r1051: added two internal parameters

rmq_rescue_size and rmq_rescue_ratio

Author: lh3

main.c

@@ -7,7 +7,7 @@
 #include "mmpriv.h"
 #include "ketopt.h"
 
-#define MM_VERSION "2.18-r1050-dirty"
+#define MM_VERSION "2.18-r1051-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>

map.c

@@ -300,9 +300,9 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
 			a = mg_lchain_dp(max_chain_gap_ref, max_chain_gap_qry, opt->bw, opt->max_chain_skip, opt->max_chain_iter, opt->min_cnt, opt->min_chain_score,
 							 opt->chain_gap_scale * 0.01 * mi->k, 0.0f, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
 		}
-	} else if (opt->bw_long > opt->bw && !(opt->flag & (MM_F_RMQ|MM_F_NO_LJOIN)) && n_segs == 1 && n_regs0 > 1) {
+	} else if (opt->bw_long > opt->bw && (opt->flag & (MM_F_RMQ|MM_F_NO_LJOIN)) == 0 && n_segs == 1 && n_regs0 > 1) {
 		int32_t st = (int32_t)a[0].y, en = (int32_t)a[(int32_t)u[0] - 1].y;
-		if (qlen_sum - (en - st) > 1000 || en - st > qlen_sum * .1) {
+		if (qlen_sum - (en - st) > opt->rmq_rescue_size || en - st > qlen_sum * opt->rmq_rescue_ratio) {
 			int32_t i;
 			for (i = 0, n_a = 0; i < n_regs0; ++i) n_a += (int32_t)u[i];
 			kfree(b->km, u);

minimap.h

@@ -122,6 +122,8 @@ typedef struct {
 	int min_chain_score; // min chaining score
 	float chain_gap_scale;
 	int rmq_size_cap, rmq_inner_dist;
+	int rmq_rescue_size;
+	float rmq_rescue_ratio;
 
 	float mask_level;
 	int mask_len;

options.c

@@ -29,6 +29,8 @@ void mm_mapopt_init(mm_mapopt_t *opt)
 	opt->max_chain_iter = 5000;
 	opt->rmq_inner_dist = 1000;
 	opt->rmq_size_cap = 100000;
+	opt->rmq_rescue_size = 1000;
+	opt->rmq_rescue_ratio = 0.1f;
 	opt->chain_gap_scale = 0.8f;
 	opt->max_max_occ = 4095;
 	opt->occ_dist = 500;

python/cmappy.pxd

@@ -24,6 +24,8 @@ cdef extern from "minimap.h":
 		int min_chain_score
 		float chain_gap_scale
 		int rmq_size_cap, rmq_inner_dist
+		int rmq_rescue_size
+		float rmq_rescue_ratio
 
 		float mask_level
 		int mask_len