adding simple q distribution calc and chart

Modules/QualityDistribution.cs

@@ -0,0 +1,66 @@
+using System;
+using System.Linq;
+
+namespace Ovation.FasterQC.Net
+{
+    public class QualityDistribution : IQcModule
+    {
+        private const byte ILLUMINA_BASE_ADJUSTMENT = 33;
+
+        private readonly ulong[] qualities = new ulong[128];
+
+        private byte lowestScore = byte.MaxValue;
+
+        private byte highestScore = byte.MinValue;
+
+        public string Name => "qualityDistribution";
+
+        public string Description => "Calculates the distribution of quality scores";
+
+        public bool IsEnabledForAll => true;
+
+        public object Data
+        {
+            get
+            {
+                return new
+                {
+                    lowestScore = lowestScore - ILLUMINA_BASE_ADJUSTMENT,
+                    highestScore = highestScore - ILLUMINA_BASE_ADJUSTMENT,
+
+                    lowestScoreUnadjusted = lowestScore,
+                    highestScoreUnadjusted = highestScore,
+
+                    qualities = qualities.Skip(lowestScore).Take(highestScore - lowestScore + 1),
+                };
+            }
+        }
+
+        public void ProcessSequence(Sequence sequence)
+        {
+            var sequenceLength = sequence.Read.Length;
+            var quals = sequence.Quality;
+
+            for (var i = 0; i < sequenceLength; i++)
+            {
+                var qual = quals[i];
+
+                lowestScore = Math.Min(lowestScore, quals[i]);
+                highestScore = Math.Max(highestScore, quals[i]);
+
+                qualities[qual]++;
+            }
+        }
+
+        public void Reset()
+        {
+            for (var p = 0; p < qualities.Length; p++)
+            {
+                qualities[p] = 0;
+            }
+
+            lowestScore = byte.MaxValue;
+            highestScore = byte.MinValue;
+        }
+    }
+}

R/fasterqc.R

@@ -31,7 +31,7 @@ multiplot <- function(..., plotlist = NULL, file, cols = 1, layout = NULL) {
     # ncol: Number of columns of plots
     # nrow: Number of rows needed, calculated from # of cols
     layout <- matrix(seq(1, cols * ceiling(num_plots / cols)),
-      ncol = cols, nrow = ceiling(num_plots / cols)
+                     ncol = cols, nrow = ceiling(num_plots / cols)
     )
   }
 
@@ -56,9 +56,8 @@ multiplot <- function(..., plotlist = NULL, file, cols = 1, layout = NULL) {
 }
 
 setwd("/Users/michaeljon/src/ovation/fasterqc.net/tmp")
-sample <- "in3257_2_S1_sorted"
+sample <- "in3257_2_S1.sorted"
 
-# load the data
 json <-
   jsonlite::fromJSON(readLines(paste(getwd(), "/", sample, ".json", sep = "")))
 
@@ -162,6 +161,28 @@ png(paste(sample, ".base-qual-dist.png", sep = ""), width = 800, height = 600)
 print(plt)
 dev.off()
 
+# plot quality distributions
+quality_dist <- data.frame(
+  qs = json$qualityDistribution$qualities
+)
+
+plt <- ggplot(quality_dist, aes(x = seq_along(qs))) +
+  geom_col(aes(y = qs), fill = "#7faf7f") +
+  scale_y_continuous(labels = scales::comma, trans = "log10") +
+  labs(
+    color = "",
+    title = "Quality distribution",
+    subtitle = paste("Sample ", sample, sep = ""),
+    x = "Quality (phred)",
+    y = "# of bases (log)",
+    caption = "Species: SARS-CoV-2"
+  ) +
+  theme_ipsum()
+
+png(paste(sample, ".qual-dist.png", sep = ""), width = 800, height = 600)
+print(plt)
+dev.off()
+
 # plot quality distributions
 quality_distribution <- data.frame(
   qual = json$meanQualityDistribution$distribution,
@@ -281,4 +302,4 @@ plt <- ggplot(histogram, aes(x = lengths)) +
 
 png(paste(sample, ".aligned.png", sep = ""), width = 800, height = 600)
 print(plt)
-dev.off()
+dev.off()