← Back to branch summary

~ubuntu-branches/ubuntu/trusty/jellyfish/trusty

« back to all changes in this revision

Viewing changes to jellyfish/dump_fastq_main_cmdline.hpp

  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2012-05-21 21:56:38 UTC
  • mfrom: (1.1.2)
  • Revision ID: package-import@ubuntu.com-20120521215638-pqynm387yv9cujk1
Tags: 1.1.5-1
http://bugs.debian.org/667214
* New upstream version fixing the FTBFS with gcc-4.7 bug
  Closes: #667214
* debian/patches/fix-unused-but-set-variable.patch: Removed
  because applied upstream

Show diffs side-by-side

added added

removed removed

Lines of Context:
jellyfish/dump_fastq_main_cmdline.hpp
22
22
    USAGE_OPT = 1000
23
23
  };
24
24
 
25
 
  dump_fastq_main_args(int argc, char *argv[]) :
26
 
    column_flag(false),
27
 
    tab_flag(false),
28
 
    lower_count_arg(), lower_count_given(false),
29
 
    upper_count_arg(), upper_count_given(false),
30
 
    verbose_flag(false),
31
 
    output_arg(""), output_given(false)
32
 
  {
 
25
  dump_fastq_main_args() : 
 
26
    column_flag(false),
 
27
    tab_flag(false),
 
28
    lower_count_arg(), lower_count_given(false),
 
29
    upper_count_arg(), upper_count_given(false),
 
30
    verbose_flag(false),
 
31
    output_arg(""), output_given(false)
 
32
  { }
 
33
 
 
34
  dump_fastq_main_args(int argc, char* argv[]) :
 
35
    column_flag(false),
 
36
    tab_flag(false),
 
37
    lower_count_arg(), lower_count_given(false),
 
38
    upper_count_arg(), upper_count_given(false),
 
39
    verbose_flag(false),
 
40
    output_arg(""), output_given(false)
 
41
  { parse(argc, argv); }
 
42
 
 
43
  void parse(int argc, char* argv[]) {
33
44
    static struct option long_options[] = {
34
45
      {"column", 0, 0, 'c'},
35
46
      {"tab", 0, 0, 't'},
93
104
        break;
94
105
      }
95
106
    }
 
107
 
 
108
    // Parse arguments
96
109
    if(argc - optind != 1)
97
110
      error("Requires exactly 1 argument.");
98
111
    db_arg = yaggo::string(argv[optind]);
99
112
    ++optind;
100
113
  }
 
114
 
101
115
#define dump_fastq_main_args_USAGE "Usage: jellyfish qdump [options] db:path"
102
116
  const char * usage() const { return dump_fastq_main_args_USAGE; }
103
117
  void error(const char *msg) { 
106
120
              << std::endl;
107
121
    exit(1);
108
122
  }
 
123
 
109
124
#define dump_fastq_main_args_HELP "Dump k-mer from a qmer database\n\nBy default, dump in a fasta format where the header is the count and\n" \
110
125
  "the sequence is the sequence of the k-mer. The column format is a 2\n" \
111
126
  "column output: k-mer count.\n\n" \
115
130
  " -L, --lower-count=double                 Don't output k-mer with count < lower-count\n" \
116
131
  " -U, --upper-count=double                 Don't output k-mer with count > upper-count\n" \
117
132
  " -v, --verbose                            Be verbose (false)\n" \
118
 
  " -o, --output=c_string                    Output file\n" \
 
133
  " -o, --output=string                      Output file\n" \
119
134
  "     --usage                              Usage\n" \
120
135
  " -h, --help                               This message\n" \
121
136
  " -V, --version                            Version"