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1 #include <assert.h>
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2 #include <ctype.h>
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3 #include <sys/stat.h>
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4 #include "bam_endian.h"
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5 #include "kstring.h"
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6 #include "bcf.h"
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7 #ifdef _USE_KNETFILE
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8 #include "knetfile.h"
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9 #endif
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10
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11 #define TAD_LIDX_SHIFT 13
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12
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13 typedef struct {
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14 int32_t n, m;
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15 uint64_t *offset;
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16 } bcf_lidx_t;
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17
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18 struct __bcf_idx_t {
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19 int32_t n;
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20 bcf_lidx_t *index2;
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21 };
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22
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23 /************
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24 * indexing *
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25 ************/
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26
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27 static inline void insert_offset2(bcf_lidx_t *index2, int _beg, int _end, uint64_t offset)
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28 {
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29 int i, beg, end;
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30 beg = _beg >> TAD_LIDX_SHIFT;
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31 end = (_end - 1) >> TAD_LIDX_SHIFT;
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32 if (index2->m < end + 1) {
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33 int old_m = index2->m;
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34 index2->m = end + 1;
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35 kroundup32(index2->m);
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36 index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8);
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37 memset(index2->offset + old_m, 0, 8 * (index2->m - old_m));
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38 }
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39 if (beg == end) {
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40 if (index2->offset[beg] == 0) index2->offset[beg] = offset;
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41 } else {
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42 for (i = beg; i <= end; ++i)
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43 if (index2->offset[i] == 0) index2->offset[i] = offset;
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44 }
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45 if (index2->n < end + 1) index2->n = end + 1;
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46 }
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47
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48 bcf_idx_t *bcf_idx_core(bcf_t *bp, bcf_hdr_t *h)
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49 {
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50 bcf_idx_t *idx;
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51 int32_t last_coor, last_tid;
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52 uint64_t last_off;
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53 kstring_t *str;
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54 BGZF *fp = bp->fp;
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55 bcf1_t *b;
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56 int ret;
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57
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58 b = calloc(1, sizeof(bcf1_t));
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59 str = calloc(1, sizeof(kstring_t));
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60 idx = (bcf_idx_t*)calloc(1, sizeof(bcf_idx_t));
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61 idx->n = h->n_ref;
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62 idx->index2 = calloc(h->n_ref, sizeof(bcf_lidx_t));
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63
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64 last_tid = 0xffffffffu;
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65 last_off = bgzf_tell(fp); last_coor = 0xffffffffu;
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66 while ((ret = bcf_read(bp, h, b)) > 0) {
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67 int end, tmp;
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68 if (last_tid != b->tid) { // change of chromosomes
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69 last_tid = b->tid;
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70 } else if (last_coor > b->pos) {
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71 fprintf(stderr, "[bcf_idx_core] the input is out of order\n");
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72 free(str->s); free(str); free(idx); bcf_destroy(b);
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73 return 0;
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74 }
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75 tmp = strlen(b->ref);
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76 end = b->pos + (tmp > 0? tmp : 1);
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77 insert_offset2(&idx->index2[b->tid], b->pos, end, last_off);
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78 last_off = bgzf_tell(fp);
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79 last_coor = b->pos;
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80 }
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81 free(str->s); free(str); bcf_destroy(b);
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82 return idx;
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83 }
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84
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85 void bcf_idx_destroy(bcf_idx_t *idx)
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86 {
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87 int i;
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88 if (idx == 0) return;
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89 for (i = 0; i < idx->n; ++i) free(idx->index2[i].offset);
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90 free(idx->index2);
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91 free(idx);
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92 }
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93
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94 /******************
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95 * index file I/O *
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96 ******************/
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97
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98 void bcf_idx_save(const bcf_idx_t *idx, BGZF *fp)
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99 {
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100 int32_t i, ti_is_be;
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101 ti_is_be = bam_is_big_endian();
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102 bgzf_write(fp, "BCI\4", 4);
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103 if (ti_is_be) {
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104 uint32_t x = idx->n;
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105 bgzf_write(fp, bam_swap_endian_4p(&x), 4);
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106 } else bgzf_write(fp, &idx->n, 4);
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107 for (i = 0; i < idx->n; ++i) {
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108 bcf_lidx_t *index2 = idx->index2 + i;
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109 // write linear index (index2)
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110 if (ti_is_be) {
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111 int x = index2->n;
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112 bgzf_write(fp, bam_swap_endian_4p(&x), 4);
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113 } else bgzf_write(fp, &index2->n, 4);
