Change the way to exclude regions in hmmratac and fix the incorrect keep-duplicate option
#689
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… utilized after reading alignments #680; 3. rename to for ; 4. update docs
philippadoherty
approved these changes
Feb 13, 2025
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hmmratac. We will remove the aligned fragments located in the 'blacklist' regions before the EM step to estimate fragment lengths distributions and HMM step to learn and predict nucleosome states. The reason is discussed in Bug: No peaks detected in not-blacklisted regions when a blacklist is given to macs3 hmmratac #680. To implement this feature, we added theexcludefunctions to PETrackI and PETrackII.hmmratacoption--keep-duplicatehad opposite effect previously as indicated by the name and description. It has been renamed as--remove-dupto reflect the actual behavior.hmmratacwill not remove duplicated fragments unless this option is set.