>
> yeah, @jakebiesinger <https://github.com/jakebiesinger> , actually I did
> that thing. the input format is readId\tReadSequence\tReadSequence. When
> processing this kind of line, I used String[] rawLine =
> value.toString().split("\t"); the rawLine[0] is readId; rawLine[1]'s mateId
> automatically is set 0 implicitly. And rawLine[1]'s matedId automatically
> is set 1 implicitly. That mean I always set left ReadSequence to 0, right
> ReadSequence to 1 in a implicit way. By doing this, we don't need add _1 or
> _2 in the end of each read. Do you think is it better?
>
That's the right behavior for setting the mateId but it's incorrect to say
that mate0 is always `thisReadSequence` and mate1 is always
`mateReadSequence`.  Does that make sense?