From 98718d0faa5beb3ada59516b6f9257e841330ee2 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 10 May 2010 14:50:22 +0000
Subject: [PATCH] Computes the error rate per cycle

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3336 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/ErrorRatePerReadPosition.java     | 153 ++++++++++++++++++
 1 file changed, 153 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/oneoffprojects/walkers/ErrorRatePerReadPosition.java

diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ErrorRatePerReadPosition.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ErrorRatePerReadPosition.java
new file mode 100755
index 000000000..9e664e0e8
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ErrorRatePerReadPosition.java
@@ -0,0 +1,153 @@
+package org.broadinstitute.sting.oneoffprojects.walkers;
+
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.utils.BaseUtils;
+
+import java.util.List;
+import java.util.HashMap;
+import java.util.HashSet;
+
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMReadGroupRecord;
+
+public class ErrorRatePerReadPosition extends LocusWalker<Integer, Integer> {
+    private HashMap<String, int[]> mismatches;
+    private HashMap<String, int[]> counts;
+    private HashMap<String, int[]> quals;
+    private HashMap<String, HashSet<Integer>> readLengthsPerReadGroup;
+    private HashSet<Integer> readLengths;
+    private int readLength = 10000;
+
+
+    public void initialize() {
+        mismatches = new HashMap<String, int[]>();
+        counts = new HashMap<String, int[]>();
+        quals = new HashMap<String, int[]>();
+        readLengthsPerReadGroup = new HashMap<String, HashSet<Integer>>();
+        readLengths = new HashSet<Integer>();
+
+        for (SAMReadGroupRecord rg : this.getToolkit().getSAMFileHeader().getReadGroups()) {
+            int[] mm = new int[readLength];
+            int[] cm = new int[readLength];
+            int[] qm = new int[readLength];
+
+            mismatches.put(rg.getReadGroupId(), mm);
+            counts.put(rg.getReadGroupId(), cm);
+            quals.put(rg.getReadGroupId(), qm);
+        }
+    }
+
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        List<Integer> offsets = context.getOffsets();
+        List<SAMRecord> reads = context.getReads();
+
+        for (int i = 0; i < offsets.size(); i++) {
+            int offset = offsets.get(i);
+            char readBase = reads.get(i).getReadString().charAt(offset);
+
+            int refIndex = ref.getBaseIndex();
+            int readIndex = BaseUtils.simpleBaseToBaseIndex(readBase);
+
+
+            if (!reads.get(i).getReadNegativeStrandFlag() && (!reads.get(i).getReadPairedFlag() || reads.get(i).getFirstOfPairFlag())) {
+                String keyName = reads.get(i).getReadGroup().getReadGroupId();
+
+                //out.printf("%d %d%n", refIndex, readIndex);
+
+                mismatches.get(keyName)[offset] += (refIndex != readIndex) ? 1 : 0;
+                counts.get(keyName)[offset]++;
+                quals.get(keyName)[offset] += reads.get(i).getBaseQualities()[offset];
+
+                //out.println(reads.get(i).getBaseQualities()[offset]);
+
+                int readLength = reads.get(i).getReadLength();
+                if (!readLengthsPerReadGroup.containsKey(keyName)) {
+                    readLengthsPerReadGroup.put(keyName, new HashSet<Integer>());
+                }
+
+                readLengthsPerReadGroup.get(keyName).add(readLength);
+                readLengths.add(readLength);
+            }
+        }
+
+        return null;
+    }
+
+    public Integer reduceInit() {
+        return null;
+    }
+
+    public Integer reduce(Integer value, Integer sum) {
+        return null;
+    }
+
+    public void onTraversalDone(Integer sum) {
+        String[] rgs = mismatches.keySet().toArray(new String[1]);
+
+        out.printf("position");
+        for (String rg : rgs) { out.printf("\t%s", rg); }
+        //out.printf("\tmean\tsd\tmin\tmax");
+
+        //for (int readLength : readLengths) {
+        //    out.printf("\t%dreadLength", readLength);
+        //}
+
+        out.println();
+
+        for (int i = 0; i < readLength; i++) {
+            boolean print = false;
+            String row = "";
+
+            row += String.format("%d", i);
+
+            double rsum = 0.0;
+            double min = 1.00;
+            double max = 0.00;
+            
+            for (String rg : rgs) {
+                double value = ((double) mismatches.get(rg)[i])/((double) counts.get(rg)[i]);
+                //double value = ((double) quals.get(rg)[i])/((double) counts.get(rg)[i]);
+
+                if (Double.isInfinite(value) || Double.isNaN(value)) {
+                    value = 0.0;
+                } else {
+                    print = true;
+                }
+
+                row += String.format("\t%f", value);
+
+                rsum += value;
+                if (value > max) { max = value; }
+                if (value < min) { min = value; }
+            }
+
+            double mean = rsum/rgs.length;
+
+            double squareDeviationSum = 0.0;
+            for (String rg : rgs) {
+                double value = ((double) mismatches.get(rg)[i])/((double) counts.get(rg)[i]);
+
+                if (Double.isInfinite(value) || Double.isNaN(value)) {
+                    value = 0.0;
+                } else {
+                    print = true;
+                }
+
+                squareDeviationSum += Math.pow(value - mean, 2.0);
+            }
+
+            double sd = Math.sqrt(squareDeviationSum/rgs.length);
+
+            //row += String.format("\t%f\t%f\t%f\t%f", mean, sd, min, max);
+
+            row += String.format("%n");
+
+            if (print) {
+                out.print(row);
+            }
+        }
+    }
+}