search

aryeelab / hichipper

A preprocessing and QC pipeline for HiChIP data
MIT License
33 stars 12 forks source link

v0.4.4 < version < v0.5.6 -- duplicates #13

Closed caleblareau closed 7 years ago

caleblareau commented 7 years ago

Need to parse the *_allValidPairs file (PCR de-duplicated) rather than the *validPairs

interactionsCall.sh line 24; simple fix.

cli.py line 109 -- need to verify the *_allValidPairs

Only affects the versions listed in the title. Will make this version 0.6.0

caleblareau commented 7 years ago

https://github.com/aryeelab/hichipper/commit/76daa85136bbfb8175f81f7974332318519003ac

Want to add a --keep-dups flag. These may not necessarily be PCR duplicates but some other sort of duplicates. In high quality samples, these should be relatively low.

If keep_dups, do the old version in the diff; else do the new version. Tweak needed for v0.6.0