Added check to make sure file passed in with sample IDs is valid (used in SelectVariants) -- throws UserException. Corresponding test checks for UserException.

public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/SampleUtils.java

@@ -28,6 +28,7 @@ package org.broadinstitute.sting.utils;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMReadGroupRecord;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
 import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
@@ -280,7 +281,7 @@ public class SampleUtils {
                         samplesFromFiles.add(line);
                     }
                 } catch (FileNotFoundException e) {
-                    // ignore exception
+                    throw new UserException.CouldNotReadInputFile(file, e);
                 }
             }
         }

public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/SampleUtilsUnitTest.java

@@ -0,0 +1,53 @@
+/*
+* Copyright (c) 2012 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.utils;
+
+import org.apache.commons.io.FileUtils;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.io.IOUtils;
+import org.testng.Assert;
+import org.broadinstitute.sting.BaseTest;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.util.*;
+
+/**
+ * Testing framework for sample utilities class.
+ *
+ * @author gauthier
+ */
+
+public class SampleUtilsUnitTest extends BaseTest {
+    @Test(expectedExceptions=UserException.class)
+    public void testBadSampleFiles() throws Exception {
+        Set<File> sampleFiles = new HashSet<File>(0);
+        sampleFiles.add(new File("fileNotHere.samples"));
+        Collection<String> samplesFromFile = SampleUtils.getSamplesFromFiles(sampleFiles);
+    }
+}