[Seqan-dev] problem in LoadReads

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

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.

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;

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;

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

Thanks in Advance,
Luis Enrique