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1 #include <ctype.h>
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2 #include <assert.h>
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3 #include "bam.h"
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4 #include "khash.h"
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5 #include "ksort.h"
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6 #include "bam_endian.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 /*!
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12 @header
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13
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14 Alignment indexing. Before indexing, BAM must be sorted based on the
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15 leftmost coordinate of alignments. In indexing, BAM uses two indices:
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16 a UCSC binning index and a simple linear index. The binning index is
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17 efficient for alignments spanning long distance, while the auxiliary
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18 linear index helps to reduce unnecessary seek calls especially for
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19 short alignments.
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20
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21 The UCSC binning scheme was suggested by Richard Durbin and Lincoln
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22 Stein and is explained by Kent et al. (2002). In this scheme, each bin
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23 represents a contiguous genomic region which can be fully contained in
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24 another bin; each alignment is associated with a bin which represents
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25 the smallest region containing the entire alignment. The binning
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26 scheme is essentially another representation of R-tree. A distinct bin
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27 uniquely corresponds to a distinct internal node in a R-tree. Bin A is
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28 a child of Bin B if region A is contained in B.
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29
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30 In BAM, each bin may span 2^29, 2^26, 2^23, 2^20, 2^17 or 2^14 bp. Bin
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31 0 spans a 512Mbp region, bins 1-8 span 64Mbp, 9-72 8Mbp, 73-584 1Mbp,
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32 585-4680 128Kbp and bins 4681-37449 span 16Kbp regions. If we want to
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33 find the alignments overlapped with a region [rbeg,rend), we need to
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34 calculate the list of bins that may be overlapped the region and test
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35 the alignments in the bins to confirm the overlaps. If the specified
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36 region is short, typically only a few alignments in six bins need to
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37 be retrieved. The overlapping alignments can be quickly fetched.
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38
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39 */
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40
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41 #define BAM_MIN_CHUNK_GAP 32768
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42 // 1<<14 is the size of minimum bin.
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43 #define BAM_LIDX_SHIFT 14
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44
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45 typedef struct {
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46 uint64_t u, v;
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47 } pair64_t;
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48
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49 #define pair64_lt(a,b) ((a).u < (b).u)
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50 KSORT_INIT(off, pair64_t, pair64_lt)
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51
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52 typedef struct {
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53 uint32_t m, n;
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54 pair64_t *list;
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55 } bam_binlist_t;
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56
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57 typedef struct {
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58 int32_t n, m;
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59 uint64_t *offset;
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60 } bam_lidx_t;
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61
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62 KHASH_MAP_INIT_INT(i, bam_binlist_t)
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63
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64 struct __bam_index_t {
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65 int32_t n;
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66 khash_t(i) **index;
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67 bam_lidx_t *index2;
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68 };
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69
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70 // requirement: len <= LEN_MASK
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71 static inline void insert_offset(khash_t(i) *h, int bin, uint64_t beg, uint64_t end)
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72 {
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73 khint_t k;
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74 bam_binlist_t *l;
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75 int ret;
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76 k = kh_put(i, h, bin, &ret);
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77 l = &kh_value(h, k);
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78 if (ret) { // not present
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79 l->m = 1; l->n = 0;
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80 l->list = (pair64_t*)calloc(l->m, 16);
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81 }
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82 if (l->n == l->m) {
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83 l->m <<= 1;
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84 l->list = (pair64_t*)realloc(l->list, l->m * 16);
