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This commit is contained in:
Haoyu Cheng
2019-12-12 20:12:52 -05:00
parent 9c25075fed
commit 90195293f1
2 changed files with 259 additions and 40 deletions
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Correct.cpp
+257 -38
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@@ -7115,7 +7115,6 @@ Cigar_record* current_cigar, long long uncorrected_window_start, Round2_alignmen
backbone_length = corrected_window_end - corrected_window_start + 1;
addUnmatchedSeqToGraph(g, backbone, backbone_length, &startNodeID, &endNodeID);
///fprintf(stderr, "startNodeID: %d, endNodeID: %d\n", startNodeID, endNodeID);
long long correct_x_pos_s;
long long matched_coverage = 0;
@@ -7125,7 +7124,7 @@ Cigar_record* current_cigar, long long uncorrected_window_start, Round2_alignmen
correct_x_pos_s = (overlap_list->list[overlapID].x_pos_s / WINDOW) * WINDOW;
windowID = (uncorrected_window_start - correct_x_pos_s) / WINDOW;
///如果这个window不匹配，跳过
///skip if window is unmatched
if (overlap_list->list[overlapID].w_list[windowID].y_end == -1)
{
continue;
@@ -7139,7 +7138,7 @@ Cigar_record* current_cigar, long long uncorrected_window_start, Round2_alignmen
/**
* There are total 3 cases:
* 1. this window of x is overlapped totally by y
* 1. this window of x is overlapped fully by y
* x: ------|------|---------
* y: ------|------|---------
* in this case, x_start == uncorrected_window_start, x_length == WINDOW
@@ -7626,24 +7625,26 @@ CIGAR* cigar, haplotype_evdience_alloc* hap)
int operation;
int operationLen;
int i;
///mismatches based on the offset of x
long long inner_offset = x_total_start - window_offset;
///note that node 0 is the start node
///0 is match, 1 is mismatch, 2 is up, 3 is left
///2是x缺字符（y多字符），而3是y缺字符（x多字符）
///2 represents thre are more bases at y
///3 represents thre are more bases at x
while (cigar_i < cigar->length)
{
operation = cigar->C_C[cigar_i];
operationLen = cigar->C_L[cigar_i];
///这种情况代表匹配和mismatch
///match
if (operation == 0)
{
x_i += operationLen;
y_i += operationLen;
}
else if(operation == 1)
else if(operation == 1) ///mismatch
{
for (i = 0; i < operationLen; i++)
{
@@ -7667,8 +7668,6 @@ CIGAR* cigar, haplotype_evdience_alloc* hap)
cigar_i++;
}
}
@@ -7693,17 +7692,19 @@ CIGAR* cigar, haplotype_evdience_alloc* hap, int snp_threshold)
///note that node 0 is the start node
///0 is match, 1 is mismatch, 2 is up, 3 is left
///2是x缺字符（y多字符），而3是y缺字符（x多字符）
///2 represents thre are more bases at y
///3 represents thre are more bases at x
while (cigar_i < cigar->length)
{
operation = cigar->C_C[cigar_i];
operationLen = cigar->C_L[cigar_i];
///这种情况代表匹配和mismatch
///matches
if (operation == 0)
{
for (i = 0; i < operationLen; i++)
{
///should be at least 2 mismatches
if(hap->flag[inner_offset] > snp_threshold)
{
ev.misBase = y_string[y_i];
@@ -7747,7 +7748,7 @@ CIGAR* cigar, haplotype_evdience_alloc* hap, int snp_threshold)
}
else if (operation == 3)
{
/****************************may have bugs********************************/
for (i = 0; i < operationLen; i++)
{
if(hap->flag[inner_offset] > snp_threshold)
@@ -7763,6 +7764,7 @@ CIGAR* cigar, haplotype_evdience_alloc* hap, int snp_threshold)
inner_offset++;
x_i++;
}
/****************************may have bugs********************************/
}
cigar_i++;
@@ -7779,10 +7781,10 @@ CIGAR* cigar, haplotype_evdience_alloc* hap, int snp_threshold)
void cluster(char* r_string, long long window_start, long long window_end,
overlap_region_alloc* overlap_list, Correct_dumy* dumy, All_reads* R_INF, haplotype_evdience_alloc* hap)
{
///window_start, window_end, and useful_length correspond to x, instead of y
