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1 #include "mrcanavar.h"
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2
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3
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4
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5 int main(int argc, char **argv){
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6
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7 int i;
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8
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9 char gzSAM;
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10
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11 char *indirSAM;
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12 char *depthFile;
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13 char *out_prefix;
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14
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15
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16 init_globals();
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17
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18 gzSAM = 0;
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19 indirSAM = NULL;
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20 depthFile = NULL;
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21 out_prefix = NULL;
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22
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23
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24 for (i=1; i<argc; i++){
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25
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26
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27 /* modes */
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28 if (!strcmp(argv[i], "--prep"))
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29 set_runmode(PREP);
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30 else if (!strcmp(argv[i], "--read"))
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31 set_runmode(READSAM);
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32 else if (!strcmp(argv[i], "--call"))
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33 set_runmode(CALL);
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34
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35
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36 /* compulsory parameters for all modes */
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37 else if (!strcmp(argv[i], "-conf"))
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38 set_str(&GENOME_CONF, argv[i+1]);
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39
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40 /* compulsory parameters for the PREP mode */
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41 else if (!strcmp(argv[i], "-fasta"))
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42 set_str(&GENOME_FASTA, argv[i+1]);
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43 else if (!strcmp(argv[i], "-gaps"))
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44 set_str(&GENOME_GAPS, argv[i+1]);
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45
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46 /* optional parameters for the PREP mode */
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47 else if (!strcmp(argv[i], "-lw_size"))
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48 LW_SIZE = atoi(argv[i+1]);
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49 else if (!strcmp(argv[i], "-sw_size"))
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50 SW_SIZE = atoi(argv[i+1]);
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51 else if (!strcmp(argv[i], "-cw_size"))
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52 CW_SIZE = atoi(argv[i+1]);
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53 else if (!strcmp(argv[i], "-lw_slide"))
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54 LW_SLIDE = atoi(argv[i+1]);
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55 else if (!strcmp(argv[i], "-sw_slide"))
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56 SW_SLIDE = atoi(argv[i+1]);
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57
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58
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59 /* compulsory parameters for both READ and CALL modes */
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60 else if (!strcmp(argv[i], "-depth"))
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61 set_str(&depthFile, argv[i+1]);
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62
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63 /* compulsory parameters for the READ mode */
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64
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65 else if (!strcmp(argv[i], "-samdir"))
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66 set_str(&indirSAM, argv[i+1]);
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67
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68
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69 /* optional parameters for the SAM mode */
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70 else if (!strcmp(argv[i], "--gz"))
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71 gzSAM = 1;
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72
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73
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74 /* compulsory parameters for the CALL mode */
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75 else if (!strcmp(argv[i], "-o"))
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76 set_str(&out_prefix, argv[i+1]);
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77
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78 /* optional parameters for the CALL mode */
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79 else if (!strcmp(argv[i], "-cont_win"))
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80 CONT_WINDOW = atoi(argv[i+1]);
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81 else if (!strcmp(argv[i], "-cut_win"))
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82 CUT_WINDOW = atoi(argv[i+1]);
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83 else if (!strcmp(argv[i], "--xx"))
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84 set_gender(FEMALE);
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85 else if (!strcmp(argv[i], "--xy"))
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86 set_gender(MALE);
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87 else if (!strcmp(argv[i], "--multgc"))
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88 MULTGC = 1;
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89
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90
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91
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92
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93 /* generic stuff */
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94 else if (!strcmp(argv[i], "-v")){
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95 fprintf (stdout, "\nmrCaNaVaR version %s.\nLast update: %s.\n\n", VERSION, LAST_UPDATE);
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96 return 0;
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97 }
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98 else if (!strcmp(argv[i], "-h")){
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99 printHelp(argv[0]);
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100 return 0;
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101 }
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102 else if (!strcmp(argv[i], "--verbose"))
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103 VERBOSE = 1;
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104 else if (!strcmp(argv[i], "--disable-sam-check"))
