module structure changes

modules now express a supported reader type (or types) so that we don't run them when there's a mismatch between source data and module (there is at least one module that requires an aligned data source). also made the module names case-insensitive on the command line and check for unknown module at startup. app fails hard on any unknown modules, but without dumping an exception or trying run the reader on an empty module set.
michaeljon · May 27, 2022 · d252be0 · d252be0
1 parent 1b94999
commit d252be0
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Showing 18 changed files with 74 additions and 15 deletions.
diff --git a/Interfaces/IQcModule.cs b/Interfaces/IQcModule.cs
@@ -9,6 +9,8 @@ public interface IQcModule
 
         bool IsEnabledForAll { get; }
 
+        ReaderType SupportedReaders { get; }
+
         void ProcessSequence(Sequence sequence);
 
         void Reset();

diff --git a/Models/BamAlignment.cs b/Models/BamAlignment.cs
@@ -1,5 +1,4 @@
 using System;
-using System.ComponentModel;
 using System.Diagnostics.CodeAnalysis;
 using System.Text;
 

diff --git a/Modules/AlignmentStatistics.cs b/Modules/AlignmentStatistics.cs
@@ -50,6 +50,8 @@ public class AlignmentStatistics : IQcModule
 
         public bool IsEnabledForAll => true;
 
+        public ReaderType SupportedReaders => ReaderType.AlignedReaders;
+
         public string Description => "Calculates alignment statistics for SAM/BAM files";
 
         public void ProcessSequence(Sequence sequence)

diff --git a/Modules/BasicStatistics.cs b/Modules/BasicStatistics.cs
@@ -28,6 +28,8 @@ public class BasicStatistics : IQcModule
 
         public bool IsEnabledForAll => true;
 
+        public ReaderType SupportedReaders => ReaderType.AllReaders;
+
         public void ProcessSequence(Sequence sequence)
         {
             var sequenceLength = sequence.Read.Length;

diff --git a/Modules/KmerContent.cs b/Modules/KmerContent.cs
@@ -24,6 +24,8 @@ public class KMerContent : IQcModule
 
         public bool IsEnabledForAll => true;
 
+        public ReaderType SupportedReaders => ReaderType.AllReaders;
+
         public object Data
         {
             get

diff --git a/Modules/MeanQualityDistribution.cs b/Modules/MeanQualityDistribution.cs
@@ -22,6 +22,8 @@ public class MeanQualityDistribution : IQcModule
 
         public bool IsEnabledForAll => true;
 
+        public ReaderType SupportedReaders => ReaderType.AllReaders;
+
         public object Data
         {
             get

diff --git a/Modules/ModuleFactory.cs b/Modules/ModuleFactory.cs
@@ -26,7 +26,7 @@ public static Dictionary<string, IQcModule> ModuleMap
 
                     foreach (var module in modules)
                     {
-                        moduleMap.Add(module.GetType().Name, module);
+                        moduleMap.Add(module.GetType().Name.ToLowerInvariant(), module);
                     }
                 }
 
@@ -36,24 +36,40 @@ public static Dictionary<string, IQcModule> ModuleMap
 
         public static IEnumerable<IQcModule> Create(CliOptions settings)
         {
+            var moduleNames = new List<string>();
+            var modules = new List<IQcModule>();
+
             if (settings.ModuleNames.Any() == false || settings.ModuleNames.First() == "all")
             {
-                var moduleNames = new List<string>();
-                var modules = new List<IQcModule>();
-
-                foreach (var module in ModuleMap.Where(m => m.Value.IsEnabledForAll == true))
+                foreach (var module in ModuleMap.Where(m => m.Value.IsEnabledForAll == true && (m.Value.SupportedReaders & settings.Format) != 0))
                 {
                     moduleNames.Add(module.Key);
                     modules.Add(module.Value);
                 }
-
-                settings.ModuleNames = moduleNames;
-                return modules;
             }
             else
             {
-                return settings.ModuleNames.Select(n => ModuleMap[n]);
+                foreach (var moduleName in settings.ModuleNames)
+                {
+                    if (ModuleMap.ContainsKey(moduleName.ToLowerInvariant()) == false)
+                    {
+                        Console.Error.WriteLine($"Unknown module name {moduleName} requested.");
+                        modules.Clear();
+                        break;
+                    }
+
+                    var module = ModuleMap[moduleName.ToLowerInvariant()];
+
+                    if (module != null)
+                    {
+                        moduleNames.Add(moduleName);
+                        modules.Add(module);
+                    }
+                }
             }
+
+            settings.ModuleNames = moduleNames;
+            return modules;
         }
     }
 }
diff --git a/Modules/NCountsAtPosition.cs b/Modules/NCountsAtPosition.cs
@@ -14,6 +14,8 @@ public class NCountsAtPosition : IQcModule
 
         public bool IsEnabledForAll => true;
 
