fast-bwa/bwamem.c

#include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include <assert.h>
#include <math.h>
#ifdef HAVE_PTHREAD
#include <pthread.h>
#endif

#include "kstring.h"
#include "bwamem.h"
#include "bntseq.h"
#include "ksw.h"
#include "kvec.h"
#include "ksort.h"
#include "utils.h"

/* Theory on probability and scoring *ungapped* alignment
 *
 * s'(a,b) = log[P(b|a)/P(b)] = log[4P(b|a)], assuming uniform base distribution
 * s'(a,a) = log(4), s'(a,b) = log(4e/3), where e is the error rate
 *
 * Scale s'(a,b) to s(a,a) s.t. s(a,a)=x. Then s(a,b) = x*s'(a,b)/log(4), or conversely: s'(a,b)=s(a,b)*log(4)/x
 *
 * If the matching score is x and mismatch penalty is -y, we can compute error rate e:
 *   e = .75 * exp[-log(4) * y/x]
 *
 * log P(seq) = \sum_i log P(b_i|a_i) = \sum_i {s'(a,b) - log(4)}
 *   = \sum_i { s(a,b)*log(4)/x - log(4) } = log(4) * (S/x - l)
 *
 * where S=\sum_i s(a,b) is the alignment score. Converting to the phred scale:
 *   Q(seq) = -10/log(10) * log P(seq) = 10*log(4)/log(10) * (l - S/x) = 6.02 * (l - S/x)
 *
 *
 * Gap open (zero gap): q' = log[P(gap-open)], r' = log[P(gap-ext)] (see Durbin et al. (1998) Section 4.1)
 * Then q = x*log[P(gap-open)]/log(4), r = x*log[P(gap-ext)]/log(4)
 *
 * When there are gaps, l should be the length of alignment matches (i.e. the M operator in CIGAR)
 */

mem_opt_t *mem_opt_init()
{
	mem_opt_t *o;
	o = calloc(1, sizeof(mem_opt_t));
	o->flag = 0;
	o->a = 1; o->b = 4; o->q = 6; o->r = 1; o->w = 100;
	o->pen_unpaired = 9;
	o->pen_clip = 5;
	o->min_seed_len = 19;
	o->split_width = 10;
	o->max_occ = 10000;
	o->max_chain_gap = 10000;
	o->max_ins = 10000;
	o->mask_level = 0.50;
	o->chain_drop_ratio = 0.50;
	o->split_factor = 1.5;
	o->chunk_size = 10000000;
	o->n_threads = 1;
	o->max_matesw = 100;
	mem_fill_scmat(o->a, o->b, o->mat);
	return o;
}

void mem_fill_scmat(int a, int b, int8_t mat[25])
{
	int i, j, k;
	for (i = k = 0; i < 4; ++i) {
		for (j = 0; j < 4; ++j)
			mat[k++] = i == j? a : -b;
		mat[k++] = 0; // ambiguous base
	}
	for (j = 0; j < 5; ++j) mat[k++] = 0;
}

/***************************
 * SMEM iterator interface *
 ***************************/

struct __smem_i {
	const bwt_t *bwt;
	const uint8_t *query;
	int start, len;
	bwtintv_v *matches; // matches; to be returned by smem_next()
	bwtintv_v *sub;     // sub-matches inside the longest match; temporary
	bwtintv_v *tmpvec[2]; // temporary arrays
};

smem_i *smem_itr_init(const bwt_t *bwt)
{
	smem_i *itr;
	itr = calloc(1, sizeof(smem_i));
	itr->bwt = bwt;
	itr->tmpvec[0] = calloc(1, sizeof(bwtintv_v));
	itr->tmpvec[1] = calloc(1, sizeof(bwtintv_v));
	itr->matches   = calloc(1, sizeof(bwtintv_v));
	itr->sub       = calloc(1, sizeof(bwtintv_v));
	return itr;
}

void smem_itr_destroy(smem_i *itr)
{
	free(itr->tmpvec[0]->a); free(itr->tmpvec[0]);
	free(itr->tmpvec[1]->a); free(itr->tmpvec[1]);
	free(itr->matches->a);   free(itr->matches);
	free(itr->sub->a);       free(itr->sub);
	free(itr);
}

void smem_set_query(smem_i *itr, int len, const uint8_t *query)
{
	itr->query = query;
	itr->start = 0;
	itr->len = len;
}

const bwtintv_v *smem_next(smem_i *itr, int split_len, int split_width)
{
	int i, max, max_i, ori_start;
	itr->tmpvec[0]->n = itr->tmpvec[1]->n = itr->matches->n = itr->sub->n = 0;
	if (itr->start >= itr->len || itr->start < 0) return 0;
	while (itr->start < itr->len && itr->query[itr->start] > 3) ++itr->start; // skip ambiguous bases
	if (itr->start == itr->len) return 0;
	ori_start = itr->start;
	itr->start = bwt_smem1(itr->bwt, itr->len, itr->query, ori_start, 1, itr->matches, itr->tmpvec); // search for SMEM
	if (itr->matches->n == 0) return itr->matches; // well, in theory, we should never come here
	for (i = max = 0, max_i = 0; i < itr->matches->n; ++i) { // look for the longest match
		bwtintv_t *p = &itr->matches->a[i];
		int len = (uint32_t)p->info - (p->info>>32);
		if (max < len) max = len, max_i = i;
	}
	if (split_len > 0 && max >= split_len && itr->matches->a[max_i].x[2] <= split_width) { // if the longest SMEM is unique and long
		int j;
		bwtintv_v *a = itr->tmpvec[0]; // reuse tmpvec[0] for merging
		bwtintv_t *p = &itr->matches->a[max_i];
		bwt_smem1(itr->bwt, itr->len, itr->query, ((uint32_t)p->info + (p->info>>32))>>1, itr->matches->a[max_i].x[2]+1, itr->sub, itr->tmpvec); // starting from the middle of the longest MEM
		i = j = 0; a->n = 0;
		while (i < itr->matches->n && j < itr->sub->n) { // ordered merge
			int64_t xi = itr->matches->a[i].info>>32<<32 | (itr->len - (uint32_t)itr->matches->a[i].info);
			int64_t xj = itr->sub->a[j].info>>32<<32 | (itr->len - (uint32_t)itr->sub->a[j].info);
			if (xi < xj) {
				kv_push(bwtintv_t, *a, itr->matches->a[i]);
				++i;
			} else if ((uint32_t)itr->sub->a[j].info - (itr->sub->a[j].info>>32) >= max>>1 && (uint32_t)itr->sub->a[j].info > ori_start) {
				kv_push(bwtintv_t, *a, itr->sub->a[j]);
				++j;
			} else ++j;
		}
		for (; i < itr->matches->n; ++i) kv_push(bwtintv_t, *a, itr->matches->a[i]);
		for (; j < itr->sub->n; ++j)
			if ((uint32_t)itr->sub->a[j].info - (itr->sub->a[j].info>>32) >= max>>1 && (uint32_t)itr->sub->a[j].info > ori_start)
				kv_push(bwtintv_t, *a, itr->sub->a[j]);
		kv_copy(bwtintv_t, *itr->matches, *a);
	}
	return itr->matches;
}

/********************************
 * Chaining while finding SMEMs *
 ********************************/

typedef struct {
	int64_t rbeg;
	int32_t qbeg, len;
} mem_seed_t;

typedef struct {
	int n, m;
	int64_t pos;
	mem_seed_t *seeds;
} mem_chain_t;

typedef struct { size_t n, m; mem_chain_t *a;  } mem_chain_v;

#include "kbtree.h"

#define chain_cmp(a, b) (((b).pos < (a).pos) - ((a).pos < (b).pos))
KBTREE_INIT(chn, mem_chain_t, chain_cmp)

static int test_and_merge(const mem_opt_t *opt, mem_chain_t *c, const mem_seed_t *p)
{
	int64_t qend, rend, x, y;
	const mem_seed_t *last = &c->seeds[c->n-1];
	qend = last->qbeg + last->len;
	rend = last->rbeg + last->len;
	if (p->qbeg >= c->seeds[0].qbeg && p->qbeg + p->len <= qend && p->rbeg >= c->seeds[0].rbeg && p->rbeg + p->len <= rend)
		return 1; // contained seed; do nothing
	x = p->qbeg - last->qbeg; // always non-negtive
	y = p->rbeg - last->rbeg;
	if (y >= 0 && x - y <= opt->w && y - x <= opt->w && x - last->len < opt->max_chain_gap && y - last->len < opt->max_chain_gap) { // grow the chain
		if (c->n == c->m) {
			c->m <<= 1;
			c->seeds = realloc(c->seeds, c->m * sizeof(mem_seed_t));
		}
		c->seeds[c->n++] = *p;
		return 1;
	}
	return 0; // request to add a new chain
}

static void mem_insert_seed(const mem_opt_t *opt, kbtree_t(chn) *tree, smem_i *itr)
{
	const bwtintv_v *a;
	int split_len = (int)(opt->min_seed_len * opt->split_factor + .499);
	split_len = split_len < itr->len? split_len : itr->len;
	while ((a = smem_next(itr, split_len, opt->split_width)) != 0) { // to find all SMEM and some internal MEM
		int i;
		for (i = 0; i < a->n; ++i) { // go through each SMEM/MEM up to itr->start
			bwtintv_t *p = &a->a[i];
			int slen = (uint32_t)p->info - (p->info>>32); // seed length
			int64_t k;
			if (slen < opt->min_seed_len || p->x[2] > opt->max_occ) continue; // ignore if too short or too repetitive
			for (k = 0; k < p->x[2]; ++k) {
				mem_chain_t tmp, *lower, *upper;
				mem_seed_t s;
				int to_add = 0;
				s.rbeg = tmp.pos = bwt_sa(itr->bwt, p->x[0] + k); // this is the base coordinate in the forward-reverse reference
				s.qbeg = p->info>>32;
				s.len  = slen;
				if (kb_size(tree)) {
					kb_intervalp(chn, tree, &tmp, &lower, &upper); // find the closest chain
					if (!lower || !test_and_merge(opt, lower, &s)) to_add = 1;
				} else to_add = 1;
				if (to_add) { // add the seed as a new chain
					tmp.n = 1; tmp.m = 4;
					tmp.seeds = calloc(tmp.m, sizeof(mem_seed_t));
					tmp.seeds[0] = s;
					kb_putp(chn, tree, &tmp);
				}
			}
		}
	}
}

