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fix bugs for overlaps of different length

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This commit is contained in:
Haoyu Cheng
2019-12-09 17:07:11 -05:00
parent fca9c8db15
commit 09603432e5
11 changed files with 1726 additions and 94 deletions
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Correct.cpp
+186 -15
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@@ -7,6 +7,7 @@
#include "edlib.h"
#include "Assembly.h"
#include "CommandLines.h"
#include "ksw2.h"
long long T_total_match=0;
long long T_total_unmatch=0;
@@ -14,6 +15,36 @@ long long T_total_mis=0;
pthread_mutex_t debug_statistics ;
void align(const char *tseq, const char *qseq, const int tl, const int ql,
const uint8_t *c, int sc_mch, int sc_mis, int gapo, int gape, int bandLen, int zdrop,
int* max_q_pos, int* max_t, int* score)
{
int i, a = sc_mch, b = sc_mis < 0? sc_mis : -sc_mis; // a>0 and b<0
int8_t mat[25] = { a,b,b,b,0, b,a,b,b,0, b,b,a,b,0, b,b,b,a,0, 0,0,0,0,0 };
uint8_t *ts, *qs;
ksw_extz_t ez;
memset(&ez, 0, sizeof(ksw_extz_t));
ts = (uint8_t*)malloc(tl);
qs = (uint8_t*)malloc(ql);
for (i = 0; i < tl; ++i) ts[i] = c[(uint8_t)tseq[i]]; // encode to 0/1/2/3
for (i = 0; i < ql; ++i) qs[i] = c[(uint8_t)qseq[i]];
///ksw_extz(0, ql, qs, tl, ts, 5, mat, gapo, gape, -1, -1, 0, &ez);
ksw_extz2_sse(0, ql, qs, tl, ts, 5, mat, gapo, gape, bandLen, zdrop, sc_mch, 0, &ez);
/**
for (i = 0; i < ez.n_cigar; ++i) // print CIGAR
printf("%d%c", ez.cigar[i]>>4, "MID"[ez.cigar[i]&0xf]);
putchar('\n');
**/
free(ez.cigar); free(ts); free(qs);
(*score) = ez.max;
}
void clear_Round2_alignment(Round2_alignment* h)
{
clear_Correct_dumy_pure(&(h->dumy));
@@ -950,6 +981,116 @@ inline double trim_error_rate(overlap_region_alloc* overlap_list, long long ID)
return error_rate;
}
///error_rate should be 30%
long long get_high_error(long long x_start, long long x_end,
long long y_start, long long y_end, long long y_id, long long y_strand, long long pre_threshold,
long long n_steps, float error_rate, All_reads* R_INF, Correct_dumy* dumy,
UC_Read* g_read)
{
long long stepLen = (x_end - x_start + 1) / n_steps;
if((x_end - x_start + 1) % n_steps != 0)
{
stepLen++;
}
long long SubLen, SubWindowLen;
long long SubThreshold = THRESHOLD_MAX_SIZE;
int extra_begin, extra_end;
long long o_len;
long long T_error = 0;
y_start = y_start + pre_threshold;
while (x_start <= x_end)
{
SubLen = x_end - x_start + 1;
if(SubLen > stepLen)
{
SubLen = stepLen;
}
SubThreshold = SubLen * error_rate;
if(SubThreshold > THRESHOLD_MAX_SIZE)
{
SubThreshold = THRESHOLD_MAX_SIZE;
}
SubThreshold = Adjust_Threshold(SubThreshold, SubLen);
SubWindowLen = SubLen + (SubThreshold << 1);
if(determine_overlap_region(SubThreshold, y_start, y_id, SubWindowLen, R_INF,
&extra_begin, &extra_end, &y_start, &o_len) == 0)
{
T_error = T_error + (x_end - x_start + 1) * error_rate * 1.5;
break;
}
fill_subregion(dumy->overlap_region, y_start, o_len, y_strand, R_INF, y_id,
extra_begin, extra_end);
char* x_string = g_read->seq + x_start;
char* y_string = dumy->overlap_region;
int end_site;
unsigned int error;