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105 CHECKSAM = 0;
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106 }
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107
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108
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109 switch(RUNMODE){
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110 case NONE:
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111 print_error("Select mode: --prep, ---read, or --call\n");
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112 break;
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113 case PREP:
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114 fprintf(stdout, "Mode: Prepare genome...\n");
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115 prep_genome();
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116 break;
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117 case READSAM:
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118 fprintf(stdout, "Mode: Read SAM ...\n");
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119 read_depth(indirSAM, depthFile, gzSAM);
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120 break;
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121 case CALL:
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122 fprintf(stdout, "Mode: Call copy numbers ...\n");
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123 call_cnv(depthFile, out_prefix);
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124 break;
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125 default:
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126 break;
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127 }
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128
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129 return 0;
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130
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131 }
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132
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133
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134 void printHelp(char *binfile){
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135
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136 fprintf (stdout, "\nmrCaNaVaR version %s\nLast update: %s\n\n", VERSION, LAST_UPDATE);
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137 fprintf (stdout, "%s --<mode> [options] \n\n", binfile);
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138
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139 fprintf (stdout, "======== RUN MODES ========\n\n");
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140
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141 fprintf (stdout, "\t--prep : Prepare reference genome configuration file.\n");
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142 fprintf (stdout, "\t--read : Read mapping information from SAM files.\n");
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143 fprintf (stdout, "\t--call : Call CNVs and predict copy numbers.\n\n");
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144
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145 fprintf (stdout, "======== PREP MODE COMPULSORY PARAMETERS ========\n\n");
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146 fprintf (stdout, "\t-fasta <fasta_file> : FASTA file for the reference genome.\n");
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147 fprintf (stdout, "\t-gaps <gaps_file> : Gap coordinates of the reference genome in BED format.\n");
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148 fprintf (stdout, "\t-conf <config_file> : Reference configuration file (output).\n\n");
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149 fprintf (stdout, "======== PREP MODE OPTIONAL PARAMETERS ========\n\n");
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150 fprintf (stdout, "\t-lw_size <lw_size> : Long window span size. Default is 5000.\n");
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151 fprintf (stdout, "\t-lw_slide <lw_slide> : Long window slide size. Default is 1000.\n");
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152 fprintf (stdout, "\t-sw_size <sw_size> : Short window span size. Default is 1000.\n");
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153 fprintf (stdout, "\t-sw_slide <sw_slide> : Short window slide size. Default is 1000.\n");
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154 fprintf (stdout, "\t-cw_size <cw_size> : Copy number window size. Default is 1000.\n\n");
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155
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156 fprintf (stdout, "======== READ MODE COMPULSORY PARAMETERS ========\n\n");
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157 fprintf (stdout, "\t-conf <config_file> : Reference configuration file (input).\n");
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158 fprintf (stdout, "\t-samdir <sam_dir> : Directory that contains SAM files for mapping information.\n");
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159 fprintf (stdout, "\t-depth <depth_file> : Read depth file (output).\n\n");
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160 fprintf (stdout, "======== READ MODE OPTIONAL PARAMETERS ========\n\n");
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161 fprintf (stdout, "\t--gz : Indicates that the SAM files are compressed in gzip format.\n\n");
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162
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163 fprintf (stdout, "======== CALL MODE COMPULSORY PARAMETERS ========\n\n");
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164 fprintf (stdout, "\t-conf <config_file> : Reference configuration file (input).\n");
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165 fprintf (stdout, "\t-depth <depth_file> : Read depth file (input).\n");
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166 fprintf (stdout, "\t-o <out_prefix> : Prefix for the output file names.\n\n");
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167
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168
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169 fprintf (stdout, "======== CALL MODE OPTIONAL PARAMETERS ========\n\n");
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170 fprintf (stdout, "\t--xx : Set gender of the sequenced sample as female. Mammalian genomes only. Default is autodetect.\n");
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171 fprintf (stdout, "\t--xy : Set gender of the sequenced sample as male. Mammalian genomes only. Default is autodetect.\n");
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172 fprintf (stdout, "\t--multgc : Perform multiplicative GC correction. Default is additive.\n");
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173 fprintf (stdout, "\t--verbose : Verbose output.\n");
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174
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175
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176 /*
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177
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178 fprintf (stdout, "======== NOT IMPLEMENTED YET ========\n\n");
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179 fprintf (stdout, "\t-cont_win <cwin_number> : Contiguous window number to look for high/low depth windows. Default is 7.\n");
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180 fprintf (stdout, "\t-cut_win <cwin_cutoff> : Window number cutoff. Default is 6.\n\n");
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181
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182
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183 */
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184
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185 }
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