Notes on partis

• bounds are in the format (begin, end), such that the relevant 0-indexed indices are begin <= i < end
• qrbounds are the bounds of the S-W match indexing sites of the query sequence
• glbounds are the bounds of the S-W match indexing sites of the GL sequence
• k_v_min is the min of the right hand qrbound across the GL matches, max is the corresponding max [link]. Thus they are the minimum and maximum length of a V match.
• A k_d is the (query index of the end of the D match) - (query index of the end of the V match for the best V) [link]. Thus k_d_min and k_d_max are the max and the min lengths of the D (plus insertion) matches.