You don't need to parse the file name in the updated version but you've misunderstood the format.  It's not `this` and `that` in the file.  It's actually `readId\tReadSequence_1\tReadSequence_2`.  You need to parse both `_1` and `_2` read sequences but when you're generating the kmers for them, when you're building `_1`'s sequence, `_1` is `this` and `_2` is `that`.  When you're building `_2`'s kmers, `this` is `_2` and `that` is `_1`.