Re: [Seqan-dev] CheckStreamFormat for FastQ

Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de> · Fri, 06 Jan 2012 15:06:25 +0100

I tested the program on the file that you attached and it worked. Does 

the program detect the format of the small file, too?

$ make file_detect
[...]
$ ./sandbox/holtgrew/demos/file_detect /tmp/lane_5_p1.fastq
Detected FASTQ.

Could you try again with a fresh checkout?

On 01/06/2012 02:35 PM, Felix Heeger wrote:

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

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