curious error when reading fastq.gz files (maybe not an issue)

[rderelle]

Hi,

Many thanks for developing and sharing seq_io!

I recently got a curious case when trying to parse a gziped fastq files sent by one of my collaborators. When using seq_io directly on these files, I get for all them the following error message:

Err value: UnexpectedEnd { pos: ErrorPosition { line: 713, id: None } }

However, if I gunzip these fastq files and re-gzip them, they get parsed as expected.

Would you know what could cause this error? Could it be an incompatibility Windows/Unix (I'm using a Unix system but I don't know how these files have been generated)?

My apologies if this is a trivial question/issue.

[markschl]

Without details about the implementation, I cannot precisely know what is going on.

However, in case you are using GzDecoder from the flate2 crate, the described error can in fact occur. Many 'fastq.gz' files are multi-member files which makes it necessary to use MultiGzDecoder instead. I've hit this problem earlier as well, since I didn't know about this. Could this be the problem in your case?

[rderelle]

Hi,

Thanks a lot for your reply and my apologies for not giving you more details!
You have indeed identified my mistake: I was using GzDecoder instead of GzDecoder. Now all files are correctly parsed.

best,
Romain