the matePairId associates two reads to a mate-pair. Thus there are at most 2 reads with the same matePairId. The alignedReadStore stores matches of reads. Every read can have multiple matches. Each match has a unique id. Two matches of reads of the same mate-pair can form a mate-pair match. If so they have the same pairMatchId which is unique for these 2 matches.
X1 X2 Y1 Y2 Y3
2 reads A and B have matches at positions Xi and Yj. Theoretically 2*3 pairs of matches are possible. If only X1-Y1 and X2-Y3 form a mate pair match (due to their insert size) the alignedReadStore could look as follows:
read, position, pairMatchId
A, X1, 23
Am 04.01.2011 um 16:47 schrieb Mat: