r703: added --max-clip-ratio

still testing the option

align.c

@@ -720,7 +720,7 @@ mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *m
 	*n_regs_ = n_regs;
 	kfree(km, qseq0[0]);
 	kfree(km, ez.cigar);
-	mm_filter_regs(km, opt, n_regs_, regs);
+	mm_filter_regs(km, opt, qlen, n_regs_, regs);
 	mm_hit_sort_by_dp(km, n_regs_, regs);
 	return regs;
 }

hit.c

@@ -245,16 +245,17 @@ void mm_select_sub(void *km, float pri_ratio, int min_diff, int best_n, int *n_,
 	}
 }
 
-void mm_filter_regs(void *km, const mm_mapopt_t *opt, int *n_regs, mm_reg1_t *regs)
+void mm_filter_regs(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs, mm_reg1_t *regs)
 { // NB: after this call, mm_reg1_t::parent can be -1 if its parent filtered out
 	int i, k;
 	for (i = k = 0; i < *n_regs; ++i) {
 		mm_reg1_t *r = &regs[i];
 		int flt = 0;
 		if (!r->inv && !r->seg_split && r->cnt < opt->min_cnt) flt = 1;
-		if (r->p) {
+		if (r->p) { // these filters are only applied when base-alignment is available
 			if (r->mlen < opt->min_chain_score) flt = 1;
 			else if (r->p->dp_max < opt->min_dp_max) flt = 1;
+			else if (r->qs > qlen * opt->max_clip_ratio && qlen - r->qe > qlen * opt->max_clip_ratio) flt = 1;
 			if (flt) free(r->p);
 		}
 		if (!flt) {
@@ -337,7 +338,7 @@ void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs_, mm_r
 					r->parent = regs[r->parent].parent;
 			}
 		}
-		mm_filter_regs(km, opt, n_regs_, regs);
+		mm_filter_regs(km, opt, qlen, n_regs_, regs);
 		mm_sync_regs(km, *n_regs_, regs);
 	}
 }

main.c

@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.8-r686-dirty"
+#define MM_VERSION "2.8-r703-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -50,6 +50,7 @@ static struct option long_options[] = {
 	{ "heap-sort",      required_argument, 0, 0 },   // 24
 	{ "all-chain",      no_argument,       0, 'P' },
 	{ "dual",           required_argument, 0, 0 },   // 26
+	{ "max-clip-ratio", required_argument, 0, 0 },   // 27
 	{ "help",           no_argument,       0, 'h' },
 	{ "max-intron-len", required_argument, 0, 'G' },
 	{ "version",        no_argument,       0, 'V' },
@@ -163,6 +164,7 @@ int main(int argc, char *argv[])
 		else if (c == 0 && long_idx ==21) opt.anchor_ext_shift = atoi(optarg); // --end-seed-pen
 		else if (c == 0 && long_idx ==22) opt.flag |= MM_F_FOR_ONLY; // --for-only
 		else if (c == 0 && long_idx ==23) opt.flag |= MM_F_REV_ONLY; // --rev-only
+		else if (c == 0 && long_idx ==27) opt.max_clip_ratio = atof(optarg); // --max-clip-ratio
 		else if (c == 0 && long_idx == 14) { // --frag
 			yes_or_no(&opt, MM_F_FRAG_MODE, long_idx, optarg, 1);
 		} else if (c == 0 && long_idx == 15) { // --secondary

minimap.h

@@ -121,6 +121,7 @@ typedef struct {
 	int min_dp_max;  // drop an alignment if the score of the max scoring segment is below this threshold
 	int min_ksw_len;
 	int anchor_ext_len, anchor_ext_shift;
+	float max_clip_ratio; // drop an alignment if BOTH ends are clipped above this ratio
 
 	int pe_ori, pe_bonus;
 

mmpriv.h

@@ -75,7 +75,7 @@ int mm_set_sam_pri(int n, mm_reg1_t *r);
 void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r, int sub_diff);
 void mm_select_sub(void *km, float pri_ratio, int min_diff, int best_n, int *n_, mm_reg1_t *r);
 void mm_select_sub_multi(void *km, float pri_ratio, float pri1, float pri2, int max_gap_ref, int min_diff, int best_n, int n_segs, const int *qlens, int *n_, mm_reg1_t *r);
-void mm_filter_regs(void *km, const mm_mapopt_t *opt, int *n_regs, mm_reg1_t *regs);
+void mm_filter_regs(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs, mm_reg1_t *regs);
 void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs, mm_reg1_t *regs, mm128_t *a);
 void mm_hit_sort_by_dp(void *km, int *n_regs, mm_reg1_t *r);
 void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, int rep_len, int is_sr);

options.c

@@ -29,6 +29,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
 	opt->min_dp_max = opt->min_chain_score * opt->a;
 	opt->min_ksw_len = 200;
 	opt->anchor_ext_len = 20, opt->anchor_ext_shift = 6;
+	opt->max_clip_ratio = 1.0f;
 	opt->mini_batch_size = 500000000;
 
 	opt->pe_ori = 0; // FF

python/cmappy.pxd

@@ -31,6 +31,7 @@ cdef extern from "minimap.h":
 		int min_dp_max
 		int min_ksw_len
 		int anchor_ext_len, anchor_ext_shift
+		float max_clip_ratio
 		int pe_ori, pe_bonus
 		float mid_occ_frac
 		int32_t mid_occ