Re: [Seqan-dev] problem in LoadReads

["Dadi, Temesgen Hailemariam" <temesgen.dadi@fu-berlin.de>]

Hi Luis,

That is exactly the same code fragment as mine.
What kind of files are fn1_i and fn2_i? Are they fasta/fastq?
zipped/compressed? Could you please upload them or attach them so that I
could investigate further? Any file producing your problem will work.

If not could you please try by assigning fn1_i and fn1_i to the fastq file
seqan-src/tests/seq_io/test_dna.fq

I suspect the files are either corrupted or contain some invalid fastq
records.
In SeqAn 2.0 we added a validity check for fastq records and may be that
is causing a problem.

Thanks,
Temesgen



On 10/03/16 18:26, "Luis Enrique Ramirez Chavez" <lramirez@mpi-inf.mpg.de>
wrote:

>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 =
>> ³~/workspace/example/reads_pe_N6000.GA.R.fastq";
>>     CharString fileNameL =
>> ³~/workspace/example/reads_pe_N6000.CT.L.fastq";
>>
>>     loadReads(store, fileNameR, fileNameR);
>>
>> and I couldn¹t. 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
>> Telephone: +49 (0)30 838-75246          |   Gebäude 35, 14163 Berlin,
>> 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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>>> seqan-dev@lists.fu-berlin.de
>>> https://lists.fu-berlin.de/listinfo/seqan-dev
>>
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