void mem_print_chain(const bntseq_t *bns, mem_chain_v *chn)
{
	int i, j;
	for (i = 0; i < chn->n; ++i) {
		mem_chain_t *p = &chn->a[i];
		printf("%d", p->n);
		for (j = 0; j < p->n; ++j) {
			bwtint_t pos;
			int is_rev, ref_id;
			pos = bns_depos(bns, p->seeds[j].rbeg, &is_rev);
			if (is_rev) pos -= p->seeds[j].len - 1;
			bns_cnt_ambi(bns, pos, p->seeds[j].len, &ref_id);
			printf("\t%d,%d,%ld(%s:%c%ld)", p->seeds[j].len, p->seeds[j].qbeg, (long)p->seeds[j].rbeg, bns->anns[ref_id].name, "+-"[is_rev], (long)(pos - bns->anns[ref_id].offset) + 1);
		}
		putchar('\n');
	}
}

mem_chain_v mem_chain(const mem_opt_t *opt, const bwt_t *bwt, int len, const uint8_t *seq)
{
	mem_chain_v chain;
	smem_i *itr;
	kbtree_t(chn) *tree;

	kv_init(chain);
	if (len < opt->min_seed_len) return chain; // if the query is shorter than the seed length, no match
	tree = kb_init(chn, KB_DEFAULT_SIZE);
	itr = smem_itr_init(bwt);
	smem_set_query(itr, len, seq);
	mem_insert_seed(opt, tree, itr);

	kv_resize(mem_chain_t, chain, kb_size(tree));

	#define traverse_func(p_) (chain.a[chain.n++] = *(p_))
	__kb_traverse(mem_chain_t, tree, traverse_func);
	#undef traverse_func

	smem_itr_destroy(itr);
	kb_destroy(chn, tree);
	return chain;
}

/********************
 * Filtering chains *
 ********************/

typedef struct {
	int beg, end, w;
	void *p, *p2;
} flt_aux_t;

#define flt_lt(a, b) ((a).w > (b).w)
KSORT_INIT(mem_flt, flt_aux_t, flt_lt)

int mem_chain_flt(const mem_opt_t *opt, int n_chn, mem_chain_t *chains)
{
	flt_aux_t *a;
	int i, j, n;
	if (n_chn <= 1) return n_chn; // no need to filter
	a = malloc(sizeof(flt_aux_t) * n_chn);
	for (i = 0; i < n_chn; ++i) {
		mem_chain_t *c = &chains[i];
		int64_t end;
		int w = 0, tmp;
		for (j = 0, end = 0; j < c->n; ++j) {
			const mem_seed_t *s = &c->seeds[j];
			if (s->qbeg >= end) w += s->len;
			else if (s->qbeg + s->len > end) w += s->qbeg + s->len - end;
			end = end > s->qbeg + s->len? end : s->qbeg + s->len;
		}
		tmp = w;
		for (j = 0, end = 0; j < c->n; ++j) {
			const mem_seed_t *s = &c->seeds[j];
			if (s->rbeg >= end) w += s->len;
			else if (s->rbeg + s->len > end) w += s->rbeg + s->len - end;
			end = end > s->qbeg + s->len? end : s->qbeg + s->len;
		}
		w = w < tmp? w : tmp;
		a[i].beg = c->seeds[0].qbeg;
		a[i].end = c->seeds[c->n-1].qbeg + c->seeds[c->n-1].len;
		a[i].w = w; a[i].p = c; a[i].p2 = 0;
	}
	ks_introsort(mem_flt, n_chn, a);
	{ // reorder chains such that the best chain appears first
		mem_chain_t *swap;
		swap = malloc(sizeof(mem_chain_t) * n_chn);
		for (i = 0; i < n_chn; ++i) {
			swap[i] = *((mem_chain_t*)a[i].p);
			a[i].p = &chains[i]; // as we will memcpy() below, a[i].p is changed
		}
		memcpy(chains, swap, sizeof(mem_chain_t) * n_chn);
		free(swap);
	}
	for (i = 1, n = 1; i < n_chn; ++i) {
		for (j = 0; j < n; ++j) {
			int b_max = a[j].beg > a[i].beg? a[j].beg : a[i].beg;
			int e_min = a[j].end < a[i].end? a[j].end : a[i].end;
			if (e_min > b_max) { // have overlap
				int min_l = a[i].end - a[i].beg < a[j].end - a[j].beg? a[i].end - a[i].beg : a[j].end - a[j].beg;
				if (e_min - b_max >= min_l * opt->mask_level) { // significant overlap
					if (a[j].p2 == 0) a[j].p2 = a[i].p;
					if (a[i].w < a[j].w * opt->chain_drop_ratio && a[j].w - a[i].w >= opt->min_seed_len<<1)
						break;
				}
			}
		}
		if (j == n) a[n++] = a[i]; // if have no significant overlap with better chains, keep it.
	}
	for (i = 0; i < n; ++i) { // mark chains to be kept
		mem_chain_t *c = (mem_chain_t*)a[i].p;
		if (c->n > 0) c->n = -c->n;
		c = (mem_chain_t*)a[i].p2;
		if (c && c->n > 0) c->n = -c->n;
	}
	free(a);
	for (i = 0; i < n_chn; ++i) { // free discarded chains
		mem_chain_t *c = &chains[i];
		if (c->n >= 0) {
			free(c->seeds);
			c->n = c->m = 0;
		} else c->n = -c->n;
	}
	for (i = n = 0; i < n_chn; ++i) { // squeeze out discarded chains
		if (chains[i].n > 0) {
			if (n != i) chains[n++] = chains[i];
			else ++n;
		}
	}
	return n;
}

