From aa86f3710dfd76cd35a355afcfd240ce6b6c2622 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 17 Dec 2009 18:25:09 +0000
Subject: [PATCH] Updating HomopolymerCovariate to only count the consecutive
 previous bases. I left in the code but commented out for if somebody wants to
 worry about carry forward homopolymer problems.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2391 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../recalibration/HomopolymerCovariate.java   | 34 +++++++++++++++----
 .../RecalibrationArgumentCollection.java      |  2 +-
 packages/GenomeAnalysisTK.xml                 |  2 +-
 3 files changed, 29 insertions(+), 9 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/HomopolymerCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/HomopolymerCovariate.java
index 0e9fb9306..e9745b6a3 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/HomopolymerCovariate.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/HomopolymerCovariate.java
@@ -32,15 +32,15 @@ import net.sf.samtools.SAMRecord;
  * User: rpoplin
  * Date: Dec 4, 2009
  *
- * The Homopolymer Run Covariate. This is the number of bases in the previous N that match the current base.
+ * The Homopolymer Run Covariate. This is the number of consecutive bases in the previous N that match the current base.
  * For example, if N = 10:
- * ATTGCCCCGTAAAAAAAAAA
- * 00100123121123456789
+ * ATTGCCCCGTAAAAAAAAATA
+ * 001001230001234567800
  */
 
 public class HomopolymerCovariate implements ExperimentalCovariate {
 
-    int numBack = 8;
+    int numBack = 7;
 
     // Initialize any member variables using the command-line arguments passed to the walkers
     public void initialize( final RecalibrationArgumentCollection RAC ) {
@@ -50,6 +50,10 @@ public class HomopolymerCovariate implements ExperimentalCovariate {
     // Used to pick out the covariate's value from attributes of the read
     public final Comparable getValue( final SAMRecord read, final int offset ) {
 
+        // This block of code is for if you don't want to only count consecutive bases
+        // ATTGCCCCGTAAAAAAAAATA
+        // 001001231211234567819
+        /*
         int numAgree = 0; // The number of bases that agree with you in the previous numBack bases of the read
         int startPos = 0;
         int stopPos = 0;
@@ -57,15 +61,31 @@ public class HomopolymerCovariate implements ExperimentalCovariate {
         byte thisBase = bases[offset];
         if( !read.getReadNegativeStrandFlag() ) { // Forward direction
             startPos = Math.max(offset - numBack, 0);
-            stopPos = offset;
+            stopPos = Math.max(offset - 1, 0);
         } else { // Negative direction
-            startPos = offset + 1;
-            stopPos = Math.min(offset + numBack + 1, read.getReadLength());
+            startPos = Math.min(offset + 2, bases.length);
+            stopPos = Math.min(offset + numBack + 1, bases.length);
         }
 
         for( int iii = startPos; iii < stopPos; iii++ ) {
             if( bases[iii] == thisBase ) { numAgree++; }
         }
+        */
+
+        int numAgree = 0; // The number of consecutive bases that agree with you in the previous numBack bases of the read
+        byte[] bases = read.getReadBases();
+        int iii = offset;
+        if( !read.getReadNegativeStrandFlag() ) { // Forward direction
+            while( iii <= bases.length-2 && bases[iii] == bases[iii+1] && numAgree < numBack ) {
+                numAgree++;
+                iii++;
+            }
+        } else { // Negative direction
+            while( iii >= 1 && bases[iii] == bases[iii-1] && numAgree < numBack ) {
+                numAgree++;
+                iii--;
+            }
+        }
 
         return numAgree;
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java
index 7a5c9cdc6..9d904e5fc 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java
@@ -58,7 +58,7 @@ public class RecalibrationArgumentCollection {
     @Argument(fullName = "window_size_nqs", shortName="nqs", doc="The window size used by MinimumNQSCovariate for its calculation", required=false)
     public int WINDOW_SIZE = 5;
     @Argument(fullName = "homopolymer_nback", shortName="nback", doc="The number of previous bases to look at in HomopolymerCovariate", required=false)
-    public int HOMOPOLYMER_NBACK = 8;
+    public int HOMOPOLYMER_NBACK = 7;
 
     public boolean checkSolidRecalMode() {
         return ( SOLID_RECAL_MODE.equalsIgnoreCase("DO_NOTHING") || SOLID_RECAL_MODE.equalsIgnoreCase("SET_Q_ZERO") ||
diff --git a/packages/GenomeAnalysisTK.xml b/packages/GenomeAnalysisTK.xml
index acffff24c..33f9f5e95 100644
--- a/packages/GenomeAnalysisTK.xml
+++ b/packages/GenomeAnalysisTK.xml
@@ -24,7 +24,7 @@
       <class>org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate</class>
       <class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
       <class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate</class>
+      <class>org.broadinstitute.sting.gatk.walkers.recalibration.HomopolymerCovariate</class>
       <!-- Local realignment around indels -->
       <class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class>
       <class>org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker</class>