From 99ddd8ab1528bd5422fa7590dca7f092b7a2a16d Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 14 Jul 2009 17:58:04 +0000
Subject: [PATCH] bug fix for transitioning between chromosomes in GLF output

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1237 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/genotype/glf/GLFWriter.java   | 29 ++++---------------
 1 file changed, 5 insertions(+), 24 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java
index b988929b5..5da2ed0e8 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java
@@ -156,6 +156,8 @@ public class GLFWriter implements GenotypeWriter {
     /**
      * add a GLF record to the output file
      *
+     * @param contigName the contig name
+     * @param contigLength the contig length
      * @param rec the GLF record to write.
      */
     public void addGLFRecord(String contigName, int contigLength, GLFRecord rec) {
@@ -183,8 +185,8 @@ public class GLFWriter implements GenotypeWriter {
     /**
      * check to see if we've jumped to a new contig
      *
-     * @param sequenceName
-     * @param seqLength
+     * @param sequenceName the name for the sequence
+     * @param seqLength the sequence length
      */
     private void checkSequence(String sequenceName, int seqLength) {
         if ((referenceSequenceName == null) || (!referenceSequenceName.equals(sequenceName))) {
@@ -193,6 +195,7 @@ public class GLFWriter implements GenotypeWriter {
             }
             referenceSequenceName = sequenceName;
             referenceSequenceLength = seqLength;
+            lastPos = 1;
             addSequence();
         }
     }
@@ -220,28 +223,6 @@ public class GLFWriter implements GenotypeWriter {
         outputBinaryCodec.close();
     }
 
-    /**
-     * normalize the values to the range of a byte (0 - 255)
-     *
-     * @param values the floating point values to normalize
-     *
-     * @return a byte array containing the normalized values
-     */
-    private byte[] normalizeToByte(double[] values) {
-        byte ret[] = new byte[values.length];
-        double min = Double.MAX_VALUE;
-        double max = Double.MIN_VALUE;
-        for (double d : values) {
-            min = (d < min) ? d : min;
-            max = (d > max) ? d : max;
-        }
-        double scale = max / 255.0;
-        for (int x = 0; x < values.length; x++) {
-            ret[x] = (byte) ((values[x] - min) / scale);
-        }
-        return ret;
-    }
-
     /**
      * get the reference sequence
      *