/******************************
 * De-overlap single-end hits *
 ******************************/

#define alnreg_slt(a, b) ((a).score > (b).score || ((a).score == (b).score && ((a).rb < (b).rb || ((a).rb == (b).rb && (a).qb < (b).qb))))
KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt)

int mem_sort_and_dedup(int n, mem_alnreg_t *a)
{
	int m, i;
	if (n <= 1) return n;
	ks_introsort(mem_ars, n, a);
	for (i = 1; i < n; ++i) { // mark identical hits
		if (a[i].score == a[i-1].score && a[i].rb == a[i-1].rb && a[i].qb == a[i-1].qb)
			a[i].qe = a[i].qb;
	}
	for (i = 1, m = 1; i < n; ++i) // exclude identical hits
		if (a[i].qe > a[i].qb) {
			if (m != i) a[m++] = a[i];
			else ++m;
		}
	return m;
}

void mem_mark_primary_se(const mem_opt_t *opt, int n, mem_alnreg_t *a) // IMPORTANT: must run mem_sort_and_dedup() before calling this function
{ // similar to the loop in mem_chain_flt()
	int i, k, tmp;
	kvec_t(int) z;
	if (n == 0) return;
	kv_init(z);
	for (i = 0; i < n; ++i) a[i].sub = 0, a[i].secondary = -1;
	tmp = opt->a + opt->b > opt->q + opt->r? opt->a + opt->b : opt->q + opt->r;
	kv_push(int, z, 0);
	for (i = 1; i < n; ++i) {
		for (k = 0; k < z.n; ++k) {
			int j = z.a[k];
			int b_max = a[j].qb > a[i].qb? a[j].qb : a[i].qb;
			int e_min = a[j].qe < a[i].qe? a[j].qe : a[i].qe;
			if (e_min > b_max) { // have overlap
				int min_l = a[i].qe - a[i].qb < a[j].qe - a[j].qb? a[i].qe - a[i].qb : a[j].qe - a[j].qb;
				if (e_min - b_max >= min_l * opt->mask_level) { // significant overlap
					if (a[j].sub == 0) a[j].sub = a[i].score;
					if (a[j].score - a[i].score <= tmp) ++a[j].sub_n;
					break;
				}
			}
		}
		if (k == z.n) kv_push(int, z, i);
		else a[i].secondary = z.a[k];
	}
	free(z.a);
}

/****************************************
 * Construct the alignment from a chain *
 ****************************************/

static inline int cal_max_gap(const mem_opt_t *opt, int qlen)
{
	int l = (int)((double)(qlen * opt->a - opt->q) / opt->r + 1.);
	l = l > 1? l : 1;
	return l < opt->w<<1? l : opt->w<<1;
}

void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain_t *c, mem_alnreg_v *av)
{ // FIXME: in general, we SHOULD check funny seed patterns such as contained seeds. When that happens, we should use a SW or extend more seeds
	int i, k;
	int64_t rlen, rmax[2], tmp, max = 0;
	const mem_seed_t *s;
	uint8_t *rseq = 0;
	uint64_t *srt;

