adding read limiter... for dev speed

Interfaces/ISequenceReader.cs

@@ -4,7 +4,7 @@ namespace Ovation.FasterQC.Net
 {
     public interface ISequenceReader : IDisposable
     {
-        int SequencesRead { get; }
+        ulong SequencesRead { get; }
 
         bool ReadSequence(out Sequence? sequence);
 

Models/ReadFlag.cs

@@ -15,6 +15,8 @@ public enum ReadFlag : ushort
         /// </summary>
         Aligned = 2,
 
+        AlignedAndPaired = Aligned | Paired,
+
         /// <summary>
         /// segment unmapped (read1 unmapped)
         /// </summary>

Modules/AlignmentStatistics.cs

@@ -9,13 +9,15 @@ public class AlignmentStatistics : IQcModule
 
         private ulong aligned;
 
+        private ulong alignedAndPaired;
+
         private ulong segmentUnmapped;
 
         private ulong nextSegmentUnmapped;
 
         private ulong reverseComplemented;
 
-        private ulong nextSegmenteverseComplemented;
+        private ulong nextSegmentReverseComplemented;
 
         private ulong nonPrimaryAlignment;
 
@@ -33,10 +35,11 @@ public void ProcessSequence(Sequence sequence)
 
             if ((sequence.ReadFlag & ReadFlag.Paired) != 0) paired++;
             if ((sequence.ReadFlag & ReadFlag.Aligned) != 0) aligned++;
+            if ((sequence.ReadFlag & ReadFlag.AlignedAndPaired) == ReadFlag.AlignedAndPaired) alignedAndPaired++;
             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.NextSegmentReverseComplemented) != 0) nextSegmentReverseComplemented++;
             if ((sequence.ReadFlag & ReadFlag.NotPrimaryAlignment) != 0) nonPrimaryAlignment++;
             if ((sequence.ReadFlag & ReadFlag.FailedQualityChecks) != 0) failedQualityChecks++;
             if ((sequence.ReadFlag & ReadFlag.OpticalDuplicate) != 0) opticalDuplicate++;
@@ -52,10 +55,11 @@ public void Reset()
             sequenceCount,
             paired,
             aligned,
+            alignedAndPaired,
             segmentUnmapped,
             nextSegmentUnmapped,
             reverseComplemented,
-            nextSegmenteverseComplemented,
+            nextSegmentReverseComplemented,
             nonPrimaryAlignment,
             failedQualityChecks,
             opticalDuplicate

Program.cs

@@ -50,7 +50,7 @@ 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))
+            while (sequenceReader.ReadSequence(out Sequence? sequence) && sequenceReader.SequencesRead < Settings.ReadLimit)
             {
                 ArgumentNullException.ThrowIfNull(sequence);
 

Readers/BamReader.cs

@@ -18,9 +18,9 @@ public class BamReader : ISequenceReader
 
         private bool disposedValue;
 
-        private int sequencesRead = 0;
+        private ulong sequencesRead = 0;
 
-        public int SequencesRead => sequencesRead;
+        public ulong SequencesRead => sequencesRead;
 
         public BamReader(string bam)
         {

Readers/FastqLineReader.cs

@@ -18,9 +18,9 @@ public class FastqLineReader : ISequenceReader
 
         private bool disposedValue;
 
-        private int sequencesRead = 0;
+        private ulong sequencesRead = 0;
 
-        public int SequencesRead => sequencesRead;
+        public ulong SequencesRead => sequencesRead;
 
         public double ApproximateCompletion =>
             100.0 * inputStream.Position / inputStream.Length;

Readers/FastqReader.cs

@@ -17,9 +17,9 @@ public class FastqReader : ISequenceReader
 
         private bool disposedValue;
 
-        private int sequencesRead = 0;
+        private ulong sequencesRead = 0;
 
-        public int SequencesRead => sequencesRead;
+        public ulong SequencesRead => sequencesRead;
 
         public double ApproximateCompletion =>
             100.0 * inputStream.Position / inputStream.Length;

Readers/SamReader.cs

@@ -19,9 +19,9 @@ public class SamReader : ISequenceReader
 
         private bool disposedValue;
 
-        private int sequencesRead = 0;
+        private ulong sequencesRead = 0;
 
-        public int SequencesRead => sequencesRead;
+        public ulong SequencesRead => sequencesRead;
 
         public SamReader(string sam, bool gzipped = true)
         {

Utils/CliOptions.cs

@@ -25,7 +25,10 @@ public class CliOptions
         public ReaderType Format { get; set; }
 
         [Option('m', "modules", Required = false, 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>();
+
+        [Option('l', "read-limit", Required = false, HelpText = "Limit the number of reads processed")]
+        public ulong ReadLimit { get; set; } = ulong.MaxValue;
 
         public static CliOptions Settings { get; set; } = null!;
 

Utils/PrettyPrintExtension.cs

@@ -2,7 +2,7 @@ namespace Ovation.FasterQC.Net.Utils
 {
     public static class PrettyPrintExtension
     {
-        public static string WithSsiUnits(this int n)
+        public static string WithSsiUnits(this ulong n)
         {
             return n switch
             {