[Seqan-dev] Reading FastQ files from GZ archive
- From: ngs geek <ngsgeek@gmail.com>
- To: seqan-dev@lists.fu-berlin.de
- Date: Fri, 30 Mar 2012 13:44:49 -0400
- Reply-to: SeqAn Development <seqan-dev@lists.fu-berlin.de>
- Subject: [Seqan-dev] Reading FastQ files from GZ archive
Hi All:
I'm trying to filter reads contained in a gz file based on quality score; I was able to stream the id and the
sequence with GZFile stream and using a singlepass reader (I don't want to keep the reads in memory).
Unfortunately, I can't access the quality string.
RecordReader<Stream<GZFile>, SinglePass<> > reader(fastq_file);
CharString id;
String<Dna5Q> seq;
CharString qual;
while (!atEnd(reader))
{
if (readRecord(id, seq, reader, Fastq()) != 0)
{
std::cerr << "Problem with your FASTQ file." << std::endl;
return 1;
}
// reading qual
}
Any idea on this? I tried assignQualities etc. with no luck.
Thanks
JD
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