Add option PRIMARY_ALIGNMENT_STRATEGY to MergeBamAlignment, which enables...

Add option PRIMARY_ALIGNMENT_STRATEGY to MergeBamAlignment, which enables selection of the strategy for selecting the primary alignment for a read if there are multiple alignments marked as primary, or if none of the alignments for a read are marked as primary.
In addition to the existing strategy, BestMapq, add a new strategy EarliestFragment which only works for fragments, and selects the alignment that maps the earliest base in a read.