q_pos and r_pos indexing

[paulaberry]

The outputs from alignment.dump() indicate a 1-indexed position number for the start and end of the matching region of the query and reference sequence. However, the output from alignment.r_pos and alignment.q_pos are 0-indexed. The output from alignment.r_end and alignment.q_end are the same as in the output from alignment.dum() and so appear to be 1-indexed. Is this expected behavior and output?

[vpradeep07]

Yes, I noticed this as well, and I agree that the 1-indexed printout of the query position is confusing, especially since the internal state variable q_pos is 0-indexed. While I'm not the author (I'm a new user of swalign), I believe this 1-indexing is expected behavior. See code snippet below:

swalign/swalign/__init__.py

Lines 446 to 458 in df1f7f4

	q_pre = 'Query: %%%ss ' % maxlen
	r_pre = 'Ref : %%%ss ' % maxlen
	m_pre = ' ' * (8 + maxlen)
	rpos = self.r_pos
	if not self.rc:
	qpos = self.q_pos
	else:
	qpos = self.q_end
	while q and r and m:
	if not self.rc:
	out.write(q_pre % (qpos + 1)) # pos is displayed as 1-based

As shown, the author explicitly is adding +1 to the query pos to make it print 1-indexed.

[mbreese]

Yes, you're correct. This is the expected behavior. Typically coordinates that are human readable are reported out as 1-based values.