From 89649bd7a8a83940a187e62f47a6e2d303b7bd53 Mon Sep 17 00:00:00 2001
From: mmguar <mmguar@caltech.edu>
Date: Wed, 26 Oct 2022 18:06:29 -0700
Subject: [PATCH] Should fix 825

---
 lib/src/state/design.dart | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/lib/src/state/design.dart b/lib/src/state/design.dart
index 8ef830287..11e135055 100644
--- a/lib/src/state/design.dart
+++ b/lib/src/state/design.dart
@@ -2125,6 +2125,23 @@ abstract class Design with UnusedFields implements Built<Design, DesignBuilder>,
         else
           start = old_base;
 
+	bool running = true;
+	while(running){
+	  switch(Design._cadnano_v2_import_extract_end_deletions(vstrands[old_helix]['skip'], start,end)){
+	    case -1:{
+	      start = start + 1;
+	    }
+	    break;
+	    case 1:{
+	      end = end-1;
+	    }
+	    break;
+	    case 0:{
+	      running = false;
+	    }
+	  }
+	}
+
         domains.add(Domain(
             is_scaffold: strand_type == 'scaf',
             helix: old_helix,
@@ -2174,6 +2191,19 @@ abstract class Design with UnusedFields implements Built<Design, DesignBuilder>,
     return to_return;
   }
 
+
+  /// Routines which finds cadnano skips that correspond to domain ends. Returns -1 if they appear at the start, +1 if they appear at the end, or 0 if there are no end deletions.
+  static int _cadnano_v2_import_extract_end_deletions(List<dynamic> skip_table, int start, int end){
+    if ((skip_table[start] == -1)){
+      return -1;
+    }
+    if (skip_table[end] == -1){
+      return 1;
+    } else {
+      return 0;
+    }
+  }
+
   /// Routines which converts cadnano skips to scadnano insertions
   static List<Insertion> _cadnano_v2_import_extract_insertions(List<dynamic> loop_table, int start, int end) {
     List<Insertion> to_return = [];