Merge pull request #2 from stephen-riley/add-null-checking

Add null checking
michaeljon · May 18, 2022 · 4e0b684 · 4e0b684
2 parents e008268 + 6cfe2e2
commit 4e0b684
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Showing 10 changed files with 34 additions and 29 deletions.
diff --git a/Interfaces/ISequenceReader.cs b/Interfaces/ISequenceReader.cs
@@ -6,7 +6,7 @@ public interface ISequenceReader : IDisposable
     {
         int SequencesRead { get; }
 
-        bool ReadSequence(out Sequence sequence);
+        bool ReadSequence(out Sequence? sequence);
 
         double ApproximateCompletion { get; }
     }

diff --git a/Models/BamAlignment.cs b/Models/BamAlignment.cs
@@ -1,6 +1,8 @@
+using System.Diagnostics.CodeAnalysis;
+
 namespace Ovation.FasterQC.Net
 {
-#pragma warning disable IDE1006
+    [SuppressMessage("Code style", "IDE1006", Justification = "Names correspond to BAM structure field names")]
     public class BamAlignment
     {
         public uint block_size { get; set; }
@@ -27,13 +29,12 @@ public class BamAlignment
 
         public int tlen { get; set; }
 
-        public byte[] read_name { get; set; }
+        public byte[] read_name { get; set; } = null!;
 
-        public uint[] cigar { get; set; }
+        public uint[] cigar { get; set; } = null!;
 
-        public byte[] seq { get; set; }
+        public byte[] seq { get; set; } = null!;
 
-        public byte[] qual { get; set; }
+        public byte[] qual { get; set; } = null!;
     }
-#pragma warning restore IDE1006
-}
+}
diff --git a/Models/Sequence.cs b/Models/Sequence.cs
@@ -34,6 +34,7 @@ public Sequence(BamAlignment bamAlignment)
             Identifier = new ReadOnlyMemory<byte>(bamAlignment.read_name).ToArray();
             Read = new ReadOnlyMemory<byte>(bamAlignment.seq).ToArray();
             Quality = new ReadOnlyMemory<byte>(bamAlignment.qual).ToArray();
+            Blank = Array.Empty<byte>();
         }
 
         public override string ToString()
@@ -48,4 +49,4 @@ public override string ToString()
             return sb.ToString();
         }
     }
-}
+}
diff --git a/Ovation.FasterQC.Net.csproj b/Ovation.FasterQC.Net.csproj
@@ -3,6 +3,7 @@
   <PropertyGroup>
     <OutputType>Exe</OutputType>
     <TargetFramework>net6.0</TargetFramework>
+    <Nullable>enable</Nullable>
   </PropertyGroup>
 
   <ItemGroup>

diff --git a/Program.cs b/Program.cs
@@ -19,7 +19,7 @@ class Program
             PropertyNamingPolicy = JsonNamingPolicy.CamelCase
         };
 
-        private TimedSequenceProgressBar progressBar;
+        private TimedSequenceProgressBar? progressBar;
 
         static void Main(string[] args)
         {
@@ -42,14 +42,16 @@ 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))
+            while (sequenceReader.ReadSequence(out Sequence? sequence))
             {
+                ArgumentNullException.ThrowIfNull(sequence);
+
                 foreach (var module in modules)
                 {
                     module.ProcessSequence(sequence);
                 }
 
-                On(Settings.ShowProgress, () => progressBar.Update());
+                On(Settings.ShowProgress, () => progressBar?.Update());
                 On(Settings.Verbose, () =>
                 {
                     if (sequenceReader.SequencesRead % UpdatePeriod == 0)
@@ -71,7 +73,7 @@ private void Run()
                 results[module.Name] = module.Data;
             }
 
-            On(Settings.ShowProgress, () => progressBar.Update(force: true));
+            On(Settings.ShowProgress, () => progressBar?.Update(force: true));
             On(Settings.Verbose, () => Console.Error.WriteLine($"{sequenceReader.SequencesRead.WithSsiUnits()} sequences completed ({sequenceReader.ApproximateCompletion:0.0}%)"));
 
             if (string.IsNullOrWhiteSpace(Settings.OutputFilename))

diff --git a/Readers/BamReader.cs b/Readers/BamReader.cs
@@ -40,7 +40,7 @@ public BamReader(string bam)
             ConsumeHeader();
         }
 
-        public bool ReadSequence(out Sequence sequence)
+        public bool ReadSequence(out Sequence? sequence)
         {
             try
             {
@@ -106,9 +106,10 @@ private BamAlignment ReadSequence()
             var bamAlignment = new BamAlignment
             {
                 block_size = block_size,
+                refID = BitConverter.ToInt32(block, offset)
             };
 
