Merge pull request #11 from michaeljon/issue-9

issue-9: add sam/bam stats

.gitignore

@@ -13,7 +13,4 @@ obj/
 !.vscode/launch.json
 !.vscode/extensions.json
 
-results.json
-
-*.gz
-*.bam
+tmp/*

Modules/AlignmentStatistics.cs

@@ -0,0 +1,64 @@
+
+namespace Ovation.FasterQC.Net
+{
+    public class AlignmentStatistics : IQcModule
+    {
+        private ulong sequenceCount;
+
+        private ulong paired;
+
+        private ulong aligned;
+
+        private ulong segmentUnmapped;
+
+        private ulong nextSegmentUnmapped;
+
+        private ulong reverseComplemented;
+
+        private ulong nextSegmenteverseComplemented;
+
+        private ulong nonPrimaryAlignment;
+
+        private ulong failedQualityChecks;
+
+        private ulong opticalDuplicate;
+
+        public string Name => "alignmentStatistics";
+
+        public string Description => "Calculates alignment statistics for SAM/BAM files";
+
+        public void ProcessSequence(Sequence sequence)
+        {
+            sequenceCount++;
+
+            if ((sequence.ReadFlag & ReadFlag.Paired) != 0) paired++;
+            if ((sequence.ReadFlag & ReadFlag.Aligned) != 0) aligned++;
+            if ((sequence.ReadFlag & ReadFlag.SegmentUnmapped) != 0) segmentUnmapped++;
+            if ((sequence.ReadFlag & ReadFlag.NextSegmentUnmapped) != 0) nextSegmentUnmapped++;
+            if ((sequence.ReadFlag & ReadFlag.ReverseComplemented) != 0) reverseComplemented++;
+            if ((sequence.ReadFlag & ReadFlag.NextSegmentReverseComplemented) != 0) nextSegmenteverseComplemented++;
+            if ((sequence.ReadFlag & ReadFlag.NotPrimaryAlignment) != 0) nonPrimaryAlignment++;
+            if ((sequence.ReadFlag & ReadFlag.FailedQualityChecks) != 0) failedQualityChecks++;
+            if ((sequence.ReadFlag & ReadFlag.OpticalDuplicate) != 0) opticalDuplicate++;
+        }
+
+        public void Reset()
+        {
+            sequenceCount = 0;
+        }
+
+        public object Data => new
+        {
+            sequenceCount,
+            paired,
+            aligned,
+            segmentUnmapped,
+            nextSegmentUnmapped,
+            reverseComplemented,
+            nextSegmenteverseComplemented,
+            nonPrimaryAlignment,
+            failedQualityChecks,
+            opticalDuplicate
+        };
+    }
+}

Modules/ModuleFactory.cs

@@ -8,6 +8,7 @@ public static class ModuleFactory
     {
         private static readonly Dictionary<string, IQcModule> moduleMap = new()
         {
+            ["AlignmentStatistics"] = new AlignmentStatistics(),
             ["BasicStatistics"] = new BasicStatistics(),
             ["KMerContent"] = new KMerContent(),
             ["NCountsAtPosition"] = new NCountsAtPosition(),