end_site = Reserve_Banded_BPM(y_string, SubWindowLen, x_string, SubLen, SubThreshold, &error);
///error等于-1说明没匹配
if (error!=(unsigned int)-1)
{
T_error = T_error + error;
y_start = y_start + end_site - extra_begin + 1;
}
else
{
T_error = T_error + SubLen * error_rate * 1.5;
y_start = y_start + SubThreshold - extra_begin + SubLen;
}
x_start = x_start + SubLen;
}
return T_error;
}
inline double non_trim_error_rate(overlap_region_alloc* overlap_list, long long ID,
All_reads* R_INF, Correct_dumy* dumy, UC_Read* g_read)
{
long long tLen, tError,i, subWinLen, subWinNum;
tLen = 0;
tError = 0;
subWinNum = overlap_list->list[ID].w_list_length;
for (i = 0; i < subWinNum; i++)
{
subWinLen = overlap_list->list[ID].w_list[i].x_end - overlap_list->list[ID].w_list[i].x_start + 1;
tLen += subWinLen;
if(overlap_list->list[ID].w_list[i].y_end != -1)
{
tError += overlap_list->list[ID].w_list[i].error;
}
else
{
tError +=
get_high_error(overlap_list->list[ID].w_list[i].x_start,
overlap_list->list[ID].w_list[i].x_end, overlap_list->list[ID].w_list[i].y_start,
overlap_list->list[ID].w_list[i].y_end, overlap_list->list[ID].y_id,
overlap_list->list[ID].y_pos_strand,
overlap_list->list[ID].w_list[i].error_threshold - overlap_list->list[ID].w_list[i].extra_begin,
3, 0.3, R_INF, dumy, g_read);
}
}
double error_rate = (double)(tError)/(double)(tLen);
return error_rate;
}
void mark_duplicate(overlap_region_alloc* overlap_list, All_reads* R_INF,
@@ -3044,7 +3185,9 @@ inline void recalcate_window(overlap_region_alloc* overlap_list, All_reads* R_IN
}
}
error_rate = trim_error_rate(overlap_list, j);
///error_rate = trim_error_rate(overlap_list, j);
error_rate = non_trim_error_rate(overlap_list, j, R_INF, dumy, g_read);
///if(error_rate <= 0.015)
if(error_rate <= 0.03)
@@ -8638,6 +8781,19 @@ uint32_t* SNPs, long long SNPLen, haplotype_evdience_alloc* hap)
for (i = 0; i < SNPLen; i++)
{
snpID = SNPs[i];
///if(overlap_list->list[0].x_id == 83735)
///if(overlap_list->list[0].x_id == 83739)
// if(overlap_list->list[0].x_id == 1185538)
// {
// fprintf(stderr, "SNPLen: %d, x_id: %d, hap->snp_stat[snpID].site: %d, occ_0: %d, occ_1: %d, occ_2: %d, overlap_num: %d\n",
// SNPLen, overlap_list->list[0].x_id, hap->snp_stat[snpID].site,
// hap->snp_stat[snpID].occ_0, hap->snp_stat[snpID].occ_1, hap->snp_stat[snpID].occ_2,
// hap->snp_stat[snpID].overlap_num);
// }
///check all overlaps
for (j = 0; j < Get_SNP_Vector_Length((*hap)); j++)
@@ -9578,6 +9734,22 @@ Correct_dumy* dumy)
}
int debug_print_snp_stat(char* name, haplotype_evdience_alloc* hap, overlap_region_alloc* overlap_list, All_reads* R_INF)
{
if(overlap_list->length > 0 &&
memcmp(name, Get_NAME((*R_INF), overlap_list->list[0].x_id),
Get_NAME_LENGTH((*R_INF), overlap_list->list[0].x_id)) == 0)
{
fprintf(stderr, "\n%s, available_snp: %d\n", name, hap->available_snp);
int i;
for (i = 0; i < hap->available_snp; i++)
{
fprintf(stderr, "site: %d, occ_0: %d, occ_1: %d, occ_2: %d\n",
hap->snp_stat[i].site, hap->snp_stat[i].occ_0,
hap->snp_stat[i].occ_1, hap->snp_stat[i].occ_2);
}
}
}
int generate_haplotypes_DP(haplotype_evdience_alloc* hap, overlap_region_alloc* overlap_list, All_reads* R_INF, long long rLen,
int force_repeat)
