fast-bwa/bwamem_pair.c

#include <stdlib.h>
#include <string.h>
#include <math.h>
#include "kstring.h"
#include "bwamem.h"
#include "kvec.h"
#include "utils.h"

#define MIN_RATIO     0.8
#define MIN_DIR_CNT   10
#define MIN_DIR_RATIO 0.05
#define OUTLIER_BOUND 2.0
#define MAPPING_BOUND 3.0
#define MAX_STDDEV    4.0
#define EXT_STDDEV    4.0

void bwa_hit2sam(kstring_t *str, const int8_t mat[25], int q, int r, int w, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, bwahit_t *p, int is_hard);

static int cal_sub(const mem_opt_t *opt, mem_alnreg_v *r)
{
	int j;
	for (j = 1; j < r->n; ++j) { // choose unique alignment
		int b_max = r->a[j].qb > r->a[0].qb? r->a[j].qb : r->a[0].qb;
		int e_min = r->a[j].qe < r->a[0].qe? r->a[j].qe : r->a[0].qe;
		if (e_min > b_max) { // have overlap
			int min_l = r->a[j].qe - r->a[j].qb < r->a[0].qe - r->a[0].qb? r->a[j].qe - r->a[j].qb : r->a[0].qe - r->a[0].qb;
			if (e_min - b_max >= min_l * opt->mask_level) break; // significant overlap
		}
	}
	return j < r->n? r->a[j].score : opt->min_seed_len * opt->a;
}

void mem_pestat(const mem_opt_t *opt, int64_t l_pac, int n, const mem_alnreg_v *regs, mem_pestat_t pes[4])
{
	int i, d, max;
	uint64_v isize[4];
	memset(pes, 0, 4 * sizeof(mem_pestat_t));
	memset(isize, 0, sizeof(kvec_t(int)) * 4);
	for (i = 0; i < n>>1; ++i) {
		int dir;
		int64_t is, pos[2];
		mem_alnreg_v *r[2];
		r[0] = (mem_alnreg_v*)&regs[i<<1|0];
		r[1] = (mem_alnreg_v*)&regs[i<<1|1];
		if (r[0]->n == 0 || r[1]->n == 0) continue;
		if (cal_sub(opt, r[0]) > MIN_RATIO * r[0]->a[0].score) continue;
		if (cal_sub(opt, r[1]) > MIN_RATIO * r[1]->a[0].score) continue;
		pos[0] = r[0]->a[0].rb < l_pac? r[0]->a[0].rb : (l_pac<<1) - 1 - r[0]->a[0].rb; // forward coordinate
		pos[1] = r[1]->a[0].rb < l_pac? r[1]->a[0].rb : (l_pac<<1) - 1 - r[1]->a[0].rb;
		if (pos[0] < pos[1]) dir = (r[0]->a[0].rb >= l_pac)<<1 | (r[1]->a[0].rb >= l_pac);
		else dir = (r[1]->a[0].rb >= l_pac)<<1 | (r[0]->a[0].rb >= l_pac);
		is = abs(pos[0] - pos[1]);
		if (is <= opt->max_ins) kv_push(uint64_t, isize[dir], is);
	}
	if (mem_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n);
	for (d = 0; d < 4; ++d) { // TODO: this block is nearly identical to the one in bwtsw2_pair.c. It would be better to merge these two.
		mem_pestat_t *r = &pes[d];
		uint64_v *q = &isize[d];
		int p25, p50, p75, x;
		if (q->n < MIN_DIR_CNT) {
			fprintf(stderr, "[M::%s] skip orientation %c%c as there are not enough pairs\n", __func__, "FR"[d>>1&1], "FR"[d&1]);
			r->failed = 1;
			continue;
		} else fprintf(stderr, "[M::%s] analyzing insert size distribution for orientation %c%c...\n", __func__, "FR"[d>>1&1], "FR"[d&1]);
		ks_introsort_64(q->n, q->a);
		p25 = q->a[(int)(.25 * q->n + .499)];
		p50 = q->a[(int)(.50 * q->n + .499)];
		p75 = q->a[(int)(.75 * q->n + .499)];
		r->low  = (int)(p25 - OUTLIER_BOUND * (p75 - p25) + .499);
		if (r->low < 1) r->low = 1;
		r->high = (int)(p75 + OUTLIER_BOUND * (p75 - p25) + .499);
		fprintf(stderr, "[M::%s] (25, 50, 75) percentile: (%d, %d, %d)\n", __func__, p25, p50, p75);
		fprintf(stderr, "[M::%s] low and high boundaries for computing mean and std.dev: (%d, %d)\n", __func__, r->low, r->high);
		for (i = x = 0, r->avg = 0; i < q->n; ++i)
			if (q->a[i] >= r->low && q->a[i] <= r->high)
				r->avg += q->a[i], ++x;
		r->avg /= x;
		for (i = 0, r->std = 0; i < q->n; ++i)
			if (q->a[i] >= r->low && q->a[i] <= r->high)
				r->std += (q->a[i] - r->avg) * (q->a[i] - r->avg);
		r->std = sqrt(r->std / x);
		fprintf(stderr, "[M::%s] mean and std.dev: (%.2f, %.2f)\n", __func__, r->avg, r->std);
		r->low  = (int)(p25 - MAPPING_BOUND * (p75 - p25) + .499);
		r->high = (int)(p75 + MAPPING_BOUND * (p75 - p25) + .499);
		if (r->low  > r->avg - MAX_STDDEV * r->std) r->low  = (int)(r->avg - MAX_STDDEV * r->std + .499);
		if (r->high < r->avg - MAX_STDDEV * r->std) r->high = (int)(r->avg + MAX_STDDEV * r->std + .499);
		if (r->low < 1) r->low = 1;
		fprintf(stderr, "[M::%s] low and high boundaries for proper pairs: (%d, %d)\n", __func__, r->low, r->high);
		free(q->a);
	}
	for (d = 0, max = 0; d < 4; ++d)
		max = max > isize[d].n? max : isize[d].n;
	for (d = 0; d < 4; ++d)
		if (pes[d].failed == 0 && isize[d].n < max * MIN_DIR_RATIO) {
			pes[d].failed = 1;
			fprintf(stderr, "[M::%s] skip orientation %c%c\n", __func__, "FR"[d>>1&1], "FR"[d&1]);
		}
}