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85 }
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86 l->list[l->n].u = beg; l->list[l->n++].v = end;
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87 }
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88
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89 static inline void insert_offset2(bam_lidx_t *index2, bam1_t *b, uint64_t offset)
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90 {
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91 int i, beg, end;
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92 beg = b->core.pos >> BAM_LIDX_SHIFT;
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93 end = (bam_calend(&b->core, bam1_cigar(b)) - 1) >> BAM_LIDX_SHIFT;
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94 if (index2->m < end + 1) {
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95 int old_m = index2->m;
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96 index2->m = end + 1;
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97 kroundup32(index2->m);
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98 index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8);
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99 memset(index2->offset + old_m, 0, 8 * (index2->m - old_m));
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100 }
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101 for (i = beg + 1; i <= end; ++i)
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102 if (index2->offset[i] == 0) index2->offset[i] = offset;
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103 index2->n = end + 1;
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104 }
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105
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106 static void merge_chunks(bam_index_t *idx)
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107 {
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108 #if defined(BAM_TRUE_OFFSET) || defined(BAM_VIRTUAL_OFFSET16)
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109 khash_t(i) *index;
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110 int i, l, m;
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111 khint_t k;
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112 for (i = 0; i < idx->n; ++i) {
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113 index = idx->index[i];
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114 for (k = kh_begin(index); k != kh_end(index); ++k) {
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115 bam_binlist_t *p;
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116 if (!kh_exist(index, k)) continue;
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117 p = &kh_value(index, k);
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118 m = 0;
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119 for (l = 1; l < p->n; ++l) {
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120 #ifdef BAM_TRUE_OFFSET
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121 if (p->list[m].v + BAM_MIN_CHUNK_GAP > p->list[l].u) p->list[m].v = p->list[l].v;
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122 #else
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123 if (p->list[m].v>>16 == p->list[l].u>>16) p->list[m].v = p->list[l].v;
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124 #endif
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125 else p->list[++m] = p->list[l];
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126 } // ~for(l)
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127 p->n = m + 1;
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128 } // ~for(k)
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129 } // ~for(i)
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130 #endif // defined(BAM_TRUE_OFFSET) || defined(BAM_BGZF)
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131 }
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132
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133 bam_index_t *bam_index_core(bamFile fp)
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134 {
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135 bam1_t *b;
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136 bam_header_t *h;
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137 int i, ret;
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138 bam_index_t *idx;
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139 uint32_t last_bin, save_bin;
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140 int32_t last_coor, last_tid, save_tid;
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141 bam1_core_t *c;
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142 uint64_t save_off, last_off;
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143
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144 idx = (bam_index_t*)calloc(1, sizeof(bam_index_t));
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145 b = (bam1_t*)calloc(1, sizeof(bam1_t));
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146 h = bam_header_read(fp);
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147 c = &b->core;
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148
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149 idx->n = h->n_targets;
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150 bam_header_destroy(h);
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151 idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*));
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152 for (i = 0; i < idx->n; ++i) idx->index[i] = kh_init(i);
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153 idx->index2 = (bam_lidx_t*)calloc(idx->n, sizeof(bam_lidx_t));
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154
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155 save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
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156 save_off = last_off = bam_tell(fp); last_coor = 0xffffffffu;
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157 while ((ret = bam_read1(fp, b)) >= 0) {
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158 if (last_tid != c->tid) { // change of chromosomes
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159 last_tid = c->tid;
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160 last_bin = 0xffffffffu;
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161 } else if (last_coor > c->pos) {
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162 fprintf(stderr, "[bam_index_core] the alignment is not sorted (%s): %u > %u in %d-th chr\n",
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163 bam1_qname(b), last_coor, c->pos, c->tid+1);
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164 exit(1);
