Changed "notboth" logic in pairToBed when inout is BAM. Changed "notboth" logic in pairToBed when inout is BAM. Changed "notboth" logic in pairToBed when inout is BAM. Changed "notboth" logic in pairToBed when inout is BAM. Changed "notboth" logic in pairToBed when inout is BAM. Changed "notboth" logic in pairToBed when inout is BAM. Changed "notboth" logic in pairToBed when inout is BAM. Changed "notboth" logic in pairToBed when inout is BAM.
Changed "notboth" logic in pairToBed when inout is BAM.
Changed "notboth" logic in pairToBed when inout is BAM.
Changed "notboth" logic in pairToBed when inout is BAM.
Changed "notboth" logic in pairToBed when inout is BAM.
Changed "notboth" logic in pairToBed when inout is BAM.
Changed "notboth" logic in pairToBed when inout is BAM.
Changed "notboth" logic in pairToBed when inout is BAM.
Changed "notboth" logic in pairToBed when inout is BAM.

jmarshall/bedtools2,jmarshall/bedtools2,arq5x/bedtools2,arq5x/bedtools2,jmarshall/bedtools2,arq5x/bedtools2,arq5x/bedtools2,arq5x/bedtools2,jmarshall/bedtools2,jmarshall/bedtools2