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1 #include <math.h>
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2 #include "sam.h"
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3 #include "khash.h"
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4 #include "klist.h"
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5
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6 #define QUEUE_CLEAR_SIZE 0x100000
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7 #define MAX_POS 0x7fffffff
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8
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9 typedef struct {
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10 int endpos;
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11 uint32_t score:31, discarded:1;
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12 bam1_t *b;
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13 } elem_t, *elem_p;
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14 #define __free_elem(p) bam_destroy1((p)->data.b)
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15 KLIST_INIT(q, elem_t, __free_elem)
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16 typedef klist_t(q) queue_t;
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17
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18 KHASH_MAP_INIT_INT(best, elem_p)
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19 typedef khash_t(best) besthash_t;
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20
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21 typedef struct {
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22 uint64_t n_checked, n_removed;
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23 besthash_t *left, *rght;
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24 } lib_aux_t;
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25 KHASH_MAP_INIT_STR(lib, lib_aux_t)
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26
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27 static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib)
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28 {
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29 khint_t k = kh_get(lib, aux, lib);
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30 if (k == kh_end(aux)) {
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31 int ret;
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32 char *p = strdup(lib);
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33 lib_aux_t *q;
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34 k = kh_put(lib, aux, p, &ret);
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35 q = &kh_val(aux, k);
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36 q->left = kh_init(best);
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37 q->rght = kh_init(best);
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38 q->n_checked = q->n_removed = 0;
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39 return q;
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40 } else return &kh_val(aux, k);
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41 }
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42
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43 static inline int sum_qual(const bam1_t *b)
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44 {
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45 int i, q;
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46 uint8_t *qual = bam1_qual(b);
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47 for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i];
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48 return q;
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49 }
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50
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51 static inline elem_t *push_queue(queue_t *queue, const bam1_t *b, int endpos, int score)
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52 {
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53 elem_t *p = kl_pushp(q, queue);
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54 p->discarded = 0;
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55 p->endpos = endpos; p->score = score;
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56 if (p->b == 0) p->b = bam_init1();
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57 bam_copy1(p->b, b);
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58 return p;
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59 }
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60
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61 static void clear_besthash(besthash_t *h, int32_t pos)
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62 {
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63 khint_t k;
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64 for (k = kh_begin(h); k != kh_end(h); ++k)
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65 if (kh_exist(h, k) && kh_val(h, k)->endpos <= pos)
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66 kh_del(best, h, k);
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67 }
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68
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69 static void dump_alignment(samfile_t *out, queue_t *queue, int32_t pos, khash_t(lib) *h)
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70 {
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71 if (queue->size > QUEUE_CLEAR_SIZE || pos == MAX_POS) {
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72 khint_t k;
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73 while (1) {
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74 elem_t *q;
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75 if (queue->head == queue->tail) break;
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76 q = &kl_val(queue->head);
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77 if (q->discarded) {
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78 q->b->data_len = 0;
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79 kl_shift(q, queue, 0);
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80 continue;
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81 }
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82 if ((q->b->core.flag&BAM_FREVERSE) && q->endpos > pos) break;
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83 samwrite(out, q->b);
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84 q->b->data_len = 0;
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85 kl_shift(q, queue, 0);
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86 }
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87 for (k = kh_begin(h); k != kh_end(h); ++k) {
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88 if (kh_exist(h, k)) {
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89 clear_besthash(kh_val(h, k).left, pos);
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90 clear_besthash(kh_val(h, k).rght, pos);
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91 }
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92 }
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93 }
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94 }
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95
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96 void bam_rmdupse_core(samfile_t *in, samfile_t *out, int force_se)
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97 {
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98 bam1_t *b;
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99 queue_t *queue;
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100 khint_t k;
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101 int last_tid = -2;
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102 khash_t(lib) *aux;
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103
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104 aux = kh_init(lib);
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105 b = bam_init1();
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106 queue = kl_init(q);
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107 while (samread(in, b) >= 0) {
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108 bam1_core_t *c = &b->core;
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109 int endpos = bam_calend(c, bam1_cigar(b));
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110 int score = sum_qual(b);
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111
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112 if (last_tid != c->tid) {
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113 if (last_tid >= 0) dump_alignment(out, queue, MAX_POS, aux);
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114 last_tid = c->tid;
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115 } else dump_alignment(out, queue, c->pos, aux);
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116 if ((c->flag&BAM_FUNMAP) || ((c->flag&BAM_FPAIRED) && !force_se)) {
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117 push_queue(queue, b, endpos, score);
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118 } else {
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119 const char *lib;
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120 lib_aux_t *q;
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121 besthash_t *h;
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122 uint32_t key;
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123 int ret;
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124 lib = bam_get_library(in->header, b);
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125 q = lib? get_aux(aux, lib) : get_aux(aux, "\t");
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126 ++q->n_checked;
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127 h = (c->flag&BAM_FREVERSE)? q->rght : q->left;
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128 key = (c->flag&BAM_FREVERSE)? endpos : c->pos;
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129 k = kh_put(best, h, key, &ret);
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130 if (ret == 0) { // in the hash table
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131 elem_t *p = kh_val(h, k);
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132 ++q->n_removed;
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133 if (p->score < score) {
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134 if (c->flag&BAM_FREVERSE) { // mark "discarded" and push the queue
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135 p->discarded = 1;
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136 kh_val(h, k) = push_queue(queue, b, endpos, score);
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137 } else { // replace
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138 p->score = score; p->endpos = endpos;
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139 bam_copy1(p->b, b);
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140 }
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141 } // otherwise, discard the alignment
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142 } else kh_val(h, k) = push_queue(queue, b, endpos, score);
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143 }
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144 }
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145 dump_alignment(out, queue, MAX_POS, aux);
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146
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147 for (k = kh_begin(aux); k != kh_end(aux); ++k) {
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148 if (kh_exist(aux, k)) {
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149 lib_aux_t *q = &kh_val(aux, k);
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150 fprintf(stderr, "[bam_rmdupse_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed,
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151 (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k));
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152 kh_destroy(best, q->left); kh_destroy(best, q->rght);
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153 free((char*)kh_key(aux, k));
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154 }
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155 }
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156 kh_destroy(lib, aux);
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157 bam_destroy1(b);
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158 kl_destroy(q, queue);
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159 }
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