long long useful_length = window_end - window_start + 1;
long long x_start;
long long x_length;
@@ -7796,23 +7798,13 @@ overlap_region_alloc* overlap_list, Correct_dumy* dumy, All_reads* R_INF, haplot
long long correct_x_pos_s;
long long inner_window_offset;
int snp_threshold;
/**
if(overlap_list->mapped_overlaps > Coverage_Threshold(coverage))
{
snp_threshold = 0;
}
else**/
{
snp_threshold = 1;
}
snp_threshold = 1;
///与当前window重叠的所有overlap
///all overlaps related to the current window [window_start, window_end]
///first mark all snp pos
for (i = 0; i < dumy->length; i++)
{
///这个是那个overlap的ID，而不是overlap里对应窗口的ID
///overlap id, instead of the window id or the y id
overlapID = dumy->overlapID[i];
///overlap_list->list[overlapID].x_pos_s is the begining of the whole overlap
@@ -7820,13 +7812,14 @@ overlap_region_alloc* overlap_list, Correct_dumy* dumy, All_reads* R_INF, haplot
///window_start is the begining of this window in the whole x_read
windowID = (window_start - correct_x_pos_s) / WINDOW;
///如果这个window不匹配，跳过
///skip if this window is not matched
if (overlap_list->list[overlapID].w_list[windowID].y_end == -1)
{
continue;
}
///both x_start and y_start are the begining of the whole x_read and y_read
///both x_start and y_start are the offsets of the whole x_read and y_read
///instead of the offsets of window
x_start = overlap_list->list[overlapID].w_list[windowID].x_start;
x_length = overlap_list->list[overlapID].w_list[windowID].x_end
- overlap_list->list[overlapID].w_list[windowID].x_start + 1;
@@ -7836,33 +7829,35 @@ overlap_region_alloc* overlap_list, Correct_dumy* dumy, All_reads* R_INF, haplot
- overlap_list->list[overlapID].w_list[windowID].y_start + 1;
markSNP(window_start, x_start, x_length, y_start, y_length, &(overlap_list->list[overlapID].w_list[windowID].cigar),
hap);
markSNP(window_start, x_start, x_length, y_start, y_length,
&(overlap_list->list[overlapID].w_list[windowID].cigar), hap);
}
/****************************may have bugs********************************/
long long last_snp = useful_length - 1;
long long last_snp = -1;
long long first_snp = -1;
for (i = 0; i < useful_length; i++)
{
if(hap->flag[i] != 0)
{
last_snp = i;
if(first_snp != -1)
if(first_snp == -1)
{
first_snp = i;
}
}
///for a real snp, the coverage should be at least 2
if(hap->flag[i] > snp_threshold)
{
hap->snp++;
}
}
if(first_snp == -1)
///if there are any >0 elements, both first_snp and last_snp should be != -1
if(first_snp == -1 || last_snp == -1)
{
first_snp = 0;
last_snp = -1;
}
/****************************may have bugs********************************/
@@ -7871,7 +7866,7 @@ overlap_region_alloc* overlap_list, Correct_dumy* dumy, All_reads* R_INF, haplot
///add the information related to snp to haplotype_evdience_alloc
for (i = 0; i < dumy->length; i++)
{
///这个是那个overlap的ID，而不是overlap里对应窗口的ID
///overlap ID, instead of the window ID
overlapID = dumy->overlapID[i];
///overlap_list->list[overlapID].x_pos_s is the begining of the whole overlap
@@ -7879,13 +7874,14 @@ overlap_region_alloc* overlap_list, Correct_dumy* dumy, All_reads* R_INF, haplot
///window_start is the begining of this window in the whole x_read
windowID = (window_start - correct_x_pos_s) / WINDOW;
///如果这个window不匹配，跳过
///skip if this window is not matched
if (overlap_list->list[overlapID].w_list[windowID].y_end == -1)
{
continue;
}
///both x_start and y_start are the begining of the whole x_read and y_read
///both x_start and y_start are the offsets of the whole x_read and y_read
///instead of the offsets of window
x_start = overlap_list->list[overlapID].w_list[windowID].x_start;
