Re: [Seqan-dev] problem in LoadReads

["Luis Enrique Ramirez Chavez" <lramirez@mpi-inf.mpg.de>]

Hi Temesgen,

Thanks for your response

typedef seqan::FragmentStore<> THMMFragStore;

THMMFragStore fragStore;

if (!loadReads(fragStore, fn1_i, fn2_i)){
     return false;
}


The reads are fastq format very small 5 megabytes each.

Regards,
Luis Ramirez


> I tried to reproduce your bug with the following simple code fragment:
>
>     FragmentStore<> store;
>
>     CharString fileNameR =
> “~/workspace/example/reads_pe_N6000.GA.R.fastq";
>     CharString fileNameL =
> “~/workspace/example/reads_pe_N6000.CT.L.fastq";
>
>     loadReads(store, fileNameR, fileNameR);
>
> and I couldn’t. All the reads were loaded correctly.
>
> Can you please provide me with a code fragment that can produce the
> problem?
>
> Thanks!
>
> Temesgen H. Dadi
> PhD Candidate (IMPRS-CBSC, JSMC)
> Skype ID: temeehi
> Freie Universität Berlin
> Institut für Informatik                 |          Institut für
> Mikrobiologie
> AG Algorithmische Bioinformatik         |                      und
> Tierseuche
> Takustraße 9, 14195 Berlin, Germany     |       Robert-von-Ostertag-Str.
> 7-13
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> Germany
>
>
>
>
>
>> On 22 Feb 2016, at 12:24, Hannes Hauswedell
>> <hannes.hauswedell@fu-berlin.de> wrote:
>>
>> Am Montag, 22. Februar 2016, 11:23:23 schrieb Luis Enrique Ramirez
>> Chavez:
>>> Hi Seqan Devs,
>>>
>>> I am currently working a project that used Seqan 1.4 and now I am
>>> updating
>>> to Seqan 2.1. I think that maybe I have found a bug in Seqan. The
>>> problem
>>> is that LoadReads from FragmentStore is not returning the same as in
>>> the
>>> previous version for the same call, I did a little research  comparing
>>> both versions.
>>
>> Thanks for your bug report and research!
>>
>>> The code of loadReads  have change from one version to the other, in
>>> both
>>> versions it's defined in seqan/store/store_io.h at line 1159 for old
>>> version and at line 1273 for the new version but the behave is
>>> different
>>> and I think here is the problem.
>>>
>>> in old version there is this part:
>>>
>>> MultiSeqFile multiSeqFileL, multiSeqFileR;
>>> if (!open(multiSeqFileL.concat, toCString(fileNameL), OPEN_RDONLY))
>>>  return false;
>>> if (!open(multiSeqFileR.concat, toCString(fileNameR), OPEN_RDONLY))
>>>  return false;
>>
>> This looks like the file is from a previous save() so it is in SeqAn
>> binary
>> format.
>>
>>
>>> The flow is working correctly and the ifs don't reach the return false
>>> but
>>> in the new version the code is like this
>>>
>>> SeqFileIn seqFileL, seqFileR;
>>> if (!open(seqFileL, toCString(fileNameL)) || !open(seqFileR,
>>> toCString(fileNameR)))
>>>   return false;
>>
>> This looks like it is trying to load it as a regular sequence file so
>> this
>> seems something different from above. You might be right, that this is
>> the
>> place!
>>
>>> here the execution always always return false. I inspected and its
>>> because
>>> a different open function its called and here is where I think is the
>>> bug.
>>>
>>> In seqan 1.4 the open function called is from  string_map defined in
>>> /include/seqan/file/string_mmap.h however in 2.x the open function that
>>> is
>>> being called is from /include/seqan/stream/formatted_file.h. The open
>>> from
>>> string_mmap.h exists in 2.x and I think is the function that wanted to
>>> be
>>> called. LoadReads calls open with SeqFileIn in the new version while in
>>> previous with MultiSeqFile but MultiSeqFile is not available in new
>>> version
>>>
>>> Can you please check if that is a bug
>>
>> I have created an issue in the bugtracker that you can follow:
>> https://github.com/seqan/seqan/issues/1484
>>
>> Best regards,
>> Hannes
>> --
>> Hannes Hauswedell
>>
>> PhD student
>> Max Planck Institute for Molecular Genetics / Freie Universität Berlin
>>
>> address     Institut für Informatik
>>            Takustraße 9
>>            Room 019
>>            14195 Berlin
>> telephone   +49 (0)30 838-75241
>> fax         +49 (0)30 838-75218
>> e-mail      hannes.hauswedell@[molgen.mpg.de|fu-berlin.de]
>>
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