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修改一些注释疏忽的问题

This commit is contained in:
zzh 2024-02-16 21:23:55 +08:00
parent 7dceae8c5d
commit 4a1c2cd3db
2 changed files with 10 additions and 8 deletions
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8
bwamem.c
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@ -176,7 +176,7 @@ static void mem_collect_intv(const mem_opt_t *opt, const bwt_t *bwt, const FMTIn
bwtintv_t *p = &a->mem1.a[i];
//fprintf(fp1, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info);
//fprintf(stderr, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info);
//int slen = (uint32_t)p->info - (p->info >> 32); // seed length
int slen = (uint32_t)p->info - (p->info >> 32); // seed length
//if (slen < 16) ++n16;
//if (slen < 17) ++n17;
//if (slen < 18) ++n18;
@ -212,7 +212,7 @@ static void mem_collect_intv(const mem_opt_t *opt, const bwt_t *bwt, const FMTIn
__sync_fetch_and_add(&time_bwt_smem1a, tmp_time);
#endif
for (i = 0; i < a->mem1.n; ++i) {
bwtintv_t *p = &a->mem1.a[i];
//bwtintv_t *p = &a->mem1.a[i];
//fprintf(fp1, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info);
//fprintf(stderr, "%ld %ld %ld %ld %d\n", p->x[0], p->x[1], p->x[2], p->info >> 32, (uint32_t)p->info);
//int slen = (uint32_t)p->info - (p->info >> 32);
@ -228,7 +228,7 @@ static void mem_collect_intv(const mem_opt_t *opt, const bwt_t *bwt, const FMTIn
//if (max_seed_len == len - start_N_num)
// goto collect_intv_end;
//goto collect_intv_end;
third_seed:
//third_seed:
// third pass: LAST-like
if (opt->max_mem_intv > 0) {
x = 0;
@ -262,7 +262,7 @@ third_seed:
}
}
collect_intv_end:
//collect_intv_end:
// sort
ks_introsort(mem_intv, a->mem.n, a->mem.a);
}

10
run.sh
View File

@ -6,15 +6,17 @@ thread=1
#reference=~/data/reference/human_g1k_v37_decoy.fasta
#n_r1=~/fastq/sn_r1.fq
#n_r2=~/fastq/sn_r2.fq
n_r1=~/fastq/tiny_n_r1.fq
n_r2=~/fastq/tiny_n_r2.fq
n_r1=~/fastq/sn_r1.fq
n_r2=~/fastq/sn_r2.fq
#n_r1=~/fastq/tiny_n_r1.fq
#n_r2=~/fastq/tiny_n_r2.fq
#n_r1=~/fastq/diff_r1.fq
#n_r2=~/fastq/diff_r2.fq
#n_r1=~/fastq/d_r1.fq
#n_r2=~/fastq/d_r2.fq
reference=~/reference/human_g1k_v37_decoy.fasta
out=./out.sam
#out=/dev/null
#out=./out.sam
out=/dev/null
#time ./bwa mem -t 12 -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
# /home/zzh/data/reference/human_g1k_v37_decoy.fasta \
# /home/zzh/data/fastq/nm1.fq \