makeDefault() factories from current defaults, and sort-check records before the caller sees them

  #1844·tfenne opened Sep 26, 2026Member·

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• Support for GTF files: GtfCodec and GtfWriter

  featuretribble
  #1744·lindenb opened Apr 15, 2025Contributor·

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• Removed 'backed' last cache hit hard references; it seems that that i…

  bugcram
  #1645·vruano opened Jan 11, 2023Contributor·

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  7

• Test case helper and fix EOF detection

  bug
  #1641·lbergelson opened Dec 2, 2022Member·

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  1

• Refactoring VariantContextComparator

  chorevcf
  #1629·lbergelson opened Oct 28, 2022Member·

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  4

  

• Require sequence dictionary MD5s when writing CRAM.

  cramfeature
  #1612·cmnbroad opened Jun 1, 2022Contributor·

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  9

• Add support for re-serializing (sharding and reassembling) CRAM containers.

  cramfeature
  #1609·cmnbroad opened May 3, 2022Contributor·

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  8

• VCFHeader and VCFHeaderLine rewrite/refactoring

  featurevcf
  #1581·cmnbroad opened Nov 9, 2021Contributor·

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  100

• 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·

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• Some improvements on CigarOperator enum.

  bamchorecramsam
  #1448·vruano opened Jan 1, 2020Contributor·

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• Proposal: handling UCSC 2bit sequences as ReferenceFile

  featureWaiting for revisions
  #1417·lindenb opened Aug 31, 2019Contributor·

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  7

• 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

  

• Adding tests revealing 0-length interval nonsense

  chore
  #1320·lbergelson opened Mar 8, 2019Member·

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  4

• Async BAM performance improvements

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

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  58

  

• Tribble writing support

  featuretribble
  #822·magicDGS opened Mar 10, 2017Member·

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  26

  

• Added validation warning if the mapped length of the read is greater than the predicted insert size for FR pairs on the same chromosome.

  bamcramfeaturesamWaiting for Review
  #816·tfenne opened Mar 3, 2017Member·

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  18