Removes invalid aligned reads and rename
alignId sequentially beginning with 0.
The fragment store.
This function removes all entries from alignedReadStore whose
alignId equals to INVALID_ID as well as orphan entries
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.
The new size of the alignedReadStore.
SeqAn - Sequence Analysis Library - www.seqan.de