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Commits on May 31, 2026

• Merge branch 'worktree-fix-gnomad-svlen-filter'

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• Fix gnomAD SVLEN-aware filtering

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• add gnomad filtering based on SVLEN/SVTYPE for both breakpoints/cigar-based indel

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Commits on May 29, 2026

• docs: add CLAUDE.md project guidance

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• chore(cli): remove duplicate getsv command

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• docs(readme): document gnomadfilter command and --gnomadaf flag

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• fix(ensemble): emit the final SV group in insilico_truth

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• feat(gnomadfilter): two-breakpoint match for cross-chrom gnomAD-SV rows

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• add bed.gz support

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Commits on May 28, 2026

• feat(cli): add --output_consensus flag to sv-cross-ref-filter

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• filtercaller: add MinisvReads.output_consensus method

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• filtercaller: drop unused gc_cmp_same_sv1 import

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• filtercaller: add _consensus_lost_by_filter set-difference helper

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• union_sv: add min_file_count kwarg to drop groups under N-caller support

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• feat: add gnomadfilter CLI command + sync __version__ to package metadata

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Commits on Mar 12, 2026

• fix trio mode option

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Commits on Feb 19, 2026

• add trio-based denovo assembly filtering interface

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Commits on Feb 11, 2026

• update the latest interface readme and test scripts

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Commits on Feb 2, 2026

• refine the filtering api

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Commits on Jan 4, 2026

• add ont platform support; add pandas dependency for collection stat

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Commits on Jan 3, 2026

• add denovo/graph genome filter interface

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Commits on Nov 11, 2025

• sync latest breakpoint signature test; add filterasm test script; add tag

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Commits on Mar 14, 2025

• refine double strand break signatures

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Commits on Feb 16, 2025

• add union api; add advunion for accepting read ids and vcfs; add double strand break analysis

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Commits on Jan 28, 2025

• sync readme between minisv.rs and minisv.py; debug translocation merge code; add ensembleunion for collapsing SV union set; add doublestrandbreak for double strand break signature analysis

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Commits on Jan 23, 2025

• add initial support for double strand break signature

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Commits on Jan 22, 2025

• add ensemble of minisv union script

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Commits on Dec 8, 2024

• update annotation and asm filter script; add test script

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Commits on Nov 7, 2024

• adjust the filter asm conditions

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Commits on Nov 6, 2024

• add module for typing and util

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• sync latest sv typings; add filtering by assembly with sv type for all sv callers

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Commits on Oct 28, 2024

• reproduce isec, merge, eval and annot; add test scripts

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Commits on Oct 23, 2024

• reproduce minisv extract

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Commits on Oct 10, 2024

• add severus/sniffles2/msv filtering from asm

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Commits on Jun 10, 2024

• 1. add whatshap haplotag for filtering SV; 2. remove cython codes; 3. clean the gafcall remaining names

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