First pass at an IndelLengthHistogram module for variant annotator. Off by default. Will be tested shortly (have to commit, so I can check out in another directory, so that compiling won't kill all my jobs running on LSF)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3440 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelLengthHistogram.java

@@ -0,0 +1,101 @@
+package org.broadinstitute.sting.gatk.walkers.varianteval;
+
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
+import org.broadinstitute.sting.playground.utils.report.utils.TableType;
+import org.broadinstitute.sting.utils.StingException;
+
+/**
+ * IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl
+ *
+ * @Author chartl
+ * @Date May 26, 2010
+ */
+public class IndelLengthHistogram extends VariantEvaluator {
+    private final int SIZE_LIMIT = 50;
+    @DataPoint(name="indelLengthHistogram",description="Histogram of indel lengths")
+    IndelHistogram indelHistogram = new IndelHistogram(SIZE_LIMIT);
+
+    /*
+     * Indel length histogram table object
+     */
+
+    class IndelHistogram implements TableType {
+        private Integer[] colKeys;
+        private int limit;
+        private String[] rowKeys = {"EventLength"};
+        private int[] indelHistogram;
+
+        public IndelHistogram(int limit) {
+            colKeys = initColKeys(limit);
+            indelHistogram = new int[limit*2];
+            this.limit = limit;
+        }
+
+        public Object[] getColumnKeys() {
+            return colKeys;
+        }
+
+        public Object[] getRowKeys() {
+            return rowKeys;
+        }
+
+        public Object getCell(int row, int col) {
+            return indelHistogram[col];
+        }
+
+        private Integer[] initColKeys(int size) {
+            Integer[] cK = new Integer[size*2+1];
+            int index = 0;
+            for ( int i = -size; i < size; i ++ ) {
+                cK[index] = i;
+                index++;
+            }
+
+            return cK;
+        }
+
+        public String getName() { return "indelHistTable"; }
+
+        public void update(int eLength) {
+            indelHistogram[len2index(eLength)]++;
+        }
+
+        private int len2index(int len) {
+            if ( len > limit || len < -limit ) {
+                throw new StingException("Indel length exceeds limit of "+limit+" please increase indel limit size");
+            }
+            return len + limit;
+        }
+    }
+
+    public IndelLengthHistogram(VariantEvalWalker parent) { super(parent); }
+
+    public boolean enabled() { return false; }
+
+    public String getName() { return "IndelLengthHistogram"; }
+
+    public int getComparisonOrder() { return 1; } // need only the evals
+
+    public String update1(VariantContext vc1, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        if ( ! vc1.isBiallelic() && vc1.isIndel() ) {
+            veWalker.getLogger().warn("[IndelLengthHistogram] Non-biallelic indel at "+ref.getLocus()+" ignored.");
+            return vc1.toString(); // biallelic sites are output
+        }
+
+        if ( vc1.isIndel() ) {
+            if ( vc1.isInsertion() ) {
+                indelHistogram.update(vc1.getAlternateAllele(0).length());
+            } else if ( vc1.isDeletion() ) {
+                indelHistogram.update(-vc1.getReference().length());
+            } else {
+                throw new StingException("Indel type that is not insertion or deletion.");
+            }
+        }
+
+        return null;
+    }
+}