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This commit is contained in:
Haoyu Cheng
2019-07-08 01:06:36 -04:00
parent 87873d6323
commit 1892b4d2db
6 changed files with 1315 additions and 940 deletions
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Correct.cpp
+212 -184
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@@ -1,6 +1,7 @@
#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#include <pthread.h>
#include "Correct.h"
#include "Levenshtein_distance.h"
#include "edlib.h"
@@ -8,6 +9,7 @@
long long T_total_match=0;
long long T_total_unmatch=0;
long long T_total_mis=0;
pthread_mutex_t debug_statistics ;
#define MAX(x, y) ((x >= y)?x:y)
@@ -286,7 +288,6 @@ long long o_len, int threashold, int error, long long* total_mis)
if (result.status == EDLIB_STATUS_OK) {
if (result.editDistance != error)
///if (result.editDistance != error && result.endLocations[0] > x_len)
{
(*total_mis)++;
@@ -310,36 +311,61 @@ long long o_len, int threashold, int error, long long* total_mis)
char* cigar = edlibAlignmentToCigar(result.alignment, result.alignmentLength, EDLIB_CIGAR_STANDARD);
int cigar_length = strlen(cigar);
/**
for (int i = cigar_length - 1; i >= 0; i--)
int i = cigar_length - 1;
int j = 0;
char tmp;
while (i >= 0)
{
switch (cigar[i])
if (up_length < 0 || left_length < 0)
{
case 'I':
break;
default:
break;
}
}
**/
///fprintf(stderr,"%s\n", cigar);
free(cigar);
/**
fprintf(stderr, "****\ni: %u, edlib: %d, alignmentLength: %d, startLocations: %d, endLocations: %d\n",
i, result.editDistance, result.alignmentLength, result.startLocations[0], result.endLocations[0]);
char* cigar = edlibAlignmentToCigar(result.alignment, result.alignmentLength, EDLIB_CIGAR_STANDARD);
fprintf(stderr,"%s\n", cigar);
free(cigar);
print_string(x_string, x_len);
print_string(y_string, o_len);
fprintf(stderr, "BPM: %d\n", error);
**/
if (cigar[i] == 'I' || cigar[i] == 'D')
{
tmp = cigar[i];
cigar[i] = '\0';
j = i - 1;
while (cigar[j] <= '9' && cigar[j] >= '0' && j >= 0)
{
j--;
}
j++;
int Len = atoi(cigar + j);
cigar[i] = tmp;
i = j - 1;
if (tmp == 'I')
{
up_length = up_length - Len;
left_length = left_length + Len;
}
else
{
left_length = left_length - Len;
up_length = up_length + Len;
}
}
else
{
i--;
}
}
if (up_length >= 0 && left_length >= 0)
{
fprintf(stderr, "****\nedlib: %d, alignmentLength: %d, startLocations: %d, endLocations: %d\n",
result.editDistance, result.alignmentLength, result.startLocations[0], result.endLocations[0]);
fprintf(stderr,"%s\n", cigar);
print_string(x_string, x_len);
print_string(y_string, o_len);
fprintf(stderr, "BPM: %d\n", error);
}
free(cigar);
}
}
edlibFreeAlignResult(result);
@@ -358,10 +384,14 @@ char* r_string)
long long x_end, x_len;
int end_site;
unsigned int error;
long long total_match=0;
long long total_unmatch=0;
long long total_mis=0;
/************需要注释掉********* */
// long long total_match=0;
// long long total_unmatch=0;
// long long total_mis=0;
/************需要注释掉********* */
int groupLen = 0;
int return_sites[GROUP_SIZE];
unsigned int return_sites_error[GROUP_SIZE];
///这些是整个window被完全覆盖的
for (i = 0; i < dumy->length; i++)
@@ -383,54 +413,136 @@ char* r_string)
///不能超过y的剩余长度
o_len = MIN(Window_Len, currentIDLen - y_start);
recover_UC_Read_sub_region(dumy->overlap_region, y_start, o_len, overlap_list->list[currentID].y_pos_strand,
R_INF, overlap_list->list[currentID].y_id);
x_string = r_string + x_start;
y_string = dumy->overlap_region;
///这个长度足够，可以用来一起比
if (Window_Len == o_len)
{
end_site = Reserve_Banded_BPM(y_string, o_len, x_string, x_len, THRESHOLD, &error);
recover_UC_Read_sub_region(dumy->overlap_region_group[groupLen], y_start, o_len, overlap_list->list[currentID].y_pos_strand,
R_INF, overlap_list->list[currentID].y_id);
