pairMatchId sequentially beginning with 0.
The fragment store.
This function renames the
pairMatchId in the alignedReadStore sequentially beginning with 0.
Two read alignments can be identified to be a pair match if they have the same pairMatchId.
Please note that paired reads not necessarily have to mapped as a pair match,
e.g. if they are on different contigs or have the same orientation or a wrong insert size.
The number of pair matches.
SeqAn - Sequence Analysis Library - www.seqan.de