Turned on the penalty for flanking region mismatches

added fixes to the cigar string generation amoung other things

fixed output issue

fixed an issue with read group identification

addressed issue with properly identifying ambiguous calls

Fixed double-counting for variant events that span the forward and reverse strands of a read

Fixed cmakelists.txt

added an error if no sample index file present

fixed overwrite sample bug

fixed sample name override bug

fixed issue with overriding sample name

fixed tabix compilation issue

force reference sequence to be evaluated as upper case

fixed merge issue

fixed another issue