	if (c->n == 0) return;
	// get the max possible span
	rmax[0] = l_pac<<1; rmax[1] = 0;
	for (i = 0; i < c->n; ++i) {
		int64_t b, e;
		const mem_seed_t *t = &c->seeds[i];
		b = t->rbeg - (t->qbeg + cal_max_gap(opt, t->qbeg));
		e = t->rbeg + t->len + ((l_query - t->qbeg - t->len) + cal_max_gap(opt, l_query - t->qbeg - t->len));
		rmax[0] = rmax[0] < b? rmax[0] : b;
		rmax[1] = rmax[1] > e? rmax[1] : e;
		if (t->len > max) max = t->len;
	}
	rmax[0] = rmax[0] > 0? rmax[0] : 0;
	rmax[1] = rmax[1] < l_pac<<1? rmax[1] : l_pac<<1;
	if (rmax[0] < l_pac && l_pac < rmax[1]) { // crossing the forward-reverse boundary; then choose one side
		if (l_pac - rmax[0] > rmax[1] - l_pac) rmax[1] = l_pac;
		else rmax[0] = l_pac;
	}
	// retrieve the reference sequence
	rseq = bns_get_seq(l_pac, pac, rmax[0], rmax[1], &rlen);
	if (rlen != rmax[1] - rmax[0]) return;

	srt = malloc(c->n * 8);
	for (i = 0; i < c->n; ++i)
		srt[i] = (uint64_t)c->seeds[i].len<<32 | i;
	ks_introsort_64(c->n, srt);

	for (k = c->n - 1; k >= 0; --k) {
		mem_alnreg_t *a;
		s = &c->seeds[(uint32_t)srt[k]];

		for (i = 0; i < av->n; ++i) { // test whether extension has been made before
			mem_alnreg_t *p = &av->a[i];
			int64_t rd;
			int qd, w, max_gap;
			if (s->rbeg < p->rb || s->rbeg + s->len > p->re || s->qbeg < p->qb || s->qbeg + s->len > p->qe) continue; // not fully contained
			// qd: distance ahead of the seed on query; rd: on reference
			qd = s->qbeg - p->qb; rd = s->rbeg - p->rb;
			max_gap = cal_max_gap(opt, qd < rd? qd : rd); // the maximal gap allowed in regions ahead of the seed
			w = max_gap < opt->w? max_gap : opt->w; // bounded by the band width
			if (qd - rd < w && rd - qd < w) break; // the seed is "around" a previous hit
			// similar to the previous four lines, but this time we look at the region behind
			qd = p->qe - (s->qbeg + s->len); rd = p->re - (s->rbeg + s->len);
			max_gap = cal_max_gap(opt, qd < rd? qd : rd);
			w = max_gap < opt->w? max_gap : opt->w;
			if (qd - rd < w && rd - qd < w) break;
		}
		if (i < av->n) continue;

		a = kv_pushp(mem_alnreg_t, *av);
		memset(a, 0, sizeof(mem_alnreg_t));

		if (s->qbeg) { // left extension
			uint8_t *rs, *qs;
			int qle, tle, gtle, gscore;
			qs = malloc(s->qbeg);
			for (i = 0; i < s->qbeg; ++i) qs[i] = query[s->qbeg - 1 - i];
			tmp = s->rbeg - rmax[0];
			rs = malloc(tmp);
			for (i = 0; i < tmp; ++i) rs[i] = rseq[tmp - 1 - i];
			a->score = ksw_extend(s->qbeg, qs, tmp, rs, 5, opt->mat, opt->q, opt->r, opt->w, s->len * opt->a, &qle, &tle, &gtle, &gscore);
			// check whether we prefer to reach the end of the query
			if (gscore <= 0 || gscore <= a->score - opt->pen_clip) a->qb = s->qbeg - qle, a->rb = s->rbeg - tle; // local hits
			else a->qb = 0, a->rb = s->rbeg - gtle; // reach the end
			free(qs); free(rs);
		} else a->score = s->len * opt->a, a->qb = 0, a->rb = s->rbeg;

		if (s->qbeg + s->len != l_query) { // right extension
			int qle, tle, qe, re, gtle, gscore;
			qe = s->qbeg + s->len;
			re = s->rbeg + s->len - rmax[0];
			a->score = ksw_extend(l_query - qe, query + qe, rmax[1] - rmax[0] - re, rseq + re, 5, opt->mat, opt->q, opt->r, opt->w, a->score, &qle, &tle, &gtle, &gscore);
			// similar to the above
			if (gscore <= 0 || gscore <= a->score - opt->pen_clip) a->qe = qe + qle, a->re = rmax[0] + re + tle;
			else a->qe = l_query, a->re = rmax[0] + re + gtle;
		} else a->qe = l_query, a->re = s->rbeg + s->len;
		if (bwa_verbose >= 4) printf("[%d] score=%d\t[%d,%d) <=> [%ld,%ld)\n", k, a->score, a->qb, a->qe, (long)a->rb, (long)a->re);

		// compute seedcov
		for (i = 0, a->seedcov = 0; i < c->n; ++i) {
			const mem_seed_t *t = &c->seeds[i];
			if (t->qbeg >= a->qb && t->qbeg + t->len <= a->qe && t->rbeg >= a->rb && t->rbeg + t->len <= a->re) // seed fully contained
				a->seedcov += t->len; // this is not very accurate, but for approx. mapQ, this is good enough
		}
	}
	free(srt); free(rseq);
}

