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1 #include <stdio.h>
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2 #include <stdlib.h>
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3 #include <ctype.h>
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4 #include <assert.h>
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5 #include "sam.h"
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6
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7 typedef struct {
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8 int k, x, y, end;
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9 } cstate_t;
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10
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11 static cstate_t g_cstate_null = { -1, 0, 0, 0 };
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12
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13 typedef struct __linkbuf_t {
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14 bam1_t b;
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15 uint32_t beg, end;
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16 cstate_t s;
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17 struct __linkbuf_t *next;
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18 } lbnode_t;
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19
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20 /* --- BEGIN: Memory pool */
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21
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22 typedef struct {
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23 int cnt, n, max;
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24 lbnode_t **buf;
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25 } mempool_t;
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26
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27 static mempool_t *mp_init()
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28 {
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29 mempool_t *mp;
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30 mp = (mempool_t*)calloc(1, sizeof(mempool_t));
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31 return mp;
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32 }
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33 static void mp_destroy(mempool_t *mp)
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34 {
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35 int k;
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36 for (k = 0; k < mp->n; ++k) {
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37 free(mp->buf[k]->b.data);
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38 free(mp->buf[k]);
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39 }
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40 free(mp->buf);
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41 free(mp);
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42 }
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43 static inline lbnode_t *mp_alloc(mempool_t *mp)
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44 {
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45 ++mp->cnt;
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46 if (mp->n == 0) return (lbnode_t*)calloc(1, sizeof(lbnode_t));
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47 else return mp->buf[--mp->n];
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48 }
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49 static inline void mp_free(mempool_t *mp, lbnode_t *p)
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50 {
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51 --mp->cnt; p->next = 0; // clear lbnode_t::next here
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52 if (mp->n == mp->max) {
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53 mp->max = mp->max? mp->max<<1 : 256;
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54 mp->buf = (lbnode_t**)realloc(mp->buf, sizeof(lbnode_t*) * mp->max);
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55 }
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56 mp->buf[mp->n++] = p;
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57 }
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58
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59 /* --- END: Memory pool */
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60
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61 /* --- BEGIN: Auxiliary functions */
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62
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63 /* s->k: the index of the CIGAR operator that has just been processed.
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64 s->x: the reference coordinate of the start of s->k
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65 s->y: the query coordiante of the start of s->k
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66 */
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67 static inline int resolve_cigar2(bam_pileup1_t *p, uint32_t pos, cstate_t *s)
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68 {
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69 #define _cop(c) ((c)&BAM_CIGAR_MASK)
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70 #define _cln(c) ((c)>>BAM_CIGAR_SHIFT)
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71
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72 bam1_t *b = p->b;
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73 bam1_core_t *c = &b->core;
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74 uint32_t *cigar = bam1_cigar(b);
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75 int k, is_head = 0;
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76 // determine the current CIGAR operation
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77 // fprintf(stderr, "%s\tpos=%d\tend=%d\t(%d,%d,%d)\n", bam1_qname(b), pos, s->end, s->k, s->x, s->y);
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78 if (s->k == -1) { // never processed
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79 is_head = 1;
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80 if (c->n_cigar == 1) { // just one operation, save a loop
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81 if (_cop(cigar[0]) == BAM_CMATCH || _cop(cigar[0]) == BAM_CEQUAL || _cop(cigar[0]) == BAM_CDIFF) s->k = 0, s->x = c->pos, s->y = 0;
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82 } else { // find the first match or deletion
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83 for (k = 0, s->x = c->pos, s->y = 0; k < c->n_cigar; ++k) {
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84 int op = _cop(cigar[k]);
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85 int l = _cln(cigar[k]);
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86 if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CEQUAL || op == BAM_CDIFF) break;
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87 else if (op == BAM_CREF_SKIP) s->x += l;
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88 else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l;
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89 }
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90 assert(k < c->n_cigar);
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91 s->k = k;
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92 }
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93 } else { // the read has been processed before
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94 int op, l = _cln(cigar[s->k]);
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95 if (pos - s->x >= l) { // jump to the next operation
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96 assert(s->k < c->n_cigar); // otherwise a bug: this function should not be called in this case
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97 op = _cop(cigar[s->k+1]);
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98 if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP || op == BAM_CEQUAL || op == BAM_CDIFF) { // jump to the next without a loop
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99 if (_cop(cigar[s->k]) == BAM_CMATCH|| _cop(cigar[s->k]) == BAM_CEQUAL || _cop(cigar[s->k]) == BAM_CDIFF) s->y += l;
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100 s->x += l;
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101 ++s->k;
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102 } else { // find the next M/D/N/=/X
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103 if (_cop(cigar[s->k]) == BAM_CMATCH|| _cop(cigar[s->k]) == BAM_CEQUAL || _cop(cigar[s->k]) == BAM_CDIFF) s->y += l;
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104 s->x += l;
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105 for (k = s->k + 1; k < c->n_cigar; ++k) {
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106 op = _cop(cigar[k]), l = _cln(cigar[k]);
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107 if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP || op == BAM_CEQUAL || op == BAM_CDIFF) break;
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108 else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l;
