pass BED regions to extd2; not tested

2026-09-17 05:57:54 +08:00 · 2018-09-17 12:31:42 -04:00
parent 2b653ecda3
commit d01369ec47
6 changed files with 40 additions and 22 deletions
--- a/align.c
+++ b/align.c
@@ -290,7 +290,7 @@ static void mm_update_cigar_eqx(mm_reg1_t *r, const uint8_t *qseq, const uint8_t
 	r->p = p;
 }

-static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint8_t *qseq, int tlen, const uint8_t *tseq, const int8_t *mat, int w, int end_bonus, int zdrop, int flag, ksw_extz_t *ez)
+static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint8_t *qseq, int tlen, const uint8_t *tseq, const int8_t *ob, const int8_t *mat, int w, int end_bonus, int zdrop, int flag, ksw_extz_t *ez)
 {
 	if (mm_dbg_flag & MM_DBG_PRINT_ALN_SEQ) {
 		int i;
@@ -305,7 +305,7 @@ static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint
 	else if (opt->q == opt->q2 && opt->e == opt->e2)
 		ksw_extz2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, w, zdrop, end_bonus, flag, ez);
 	else
-		ksw_extd2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->e2, w, zdrop, end_bonus, flag, ez);
+		ksw_extd2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->e2, w, zdrop, end_bonus, flag, ob, ez);
 	if (mm_dbg_flag & MM_DBG_PRINT_ALN_SEQ) {
 		int i;
 		fprintf(stderr, "score=%d, cigar=", ez->score);
@@ -547,7 +547,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 	int32_t i, l, bw, dropped = 0, extra_flag = 0, rs0, re0, qs0, qe0;
 	int32_t rs, re, qs, qe;
 	int32_t rs1, qs1, re1, qe1;
-	int8_t mat[25];
+	int8_t mat[25], *ob;

 	if (is_sr) assert(!(mi->flag & MM_I_HPC)); // HPC won't work with SR because with HPC we can't easily tell if there is a gap

@@ -660,13 +660,14 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int

 	assert(re0 > rs0);
 	tseq = (uint8_t*)kmalloc(km, re0 - rs0);
+	ob = (int8_t*)kmalloc(km, re0 - rs0);

 	if (qs > 0 && rs > 0) { // left extension
 		qseq = &qseq0[rev][qs0];
-		mm_idx_getseq(mi, rid, rs0, rs, tseq);
+		mm_idx_getseq2(mi, rid, rs0, rs, tseq, ob);
 		mm_seq_rev(qs - qs0, qseq);
 		mm_seq_rev(rs - rs0, tseq);
-		mm_align_pair(km, opt, qs - qs0, qseq, rs - rs0, tseq, mat, bw, opt->end_bonus, r->split_inv? opt->zdrop_inv : opt->zdrop, extra_flag|KSW_EZ_EXTZ_ONLY|KSW_EZ_RIGHT|KSW_EZ_REV_CIGAR, ez);
+		mm_align_pair(km, opt, qs - qs0, qseq, rs - rs0, tseq, ob, mat, bw, opt->end_bonus, r->split_inv? opt->zdrop_inv : opt->zdrop, extra_flag|KSW_EZ_EXTZ_ONLY|KSW_EZ_RIGHT|KSW_EZ_REV_CIGAR, ez);
 		if (ez->n_cigar > 0) {
 			mm_append_cigar(r, ez->n_cigar, ez->cigar);
 			r->p->dp_score += ez->max;
@@ -691,7 +692,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 				bw1 = qe - qs > re - rs? qe - qs : re - rs;
 			// perform alignment
 			qseq = &qseq0[rev][qs];
-			mm_idx_getseq(mi, rid, rs, re, tseq);
+			mm_idx_getseq2(mi, rid, rs, re, tseq, ob);
 			if (is_sr) { // perform ungapped alignment
 				assert(qe - qs == re - rs);
 				ksw_reset_extz(ez);
@@ -701,11 +702,11 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 				}
 				ez->cigar = ksw_push_cigar(km, &ez->n_cigar, &ez->m_cigar, ez->cigar, 0, qe - qs);
 			} else { // perform normal gapped alignment
-				mm_align_pair(km, opt, qe - qs, qseq, re - rs, tseq, mat, bw1, -1, opt->zdrop, extra_flag|KSW_EZ_APPROX_MAX, ez); // first pass: with approximate Z-drop
+				mm_align_pair(km, opt, qe - qs, qseq, re - rs, tseq, ob, mat, bw1, -1, opt->zdrop, extra_flag|KSW_EZ_APPROX_MAX, ez); // first pass: with approximate Z-drop
 			}
 			// test Z-drop and inversion Z-drop
 			if ((zdrop_code = mm_test_zdrop(km, opt, qseq, tseq, ez->n_cigar, ez->cigar, mat)) != 0)
-				mm_align_pair(km, opt, qe - qs, qseq, re - rs, tseq, mat, bw1, -1, zdrop_code == 2? opt->zdrop_inv : opt->zdrop, extra_flag, ez); // second pass: lift approximate
+				mm_align_pair(km, opt, qe - qs, qseq, re - rs, tseq, ob, mat, bw1, -1, zdrop_code == 2? opt->zdrop_inv : opt->zdrop, extra_flag, ez); // second pass: lift approximate
 			// update CIGAR
 			if (ez->n_cigar > 0)
 				mm_append_cigar(r, ez->n_cigar, ez->cigar);
@@ -730,8 +731,8 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int

