r176: removed seedcov_ratio; changed default opt

min_seedcov_ratio is not used

hit.c

@@ -197,10 +197,6 @@ void mm_filter_regs(void *km, const mm_mapopt_t *opt, int *n_regs, mm_reg1_t *re
 		mm_reg1_t *r = &regs[i];
 		int flt = 0;
 		if (r->cnt < opt->min_cnt) flt = 1;
-		else {
-			int blen = r->qe - r->qs < r->re - r->rs? r->qe - r->qs : r->re - r->rs;
-			if (r->score < blen * opt->min_seedcov_ratio * opt->a) flt = 1;
-		}
 		if (r->p) {
 			if (r->p->blen - r->p->n_ambi - r->p->n_diff < opt->min_chain_score) flt = 1;
 			else if (r->p->dp_max < opt->min_dp_max) flt = 1;

main.c

@@ -10,7 +10,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r175-pre"
+#define MM_VERSION "2.0-r176-pre"
 
 void liftrlimit()
 {
@@ -43,7 +43,7 @@ static int test_idx(const char *fn)
 
 static struct option long_options[] = {
 	{ "bucket-bits",    required_argument, 0, 0 },
-	{ "mb-size",        required_argument, 0, 0 },
+	{ "mb-size",        required_argument, 0, 'K' },
 	{ "int-rname",      no_argument,       0, 0 },
 	{ "no-kalloc",      no_argument,       0, 0 },
 	{ "print-qname",    no_argument,       0, 0 },
@@ -73,7 +73,7 @@ int main(int argc, char *argv[])
 	mm_realtime0 = realtime();
 	mm_mapopt_init(&opt);
 
-	while ((c = getopt_long(argc, argv, "aw:k:t:r:f:Vv:g:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:D:N:Q", long_options, &long_idx)) >= 0) {
+	while ((c = getopt_long(argc, argv, "aw:k:K:t:r:f:Vv:g:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Q", long_options, &long_idx)) >= 0) {
 		if (c == 'w') w = atoi(optarg);
 		else if (c == 'k') k = atoi(optarg);
 		else if (c == 'H') is_hpc = 1;
@@ -85,7 +85,6 @@ int main(int argc, char *argv[])
 		else if (c == 'g') opt.max_gap = atoi(optarg);
 		else if (c == 'N') opt.best_n = atoi(optarg);
 		else if (c == 'p') opt.pri_ratio = atof(optarg);
-		else if (c == 'D') opt.min_seedcov_ratio = atof(optarg);
 		else if (c == 'M') opt.mask_level = atof(optarg);
 		else if (c == 'c') opt.flag |= MM_F_CIGAR;
 		else if (c == 'X') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
@@ -114,7 +113,7 @@ int main(int argc, char *argv[])
 		} else if (c == 'E') {
 			opt.e = opt.e2 = strtol(optarg, &s, 10);
 			if (*s == ',') opt.e2 = strtol(s + 1, &s, 10);
-		} else if (c == 'I' || (c == 0 && long_idx == 1)) {
+		} else if (c == 'I' || c == 'K') {
 			double x;
 			char *p;
 			x = strtod(optarg, &p);
@@ -126,11 +125,13 @@ int main(int argc, char *argv[])
 		} else if (c == 'x') {
 			if (strcmp(optarg, "ava-ont") == 0) {
 				opt.flag |= MM_F_AVA | MM_F_NO_SELF;
-				opt.min_chain_score = 100, opt.pri_ratio = 0.0f, opt.min_seedcov_ratio = 0.05f, opt.max_gap = 10000, opt.max_chain_skip = 25;
+				opt.min_chain_score = 100, opt.pri_ratio = 0.0f, opt.max_gap = 10000, opt.max_chain_skip = 25;
+				minibatch_size = 500000000;
 				k = 15, w = 5;
 			} else if (strcmp(optarg, "ava-pb") == 0) {
 				opt.flag |= MM_F_AVA | MM_F_NO_SELF;
-				opt.min_chain_score = 100, opt.pri_ratio = 0.0f, opt.min_seedcov_ratio = 0.05f, opt.max_gap = 10000, opt.max_chain_skip = 25;
+				opt.min_chain_score = 100, opt.pri_ratio = 0.0f, opt.max_gap = 10000, opt.max_chain_skip = 25;
+				minibatch_size = 500000000;
 				is_hpc = 1, k = 19, w = 5;
 			} else if (strcmp(optarg, "map10k") == 0) {
 				is_hpc = 1, k = 19;
@@ -163,10 +164,9 @@ int main(int argc, char *argv[])
 		fprintf(stderr, "    -X           skip self and dual mappings (for the all-vs-all mode)\n");
 		fprintf(stderr, "    -p FLOAT     min secondary-to-primary score ratio [%g]\n", opt.pri_ratio);
 		fprintf(stderr, "    -N INT       retain at most INT secondary alignments [%d]\n", opt.best_n);
-		fprintf(stderr, "    -D FLOAT     min fraction of minimizer matches [%g]\n", opt.min_seedcov_ratio);
 		fprintf(stderr, "    -x STR       preset (recommended to be applied before other options) []\n");
-		fprintf(stderr, "                 ava-pb: -Hk19 -w5 -Xp0 -m100 -D.05 -g10000 --max-chain-skip 25 (PacBio read overlap)\n");
+		fprintf(stderr, "                 ava-pb: -Hk19 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (PacBio read overlap)\n");
-		fprintf(stderr, "                 ava-ont: -k15 -w5 -Xp0 -m100 -D.05 -g10000 --max-chain-skip 25 (ONT read overlap)\n");
+		fprintf(stderr, "                 ava-ont: -k15 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (ONT read overlap)\n");
 		fprintf(stderr, "                 map10k: -Hk19   (PacBio/ONT vs reference mapping)\n");
 		fprintf(stderr, "                 asm1m:  -k19 -w19   (intra-species assembly to ref mapping)\n");
 		fprintf(stderr, "  Alignment:\n");
@@ -181,6 +181,7 @@ int main(int argc, char *argv[])
 		fprintf(stderr, "    -a           output in the SAM format (PAF by default)\n");
 		fprintf(stderr, "    -c           output CIGAR in PAF\n");
 		fprintf(stderr, "    -t INT       number of threads [%d]\n", n_threads);
+		fprintf(stderr, "    -K NUM       minibatch size [200M]\n");
 //		fprintf(stderr, "    -v INT       verbose level [%d]\n", mm_verbose);
 		fprintf(stderr, "    -V           show version number\n");
 		fprintf(stderr, "\nSee `man ./minimap2.1' for detailed description of command-line options.\n");

