Changes

| <code>uint32_t SamFile::GetNumOverlaps(SamRecord& samRecord)</code>

| <code>uint32_t SamFile::GetNumOverlaps(SamRecord& samRecord)</code>

| Returns the number of bases in the passed in read that overlap the region that is currently set for this file.

| Returns the number of bases in the passed in read that overlap the region that is currently set for this file.

| Overlapping means that the bases occur in both the read and the reference as either matches or mismatches.  This does not count insertions, deletions, clips, pads, or skips.

Overlapping means that the bases occur in both the read and the reference as either matches or mismatches.  This does not count insertions, deletions, clips, pads, or skips.

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