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

This commit is contained in:
Christopher Hartl 2011-08-18 12:23:32 -04:00
parent ff45fc9d5a c787fd0b70
commit 3a6a206940
6 changed files with 49 additions and 20 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
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@ -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();
}

2
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -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);

4
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java
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@ -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);

2
public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java
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@ -71,7 +71,7 @@ public abstract class DocumentedGATKFeatureHandler {
* @return
*/
public String getDestinationFilename(ClassDoc doc, Class clazz) {
return HelpUtils.htmlFilenameForClass(clazz);
return GATKDocUtils.htmlFilenameForClass(clazz);
}
/**

44
public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java 100644
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@ -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();
}
}

15
public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java
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@ -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();
}
}