findOpticalDuplicates
public boolean[] findOpticalDuplicates(List<? extends PhysicalLocation> list,
PhysicalLocation keeper)
Finds which reads within the list of duplicates that are likely to be optical/co-localized duplicates of
one another. Within each cluster of optical duplicates that is found, one read remains un-flagged for
optical duplication and the rest are flagged as optical duplicates. The set of reads that are considered
optical duplicates are indicated by returning "true" at the same index in the resulting boolean[] as the
read appeared in the input list of physical locations.
- Parameters:
list
- a list of reads that are determined to be duplicates of one another
keeper
- a single PhysicalLocation that is the one being kept as non-duplicate, and thus should never be
annotated as an optical duplicate. May in some cases be null, or a PhysicalLocation not
contained within the list!
- Returns:
- a boolean[] of the same length as the incoming list marking which reads are optical duplicates