[Bioperl-l] warning: Bio::Index::Fastq;

[Fields, Christopher J]

Validation checks like this are done at the level of full parsing of the data, yes (via Bio::SeqIO).  Bio::Index::Fastq is meant as a rapid indexing tool, though, hence my comment re: using a simple 4-line convention by default vs. complete parsing.  

We can also implement a more stringent indexer that validates as it parses, but for the purpose of the module we care more about getting it to run ‘fast' on the majority of inputs (e.g. use the 4-line convention) and ‘well’ on all of them (e.g. using any convention).

I noticed yesterday when delving into it there aren’t any tests yet for this module, so I’ll likely add these in as well.  Don’t expect it to be fast, though.

chris

On Mar 12, 2014, at 12:21 PM, Daisie Huang <daisieh at zoology.ubc.ca> wrote:

> Perhaps this is naive, but isn't a quality line always going to be the same
> length as the sequence line it follows? It seems like quality lines
> shouldn't be confirmed by any sort of regex match, they should be confirmed
> by string length following the corresponding sequence string.
> 
> 
> 
> --
> View this message in context: http://bioperl.996286.n3.nabble.com/warning-Bio-Index-Fastq-tp17362p17385.html
> Sent from the Bioperl-L mailing list archive at Nabble.com.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l