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165 }
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166 if (b->core.tid >= 0 && b->core.bin < 4681) insert_offset2(&idx->index2[b->core.tid], b, last_off);
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167 if (c->bin != last_bin) { // then possibly write the binning index
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168 if (save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record
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169 insert_offset(idx->index[save_tid], save_bin, save_off, last_off);
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170 save_off = last_off;
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171 save_bin = last_bin = c->bin;
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172 save_tid = c->tid;
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173 if (save_tid < 0) break;
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174 }
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175 if (bam_tell(fp) <= last_off) {
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176 fprintf(stderr, "[bam_index_core] bug in BGZF/RAZF: %llx < %llx\n",
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177 (unsigned long long)bam_tell(fp), (unsigned long long)last_off);
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178 exit(1);
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179 }
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180 last_off = bam_tell(fp);
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181 last_coor = b->core.pos;
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182 }
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183 if (save_tid >= 0) insert_offset(idx->index[save_tid], save_bin, save_off, bam_tell(fp));
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184 merge_chunks(idx);
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185 if (ret < -1) fprintf(stderr, "[bam_index_core] truncated file? Continue anyway. (%d)\n", ret);
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186 free(b->data); free(b);
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187 return idx;
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188 }
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189
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190 void bam_index_destroy(bam_index_t *idx)
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191 {
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192 khint_t k;
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193 int i;
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194 if (idx == 0) return;
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195 for (i = 0; i < idx->n; ++i) {
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196 khash_t(i) *index = idx->index[i];
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197 bam_lidx_t *index2 = idx->index2 + i;
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198 for (k = kh_begin(index); k != kh_end(index); ++k) {
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199 if (kh_exist(index, k))
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200 free(kh_value(index, k).list);
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201 }
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202 kh_destroy(i, index);
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203 free(index2->offset);
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204 }
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205 free(idx->index); free(idx->index2);
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206 free(idx);
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207 }
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208
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209 void bam_index_save(const bam_index_t *idx, FILE *fp)
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210 {
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211 int32_t i, size;
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212 khint_t k;
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213 fwrite("BAI\1", 1, 4, fp);
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214 if (bam_is_be) {
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215 uint32_t x = idx->n;
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216 fwrite(bam_swap_endian_4p(&x), 4, 1, fp);
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217 } else fwrite(&idx->n, 4, 1, fp);
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218 for (i = 0; i < idx->n; ++i) {
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219 khash_t(i) *index = idx->index[i];
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220 bam_lidx_t *index2 = idx->index2 + i;
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221 // write binning index
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222 size = kh_size(index);
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223 if (bam_is_be) { // big endian
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224 uint32_t x = size;
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225 fwrite(bam_swap_endian_4p(&x), 4, 1, fp);
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226 } else fwrite(&size, 4, 1, fp);
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227 for (k = kh_begin(index); k != kh_end(index); ++k) {
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228 if (kh_exist(index, k)) {
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229 bam_binlist_t *p = &kh_value(index, k);
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230 if (bam_is_be) { // big endian
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231 uint32_t x;
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232 x = kh_key(index, k); fwrite(bam_swap_endian_4p(&x), 4, 1, fp);
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233 x = p->n; fwrite(bam_swap_endian_4p(&x), 4, 1, fp);
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234 for (x = 0; (int)x < p->n; ++x) {
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235 bam_swap_endian_8p(&p->list[x].u);
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236 bam_swap_endian_8p(&p->list[x].v);
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237 }
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238 fwrite(p->list, 16, p->n, fp);
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239 for (x = 0; (int)x < p->n; ++x) {
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240 bam_swap_endian_8p(&p->list[x].u);
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241 bam_swap_endian_8p(&p->list[x].v);
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242 }
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243 } else {
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244 fwrite(&kh_key(index, k), 4, 1, fp);