/*****************************
 * Basic hit->SAM conversion *
 *****************************/

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, const bwahit_t *p_, int is_hard, const bwahit_t *m)
{
#define is_mapped(x) ((x)->rb >= 0 && (x)->rb < (x)->re && (x)->re <= bns->l_pac<<1)
	int score, n_cigar, is_rev = 0, rid, mid, copy_mate = 0, NM = -1;
	uint32_t *cigar = 0;
	int64_t pos;
	bwahit_t ptmp, *p = &ptmp;

	if (!p_) { // in this case, generate an unmapped alignment
		memset(&ptmp, 0, sizeof(bwahit_t));
		ptmp.rb = ptmp.re = -1;
	} else ptmp = *p_;
	p->flag |= m? 1 : 0; // is paired in sequencing
	p->flag |= !is_mapped(p)? 4 : 0; // is mapped
	p->flag |= m && !is_mapped(m)? 8 : 0; // is mate mapped
	if (m && !is_mapped(p) && is_mapped(m)) {
		p->rb = m->rb; p->re = m->re; p->qb = 0; p->qe = s->l_seq;
		copy_mate = 1;
	}
	p->flag |= p->rb >= bns->l_pac? 0x10 : 0; // is reverse strand
	p->flag |= m && m->rb >= bns->l_pac? 0x20 : 0; // is mate on reverse strand
	kputs(s->name, str); kputc('\t', str);
	if (is_mapped(p)) { // has a coordinate, no matter whether it is mapped or copied from the mate
		int sam_flag = p->flag&0xff; // the flag that will be outputed to SAM; it is not always the same as p->flag
		if (p->flag&0x10000) sam_flag |= 0x100;
		if (!copy_mate) {
			cigar = bwa_gen_cigar(mat, q, r, w, bns->l_pac, pac, p->qe - p->qb, (uint8_t*)&s->seq[p->qb], p->rb, p->re, &score, &n_cigar, &NM);
			p->flag |= n_cigar == 0? 4 : 0; // FIXME: check why this may happen (this has already happened)
		} else n_cigar = 0, cigar = 0;
		pos = bns_depos(bns, p->rb < bns->l_pac? p->rb : p->re - 1, &is_rev);
		bns_cnt_ambi(bns, pos, p->re - p->rb, &rid);
		kputw(sam_flag, str); kputc('\t', str);
		kputs(bns->anns[rid].name, str); kputc('\t', str); kputuw(pos - bns->anns[rid].offset + 1, str); kputc('\t', str);
		kputw(p->qual, str); kputc('\t', str);
		if (n_cigar) {
			int i, clip5, clip3;
			clip5 = is_rev? s->l_seq - p->qe : p->qb;
			clip3 = is_rev? p->qb : s->l_seq - p->qe;
			if (clip5) { kputw(clip5, str); kputc("SH"[(is_hard!=0)], str); }
			for (i = 0; i < n_cigar; ++i) {
				kputw(cigar[i]>>4, str); kputc("MIDSH"[cigar[i]&0xf], str);
			}
			if (clip3) { kputw(clip3, str); kputc("SH"[(is_hard!=0)], str); }
		} else kputc('*', str);
	} else { // no coordinate
		kputw(p->flag, str);
		kputs("\t*\t0\t0\t*", str);
		rid = -1;
	}
	if (m && is_mapped(m)) { // then print mate pos and isize
		pos = bns_depos(bns, m->rb < bns->l_pac? m->rb : m->re - 1, &is_rev);
		bns_cnt_ambi(bns, pos, m->re - m->rb, &mid);
		kputc('\t', str);
		if (mid == rid) kputc('=', str);
		else kputs(bns->anns[mid].name, str);
		kputc('\t', str); kputuw(pos - bns->anns[mid].offset + 1, str);
		kputc('\t', str);
		if (mid == rid) {
			int64_t p0 = p->rb < bns->l_pac? p->rb : (bns->l_pac<<1) - 1 - p->rb;
			int64_t p1 = m->rb < bns->l_pac? m->rb : (bns->l_pac<<1) - 1 - m->rb;
			kputw(p0 - p1 + (p0 > p1? 1 : -1), str);
		} else kputw(0, str);
		kputc('\t', str);
	} else kputsn("\t*\t0\t0\t", 7, str);
	if (p->flag&0x100) { // for secondary alignments, don't write SEQ and QUAL
		kputsn("*\t*", 3, str);
	} else if (!(p->flag&0x10)) { // print SEQ and QUAL, the forward strand
		int i, qb = 0, qe = s->l_seq;
		if (!(p->flag&4) && is_hard) qb = p->qb, qe = p->qe;
		ks_resize(str, str->l + (qe - qb) + 1);
		for (i = qb; i < qe; ++i) str->s[str->l++] = "ACGTN"[(int)s->seq[i]];
		kputc('\t', str);
		if (s->qual) { // printf qual
			ks_resize(str, str->l + (qe - qb) + 1);
			for (i = qb; i < qe; ++i) str->s[str->l++] = s->qual[i];
			str->s[str->l] = 0;
		} else kputc('*', str);
	} else { // the reverse strand
		int i, qb = 0, qe = s->l_seq;
		if (!(p->flag&4) && is_hard) qb = p->qb, qe = p->qe;
		ks_resize(str, str->l + (qe - qb) + 1);
		for (i = qe-1; i >= qb; --i) str->s[str->l++] = "TGCAN"[(int)s->seq[i]];
		kputc('\t', str);
		if (s->qual) { // printf qual
			ks_resize(str, str->l + (qe - qb) + 1);
			for (i = qe-1; i >= qb; --i) str->s[str->l++] = s->qual[i];
			str->s[str->l] = 0;
		} else kputc('*', str);
	}
	if (NM >= 0) { kputsn("\tNM:i:", 6, str); kputw(NM, str); }
	if (p->score >= 0) { kputsn("\tAS:i:", 6, str); kputw(p->score, str); }
	if (p->sub >= 0) { kputsn("\tXS:i:", 6, str); kputw(p->sub, str); }
	if (bwa_rg_id[0]) { kputsn("\tRG:Z:", 6, str); kputs(bwa_rg_id, str); }
	if (s->comment) { kputc('\t', str); kputs(s->comment, str); }
	kputc('\n', str);
	free(cigar);
#undef is_mapped
}

