From b3118747eafb1a71ed0a508e9ef127db4252c8a1 Mon Sep 17 00:00:00 2001
From: Michaeljon Miller <michaeljon.miller@outlook.com>
Date: Fri, 20 May 2022 11:21:07 -0700
Subject: [PATCH] adding a polyx module

---
 Modules/PolyX.cs | 105 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 105 insertions(+)
 create mode 100644 Modules/PolyX.cs

diff --git a/Modules/PolyX.cs b/Modules/PolyX.cs
new file mode 100644
index 0000000..e382f51
--- /dev/null
+++ b/Modules/PolyX.cs
@@ -0,0 +1,105 @@
+namespace Ovation.FasterQC.Net
+{
+    public class PolyX : IQcModule
+    {
+        private const byte POLY_SIZE = 10;
+
+        private readonly ulong[] polyA = new ulong[2];
+
+        private readonly ulong[] polyT = new ulong[2];
+
+        private readonly ulong[] polyC = new ulong[2];
+
+        private readonly ulong[] polyG = new ulong[2];
+
+        private ulong sequenceCount;
+
+        private ulong tooShort;
+
+        public string Name => "polyX";
+
+        public string Description => "Calculates the the number of reads with polyX heads / tails";
+
+        public bool IsEnabledForAll => true;
+
+        public object Data
+        {
+            get
+            {
+                return new
+                {
+                    sequenceCount,
+                    tooShort,
+                    target = POLY_SIZE,
+                    head = new { a = polyA[0], t = polyT[0], c = polyC[0], g = polyG[0] },
+                    tail = new { a = polyA[1], t = polyT[1], c = polyC[1], g = polyG[1] },
+                };
+            }
+        }
+
+        public void ProcessSequence(Sequence sequence)
+        {
+            sequenceCount++;
+
+            if (sequence.Read.Length < POLY_SIZE)
+            {
+                tooShort++;
+                return;
+            }
+
+            if (CheckPolyHead((byte)'A', sequence.Read) == true) polyA[0]++;
+            if (CheckPolyTail((byte)'A', sequence.Read) == true) polyA[1]++;
+
+            if (CheckPolyHead((byte)'T', sequence.Read) == true) polyT[0]++;
+            if (CheckPolyTail((byte)'T', sequence.Read) == true) polyT[1]++;
+
+            if (CheckPolyHead((byte)'C', sequence.Read) == true) polyC[0]++;
+            if (CheckPolyTail((byte)'C', sequence.Read) == true) polyC[1]++;
+
+            if (CheckPolyHead((byte)'G', sequence.Read) == true) polyG[0]++;
+            if (CheckPolyTail((byte)'G', sequence.Read) == true) polyG[1]++;
+        }
+
+        public void Reset()
+        {
+            polyA[0] = 0; polyA[1] = 0;
+            polyT[0] = 0; polyT[1] = 0;
+            polyC[0] = 0; polyC[1] = 0;
+            polyG[0] = 0; polyG[1] = 0;
+
+            sequenceCount = 0;
+            tooShort = 0;
+        }
+
+        private static bool CheckPolyHead(byte test, byte[] sequence)
+        {
+            // consider a loop unroll here
+            for (var i = 0; i < POLY_SIZE; i++)
+            {
+                if (sequence[i] != test)
+                {
+                    return false;
+                }
+            }
+
+            return true;
+        }
+
+        private static bool CheckPolyTail(byte test, byte[] sequence)
+        {
+            var endOfRead = sequence.Length - 1;
+            var endOfPoly = sequence.Length - (POLY_SIZE + 1);
+
+            // consider a loop unroll here
+            for (var i = endOfRead; i > endOfPoly; i--)
+            {
+                if (sequence[i] != test)
+                {
+                    return false;
+                }
+            }
+
+            return true;
+        }
+    }
+}