All pull requests

Pull requests

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

  #5063·parsaeskandar opened Oct 15, 2026Contributor·

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  2

• Description for main lines in alignment_to_bam

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

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• GAF version 1.1 with reference-free difference strings

  #5060·jltsiren opened Oct 12, 2026Contributor·

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• snarls: add SnarlManagerDecomposition, decomposition_sites and SiteTraversalFinder

  #5057·benedictpaten opened Oct 7, 2026Contributor·

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  66

• surject changes: support paired diploid placements

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

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

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

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

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

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  7

• surject changes: classify secondary and supplementary alignments

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

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  9

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

  #5050·Sagorikanag opened Oct 2, 2026·1/5·

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  18

• 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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  10

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

  #5026·Sagorikanag opened Aug 31, 2026·

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• 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, 2026·

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• surject: realign anchors containing substitutions

  #5010·Sagorikanag opened Aug 13, 2026·

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• surject: rank paths by their best alignment

  #5009·Sagorikanag opened Aug 13, 2026·

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• Diploid map interleaved

  #5008·Sagorikanag opened Aug 13, 2026·

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• test: strip BSD wc padding so the test suite is usable on macOS

  #5003·benedictpaten opened Aug 8, 2026Contributor·

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  3

• Diploid map long read changes

  #4994·Sagorikanag opened Aug 2, 2026·

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• surject: classify disjoint interval alignments

  #4993·Sagorikanag opened Aug 1, 2026·

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• call: add opt-in read-level genotype likelihoods (--read-likelihood)

  #4990·benedictpaten opened Jul 29, 2026Contributor·

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  325

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

  #4986·Sagorikanag opened Jul 29, 2026·

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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

  103

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

  #4953·faithokamoto opened Jul 1, 2026Contributor·

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  33