/************************
 * Integrated interface *
 ************************/

int mem_approx_mapq_se(const mem_opt_t *opt, const mem_alnreg_t *a)
{
	int mapq, l, sub = a->sub? a->sub : opt->min_seed_len * opt->a;
	double identity;
	sub = a->csub > sub? a->csub : sub;
	if (sub >= a->score) return 0;
	l = a->qe - a->qb > a->re - a->rb? a->qe - a->qb : a->re - a->rb;
	mapq = a->score? (int)(MEM_MAPQ_COEF * (1. - (double)sub / a->score) * log(a->seedcov) + .499) : 0;
	identity = 1. - (double)(l * opt->a - a->score) / (opt->a + opt->b) / l;
	mapq = identity < 0.95? (int)(mapq * identity * identity + .499) : mapq;
	if (a->sub_n > 0) mapq -= (int)(4.343 * log(a->sub_n+1) + .499);
	if (mapq > 60) mapq = 60;
	if (mapq < 0) mapq = 0;
	return mapq;
}

void mem_alnreg2hit(const mem_alnreg_t *a, bwahit_t *h)
{
	h->rb = a->rb; h->re = a->re; h->qb = a->qb; h->qe = a->qe;
	h->score = a->score;
	h->sub = a->secondary >= 0? -1 : a->sub > a->csub? a->sub : a->csub;
	h->qual = 0; // quality unset
	h->flag = a->secondary >= 0? 0x100 : 0; // only the "secondary" bit is set
}

void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const bwahit_t *m)
{
	int k;
	kstring_t str;
	str.l = str.m = 0; str.s = 0;
	if (a->n > 0) {
		int mapq0 = -1;
		for (k = 0; k < a->n; ++k) {
			bwahit_t h;
			mem_alnreg_t *p = &a->a[k];
			if (p->secondary >= 0 && !(opt->flag&MEM_F_ALL)) continue;
			if (p->secondary >= 0 && p->score < a->a[p->secondary].score * .5) continue;
			mem_alnreg2hit(p, &h);
			bwa_fix_xref(opt->mat, opt->q, opt->r, opt->w, bns, pac, (uint8_t*)s->seq, &h.qb, &h.qe, &h.rb, &h.re);
			h.flag |= extra_flag;
			if ((opt->flag&MEM_F_NO_MULTI) && k && p->secondary < 0) h.flag |= 0x10000; // print the sequence, but flag as secondary (for Picard)
			h.qual = p->secondary >= 0? 0 : mem_approx_mapq_se(opt, p);
			if (k == 0) mapq0 = h.qual;
			else if (h.qual > mapq0) h.qual = mapq0;
			bwa_hit2sam(&str, opt->mat, opt->q, opt->r, opt->w, bns, pac, s, &h, opt->flag&MEM_F_HARDCLIP, m);
		}
	} else bwa_hit2sam(&str, opt->mat, opt->q, opt->r, opt->w, bns, pac, s, 0, opt->flag&MEM_F_HARDCLIP, m);
	s->sam = str.s;
}

mem_alnreg_v mem_align1(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int l_seq, char *seq)
{
	int i;
	mem_chain_v chn;
	mem_alnreg_v regs;

	for (i = 0; i < l_seq; ++i) // convert to 2-bit encoding if we have not done so
		seq[i] = seq[i] < 4? seq[i] : nst_nt4_table[(int)seq[i]];

