Change the way to exclude regions in `hmmratac` and fix the incorrect `keep-duplicate` option#689

Merged

taoliu merged 1 commit intomasterfrom feat/macs3/fragsupport

Feb 13, 2025

+445-273

Commits on Feb 12, 2025

1. implement function for PETrackI/II; 2. blacklisted regions will be utilized after reading alignments #680 ; 3. rename to for ; 4. update docs
taoliu
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