Drop all paired or unpaired reads. Relies on the accuracy and disjoint nature of the FIRST_OF_PAIR and SECOND_OF_PAIR flags, and that each paired-end read has a unique id (qname). Maintains multiple alignments for any kept read ends.
The Sam object to filter.
This allows dropping unpaired reads after filtering that might only drop one read of a pair, such as filtering by quality.
A sam object with only paired reads, or with only unpaired reads.
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