MaskPrimers primer alignment log not displaying indels correctly

[Jason Vander Heiden]

When MaskPrimers align finds a best match with a deletion in the input sequence, the log file does not convey this correctly, but instead adds the gap of the head/tail of the input sequence instead of the correct inner position. Need to correct log by stitching alignment and input sequence together, probably by cutting at the max_len boundary.

[Jason Vander Heiden]

Stopped trusting the start/end alignment positions from Bio.pairwise2.localds(), and instead manually parsed them from the alignment length and leading/trailing gap character counts.