Merge branch 'dev'

bwamem.c

@@ -968,6 +968,30 @@ int mem_approx_mapq_se(const mem_opt_t *opt, const mem_alnreg_t *a)
 	return mapq;
 }
 
+void mem_reorder_primary5(int T, mem_alnreg_v *a)
+{
+	int k, n_pri = 0, left_st = INT_MAX, left_k = -1;
+	mem_alnreg_t t;
+	for (k = 0; k < a->n; ++k)
+		if (a->a[k].secondary < 0 && !a->a[k].is_alt && a->a[k].score >= T) ++n_pri;
+	if (n_pri <= 1) return; // only one alignment
+	for (k = 0; k < a->n; ++k) {
+		mem_alnreg_t *p = &a->a[k];
+		if (p->secondary >= 0 || p->is_alt || p->score < T) continue;
+		if (p->qb < left_st) left_st = p->qb, left_k = k;
+	}
+	assert(a->a[0].secondary < 0);
+	if (left_k == 0) return; // no need to reorder
+	t = a->a[0], a->a[0] = a->a[left_k], a->a[left_k] = t;
+	for (k = 1; k < a->n; ++k) { // update secondary and secondary_all
+		mem_alnreg_t *p = &a->a[k];
+		if (p->secondary == 0) p->secondary = left_k;
+		else if (p->secondary == left_k) p->secondary = 0;
+		if (p->secondary_all == 0) p->secondary_all = left_k;
+		else if (p->secondary_all == left_k) p->secondary_all = 0;
+	}
+}
+
 // TODO (future plan): group hits into a uint64_t[] array. This will be cleaner and more flexible
 void mem_reg2sam(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const mem_aln_t *m)
 {
@@ -1160,6 +1184,7 @@ static void worker2(void *data, int i, int tid)
 	if (!(w->opt->flag&MEM_F_PE)) {
 		if (bwa_verbose >= 4) printf("=====> Finalizing read '%s' <=====\n", w->seqs[i].name);
 		mem_mark_primary_se(w->opt, w->regs[i].n, w->regs[i].a, w->n_processed + i);
+		if (w->opt->flag & MEM_F_PRIMARY5) mem_reorder_primary5(w->opt->T, &w->regs[i]);
 		mem_reg2sam(w->opt, w->bns, w->pac, &w->seqs[i], &w->regs[i], 0, 0);
 		free(w->regs[i].a);
 	} else {

bwamem.h

@@ -19,6 +19,7 @@ typedef struct __smem_i smem_i;
 #define MEM_F_REF_HDR	0x100
 #define MEM_F_SOFTCLIP  0x200
 #define MEM_F_SMARTPE   0x400
+#define MEM_F_PRIMARY5  0x800
 
 typedef struct {
 	int a, b;               // match score and mismatch penalty

bwamem_pair.c

@@ -243,6 +243,7 @@ int mem_pair(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, cons
 }
 
 void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const mem_aln_t *list, int which, const mem_aln_t *m);
+void mem_reorder_primary5(int T, mem_alnreg_v *a);
 
 #define raw_mapq(diff, a) ((int)(6.02 * (diff) / (a) + .499))
 
@@ -275,6 +276,10 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
 	}
 	n_pri[0] = mem_mark_primary_se(opt, a[0].n, a[0].a, id<<1|0);
 	n_pri[1] = mem_mark_primary_se(opt, a[1].n, a[1].a, id<<1|1);
+	if (opt->flag & MEM_F_PRIMARY5) {
+		mem_reorder_primary5(opt->T, &a[0]);
+		mem_reorder_primary5(opt->T, &a[1]);
+	}
 	if (opt->flag&MEM_F_NOPAIRING) goto no_pairing;
 	// pairing single-end hits
 	if (n_pri[0] && n_pri[1] && (o = mem_pair(opt, bns, pac, pes, s, a, id, &subo, &n_sub, z, n_pri)) > 0) {

fastmap.c

@@ -130,7 +130,7 @@ int main_mem(int argc, char *argv[])
 
 	aux.opt = opt = mem_opt_init();
 	memset(&opt0, 0, sizeof(mem_opt_t));
-	while ((c = getopt(argc, argv, "1paMCSPVYjk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:y:K:X:H:")) >= 0) {
+	while ((c = getopt(argc, argv, "51paMCSPVYjk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:y:K:X:H:")) >= 0) {
 		if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
 		else if (c == '1') no_mt_io = 1;
 		else if (c == 'x') mode = optarg;
@@ -147,6 +147,7 @@ int main_mem(int argc, char *argv[])
 		else if (c == 'S') opt->flag |= MEM_F_NO_RESCUE;
 		else if (c == 'Y') opt->flag |= MEM_F_SOFTCLIP;
 		else if (c == 'V') opt->flag |= MEM_F_REF_HDR;
+		else if (c == '5') opt->flag |= MEM_F_PRIMARY5;
 		else if (c == 'c') opt->max_occ = atoi(optarg), opt0.max_occ = 1;
 		else if (c == 'd') opt->zdrop = atoi(optarg), opt0.zdrop = 1;
 		else if (c == 'v') bwa_verbose = atoi(optarg);
@@ -265,6 +266,7 @@ int main_mem(int argc, char *argv[])
 		fprintf(stderr, "       -R STR        read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n");
 		fprintf(stderr, "       -H STR/FILE   insert STR to header if it starts with @; or insert lines in FILE [null]\n");
 		fprintf(stderr, "       -j            treat ALT contigs as part of the primary assembly (i.e. ignore <idxbase>.alt file)\n");
+		fprintf(stderr, "       -5            always take the leftmost alignment on a read as primary\n");
 		fprintf(stderr, "\n");
 		fprintf(stderr, "       -v INT        verbose level: 1=error, 2=warning, 3=message, 4+=debugging [%d]\n", bwa_verbose);
 		fprintf(stderr, "       -T INT        minimum score to output [%d]\n", opt->T);

main.c

@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.15-r1140"
+#define PACKAGE_VERSION "0.7.15-r1142-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);