Re: [Seqan-dev] double pass record reader
On 03/09/2012 08:18 AM, Bernd Jagla wrote:
Hi,
I have one comment:
the link in the web page http://trac.seqan.de/wiki/Tutorial/FileIO2 that
should link to "Double-Pass Record Reader
<http://docs.seqan.de/seqan/dev/SPEC_Double-_Pass+_Record+_Reader.html>:" is
not workin...
Good catch, I fixed this.
and I have one question:
is it possible to write out to a file the things done in the first pass
of the "double pass record reader"?
I would like to write a function/program that is only working on a given
partition. If I repeat this n times I think it would be beneficial to
put the first pass of the reading into an external program...
Hm, you could try to use MultiSeqFile, following this tutorial here:
http://trac.seqan.de/wiki/HowTo/EfficientImportOfMillionsOfSequences
This gives you random access, albeit without storing an index into your
reads file. Currently, storing such indices is not possible.
However: I can see how this would be useful for processing chunks of
data. Let me see whether we can cook up something reuseable in this
direction. There is the FAI index format from samtools, but that's only
for FASTA files.
*m
