Re: [Seqan-dev] CheckStreamFormat for FastQ

Felix Heeger <fheeger@mi.fu-berlin.de> · Fri, 06 Jan 2012 14:35:36 +0100

Hi Manual,

thank you for your effort. I checked your suggestion today and it did
not fix my problem. Also your example program can not identify my FASTQ
file. I am pretty sure it is valid FASTQ as other programs work fine on
it. I attached the first part of the file, if you want to have a look at
it.

felix

On Wed, 2011-12-21 at 18:31 +0100, Manuel Holtgrewe wrote:
> Felix,
> 
> The documentation of checkStreamFormat() was misleading. I fixed it in 
> [10948].
> 
> http://docs.seqan.de/seqan/dev2/?i=Function.checkStreamFormat
> 
> (The documentation is regenerated every hour, so you might wait for a 
> bit to see it).
> 
> The following is a simple example program I compiled and tested. Please 
> write another email, if the problem persists.
> 
> HTH,
> Manuel
> 
> #include <fstream>
> #include <iostream>
> 
> #include <seqan/sequence.h>
> #include <seqan/stream.h>
> 
> int main(int argc, char ** argv)
> {
>      using namespace seqan;
> 
>      if (argc != 2)
>          return 1;
>      std::fstream in(argv[1]);
> 
>      RecordReader<std::fstream, SinglePass<> > reader(in);
>      AutoSeqStreamFormat tagSelector;
>      bool b = checkStreamFormat(reader, tagSelector);
>      if (!b)
>      {
>          std::cerr << "Could not detect file format!" << std::endl;
>          return 1;
>      }
> 
>      // b is true if any format was detected successfully.
>      if (tagSelector.tagId == 1)
>          std::cerr << "Detected FASTA." << std::endl;
>      else if (tagSelector.tagId == 2)
>          std::cerr << "Detected FASTQ." << std::endl;
>      else
>          std::cerr << "Unknown file format!" << std::endl;
>      return 0;
> }
> 
> 
> On 12/21/2011 05:15 PM, Felix Heeger wrote:
> > Hi,
> >
> > I have to different functions I want to call depending on the fact if a
> > input file is fasta or fastq format.
> >
> > My approach to this is:
> >
> >> RecordReader<std::ifstream, SinglePass<>  >  reader(inFile);
> >> if (checkStreamFormat(reader, Fasta()))
> >> {
> >>      std::cerr<<  "Input file format is fasta."<<  std::endl;
> >>      [call function for fasta]
> >> }
> >> else if (checkStreamFormat(reader, Fastq()))
> >> {
> >>      std::cerr<<  "Input file format is fastq."<<  std::endl;
> >>      [call function for fastq]
> >> }
> >> else
> >> {
> >>      std::cerr<<  "ERORR: Input file format is not fasta or fastq."<<  std::endl;
> >>      return -1;
> >> }
> >
> > This works fine for fasta. However my fastq file is not recognized.
> > I looked into the code for checkStreamFormat a bit and the file is not
> > recognized because the iterator in the readRecord function reaches
> > atEnd before the quality meta data for the 35th record is finished (l. 392).
> > This happens with two different fastq files.
> >
> > So my theory is the following:
> > In the checkStreamFormat function LimitRecordReaderInScope
> > is used. The documentation states that this prevents the stream from
> > "rebuffering". This probably prevents the reader from finishing to read
> > the complete record and the recognition of the file fails.
> >
> > I hope I could make myself clear. I can also provide my code and a sample
> > fastq file if it would be helpful.
> >
> > Cheers,
> > felix
> >
> >
> >
> > _______________________________________________
> > seqan-dev mailing list
> > seqan-dev@lists.fu-berlin.de
> > https://lists.fu-berlin.de/listinfo/seqan-dev
> 
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