Function
compactAlignedReads
Removes invalid aligned reads and rename alignId  sequentially beginning with 0.
Include Headers
seqan/store.h
Parameters
|  The fragment store. Types:  FragmentStore | 
Remarks
 This function removes all entries from alignedReadStore whose alignId  equals to INVALID_ID  as well as orphan entries
in alignQualityStore.
Afterwards the alignIds are renamed sequentially beginning with 0.
This function can be used to remove alignments which are selected by previously setting their id to INVALID_ID .
Return Values
 The new size of the alignedReadStore.
SeqAn - Sequence Analysis Library - www.seqan.de