Lines 88-93 in parse_ssearch.py

[markcharder]

Hey, really great tool, thanks.

Not sure whether lines 88-93 of parse_ssearch.py are behaving as expected:

if match:
            diff_start = int(match.group(1)) - 1
            diff_end = int(curr_query_length)
            start = int(match.group(3)) - diff_start
            end = int(match.group(4)) + diff_end
            hsp = int(match.group(4)) - int(match.group(3))

If this is a miRNA passed with the '-i' switch to ssearch36, it will give you:
mRNA start = [original start] - [sRNA end - 1]
mRNA end = [original end] + [sRNA length]

Since the option passed to ssearch36 is '-W 10', shouldn't it just be:
mRNA start = [original start] - 10
mRNA end = [original end] + 10

I think there should also be something in there to account for the fact that, for some mRNAs, 10 nucleotides before the start may be negative and 10 nucleotides after the end may be beyond the mRNA length.