From a69a4dda2fcf14ef3f7e8c6e97b92645fdf62e6d Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Fri, 30 Sep 2011 09:56:23 -0400
Subject: [PATCH] SamplesDB no longer has null sample

-- Updated getSamples().size() == 2 test in CallableLociWalker that really ensured there was one sample in the system
---
 .../sting/gatk/samples/SampleDataSource.java  |  2 +-
 .../walkers/coverage/CallableLociWalker.java  |  3 +--
 .../gatk/walkers/qc/CountMalesWalker.java     | 24 +++++++++++++++++++
 3 files changed, 26 insertions(+), 3 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDataSource.java
index 9543c834a..d5285271b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDataSource.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDataSource.java
@@ -35,7 +35,7 @@ public class SampleDataSource {
      * Constructor takes both a SAM header and sample files because the two must be integrated.
      */
     public SampleDataSource() {
-        samples.put(null, new Sample(null, this));
+
     }
 
     public SampleDataSource(final SAMFileHeader header, final List<File> sampleFiles) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java
index 1e2d40271..1dfc6fea0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java
@@ -227,8 +227,7 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
 
     @Override
     public void initialize() {
-        if ( getSampleDB().getSamples().size() != 2 ) {
-            // unbelievably there are actually two samples even when there's just one in the header.  God I hate this Samples system
+        if ( getSampleDB().getSamples().size() != 1 ) {
             throw new UserException.BadArgumentValue("-I", "CallableLoci only works for a single sample, but multiple samples were found in the provided BAM files: " + getSampleDB().getSamples());
         }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMalesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMalesWalker.java
index f2c035c3c..d776fe415 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMalesWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMalesWalker.java
@@ -1,3 +1,27 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.qc;
 
 import net.sf.samtools.SAMRecord;