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Old 04-02-2010, 03:45 PM   #1
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Location: Texas

Join Date: Mar 2010
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Default Filter BAM records by positions using picard

I am filtering out reads in a BAM that do not overlap a set of regions by iterating over a list of SAMRecords and comparing their alignment starts and ends to the regions.

There's a queryOverlapping in the SAMFileReader Class that seems to be doing what i want. It queries record overlapping a range by passing in a range and a sequence. I don't understand why the sequence is necessary for such operation.

Any explanation?

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