Function
compactPairMatchIds
Renames pairMatchId  sequentially beginning with 0.
Include Headers
seqan/store.h
Parameters
|  The fragment store. Types:  FragmentStore | 
Remarks
 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.
Return Values
 The number of pair matches.
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