From cc75e8f712d881d4603f0a495ef3b0ce2211a90a Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 14 Apr 2009 00:53:58 +0000
Subject: [PATCH] Uses the cleaner new GenomeLoc(read) syntax

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@393 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/gatk/iterators/SortSamIterator.java  | 4 ++--
 .../sting/gatk/iterators/VerifyingSamIterator.java            | 4 ++--
 .../broadinstitute/sting/gatk/traversals/TraverseByReads.java | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/SortSamIterator.java b/java/src/org/broadinstitute/sting/gatk/iterators/SortSamIterator.java
index dfa9d8fb2..68d46ba5a 100755
--- a/java/src/org/broadinstitute/sting/gatk/iterators/SortSamIterator.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/SortSamIterator.java
@@ -53,8 +53,8 @@ public class SortSamIterator implements Iterator<SAMRecord> {
         }
 
         public int compareTo(ComparableSAMRecord o) {
-            GenomeLoc myLoc = GenomeLoc.genomicLocationOf(record);
-            GenomeLoc hisLoc = GenomeLoc.genomicLocationOf(o.getRecord());
+            GenomeLoc myLoc = new GenomeLoc(record);
+            GenomeLoc hisLoc = new GenomeLoc(o.getRecord());
             return myLoc.compareTo(hisLoc);
         }
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java b/java/src/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java
index 373c45bae..93f5f81a3 100644
--- a/java/src/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java
@@ -55,8 +55,8 @@ public class VerifyingSamIterator implements Iterator<SAMRecord> {
         if ( last == null || cur.getReadUnmappedFlag() )
             return false;
         else {
-            GenomeLoc lastLoc = GenomeLoc.genomicLocationOf( last );
-            GenomeLoc curLoc = GenomeLoc.genomicLocationOf( cur );
+            GenomeLoc lastLoc = new GenomeLoc( last );
+            GenomeLoc curLoc = new GenomeLoc( cur );
             return curLoc.compareTo(lastLoc) == -1;
         }
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java
index dc6219ff4..593e9dd54 100644
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java
@@ -81,7 +81,7 @@ public class TraverseByReads extends TraversalEngine {
             // get the next read
             final SAMRecord read = samReadIter.next();
             final List<SAMRecord> reads = Arrays.asList(read);
-            GenomeLoc loc = GenomeLoc.genomicLocationOf(read);
+            GenomeLoc loc = new GenomeLoc(read);
 
             // Jump forward in the reference to this locus location
             LocusContext locus = new LocusContext(loc, reads, offsets);