-            bamAlignment.refID = BitConverter.ToInt32(block, offset); offset += 4;
+            offset += 4;
             bamAlignment.pos = BitConverter.ToInt32(block, offset) + 1; offset += 4;
             bamAlignment.l_read_name = block[offset]; offset += 1;
             bamAlignment.mapq = block[offset]; offset += 1;

diff --git a/Readers/FastqLineReader.cs b/Readers/FastqLineReader.cs
@@ -10,7 +10,7 @@ public class FastqLineReader : ISequenceReader
     {
         private readonly FileStream inputStream;
 
-        private readonly GZipStream gzipStream;
+        private readonly GZipStream? gzipStream;
 
         private readonly BufferedStream bufferedStream;
 
@@ -50,7 +50,7 @@ public FastqLineReader(string fastq, bool gzipped = true)
             }
         }
 
-        public bool ReadSequence(out Sequence sequence)
+        public bool ReadSequence(out Sequence? sequence)
         {
             try
             {
@@ -61,10 +61,10 @@ public bool ReadSequence(out Sequence sequence)
                     return false;
                 }
 
-                var identifier = Encoding.ASCII.GetBytes(streamReader.ReadLine());
-                var read = Encoding.ASCII.GetBytes(streamReader.ReadLine());
-                var blank = Encoding.ASCII.GetBytes(streamReader.ReadLine());
-                var quality = Encoding.ASCII.GetBytes(streamReader.ReadLine());
+                var identifier = Encoding.ASCII.GetBytes(streamReader.ReadLine() ?? "");
+                var read = Encoding.ASCII.GetBytes(streamReader.ReadLine() ?? "");
+                var blank = Encoding.ASCII.GetBytes(streamReader.ReadLine() ?? "");
+                var quality = Encoding.ASCII.GetBytes(streamReader.ReadLine() ?? "");
 
                 sequence = new Sequence(identifier, read, blank, quality);
                 sequencesRead++;

diff --git a/Readers/FastqReader.cs b/Readers/FastqReader.cs
@@ -9,7 +9,7 @@ public class FastqReader : ISequenceReader
     {
         private readonly FileStream inputStream;
 
-        private readonly GZipStream gzipStream;
+        private readonly GZipStream? gzipStream;
 
         private readonly BufferedStream bufferedStream;
 
@@ -49,7 +49,7 @@ public FastqReader(string fastq, bool gzipped = true)
             }
         }
 
-        public bool ReadSequence(out Sequence sequence)
+        public bool ReadSequence(out Sequence? sequence)
         {
             // this is clearly dangerous, instead read a large chunk of the file
             // and then walk through it returning only the consumed portion while

diff --git a/Readers/ReaderFactory.cs b/Readers/ReaderFactory.cs
@@ -9,7 +9,7 @@ public static ISequenceReader Create(CliOptions settings)
         {
             return settings switch
             {
-                { Fastq: true } => new FastqLineReader(settings.InputFilename, true),
+                { Fastq: true } => new FastqLineReader(settings.InputFilename, settings.Zipped),
                 { Bam: true } => new BamReader(settings.InputFilename),
                 _ => throw new InvalidOperationException($"could not determine file type of {settings.InputFilename}")
             };

diff --git a/Utils/CliOptions.cs b/Utils/CliOptions.cs
@@ -17,10 +17,10 @@ public class CliOptions
         public bool ShowProgress { get; set; }
 
         [Option('i', "input", Required = true, HelpText = "Input filename.")]
-        public string InputFilename { get; set; }
+        public string InputFilename { get; set; } = null!;
 
         [Option('o', "output", Required = false, HelpText = "Output filename.  Defaults to STDOUT.")]
-        public string OutputFilename { get; set; }
+        public string OutputFilename { get; set; } = null!;
 
         [Option('b', "bam", Required = false, HelpText = "Assume BAM format.")]
         public bool Bam { get; set; }
@@ -32,10 +32,9 @@ public class CliOptions
         public bool Zipped { get; set; }
 
         [Option('m', "modules", Required = true, Min = 1, HelpText = "Space-separated list of modules to run, or 'all'.")]
-        public IEnumerable<string> ModuleNames { get; set; }
+        public IEnumerable<string> ModuleNames { get; set; } = Array.Empty<string>();
 
-        public static CliOptions Settings
-        { get; set; }
+        public static CliOptions Settings { get; set; } = null!;
 
         public const int UpdatePeriod = 100_000;