if (error!=(unsigned int)-1)
x_string = r_string + x_start;
groupLen++;
if (groupLen == GROUP_SIZE)
{
total_match++;
}
else
{
total_unmatch++;
}
test_edit_distance_by_edlib(x_string, y_string, x_len,
o_len, THRESHOLD, error, &total_mis);
Reserve_Banded_BPM_4_SSE_only(dumy->overlap_region_group[0], dumy->overlap_region_group[1],
dumy->overlap_region_group[2], dumy->overlap_region_group[3], o_len, x_string, x_len,
return_sites, return_sites_error, THRESHOLD, dumy->Peq_SSE);
groupLen = 0;
// end_site = Reserve_Banded_BPM(dumy->overlap_region_group[0], o_len, x_string, x_len, THRESHOLD, &error);
// if (error!=return_sites_error[0])
// {
// fprintf(stderr, "error\n");
// }
// end_site = Reserve_Banded_BPM(dumy->overlap_region_group[1], o_len, x_string, x_len, THRESHOLD, &error);
// if (error!=return_sites_error[1])
// {
// fprintf(stderr, "error\n");
// }
// end_site = Reserve_Banded_BPM(dumy->overlap_region_group[2], o_len, x_string, x_len, THRESHOLD, &error);
// if (error!=return_sites_error[2])
// {
// fprintf(stderr, "error\n");
// }
// end_site = Reserve_Banded_BPM(dumy->overlap_region_group[3], o_len, x_string, x_len, THRESHOLD, &error);
// if (error!=return_sites_error[3])
// {
// fprintf(stderr, "error\n");
// }
// /************需要注释掉**********/
// for (size_t ijk = 0; ijk < GROUP_SIZE; ijk++)
// {
// if (return_sites_error[ijk]!=(unsigned int)-1)
// {
// total_match++;
// }
// else
// {
// total_unmatch++;
// }
// test_edit_distance_by_edlib(x_string, dumy->overlap_region_group[ijk], x_len, o_len, THRESHOLD,
// return_sites_error[ijk], &total_mis);
// }
// /************需要注释掉********* */
}
}
else ///这个不够，只能单个比 ///不够的地方要置N
{
/**
recover_UC_Read_sub_region(dumy->overlap_region, y_start, o_len, overlap_list->list[currentID].y_pos_strand,
R_INF, overlap_list->list[currentID].y_id);
x_string = r_string + x_start;
y_string = dumy->overlap_region;
///o_len < Window_Len, 说明y的长度不够，需要在y后面补N
memset (y_string + o_len, 0, Window_Len - o_len);
end_site = Reserve_Banded_BPM(y_string, o_len, x_string, x_len, THRESHOLD, &error);
if (error!=-1)
{
total_match++;
}
else
{
total_unmatch++;
}
**/
// /************需要注释掉**********/
// if (error!=(unsigned int)-1)
// {
// total_match++;
// }
// else
// {
// total_unmatch++;
// }
// test_edit_distance_by_edlib(x_string, y_string, x_len, o_len, THRESHOLD, error, &total_mis);
// /************需要注释掉********* */
}
}
if (groupLen == 1)
{
end_site = Reserve_Banded_BPM(dumy->overlap_region_group[0], o_len, x_string, x_len, THRESHOLD, &error);
// /************需要注释掉**********/
// if (error!=(unsigned int)-1)
// {
// total_match++;
// }
// else
// {
// total_unmatch++;
// }
// test_edit_distance_by_edlib(x_string, dumy->overlap_region_group[0], x_len, o_len, THRESHOLD, error, &total_mis);
// /************需要注释掉********* */
}
else if (groupLen > 1)
{
Reserve_Banded_BPM_4_SSE_only(dumy->overlap_region_group[0], dumy->overlap_region_group[1],
dumy->overlap_region_group[2], dumy->overlap_region_group[3], o_len, x_string, x_len,
return_sites, return_sites_error, THRESHOLD, dumy->Peq_SSE);
// /************需要注释掉**********/
// for (size_t ijk = 0; ijk < groupLen; ijk++)
// {
// if (return_sites_error[ijk]!=(unsigned int)-1)
// {
// total_match++;
// }
// else
// {
// total_unmatch++;
// }
// test_edit_distance_by_edlib(x_string, dumy->overlap_region_group[ijk], x_len, o_len, THRESHOLD,
// return_sites_error[ijk], &total_mis);
// }
// /************需要注释掉**********/
groupLen = 0;
}
long long reverse_i = dumy->size - 1;
///这些是整个window被部分覆盖的
@@ -471,41 +583,38 @@ char* r_string)
y_string = dumy->overlap_region;
///不够的地方要置N
if (Window_Len != o_len)
{
///o_len < Window_Len, 说明y的长度不够，需要在y后面补N
memset (y_string + o_len, 0, Window_Len - o_len);
