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This commit is contained in:
Haoyu Cheng
2019-07-09 22:15:58 -04:00
parent 4eddb02dbd
commit 3d88530385
4 changed files with 500 additions and 17 deletions
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Correct.cpp
+85 -1
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@@ -674,7 +674,11 @@ char* r_string)
}
void correct_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF, UC_Read* g_read, Correct_dumy* dumy)
void correct_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF,
UC_Read* g_read, Correct_dumy* dumy, UC_Read* overlap_read,
long long* matched_overlap_0, long long* matched_overlap_1,
long long* potiental_matched_overlap_0, long long* potiental_matched_overlap_1)
{
reverse_complement(g_read->seq, g_read->length);
@@ -733,6 +737,86 @@ void correct_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF, UC_Re
// T_total_match, T_total_unmatch, T_total_mis);
// pthread_mutex_unlock(&debug_statistics);
/************需要注释掉********* */
/**
long long j;
long long Len_x;
int threshold;
long long y_start;
long long Len_y;
long long currentIDLen;
for (j = 0; j < overlap_list->length; j++)
{
Len_x = overlap_list->list[j].x_pos_e - overlap_list->list[j].x_pos_s + 1;
if (Len_x * 0.6 <= overlap_list->list[j].align_length)
{
threshold = Len_x * 0.04;
y_start = overlap_list->list[j].y_pos_s - threshold;
if (y_start < 0)
{
y_start = 0;
}
///当前y的长度
currentIDLen = Get_READ_LENGTH((*R_INF), overlap_list->list[j].y_id);
///不能超过y的剩余长度
Len_y = MIN(Len_x + 2 * threshold, currentIDLen - y_start);
if (overlap_list->list[j].y_pos_strand == 0)
{
recover_UC_Read(overlap_read, R_INF, overlap_list->list[j].y_id);
(*matched_overlap_0)++;
}
else
{
recover_UC_Read_RC(overlap_read, R_INF, overlap_list->list[j].y_id);
(*matched_overlap_1)++;
}
EdlibAlignResult result = edlibAlign(g_read->seq + overlap_list->list[j].x_pos_s, Len_x,
overlap_read->seq + y_start, Len_y,
edlibNewAlignConfig(threshold, EDLIB_MODE_HW, EDLIB_TASK_PATH, NULL, 0));
if (result.status == EDLIB_STATUS_OK && result.editDistance != -1) {
char* cigar = edlibAlignmentToCigar(result.alignment, result.alignmentLength, EDLIB_CIGAR_STANDARD);
int cigar_length = strlen(cigar);
free(cigar);
if (overlap_list->list[j].y_pos_strand == 0)
{
(*potiental_matched_overlap_0)++;
}
else
{
(*potiental_matched_overlap_1)++;
}
// if (overlap_list->list[j].shared_seed == 1 && Len_x >= 1000)
// {
// (*matched_overlap_0)++;
// }
// if (overlap_list->list[j].shared_seed == 2 && Len_x >= 1000)
// {
// (*matched_overlap_1)++;
// }
}
edlibFreeAlignResult(result);
}
}
**/
}