From 7f74303f2b4b23d81bbd1fe444031d48f2cc1f9e Mon Sep 17 00:00:00 2001
From: vruano <valentin.ruano@gmail.com>
Date: Wed, 15 Jul 2015 17:58:51 -0400
Subject: [PATCH] Removes a very inefficient way to iterate in
 ReferenceConfidenceModel.isReadInformativeAboutIndelsOfSize(...)

Addresses performance issue #1048.
---
 .../ReferenceConfidenceModel.java             | 20 ++++++-------------
 1 file changed, 6 insertions(+), 14 deletions(-)

diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java
index d674800ad..8247af4b9 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java
@@ -491,20 +491,12 @@ public class ReferenceConfidenceModel {
         // consider each indel size up to max in term, checking if an indel that deletes either the ref bases (deletion
         // or read bases (insertion) would fit as well as the origin baseline sum of mismatching quality scores
         for ( int indelSize = 1; indelSize <= maxIndelSize; indelSize++ ) {
-            for ( final boolean checkInsertion : Arrays.asList(true, false) ) {
-                final int readI, refI;
-                if ( checkInsertion ) {
-                    readI = readStart + indelSize;
-                    refI = refStart;
-                } else {
-                    readI = readStart;
-                    refI = refStart + indelSize;
-                }
-
-                final int score = sumMismatchingQualities(readBases, readQuals, readI, refBases, refI, baselineMMSum);
-                if ( score <= baselineMMSum )
-                    return false;
-            }
+            // check insertions:
+            if (sumMismatchingQualities(readBases, readQuals, readStart + indelSize, refBases, refStart, baselineMMSum) <= baselineMMSum)
+                return false;
+            // check deletions:
+            if (sumMismatchingQualities(readBases, readQuals, readStart, refBases, refStart + indelSize, baselineMMSum) <= baselineMMSum)
+                return false;
         }
 
         return true;