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109 }
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110 s->k = k;
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111 }
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112 assert(s->k < c->n_cigar); // otherwise a bug
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113 } // else, do nothing
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114 }
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115 { // collect pileup information
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116 int op, l;
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117 op = _cop(cigar[s->k]); l = _cln(cigar[s->k]);
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118 p->is_del = p->indel = p->is_refskip = 0;
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119 if (s->x + l - 1 == pos && s->k + 1 < c->n_cigar) { // peek the next operation
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120 int op2 = _cop(cigar[s->k+1]);
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121 int l2 = _cln(cigar[s->k+1]);
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122 if (op2 == BAM_CDEL) p->indel = -(int)l2;
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123 else if (op2 == BAM_CINS) p->indel = l2;
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124 else if (op2 == BAM_CPAD && s->k + 2 < c->n_cigar) { // no working for adjacent padding
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125 int l3 = 0;
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126 for (k = s->k + 2; k < c->n_cigar; ++k) {
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127 op2 = _cop(cigar[k]); l2 = _cln(cigar[k]);
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128 if (op2 == BAM_CINS) l3 += l2;
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129 else if (op2 == BAM_CDEL || op2 == BAM_CMATCH || op2 == BAM_CREF_SKIP || op2 == BAM_CEQUAL || op2 == BAM_CDIFF) break;
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130 }
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131 if (l3 > 0) p->indel = l3;
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132 }
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133 }
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134 if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
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135 p->qpos = s->y + (pos - s->x);
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136 } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) {
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137 p->is_del = 1; p->qpos = s->y; // FIXME: distinguish D and N!!!!!
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138 p->is_refskip = (op == BAM_CREF_SKIP);
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139 } // cannot be other operations; otherwise a bug
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140 p->is_head = (pos == c->pos); p->is_tail = (pos == s->end);
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141 }
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142 return 1;
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143 }
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144
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145 /* --- END: Auxiliary functions */
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146
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147 /*******************
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148 * pileup iterator *
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149 *******************/
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150
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151 struct __bam_plp_t {
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152 mempool_t *mp;
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153 lbnode_t *head, *tail, *dummy;
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154 int32_t tid, pos, max_tid, max_pos;
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155 int is_eof, flag_mask, max_plp, error, maxcnt;
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156 bam_pileup1_t *plp;
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157 // for the "auto" interface only
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158 bam1_t *b;
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159 bam_plp_auto_f func;
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160 void *data;
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161 };
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162
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163 bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data)
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164 {
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165 bam_plp_t iter;
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166 iter = calloc(1, sizeof(struct __bam_plp_t));
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167 iter->mp = mp_init();
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168 iter->head = iter->tail = mp_alloc(iter->mp);
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169 iter->dummy = mp_alloc(iter->mp);
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170 iter->max_tid = iter->max_pos = -1;
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171 iter->flag_mask = BAM_DEF_MASK;
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172 iter->maxcnt = 8000;
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173 if (func) {
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174 iter->func = func;
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175 iter->data = data;
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176 iter->b = bam_init1();
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177 }
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178 return iter;
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179 }
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180
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181 void bam_plp_destroy(bam_plp_t iter)
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182 {
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183 mp_free(iter->mp, iter->dummy);
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184 mp_free(iter->mp, iter->head);
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185 if (iter->mp->cnt != 0)
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186 fprintf(stderr, "[bam_plp_destroy] memory leak: %d. Continue anyway.\n", iter->mp->cnt);
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187 mp_destroy(iter->mp);
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188 if (iter->b) bam_destroy1(iter->b);
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189 free(iter->plp);
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190 free(iter);
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191 }
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192
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193 const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
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194 {
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195 if (iter->error) { *_n_plp = -1; return 0; }
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196 *_n_plp = 0;
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197 if (iter->is_eof && iter->head->next == 0) return 0;
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198 while (iter->is_eof || iter->max_tid > iter->tid || (iter->max_tid == iter->tid && iter->max_pos > iter->pos)) {
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199 int n_plp = 0;
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200 lbnode_t *p, *q;
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201 // write iter->plp at iter->pos
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202 iter->dummy->next = iter->head;
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203 for (p = iter->head, q = iter->dummy; p->next; q = p, p = p->next) {
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204 if (p->b.core.tid < iter->tid || (p->b.core.tid == iter->tid && p->end <= iter->pos)) { // then remove
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205 q->next = p->next; mp_free(iter->mp, p); p = q;
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206 } else if (p->b.core.tid == iter->tid && p->beg <= iter->pos) { // here: p->end > pos; then add to pileup
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207 if (n_plp == iter->max_plp) { // then double the capacity
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208 iter->max_plp = iter->max_plp? iter->max_plp<<1 : 256;
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209 iter->plp = (bam_pileup1_t*)realloc(iter->plp, sizeof(bam_pileup1_t) * iter->max_plp);
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210 }
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211 iter->plp[n_plp].b = &p->b;
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212 if (resolve_cigar2(iter->plp + n_plp, iter->pos, &p->s)) ++n_plp; // actually always true...
