Ref based sim#11

Merged

zrm22 merged 15 commits intomainfrom

Feb 6, 2026

Commits on Dec 23, 2025

Refactor and initial functions for recombining gvcf files based on picked crossover points.
zrm22
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Commits on Jan 7, 2026

Adding in more functionality for the recombine gvcf code
zrm22
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Commits on Jan 9, 2026

Commits on Jan 12, 2026

Unit tests and Associated files
zrm22
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Commits on Jan 14, 2026

Adding in more unit tests and fixing the sample names in the gvcfs
zrm22
committed

Commits on Jan 15, 2026

Fixing resizing algorithm to correctly prevent overlaps
zrm22
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Commits on Jan 16, 2026

Commits on Feb 3, 2026

Commits on Feb 6, 2026

Updating with review comments.
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