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Old 12-28-2008, 11:33 AM   #1
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Default MAQ: finding the stop position of an alignment

I am using MAQ and have a short alignment question.
For each aligned sequence I want to find the start and stop position of the reference sequence.
The start position is given by MAQ and the stop position is start+ total alignment length.
So is the total alignment length the same as the "length of the read" (output from MAQ) and does that value include gaps/insertions introduced by MAQ-aligment?
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