Merge branch 'main' into issue-6

.vscode/launch.json

@@ -12,12 +12,23 @@
       // If you have changed target frameworks, make sure to update the program path.
       "program": "${workspaceFolder}/bin/Debug/net6.0/Ovation.FasterQC.Net.dll",
       "args": [
-        "-p", "-i", "/tmp/zr6254_1/zr6254_1.sorted.bam", "-o", "/tmp/bob.json", "-m", "BasicStatistics", "NCountsAtPosition"
+        "-v",
+        "-d",
+        "-f",
+        "sam",
+        "-i",
+        "./tmp/in3257_2_S1.sorted.sam",
+        "-o",
+        "./tmp/bob.json",
+        "-m",
+        "BasicStatistics",
+        "NCountsAtPosition"
       ],
       "cwd": "${workspaceFolder}",
       // For more information about the 'console' field, see https://aka.ms/VSCode-CS-LaunchJson-Console
       "console": "internalConsole",
-      "stopAtEntry": false
+      "stopAtEntry": false,
+      "requireExactSource": false
     },
     {
       "name": ".NET Core Attach",

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; }
     }

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
-}
+}

Models/ReadFlag.cs

@@ -0,0 +1,68 @@
+using System;
+
+namespace Ovation.FasterQC.Net
+{
+    [Flags]
+    public enum ReadFlag : ushort
+    {
+        /// <summary>
+        /// template having multiple templates in sequencing (read is paired)
+        /// </summary>
+        Paired = 1,
+
+        /// <summary>
+        /// each segment properly aligned according to the aligner (read mapped in proper pair)
+        /// </summary>
+        Aligned = 2,
+
+        /// <summary>
+        /// segment unmapped (read1 unmapped)
+        /// </summary>
+        SegmentUnmapped = 4,
+
+        /// <summary>
+        /// next segment in the template unmapped (read2 unmapped)
+        /// </summary>
+        NextSegmentUnmapped = 8,
+
+        /// <summary>
+        /// SEQ being reverse complemented (read1 reverse complemented)
+        /// </summary>
+        ReverseComplemented = 16,
+
+        /// <summary>
+        /// SEQ of the next segment in the template being reverse complemented (read2 reverse complemented)
+        /// </summary>
+        NextSegmentReverseComplemented = 32,
+
+        /// <summary>
+        /// the first segment in the template (is read1)
+        /// </summary>
+        FirstSegment = 64,
+
+        /// <summary>
+        /// the last segment in the template (is read2)
+        /// </summary>
+        LastSegment = 128,
+
+        /// <summary>
+        /// not primary alignment
+        /// </summary>
+        NotPrimaryAlignment = 256,
+
+        /// <summary>
+        /// alignment fails quality checks
+        /// </summary>
+        FailedQualityChecks = 512,
+
+        /// <summary>
+        /// PCR or optical duplicate
+        /// </summary>
+        OpticalDuplicate = 1024,
+
+        /// <summary>
+        /// supplementary alignment (e.g. aligner specific, could be a portion of a split read or a tied region)
+        /// </summary>
+        SupplementaryAlignment = 2048
+    }
+}

Models/Sequence.cs

@@ -5,6 +5,8 @@ namespace Ovation.FasterQC.Net
 {
     public class Sequence
     {
+        public ReadFlag ReadFlag { get; }
+
         public byte[] Identifier { get; }
 
         public byte[] Read { get; }
@@ -21,8 +23,9 @@ public Sequence(byte[] lines, int[] endOfLines)
             Quality = new ReadOnlyMemory<byte>(lines, endOfLines[2], endOfLines[3] - endOfLines[2]).ToArray();
         }
 
