From cdc2a1e29faa502f4172ef01dd2e9b3d75757a21 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Tue, 27 Jun 2017 22:03:31 -0400
Subject: [PATCH] r92: fixed a bug for overlapping alignment

On the PBcR example E. coli reads, miniasm gives one circular unitig.
---
 main.c   | 6 +++---
 map.c    | 1 +
 mmpriv.h | 2 ++
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/main.c b/main.c
index 101bbaa..c81f747 100644
--- a/main.c
+++ b/main.c
@@ -10,7 +10,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r90-pre"
+#define MM_VERSION "2.0-r92-pre"
 
 void liftrlimit()
 {
@@ -112,7 +112,7 @@ int main(int argc, char *argv[])
 		} else if (c == 'x') {
 			if (strcmp(optarg, "ava10k") == 0) {
 				opt.flag |= MM_F_AVA | MM_F_NO_SELF;
-				opt.min_score = 100;
+				opt.min_score = 100, opt.pri_ratio = 0.0f;
 				is_hpc = 1, k = 19, w = 5;
 			}
 		}
@@ -138,7 +138,7 @@ int main(int argc, char *argv[])
 		fprintf(stderr, "    -S         skip self and dual mappings\n");
 		fprintf(stderr, "    -p FLOAT   threshold to output a mapping [%g]\n", opt.pri_ratio);
 		fprintf(stderr, "    -x STR     preset (recommended to be applied before other options) []\n");
-		fprintf(stderr, "               ava10k: -Hk19 -Sw5 -s100 (PacBio/ONT all-vs-all read mapping)\n");
+		fprintf(stderr, "               ava10k: -Hk19 -Sw5 -p0 -s100 (PacBio/ONT all-vs-all read mapping)\n");
 		fprintf(stderr, "  Alignment:\n");
 		fprintf(stderr, "    -A INT     matching score [%d]\n", opt.a);
 		fprintf(stderr, "    -B INT     mismatch penalty [%d]\n", opt.b);
diff --git a/map.c b/map.c
index 9657915..c1ac90e 100644
--- a/map.c
+++ b/map.c
@@ -281,6 +281,7 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
 			}
 		}
 	}
+	n_a = j;
 	radix_sort_128x(a, a + n_a);
 	for (i = 0; i < n; ++i)
 		if (m[i].is_alloc) kfree(b->km, m[i].x.r);
diff --git a/mmpriv.h b/mmpriv.h
index cc56ad0..164e050 100644
--- a/mmpriv.h
+++ b/mmpriv.h
@@ -1,6 +1,7 @@
 #ifndef MMPRIV2_H
 #define MMPRIV2_H
 
+#include <assert.h>
 #include "minimap.h"
 #include "bseq.h"
 
@@ -41,6 +42,7 @@ static inline void mm_reg_set_coor(mm_reg1_t *r, int32_t qlen, const mm128_t *a)
 	int32_t k = r->as;
 	r->rev = a[k].x>>63;
 	r->rid = a[k].x<<1>>33;
+	assert(r->rid != 0x7fffffff);
 	r->rs = (int32_t)a[k].x + 1 > (int32_t)(a[k].y>>32)? (int32_t)a[k].x + 1 - (int32_t)(a[k].y>>32) : 0;
 	r->re = (int32_t)a[k + r->cnt - 1].x + 1;
 	if (!r->rev) {