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245 fwrite(&p->n, 4, 1, fp);
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246 fwrite(p->list, 16, p->n, fp);
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247 }
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248 }
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249 }
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250 // write linear index (index2)
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251 if (bam_is_be) {
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252 int x = index2->n;
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253 fwrite(bam_swap_endian_4p(&x), 4, 1, fp);
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254 } else fwrite(&index2->n, 4, 1, fp);
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255 if (bam_is_be) { // big endian
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256 int x;
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257 for (x = 0; (int)x < index2->n; ++x)
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258 bam_swap_endian_8p(&index2->offset[x]);
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259 fwrite(index2->offset, 8, index2->n, fp);
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260 for (x = 0; (int)x < index2->n; ++x)
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261 bam_swap_endian_8p(&index2->offset[x]);
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262 } else fwrite(index2->offset, 8, index2->n, fp);
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263 }
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264 fflush(fp);
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265 }
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266
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267 static bam_index_t *bam_index_load_core(FILE *fp)
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268 {
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269 int i;
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270 char magic[4];
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271 bam_index_t *idx;
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272 if (fp == 0) {
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273 fprintf(stderr, "[bam_index_load_core] fail to load index.\n");
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274 return 0;
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275 }
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276 fread(magic, 1, 4, fp);
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277 if (strncmp(magic, "BAI\1", 4)) {
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278 fprintf(stderr, "[bam_index_load] wrong magic number.\n");
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279 fclose(fp);
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280 return 0;
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281 }
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282 idx = (bam_index_t*)calloc(1, sizeof(bam_index_t));
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283 fread(&idx->n, 4, 1, fp);
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284 if (bam_is_be) bam_swap_endian_4p(&idx->n);
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285 idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*));
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286 idx->index2 = (bam_lidx_t*)calloc(idx->n, sizeof(bam_lidx_t));
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287 for (i = 0; i < idx->n; ++i) {
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288 khash_t(i) *index;
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289 bam_lidx_t *index2 = idx->index2 + i;
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290 uint32_t key, size;
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291 khint_t k;
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292 int j, ret;
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293 bam_binlist_t *p;
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294 index = idx->index[i] = kh_init(i);
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295 // load binning index
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296 fread(&size, 4, 1, fp);
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297 if (bam_is_be) bam_swap_endian_4p(&size);
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298 for (j = 0; j < (int)size; ++j) {
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299 fread(&key, 4, 1, fp);
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300 if (bam_is_be) bam_swap_endian_4p(&key);
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301 k = kh_put(i, index, key, &ret);
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302 p = &kh_value(index, k);
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303 fread(&p->n, 4, 1, fp);
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304 if (bam_is_be) bam_swap_endian_4p(&p->n);
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305 p->m = p->n;
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306 p->list = (pair64_t*)malloc(p->m * 16);
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307 fread(p->list, 16, p->n, fp);
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308 if (bam_is_be) {
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309 int x;
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310 for (x = 0; x < p->n; ++x) {
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311 bam_swap_endian_8p(&p->list[x].u);
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312 bam_swap_endian_8p(&p->list[x].v);
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313 }
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314 }
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315 }
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316 // load linear index
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317 fread(&index2->n, 4, 1, fp);
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318 if (bam_is_be) bam_swap_endian_4p(&index2->n);
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319 index2->m = index2->n;
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320 index2->offset = (uint64_t*)calloc(index2->m, 8);
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321 fread(index2->offset, index2->n, 8, fp);
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322 if (bam_is_be)
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323 for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]);
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324 }
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325 return idx;
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326 }
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327
