Re: [Seqan-dev] CheckStreamFormat for FastQ

[Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>]

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
>
>
>
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