x_length = overlap_list->list[overlapID].w_list[windowID].x_end
- overlap_list->list[overlapID].w_list[windowID].x_start + 1;
@@ -7907,7 +7903,133 @@ overlap_region_alloc* overlap_list, Correct_dumy* dumy, All_reads* R_INF, haplot
hap, snp_threshold);
}
RsetInitHaplotypeEvdienceFlag(hap + first_snp, last_snp + 1);
RsetInitHaplotypeEvdienceFlag(hap, first_snp, last_snp + 1 - first_snp);
}
void cluster_advance(char* r_string, long long window_start, long long window_end,
overlap_region_alloc* overlap_list, Correct_dumy* dumy, All_reads* R_INF, haplotype_evdience_alloc* hap)
{
///window_start, window_end, and useful_length correspond to x, instead of y
long long useful_length = window_end - window_start + 1;
long long x_start;
long long x_length;
char* x_string;
char* y_string;
long long i;
long long y_start, y_length;
long long overlapID, windowID;
long long startNodeID, endNodeID, currentNodeID;
long long correct_x_pos_s;
long long inner_window_offset;
int snp_threshold;
snp_threshold = 1;
///all overlaps related to the current window [window_start, window_end]
///first mark all snp pos
for (i = 0; i < dumy->length; i++)
{
///overlap id, instead of the window id or the y id
overlapID = dumy->overlapID[i];
///overlap_list->list[overlapID].x_pos_s is the begining of the whole overlap
correct_x_pos_s = (overlap_list->list[overlapID].x_pos_s / WINDOW) * WINDOW;
///window_start is the begining of this window in the whole x_read
windowID = (window_start - correct_x_pos_s) / WINDOW;
///skip if this window is not matched
if (overlap_list->list[overlapID].w_list[windowID].y_end == -1)
{
continue;
}
///both x_start and y_start are the offsets of the whole x_read and y_read
///instead of the offsets of window
x_start = overlap_list->list[overlapID].w_list[windowID].x_start;
x_length = overlap_list->list[overlapID].w_list[windowID].x_end
- overlap_list->list[overlapID].w_list[windowID].x_start + 1;
y_start = overlap_list->list[overlapID].w_list[windowID].y_start;
y_length = overlap_list->list[overlapID].w_list[windowID].y_end
- overlap_list->list[overlapID].w_list[windowID].y_start + 1;
markSNP(window_start, x_start, x_length, y_start, y_length,
&(overlap_list->list[overlapID].w_list[windowID].cigar), hap);
}
/****************************may have bugs********************************/
long long last_snp = -1;
long long first_snp = -1;
for (i = 0; i < useful_length; i++)
{
if(hap->flag[i] != 0)
{
last_snp = i;
if(first_snp == -1)
{
first_snp = i;
}
}
///for a real snp, the coverage should be at least 2
if(hap->flag[i] > snp_threshold)
{
hap->snp++;
}
}
///if there are any >0 elements, both first_snp and last_snp should be != -1
if(first_snp == -1 || last_snp == -1)
{
first_snp = 0;
last_snp = -1;
}
/****************************may have bugs********************************/
///add the information related to snp to haplotype_evdience_alloc
for (i = 0; i < dumy->length; i++)
{
///overlap ID, instead of the window ID
overlapID = dumy->overlapID[i];
///overlap_list->list[overlapID].x_pos_s is the begining of the whole overlap
correct_x_pos_s = (overlap_list->list[overlapID].x_pos_s / WINDOW) * WINDOW;
///window_start is the begining of this window in the whole x_read
windowID = (window_start - correct_x_pos_s) / WINDOW;
///skip if this window is not matched
if (overlap_list->list[overlapID].w_list[windowID].y_end == -1)
{
continue;
}
///both x_start and y_start are the offsets of the whole x_read and y_read
///instead of the offsets of window
x_start = overlap_list->list[overlapID].w_list[windowID].x_start;
x_length = overlap_list->list[overlapID].w_list[windowID].x_end