	chn = mem_chain(opt, bwt, l_seq, (uint8_t*)seq);
	chn.n = mem_chain_flt(opt, chn.n, chn.a);
	if (bwa_verbose >= 4) mem_print_chain(bns, &chn);

	kv_init(regs);
	for (i = 0; i < chn.n; ++i) {
		mem_chain_t *p = &chn.a[i];
		mem_chain2aln(opt, bns->l_pac, pac, l_seq, (uint8_t*)seq, p, &regs);
		free(chn.a[i].seeds);
	}
	free(chn.a);
	regs.n = mem_sort_and_dedup(regs.n, regs.a);
	return regs;
}

typedef struct {
	int start, step, n;
	const mem_opt_t *opt;
	const bwt_t *bwt;
	const bntseq_t *bns;
	const uint8_t *pac;
	const mem_pestat_t *pes;
	bseq1_t *seqs;
	mem_alnreg_v *regs;
} worker_t;

static void *worker1(void *data)
{
	worker_t *w = (worker_t*)data;
	int i;
	if (!(w->opt->flag&MEM_F_PE)) {
		for (i = w->start; i < w->n; i += w->step)
			w->regs[i] = mem_align1(w->opt, w->bwt, w->bns, w->pac, w->seqs[i].l_seq, w->seqs[i].seq);
	} else { // for PE we align the two ends in the same thread in case the 2nd read is of worse quality, in which case some threads may be faster/slower
		for (i = w->start; i < w->n>>1; i += w->step) {
			w->regs[i<<1|0] = mem_align1(w->opt, w->bwt, w->bns, w->pac, w->seqs[i<<1|0].l_seq, w->seqs[i<<1|0].seq);
			w->regs[i<<1|1] = mem_align1(w->opt, w->bwt, w->bns, w->pac, w->seqs[i<<1|1].l_seq, w->seqs[i<<1|1].seq);
		}
	}
	return 0;
}

static void *worker2(void *data)
{
	extern int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_pestat_t pes[4], uint64_t id, bseq1_t s[2], mem_alnreg_v a[2]);
	worker_t *w = (worker_t*)data;
	int i;
	if (!(w->opt->flag&MEM_F_PE)) {
		for (i = w->start; i < w->n; i += w->step) {
			mem_mark_primary_se(w->opt, w->regs[i].n, w->regs[i].a);
			mem_sam_se(w->opt, w->bns, w->pac, &w->seqs[i], &w->regs[i], 0, 0);
			free(w->regs[i].a);
		}
	} else {
		int n = 0;
		for (i = w->start; i < w->n>>1; i += w->step) { // not implemented yet
			n += mem_sam_pe(w->opt, w->bns, w->pac, w->pes, i, &w->seqs[i<<1], &w->regs[i<<1]);
			free(w->regs[i<<1|0].a); free(w->regs[i<<1|1].a);
		}
		fprintf(stderr, "[M::%s@%d] performed mate-SW for %d reads\n", __func__, w->start, n);
	}
	return 0;
}

void mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int n, bseq1_t *seqs)
{
	int i;
	worker_t *w;
	mem_alnreg_v *regs;
	mem_pestat_t pes[4];

	w = calloc(opt->n_threads, sizeof(worker_t));
	regs = malloc(n * sizeof(mem_alnreg_v));
	for (i = 0; i < opt->n_threads; ++i) {
		worker_t *p = &w[i];
		p->start = i; p->step = opt->n_threads; p->n = n;
		p->opt = opt; p->bwt = bwt; p->bns = bns; p->pac = pac;
		p->seqs = seqs; p->regs = regs;
		p->pes = &pes[0];
	}
#ifdef HAVE_PTHREAD
	if (opt->n_threads == 1) {
		worker1(w);
		if (opt->flag&MEM_F_PE) mem_pestat(opt, bns->l_pac, n, regs, pes);
		worker2(w);
	} else {
		pthread_t *tid;
		tid = (pthread_t*)calloc(opt->n_threads, sizeof(pthread_t));
		for (i = 0; i < opt->n_threads; ++i) pthread_create(&tid[i], 0, worker1, &w[i]);
		for (i = 0; i < opt->n_threads; ++i) pthread_join(tid[i], 0);
		if (opt->flag&MEM_F_PE) mem_pestat(opt, bns->l_pac, n, regs, pes);
		for (i = 0; i < opt->n_threads; ++i) pthread_create(&tid[i], 0, worker2, &w[i]);
		for (i = 0; i < opt->n_threads; ++i) pthread_join(tid[i], 0);
		free(tid);
	}
#else
	worker1(w);
	if (opt->flag&MEM_F_PE) mem_pestat(opt, bns->l_pac, n, regs, pes);
	worker2(w);
#endif
	for (i = 0; i < n; ++i) {
		fputs(seqs[i].sam, stdout);
		free(seqs[i].name); free(seqs[i].comment); free(seqs[i].seq); free(seqs[i].qual); free(seqs[i].sam);
	}
	free(regs); free(w);
}