From 10db6b0434191ccd323b72a7429cce230f88ca63 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Thu, 4 May 2017 17:45:19 +0800
Subject: [PATCH] wrong HPC

---
 map.c    | 8 +++++---
 sketch.c | 2 +-
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/map.c b/map.c
index 88d62e1..2c22899 100644
--- a/map.c
+++ b/map.c
@@ -10,7 +10,7 @@
 void mm_mapopt_init(mm_mapopt_t *opt)
 {
 	memset(opt, 0, sizeof(mm_mapopt_t));
-	opt->n_frag_mini = 100;
+	opt->n_frag_mini = 1000;
 	opt->max_occ_frac = 1e-5f;
 	opt->mid_occ_frac = 2e-4f;
 	opt->sdust_thres = 0;
@@ -261,7 +261,7 @@ void mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b, uint3
 		}
 	}
 	radix_sort_128x(a, a + n_a);
-//	for (i = 0; i < n_a; ++i) printf("%c\t%d\t%d\n", "+-"[a[i].x>>63], (uint32_t)a[i].x>>1, (uint32_t)a[i].y);
+	//for (i = 0; i < n_a; ++i) printf("%c\t%s\t%d\t%d\n", "+-"[a[i].x>>63], mi->seq[a[i].x<<1>>33].name, (uint32_t)a[i].x>>1, (uint32_t)a[i].y);
 
 	t = (int*)kmalloc(b->km_fixed, (n_a + opt->min_cnt - 1) / opt->min_cnt * sizeof(int));
 	n_t = mm_liss(opt->radius, opt->min_cnt, b->km_fixed, n_a, a, t);
@@ -278,7 +278,9 @@ void mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b, uint3
 		else if (t[i] > max2) max2 = t[i];
 		off += t[i];
 	}
-	printf("%s\t%d\t%d\t", qname, max, max2);
+	if (a_st) printf("%s:%d-%d", qname, (uint32_t)a_st->y, (uint32_t)(a_en-1)->y);
+	else printf("%s:*", qname);
+	printf("\t%d\t%d\t", max, max2);
 	if (max_i >= 0) printf("%s:%d-%d", mi->seq[a_st->x<<1>>33].name, (uint32_t)a_st->x>>1, (uint32_t)(a_en-1)->x>>1);
 	else printf("*");
 	printf("\t%d\t%d\t%d\t%d\t%d\n", n_tot, n_low, s_low, n, n_t);
diff --git a/sketch.c b/sketch.c
index c5da0d9..b141cba 100644
--- a/sketch.c
+++ b/sketch.c
@@ -112,7 +112,7 @@ void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, i
 				info.x = hash64(kmer[z], mask) << 8 | kmer_span;
 				info.y = (uint64_t)rid<<32 | (uint32_t)i<<1 | z;
 			}
-		} else l = 0, tq.count = tq.front = 0;
+		} else l = 0, tq.count = tq.front = 0, kmer_span = 0;
 		buf[buf_pos] = info; // need to do this here as appropriate buf_pos and buf[buf_pos] are needed below
 		if (l == w + k - 1) { // special case for the first window - because identical k-mers are not stored yet
 			for (j = buf_pos + 1; j < w; ++j)