- overlap_list->list[overlapID].w_list[windowID].x_start + 1;
y_start = overlap_list->list[overlapID].w_list[windowID].y_start;
y_length = overlap_list->list[overlapID].w_list[windowID].y_end
- overlap_list->list[overlapID].w_list[windowID].y_start + 1;
recover_UC_Read_sub_region(dumy->overlap_region, y_start, y_length, overlap_list->list[overlapID].y_pos_strand,
R_INF, overlap_list->list[overlapID].y_id);
x_string = r_string + x_start;
y_string = dumy->overlap_region;
addSNPtohaplotype(window_start, overlapID, x_string, x_start, x_length,
y_string, y_start, y_length, &(overlap_list->list[overlapID].w_list[windowID].cigar),
hap, snp_threshold);
}
RsetInitHaplotypeEvdienceFlag(hap, first_snp, last_snp + 1 - first_snp);
}
int cmp_haplotype_evdience(const void * a, const void * b)
@@ -11245,7 +11367,103 @@ void partition_overlaps(overlap_region_alloc* overlap_list, All_reads* R_INF,
}
void partition_overlaps_advance(overlap_region_alloc* overlap_list, All_reads* R_INF,
UC_Read* g_read, Correct_dumy* dumy, haplotype_evdience_alloc* hap,
int force_repeat)
{
ResizeInitHaplotypeEvdience(hap);
long long i, j, overlap_length;
long long window_start, window_end;
long long num_availiable_win = 0;
Window_Pool w_inf;
init_Window_Pool(&w_inf, g_read->length, WINDOW, TAIL_LENGTH);
int flag = 0;
while(get_Window(&w_inf, &window_start, &window_end) && flag != -2)
{
dumy->length = 0;
dumy->lengthNT = 0;
///flag返回的是重叠数量
///dumy->length返回的是有效完全重叠的数量
///dumy->lengthNT返回的是有效不完全重叠的数量
///return overlaps that is overlaped with [window_start, window_end]
flag = get_available_interval(window_start, window_end, overlap_list, dumy);
switch (flag)
{
case 1: ///找到匹配
break;
case 0: ///没找到匹配
break;
case -2: ///下一个window也不会存在匹配, 直接跳出
break;
}
///这个是available overlap里所有window的数量...
///num_availiable_win = num_availiable_win + dumy->length + dumy->lengthNT;
num_availiable_win = num_availiable_win + dumy->length;
cluster_advance(g_read->seq, window_start, window_end, overlap_list, dumy, R_INF, hap);
}
///very time-consuming
qsort(hap->list, hap->length, sizeof(haplotype_evdience), cmp_haplotype_evdience);
///debug_hap_information(overlap_list, R_INF, g_read, hap, dumy);
SetSnpMatrix(hap, hap->snp, overlap_list->length);
uint64_t pre_site = (uint64_t)-1;
uint64_t num_of_snps = 0;
long long pre_i = -1;
long long sub_length;
haplotype_evdience* sub_list;
///long long debug_total_length = 0;
////split reads
for (i = 0; i < hap->length; i++)
{
if(pre_site != hap->list[i].site)
{
if(i != 0)
{
sub_list = hap->list + pre_i;
sub_length = i - pre_i;
///debug_total_length = debug_total_length + sub_length;
split_sub_list(hap, sub_list, sub_length, hap->snp, overlap_list, R_INF, g_read);
}
num_of_snps++;
pre_site = hap->list[i].site;
pre_i = i;
}
}
if(pre_i != -1)
{
sub_list = hap->list + pre_i;
sub_length = i - pre_i;
///debug_total_length = debug_total_length + sub_length;
split_sub_list(hap, sub_list, sub_length, hap->snp, overlap_list, R_INF, g_read);
}
///debug_snp_matrix(hap);
generate_haplotypes_DP(hap, overlap_list, R_INF, g_read->length, force_repeat);
///generate_haplotypes_naive(hap, overlap_list, R_INF, g_read->length, force_repeat);
lable_large_indels(overlap_list, R_INF, g_read->length, dumy);
///debug_snp_matrix(hap);
}
@@ -11545,7 +11763,8 @@ void correct_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF,
partition_overlaps(overlap_list, R_INF, g_read, dumy, hap, force_repeat);
////partition_overlaps(overlap_list, R_INF, g_read, dumy, hap, force_repeat);
partition_overlaps_advance(overlap_list, R_INF, g_read, dumy, hap, force_repeat);
// print_overlap("m64016_190918_162737/174131552/ccs",