[Seqan-dev] createQGramIndex example

[Aaron Quinlan <aaronquinlan@gmail.com>]

Hi all,
   
   I would like to use SeqAn to create a qgram/kmer index of the mouse genome and would like to have control over the kmer and step sizes.  I have tried combined bits of example code on the website to do this, but either cannot get it compile or cause segfaults.  

   Is there a clear working example (perhaps I've missed it) of creating a qgram index from a genome StringSet and then using it to seed alignments from say a FASTQ file?

   That said, as has been noted in an earlier post to this list, I find that the readMeta function does not work with FASTQ.  What idiom should be followed for extracting ids, sequences and qualities from a FASTQ file?

All the best and thanks for creating this library...I think once I can get rolling it will be incredibly useful and powerful.

Best,
Aaron Quinlan
University of Virginia