map.c

@@ -20,7 +20,6 @@ void mm_mapopt_init(mm_mapopt_t *opt)
 	opt->bw = 500;
 	opt->max_gap = 5000;
 	opt->max_chain_skip = 25;
-	opt->min_seedcov_ratio = 0.0f;
 
 	opt->mask_level = 0.5f;
 	opt->pri_ratio = 0.8f;

minimap.h

@@ -77,7 +77,6 @@ typedef struct {
 	int max_chain_skip;
 	int min_cnt;
 	int min_chain_score;
-	float min_seedcov_ratio;
 
 	float mask_level;
 	float pri_ratio;

minimap2.1

@@ -164,12 +164,6 @@ secondary alignments [5]. This option has no effect when
 .B -X
 is applied.
 .TP
-.BI -D \ FLOAT
-Discard a chain if the fraction of matching bases over the length of
-query/target sequences in the chain is
-.RI < FLOAT
-[0].
-.TP
 .BI -x \ STR
 Preset []. This option applies multiple options at the same time. It should be
 applied before other options because options applied later will overwrite the
@@ -181,10 +175,10 @@ are:
 .RS
 .TP 8
 .B ava-pb
-PacBio all-vs-all overlap mapping (-Hk19 -w5 -Xp0 -m100 -D.05 -g10000)
+PacBio all-vs-all overlap mapping (-Hk19 -w5 -Xp0 -m100 -K500m -g10000 --max-chain-skip 25)
 .TP 8
 .B ava-ont
-Oxford Nanopore all-vs-all overlap mapping (-k15 -w5 -Xp0 -m100 -D.05 -g10000)
+Oxford Nanopore all-vs-all overlap mapping (-k15 -w5 -Xp0 -m100 -K500m -g10000 --max-chain-skip 25)
 .TP
 .B map10k
 PacBio/Oxford Nanopore read to reference mapping (-Hk19)
@@ -249,14 +243,22 @@ sequences, and uses up to
 threads when mapping (the extra thread is for I/O, which is frequently idle and
 takes little CPU time).
 .TP
-.B -V
+.BI -K \ NUM
-Print version number to stdout
-.TP
-.BI --mb-size \ STR
 Number of bases loaded into memory to process in a mini-batch [200M].
 Similar to option
 .BR -I ,
-K/M/G/k/m/g suffix is accepted. This option affects both indexing and mapping.
+K/M/G/k/m/g suffix is accepted. A large
+.I NUM
+helps load balancing in the multi-threading mode, at the cost of increased
+memory. Preset
+.B ava-pb
+and
+.B ava-ont
+use
+.BR -K500m .
+.TP
+.B -V
+Print version number to stdout
 .SS Miscellaneous options
 .TP 10
 .B --no-kalloc