Develop#296

Merged

joshfactorial merged 11 commits into

mainfrom

May 19, 2026

Commits on May 19, 2026

Vectorize map_local_trinuc_bias; index indels by position for O(1) overlap check

joshfactorial
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claude
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Vectorize write_bam_record; bump to 4.4.4

joshfactorial
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claude
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ChangeLog: v4.4.4 entry summarizing variant + BAM-encoding optimizations

joshfactorial
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claude
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README cleanup pass: fix outdated config keys, version refs, examples

joshfactorial
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claude
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Remove parallel_mode from the user-facing config; derive splitting from threads

joshfactorial
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claude
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ChangeLog: note parallel_mode removal in v4.4.3 entry

joshfactorial
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claude
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GC bias coverage-semantics fix; bump to v4.5.0

joshfactorial
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claude
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Drop stale TODOs and orphaned shape-curve scaffolding

joshfactorial
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claude
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Remove orphaned common_variants + high_mut_regions scaffolding (#295)

joshfactorial
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claude
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Revert version to 4.4.4 (was 4.5.0)

joshfactorial
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claude
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Merge branch 'main' into develop
joshfactorial
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