vcfdist v3.0.0#37

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TimD1 wants to merge 131 commits intomasterfrom

Commits on Mar 25, 2024

Commits on Apr 5, 2024

Variant information is merged across haplotypes
TimD1
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Commits on May 8, 2024

Started making graph data structure.
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Commits on Jul 14, 2024

Commits on Jul 17, 2024

Commits on Jul 21, 2024

Updated graph definition to make truth a graph.
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Commits on Jul 22, 2024

Forward alignment uses new algorithm
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Commits on Jul 24, 2024

Added precision-recall calculation.
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Commits on Aug 3, 2024

Updated phasing and printing
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Commits on Sep 29, 2024

docs: added v2.5.3 to cache
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Commits on Nov 2, 2024

Commits on Nov 4, 2024

printing mostly fixed, just switch errors
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Commits on Nov 5, 2024

feat: finally fixed printing summary.vcf!
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Commits on Nov 6, 2024

fix: update simple_gt if corresponding variant filtered
TimD1
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Commits on Nov 11, 2024

feat: print switch/flip error rates to summary TSV
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Commits on Nov 16, 2024

Commits on Nov 18, 2024

fix: ref_dist calculated using wf_ed, not variants.
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Commits on Nov 19, 2024

fix: disallow non-ref sync points unless both submatrices change
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Commits on Nov 21, 2024

fix: fix GT fixing tie for FP variants
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Commits on Nov 24, 2024

Commits on Nov 26, 2024

fix: decrement TRUTH_TP count for AC_ERR_2_TO_1
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Commits on Nov 30, 2024

Commits on Dec 2, 2024

fix: RAM calculation
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Commits on Dec 4, 2024

fix: loop bug in query graph
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Commits on Dec 7, 2024

Commits on Dec 11, 2024

feat: large variants pulled out for second round eval
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Commits on Dec 13, 2024

wip: added skeleton for second-round eval
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Commits on Dec 20, 2024

feat: removed all usage of vars->clusters[]
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Commits on Dec 22, 2024

Commits on Dec 27, 2024

feat: added WFA forward pass
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Commits on Dec 31, 2024

feat: added parse_wfa_path()
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Commits on Jan 1, 2025

Commits on Jan 12, 2025

Commits on Jan 19, 2025

Commits on Feb 9, 2025

fix: memory error on empty contig
TimD1
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Commits on Apr 5, 2025

Commits on Apr 6, 2025

fix: remove git-aware from pytest
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Commits on Apr 18, 2025

fix: WFA error when variants are adjacent to contig ends
TimD1
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Commits on May 3, 2025

Commits on May 5, 2025

Commits on May 30, 2025

Commits on Jun 3, 2025

chore: removed cluster and variant merging
TimD1
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Commits on Jun 8, 2025

feat: added --max-supercluster-size from v2
TimD1
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Commits on Jun 21, 2025

Commits on Jul 4, 2025