making module factory dynamic

michaeljon · May 18, 2022 · 6f79480 · 6f79480
1 parent 8ab1a9b
commit 6f79480
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Showing 13 changed files with 120 additions and 23 deletions.
diff --git a/Interfaces/IQcModule.cs b/Interfaces/IQcModule.cs
@@ -7,6 +7,8 @@ public interface IQcModule
 
         string Description { get; }
 
+        bool IsEnabledForAll { get; }
+
         void ProcessSequence(Sequence sequence);
 
         void Reset();

diff --git a/Modules/AlignmentStatistics.cs b/Modules/AlignmentStatistics.cs
@@ -1,10 +1,15 @@
 
+using System.Collections.Generic;
+using System.Linq;
+
 namespace Ovation.FasterQC.Net
 {
     public class AlignmentStatistics : IQcModule
     {
         private ulong sequenceCount;
 
+        private ulong baseCount;
+
         private ulong paired;
 
         private ulong aligned;
@@ -25,16 +30,39 @@ public class AlignmentStatistics : IQcModule
 
         private ulong opticalDuplicate;
 
+        private ulong alignedBases;
+
+        private readonly Dictionary<int, ReadPair> readLengthHistogram = new();
+
         public string Name => "alignmentStatistics";
 
+        public bool IsEnabledForAll => true;
+
         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++;
+            baseCount += (ulong)sequence.Read.Length;
+
+            if (readLengthHistogram.ContainsKey(sequence.Read.Length) == false)
+            {
+                readLengthHistogram.Add(sequence.Read.Length, new ReadPair());
+            }
+
+            var readPair = readLengthHistogram[sequence.Read.Length];
+
+            if ((sequence.ReadFlag & ReadFlag.Paired) != 0)
+            {
+                paired++;
+                readPair.Paired++;
+            }
+            if ((sequence.ReadFlag & ReadFlag.Aligned) != 0)
+            {
+                aligned++;
+                alignedBases += (ulong)sequence.Read.Length;
+                readPair.AlignedAndPaired++;
+            }
             if ((sequence.ReadFlag & ReadFlag.AlignedAndPaired) == ReadFlag.AlignedAndPaired) alignedAndPaired++;
             if ((sequence.ReadFlag & ReadFlag.SegmentUnmapped) != 0) segmentUnmapped++;
             if ((sequence.ReadFlag & ReadFlag.NextSegmentUnmapped) != 0) nextSegmentUnmapped++;
@@ -62,7 +90,19 @@ public void Reset()
             nextSegmentReverseComplemented,
             nonPrimaryAlignment,
             failedQualityChecks,
-            opticalDuplicate
+            opticalDuplicate,
+            alignedBases,
+            averageReadLength = (double)baseCount / (double)sequenceCount,
+            histogram = readLengthHistogram
+                .Select((k, v) => new ulong[] { (ulong)k.Key, k.Value.Paired, k.Value.AlignedAndPaired })
+                .OrderBy(a => a[0])
         };
+
+        class ReadPair
+        {
+            public ulong AlignedAndPaired { get; set; }
+
+            public ulong Paired { get; set; }
+        }
     }
 }
diff --git a/Modules/BasicStatistics.cs b/Modules/BasicStatistics.cs
@@ -24,6 +24,8 @@ public class BasicStatistics : IQcModule
 
         public string Description => "Calculates basic quality statistics";
 
+        public bool IsEnabledForAll => true;
+
         public void ProcessSequence(Sequence sequence)
         {
             var sequenceLength = sequence.Read.Length;

diff --git a/Modules/KmerContent.cs b/Modules/KmerContent.cs
@@ -22,6 +22,8 @@ public class KMerContent : IQcModule
 
         public string Description => "Computes 4-mer counts across all sequences";
 
+        public bool IsEnabledForAll => true;
+
         public object Data
         {
             get

diff --git a/Modules/MeanQualityDistribution.cs b/Modules/MeanQualityDistribution.cs
@@ -20,6 +20,8 @@ public class MeanQualityDistribution : IQcModule
 
         public string Description => "Calculates the quality distribution across all sequences";
 
