r406: allow to use diff clipping penalties

for 5'-end or for 3'-end

bwamem.c

@@ -51,7 +51,7 @@ mem_opt_t *mem_opt_init()
 	o->T = 30;
 	o->zdrop = 100;
 	o->pen_unpaired = 17;
-	o->pen_clip = 5;
+	o->pen_clip5 = o->pen_clip3 = 5;
 	o->min_seed_len = 19;
 	o->split_width = 10;
 	o->max_occ = 10000;
@@ -572,12 +572,12 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
 			for (i = 0; i < MAX_BAND_TRY; ++i) {
 				int prev = a->score;
 				aw[0] = opt->w << i;
-				a->score = ksw_extend(s->qbeg, qs, tmp, rs, 5, opt->mat, opt->q, opt->r, aw[0], opt->pen_clip, opt->zdrop, s->len * opt->a, &qle, &tle, &gtle, &gscore, &max_off[0]);
+				a->score = ksw_extend(s->qbeg, qs, tmp, rs, 5, opt->mat, opt->q, opt->r, aw[0], opt->pen_clip5, opt->zdrop, s->len * opt->a, &qle, &tle, &gtle, &gscore, &max_off[0]);
 				if (bwa_verbose >= 4) { printf("L\t%d < %d; w=%d; max_off=%d\n", prev, a->score, aw[0], max_off[0]); fflush(stdout); }
 				if (a->score == prev || max_off[0] < (aw[0]>>1) + (aw[0]>>2)) break;
 			}
 			// check whether we prefer to reach the end of the query
-			if (gscore <= 0 || gscore <= a->score - opt->pen_clip) { // local extension
+			if (gscore <= 0 || gscore <= a->score - opt->pen_clip5) { // local extension
 				a->qb = s->qbeg - qle, a->rb = s->rbeg - tle;
 				a->truesc = a->score;
 			} else { // to-end extension
@@ -595,12 +595,12 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
 			for (i = 0; i < MAX_BAND_TRY; ++i) {
 				int prev = a->score;
 				aw[1] = opt->w << i;
-				a->score = ksw_extend(l_query - qe, query + qe, rmax[1] - rmax[0] - re, rseq + re, 5, opt->mat, opt->q, opt->r, aw[1], opt->pen_clip, opt->zdrop, sc0, &qle, &tle, &gtle, &gscore, &max_off[1]);
+				a->score = ksw_extend(l_query - qe, query + qe, rmax[1] - rmax[0] - re, rseq + re, 5, opt->mat, opt->q, opt->r, aw[1], opt->pen_clip3, opt->zdrop, sc0, &qle, &tle, &gtle, &gscore, &max_off[1]);
 				if (bwa_verbose >= 4) { printf("R\t%d < %d; w=%d; max_off=%d\n", prev, a->score, aw[1], max_off[1]); fflush(stdout); }
 				if (a->score == prev || max_off[1] < (aw[1]>>1) + (aw[1]>>2)) break;
 			}
 			// similar to the above
-			if (gscore <= 0 || gscore <= a->score - opt->pen_clip) { // local extension
+			if (gscore <= 0 || gscore <= a->score - opt->pen_clip3) { // local extension
 				a->qe = qe + qle, a->re = rmax[0] + re + tle;
 				a->truesc += a->score - sc0;
 			} else { // to-end extension

bwamem.h

@@ -20,7 +20,7 @@ typedef struct __smem_i smem_i;
 typedef struct {
 	int a, b, q, r;         // match score, mismatch penalty and gap open/extension penalty. A gap of size k costs q+k*r
 	int pen_unpaired;       // phred-scaled penalty for unpaired reads
-	int pen_clip;           // clipping penalty. This score is not deducted from the DP score.
+	int pen_clip5,pen_clip3;// clipping penalty. This score is not deducted from the DP score.
 	int w;                  // band width
 	int zdrop;              // Z-dropoff
 

fastmap.c

@@ -2,6 +2,7 @@
 #include <stdio.h>
 #include <unistd.h>
 #include <stdlib.h>
+#include <ctype.h>
 #include "bwa.h"
 #include "bwamem.h"
 #include "kvec.h"
@@ -35,7 +36,6 @@ int main_mem(int argc, char *argv[])
 		else if (c == 'O') opt->q = atoi(optarg);
 		else if (c == 'E') opt->r = atoi(optarg);
 		else if (c == 'T') opt->T = atoi(optarg);
-		else if (c == 'L') opt->pen_clip = atoi(optarg);
 		else if (c == 'U') opt->pen_unpaired = atoi(optarg);
 		else if (c == 't') opt->n_threads = atoi(optarg), opt->n_threads = opt->n_threads > 1? opt->n_threads : 1;
 		else if (c == 'P') opt->flag |= MEM_F_NOPAIRING;
@@ -48,7 +48,13 @@ int main_mem(int argc, char *argv[])
 		else if (c == 'v') bwa_verbose = atoi(optarg);
 		else if (c == 'r') opt->split_factor = atof(optarg);
 		else if (c == 'C') copy_comment = 1;
-		else if (c == 'R') {
+		else if (c == 'L') {
+			char *p;
+			opt->pen_clip5 = opt->pen_clip3 = strtol(optarg, &p, 10);
+			if (*p != 0 && ispunct(*p) && isdigit(p[1]))
+				opt->pen_clip3 = strtol(p+1, &p, 10);
+			fprintf(stderr, "%d,%d\n", opt->pen_clip5, opt->pen_clip3);
+		} else if (c == 'R') {
 			if ((rg_line = bwa_set_rg(optarg)) == 0) return 1; // FIXME: memory leak
 		} else if (c == 's') opt->split_width = atoi(optarg);
 		else return 1;
@@ -71,7 +77,7 @@ int main_mem(int argc, char *argv[])
 		fprintf(stderr, "       -B INT     penalty for a mismatch [%d]\n", opt->b);
 		fprintf(stderr, "       -O INT     gap open penalty [%d]\n", opt->q);
 		fprintf(stderr, "       -E INT     gap extension penalty; a gap of size k cost {-O} + {-E}*k [%d]\n", opt->r);
-		fprintf(stderr, "       -L INT     penalty for clipping [%d]\n", opt->pen_clip);
+		fprintf(stderr, "       -L INT     penalty for clipping [%d]\n", opt->pen_clip5);
 		fprintf(stderr, "       -U INT     penalty for an unpaired read pair [%d]\n", opt->pen_unpaired);
 		fprintf(stderr, "\nInput/output options:\n\n");
 		fprintf(stderr, "       -p         first query file consists of interleaved paired-end sequences\n");

main.c

@@ -3,7 +3,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.5a-r405"
+#define PACKAGE_VERSION "0.7.5a-r406"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);