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revision 1.4, Thu Sep 4 17:46:10 2008 UTC revision 1.5, Sun Sep 7 23:23:31 2008 UTC
# Line 44  Line 44 
44  #... Parse argument list  #... Parse argument list
45  #-----------------------------------------------------------------------  #-----------------------------------------------------------------------
46  my $trouble = 0;  my $trouble = 0;
47  while (@ARGV && ($ARGV[0] =~ m/^-/))  for (my $arg=$#ARGV; ($arg >= 0); $arg--)
48  {  {
49      if ($ARGV[0] =~ m/^-{1,2}code=(\d+)/) {      if ($ARGV[$arg] =~ m/^-{1,2}code=(\d+)/) {
50          $genetic_code = $1;          $genetic_code = $1;
51            splice(@ARGV,$arg,1);
52      }      }
53      elsif ($ARGV[0] =~ m/^-{1,2}train=(\S+)/) {      elsif ($ARGV[$arg] =~ m/^-{1,2}train=(\S+)/) {
54          $train = $1;          $train = $1;
55          ($training_tbl, $training_contigs) = split /,/, $train;          ($training_tbl, $training_contigs) = split /,/, $train;
56    
# Line 76  Line 77 
77              $trouble = 1;              $trouble = 1;
78              warn "Training argument $train is invalid";              warn "Training argument $train is invalid";
79          }          }
80            splice(@ARGV,$arg,1);
81      }      }
82      elsif ($ARGV[0] =~ m/^-{1,2}skip_called/) {      elsif ($ARGV[$arg] =~ m/^-{1,2}skip_called/) {
83          $skip_called = $ARGV[0];          $skip_called = $ARGV[$arg];
84          print STDERR "Skip option is set\n" if $ENV{VERBOSE};          print STDERR "Skip option is set\n" if $ENV{VERBOSE};
85            splice(@ARGV,$arg,1);
86      }      }
87      else {      elsif ($ARGV[$arg] =~ /^-/) {
88          $trouble = 1;          $trouble = 1;
89          warn "Unrecognized argument $ARGV[0]";          warn "Unrecognized argument $ARGV[$arg]";
90      }      }
   
     shift @ARGV;  
91  }  }
92    
93  my $genetic_code_switch = qq(-z $genetic_code);  my $genetic_code_switch = qq(-z $genetic_code);

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