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114 if (ti_is_be) { // big endian
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115 int x;
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116 for (x = 0; (int)x < index2->n; ++x)
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117 bam_swap_endian_8p(&index2->offset[x]);
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118 bgzf_write(fp, index2->offset, 8 * index2->n);
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119 for (x = 0; (int)x < index2->n; ++x)
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120 bam_swap_endian_8p(&index2->offset[x]);
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121 } else bgzf_write(fp, index2->offset, 8 * index2->n);
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122 }
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123 }
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124
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125 static bcf_idx_t *bcf_idx_load_core(BGZF *fp)
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126 {
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127 int i, ti_is_be;
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128 char magic[4];
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129 bcf_idx_t *idx;
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130 ti_is_be = bam_is_big_endian();
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131 if (fp == 0) {
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132 fprintf(stderr, "[%s] fail to load index.\n", __func__);
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133 return 0;
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134 }
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135 bgzf_read(fp, magic, 4);
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136 if (strncmp(magic, "BCI\4", 4)) {
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137 fprintf(stderr, "[%s] wrong magic number.\n", __func__);
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138 return 0;
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139 }
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140 idx = (bcf_idx_t*)calloc(1, sizeof(bcf_idx_t));
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141 bgzf_read(fp, &idx->n, 4);
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142 if (ti_is_be) bam_swap_endian_4p(&idx->n);
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143 idx->index2 = (bcf_lidx_t*)calloc(idx->n, sizeof(bcf_lidx_t));
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144 for (i = 0; i < idx->n; ++i) {
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145 bcf_lidx_t *index2 = idx->index2 + i;
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146 int j;
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147 bgzf_read(fp, &index2->n, 4);
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148 if (ti_is_be) bam_swap_endian_4p(&index2->n);
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149 index2->m = index2->n;
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150 index2->offset = (uint64_t*)calloc(index2->m, 8);
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151 bgzf_read(fp, index2->offset, index2->n * 8);
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152 if (ti_is_be)
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153 for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]);
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154 }
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155 return idx;
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156 }
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157
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158 bcf_idx_t *bcf_idx_load_local(const char *fnidx)
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159 {
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160 BGZF *fp;
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161 fp = bgzf_open(fnidx, "r");
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162 if (fp) {
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163 bcf_idx_t *idx = bcf_idx_load_core(fp);
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164 bgzf_close(fp);
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165 return idx;
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166 } else return 0;
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167 }
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168
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169 #ifdef _USE_KNETFILE
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170 static void download_from_remote(const char *url)
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171 {
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172 const int buf_size = 1 * 1024 * 1024;
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173 char *fn;
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174 FILE *fp;
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175 uint8_t *buf;
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176 knetFile *fp_remote;
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177 int l;
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178 if (strstr(url, "ftp://") != url && strstr(url, "http://") != url) return;
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179 l = strlen(url);
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180 for (fn = (char*)url + l - 1; fn >= url; --fn)
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181 if (*fn == '/') break;
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182 ++fn; // fn now points to the file name
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183 fp_remote = knet_open(url, "r");
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184 if (fp_remote == 0) {
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185 fprintf(stderr, "[download_from_remote] fail to open remote file.\n");
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186 return;
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187 }
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188 if ((fp = fopen(fn, "w")) == 0) {
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189 fprintf(stderr, "[download_from_remote] fail to create file in the working directory.\n");
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190 knet_close(fp_remote);
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191 return;
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192 }
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193 buf = (uint8_t*)calloc(buf_size, 1);
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194 while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
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195 fwrite(buf, 1, l, fp);
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196 free(buf);
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197 fclose(fp);
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198 knet_close(fp_remote);
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199 }
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200 #else
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201 static void download_from_remote(const char *url)
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202 {
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203 return;
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204 }
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205 #endif
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206
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207 static char *get_local_version(const char *fn)
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208 {
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209 struct stat sbuf;
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210 char *fnidx = (char*)calloc(strlen(fn) + 5, 1);
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211 strcat(strcpy(fnidx, fn), ".bci");
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212 if ((strstr(fnidx, "ftp://") == fnidx || strstr(fnidx, "http://") == fnidx)) {
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213 char *p, *url;
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214 int l = strlen(fnidx);
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215 for (p = fnidx + l - 1; p >= fnidx; --p)
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216 if (*p == '/') break;
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217 url = fnidx; fnidx = strdup(p + 1);
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218 if (stat(fnidx, &sbuf) == 0) {
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219 free(url);
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220 return fnidx;
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221 }
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222 fprintf(stderr, "[%s] downloading the index file...\n", __func__);
