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1 #include <string.h>
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2 #include <stdlib.h>
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3 #include <sys/stat.h>
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4 #include <unistd.h>
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5 #include "knetfile.h"
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6 #include "bcf.h"
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7
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8 #include "kseq.h"
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9 KSTREAM_INIT(gzFile, gzread, 0x10000)
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10
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11 int bcfview(int argc, char *argv[]);
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12 int bcf_main_index(int argc, char *argv[]);
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13
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14 #define BUF_SIZE 0x10000
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15
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16 int bcf_cat(int n, char * const *fn)
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17 {
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18 int i;
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19 bcf_t *out;
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20 uint8_t *buf;
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21 buf = malloc(BUF_SIZE);
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22 out = bcf_open("-", "w");
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23 for (i = 0; i < n; ++i) {
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24 bcf_t *in;
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25 bcf_hdr_t *h;
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26 off_t end;
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27 struct stat s;
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28 in = bcf_open(fn[i], "r");
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29 h = bcf_hdr_read(in);
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30 if (i == 0) bcf_hdr_write(out, h);
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31 bcf_hdr_destroy(h);
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32 #ifdef _USE_KNETFILE
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33 fstat(knet_fileno((knetFile*)in->fp->fp), &s);
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34 end = s.st_size - 28;
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35 while (knet_tell((knetFile*)in->fp->fp) < end) {
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36 int size = knet_tell((knetFile*)in->fp->fp) + BUF_SIZE < end? BUF_SIZE : end - knet_tell((knetFile*)in->fp->fp);
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37 knet_read(in->fp->fp, buf, size);
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38 fwrite(buf, 1, size, out->fp->fp);
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39 }
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40 #else
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41 abort(); // FIXME: not implemented
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42 #endif
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43 bcf_close(in);
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44 }
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45 bcf_close(out);
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46 free(buf);
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47 return 0;
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48 }
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49
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50 extern double bcf_pair_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4]);
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51
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52 int bcf_main_ldpair(int argc, char *argv[])
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53 {
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54 bcf_t *fp;
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55 bcf_hdr_t *h;
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56 bcf1_t *b0, *b1;
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57 bcf_idx_t *idx;
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58 kstring_t str;
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59 void *str2id;
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60 gzFile fplist;
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61 kstream_t *ks;
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62 int dret, lineno = 0;
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63 if (argc < 3) {
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64 fprintf(stderr, "Usage: bcftools ldpair <in.bcf> <in.list>\n");
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65 return 1;
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66 }
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67 fplist = gzopen(argv[2], "rb");
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68 ks = ks_init(fplist);
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69 memset(&str, 0, sizeof(kstring_t));
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70 fp = bcf_open(argv[1], "rb");
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71 h = bcf_hdr_read(fp);
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72 str2id = bcf_build_refhash(h);
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73 idx = bcf_idx_load(argv[1]);
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74 if (idx == 0) {
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75 fprintf(stderr, "[%s] No bcf index is found. Abort!\n", __func__);
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76 return 1;
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77 }
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78 b0 = calloc(1, sizeof(bcf1_t));
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79 b1 = calloc(1, sizeof(bcf1_t));
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80 while (ks_getuntil(ks, '\n', &str, &dret) >= 0) {
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81 char *p, *q;
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82 int k;
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83 int tid0 = -1, tid1 = -1, pos0 = -1, pos1 = -1;
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84 ++lineno;
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85 for (p = q = str.s, k = 0; *p; ++p) {
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86 if (*p == ' ' || *p == '\t') {
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87 *p = '\0';
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88 if (k == 0) tid0 = bcf_str2id(str2id, q);
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89 else if (k == 1) pos0 = atoi(q) - 1;
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90 else if (k == 2) tid1 = strcmp(q, "=")? bcf_str2id(str2id, q) : tid0;
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91 else if (k == 3) pos1 = atoi(q) - 1;
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92 q = p + 1;
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93 ++k;
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94 }
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95 }
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96 if (k == 3) pos1 = atoi(q) - 1;
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97 if (tid0 >= 0 && tid1 >= 0 && pos0 >= 0 && pos1 >= 0) {
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98 uint64_t off;
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99 double r, f[4];