 	if (!dropped && qe < qe0 && re < re0) { // right extension
 		qseq = &qseq0[rev][qe];
-		mm_idx_getseq(mi, rid, re, re0, tseq);
-		mm_align_pair(km, opt, qe0 - qe, qseq, re0 - re, tseq, mat, bw, opt->end_bonus, opt->zdrop, extra_flag|KSW_EZ_EXTZ_ONLY, ez);
+		mm_idx_getseq2(mi, rid, re, re0, tseq, ob);
+		mm_align_pair(km, opt, qe0 - qe, qseq, re0 - re, tseq, ob, mat, bw, opt->end_bonus, opt->zdrop, extra_flag|KSW_EZ_EXTZ_ONLY, ez);
 		if (ez->n_cigar > 0) {
 			mm_append_cigar(r, ez->n_cigar, ez->cigar);
 			r->p->dp_score += ez->max;
@@ -747,7 +748,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int

 	assert(re1 - rs1 <= re0 - rs0);
 	if (r->p) {
-		mm_idx_getseq(mi, rid, rs1, re1, tseq);
+		mm_idx_getseq2(mi, rid, rs1, re1, tseq, ob);
 		mm_update_extra(r, &qseq0[r->rev][qs1], tseq, mat, opt->q, opt->e);
 		if (opt->flag & MM_F_EQX) mm_update_cigar_eqx(r, &qseq0[r->rev][qs1], tseq);
 		if (rev && r->p->trans_strand)
@@ -755,6 +756,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 	}

 	kfree(km, tseq);
+	kfree(km, ob);
 }

 static int mm_align1_inv(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, uint8_t *qseq0[2], const mm_reg1_t *r1, const mm_reg1_t *r2, mm_reg1_t *r_inv, ksw_extz_t *ez)
@@ -788,7 +790,7 @@ static int mm_align1_inv(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, i
 	mm_seq_rev(tl, tseq);
 	if (score < opt->min_dp_max) goto end_align1_inv;
 	q_off = ql - (q_off + 1), t_off = tl - (t_off + 1);
-	mm_align_pair(km, opt, ql - q_off, qseq + q_off, tl - t_off, tseq + t_off, mat, (int)(opt->bw * 1.5), -1, opt->zdrop, KSW_EZ_EXTZ_ONLY, ez);
+	mm_align_pair(km, opt, ql - q_off, qseq + q_off, tl - t_off, tseq + t_off, 0, mat, (int)(opt->bw * 1.5), -1, opt->zdrop, KSW_EZ_EXTZ_ONLY, ez);
 	if (ez->n_cigar == 0) goto end_align1_inv; // should never be here
 	mm_append_cigar(r_inv, ez->n_cigar, ez->cigar);
 	r_inv->p->dp_score = ez->max;
--- a/index.c
+++ b/index.c
@@ -134,7 +134,7 @@ int mm_idx_name2id(const mm_idx_t *mi, const char *name)
 	return k == kh_end(h)? -1 : kh_val(h, k);
 }

