Re: [Seqan-dev] Saving an index for StringSet to disk: lots of files

[Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>]

Am Freitag 16 März 2018, 20:40:00 schrieb Lucas van Dijk:
> Hi all,
> 
> I'm trying to build a simple (short) read filter: given a list of k-mers,
> keep only reads that contains at least one of the given k-mers. This will
> be used to analyse the behaviour of a tool we're working on. It doesn't
> need to be super memory efficient, it'll mostly be a debugging tool.
> 
> My strategy was to use SeqAn and built a suffix array index for the
> StringSet of reads, and quickly enumerate which reads contain a given
> k-mer. I got a simple prototype working that reads the whole FASTQ file in
> memory as StringSet, and then build an Index<StringSet<Dna5String>,
> IndexSa<>>.


You should use the StringSet<Dna5String, Owncer<ConcatDirect<>>> 
specialisation here, it will result in only two files being written for the 
StringSet (the concatenation of all strings plus a vector of delimiters).

Hope that helps,
Hannes
-- 
Hannes Hauswedell

Scientific staff & PhD candidate
Freie Universität Berlin / Max Planck Institute for Molecular Genetics

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