zzh
/
fast-bwa
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

清理一些fprintf

This commit is contained in:
zzh 2024-04-06 16:08:43 +08:00
parent 3e20d7ee0f
commit d41c038616
5 changed files with 10 additions and 8 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
Makefile
View File

@ -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

2
bwa.c
View File

@ -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);

2
fastmap.c
View File

@ -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");

2
fmt_idx.c
View File

@ -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)) \

10
run.sh
View File

@ -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