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213 }
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214 }
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215 iter->head = iter->dummy->next; // dummy->next may be changed
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216 *_n_plp = n_plp; *_tid = iter->tid; *_pos = iter->pos;
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217 // update iter->tid and iter->pos
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218 if (iter->head->next) {
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219 if (iter->tid > iter->head->b.core.tid) {
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220 fprintf(stderr, "[%s] unsorted input. Pileup aborts.\n", __func__);
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221 iter->error = 1;
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222 *_n_plp = -1;
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223 return 0;
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224 }
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225 }
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226 if (iter->tid < iter->head->b.core.tid) { // come to a new reference sequence
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227 iter->tid = iter->head->b.core.tid; iter->pos = iter->head->beg; // jump to the next reference
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228 } else if (iter->pos < iter->head->beg) { // here: tid == head->b.core.tid
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229 iter->pos = iter->head->beg; // jump to the next position
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230 } else ++iter->pos; // scan contiguously
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231 // return
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232 if (n_plp) return iter->plp;
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233 if (iter->is_eof && iter->head->next == 0) break;
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234 }
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235 return 0;
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236 }
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237
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238 int bam_plp_push(bam_plp_t iter, const bam1_t *b)
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239 {
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240 if (iter->error) return -1;
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241 if (b) {
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242 if (b->core.tid < 0) return 0;
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243 if (b->core.flag & iter->flag_mask) return 0;
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244 if (iter->tid == b->core.tid && iter->pos == b->core.pos && iter->mp->cnt > iter->maxcnt) return 0;
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245 bam_copy1(&iter->tail->b, b);
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246 iter->tail->beg = b->core.pos; iter->tail->end = bam_calend(&b->core, bam1_cigar(b));
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247 iter->tail->s = g_cstate_null; iter->tail->s.end = iter->tail->end - 1; // initialize cstate_t
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248 if (b->core.tid < iter->max_tid) {
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249 fprintf(stderr, "[bam_pileup_core] the input is not sorted (chromosomes out of order)\n");
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250 iter->error = 1;
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251 return -1;
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252 }
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253 if ((b->core.tid == iter->max_tid) && (iter->tail->beg < iter->max_pos)) {
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254 fprintf(stderr, "[bam_pileup_core] the input is not sorted (reads out of order)\n");
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255 iter->error = 1;
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256 return -1;
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257 }
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258 iter->max_tid = b->core.tid; iter->max_pos = iter->tail->beg;
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259 if (iter->tail->end > iter->pos || iter->tail->b.core.tid > iter->tid) {
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260 iter->tail->next = mp_alloc(iter->mp);
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261 iter->tail = iter->tail->next;
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262 }
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263 } else iter->is_eof = 1;
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264 return 0;
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265 }
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266
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267 const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
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268 {
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269 const bam_pileup1_t *plp;
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270 if (iter->func == 0 || iter->error) { *_n_plp = -1; return 0; }
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271 if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
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272 else { // no pileup line can be obtained; read alignments
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273 *_n_plp = 0;
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274 if (iter->is_eof) return 0;
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275 while (iter->func(iter->data, iter->b) >= 0) {
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276 if (bam_plp_push(iter, iter->b) < 0) {
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277 *_n_plp = -1;
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278 return 0;
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279 }
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280 if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
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281 // otherwise no pileup line can be returned; read the next alignment.
