Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java

@@ -175,7 +175,7 @@ public class CommandLineGATK extends CommandLineExecutable {
         Formatter formatter = new Formatter(additionalHelp);
 
         formatter.format("For a full description of this walker, see its GATKdocs at:%n");
-        formatter.format("%s%n", HelpUtils.helpLinksToGATKDocs(walkerType));
+        formatter.format("%s%n", GATKDocUtils.helpLinksToGATKDocs(walkerType));
 
         return additionalHelp.toString();
     }

public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -689,8 +689,6 @@ public class GenomeAnalysisEngine {
         validateSuppliedReads();
         readsDataSource = createReadsDataSource(argCollection,genomeLocParser,referenceDataSource.getReference());
 
-        sampleDataSource = new SampleDataSource(getSAMFileHeader(), argCollection.sampleFiles);
-
         for (ReadFilter filter : filters)
             filter.initialize(this);
 

public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java

@@ -223,8 +223,10 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
 
     @Override
     public void initialize() {
-        if ( getToolkit().getSamples().size() > 1 )
+        if ( getToolkit().getSamples().size() != 2 ) {
+            // unbelievably there are actually two samples even when there's just one in the header.  God I hate this Samples system
             throw new UserException.BadArgumentValue("-I", "CallableLoci only works for a single sample, but multiple samples were found in the provided BAM files: " + getToolkit().getSamples());
+        }
 
         try {
             PrintStream summaryOut = new PrintStream(summaryFile);

public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java

@@ -71,7 +71,7 @@ public abstract class DocumentedGATKFeatureHandler {
      * @return
      */
     public String getDestinationFilename(ClassDoc doc, Class clazz) {
-        return HelpUtils.htmlFilenameForClass(clazz);
+        return GATKDocUtils.htmlFilenameForClass(clazz);
     }
 
     /**

public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java

@@ -0,0 +1,44 @@
+/*
+ * 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.utils.help;
+
+public class GATKDocUtils {
+    public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gsa/gatkdocs/release/";
+    public final static String URL_ROOT_FOR_STABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/stable/";
+    public final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/";
+
+    public static String htmlFilenameForClass(Class c) {
+        return c.getName().replace(".", "_") + ".html";
+    }
+
+    public static String helpLinksToGATKDocs(Class c) {
+        String classPath = htmlFilenameForClass(c);
+        StringBuilder b = new StringBuilder();
+        b.append("release  version: ").append(URL_ROOT_FOR_RELEASE_GATKDOCS).append(classPath).append("\n");
+        b.append("stable   version: ").append(URL_ROOT_FOR_STABLE_GATKDOCS).append(classPath).append("\n");
+        b.append("unstable version: ").append(URL_ROOT_FOR_UNSTABLE_GATKDOCS).append(classPath).append("\n");
+        return b.toString();
+    }
+}

public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java

@@ -32,9 +32,6 @@ import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import java.lang.reflect.Field;
 
 public class HelpUtils {
-    public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gsa/gatkdocs/release/";
-    public final static String URL_ROOT_FOR_STABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/stable/";
-    public final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/";
 
     protected static boolean implementsInterface(ProgramElementDoc classDoc, Class... interfaceClasses) {
         for (Class interfaceClass : interfaceClasses)
@@ -79,16 +76,4 @@ public class HelpUtils {
                 String.format("%s", doc.name());
     }
 
-    public static String htmlFilenameForClass(Class c) {
-        return c.getName().replace(".", "_") + ".html";
-    }
-
-    public static String helpLinksToGATKDocs(Class c) {
-        String classPath = htmlFilenameForClass(c);
-        StringBuilder b = new StringBuilder();
-        b.append("release  version: ").append(URL_ROOT_FOR_RELEASE_GATKDOCS).append(classPath).append("\n");
-        b.append("stable   version: ").append(URL_ROOT_FOR_STABLE_GATKDOCS).append(classPath).append("\n");
-        b.append("unstable version: ").append(URL_ROOT_FOR_UNSTABLE_GATKDOCS).append(classPath).append("\n");
-        return b.toString();
-    }
 }