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328 bam_index_t *bam_index_load_local(const char *_fn)
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329 {
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330 FILE *fp;
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331 char *fnidx, *fn;
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332
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333 if (strstr(_fn, "ftp://") == _fn || strstr(_fn, "http://") == _fn) {
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334 const char *p;
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335 int l = strlen(_fn);
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336 for (p = _fn + l - 1; p >= _fn; --p)
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337 if (*p == '/') break;
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338 fn = strdup(p + 1);
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339 } else fn = strdup(_fn);
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340 fnidx = (char*)calloc(strlen(fn) + 5, 1);
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341 strcpy(fnidx, fn); strcat(fnidx, ".bai");
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342 fp = fopen(fnidx, "r");
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343 if (fp == 0) { // try "{base}.bai"
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344 char *s = strstr(fn, "bam");
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345 if (s == fn + strlen(fn) - 3) {
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346 strcpy(fnidx, fn);
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347 fnidx[strlen(fn)-1] = 'i';
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348 fp = fopen(fnidx, "r");
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349 }
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350 }
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351 free(fnidx); free(fn);
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352 if (fp) {
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353 bam_index_t *idx = bam_index_load_core(fp);
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354 fclose(fp);
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355 return idx;
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356 } else return 0;
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357 }
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358
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359 #ifdef _USE_KNETFILE
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360 static void download_from_remote(const char *url)
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361 {
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362 const int buf_size = 1 * 1024 * 1024;
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363 char *fn;
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364 FILE *fp;
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365 uint8_t *buf;
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366 knetFile *fp_remote;
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367 int l;
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368 if (strstr(url, "ftp://") != url && strstr(url, "http://") != url) return;
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369 l = strlen(url);
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370 for (fn = (char*)url + l - 1; fn >= url; --fn)
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371 if (*fn == '/') break;
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372 ++fn; // fn now points to the file name
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373 fp_remote = knet_open(url, "r");
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374 if (fp_remote == 0) {
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375 fprintf(stderr, "[download_from_remote] fail to open remote file.\n");
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376 return;
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377 }
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378 if ((fp = fopen(fn, "w")) == 0) {
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379 fprintf(stderr, "[download_from_remote] fail to create file in the working directory.\n");
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380 knet_close(fp_remote);
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381 return;
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382 }
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383 buf = (uint8_t*)calloc(buf_size, 1);
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384 while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
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385 fwrite(buf, 1, l, fp);
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386 free(buf);
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387 fclose(fp);
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388 knet_close(fp_remote);
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389 }
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390 #else
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391 static void download_from_remote(const char *url)
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392 {
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393 return;
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394 }
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395 #endif
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396
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397 bam_index_t *bam_index_load(const char *fn)
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398 {
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399 bam_index_t *idx;
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400 idx = bam_index_load_local(fn);
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401 if (idx == 0 && (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn)) {
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402 char *fnidx = calloc(strlen(fn) + 5, 1);
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403 strcat(strcpy(fnidx, fn), ".bai");
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404 fprintf(stderr, "[bam_index_load] attempting to download the remote index file.\n");
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405 download_from_remote(fnidx);
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406 idx = bam_index_load_local(fn);
|
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407 }
|
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408 if (idx == 0) fprintf(stderr, "[bam_index_load] fail to load BAM index.\n");
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409 return idx;
|
|
410 }
|
|
411
|
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412 int bam_index_build2(const char *fn, const char *_fnidx)
