Added a DiskBackedQueue and began alterations t...
replaced boolean wrappedRecord with a record->b...
replaced alignmentStartSortedCounts with a bool...
Fixed multiple bugs in the MarkDuplicatesWithMa...
Moved output directory creation to constructor....
Fixed two bugs related to subtracting alignment...
Fixed two bugs related to subtracting alignment...
Moved DuplicationMetrics back out of markduplic...