From 9c25075feda2ebf34682238cd7153247a5abd341 Mon Sep 17 00:00:00 2001
From: Haoyu Cheng <hcheng@jimmy.harvard.edu>
Date: Thu, 12 Dec 2019 03:06:47 -0500
Subject: [PATCH] update for base-level alignment

---
 Correct.cpp  | 32 ++++++++++++++++++++++++--------
 Overlaps.cpp |  2 +-
 2 files changed, 25 insertions(+), 9 deletions(-)

diff --git a/Correct.cpp b/Correct.cpp
index e3a7b36..9e04f41 100644
--- a/Correct.cpp
+++ b/Correct.cpp
@@ -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)
diff --git a/Overlaps.cpp b/Overlaps.cpp
index 5862bb1..0abeeff 100644
--- a/Overlaps.cpp
+++ b/Overlaps.cpp
@@ -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);