backup

Makefile

@@ -3,7 +3,7 @@ CFLAGS=		-g -Wall -O2 -Wc++-compat -Wno-unused-function
 CPPFLAGS=	-DHAVE_KALLOC
 INCLUDES=	-I.
 OBJS=		kalloc.o kthread.o misc.o bseq.o sketch.o chain.o align.o sdust.o \
-			index.o format.o map.o ksw2_extz2_sse.o
+			index.o patch.o format.o map.o ksw2_extz2_sse.o
 PROG=		minimap2
 PROG_EXTRA=	sdust
 LIBS=		-lm -lz -lpthread
@@ -48,5 +48,6 @@ ksw2_extz2_sse.o: ksw2.h
 main.o: bseq.h minimap.h mmpriv.h
 map.o: kthread.h kvec.h kalloc.h sdust.h mmpriv.h minimap.h bseq.h
 misc.o: minimap.h ksort.h
+patch.o: mmpriv.h minimap.h bseq.h kalloc.h
 sdust.o: kalloc.h kdq.h kvec.h sdust.h
 sketch.o: kvec.h kalloc.h minimap.h

align.c

@@ -230,7 +230,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 			for (k = 0; k < ql; ++k) fputc("ACGTN"[qseq[k]], stderr); fputc('\n', stderr);
 			#endif
 			ksw_extz2_sse(km, qe - qs, qseq, re - rs, tseq, 5, mat, opt->q, opt->e, bw, opt->zdrop, KSW_EZ_APPROX_MAX, ez);
-			if (ez->zdropped || ez->score < 0 || mm_check_zdrop(qseq, tseq, ez->n_cigar, ez->cigar, mat, opt->q, opt->e, opt->zdrop))
+			if (mm_check_zdrop(qseq, tseq, ez->n_cigar, ez->cigar, mat, opt->q, opt->e, opt->zdrop))
 				ksw_extz2_sse(km, qe - qs, qseq, re - rs, tseq, 5, mat, opt->q, opt->e, bw, opt->zdrop, 0, ez);
 			if (ez->n_cigar > 0) {
 				mm_append_cigar(r, ez->n_cigar, ez->cigar);

chain.c

@@ -35,7 +35,7 @@ int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int
 	// fill the score and backtrack arrays
 	for (i = 0; i < n; ++i) {
 		uint64_t ri = a[i].x;
-		int32_t qi = (int32_t)a[i].y, q_span = a[i].y>>32;
+		int32_t qi = (int32_t)a[i].y, q_span = a[i].y>>32&0xff; // NB: only 8 bits of span is used!!!
 		int32_t max_f = -INT32_MAX, max_j = -1, n_skip = 0;
 		while (st < i && ri - a[st].x > max_dist) ++st;
 		for (j = i - 1; j >= st; --j) {

ksw2.h

@@ -8,10 +8,11 @@
 #define KSW_EZ_SCORE_ONLY  0x01 // don't record alignment path/cigar
 #define KSW_EZ_RIGHT       0x02 // right-align gaps
 #define KSW_EZ_GENERIC_SC  0x04 // without this flag: match/mismatch only; last symbol is a wildcard
-#define KSW_EZ_APPROX_MAX  0x08 // approximate max and Z-drop; this is faster
+#define KSW_EZ_APPROX_MAX  0x08 // approximate max; this is faster with sse
-#define KSW_EZ_DYN_BAND    0x10 // once used, ksw_extz_t::{mqe,mte} may be wrong
+#define KSW_EZ_APPROX_DROP 0x10 // approximate Z-drop; faster with sse
-#define KSW_EZ_EXTZ_ONLY   0x20 // only perform extension
+#define KSW_EZ_DYN_BAND    0x20 // once used, ksw_extz_t::{mqe,mte} may be wrong
-#define KSW_EZ_REV_CIGAR   0x40 // reverse CIGAR in the output
+#define KSW_EZ_EXTZ_ONLY   0x40 // only perform extension
+#define KSW_EZ_REV_CIGAR   0x80 // reverse CIGAR in the output
 
 typedef struct {
 	uint32_t max:31, zdropped:1;

ksw2_extz2_sse.c

@@ -295,7 +295,7 @@ void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 				} else {
 					++last_H0_t, H0 += u8[last_H0_t] - qe;
 				}
-				if (apply_zdrop(ez, H0, r, last_H0_t, zdrop, e)) break;
+				if ((flag & KSW_EZ_APPROX_DROP) && apply_zdrop(ez, H0, r, last_H0_t, zdrop, e)) break;
 			} else H0 = v8[0] - qe - qe, last_H0_t = 0;
 			if (r == qlen + tlen - 2 && en0 == tlen - 1)
 				ez->score = H0;

