[Seqan-dev] Dna5Q - how do you access qual or seq ?

["Henderson, Stephen" <s.henderson@ucl.ac.uk>]

Hello

I am enjoying using your excellent seqan tools. I have a couple of queries too though.

Partly as a learning exercise I have been trying to use seqan to re-create a version of the fastqc software accessed from R - which I pass summary data for graphics and trivial stats.

I'm using the double pass-reader to minimise memory of fastq - which works nicely for a minimal speed penalty (nice). So I can do most of what I want using the longer version of quality reads..

...

seqan::StringSet<seqan::CharString> ids;

seqan::StringSet<seqan::CharString> seqs; // a Charstring

seqan::StringSet<seqan::CharString> quals;

if (read2(ids, seqs, quals, reader, seqan::Fastq()) != 0)

etc...

However it strikes me that it would be preferable to be able to use the Dna5Q Stringset and half the code and runtime:

...

seqan::StringSet<seqan::CharString> ids;

seqan::StringSet<seqan::Dna5Q> seqsQ; // Dna5Q

if (read2(ids, seqsQ, reader, seqan::Fastq()) != 0)

etc...

This because I would prefer for efficiency (i.e not double passing) and code legibility (laziness???) to iterate a single loop through a StringSet seqsQ for QC calculations. However I cannot see how to obtain the quality value from the score. The tutorial material and the documentation I can find suggests to me that this should be possible though I cannot find an actual example... 

ordValue I find works for qual CharString but is not overloaded for Dna5Q. Nor does getQualityValue seem to work as I think it is described in the documentation...

//where seqs is the StringSet of Dna5Q read in above

seqan::Dna5Q seq= seqs[0];

Rcpp::Rcout << getQualityValue(seq[0]) << std::endl;    // error

Rcpp::Rcout << (int)(ordValue(seq[0]) - 33) << std::endl;    //error

So ... sorry for the lengthy post but how do I access the qualities?... or indeed the sequences of the Dna5Q when I have read in both? 

I realise this is probably a trivial syntactic error but it has stumped me for a couple of days now.

Thanks

Stephen Henderson

UCL Cancer Institute