[mem] reads are not labelled as proper pair

[ftian9]

In bwa mem, when the insertion size cutoff is set as [a, b] (using the -I option), only the reads with the insertion size of [a + 1, b + 1] will have the change to be labeled with "proper pair" (flag 2).

Reason: The dist variable (the distance between R1 and R2 starting position) instead of the insertion size was used to compare with the cutoff. https://github.com/lh3/bwa/blob/master/bwamem_pair.c#L239-L242

Solution: From:

if (dist > pes[dir].high) break;
if (dist < pes[dir].low)  continue;

To:

if (dist + 1 > pes[dir].high) break;
if (dist + 1 < pes[dir].low)  continue;