Intersect library fragments and not alignment in multibamcov#72

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dawe wants to merge 3 commits intoarq5x:masterfrom dawe:master

+47-4

Commits on May 28, 2013

Added extension option to multiBamCov. In principle this should count library fragments instead of alignments
dawe
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If R1 is on the reverse strand, the extension should be negative
dawe
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Correct handling of R1 on reverse strand
dawe
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