Re: [Seqan-dev] Reading FastQ files from GZ archive

[ngs geek <ngsgeek@gmail.com>]

I forgot to add an example:

raw quality string:

bbbeeeeegfggfiiiiiiidgfagdghfdfhdcdfdfb_ca`BOWU^GBBOLGLU_H_Z_BLLLGLLFX]aNWWWY_bb_``BBBBBBBBBBBBBBBBB

seqan quality string:

___________________________________________!OWU^G!!OLGLU_H_Z_!LLLGLLFX]_NWWWY______B!BBBBBBBBBBBBBBB

Best

JD

On Sat, Mar 31, 2012 at 3:39 PM, ngs geek <ngsgeek@gmail.com> wrote:

Thanks! I'm seeing that the quality string is not the same that I read from the fastq file.

Are they scaled? I read the doc here http://trac.seqan.de/wiki/WhitePapers/QualityHandling

but I can't figure out if these are guess by assignQualityValues ... in any case, I can't see

consistent results for my Illumina 1.3+ reads.

Thanks

JD 

On Sat, Mar 31, 2012 at 5:22 AM, Holtgrewe, Manuel <manuel.holtgrewe@fu-berlin.de> wrote:

Hi JD,

good catch, you found a bug I just fixed. The problem was that assignQualityValues() did not resize the target string, it does now. Update your SVN checkout and it should work.

Also, there now is a demo for reading FASTQ from gzipped files in core/demos/stream_read_fastq_gz.cpp

HTH

Manuel

---

From: ngs geek [ngsgeek@gmail.com]
Sent: Friday, March 30, 2012 7:44 PM
To: 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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