xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-23 12:58:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

debug hic_hits

Browse Source
This commit is contained in:
chhylp123
2021-02-09 18:40:49 -05:00
parent 8467d58ef1
commit 5bb22f701c
3 changed files with 14 additions and 27 deletions
Download Patch File Download Diff File Expand all files Collapse all files
hic.cpp
+9 -12
View File
@@ -11401,19 +11401,17 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx)
return 1;
}
int hic_short_align_debug(const char *fn1, const char *fn2, ha_ug_index* idx)
int hic_short_align_back(const char *fn1, const char *fn2, ha_ug_index* idx)
{
double index_time = yak_realtime();
sldat_t sl;
gzFile fp1, fp2;
kvec_hc_edge back_hc_edge;
kv_init(back_hc_edge.a);
gzFile fp1, fp2;
if ((fp1 = gzopen(fn1, "r")) == 0) return 0;
if ((fp2 = gzopen(fn2, "r")) == 0) return 0;
sl.ks1 = kseq_init(fp1);
sl.ks2 = kseq_init(fp2);
sl.idx = idx;
sl.link = idx->link;
sl.chunk_size = 20000000;
@@ -11430,20 +11428,20 @@ int hic_short_align_debug(const char *fn1, const char *fn2, ha_ug_index* idx)
// load_reads(&R2, fn2);
// test_reads(&R1, fn1);
/*******************************for debug************************************/
fprintf(stderr, "+sl->hits.a.n: %u\n", (uint32_t)sl.hits.a.n);
kt_pipeline(3, worker_pipeline, &sl, 3);
fprintf(stderr, "+sl->hits.a.n: %u\n", (uint32_t)sl.hits.a.n);
dedup_hits(&sl.hits);
fprintf(stderr, "+sl->hits.a.n: %u\n", (uint32_t)sl.hits.a.n);
fprintf(stderr, "-sl->hits.a.n: %u\n", (uint32_t)sl.hits.a.n);
fprintf(stderr, "fn1: %s, fn2: %s\n", fn1, fn2);
/*******************************for debug************************************/
// sort_hits(&sl.hits);
// print_hits(idx, &sl.hits, fn1);
/*******************************for debug************************************/
dedup_hits(&sl.hits);
write_hc_hits(&sl.hits, asm_opt.output_file_name);
}
///fprintf(stderr, "u.n: %d, uID_bits: %lu, pos_bits: %lu, sl.hits.a.n: %u\n", (uint32_t)idx->ug->u.n, idx->uID_bits, idx->pos_bits, (uint32_t)sl.hits.a.n);
fprintf(stderr, "u.n: %d, uID_bits: %lu, pos_bits: %lu, sl.hits.a.n: %u\n", (uint32_t)idx->ug->u.n, idx->uID_bits, idx->pos_bits, (uint32_t)sl.hits.a.n);
H_partition hap;
MT M;
@@ -11515,7 +11513,6 @@ int hic_short_align_debug(const char *fn1, const char *fn2, ha_ug_index* idx)
destory_G_partition(gp); free(gp);
kv_destroy(sl.hits.a);
destory_bubbles(&bub);
kseq_destroy(sl.ks1);
kseq_destroy(sl.ks2);
gzclose(fp1);
@@ -11537,7 +11534,7 @@ void hic_analysis(ma_ug_t *ug, asg_t* read_g, hc_links* link)
ug_index->link = link;
///test_unitig_index(ug_index, ug);
///hic_short_align(asm_opt.hic_reads[0], asm_opt.hic_reads[1], ug_index);
hic_short_align_debug(asm_opt.hic_reads[0]->a[0], asm_opt.hic_reads[1]->a[0], ug_index);
hic_short_align_back(asm_opt.hic_reads[0]->a[0], asm_opt.hic_reads[1]->a[0], ug_index);
destory_hc_pt_index(ug_index);
}