Display leading insertions differently in alignment + bugfix

snijderlab · Jan 23, 2023 · 4cdbf7a · 4cdbf7a
1 parent 3594726
commit 4cdbf7a
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Showing 3 changed files with 13 additions and 4 deletions.
diff --git a/stitch/Reporting/HTMLReport/Asides.cs b/stitch/Reporting/HTMLReport/Asides.cs
@@ -393,7 +393,9 @@ static public (HtmlBuilder, int[]) CreateTemplateAlignment(Template template, st
                             seq.Append(new string(non_breaking_space, Math.Max(0, gaps[pos_a] - len_start)));
                             inserted += Math.Max(0, gaps[pos_a] - len_start);
                         }
+                        if (pos_a == alignment.StartA) html.Open(HtmlTag.span, "class='insertion'");
                         html.Content(AminoAcid.ArrayToString(alignment.ReadB.Sequence.AminoAcids.SubArray(pos_b, piece.StepB)));
+                        if (pos_a == alignment.StartA) html.Close(HtmlTag.span);
                         seq.Append(AminoAcid.ArrayToString(alignment.ReadB.Sequence.AminoAcids.SubArray(pos_b, piece.StepB)));
                         inserted += piece.StepB;
                     } else if (piece.StepB == 0) {

diff --git a/stitch/Reporting/HTMLReport/Report.cs b/stitch/Reporting/HTMLReport/Report.cs
@@ -433,10 +433,10 @@ private HtmlBuilder CreateSegmentJoining(int group) {
                 var bars_a = new HtmlBuilder();
                 var bars_b = new HtmlBuilder();
                 var max_doc = new double[] {
-                    set.EndAlignment.ReadA.Sequence.PositionalScore.SubArray(set.EndAlignment.StartA, set.EndAlignment.LenA).Max(),
-                    set.EndAlignment.ReadB.Sequence.PositionalScore.SubArray(set.EndAlignment.StartB, set.EndAlignment.LenB).Max(),
-                    set.SeqA.Sequence.PositionalScore.SubArray(set.SeqA.Sequence.Length - set.EndAlignment.LenA - padding, padding).Max(),
-                    set.SeqB.Sequence.PositionalScore.SubArray(set.EndAlignment.LenB, padding).Max(),
+                    set.EndAlignment.ReadA.Sequence.PositionalScore.SubArray(set.EndAlignment.StartA, set.EndAlignment.LenA).Max(0),
+                    set.EndAlignment.ReadB.Sequence.PositionalScore.SubArray(set.EndAlignment.StartB, set.EndAlignment.LenB).Max(0),
+                    set.SeqA.Sequence.PositionalScore.SubArray(set.SeqA.Sequence.Length - set.EndAlignment.LenA - padding, padding).Max(0),
+                    set.SeqB.Sequence.PositionalScore.SubArray(set.EndAlignment.LenB, padding).Max(0),
                 }.Max();
                 bars_a.Open(HtmlTag.div, $"class='joining a' style='--max:{max_doc}'");
                 bars_b.Open(HtmlTag.div, $"class='joining b' style='--max:{max_doc}'");

diff --git a/stitch/Structs/HelperFunctionality.cs b/stitch/Structs/HelperFunctionality.cs
@@ -153,6 +153,13 @@ public static int IntPow(int x, uint pow) {
             return ret;
         }
 
+        public static double Max(this IEnumerable<double> data, double fallback) {
+            if (data.Count() > 0)
+                return data.Max();
+            else
+                return fallback;
+        }
+
         public static int SmithWatermanStrings(string template, string query) {
             var score_matrix = new (int, Direction)[template.Length + 1, query.Length + 1]; // Default value of 0
             int[] indices_template = new int[template.Length];