bam_rmdupse.c

#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);
}