From d41c03861644fb082820d038b08380a96826b244 Mon Sep 17 00:00:00 2001
From: zzh <zzhofhust@gmail.com>
Date: Sat, 6 Apr 2024 16:08:43 +0800
Subject: [PATCH] =?UTF-8?q?=E6=B8=85=E7=90=86=E4=B8=80=E4=BA=9Bfprintf?=
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---
 Makefile  |  2 +-
 bwa.c     |  2 +-
 fastmap.c |  2 +-
 fmt_idx.c |  2 ++
 run.sh    | 10 +++++-----
 5 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/Makefile b/Makefile
index 10e9363..3fd821a 100644
--- a/Makefile
+++ b/Makefile
@@ -22,7 +22,7 @@ PROG=		fastbwa
 INCLUDES=	
 LIBS=		-lm -lz -lpthread -ldl
 SUBDIRS=	.
-JE_MALLOC=#/home/zzh/work/jemalloc/lib/libjemalloc.a
+JE_MALLOC=/home/zzh/work/jemalloc/lib/libjemalloc.a
 
 ifeq ($(shell uname -s),Linux)
 	LIBS += -lrt
diff --git a/bwa.c b/bwa.c
index db2973c..c02f9ea 100644
--- a/bwa.c
+++ b/bwa.c
@@ -470,7 +470,7 @@ FMTIndex *bwa_idx_load_fmt(const char *hint)
 		return 0;
 	}
 	fmt = fmt_restore_fmt(fmt_idx_fn);
-	fprintf(stderr, "%s\n", kmer_idx_fn);
+	// fprintf(stderr, "%s\n", kmer_idx_fn);
 	fmt->kmer_hash = fmt_restore_kmer_idx(kmer_idx_fn);
 
 	strcpy(sa_fn, hint);
diff --git a/fastmap.c b/fastmap.c
index 13025c2..f2c160a 100644
--- a/fastmap.c
+++ b/fastmap.c
@@ -566,7 +566,7 @@ int main_mem(int argc, char *argv[])
 
 	if (opt->n_threads < 1) opt->n_threads = 1;
 	if (opt->batch_size < 1) opt->batch_size = 256;
-	fprintf(stderr, "batch_size: %d\n", opt->batch_size);
+	// fprintf(stderr, "batch_size: %d\n", opt->batch_size);
 
 	if (optind + 1 >= argc || optind + 3 < argc) {
 		fprintf(stderr, "\n");
diff --git a/fmt_idx.c b/fmt_idx.c
index 706dce2..d27faec 100644
--- a/fmt_idx.c
+++ b/fmt_idx.c
@@ -1053,6 +1053,8 @@ backward_search:
     fmt_reverse_intvs(curr); // s.t. smaller intervals (i.e. longer matches) visited first
     if (mt.num_match == 0)
         ret = curr->a[0].info; // this will be the returned value，扩展到的最远的位置
+    else
+        ret = (uint32_t)mt.info;
         // 按照种子进行遍历，反向扩展
 #define CHECK_ADD_MEM(pos, intv, mem)                                                                           \
     if (((int)((intv).info) - (pos) >= min_seed_len) && (mem->n == 0 || (pos) < mem->a[mem->n - 1].info >> 32)) \
diff --git a/run.sh b/run.sh
index 0fd12e7..ed1408b 100755
--- a/run.sh
+++ b/run.sh
@@ -10,8 +10,8 @@ thread=64
 ## d2
 #n_r1=~/data/fastq/dataset/na12878_wgs_101/s_1.fq
 #n_r2=~/data/fastq/dataset/na12878_wgs_101/s_2.fq
-n_r1=~/data/fastq/dataset/na12878_wgs_101/45m_r1.fq
-n_r2=~/data/fastq/dataset/na12878_wgs_101/45m_r2.fq
+#n_r1=~/data/fastq/dataset/na12878_wgs_101/45m_r1.fq
+#n_r2=~/data/fastq/dataset/na12878_wgs_101/45m_r2.fq
 # d3
 #n_r1=~/data/fastq/dataset/na12878_wgs_150/s_1.fq
 #n_r2=~/data/fastq/dataset/na12878_wgs_150/s_2.fq
@@ -20,8 +20,8 @@ n_r2=~/data/fastq/dataset/na12878_wgs_101/45m_r2.fq
 ## d4
 #n_r1=~/data/fastq/dataset/zy_wes/s_1.fq
 #n_r2=~/data/fastq/dataset/zy_wes/s_2.fq
-#n_r1=~/data/fastq/dataset/zy_wes/45mr1.fq.gz
-#n_r2=~/data/fastq/dataset/zy_wes/45mr2.fq.gz
+n_r1=~/data/fastq/dataset/zy_wes/45mr1.fq.gz
+n_r2=~/data/fastq/dataset/zy_wes/45mr2.fq.gz
 ## d5
 #n_r1=~/data/fastq/dataset/zy_wgs/45mr1.fq.gz
 #n_r2=~/data/fastq/dataset/zy_wgs/45mr2.fq.gz
@@ -36,7 +36,7 @@ reference=~/data1/fmt_ref/human_g1k_v37_decoy.fasta
 #out=./all.sam
 #out=./sn.sam
 #out=./ssn-x1.sam
-out=~/data1/d2-45m.sam
+out=~/data1/d4-45m.sam
 #out=~/data/out1.sam
 #out=/dev/null
 #out=./na12878.sam