Jri test#16

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rossibarra wants to merge 8 commits intomainfrom

Commits on Feb 16, 2026

Select default contigs from shared MAF intersection
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updated config, gitignore
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Commits on Feb 19, 2026

Add missing-GT exclusion histogram to summary report
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Commits on Feb 20, 2026

Handle gz missing BED inputs and tighten summary warning parsing
rossibarra
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Commits on Feb 23, 2026

Fix summary remap warning dedupe and expand tests
rossibarra
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Add changelog file
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Summarize changes since v0.3 in changelog
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Commits on Feb 24, 2026

Default to bgzip and rename clean/mask outputs
rossibarra
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