+        public bool IsEnabledForAll => true;
+
         public object Data
         {
             get

diff --git a/Modules/ModuleFactory.cs b/Modules/ModuleFactory.cs
@@ -1,35 +1,58 @@
+using System;
 using System.Collections.Generic;
 using System.Linq;
+using System.Reflection;
 using Ovation.FasterQC.Net.Utils;
 
 namespace Ovation.FasterQC.Net.Modules
 {
     public static class ModuleFactory
     {
-        private static readonly Dictionary<string, IQcModule> moduleMap = new()
+        private static Dictionary<string, IQcModule>? moduleMap;
+
+        private static Dictionary<string, IQcModule> ModuleMap
         {
-            ["AlignmentStatistics"] = new AlignmentStatistics(),
-            ["BasicStatistics"] = new BasicStatistics(),
-            ["KMerContent"] = new KMerContent(),
-            ["NCountsAtPosition"] = new NCountsAtPosition(),
-            ["PerPositionSequenceContent"] = new PerPositionSequenceContent(),
-            ["PerSequenceGcContent"] = new PerSequenceGcContent(),
-            ["QualityDistributionByBase"] = new QualityDistributionByBase(),
-            ["MeanQualityDistribution"] = new MeanQualityDistribution(),
-            ["SequenceLengthDistribution"] = new SequenceLengthDistribution(),
-            ["PerPositionQuality"] = new PerPositionQuality(),
-        };
+            get
+            {
+                if (moduleMap == null)
+                {
+                    moduleMap = new Dictionary<string, IQcModule>();
+
+                    var modules = Assembly.GetExecutingAssembly()
+                        .GetTypes()
+                        .Where(t => string.IsNullOrEmpty(t.Namespace) == false && t.GetInterface(nameof(IQcModule)) != null)
+                        .Select(t => Activator.CreateInstance(t))
+                        .Cast<IQcModule>();
+
+                    foreach (var module in modules)
+                    {
+                        moduleMap.Add(module.GetType().Name, module);
+                    }
+                }
+
+                return moduleMap;
+            }
+        }
 
         public static IEnumerable<IQcModule> Create(CliOptions settings)
         {
             if (settings.ModuleNames.Any() == false || settings.ModuleNames.First() == "all")
             {
-                settings.ModuleNames = moduleMap.Keys;
-                return moduleMap.Values;
+                var moduleNames = new List<string>();
+                var modules = new List<IQcModule>();
+
+                foreach (var module in ModuleMap.Where(m => m.Value.IsEnabledForAll == true))
+                {
+                    moduleNames.Add(module.Key);
+                    modules.Add(module.Value);
+                }
+
+                settings.ModuleNames = moduleNames;
+                return modules;
             }
             else
             {
-                return settings.ModuleNames.Select(n => moduleMap[n]);
+                return settings.ModuleNames.Select(n => ModuleMap[n]);
             }
         }
     }

diff --git a/Modules/NCountsAtPosition.cs b/Modules/NCountsAtPosition.cs
@@ -5,12 +5,15 @@ namespace Ovation.FasterQC.Net
     public class NCountsAtPosition : IQcModule
     {
         private int[] nCounts = Array.Empty<int>();
+
         private int[] notNCounts = Array.Empty<int>();
 
         public string Name => "nPercentages";
 
         public string Description => "Calculates N counts at position along sequence";
 
+        public bool IsEnabledForAll => true;
+
         public object Data
         {
             get

diff --git a/Modules/PerPositionQuality.cs b/Modules/PerPositionQuality.cs
@@ -8,12 +8,15 @@ public class PerPositionQuality : IQcModule
         private QualityMetric[] qualities = Array.Empty<QualityMetric>();
 
         private int minimumReadLength = int.MaxValue;
+
         private int maximumReadLength = int.MinValue;
 
         public string Name => "perPositionQuality";
 
         public string Description => "Calculates the per-position quality metrics";
 
+        public bool IsEnabledForAll => true;
+
         public object Data
         {
             get

diff --git a/Modules/PerPositionSequenceContent.cs b/Modules/PerPositionSequenceContent.cs
@@ -6,15 +6,20 @@ namespace Ovation.FasterQC.Net
     public class PerPositionSequenceContent : IQcModule
     {
         private ulong[] aCounts = Array.Empty<ulong>();
+
         private ulong[] cCounts = Array.Empty<ulong>();
+
         private ulong[] tCounts = Array.Empty<ulong>();
+
         private ulong[] gCounts = Array.Empty<ulong>();
         private ulong sequenceCount;
 
         public string Name => "baseCounts";
 
         public string Description => "Calculates ATCG counts at position along sequence";
 