void mem_pair(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_pestat_t pes[4], bseq1_t s[2], mem_alnreg_v a[2], bwahit_t h[2])
{
	pair64_v v;
	pair64_t o, subo; // score<<32 | raw_score<<8 | hash
	int r, i, y[4]; // y[] keeps the last hit
	kv_init(v);
	for (r = 0; r < 2; ++r) { // loop through read number
		for (i = 0; i < a[r].n; ++i) {
			pair64_t key;
			mem_alnreg_t *e = &a[r].a[i];
			key.x = e->rb < bns->l_pac? e->rb : (bns->l_pac<<1) - 1 - e->rb; // forward position
			key.y = (uint64_t)e->score << 32 | i << 2 | (e->rb >= bns->l_pac)<<1 | r;
			kv_push(pair64_t, v, key);
		}
	}
	ks_introsort_128(v.n, v.a);
	y[0] = y[1] = y[2] = y[3] = -1;
	o.x = o.y = subo.x = subo.y = 0;
	for (i = 0; i < v.n; ++i) {
		for (r = 0; r < 2; ++r) { // loop through direction
			int dir = r<<1 | (v.a[i].y>>1&1), which, k;
			if (pes[dir].failed) continue; // invalid orientation
			which = r<<1 | ((v.a[i].y&1)^1);
			if (y[which] < 0) continue; // no previous hits
			for (k = y[which]; k >= 0; --k) { // TODO: this is a O(n^2) solution in the worst case; remember to check if this loop takes a lot of time (I doubt)
				int64_t dist;
				int raw_score, score;
				double ns;
				uint64_t x, pair;
				if ((v.a[k].y&3) != which) continue;
				dist = (int64_t)v.a[i].x - v.a[k].x;
				if (dist > pes[dir].high) break;
				if (dist < pes[dir].low)  continue;
				raw_score = (v.a[i].y>>32) + (v.a[i].y>>32);
				if (raw_score + 20 * opt->a < (subo.x>>8&0xffffff)) continue; // skip the following if the score is too small
				ns = (dist - pes[dir].avg) / pes[dir].std;
				score = (int)(23. * raw_score / (opt->a + opt->b) - 4.343 * log(.5 * erfc(fabs(ns) * M_SQRT1_2)) + .499);
				pair = (uint64_t)k<<32 | i;
				x = (uint64_t)score<<32 | (int64_t)raw_score<<8 | (hash_64(pair)&0xff);
				if (x > o.x) subo = o, o.x = x, o.y = pair;
				else if (x > subo.x) subo.x = x, subo.y = pair;
			}
		}
		y[v.a[i].y&3] = i;
	}
	free(v.a);
}

void mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_pestat_t pes[4], bseq1_t s[2], mem_alnreg_v a[2])
{
	kstring_t str;
	bwahit_t h[2];
	str.l = str.m = 0; str.s = 0;
	mem_pair(opt, bns, pac, pes, s, a, h);
	/*
	bwa_hit2sam(&str, opt->mat, opt->q, opt->r, opt->w, bns, pac, &s[0], &h[0], opt->is_hard);
	s[0].sam = strdup(str.s); str.l = 0;
	bwa_hit2sam(&str, opt->mat, opt->q, opt->r, opt->w, bns, pac, &s[1], &h[1], opt->is_hard);
	s[1].sam = str.s;
	*/
}