mmpriv.h

@@ -39,18 +39,17 @@ mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *m
 
 static inline void mm_reg_set_coor(mm_reg1_t *r, int32_t qlen, const mm128_t *a)
 {
-	int32_t k = r->as;
+	int32_t k = r->as, q_span = (int32_t)(a[k].y>>32&0xff);
 	r->rev = a[k].x>>63;
 	r->rid = a[k].x<<1>>33;
-	assert(r->rid != 0x7fffffff);
+	r->rs = (int32_t)a[k].x + 1 > q_span? (int32_t)a[k].x + 1 - q_span : 0; // NB: target span may be shorter, so this test is necessary
-	r->rs = (int32_t)a[k].x + 1 > (int32_t)(a[k].y>>32)? (int32_t)a[k].x + 1 - (int32_t)(a[k].y>>32) : 0;
 	r->re = (int32_t)a[k + r->cnt - 1].x + 1;
 	if (!r->rev) {
-		r->qs = (int32_t)a[k].y + 1 - (int32_t)(a[k].y>>32);
+		r->qs = (int32_t)a[k].y + 1 - q_span;
 		r->qe = (int32_t)a[k + r->cnt - 1].y + 1;
 	} else {
 		r->qs = qlen - ((int32_t)a[k + r->cnt - 1].y + 1);
-		r->qe = qlen - ((int32_t)a[k].y + 1 - (int32_t)(a[k].y>>32));
+		r->qe = qlen - ((int32_t)a[k].y + 1 - q_span);
 	}
 }
 

patch.c

@@ -0,0 +1,57 @@
+#include <string.h>
+#include <assert.h>
+#include "mmpriv.h"
+#include "kalloc.h"
+
+static int mm_squeeze_a_core(void *km, int n_regs, mm_reg1_t *regs, mm128_t *a, const uint64_t *aux)
+{ // squeeze out regions in a[] that are not referenced by regs[]
+	int i, as = 0;
+	for (i = 0; i < n_regs; ++i) {
+		mm_reg1_t *r = &regs[i];
+		if (r->as != as) {
+			memmove(&a[as], &a[r->as], r->cnt * 16);
+			r->as = as;
+		}
+		as += r->cnt;
+	}
+	return as;
+}
+
+void mm_join_long(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, int n_regs, mm_reg1_t *regs, mm128_t *a)
+{
+	int i, n_aux;
+	uint64_t *aux;
+
+	if (n_regs < 2) return; // nothing to join
+	aux = (uint64_t*)kmalloc(km, n_regs * 8);
+	for (i = n_aux = 0; i < n_regs; ++i)
+		aux[n_aux++] = (uint64_t)regs[i].as << 32 | i;
+	assert(n_aux == n_regs); // TODO: may be relaxed in future for other use cases
+	radix_sort_64(aux, aux + n_aux);
+	mm_squeeze_a_core(km, n_regs, regs, a, aux);
+
+	for (i = n_aux - 1; i >= 1; --i) {
+		mm_reg1_t *r0 = &regs[(int32_t)aux[i-1]], *r1 = &regs[(int32_t)aux[i]];
+		mm128_t *a0e, *a1s;
+		int max_gap, min_gap;
+
+		// test
+		if (r0->as + r0->cnt != r1->as) continue; // not adjacent in a[]
+		if (r0->rid != r1->rid || r0->rev != r1->rev) continue; // make sure on the same target and strand
+		if (r0->score < opt->min_join_flank_sc || r1->score < opt->min_join_flank_sc) continue; // require good flanking chains
+		a0e = &a[r0->as + r0->cnt - 1];
+		a1s = &a[r1->as];
+		if (a1s->x <= a0e->x || (int32_t)a1s->y <= (int32_t)a0e->y) continue; // keep colinearity
+		max_gap = min_gap = (int32_t)a1s->y - (int32_t)a0e->y;
+		max_gap = max_gap > a1s->x - a0e->x? max_gap : a1s->x - a0e->x;
+		min_gap = min_gap < a1s->x - a0e->x? min_gap : a1s->x - a0e->x;
+		if (max_gap > opt->max_join_long || min_gap > opt->max_join_short) continue;
+
+		// all conditions satisfied; join
+		a[r1->as].y |= 1ULL<<40;
+		r0->cnt += r1->cnt, r0->score += r1->score;
+		mm_reg_set_coor(r0, qlen, a);
+		r1->cnt = 0;
+	}
+	kfree(km, aux);
+}