Re: [Seqan-dev] problem in LoadReads

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

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

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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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