+++ /dev/null
-#include <math.h>
-#include "sam.h"
-#include "khash.h"
-#include "klist.h"
-
-#define QUEUE_CLEAR_SIZE 0x100000
-#define MAX_POS 0x7fffffff
-
-typedef struct {
- int endpos;
- uint32_t score:31, discarded:1;
- bam1_t *b;
-} elem_t, *elem_p;
-#define __free_elem(p) bam_destroy1((p)->data.b)
-KLIST_INIT(q, elem_t, __free_elem)
-typedef klist_t(q) queue_t;
-
-KHASH_MAP_INIT_INT(best, elem_p)
-typedef khash_t(best) besthash_t;
-
-typedef struct {
- uint64_t n_checked, n_removed;
- besthash_t *left, *rght;
-} lib_aux_t;
-KHASH_MAP_INIT_STR(lib, lib_aux_t)
-
-static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib)
-{
- khint_t k = kh_get(lib, aux, lib);
- if (k == kh_end(aux)) {
- int ret;
- char *p = strdup(lib);
- lib_aux_t *q;
- k = kh_put(lib, aux, p, &ret);
- q = &kh_val(aux, k);
- q->left = kh_init(best);
- q->rght = kh_init(best);
- q->n_checked = q->n_removed = 0;
- return q;
- } else return &kh_val(aux, k);
-}
-
-static inline int sum_qual(const bam1_t *b)
-{
- int i, q;
- uint8_t *qual = bam1_qual(b);
- for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i];
- return q;
-}
-
-static inline elem_t *push_queue(queue_t *queue, const bam1_t *b, int endpos, int score)
-{
- elem_t *p = kl_pushp(q, queue);
- p->discarded = 0;
- p->endpos = endpos; p->score = score;
- if (p->b == 0) p->b = bam_init1();
- bam_copy1(p->b, b);
- return p;
-}
-
-static void clear_besthash(besthash_t *h, int32_t pos)
-{
- khint_t k;
- for (k = kh_begin(h); k != kh_end(h); ++k)
- if (kh_exist(h, k) && kh_val(h, k)->endpos <= pos)
- kh_del(best, h, k);
-}
-
-static void dump_alignment(samfile_t *out, queue_t *queue, int32_t pos, khash_t(lib) *h)
-{
- if (queue->size > QUEUE_CLEAR_SIZE || pos == MAX_POS) {
- khint_t k;
- while (1) {
- elem_t *q;
- if (queue->head == queue->tail) break;
- q = &kl_val(queue->head);
- if (q->discarded) {
- q->b->data_len = 0;
- kl_shift(q, queue, 0);
- continue;
- }
- if ((q->b->core.flag&BAM_FREVERSE) && q->endpos > pos) break;
- samwrite(out, q->b);
- q->b->data_len = 0;
- kl_shift(q, queue, 0);
- }
- for (k = kh_begin(h); k != kh_end(h); ++k) {
- if (kh_exist(h, k)) {
- clear_besthash(kh_val(h, k).left, pos);
- clear_besthash(kh_val(h, k).rght, pos);
- }
- }
- }
-}
-
-void bam_rmdupse_core(samfile_t *in, samfile_t *out, int force_se)
-{
- bam1_t *b;
- queue_t *queue;
- khint_t k;
- int last_tid = -2;
- khash_t(lib) *aux;
-
- aux = kh_init(lib);
- b = bam_init1();
- queue = kl_init(q);
- while (samread(in, b) >= 0) {
- bam1_core_t *c = &b->core;
- int endpos = bam_calend(c, bam1_cigar(b));
- int score = sum_qual(b);
-
- if (last_tid != c->tid) {
- if (last_tid >= 0) dump_alignment(out, queue, MAX_POS, aux);
- last_tid = c->tid;
- } else dump_alignment(out, queue, c->pos, aux);
- if ((c->flag&BAM_FUNMAP) || ((c->flag&BAM_FPAIRED) && !force_se)) {
- push_queue(queue, b, endpos, score);
- } else {
- const char *lib;
- lib_aux_t *q;
- besthash_t *h;
- uint32_t key;
- int ret;
- lib = bam_get_library(in->header, b);
- q = lib? get_aux(aux, lib) : get_aux(aux, "\t");
- ++q->n_checked;
- h = (c->flag&BAM_FREVERSE)? q->rght : q->left;
- key = (c->flag&BAM_FREVERSE)? endpos : c->pos;
- k = kh_put(best, h, key, &ret);
- if (ret == 0) { // in the hash table
- elem_t *p = kh_val(h, k);
- ++q->n_removed;
- if (p->score < score) {
- if (c->flag&BAM_FREVERSE) { // mark "discarded" and push the queue
- p->discarded = 1;
- kh_val(h, k) = push_queue(queue, b, endpos, score);
- } else { // replace
- p->score = score; p->endpos = endpos;
- bam_copy1(p->b, b);
- }
- } // otherwise, discard the alignment
- } else kh_val(h, k) = push_queue(queue, b, endpos, score);
- }
- }
- dump_alignment(out, queue, MAX_POS, aux);
-
- for (k = kh_begin(aux); k != kh_end(aux); ++k) {
- if (kh_exist(aux, k)) {
- lib_aux_t *q = &kh_val(aux, k);
- fprintf(stderr, "[bam_rmdupse_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed,
- (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k));
- kh_destroy(best, q->left); kh_destroy(best, q->rght);
- free((char*)kh_key(aux, k));
- }
- }
- kh_destroy(lib, aux);
- bam_destroy1(b);
- kl_destroy(q, queue);
-}
projects / pysam.git / blobdiff