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update for base-level alignment

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This commit is contained in:
Haoyu Cheng
2019-12-12 03:06:47 -05:00
parent f1cde019a9
commit 9c25075fed
2 changed files with 25 additions and 9 deletions
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Correct.cpp
+24 -8
View File
@@ -1164,8 +1164,8 @@ All_reads* R_INF, Correct_dumy* dumy, UC_Read* g_read)
y_beg_right = 1 + overlap_list->list[ID].w_list[i + 1].y_start - 1 - x_len;
}
///cannot apply this strategy to the leftmost and the rightmost window
if(y_beg_left == -1 && y_beg_right == -1 && i > 0 && i < subWinNum - 1)
if(y_beg_left == -1 && y_beg_right == -1)
{
y_beg_left = overlap_list->list[ID].w_list[i].y_start;
if(overlap_list->list[ID].w_list[i].extra_begin >= 0)
@@ -1176,6 +1176,16 @@ All_reads* R_INF, Correct_dumy* dumy, UC_Read* g_read)
y_beg_right = y_beg_left;
}
if(y_beg_left == -1 && y_beg_right != -1)
{
y_beg_left = y_beg_right;
}
if(y_beg_right == -1 && y_beg_left != -1)
{
y_beg_right = y_beg_left;
}
if(y_beg_left != -1)
{
@@ -1191,12 +1201,18 @@ All_reads* R_INF, Correct_dumy* dumy, UC_Read* g_read)
threshold, 1, &r_error_right, &r_y_end_right, &r_x_end_right, &aligned_xLen_right);
}
///here one of aligned_xLen_left and aligned_xLen_right must be 0
if((i == 0 || i == subWinNum - 1) &&
(x_len - (aligned_xLen_left + aligned_xLen_right) > 10))
{
return 1.0;
}
/**
if(i == 0 || i == subWinNum - 1)
{
if(((aligned_xLen_left + aligned_xLen_right) < x_len)
&&
(x_len - (aligned_xLen_left + aligned_xLen_right) > 20))
{
return 1.0;
}
}
**/
///aligned in both direction
if(aligned_xLen_left != 0 && aligned_xLen_right != 0)
Overlaps.cpp
+1 -1
View File
@@ -9617,7 +9617,7 @@ char* output_file_name, long long bubble_dist, int read_graph, int write)
ma_hit_sub(min_dp, sources, n_read, readLen, mini_overlap_length, &coverage_cut);
////这个会断开
ma_hit_chimeric(1, sources, reverse_sources, n_read, readLen, coverage_cut);
ma_hit_cut(min_dp, sources, n_read, readLen, mini_overlap_length, &coverage_cut);