Merge pull request #110 from holtgrewe/hotfix/empty_line_write_fasta

[FIX] Not writing out empty lines to FASTA any more.
[FIX] fixed bug that aligned reads with insertions instead of mismatches at the read
 end (wrong sinkPos)
Merge pull request #126 from weese/razers3-hotfix

[FIX] fixed bug that aligned reads with insertions instead of mismatches...
[FIX] Fixing assertion in graph_algorithm_refine_inexact.h.

As reported and fixed by Birte Kehr.

Also see http://trac.seqan.de/ticket/1128
[FIX] Fixing a bug in removeGaps() for gaps_array.h.

Reported and fixed by Birte Kehr.