-        public Sequence(byte[] identifer, byte[] read, byte[] blank, byte[] quality)
+        public Sequence(ushort readFlag, byte[] identifer, byte[] read, byte[] blank, byte[] quality)
         {
+            ReadFlag = (ReadFlag)readFlag;
             Identifier = new ReadOnlyMemory<byte>(identifer).ToArray();
             Read = new ReadOnlyMemory<byte>(read).ToArray();
             Blank = new ReadOnlyMemory<byte>(blank).ToArray();
@@ -31,15 +34,18 @@ public Sequence(byte[] identifer, byte[] read, byte[] blank, byte[] quality)
 
         public Sequence(BamAlignment bamAlignment)
         {
+            ReadFlag = (ReadFlag)bamAlignment.flag;
             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()
         {
             var sb = new StringBuilder("sequence: \n");
 
+            sb.AppendLine(ReadFlag.ToString());
             sb.AppendLine(new string(Encoding.ASCII.GetChars(Identifier)));
             sb.AppendLine(new string(Encoding.ASCII.GetChars(Read)));
             sb.AppendLine(new string(Encoding.ASCII.GetChars(Blank)));
@@ -48,4 +54,4 @@ public override string ToString()
             return sb.ToString();
         }
     }
-}
+}

Ovation.FasterQC.Net.csproj

@@ -3,6 +3,7 @@
   <PropertyGroup>
     <OutputType>Exe</OutputType>
     <TargetFramework>net6.0</TargetFramework>
+    <Nullable>enable</Nullable>
   </PropertyGroup>
 
   <ItemGroup>

Program.cs

@@ -1,6 +1,7 @@
 using System;
 using System.Collections.Generic;
 using System.IO;
+using System.Linq;
 using System.Text.Json;
 using CommandLine;
 using Ovation.FasterQC.Net.Modules;
@@ -19,17 +20,24 @@ class Program
             PropertyNamingPolicy = JsonNamingPolicy.CamelCase
         };
 
-        private TimedSequenceProgressBar progressBar;
+        private TimedSequenceProgressBar? progressBar;
 
         static void Main(string[] args)
         {
-            Parser.Default.ParseArguments<CliOptions>(args)
-                .WithParsed(o =>
+            var parser = new Parser(config =>
                 {
-                    o.Validate();
-                    Settings = o;
-                    new Program().Run();
-                });
+                    config.AutoHelp = true;
+                    config.AutoVersion = true;
+                    config.CaseInsensitiveEnumValues = true;
+                }
+            );
+
+            parser.ParseArguments<CliOptions>(args)
+                .WithParsed(o =>
+                    {
+                        Settings = o;
+                        new Program().Run();
+                    });
         }
 
         private void Run()
@@ -42,14 +50,16 @@ 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 +81,7 @@ 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))

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;

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
             {
@@ -61,12 +61,12 @@ 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);
+                sequence = new Sequence(0, identifier, read, blank, quality);
                 sequencesRead++;
                 return true;
             }

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

Readers/ReaderFactory.cs

@@ -7,10 +7,19 @@ public static class ReaderFactory
     {
         public static ISequenceReader Create(CliOptions settings)
         {
-            return settings switch
+            return settings.Format switch
             {
-                { Fastq: true } => new FastqLineReader(settings.InputFilename, true),
-                { Bam: true } => new BamReader(settings.InputFilename),
+                ReaderType.Fastq => new FastqReader(settings.InputFilename, false),
+                ReaderType.FastqGz => new FastqReader(settings.InputFilename, true),
+
+                ReaderType.FastqLine => new FastqLineReader(settings.InputFilename, false),
+                ReaderType.FastqLineGz => new FastqLineReader(settings.InputFilename, true),
+
+                ReaderType.Sam => new SamReader(settings.InputFilename, false),
+                ReaderType.SamGz => new SamReader(settings.InputFilename, true),
+
+                ReaderType.Bam => new BamReader(settings.InputFilename),
+
                 _ => throw new InvalidOperationException($"could not determine file type of {settings.InputFilename}")
             };
         }

Readers/ReaderType.cs

@@ -0,0 +1,19 @@
+namespace Ovation.FasterQC.Net
+{
+    public enum ReaderType
+    {
+        Fastq,
+
+        FastqGz,
+
+        FastqLine,
+
+        FastqLineGz,
+
+        Sam,
+
+        SamGz,
+
+        Bam
+    }
+}