gcphrap 1.4 does not work with phrap 1.08 ?

2008-09-20
2013-04-18
  • Hi guys,

    I have been using gcphrap and phrap without problems. I got a new version of phrap (phrap version 1.080812), which does not use manyreads and longreads. Now when I try to compile gcphrap 1.4 com the new version of phrap I get a error in the compilation problem.

    >make gcphrap
    cc -O2 -o gcphrap gcphrap.o gccall_subs.o contigs.o tig_node.o nodes.o readin.o words.o segments.o recursive_swat.o log_file.o pairs.o cand_pairs.o diffs.o names.o anomalies.o qual.o tags.o analyze_splices.o alignments.o db.o smith_wat.o full_smith_wat.o quick_smith_wat.o utilities.o nw.o full_nw.o profile.o parameters.o  exp_file.o seqInfo.o expFileIO.o array.o compress.o scf_bits.o -lm
    compress.o(.text+0x72): In function `fopen_compressed':
    : warning: the use of `tmpnam' is dangerous, better use `mkstemp'
    exp_file.o(.text+0x17a0): In function `write_exp_files':
    : undefined reference to `comp_mat'
    exp_file.o(.text+0x17c0): In function `write_exp_files':
    : undefined reference to `comp_mat'
    exp_file.o(.text+0x38f0): In function `append_exp_db':
    : undefined reference to `alph_mat'
    exp_file.o(.text+0x3900): In function `append_exp_db':
    : undefined reference to `alph_mat'
    exp_file.o(.text+0x44b1): In function `append_exp_db':
    : undefined reference to `comp_mat'
    exp_file.o(.text+0x44c0): In function `append_exp_db':
    : undefined reference to `comp_mat'
    collect2: ld returned 1 exit status
    make: *** [gcphrap] Error 1

    Do I need a new version of gcphrap ? 
    Does anyone have a hint about it ?

    Cheers,

     
    • Hi, I'm having the same issue over here.
      gcphrap 1.4 with phrap 1.080812 is giving compilation errors:

      > make gcphrap
      cc -O2   -c -o exp_file.o exp_file.c
      exp_file.c: In function âwrite_exp_filesâ:
      exp_file.c:1114: error: incompatible implicit declaration of function âour_allocâ
      exp_file.c:910: error: previous implicit declaration of âour_allocâ was here
      exp_file.c:1114: warning: cast to pointer from integer of different size
      make: *** [exp_file.o] Error 1

      Any help is much appreciated!
      Thanks

       
    • James Bonfield
      James Bonfield
      2009-07-07

      Gcphrap is no longer supported I'm afraid, partly due to time but also because I do not routinely get source updates for phrap to test it against.

      Internally at Sanger we use caftools (caf2gap, gap2caf, phrap2gap, etc) - these can be downloaded from the panel on the left side of http://www.sanger.ac.uk/Software/formats/CAF/

      CAF has the big advantage that it doesn't created 1000s of intermediate small files (eg the experiment files) and it also works with the standard command-line phrap rather than needing to compile a variant.

      James