-int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq)
+int mm_idx_getseq2(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq, int8_t *b)
 {
 	uint64_t i, st1, en1;
 	if (rid >= mi->n_seq || st >= mi->seq[rid].len) return -1;
@@ -143,9 +143,24 @@ int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, ui
 	en1 = mi->seq[rid].offset + en;
 	for (i = st1; i < en1; ++i)
 		seq[i - st1] = mm_seq4_get(mi->S, i);
+	if (b && mi->R) {
+		uint32_t i, z;
+		memset(b, 0, en - st);
+		z = mm_idx_bed_query(mi, (uint64_t)rid << 32 | st);
+		for (i = z + 1; i < mi->n_R; ++i) {
+			uint32_t j, rr, rs, re;
+			rr = mi->R[i].x >> 32, rs = (uint32_t)mi->R[i].x, re = mi->R[i].end;
+			if (rr != rid || rs >= en) break;
+			assert(rs >= st);
+			for (j = rs; j < re; ++j)
+				b[j - st] = 1;
+		}
+	}
 	return en - st;
 }

+int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq) { return mm_idx_getseq2(mi, rid, st, en, seq, 0); }
+
 int32_t mm_idx_cal_max_occ(const mm_idx_t *mi, float f)
 {
 	int i;
--- a/ksw2.h
+++ b/ksw2.h
@@ -58,7 +58,7 @@ void ksw_extd(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t
 			  int8_t gapo, int8_t gape, int8_t gapo2, int8_t gape2, int w, int zdrop, int flag, ksw_extz_t *ez);

 void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
-				   int8_t gapo, int8_t gape, int8_t gapo2, int8_t gape2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez);
+				   int8_t gapo, int8_t gape, int8_t gapo2, int8_t gape2, int w, int zdrop, int end_bonus, int flag, const int8_t *qd, ksw_extz_t *ez);

 void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
 				   int8_t gapo, int8_t gape, int8_t gapo2, int8_t noncan, int zdrop, int flag, ksw_extz_t *ez);
--- a/ksw2_dispatch.c
+++ b/ksw2_dispatch.c
@@ -64,18 +64,18 @@ void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 }

 void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
-				   int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)
+				   int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, const int8_t *qd, ksw_extz_t *ez)
 {
 	extern void ksw_extd2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
-				   int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez);
+				   int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, const int8_t *qd, ksw_extz_t *ez);
 	extern void ksw_extd2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
-				   int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez);
+				   int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, const int8_t *qd, ksw_extz_t *ez);
 	unsigned simd;
 	simd = x86_simd();
 	if (simd & SIMD_SSE4_1)
-		ksw_extd2_sse41(km, qlen, query, tlen, target, m, mat, q, e, q2, e2, w, zdrop, end_bonus, flag, ez);
+		ksw_extd2_sse41(km, qlen, query, tlen, target, m, mat, q, e, q2, e2, w, zdrop, end_bonus, flag, qd, ez);
 	else if (simd & SIMD_SSE2)
-		ksw_extd2_sse2(km, qlen, query, tlen, target, m, mat, q, e, q2, e2, w, zdrop, end_bonus, flag, ez);
+		ksw_extd2_sse2(km, qlen, query, tlen, target, m, mat, q, e, q2, e2, w, zdrop, end_bonus, flag, qd, ez);
 	else abort();
 }

--- a/ksw2_extd2_sse.c
+++ b/ksw2_extd2_sse.c
@@ -17,14 +17,14 @@
 #ifdef KSW_CPU_DISPATCH
 #ifdef __SSE4_1__
 void ksw_extd2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
-				   int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)
+				   int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, const int8_t *qd, ksw_extz_t *ez)
 #else
 void ksw_extd2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
-				   int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)
+				   int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, const int8_t *qd, ksw_extz_t *ez)
 #endif
 #else
 void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
-				   int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)
+				   int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, const int8_t *qd, ksw_extz_t *ez)
 #endif // ~KSW_CPU_DISPATCH
 {
 #define __dp_code_block1 \
--- a/mmpriv.h
+++ b/mmpriv.h
@@ -74,6 +74,7 @@ void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
 void mm_idxopt_init(mm_idxopt_t *opt);
 const uint64_t *mm_idx_get(const mm_idx_t *mi, uint64_t minier, int *n);
 int32_t mm_idx_cal_max_occ(const mm_idx_t *mi, float f);
+int mm_idx_getseq2(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq, int8_t *b);
 mm128_t *mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int min_cnt, int min_sc, int is_cdna, int n_segs, int64_t n, mm128_t *a, int *n_u_, uint64_t **_u, void *km);
 mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int *n_regs_, mm_reg1_t *regs, mm128_t *a);