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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 int bam_aux_drop_other(bam1_t *b, uint8_t *s)
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63 {
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64 if (s) {
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65 uint8_t *p, *aux;
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66 aux = bam1_aux(b);
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67 p = s - 2;
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68 __skip_tag(s);
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69 memmove(aux, p, s - p);
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70 b->data_len -= b->l_aux - (s - p);
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71 b->l_aux = s - p;
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72 } else {
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73 b->data_len -= b->l_aux;
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74 b->l_aux = 0;
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75 }
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76 return 0;
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77 }
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78
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79 void bam_init_header_hash(bam_header_t *header)
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80 {
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81 if (header->hash == 0) {
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82 int ret, i;
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83 khiter_t iter;
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84 khash_t(s) *h;
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85 header->hash = h = kh_init(s);
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86 for (i = 0; i < header->n_targets; ++i) {
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87 iter = kh_put(s, h, header->target_name[i], &ret);
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88 kh_value(h, iter) = i;
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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 void bam_destroy_header_hash(bam_header_t *header)
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94 {
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95 if (header->hash)
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96 kh_destroy(s, (khash_t(s)*)header->hash);
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97 }
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98
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99 int32_t bam_get_tid(const bam_header_t *header, const char *seq_name)
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100 {
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101 khint_t k;
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102 khash_t(s) *h = (khash_t(s)*)header->hash;
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103 k = kh_get(s, h, seq_name);
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104 return k == kh_end(h)? -1 : kh_value(h, k);
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105 }
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106
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107 int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *beg, int *end)
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108 {
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109 char *s;
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110 int i, l, k, name_end;
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111 khiter_t iter;
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112 khash_t(s) *h;
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113
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114 bam_init_header_hash(header);
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115 h = (khash_t(s)*)header->hash;
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116
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117 *ref_id = *beg = *end = -1;
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118 name_end = l = strlen(str);
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119 s = (char*)malloc(l+1);
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120 // remove space
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121 for (i = k = 0; i < l; ++i)
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122 if (!isspace(str[i])) s[k++] = str[i];
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123 s[k] = 0; l = k;
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124 // determine the sequence name
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125 for (i = l - 1; i >= 0; --i) if (s[i] == ':') break; // look for colon from the end
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126 if (i >= 0) name_end = i;
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127 if (name_end < l) { // check if this is really the end
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128 int n_hyphen = 0;
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129 for (i = name_end + 1; i < l; ++i) {
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130 if (s[i] == '-') ++n_hyphen;
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131 else if (!isdigit(s[i]) && s[i] != ',') break;
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132 }
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133 if (i < l || n_hyphen > 1) name_end = l; // malformated region string; then take str as the name
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134 s[name_end] = 0;
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135 iter = kh_get(s, h, s);
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136 if (iter == kh_end(h)) { // cannot find the sequence name
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137 iter = kh_get(s, h, str); // try str as the name
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138 if (iter == kh_end(h)) {
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139 if (bam_verbose >= 2) fprintf(stderr, "[%s] fail to determine the sequence name.\n", __func__);
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140 free(s); return -1;
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141 } else s[name_end] = ':', name_end = l;
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142 }
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143 } else iter = kh_get(s, h, str);
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144 if (iter == kh_end(h)) {
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145 free(s);
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146 return -1;
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147 }
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148 *ref_id = kh_val(h, iter);
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149 // parse the interval
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150 if (name_end < l) {
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151 for (i = k = name_end + 1; i < l; ++i)
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152 if (s[i] != ',') s[k++] = s[i];
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153 s[k] = 0;
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154 *beg = atoi(s + name_end + 1);
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155 for (i = name_end + 1; i != k; ++i) if (s[i] == '-') break;
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156 *end = i < k? atoi(s + i + 1) : 1<<29;
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157 if (*beg > 0) --*beg;
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158 } else *beg = 0, *end = 1<<29;
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159 free(s);
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160 return *beg <= *end? 0 : -1;
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161 }
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162
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163 int32_t bam_aux2i(const uint8_t *s)
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164 {
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165 int type;
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166 if (s == 0) return 0;
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167 type = *s++;
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168 if (type == 'c') return (int32_t)*(int8_t*)s;
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169 else if (type == 'C') return (int32_t)*(uint8_t*)s;
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170 else if (type == 's') return (int32_t)*(int16_t*)s;
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171 else if (type == 'S') return (int32_t)*(uint16_t*)s;
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172 else if (type == 'i' || type == 'I') return *(int32_t*)s;
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173 else return 0;
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174 }
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175
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176 float bam_aux2f(const uint8_t *s)
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177 {
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178 int type;
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179 type = *s++;
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180 if (s == 0) return 0.0;
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181 if (type == 'f') return *(float*)s;
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182 else return 0.0;
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183 }
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184
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185 double bam_aux2d(const uint8_t *s)
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186 {
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187 int type;
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188 type = *s++;
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189 if (s == 0) return 0.0;
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190 if (type == 'd') return *(double*)s;
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191 else return 0.0;
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192 }
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193
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194 char bam_aux2A(const uint8_t *s)
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195 {
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196 int type;
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197 type = *s++;
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198 if (s == 0) return 0;
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199 if (type == 'A') return *(char*)s;
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200 else return 0;
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201 }
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202
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203 char *bam_aux2Z(const uint8_t *s)
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204 {
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205 int type;
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206 type = *s++;
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207 if (s == 0) return 0;
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208 if (type == 'Z' || type == 'H') return (char*)s;
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209 else return 0;
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210 }
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211
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212 #ifdef _WIN32
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213 double drand48()
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214 {
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215 return (double)rand() / RAND_MAX;
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216 }
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217 #endif
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