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100 off = bcf_idx_query(idx, tid0, pos0);
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101 bgzf_seek(fp->fp, off, SEEK_SET);
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102 while (bcf_read(fp, h, b0) >= 0 && b0->pos != pos0);
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103 off = bcf_idx_query(idx, tid1, pos1);
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104 bgzf_seek(fp->fp, off, SEEK_SET);
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105 while (bcf_read(fp, h, b1) >= 0 && b1->pos != pos1);
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106 r = bcf_pair_freq(b0, b1, f);
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107 r *= r;
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108 printf("%s\t%d\t%s\t%d\t%.4g\t%.4g\t%.4g\t%.4g\t%.4g\n", h->ns[tid0], pos0+1, h->ns[tid1], pos1+1,
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109 r, f[0], f[1], f[2], f[3]);
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110 } //else fprintf(stderr, "[%s] Parse error at line %d.\n", __func__, lineno);
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111 }
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112 bcf_destroy(b0); bcf_destroy(b1);
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113 bcf_idx_destroy(idx);
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114 bcf_str2id_destroy(str2id);
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115 bcf_hdr_destroy(h);
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116 bcf_close(fp);
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117 free(str.s);
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118 ks_destroy(ks);
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119 gzclose(fplist);
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120 return 0;
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121 }
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122
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123 int bcf_main_ld(int argc, char *argv[])
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124 {
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125 bcf_t *fp;
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126 bcf_hdr_t *h;
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127 bcf1_t **b, *b0;
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128 int i, j, m, n;
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129 double f[4];
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130 if (argc == 1) {
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131 fprintf(stderr, "Usage: bcftools ld <in.bcf>\n");
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132 return 1;
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133 }
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134 fp = bcf_open(argv[1], "rb");
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135 h = bcf_hdr_read(fp);
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136 // read the entire BCF
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137 m = n = 0; b = 0;
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138 b0 = calloc(1, sizeof(bcf1_t));
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139 while (bcf_read(fp, h, b0) >= 0) {
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140 if (m == n) {
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141 m = m? m<<1 : 16;
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142 b = realloc(b, sizeof(void*) * m);
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143 }
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144 b[n] = calloc(1, sizeof(bcf1_t));
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145 bcf_cpy(b[n++], b0);
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146 }
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147 bcf_destroy(b0);
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148 // compute pair-wise r^2
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149 printf("%d\n", n); // the number of loci
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150 for (i = 0; i < n; ++i) {
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151 printf("%s:%d", h->ns[b[i]->tid], b[i]->pos + 1);
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152 for (j = 0; j < i; ++j) {
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153 double r = bcf_pair_freq(b[i], b[j], f);
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154 printf("\t%.3f", r*r);
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155 }
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156 printf("\t1.000\n");
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157 }
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158 // free
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159 for (i = 0; i < n; ++i) bcf_destroy(b[i]);
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160 free(b);
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161 bcf_hdr_destroy(h);
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162 bcf_close(fp);
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163 return 0;
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164 }
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165
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166 int main(int argc, char *argv[])
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167 {
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168 if (argc == 1) {
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169 fprintf(stderr, "\n");
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170 fprintf(stderr, "Program: bcftools (Tools for data in the VCF/BCF formats)\n");
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171 fprintf(stderr, "Version: %s\n\n", BCF_VERSION);
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172 fprintf(stderr, "Usage: bcftools <command> <arguments>\n\n");
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173 fprintf(stderr, "Command: view print, extract, convert and call SNPs from BCF\n");
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174 fprintf(stderr, " index index BCF\n");
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175 fprintf(stderr, " cat concatenate BCFs\n");
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176 fprintf(stderr, " ld compute all-pair r^2\n");
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177 fprintf(stderr, " ldpair compute r^2 between requested pairs\n");
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178 fprintf(stderr, "\n");
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179 return 1;
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180 }
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181 if (strcmp(argv[1], "view") == 0) return bcfview(argc-1, argv+1);
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182 else if (strcmp(argv[1], "index") == 0) return bcf_main_index(argc-1, argv+1);
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183 else if (strcmp(argv[1], "ld") == 0) return bcf_main_ld(argc-1, argv+1);
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184 else if (strcmp(argv[1], "ldpair") == 0) return bcf_main_ldpair(argc-1, argv+1);
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185 else if (strcmp(argv[1], "cat") == 0) return bcf_cat(argc-2, argv+2); // cat is different ...
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186 else {
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187 fprintf(stderr, "[main] Unrecognized command.\n");
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188 return 1;
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189 }
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190 return 0;
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191 }
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