Add 'supplementary_alignment_flag' to GMT::Bwa

Add 'supplementary_alignment_flag' feature to GMT::Bwa. This feature is
available (so far) in Bwa 0.7.5 and 0.7.5a.
Use debug_message in AlignmentResult/Bwamem.
Parameter handling in AlignmentResult/Bwamem.
Fix _check_read_count in Bwamem for 0x800 flag
Fix CPU count (-t) parameter handling in Bwamem
Skip BamQc error_rate on bwamem 0.7.5a