From 4ee6a478e30b6244bb9a85925ce1a4558e1dd6d1 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 22 Dec 2009 20:43:44 +0000
Subject: [PATCH] Creates a table of reference allele percentage and alternate
 allele percentage at Hapmap-chip sites in a BAM file.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2428 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../diagnostics/AlleleBalanceInspector.java   | 86 +++++++++++++++++++
 1 file changed, 86 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/AlleleBalanceInspector.java

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/AlleleBalanceInspector.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/AlleleBalanceInspector.java
new file mode 100755
index 000000000..1d838d15c
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/AlleleBalanceInspector.java
@@ -0,0 +1,86 @@
+package org.broadinstitute.sting.playground.gatk.walkers.diagnostics;
+
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.gatk.refdata.RodGenotypeChipAsGFF;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.utils.BaseUtils;
+
+/**
+ * Takes a BAM file and a Hapmap-chip file (via the -hc argument) and creates a table of reference allele
+ * percentage and alternate allele percentage for het, homvar, and other genotypes.
+ */
+public class AlleleBalanceInspector extends LocusWalker<Integer, Integer> {
+    private int item = 1;
+    public void initialize() {
+        out.printf("item\tlocus\tref\tgenotype\tstate\tdepth\trefdepth\taltdepth\trefpct\taltpct%n");
+    }
+
+    public boolean filter(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        RodGenotypeChipAsGFF hc = (RodGenotypeChipAsGFF) tracker.lookup("hapmap-chip", null);
+
+        return hc != null && hc.getCalledGenotype().isVariant(ref.getBase());
+    }
+
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        RodGenotypeChipAsGFF hc = (RodGenotypeChipAsGFF) tracker.lookup("hapmap-chip", null);
+
+        String state;
+        if (hc.getCalledGenotype().isHet()) {
+            state = "het";
+        } else if (hc.getCalledGenotype().isHom()) {
+            state = "homvar";
+        } else {
+            state = "other";
+        }
+
+        int refIndex = ref.getBaseIndex();
+        int altIndex = -1;
+        for (char base : hc.getCalledGenotype().getBases().toCharArray()) {
+            int baseIndex = BaseUtils.simpleBaseToBaseIndex(base);
+
+            if (baseIndex != refIndex) {
+                altIndex = baseIndex;
+            }
+        }
+
+        int[] baseCounts = context.getPileup().getBaseCounts();
+        double sum = (double) (baseCounts[refIndex] + baseCounts[altIndex]);
+        double refPct = ((double) baseCounts[refIndex])/sum;
+        double altPct = ((double) baseCounts[altIndex])/sum;
+
+        out.printf("%d\t%s\t%c\t%s\t%s\t%d\t%d\t%d\t%f\t%f%n",
+                   item++,
+                   context.getLocation(),
+                   ref.getBase(),
+                   hc.getCalledGenotype().getBases(),
+                   state,
+                   context.getPileup().getReads().size(),
+                   baseCounts[refIndex],
+                   baseCounts[altIndex], refPct, altPct);
+
+        return null;
+    }
+
+    /**
+     * Provide an initial value for reduce computations.
+     *
+     * @return Initial value of reduce.
+     */
+    public Integer reduceInit() {
+        return null;  //To change body of implemented methods use File | Settings | File Templates.
+    }
+
+    /**
+     * Reduces a single map with the accumulator provided as the ReduceType.
+     *
+     * @param value result of the map.
+     * @param sum   accumulator for the reduce.
+     * @return accumulator with result of the map taken into account.
+     */
+    public Integer reduce(Integer value, Integer sum) {
+        return null;  //To change body of implemented methods use File | Settings | File Templates.
+    }
+}