|
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413 {
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414 char *fnidx;
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415 FILE *fpidx;
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416 bamFile fp;
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417 bam_index_t *idx;
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418 if ((fp = bam_open(fn, "r")) == 0) {
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419 fprintf(stderr, "[bam_index_build2] fail to open the BAM file.\n");
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420 return -1;
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421 }
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422 idx = bam_index_core(fp);
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423 bam_close(fp);
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424 if (_fnidx == 0) {
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425 fnidx = (char*)calloc(strlen(fn) + 5, 1);
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426 strcpy(fnidx, fn); strcat(fnidx, ".bai");
|
|
427 } else fnidx = strdup(_fnidx);
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428 fpidx = fopen(fnidx, "w");
|
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429 if (fpidx == 0) {
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430 fprintf(stderr, "[bam_index_build2] fail to create the index file.\n");
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431 free(fnidx);
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432 return -1;
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433 }
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434 bam_index_save(idx, fpidx);
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435 bam_index_destroy(idx);
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436 fclose(fpidx);
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437 free(fnidx);
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438 return 0;
|
|
439 }
|
|
440
|
|
441 int bam_index_build(const char *fn)
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442 {
|
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443 return bam_index_build2(fn, 0);
|
|
444 }
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445
|
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446 int bam_index(int argc, char *argv[])
|
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447 {
|
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448 if (argc < 2) {
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449 fprintf(stderr, "Usage: samtools index <in.bam> [<out.index>]\n");
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450 return 1;
|
|
451 }
|
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452 if (argc >= 3) bam_index_build2(argv[1], argv[2]);
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453 else bam_index_build(argv[1]);
|
|
454 return 0;
|
|
455 }
|
|
456
|
|
457 #define MAX_BIN 37450 // =(8^6-1)/7+1
|
|
458
|
|
459 static inline int reg2bins(uint32_t beg, uint32_t end, uint16_t list[MAX_BIN])
|
|
460 {
|
|
461 int i = 0, k;
|
|
462 --end;
|
|
463 list[i++] = 0;
|
|
464 for (k = 1 + (beg>>26); k <= 1 + (end>>26); ++k) list[i++] = k;
|
|
465 for (k = 9 + (beg>>23); k <= 9 + (end>>23); ++k) list[i++] = k;
|
|
466 for (k = 73 + (beg>>20); k <= 73 + (end>>20); ++k) list[i++] = k;
|
|
467 for (k = 585 + (beg>>17); k <= 585 + (end>>17); ++k) list[i++] = k;
|
|
468 for (k = 4681 + (beg>>14); k <= 4681 + (end>>14); ++k) list[i++] = k;
|
|
469 return i;
|
|
470 }
|
|
471
|
|
472 static inline int is_overlap(uint32_t beg, uint32_t end, const bam1_t *b)
|
|
473 {
|
|
474 uint32_t rbeg = b->core.pos;
|
|
475 uint32_t rend = b->core.n_cigar? bam_calend(&b->core, bam1_cigar(b)) : b->core.pos + 1;
|
|
476 return (rend > beg && rbeg < end);
|
|
477 }
|
|
478
|
|
479 int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func)
|
|
480 {
|
|
481 uint16_t *bins;
|
|
482 int i, n_bins, n_off;
|
|
483 pair64_t *off;
|
|
484 khint_t k;
|
|
485 khash_t(i) *index;
|
|
486 uint64_t min_off;
|
|
487
|
|
488 bins = (uint16_t*)calloc(MAX_BIN, 2);
|
|
489 n_bins = reg2bins(beg, end, bins);
|
|
490 index = idx->index[tid];
|
|
491 min_off = (beg>>BAM_LIDX_SHIFT >= idx->index2[tid].n)? 0 : idx->index2[tid].offset[beg>>BAM_LIDX_SHIFT];
|
|
492 for (i = n_off = 0; i < n_bins; ++i) {
|
|
493 if ((k = kh_get(i, index, bins[i])) != kh_end(index))
|
|
494 n_off += kh_value(index, k).n;
|
|
495 }
|
|
496 if (n_off == 0) {
|
|
497 free(bins); return 0;
|
|
498 }
|
|
499 off = (pair64_t*)calloc(n_off, 16);
|
|
500 for (i = n_off = 0; i < n_bins; ++i) {
|
|
501 if ((k = kh_get(i, index, bins[i])) != kh_end(index)) {
|
|
502 int j;
|
|
503 bam_binlist_t *p = &kh_value(index, k);
|
|
504 for (j = 0; j < p->n; ++j)
|
|
505 if (p->list[j].v > min_off) off[n_off++] = p->list[j];
|
|
506 }
|
|
507 }
|
|
508 free(bins);
|
|
509 {
|
|
510 bam1_t *b;
|
|
511 int l, ret, n_seeks;
|
|
512 uint64_t curr_off;
|
|
513 b = (bam1_t*)calloc(1, sizeof(bam1_t));
|
|
514 ks_introsort(off, n_off, off);
|
|
515 // resolve completely contained adjacent blocks
|
|
516 for (i = 1, l = 0; i < n_off; ++i)
|
|
517 if (off[l].v < off[i].v)
|
|
518 off[++l] = off[i];
|
|
519 n_off = l + 1;
|
|
520 // resolve overlaps between adjacent blocks; this may happen due to the merge in indexing
|
|
521 for (i = 1; i < n_off; ++i)
|
|
522 if (off[i-1].v >= off[i].u) off[i-1].v = off[i].u;
|
|
523 { // merge adjacent blocks
|
|
524 #if defined(BAM_TRUE_OFFSET) || defined(BAM_VIRTUAL_OFFSET16)
|
|
525 for (i = 1, l = 0; i < n_off; ++i) {
|
|
526 #ifdef BAM_TRUE_OFFSET
|
|
527 if (off[l].v + BAM_MIN_CHUNK_GAP > off[i].u) off[l].v = off[i].v;
|
|
528 #else
|
|
529 if (off[l].v>>16 == off[i].u>>16) off[l].v = off[i].v;
|
|
530 #endif
|
|
531 else off[++l] = off[i];
|
|
532 }
|
|
533 n_off = l + 1;
|
|
534 #endif
|
|
535 }
|
|
536 // retrive alignments
|
|
537 n_seeks = 0; i = -1; curr_off = 0;
|
|
538 for (;;) {
|
|
539 if (curr_off == 0 || curr_off >= off[i].v) { // then jump to the next chunk
|
|
540 if (i == n_off - 1) break; // no more chunks
|
|
541 if (i >= 0) assert(curr_off == off[i].v); // otherwise bug
|
|
542 if (i < 0 || off[i].v != off[i+1].u) { // not adjacent chunks; then seek
|
|
543 bam_seek(fp, off[i+1].u, SEEK_SET);
|
|
544 curr_off = bam_tell(fp);
|
|
545 ++n_seeks;
|
|
546 }
|
|
547 ++i;
|
|
548 }
|
|
549 if ((ret = bam_read1(fp, b)) > 0) {
|
|
550 curr_off = bam_tell(fp);
|
|
551 if (b->core.tid != tid || b->core.pos >= end) break; // no need to proceed
|
|
552 else if (is_overlap(beg, end, b)) func(b, data);
|
|
553 } else break; // end of file
|
|
554 }
|
|
555 // fprintf(stderr, "[bam_fetch] # seek calls: %d\n", n_seeks);
|
|
556 bam_destroy1(b);
|
|
557 }
|
|
558 free(off);
|
|
559 return 0;
|
|
560 }
|