#3 Errors in compiling Scalpel

[Miika Ahdesmaki]

Hi Giuseppe,
Many thanks for releasing Scalpel. I'm trying to compile the latest code, which contains vcf output, but I'm getting the following errors in compilation (Microassembler):

g++ -Wno-deprecated -Wall -g -Wl,-rpath,/home/ahdesmak/Desktop/NextGen/scalpel-code/bamtools-2.3.0/lib/ -I/home/ahdesmak/Desktop/NextGen/scalpel-code/bamtools-2.3.0/include/ -L/home/ahdesmak/Desktop/NextGen/scalpel-code/bamtools-2.3.0/lib/ Microassembler.cc Edge.cc Node.cc Graph.cc Path.cc ContigLink.cc align.cc util.cc -o Microassembler -lbamtools -lz
Microassembler.cc: In member function ‘int Microassembler::run(int, char**)’:
Microassembler.cc:447:2: error: ‘optarg’ was not declared in this scope
  optarg = NULL;
  ^
Microassembler.cc:449:99: error: ‘getopt’ was not declared in this scope
  while (!errflg && ((ch = getopt (argc, argv, "m:r:g:s:k:K:l:t:c:d:x:BDRACIhSL:T:M:vF:q:b:Q:P:p:E")) != EOF))
                                                                                                   ^
Microassembler.cc:491:50: error: ‘optopt’ was not declared in this scope
    fprintf (stderr, "Unrecognized option -%c\n", optopt);
                                                  ^
Graph.cc: In member function ‘Node_t* Graph_t::getNode(Mer_t)’:
Graph.cc:1768:36: warning: converting ‘false’ to pointer type ‘Node_t*’ [-Wconversion-null]
  if (ni == nodes_m.end()) { return false; }
                                    ^
Graph.cc: In member function ‘Node_t* Graph_t::getNode(Edge_t&)’:
Graph.cc:1789:36: warning: converting ‘false’ to pointer type ‘Node_t*’ [-Wconversion-null]
  if (ni == nodes_m.end()) { return false; }
                                    ^
make[1]: *** [Microassembler] Error 1

Any pointers as to what I might be doing wrong?

[Miika Ahdesmaki]

Ah, adding

    #include unistd.h

into Microassembler.hh seems to have solved the getopt and optopt problem (the above is missing the less-than and more-than symbols because I can't get them to display correctly here)

[Giuseppe Narzisi]

Thank you Miika for reporting the problem.
I included your fix in the src code.