Amplicov will pull out incorrect references in bedpe if reference is a substring of another

[JalealCDC]

If one reference name is a substring of another, e.g. RSV_A and RSV_AD, then amplicov will pull the RSV_AD primer locations along with RSV_A primer locations. The reason is that

amplicon_coverage_plot/amplicov/amplicov

Line 124 in 1734e66

cmd = 'grep %s %s | cut -f 2,3,5,6,7 ' % (RefID, input_bedpe)

used a default grep, which does not do exact matching.