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282 }
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283 bam_plp_push(iter, 0);
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284 if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
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285 return 0;
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286 }
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287 }
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288
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289 void bam_plp_reset(bam_plp_t iter)
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290 {
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291 lbnode_t *p, *q;
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292 iter->max_tid = iter->max_pos = -1;
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293 iter->tid = iter->pos = 0;
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294 iter->is_eof = 0;
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295 for (p = iter->head; p->next;) {
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296 q = p->next;
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297 mp_free(iter->mp, p);
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298 p = q;
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299 }
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300 iter->head = iter->tail;
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301 }
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302
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303 void bam_plp_set_mask(bam_plp_t iter, int mask)
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304 {
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305 iter->flag_mask = mask < 0? BAM_DEF_MASK : (BAM_FUNMAP | mask);
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306 }
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307
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308 void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt)
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309 {
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310 iter->maxcnt = maxcnt;
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311 }
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312
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313 /*****************
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314 * callback APIs *
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315 *****************/
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316
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317 int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data)
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318 {
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319 bam_plbuf_t *buf;
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320 int ret;
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321 bam1_t *b;
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322 b = bam_init1();
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323 buf = bam_plbuf_init(func, func_data);
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324 bam_plbuf_set_mask(buf, mask);
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325 while ((ret = bam_read1(fp, b)) >= 0)
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326 bam_plbuf_push(b, buf);
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327 bam_plbuf_push(0, buf);
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328 bam_plbuf_destroy(buf);
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329 bam_destroy1(b);
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330 return 0;
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331 }
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332
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333 void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask)
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334 {
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335 bam_plp_set_mask(buf->iter, mask);
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336 }
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337
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338 void bam_plbuf_reset(bam_plbuf_t *buf)
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339 {
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340 bam_plp_reset(buf->iter);
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341 }
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342
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343 bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data)
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344 {
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345 bam_plbuf_t *buf;
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346 buf = calloc(1, sizeof(bam_plbuf_t));
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347 buf->iter = bam_plp_init(0, 0);
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348 buf->func = func;
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349 buf->data = data;
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350 return buf;
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351 }
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352
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353 void bam_plbuf_destroy(bam_plbuf_t *buf)
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354 {
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355 bam_plp_destroy(buf->iter);
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356 free(buf);
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357 }
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358
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359 int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf)
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360 {
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361 int ret, n_plp, tid, pos;
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362 const bam_pileup1_t *plp;
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363 ret = bam_plp_push(buf->iter, b);
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364 if (ret < 0) return ret;
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365 while ((plp = bam_plp_next(buf->iter, &tid, &pos, &n_plp)) != 0)
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366 buf->func(tid, pos, n_plp, plp, buf->data);
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367 return 0;
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368 }
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369
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370 /***********
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371 * mpileup *
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372 ***********/
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373
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374 struct __bam_mplp_t {
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375 int n;
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376 uint64_t min, *pos;
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377 bam_plp_t *iter;
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378 int *n_plp;
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379 const bam_pileup1_t **plp;
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380 };
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381
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382 bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data)
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383 {
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384 int i;
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385 bam_mplp_t iter;
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386 iter = calloc(1, sizeof(struct __bam_mplp_t));
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387 iter->pos = calloc(n, 8);
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388 iter->n_plp = calloc(n, sizeof(int));
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389 iter->plp = calloc(n, sizeof(void*));
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390 iter->iter = calloc(n, sizeof(void*));
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391 iter->n = n;
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392 iter->min = (uint64_t)-1;
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393 for (i = 0; i < n; ++i) {
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394 iter->iter[i] = bam_plp_init(func, data[i]);
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395 iter->pos[i] = iter->min;
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396 }
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397 return iter;
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398 }
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399
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400 void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt)
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401 {
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402 int i;
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403 for (i = 0; i < iter->n; ++i)
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404 iter->iter[i]->maxcnt = maxcnt;
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405 }
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406
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407 void bam_mplp_destroy(bam_mplp_t iter)
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408 {
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409 int i;
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410 for (i = 0; i < iter->n; ++i) bam_plp_destroy(iter->iter[i]);
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411 free(iter->iter); free(iter->pos); free(iter->n_plp); free(iter->plp);
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412 free(iter);
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413 }
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414
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415 int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp)
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416 {
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417 int i, ret = 0;
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418 uint64_t new_min = (uint64_t)-1;
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419 for (i = 0; i < iter->n; ++i) {
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420 if (iter->pos[i] == iter->min) {
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421 int tid, pos;
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422 iter->plp[i] = bam_plp_auto(iter->iter[i], &tid, &pos, &iter->n_plp[i]);
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423 iter->pos[i] = (uint64_t)tid<<32 | pos;
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424 }
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425 if (iter->plp[i] && iter->pos[i] < new_min) new_min = iter->pos[i];
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426 }
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427 iter->min = new_min;
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428 if (new_min == (uint64_t)-1) return 0;
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429 *_tid = new_min>>32; *_pos = (uint32_t)new_min;
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430 for (i = 0; i < iter->n; ++i) {
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431 if (iter->pos[i] == iter->min) { // FIXME: valgrind reports "uninitialised value(s) at this line"
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432 n_plp[i] = iter->n_plp[i], plp[i] = iter->plp[i];
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433 ++ret;
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434 } else n_plp[i] = 0, plp[i] = 0;
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435 }
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436 return ret;
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437 }
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