From 2869270c11fd41b636d76c38d860f049ff574343 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 10 Dec 2009 21:11:42 +0000
Subject: [PATCH] Fixed deletion depth calculation plus mis-spelling in
 ReadBackedPileup method.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2315 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/genotyper/UnifiedGenotyper.java        | 2 +-
 .../broadinstitute/sting/utils/pileup/ReadBackedPileup.java   | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 3f4a02949..2bf421644 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -205,7 +205,7 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
         // are there too many deletions in the pileup?
         ReadBackedPileup pileup = context.getPileup();
         if ( isValidDeletionFraction(UAC.MAX_DELETION_FRACTION) &&
-             (double)pileup.getNumberOfDeletions() / (double)pileup.size() > UAC.MAX_DELETION_FRACTION )
+             (double)pileup.getPileupWithoutMappingQualityZeroReads().getNumberOfDeletions() / (double)(pileup.size() - pileup.getNumberOfMappingQualityZeroReads()) > UAC.MAX_DELETION_FRACTION )
             return null;
 
         // stratify the AlignmentContext and cut by sample
diff --git a/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java b/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java
index b7b18332d..4ae03cde0 100755
--- a/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java
+++ b/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java
@@ -382,7 +382,7 @@ public class ReadBackedPileup implements Iterable<PileupElement> {
      * Get an array of the mapping qualities
      * @return
      */
-    public byte[] getMapppingQuals() {
+    public byte[] getMappingQuals() {
        byte[] v = new byte[size()];
        for ( ExtendedPileupElement pile : this.extendedForeachIterator() ) { v[pile.getPileupOffset()] = (byte)pile.getRead().getMappingQuality(); }
        return v;
@@ -393,7 +393,7 @@ public class ReadBackedPileup implements Iterable<PileupElement> {
     // Private functions for printing pileups
     //
     private String getMappingQualsString() {
-        return quals2String(getMapppingQuals());
+        return quals2String(getMappingQuals());
     }
 
     private static String quals2String( byte[] quals ) {