+        public bool IsEnabledForAll => true;
+
         public object Data
         {
             get

diff --git a/Modules/PerSequenceGcContent.cs b/Modules/PerSequenceGcContent.cs
@@ -6,12 +6,15 @@ namespace Ovation.FasterQC.Net
     public class PerSequenceGcContent : IQcModule
     {
         private ulong[] gcCounts = Array.Empty<ulong>();
+
         private ulong sequenceCount;
 
         public string Name => "gcDistribution";
 
         public string Description => "Distribution of GC content percentages";
 
+        public bool IsEnabledForAll => true;
+
         public object Data => gcCounts.Select(a => Math.Round((double)a / (double)sequenceCount * 100.0, 3));
 
         public void ProcessSequence(Sequence sequence)

diff --git a/Modules/QualityDistributionByBase.cs b/Modules/QualityDistributionByBase.cs
@@ -8,8 +8,11 @@ public class QualityDistributionByBase : IQcModule
         private const byte ILLUMINA_BASE_ADJUSTMENT = 33;
 
         private readonly ulong[] aQuality = new ulong[128];
+
         private readonly ulong[] cQuality = new ulong[128];
+
         private readonly ulong[] tQuality = new ulong[128];
+
         private readonly ulong[] gQuality = new ulong[128];
 
         private byte lowestScore = byte.MaxValue;
@@ -20,6 +23,8 @@ public class QualityDistributionByBase : IQcModule
 
         public string Description => "Calculates the quality distribution across all sequences";
 
+        public bool IsEnabledForAll => true;
+
         public object Data
         {
             get

diff --git a/Modules/SequenceLengthDistribution.cs b/Modules/SequenceLengthDistribution.cs
@@ -6,6 +6,7 @@ namespace Ovation.FasterQC.Net
     public class SequenceLengthDistribution : IQcModule
     {
         private int minimumReadLength = int.MaxValue;
+
         private int maximumReadLength = int.MinValue;
 
         private readonly IDictionary<int, ulong> lengths = new Dictionary<int, ulong>();
@@ -14,6 +15,8 @@ public class SequenceLengthDistribution : IQcModule
 
         public string Description => "Calculates the sequence length distributions";
 
+        public bool IsEnabledForAll => true;
+
         public object Data
         {
             get

diff --git a/Program.cs b/Program.cs
@@ -49,7 +49,7 @@ private void Run()
             On(Settings.ShowProgress, () => progressBar = new TimedSequenceProgressBar(sequenceReader));
             On(Settings.Verbose, () => Console.Error.WriteLine($"Processing {Settings.InputFilename}..."));
 
-            while (sequenceReader.ReadSequence(out Sequence? sequence) && sequenceReader.SequencesRead < Settings.ReadLimit)
+            while (sequenceReader.SequencesRead < Settings.ReadLimit && sequenceReader.ReadSequence(out Sequence? sequence))
             {
                 ArgumentNullException.ThrowIfNull(sequence);
 
@@ -70,9 +70,13 @@ private void Run()
 
             Dictionary<string, object>? results = new()
             {
-                ["_modules"] = Settings.ModuleNames,
-                ["_inputFilename"] = Settings.InputFilename,
-                ["_outputFilename"] = string.IsNullOrWhiteSpace(Settings.OutputFilename) ? "STDOUT" : Settings.OutputFilename,
+                ["_metadata"] = new
+                {
+                    _modules = Settings.ModuleNames,
+                    _inputFilename = Settings.InputFilename,
+                    _outputFilename = string.IsNullOrWhiteSpace(Settings.OutputFilename) ? "STDOUT" : Settings.OutputFilename,
+                    _sequences = sequenceReader.SequencesRead
+                }
             };
 
             foreach (IQcModule? module in modules)
-Original file line number
+Diff line change
@@ Expand Up / @@ -22,6 +22,8 @@ public class KMerContent : IQcModule @@
             public string Description => "Computes 4-mer counts across all sequences";
+            public bool IsEnabledForAll => true;
             public object Data
             {
                 get
@@ Expand Down @@