From 1db2d1ba82dc84ec8e5c435ddeb89a6ca7af795f Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Thu, 26 Apr 2012 13:32:38 -0400
Subject: [PATCH] Do not add the first and last 4 cycles to the recalibration
 tables.

---
 .../sting/gatk/walkers/bqsr/CycleCovariate.java             | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariate.java
index 54a90a959..50e9b0447 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariate.java
@@ -78,8 +78,10 @@ public class CycleCovariate implements StandardCovariate {
                 increment = readOrderFactor;
             }
 
-            for (int i = 0; i < read.getReadLength(); i++) {
-                cycles[i] = BitSetUtils.bitSetFrom(cycle);
+            final int CUSHION = 4;
+            final int MAX_CYCLE = read.getReadLength() - CUSHION - 1;
+            for (int i = 0; i < MAX_CYCLE; i++) {
+                cycles[i] = (i<CUSHION || i>MAX_CYCLE) ? null : BitSetUtils.bitSetFrom(cycle);
                 cycle += increment;
             }
         }