fixing percent complete on read-limited runs

.vscode/launch.json

@@ -14,6 +14,8 @@
       "args": [
         "-v",
         "-d",
+        "-l",
+        "1000000",
         "-f",
         "sam",
         "-i",

Program.cs

@@ -64,7 +64,17 @@ private void Run()
                 {
                     if (sequenceReader.SequencesRead % UpdatePeriod == 0)
                     {
-                        Console.Error.WriteLine($"{sequenceReader.SequencesRead.WithSsiUnits()} sequences completed ({sequenceReader.ApproximateCompletion:0.0}%)");
+                        var approximateCompletion = sequenceReader.ApproximateCompletion;
+
+                        // if we're limiting the number of reads then the reader's
+                        // approximation will be incorrect (it's based on file positions),
+                        // so we'll do the math ourselves
+                        if (Settings.ReadLimit < ulong.MaxValue)
+                        {
+                            approximateCompletion = 100.0 * (double)sequenceReader.SequencesRead / (double)Settings.ReadLimit;
+                        }
+
+                        Console.Error.WriteLine($"{sequenceReader.SequencesRead.WithSsiUnits()} sequences completed ({approximateCompletion:0.0}%)");
                     }
                 });
             }