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223 download_from_remote(url);
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224 free(url);
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225 }
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226 if (stat(fnidx, &sbuf) == 0) return fnidx;
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227 free(fnidx); return 0;
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228 }
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229
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230 bcf_idx_t *bcf_idx_load(const char *fn)
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231 {
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232 bcf_idx_t *idx;
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233 char *fname = get_local_version(fn);
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234 if (fname == 0) return 0;
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235 idx = bcf_idx_load_local(fname);
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236 free(fname);
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237 return idx;
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238 }
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239
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240 int bcf_idx_build2(const char *fn, const char *_fnidx)
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241 {
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242 char *fnidx;
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243 BGZF *fpidx;
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244 bcf_t *bp;
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245 bcf_idx_t *idx;
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246 bcf_hdr_t *h;
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247 if ((bp = bcf_open(fn, "r")) == 0) {
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248 fprintf(stderr, "[bcf_idx_build2] fail to open the BAM file.\n");
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249 return -1;
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250 }
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251 h = bcf_hdr_read(bp);
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252 idx = bcf_idx_core(bp, h);
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253 bcf_close(bp);
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254 if (_fnidx == 0) {
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255 fnidx = (char*)calloc(strlen(fn) + 5, 1);
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256 strcpy(fnidx, fn); strcat(fnidx, ".bci");
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257 } else fnidx = strdup(_fnidx);
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258 fpidx = bgzf_open(fnidx, "w");
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259 if (fpidx == 0) {
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260 fprintf(stderr, "[bcf_idx_build2] fail to create the index file.\n");
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261 free(fnidx);
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262 return -1;
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263 }
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264 bcf_idx_save(idx, fpidx);
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265 bcf_idx_destroy(idx);
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266 bgzf_close(fpidx);
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267 free(fnidx);
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268 return 0;
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269 }
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270
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271 int bcf_idx_build(const char *fn)
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272 {
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273 return bcf_idx_build2(fn, 0);
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274 }
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275
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276 /********************************************
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277 * parse a region in the format chr:beg-end *
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278 ********************************************/
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279
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280 int bcf_parse_region(void *str2id, const char *str, int *tid, int *begin, int *end)
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281 {
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282 char *s, *p;
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283 int i, l, k;
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284 l = strlen(str);
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285 p = s = (char*)malloc(l+1);
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286 /* squeeze out "," */
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287 for (i = k = 0; i != l; ++i)
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288 if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i];
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289 s[k] = 0;
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290 for (i = 0; i != k; ++i) if (s[i] == ':') break;
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291 s[i] = 0;
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292 if ((*tid = bcf_str2id(str2id, s)) < 0) {
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293 free(s);
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294 return -1;
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295 }
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296 if (i == k) { /* dump the whole sequence */
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297 *begin = 0; *end = 1<<29; free(s);
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298 return 0;
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299 }
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300 for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
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301 *begin = atoi(p);
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302 if (i < k) {
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303 p = s + i + 1;
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304 *end = atoi(p);
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305 } else *end = 1<<29;
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306 if (*begin > 0) --*begin;
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307 free(s);
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308 if (*begin > *end) return -1;
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309 return 0;
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310 }
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311
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312 /*******************************
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313 * retrieve a specified region *
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314 *******************************/
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315
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316 uint64_t bcf_idx_query(const bcf_idx_t *idx, int tid, int beg)
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317 {
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318 uint64_t min_off, *offset;
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319 int i;
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320 if (beg < 0) beg = 0;
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321 offset = idx->index2[tid].offset;
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322 for (i = beg>>TAD_LIDX_SHIFT; i < idx->index2[tid].n && offset[i] == 0; ++i);
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323 min_off = (i == idx->index2[tid].n)? offset[idx->index2[tid].n-1] : offset[i];
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324 return min_off;
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325 }
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326
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327 int bcf_main_index(int argc, char *argv[])
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328 {
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329 if (argc == 1) {
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330 fprintf(stderr, "Usage: bcftools index <in.bcf>\n");
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331 return 1;
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332 }
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333 bcf_idx_build(argv[1]);
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334 return 0;
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335 }
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