All pull requests

Pull requests

• call: let groups of a site's walks choose its genotype under --read-likelihood, and refuse --top-down there

  #5083·benedictpaten opened Oct 30, 2026Contributor·

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• Option to ignore homopolymers

  #5082·jltsiren opened Oct 29, 2026Contributor·

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  1

• Faster per-sample index construction: haplotype information, haplotype sampling, distance index, minimizer index

  enhancement
  #5063·parsaeskandar opened Oct 15, 2026Contributor·

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  9

• Description for main lines in alignment_to_bam

  #5062·adhirakunnath-hue opened Oct 14, 2026·

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  5

• surject changes: support paired diploid placements

  #5055·Sagorikanag opened Oct 5, 2026Contributor·5/5·

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• surject changes: --diploid-map for long-read placements

  #5054·Sagorikanag opened Oct 2, 2026Contributor·4/5·

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• surject changes: detect target-path repeats during anchor pruning

  #5052·Sagorikanag opened Oct 2, 2026Contributor·3/5·

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  7

• surject changes: classify secondary and supplementary alignments

  #5051·Sagorikanag opened Oct 2, 2026Contributor·2/5·

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  9

• List path offsets in a node

  #5042·xchang1 opened Sep 17, 2026Contributor·

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• Update README.md to include Clang version

  #5028·adhirakunnath-hue opened Sep 2, 2026·

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  12

• vg surject : --diploid-map and other code changes

  #5026·Sagorikanag opened Aug 31, 2026Contributor·

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  24

• Automatic manapge generation with vg help --man

  #5018·faithokamoto opened Aug 21, 2026Contributor·

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  20

• surject: check anchor sliding on target paths

  #5011·Sagorikanag opened Aug 13, 2026Contributor·

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• surject: realign anchors containing substitutions

  #5010·Sagorikanag opened Aug 13, 2026Contributor·

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• surject: rank paths by their best alignment

  #5009·Sagorikanag opened Aug 13, 2026Contributor·

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• Diploid map interleaved

  #5008·Sagorikanag opened Aug 13, 2026Contributor·

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• Diploid map long read changes

  #4994·Sagorikanag opened Aug 2, 2026Contributor·

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• surject: classify disjoint interval alignments

  #4993·Sagorikanag opened Aug 1, 2026Contributor·

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• vg surject: prune anchors in mapper-declared tail regions

  #4986·Sagorikanag opened Jul 29, 2026Contributor·

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• Promote secondary when primary alignment fails to surject

  #4973·gaoj66-roche opened Jul 20, 2026·

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  5

• new vg combine, adding new options

  #4965·xinzilan opened Jul 14, 2026·

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  1

  151

• Allow long-read Giraffe to take self-loops/reversals between seeds

  #4953·faithokamoto opened Jul 1, 2026Contributor·

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  33

• Use vg WDL that gives RTG a defined memory limit

  #4918·adamnovak opened May 29, 2026Member·

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  2

• Giraffe server engine

  #4879·parsaeskandar opened Apr 20, 2026Contributor·

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  1

  15

• More-scalable reachability edge finding for surject

  #4764·adamnovak opened Dec 3, 2025Member·

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