r444: changed the way orientation is specified

The old model doesn't work with RF or RR orientation. The new model only works
with paired-end reads. For >2 segments, only FF is supported.

main.c

@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.2-r443-dirty"
+#define MM_VERSION "2.2-r444-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -38,7 +38,6 @@ static struct option long_options[] = {
 	{ "no-sam-sq",      no_argument,       0, 0 },
 	{ "sr",             no_argument,       0, 0 },
 	{ "multi-seg",      optional_argument, 0, 0 },
-	{ "2nd-seg-rev",    optional_argument, 0, 0 },
 	{ "help",           no_argument,       0, 'h' },
 	{ "max-intron-len", required_argument, 0, 'G' },
 	{ "version",        no_argument,       0, 'V' },
@@ -121,10 +120,6 @@ int main(int argc, char *argv[])
 			if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
 				opt.flag |= MM_F_MULTI_SEG;
 			else opt.flag &= ~MM_F_MULTI_SEG;
-		} else if (c == 0 && long_idx ==15) { // --2nd-seg-rev
-			if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
-				opt.flag |= MM_F_SEG_REV;
-			else opt.flag &= ~MM_F_SEG_REV;
 		} else if (c == 'V') {
 			puts(MM_VERSION);
 			return 0;

map.c

@@ -12,7 +12,8 @@ void mm_mapopt_init(mm_mapopt_t *opt)
 {
 	memset(opt, 0, sizeof(mm_mapopt_t));
 	opt->mid_occ_frac = 2e-4f;
-	opt->sdust_thres = 0;
+	opt->sdust_thres = 0; // no SDUST masking
+	opt->pe_ori = 0; // FF
 
 	opt->min_cnt = 3;
 	opt->min_chain_score = 40;
@@ -75,7 +76,8 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
 		mo->min_dp_max = 200;
 	} else if (strcmp(preset, "short") == 0 || strcmp(preset, "sr") == 0) {
 		io->is_hpc = 0, io->k = 21, io->w = 11;
-		mo->flag |= MM_F_SR | MM_F_MULTI_SEG | MM_F_SEG_REV;
+		mo->flag |= MM_F_SR | MM_F_MULTI_SEG;
+		mo->pe_ori = 0<<1|1; // FR
 		mo->a = 2, mo->b = 8, mo->q = 12, mo->e = 2, mo->q2 = 32, mo->e2 = 1;
 		mo->max_gap = 200;
 		mo->max_gap_ref = 1000;
@@ -339,7 +341,7 @@ typedef struct {
 static void worker_for(void *_data, long i, int tid) // kt_for() callback
 {
     step_t *s = (step_t*)_data;
-	int *qlens, j, off = s->seg_off[i];
+	int *qlens, j, off = s->seg_off[i], pe_ori = s->p->opt->pe_ori;
 	const char **qseqs;
 	mm_tbuf_t *b = s->buf[tid];
 	if (mm_dbg_flag & MM_DBG_PRINT_QNAME)
@@ -347,14 +349,14 @@ static void worker_for(void *_data, long i, int tid) // kt_for() callback
 	qlens = (int*)kmalloc(b->km, s->n_seg[i] * sizeof(int));
 	qseqs = (const char**)kmalloc(b->km, s->n_seg[i] * sizeof(const char**));
 	for (j = 0; j < s->n_seg[i]; ++j) {
-		if (j > 0 && (s->p->opt->flag & MM_F_SEG_REV))
+		if (s->n_seg[i] == 2 && ((j == 0 && (pe_ori>>1&1)) || (j == 1 && (pe_ori&1))))
 			mm_revcomp_bseq(&s->seq[off + j]);
 		qlens[j] = s->seq[off + j].l_seq;
 		qseqs[j] = s->seq[off + j].seq;
 	}
 	mm_map_multi(s->p->mi, s->n_seg[i], qlens, qseqs, &s->n_reg[off], &s->reg[off], b, s->p->opt, s->seq[off].name);
-	if (s->n_seg[i] > 1 && (s->p->opt->flag & MM_F_SEG_REV))
-		for (j = 1; j < s->n_seg[i]; ++j) { // flip the query strand and coordinate to the original read strand
+	for (j = 0; j < s->n_seg[i]; ++j) // flip the query strand and coordinate to the original read strand
+		if (s->n_seg[i] == 2 && ((j == 0 && (pe_ori>>1&1)) || (j == 1 && (pe_ori&1)))) {
 			int k, t;
 			mm_revcomp_bseq(&s->seq[off + j]);
 			for (k = 0; k < s->n_reg[off + j]; ++k) {

minimap.h

@@ -18,7 +18,6 @@
 #define MM_F_NO_SAM_SQ   0x800
 #define MM_F_SR          0x1000
 #define MM_F_MULTI_SEG   0x2000
-#define MM_F_SEG_REV     0x4000
 
 #define MM_IDX_MAGIC   "MMI\2"
 
@@ -82,6 +81,7 @@ typedef struct {
 typedef struct {
 	int sdust_thres; // score threshold for SDUST; 0 to disable
 	int flag;        // see MM_F_* macros
+	int pe_ori;
 
 	int bw;          // bandwidth
 	int max_gap, max_gap_ref; // break a chain if there are no minimizers in a max_gap window

pe.c

@@ -40,3 +40,32 @@ void mm_select_sub_multi(void *km, float pri_ratio, float pri1, float pri2, int
 	}
 }
 
+#include "ksort.h"
+
+typedef struct {
+	int s;
+	uint64_t key;
+	mm_reg1_t *r;
+} pair_arr_t;
+
+#define sort_key_pair(a) ((a).key)
+KRADIX_SORT_INIT(pair, pair_arr_t, sort_key_pair, 8)
+/*
+void mm_pair(void *km, int max_gap_ref, int *n_regs, mm_reg1_t **regs)
+{
+	int i, j, s, n, last = -1;
+	pair_arr_t *a;
+	a = (pair_arr_t*)kmalloc(km, (n_regs[0] + n_regs[1]) * sizeof(pair_arr_t));
+	for (s = n = 0; s < 2; ++s)
+		for (i = 0; i < n_regs[s]; ++i) {
+			a[n].s = s;
+			a[n].r = &regs[s][i];
+			a[n++].key = (uint64_t)a[n].r->rid << 32 | a[n].r->rs;
+		}
+	radix_sort_pair(n, a);
+	for (i = 0; i < n; ++i) {
+		int pre_dir = seg_rev? !a[i].r->rev : a[i].r->rev;
+	}
+	kfree(km, a);
+}
+*/