+        public ReaderType SupportedReaders => ReaderType.AllReaders;
+
         public object Data
         {
             get

diff --git a/Modules/NullProcessor.cs b/Modules/NullProcessor.cs
@@ -10,6 +10,8 @@ public class NullProcessor : IQcModule
 
         public bool IsEnabledForAll => false;
 
+        public ReaderType SupportedReaders => ReaderType.AllReaders;
+
         public object Data => sequenceCount;
 
         public void ProcessSequence(Sequence sequence)

diff --git a/Modules/PerPositionQuality.cs b/Modules/PerPositionQuality.cs
@@ -17,6 +17,8 @@ public class PerPositionQuality : IQcModule
 
         public bool IsEnabledForAll => true;
 
+        public ReaderType SupportedReaders => ReaderType.AllReaders;
+
         public object Data
         {
             get

diff --git a/Modules/PerPositionSequenceContent.cs b/Modules/PerPositionSequenceContent.cs
@@ -18,6 +18,8 @@ public class PerPositionSequenceContent : IQcModule
 
         public string Description => "Calculates ATCG counts at position along sequence";
 
+        public ReaderType SupportedReaders => ReaderType.AllReaders;
+
         public bool IsEnabledForAll => true;
 
         public object Data

diff --git a/Modules/PerSequenceGcContent.cs b/Modules/PerSequenceGcContent.cs
@@ -15,6 +15,8 @@ public class PerSequenceGcContent : IQcModule
 
         public bool IsEnabledForAll => true;
 
+        public ReaderType SupportedReaders => ReaderType.AllReaders;
+
         public object Data => gcCounts.Select(a => Math.Round((double)a / (double)sequenceCount * 100.0, 3));
 
         public void ProcessSequence(Sequence sequence)

diff --git a/Modules/PolyX.cs b/Modules/PolyX.cs
@@ -24,6 +24,8 @@ public class PolyX : IQcModule
 
         public bool IsEnabledForAll => true;
 
+        public ReaderType SupportedReaders => ReaderType.AllReaders;
+
         public object Data
         {
             get

diff --git a/Modules/QualityDistribution.cs b/Modules/QualityDistribution.cs
@@ -19,6 +19,8 @@ public class QualityDistribution : IQcModule
 
         public bool IsEnabledForAll => true;
 
+        public ReaderType SupportedReaders => ReaderType.AllReaders;
+
         public object Data
         {
             get

diff --git a/Modules/QualityDistributionByBase.cs b/Modules/QualityDistributionByBase.cs
@@ -25,6 +25,8 @@ public class QualityDistributionByBase : IQcModule
 
         public bool IsEnabledForAll => true;
 
+        public ReaderType SupportedReaders => ReaderType.AllReaders;
+
         public object Data
         {
             get

diff --git a/Modules/SequenceLengthDistribution.cs b/Modules/SequenceLengthDistribution.cs
@@ -17,6 +17,8 @@ public class SequenceLengthDistribution : IQcModule
 
         public bool IsEnabledForAll => true;
 
+        public ReaderType SupportedReaders => ReaderType.AllReaders;
+
         public object Data
         {
             get

diff --git a/Program.cs b/Program.cs
@@ -1,6 +1,7 @@
 using System;
 using System.Collections.Generic;
 using System.IO;
+using System.Linq;
 using System.Text;
 using System.Text.Json;
 using CommandLine;
@@ -72,6 +73,12 @@ private void Run()
             using ISequenceReader? sequenceReader = ReaderFactory.Create(Settings);
             IEnumerable<IQcModule>? modules = ModuleFactory.Create(Settings);
 
+            if (modules.Any() == false)
+            {
+                Console.Error.WriteLine($"No modules matched or at least one unknown module requested.");
+                return;
+            }
+
             Console.Error.WriteLine($"Running modules:\n  {string.Join("\n  ", Settings.ModuleNames)}");
 
             On(Settings.ShowProgress, () => progressBar = new TimedSequenceProgressBar(sequenceReader));

diff --git a/Readers/ReaderType.cs b/Readers/ReaderType.cs
@@ -1,15 +1,24 @@
+using System;
+
 namespace Ovation.FasterQC.Net
 {
+    [Flags]
     public enum ReaderType
     {
-        Fastq,
+        Fastq = 1,
+
+        FastqGz = 2,
+
+        UnalignedReaders = Fastq | FastqGz,
+
+        Sam = 4,
 
-        FastqGz,
+        SamGz = 8,
 
-        Sam,
+        Bam = 16,
 
-        SamGz,
+        AlignedReaders = Sam | SamGz | Bam,
 
-        Bam
+        AllReaders = UnalignedReaders | AlignedReaders
     }
 }
-Original file line number
+Diff line change
@@ Expand Up / @@ -24,6 +24,8 @@ public class KMerContent : IQcModule @@
             public bool IsEnabledForAll => true;
+            public ReaderType SupportedReaders => ReaderType.AllReaders;
             public object Data
             {
                 get
@@ Expand Down @@