Mark Duplicate Bitflag & include secondary & Supplimentary Reads #934
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…etection strategies. Set duplicate flag as needed on all reads inside Template which are not the top scoring read set.
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My apologies @JoeVieira - this is definitely on my list to look at, I've just been swamped recently. In all honestly it'll probably be another week or so until I have the time to do a thorough review. |
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@tfenne thanks for the response - no worries, appreciate the transparency! |
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Closes #906 & #920
This exposes a few new options
-dSet duplicate bit flag on all non-representative reads-Drepresentative read strategy, accepts strategies from htslib.Representative read is chosen by the sum scores ( from the scoring strategy ) across all primary reads, ties are broken with sum of mapping qualities from primary reads.
-Sinclude secondary reads in output ( also mark duplicates on as needed )-Uinclude supplementary reads in output ( mark as needed )