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Merge branch 'master' into rodRefactor

This commit is contained in:
Mark DePristo 2011-08-08 15:25:55 -04:00
parent 4f8fc0f2f1 0db79207e8
commit 383bb6f0e0
5 changed files with 52 additions and 18 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
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@ -36,6 +36,7 @@ import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.ApplicationDetails;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.GATKDocUtils;
import org.broadinstitute.sting.utils.help.GATKDoclet;
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
@ -177,7 +178,7 @@ 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", GATKDoclet.helpLinksToGATKDocs(walkerType));
formatter.format("%s%n", GATKDocUtils.helpLinksToGATKDocs(walkerType));
return additionalHelp.toString();
}

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 GATKDoclet.htmlFilenameForClass(clazz);
return GATKDocUtils.htmlFilenameForClass(clazz);
}
/**

48
public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java 100644
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@ -0,0 +1,48 @@
/*
* 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;
/**
* @author depristo
* @since 8/8/11
*/
public class GATKDocUtils {
private final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gsa/gatkdocs/release/";
private final static String URL_ROOT_FOR_STABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/stable/";
private 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();
}
}

16
public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java
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@ -42,9 +42,6 @@ import java.util.*;
*
*/
public class GATKDoclet {
private final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gsa/gatkdocs/release/";
private final static String URL_ROOT_FOR_STABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/stable/";
private final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/";
final protected static File SETTINGS_DIR = new File("settings/helpTemplates");
final protected static File DESTINATION_DIR = new File("gatkdocs");
final protected static Logger logger = Logger.getLogger(GATKDoclet.class);
@ -92,19 +89,6 @@ public class GATKDoclet {
return showHiddenFeatures;
}
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 Set<GATKDocWorkUnit> workUnits() {
TreeSet<GATKDocWorkUnit> m = new TreeSet<GATKDocWorkUnit>();

1
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -313,6 +313,7 @@ class DataProcessingPipeline extends QScript {
}
case class clean (inBams: File, tIntervals: File, outBam: File) extends IndelRealigner with CommandLineGATKArgs {
@Output(doc="output bai file") var bai = swapExt(outBam, ".bam", ".bai")
this.input_file :+= inBams
this.targetIntervals = tIntervals
this.out = outBam