6 #define QUEUE_CLEAR_SIZE 0x100000
7 #define MAX_POS 0x7fffffff
11 uint32_t score:31, discarded:1;
14 #define __free_elem(p) bam_destroy1((p)->data.b)
15 KLIST_INIT(q, elem_t, __free_elem)
16 typedef klist_t(q) queue_t;
18 KHASH_MAP_INIT_INT(best, elem_p)
19 typedef khash_t(best) besthash_t;
22 uint64_t n_checked, n_removed;
23 besthash_t *left, *rght;
25 KHASH_MAP_INIT_STR(lib, lib_aux_t)
27 static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib)
29 khint_t k = kh_get(lib, aux, lib);
30 if (k == kh_end(aux)) {
32 char *p = strdup(lib);
34 k = kh_put(lib, aux, p, &ret);
36 q->left = kh_init(best);
37 q->rght = kh_init(best);
38 q->n_checked = q->n_removed = 0;
40 } else return &kh_val(aux, k);
43 static inline int sum_qual(const bam1_t *b)
46 uint8_t *qual = bam1_qual(b);
47 for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i];
51 static inline elem_t *push_queue(queue_t *queue, const bam1_t *b, int endpos, int score)
53 elem_t *p = kl_pushp(q, queue);
55 p->endpos = endpos; p->score = score;
56 if (p->b == 0) p->b = bam_init1();
61 static void clear_besthash(besthash_t *h, int32_t pos)
64 for (k = kh_begin(h); k != kh_end(h); ++k)
65 if (kh_exist(h, k) && kh_val(h, k)->endpos <= pos)
69 static void dump_alignment(samfile_t *out, queue_t *queue, int32_t pos, khash_t(lib) *h)
71 if (queue->size > QUEUE_CLEAR_SIZE || pos == MAX_POS) {
75 if (queue->head == queue->tail) break;
76 q = &kl_val(queue->head);
79 kl_shift(q, queue, 0);
82 if ((q->b->core.flag&BAM_FREVERSE) && q->endpos > pos) break;
85 kl_shift(q, queue, 0);
87 for (k = kh_begin(h); k != kh_end(h); ++k) {
89 clear_besthash(kh_val(h, k).left, pos);
90 clear_besthash(kh_val(h, k).rght, pos);
96 void bam_rmdupse_core(samfile_t *in, samfile_t *out, int force_se)
107 while (samread(in, b) >= 0) {
108 bam1_core_t *c = &b->core;
109 int endpos = bam_calend(c, bam1_cigar(b));
110 int score = sum_qual(b);
112 if (last_tid != c->tid) {
113 if (last_tid >= 0) dump_alignment(out, queue, MAX_POS, aux);
115 } else dump_alignment(out, queue, c->pos, aux);
116 if ((c->flag&BAM_FUNMAP) || ((c->flag&BAM_FPAIRED) && !force_se)) {
117 push_queue(queue, b, endpos, score);
124 lib = bam_get_library(in->header, b);
125 q = lib? get_aux(aux, lib) : get_aux(aux, "\t");
127 h = (c->flag&BAM_FREVERSE)? q->rght : q->left;
128 key = (c->flag&BAM_FREVERSE)? endpos : c->pos;
129 k = kh_put(best, h, key, &ret);
130 if (ret == 0) { // in the hash table
131 elem_t *p = kh_val(h, k);
133 if (p->score < score) {
134 if (c->flag&BAM_FREVERSE) { // mark "discarded" and push the queue
136 kh_val(h, k) = push_queue(queue, b, endpos, score);
138 p->score = score; p->endpos = endpos;
141 } // otherwise, discard the alignment
142 } else kh_val(h, k) = push_queue(queue, b, endpos, score);
145 dump_alignment(out, queue, MAX_POS, aux);
147 for (k = kh_begin(aux); k != kh_end(aux); ++k) {
148 if (kh_exist(aux, k)) {
149 lib_aux_t *q = &kh_val(aux, k);
150 fprintf(stderr, "[bam_rmdupse_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed,
151 (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k));
152 kh_destroy(best, q->left); kh_destroy(best, q->rght);
153 free((char*)kh_key(aux, k));
156 kh_destroy(lib, aux);
158 kl_destroy(q, queue);