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r495-reuse misjoin detection

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chhylp123
2023-01-12 00:21:43 -05:00
parent 0613b18af9
commit 7ad498f631
3 changed files with 20 additions and 2 deletions
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2
CommandLines.h
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@@ -4,7 +4,7 @@
#include <pthread.h>
#include <stdint.h>
#define HA_VERSION "0.18.3-r493"
#define HA_VERSION "0.18.3-r495"
#define VERBOSE 0

18
Correct.cpp
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@@ -3485,6 +3485,24 @@ inline void recalcate_window_advance(overlap_region_alloc* overlap_list, All_rea
///note!!! need notification
end_site = Reserve_Banded_BPM_PATH(y_string, Window_Len, x_string, x_len, threshold, &error, &real_y_start,
&(dumy->path_length), dumy->matrix_bit, dumy->path, p->error, p->y_end - y_start);
// if(!(error != (unsigned int)-1)) {
// fprintf(stderr, "[M::%s::]\tqid::%u\tqlen::%lu\tq::[%d,\t%d)\ttid::%u\ttlen::%lu\tt::[%d,\t%d)\te_beg::%d\te_end::%d\terr::%d\n", __func__,
// overlap_list->list[j].x_id, Get_READ_LENGTH((*rref), overlap_list->list[j].x_id),
// p->x_start, p->x_end+1,
// overlap_list->list[j].y_id, Get_READ_LENGTH((*rref), overlap_list->list[j].y_id),
// p->y_start, p->y_end+1,
// p->extra_begin, p->extra_end, p->error);
// fprintf(stderr, "[M::%s::]\tqcal_len::%lld\ttcal_len::%lld\tthres::%d\n", __func__,
// x_len, Window_Len, threshold);
// fprintf(stderr, "qid::%u\nqname::%.*s\n\t%.*s\n", overlap_list->list[j].x_id,
// (int32_t)Get_NAME_LENGTH((*rref), overlap_list->list[j].x_id),
// Get_NAME((*rref), overlap_list->list[j].x_id), (int32_t)x_len, x_string);
// fprintf(stderr, "tid::%u\ntname::%.*s\n\t%.*s\n", overlap_list->list[j].y_id,
// (int32_t)Get_NAME_LENGTH((*rref), overlap_list->list[j].y_id),
// Get_NAME((*rref), overlap_list->list[j].y_id), (int32_t)Window_Len, y_string);
// }
assert(error != (unsigned int)-1);
{

2
hic.cpp
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@@ -16746,7 +16746,7 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
////dedup_hits(&(sl.hits), sl.idx);
///write_hc_hits_v14(&sl.hits, asm_opt.output_file_name);
if(asm_opt.misjoin_len > 0)
if(asm_opt.misjoin_len > 0/** && (!(asm_opt.ar))**/)//disable it for the UL assembly
{
update_switch_unitig(idx->ug, idx->read_g, &(sl.hits), &(idx->t_ch->k_trans), 10, 20, asm_opt.misjoin_len, 0.15);
renew_idx_para(idx, idx->ug);