[FIX] Fixed one issues with "S" in cigar string.

The "S" in the cigar string was treated wrongly. However, this commit does not fully fix the problem as can be seen in the output of the test. The second line of the alignment is shifted by one. Since I don't know how this problem should be fixed (remove the first character in the second row, insert an gap in the first row, ...) I did not finish the test.

Note that this problem is also related to https://lists.fu-berlin.de/htdig/seqan-dev/2014-September/msg00015.html