Fix for "Signed Integer Overflow in MAPQ"
Fix for "Signed Integer Overflow in MAPQ"

When some read doesn't map at all the MAPQ is a "Signed Integer".
SAM example of a aligned read that does not map:
"597843e1-50df-4887-ab2c-c78a4d9ac28d    2048    chrXV   638441  -2147483648     4870S25M2I7M1I3M1D14M1D7M1I19M101S ..."
The MAPQ in this case is -2147483648. This creates some problems for samtools. "[W::sam_read1_sam] Parse error at line YYYY"
This happens because "mqCount" is zero on return of method "AlignmentBuffer::computeMappingQuality"
philres/ngmlr,philres/ngmlr,philres/ngmlr,philres/ngmlr