FATAL ERROR :: must exit with non zero value

[EricDeveaud]

Hello,

when my_error_handler with fatal == true, exit value must be non zero even if breseq was compiled whithout DEBUG defined

when loocking at the code of my_error_handler one can notice the last lines of code.

    if (fatal) {
#ifdef DEBUG
    assert(false);
#else
    exit(0);
#endif
    }

should be instead

    if (fatal) {
#ifdef DEBUG
    assert(false);
#else
    exit(1);
#endif
    }

regards

Eric

[EricDeveaud]

with this small change we got the expected behavior for fatal error

see:

bigmess:breseq/0.33.2 > breseq -b 0 -o tmp -r none.gbk none.fastq.gz
================================================================================
breseq 0.33.2     http://barricklab.org/breseq

Active Developers: Barrick JE, Deatherage DE
Contact:           <jeffrey.e.barrick@gmail.com>

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software 
Foundation; either version 2, or (at your option) any later version.

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin

If you use breseq in your research, please cite:

  Deatherage, D.E., Barrick, J.E. (2014) Identification of mutations
  in laboratory-evolved microbes from next-generation sequencing
  data using breseq. Methods Mol. Biol. 1151: 165â188.

If you use structural variation (junction) predictions, please cite:

  Barrick, J.E., Colburn, G., Deatherage D.E., Traverse, C.C.,
  Strand, M.D., Borges, J.J., Knoester, D.B., Reba, A., Meyer, A.G. 
  (2014) Identifying structural variation in haploid microbial genomes 
  from short-read resequencing data using breseq. BMC Genomics 15:1039.
================================================================================
---> bowtie2  :: version 2.1.0 [/local/gensoft2/exe/bowtie2/2.1.0/scripts/bowtie2]
---> R        :: version 2.15.2 [/local/gensoft2/exe/R/2.15.2/scripts/R]
+++   NOW PROCESSING Read and reference sequence file input
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> FATAL ERROR <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Could not open reference file: none.gbk
FILE: reference_sequence.cpp   LINE: 807
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> STACK TRACE <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
0x00000000005de078 _ZN6breseq19cReferenceSequences15PrivateLoadFileERKSs
0x00000000005de54a _ZN6breseq19cReferenceSequences9LoadFilesERKSt6vectorISsSaISsEE
0x0000000000420714 _Z21breseq_default_actioniPPc
0x0000000000454b6a main
0x000000353021ed20 __libc_start_main
0x0000000000410f41 _start
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
bigmess:breseq/0.33.2 > echo $?
1

[jeffreybarrick]

Thanks for pointing this out! I've added your fix to the repository version.