From 12e1f192c48a8333eaee644fe241724c22939ca3 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 16 Apr 2009 18:42:00 +0000
Subject: [PATCH] Fixed a bug in this code where it would eat reads that didn't
 start at the beginning of the provided interval.  This should fix / help fix
 Kristian problem

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@453 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../providers/LocusContextProvider.java       | 29 ++++++++++---------
 1 file changed, 15 insertions(+), 14 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusContextProvider.java b/java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusContextProvider.java
index 1f2afd78d..2a2bf2c7c 100755
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusContextProvider.java
+++ b/java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusContextProvider.java
@@ -1,18 +1,17 @@
 package org.broadinstitute.sting.gatk.dataSources.providers;
 
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.gatk.iterators.LocusIterator;
-import org.broadinstitute.sting.gatk.iterators.LocusIteratorByHanger;
-import org.broadinstitute.sting.gatk.LocusContext;
-import org.broadinstitute.sting.gatk.traversals.TraversalStatistics;
-import org.apache.log4j.Logger;
-import net.sf.samtools.SAMRecord;
-
-import java.util.Iterator;
-import java.util.ArrayList;
-
 import edu.mit.broad.picard.filter.FilteringIterator;
 import edu.mit.broad.picard.filter.SamRecordFilter;
+import net.sf.samtools.SAMRecord;
+import org.apache.log4j.Logger;
+import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.gatk.iterators.LocusIterator;
+import org.broadinstitute.sting.gatk.iterators.LocusIteratorByHanger;
+import org.broadinstitute.sting.gatk.traversals.TraversalStatistics;
+import org.broadinstitute.sting.utils.GenomeLoc;
+
+import java.util.ArrayList;
+import java.util.Iterator;
 
 /**
  * Created by IntelliJ IDEA.
@@ -27,7 +26,7 @@ public class LocusContextProvider {
     // What's the last locus accessed?  Used for sanity checking.
     private GenomeLoc lastLoc = null;
     private LocusIterator loci;
-
+    private LocusContext locus;
     protected static Logger logger = Logger.getLogger(LocusContextProvider.class);
 
     public LocusContextProvider( Iterator<SAMRecord> reads ) {
@@ -60,9 +59,11 @@ public class LocusContextProvider {
         if ( ! locusIter.hasNext() )
             return null;
 
-        LocusContext locus = locusIter.next();
+        if (locus == null) {
+            locus = locusIter.next();
+        }
 
-        while ( ! target.containsP(locus.getLocation()) && locusIter.hasNext() ) {
+        while (target.isPast(locus.getLocation()) && locusIter.hasNext() ) {
             logger.debug(String.format("  current locus is %s vs %s => %d", locus.getLocation(), target, locus.getLocation().compareTo(target)));
             locus = locusIter.next();
         }