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1 #include <ctype.h>
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2 #include "bam.h"
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3 #include "khash.h"
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4 typedef char *str_p;
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5 KHASH_MAP_INIT_STR(s, int)
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6 KHASH_MAP_INIT_STR(r2l, str_p)
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7
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8 void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data)
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9 {
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10 int ori_len = b->data_len;
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11 b->data_len += 3 + len;
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12 b->l_aux += 3 + len;
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13 if (b->m_data < b->data_len) {
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14 b->m_data = b->data_len;
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15 kroundup32(b->m_data);
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16 b->data = (uint8_t*)realloc(b->data, b->m_data);
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17 }
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18 b->data[ori_len] = tag[0]; b->data[ori_len + 1] = tag[1];
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19 b->data[ori_len + 2] = type;
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20 memcpy(b->data + ori_len + 3, data, len);
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21 }
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22
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23 uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2])
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24 {
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25 return bam_aux_get(b, tag);
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26 }
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27
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28 #define __skip_tag(s) do { \
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29 int type = toupper(*(s)); \
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30 ++(s); \
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31 if (type == 'Z' || type == 'H') { while (*(s)) ++(s); ++(s); } \
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32 else if (type == 'B') (s) += 5 + bam_aux_type2size(*(s)) * (*(int32_t*)((s)+1)); \
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33 else (s) += bam_aux_type2size(type); \
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34 } while(0)
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35
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36 uint8_t *bam_aux_get(const bam1_t *b, const char tag[2])
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37 {
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38 uint8_t *s;
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39 int y = tag[0]<<8 | tag[1];
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40 s = bam1_aux(b);
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41 while (s < b->data + b->data_len) {
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42 int x = (int)s[0]<<8 | s[1];
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43 s += 2;
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44 if (x == y) return s;
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45 __skip_tag(s);
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46 }
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47 return 0;
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48 }
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49 // s MUST BE returned by bam_aux_get()
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50 int bam_aux_del(bam1_t *b, uint8_t *s)
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51 {
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52 uint8_t *p, *aux;
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53 aux = bam1_aux(b);
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54 p = s - 2;
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55 __skip_tag(s);
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56 memmove(p, s, b->l_aux - (s - aux));
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57 b->data_len -= s - p;
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58 b->l_aux -= s - p;
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59 return 0;
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60 }
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61
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62 void bam_init_header_hash(bam_header_t *header)
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63 {
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64 if (header->hash == 0) {
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65 int ret, i;
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66 khiter_t iter;
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67 khash_t(s) *h;
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68 header->hash = h = kh_init(s);
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69 for (i = 0; i < header->n_targets; ++i) {
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70 iter = kh_put(s, h, header->target_name[i], &ret);
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71 kh_value(h, iter) = i;
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72 }
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73 }
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74 }
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75
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76 void bam_destroy_header_hash(bam_header_t *header)
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77 {
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78 if (header->hash)
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79 kh_destroy(s, (khash_t(s)*)header->hash);
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80 }
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81
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82 int32_t bam_get_tid(const bam_header_t *header, const char *seq_name)
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83 {
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84 khint_t k;
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85 khash_t(s) *h = (khash_t(s)*)header->hash;
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86 k = kh_get(s, h, seq_name);
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87 return k == kh_end(h)? -1 : kh_value(h, k);
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88 }
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89
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90 int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end)
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91 {
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92 char *s, *p;
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93 int i, l, k;
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94 khiter_t iter;
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95 khash_t(s) *h;
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96
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97 bam_init_header_hash(header);
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98 h = (khash_t(s)*)header->hash;
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99
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100 l = strlen(str);
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101 p = s = (char*)malloc(l+1);
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102 /* squeeze out "," */
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103 for (i = k = 0; i != l; ++i)
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104 if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i];
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105 s[k] = 0;
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106 for (i = 0; i != k; ++i) if (s[i] == ':') break;
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107 s[i] = 0;
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108 iter = kh_get(s, h, s); /* get the ref_id */
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109 if (iter == kh_end(h)) { // name not found
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110 *ref_id = -1; free(s);
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111 return -1;
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112 }
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113 *ref_id = kh_value(h, iter);
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114 if (i == k) { /* dump the whole sequence */
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115 *begin = 0; *end = 1<<29; free(s);
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116 return 0;
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117 }
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118 for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
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119 *begin = atoi(p);
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120 if (i < k) {
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121 p = s + i + 1;
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122 *end = atoi(p);
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123 } else *end = 1<<29;
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124 if (*begin > 0) --*begin;
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125 free(s);
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126 if (*begin > *end) {
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127 fprintf(stderr, "[bam_parse_region] invalid region.\n");
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128 return -1;
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129 }
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130 return 0;
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131 }
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132
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133 int32_t bam_aux2i(const uint8_t *s)
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134 {
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135 int type;
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136 if (s == 0) return 0;
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137 type = *s++;
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138 if (type == 'c') return (int32_t)*(int8_t*)s;
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139 else if (type == 'C') return (int32_t)*(uint8_t*)s;
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140 else if (type == 's') return (int32_t)*(int16_t*)s;
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141 else if (type == 'S') return (int32_t)*(uint16_t*)s;
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142 else if (type == 'i' || type == 'I') return *(int32_t*)s;
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143 else return 0;
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144 }
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145
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146 float bam_aux2f(const uint8_t *s)
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147 {
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148 int type;
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149 type = *s++;
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150 if (s == 0) return 0.0;
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151 if (type == 'f') return *(float*)s;
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152 else return 0.0;
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153 }
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154
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155 double bam_aux2d(const uint8_t *s)
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156 {
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157 int type;
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158 type = *s++;
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159 if (s == 0) return 0.0;
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160 if (type == 'd') return *(double*)s;
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161 else return 0.0;
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162 }
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163
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164 char bam_aux2A(const uint8_t *s)
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165 {
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166 int type;
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167 type = *s++;
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168 if (s == 0) return 0;
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169 if (type == 'A') return *(char*)s;
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170 else return 0;
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171 }
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172
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173 char *bam_aux2Z(const uint8_t *s)
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174 {
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175 int type;
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176 type = *s++;
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177 if (s == 0) return 0;
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178 if (type == 'Z' || type == 'H') return (char*)s;
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179 else return 0;
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180 }
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181
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182 #ifdef _WIN32
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183 double drand48()
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184 {
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185 return (double)rand() / RAND_MAX;
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186 }
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187 #endif
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