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BamUtil: clipOverlap

71 bytes added, 14:15, 22 February 2012
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It also checks strand. If a forward strand extends past the end of a reverse strand, that will be clipped. Similarly, if a reverse strand starts before the forward strand, the region prior to the forward strand will be clipped. If the reverse strand occurs entirely before the forward strand, both strands will be entirely clipped.
 
The qualities on the two strands remain unchanged even with clipping.

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