From e6f468b647518f8e3ef8fb030bb4d4eee95eceea Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 17 Dec 2012 11:54:47 -0500
Subject: [PATCH] Refactored the quasi-useful IndelType annotation into the
 more useful VariantType. The indels are still annotated as before, but now
 all other variant types are annotated too. I'm doing this because of requests
 on the forum but am not making it standard.  If we find it to be useful we
 can turn it on by default later.

---
 .../{IndelType.java => VariantType.java}      | 56 +++++++++----------
 .../sting/utils/IndelUtils.java               |  4 +-
 2 files changed, 27 insertions(+), 33 deletions(-)
 rename public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/{IndelType.java => VariantType.java} (52%)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java
similarity index 52%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java
index c67d829c2..a5c2b32f0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java
@@ -15,9 +15,9 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import java.util.*;
 
 /**
- * Rough category of indel type (insertion, deletion, multi-allelic, other)
+ * Assigns a roughly correct category of the variant type (SNP, MNP, insertion, deletion, etc.)
  */
-public class IndelType extends InfoFieldAnnotation implements ExperimentalAnnotation {
+public class VariantType extends InfoFieldAnnotation implements ExperimentalAnnotation {
 
     public Map<String, Object> annotate(final RefMetaDataTracker tracker,
                                         final AnnotatorCompatible walker,
@@ -26,41 +26,35 @@ public class IndelType extends InfoFieldAnnotation implements ExperimentalAnnota
                                         final VariantContext vc,
                                         final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
 
-        int run;
-        if (vc.isMixed()) {
-            Map<String, Object> map = new HashMap<String, Object>();
-            map.put(getKeyNames().get(0), String.format("%s", "MIXED"));
-            return map;
-
-        }
-        else if ( vc.isIndel() ) {
-            String type="";
-            if (!vc.isBiallelic())
-                type = "MULTIALLELIC_INDEL";
-            else {
-                if (vc.isSimpleInsertion())
-                    type = "INS.";
-                else if (vc.isSimpleDeletion())
-                    type = "DEL.";
-                else
-                    type = "OTHER.";
-                ArrayList<Integer> inds = IndelUtils.findEventClassificationIndex(vc, ref);
-                for (int k : inds) {
-                    type = type+ IndelUtils.getIndelClassificationName(k)+".";
-                }
-            }
-            Map<String, Object> map = new HashMap<String, Object>();
-            map.put(getKeyNames().get(0), String.format("%s", type));
-            return map;
+        StringBuffer type = new StringBuffer("");
+        if ( vc.isVariant() && !vc.isBiallelic() )
+            type.append("MULTIALLELIC_");
 
+        if ( !vc.isIndel() ) {
+            type.append(vc.getType().toString());
         } else {
-            return null;
+            if (vc.isSimpleInsertion())
+                type.append("INSERTION.");
+            else if (vc.isSimpleDeletion())
+                type.append("DELETION.");
+            else
+                type.append("COMPLEX.");
+            ArrayList<Integer> inds = IndelUtils.findEventClassificationIndex(vc, ref);
+            type.append(IndelUtils.getIndelClassificationName(inds.get(0)));
+
+            for (int i = 1; i < inds.size(); i++ ) {
+                type.append(".");
+                type.append(IndelUtils.getIndelClassificationName(inds.get(i)));
+            }
         }
 
+        Map<String, Object> map = new HashMap<String, Object>();
+        map.put(getKeyNames().get(0), String.format("%s", type));
+        return map;
     }
 
-    public List<String> getKeyNames() { return Arrays.asList("IndelType"); }
+    public List<String> getKeyNames() { return Arrays.asList("VariantType"); }
 
-    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("IndelType", 1, VCFHeaderLineType.String, "Indel type description")); }
+    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("VariantType", 1, VCFHeaderLineType.String, "Variant type description")); }
 
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java b/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java
index c6ca39f4b..9b1cc9733 100755
--- a/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java
@@ -122,9 +122,9 @@ public class IndelUtils {
 
         ArrayList<Integer> inds = new ArrayList<Integer>();
         if ( vc.isSimpleInsertion() ) {
-            indelAlleleString = vc.getAlternateAllele(0).getDisplayString();
+            indelAlleleString = vc.getAlternateAllele(0).getDisplayString().substring(1);
         } else if ( vc.isSimpleDeletion() ) {
-            indelAlleleString = vc.getReference().getDisplayString();
+            indelAlleleString = vc.getReference().getDisplayString().substring(1);
         }
         else {
             inds.add(IND_FOR_OTHER_EVENT);