Post

You find yourself in the middle of a fastq file. You see + and @ all over the place. How do you find the start of the current record?

9/1/26, 1:29 am1 repost10 likes

Ragnar {Groot Koerkamp}

@curiouscoding.nl

9 Jan

You look to your right and see an @! Even better, it's indeed at the start of a line. But no, it's the start of the quality string.

Ragnar {Groot Koerkamp}

@curiouscoding.nl

9 Jan

You look to your left and see a + and the end of a line. Great! Must be the separator. But no, it's the end of the quality string. Or wait, on closer inspection. It's the end of the header.

Ragnar {Groot Koerkamp}

@curiouscoding.nl

9 Jan

In the distance, you see a + completely alone on a line. Great success!! Again, you come back disappointed. It was a 1 bp quality string.

Ragnar {Groot Koerkamp}

@curiouscoding.nl

9 Jan

After some thinking, you realize: you want a line that starts with an @, which can only be the header or the quality, but not the one that is preceded by a line with just a +! Again, disappointment: a header-@ preceded by a single-+ quality string hides around the corner.

Alexey Sergushichev

@asergushichev.bsky.social

9 Jan

Start parsing from all shifts in parallel, but withhold the data until you end up with one shift? Probably shouldn't be a big overhead if done only in the beginning of a large chunk