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genome / breakdancer

SV detection from paired end reads mapping
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Fix end position calculation. #11

Closed gatoravi closed 8 years ago

gatoravi commented 8 years ago

Related to #10

gatoravi commented 8 years ago

Actually, I think this should be y.pos() + y.query_length() + 1 and not y.pos() + y.query_length() - 1?

ernfrid commented 8 years ago

I think you are correct unless pos is 0-based. In that case, no addition is needed. If I remember correctly, BAM natively represents position as a 0-based number, but I need to go back and check to see if that gets corrected somewhere.

gatoravi commented 8 years ago

Looks like it is converted to 1-based co-ordinates here.