fixed mqd computations

michaeljon · May 19, 2022 · 0d7b86b · 0d7b86b
1 parent ec7dcd3
commit 0d7b86b
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Showing 3 changed files with 18 additions and 16 deletions.
diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -23,8 +23,7 @@
         "-o",
         "./tmp/bob.json",
         "-m",
-        "BasicStatistics",
-        "NCountsAtPosition"
+        "MeanQualityDistribution"
       ],
       "cwd": "${workspaceFolder}",
       // For more information about the 'console' field, see https://aka.ms/VSCode-CS-LaunchJson-Console

diff --git a/Modules/BasicStatistics.cs b/Modules/BasicStatistics.cs
@@ -4,6 +4,8 @@ namespace Ovation.FasterQC.Net
 {
     public class BasicStatistics : IQcModule
     {
+        private const byte ILLUMINA_BASE_ADJUSTMENT = 33;
+
         private ulong sequenceCount;
 
         private int minimumReadLength = int.MaxValue;
@@ -87,7 +89,7 @@ public void Reset()
             nCount,
             xCount,
 
-            minimumQuality,
+            minimumQuality = Math.Min(minimumQuality - ILLUMINA_BASE_ADJUSTMENT, 0),
 
             gcContent = Math.Round((double)(cCount + gCount) / (double)totalBases * 100.0, 3),
 

diff --git a/Modules/MeanQualityDistribution.cs b/Modules/MeanQualityDistribution.cs
@@ -12,9 +12,9 @@ public class MeanQualityDistribution : IQcModule
         // position and fix it when someone asks
         private readonly ulong[] qualityScores = new ulong[128];
 
-        private byte lowestScore = byte.MaxValue;
+        private uint lowestMean = uint.MaxValue;
 
-        private byte highestScore = byte.MinValue;
+        private uint highestMean = uint.MinValue;
 
         public string Name => "meanQualityDistribution";
 
@@ -28,9 +28,9 @@ public object Data
             {
                 return new
                 {
-                    lowestScore = lowestScore - ILLUMINA_BASE_ADJUSTMENT,
-                    highestScore = highestScore - ILLUMINA_BASE_ADJUSTMENT,
-                    distribution = qualityScores.Skip(lowestScore).Take(highestScore - lowestScore + 1)
+                    lowestMean = lowestMean - ILLUMINA_BASE_ADJUSTMENT,
+                    highestMean = highestMean - ILLUMINA_BASE_ADJUSTMENT,
+                    distribution = qualityScores.Skip((int)lowestMean).Take((int)(highestMean - lowestMean + 1))
                 };
             }
         }
@@ -43,16 +43,17 @@ public void ProcessSequence(Sequence sequence)
             var count = 0;
 
             var qual = sequence.Quality;
-            for (var q = 0; q < sequenceLength; q++)
+            for (var i = 0; i < sequenceLength; i++)
             {
-                lowestScore = Math.Min(lowestScore, qual[q]);
-                highestScore = Math.Max(highestScore, qual[q]);
-
-                sum += qual[q];
+                sum += qual[i];
                 count++;
             }
 
-            var mean = sum / count;
+            var mean = (uint)(sum / count);
+
+            lowestMean = Math.Min(lowestMean, mean);
+            highestMean = Math.Max(highestMean, mean);
+
             qualityScores[mean]++;
         }
 
@@ -63,8 +64,8 @@ public void Reset()
                 qualityScores[p] = 0;
             }
 
-            lowestScore = byte.MaxValue;
-            highestScore = byte.MinValue;
+            lowestMean = uint.MaxValue;
+            highestMean = uint.MinValue;
         }
     }
 }