}
end_site = Reserve_Banded_BPM(y_string, o_len, x_string, x_len, THRESHOLD, &error);
/**
if (error!=-1)
{
total_match++;
}
else
{
total_unmatch++;
}
**/
// /************需要注释掉********* */
// if (error!=(unsigned int)-1)
// {
// total_match++;
// }
// else
// {
// total_unmatch++;
// }
// test_edit_distance_by_edlib(x_string, y_string, x_len, o_len, THRESHOLD, error, &total_mis);
// /************需要注释掉********* */
}
/**
if (total_match!=0)
{
// /************需要注释掉********* */
// pthread_mutex_lock(&debug_statistics);
// T_total_match = T_total_match + total_match;
// T_total_unmatch = T_total_unmatch + total_unmatch;
// T_total_mis = T_total_mis + total_mis;
// pthread_mutex_unlock(&debug_statistics);
// /************需要注释掉********* */
fprintf(stderr, "total_match: %u\n", total_match);
fprintf(stderr, "total_unmatch: %u\n", total_unmatch);
fprintf(stderr, "total_mis: %u\n", total_mis);
}
**/
T_total_match = T_total_match + total_match;
T_total_unmatch = T_total_unmatch + total_unmatch;
T_total_mis = T_total_mis + total_mis;
}
void correct_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF, UC_Read* g_read, Correct_dumy* dumy)
@@ -522,90 +631,6 @@ void correct_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF, UC_Re
window_start = 0;
window_end = WINDOW - 1;
/**
UC_Read debug_read;
init_UC_Read(&debug_read);
for (i = 0; i < overlap_list->length; i++)
{
if (overlap_list->list[i].y_pos_strand)
{
recover_UC_Read_RC(&debug_read, R_INF, overlap_list->list[i].y_id);
}
else
{
recover_UC_Read(&debug_read, R_INF, overlap_list->list[i].y_id);
}
long long x_length = overlap_list->list[i].x_pos_e - overlap_list->list[i].x_pos_s + 1;
long long y_length = overlap_list->list[i].y_pos_e - overlap_list->list[i].y_pos_s + 1;
EdlibAlignResult result = edlibAlign(g_read->seq+overlap_list->list[i].x_pos_s,
x_length,
debug_read.seq + overlap_list->list[i].y_pos_s,
y_length,
edlibNewAlignConfig(-1, EDLIB_MODE_NW, EDLIB_TASK_DISTANCE, NULL, 0));
if (result.status == EDLIB_STATUS_OK) {
if (result.editDistance>0 && result.editDistance < x_length*0.02)
{
fprintf(stderr, "inner_i: %u, x_length: %u, y_length: %u, editDistance: %u\n",
i, x_length, y_length, result.editDistance);
fprintf(stderr, "x_pos_s: %u, x_pos_e: %u\n",
overlap_list->list[i].x_pos_s, overlap_list->list[i].x_pos_e);
fprintf(stderr, "y_pos_s: %u, y_pos_e: %u, y_pos_strand: %u\n",
overlap_list->list[i].y_pos_s, overlap_list->list[i].y_pos_e, overlap_list->list[i].y_pos_strand);
EdlibAlignResult n_result = edlibAlign(g_read->seq+overlap_list->list[i].x_pos_s,
350,
debug_read.seq + overlap_list->list[i].y_pos_s - 15,
380,
edlibNewAlignConfig(-1, EDLIB_MODE_HW, EDLIB_TASK_DISTANCE, NULL, 0));
fprintf(stderr, "n_editDistance: %u\n",
n_result.editDistance);
edlibFreeAlignResult(n_result);
}
}
edlibFreeAlignResult(result);
}
destory_UC_Read(&debug_read);
**/
///return;
int flag;
for (i = 0; i < window_num; i++)
@@ -641,18 +666,16 @@ void correct_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF, UC_Re
{
window_end = g_read->length - 1;
}
///break;
}
fprintf(stderr, "total_match: %u, total_unmatch: %u, total_mis: %u\n",
T_total_match, T_total_unmatch, T_total_mis);
// /************需要注释掉********* */
// pthread_mutex_lock(&debug_statistics);
// fprintf(stderr, "total_match: %u, total_unmatch: %u, total_mis: %u\n",
// T_total_match, T_total_unmatch, T_total_mis);
// pthread_mutex_unlock(&debug_statistics);
// /************需要注释掉********* */
}
@@ -663,6 +686,11 @@ void init_Correct_dumy(Correct_dumy* list)
list->lengthNT = 0;
list->start_i = 0;
list->overlapID = NULL;
int i;
for (i = 0; i < 256; i++)
{
list->Peq_SSE[i] = _mm_setzero_si128();
}
}
void destory_Correct_dumy(Correct_dumy* list)