@@ -9595,8 +9767,9 @@ int force_repeat)
return 0;
}
// debug_print_snp_stat("m64016_190918_162737/174131552/ccs", hap, overlap_list, R_INF);
///if hap->available_snp == 1, the following codes would have bugs
///filter snps that are highly likly false
if(hap->available_snp > 1)
@@ -9817,6 +9990,8 @@ int force_repeat)
}
}
// debug_print_snp_stat("m64016_190918_162737/174131552/ccs", hap, overlap_list, R_INF);
//if(hap->dp.max_snp_num > 0)
if(hap->available_snp > 0)
@@ -10537,7 +10712,6 @@ void correct_overlap_back(overlap_region_alloc* overlap_list, All_reads* R_INF,
}
void print_overlap(char* name, long long readID,
overlap_region_alloc* overlap_list, All_reads* R_INF, int output_reads)
{
@@ -10545,8 +10719,8 @@ overlap_region_alloc* overlap_list, All_reads* R_INF, int output_reads)
Get_NAME_LENGTH((*R_INF),readID)) == 0)
{
long long i, j;
fprintf(stderr, "\n\n****************ref_read: %.*s****************\n",
Get_NAME_LENGTH((*R_INF),readID), Get_NAME((*R_INF),readID));
fprintf(stderr, "\n\n****************ref_read: %.*s, id: %d****************\n",
Get_NAME_LENGTH((*R_INF),readID), Get_NAME((*R_INF),readID), readID);
fprintf(stderr, "\n###flag: 1\n");
@@ -10618,10 +10792,10 @@ overlap_region_alloc* overlap_list, All_reads* R_INF, int output_reads)
fprintf(stderr, ">%.*s\n", Get_NAME_LENGTH((*R_INF),readID), Get_NAME((*R_INF),readID));
fprintf(stderr, "%.*s\n", g_read.length, g_read.seq);
fprintf(stderr, "query_read:\n");
///fprintf(stderr, "query_read:\n");
for (i = 0; i < overlap_list->length; i++)
{
fprintf(stderr, "i: %d\n", i);
///fprintf(stderr, "i: %d\n", i);
recover_UC_Read(&g_read, R_INF, overlap_list->list[i].y_id);
fprintf(stderr, ">%.*s\n",
Get_NAME_LENGTH((*R_INF),overlap_list->list[i].y_id),
@@ -10629,6 +10803,8 @@ overlap_region_alloc* overlap_list, All_reads* R_INF, int output_reads)
fprintf(stderr, "%.*s\n", g_read.length, g_read.seq);
}
fprintf(stderr, "Has already output all related reads\n\n");
destory_UC_Read(&g_read);
@@ -10684,13 +10860,14 @@ overlap_region_alloc* overlap_list, All_reads* R_INF, int output_reads)
}
void correct_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF,
UC_Read* g_read, Correct_dumy* dumy, UC_Read* overlap_read, Graph* g, Graph* DAGCon,
long long* matched_overlap_0, long long* matched_overlap_1,
long long* potiental_matched_overlap_0, long long* potiental_matched_overlap_1,
Cigar_record* current_cigar, haplotype_evdience_alloc* hap,
Round2_alignment* second_round, int force_repeat, int is_consensus,
int* fully_cov, int* abnormal)
int* fully_cov, int* abnormal, uint8_t* c2n)
{
reverse_complement(g_read->seq, g_read->length);
@@ -10735,18 +10912,12 @@ void correct_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF,
recalcate_window(overlap_list, R_INF, g_read, dumy, overlap_read);
// print_overlap("m64011_190329_072846/59507330/ccs",
// overlap_list->list[0].x_id, overlap_list, R_INF);
partition_overlaps(overlap_list, R_INF, g_read, dumy, hap, force_repeat);
// print_overlap("m64016_190918_162737/53545052/ccs",
// print_overlap("m64016_190918_162737/174131552/ccs",
// overlap_list->list[0].x_id, overlap_list, R_INF, 1);
if(is_consensus)
{