seqare/novelIndelFilter.h at master · ruping/seqare · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
#include <cstdio>
#include <getopt.h>
#include <cstdlib>
#include <cstring>


struct parameters {
  char* var_f;
  char* mapping_f;
  char* type;
  unsigned int unique;
  unsigned int skipPileup;
  char* chr;
};

struct parameters* interface(struct parameters* param,int argc, char *argv[]);
void delete_param(struct parameters* param);
void usage(void);

const char* program_name;

struct parameters* interface(struct parameters* param, int argc, char *argv[]){

  program_name = argv[0];
  int c;     // the next argument
  int help = 0;

  if (argc < 2) {
    usage();
    exit(0);
  }

  param = new struct parameters;
  param->var_f = new char;
  param->mapping_f = new char;
  param->type = new char;
  param->chr = new char;

  const struct option long_options[] ={
    {"var",1,0, 'v'},
    {"mapping",1,0,'m'},
    {"type",1,0,'t'},
    {"unique",0,0,'u'},
    {"skipPileup",0,0,'s'},
    {"chr",1,0,'c'},
    {"help",0,0,'h'},
    {0, 0, 0, 0}
  };

  while (1) {

    int option_index = 0;
    c = getopt_long_only (argc, argv,"husv:m:t:c:",long_options, &option_index);

    if (c == -1) {
      break;
    }

    switch(c) {
    case 0:
      break;
    case 'v':
      param->var_f = optarg;
      break;
    case 'm':
      param->mapping_f = optarg;
      break;
    case 't':
      param->type = optarg;
      break;
    case 'u':
      param->unique = 1;
      break;
    case 's':
      param->skipPileup = 1;
      break;
    case 'c':
      param->chr = optarg;
      break;
    case 'h':
      help = 1;
      break;
    case '?':
      help = 1;
      break;
    default:
      help = 1;
      break;
    }
  }

  if(help) {
    usage();
    delete_param(param);
    exit(0);
  }

  return param;
}

void usage()
{
  fprintf(stdout, "\nnovelSnvFilter.cpp, Copyright (C) 2016 Sun Ruping <ruping@stanford.edu>\n");
  fprintf(stdout, "\n");
  fprintf(stdout, "Usage: %s options [inputfile] \n\n", program_name);
  fprintf(stdout, "-h --help                print the help message\n");
  fprintf(stdout, "-v --var     <filename>  sorted vcf file contains only variants that are novel.\n");
  fprintf(stdout, "-m --mapping <filename>  mapping_file (coordinates' sorted bam-file or file of bam-file names).\n");
  fprintf(stdout, "-q --unique              only calculate for uniquely mapped reads (set this when the bam files contain multi-mapping reads).\n");
  fprintf(stdout, "-s --skipPileup          skip piled up reads.\n");
  fprintf(stdout, "-c --chr     <prefix>    set to prefix when the chromosome names in bam files starting with a prefix, e.g., chr, Chr, CHR.\n");
  fprintf(stdout, "-t --type    <p/s>       under development\n");
  fprintf(stdout, "\n");
}


void delete_param(struct parameters* param)
{
  delete(param->var_f);
  delete(param->mapping_f);
  delete(param->type);
  delete(param->chr);
  delete(param);
}