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Merge branch 'master' into rodRefactor

This commit is contained in:
Mark DePristo 2011-08-08 10:08:43 -04:00
parent 526b524c3c 88061ed5fa
commit e5fde0d16b
9 changed files with 112 additions and 33 deletions
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11
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.GATKDoclet;
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import java.util.*;
@ -175,12 +176,8 @@ public class CommandLineGATK extends CommandLineExecutable {
StringBuilder additionalHelp = new StringBuilder();
Formatter formatter = new Formatter(additionalHelp);
formatter.format("Description:%n");
WalkerManager walkerManager = engine.getWalkerManager();
String walkerHelpText = walkerManager.getWalkerDescriptionText(walkerType);
printDescriptorLine(formatter,WALKER_INDENT,"",WALKER_INDENT,FIELD_SEPARATOR,walkerHelpText,TextFormattingUtils.DEFAULT_LINE_WIDTH);
formatter.format("For a full description of this walker, see its GATKdocs at:%n");
formatter.format("%s%n", GATKDoclet.helpLinksToGATKDocs(walkerType));
return additionalHelp.toString();
}
@ -194,8 +191,6 @@ public class CommandLineGATK extends CommandLineExecutable {
StringBuilder additionalHelp = new StringBuilder();
Formatter formatter = new Formatter(additionalHelp);
formatter.format("Available analyses:%n");
// Get the list of walker names from the walker manager.
WalkerManager walkerManager = engine.getWalkerManager();

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
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@ -50,7 +50,7 @@ public class VariantRecalibratorArgumentCollection {
@Argument(fullName="numKMeans", shortName="nKM", doc="The number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model.", required=false)
public int NUM_KMEANS_ITERATIONS = 30;
@Argument(fullName="stdThreshold", shortName="std", doc="If a variant has annotations more than -std standard deviations away from mean then don't use it for building the Gaussian mixture model.", required=false)
public double STD_THRESHOLD = 8.0;
public double STD_THRESHOLD = 14.0;
@Argument(fullName="qualThreshold", shortName="qual", doc="If a known variant has raw QUAL value less than -qual then don't use it for building the Gaussian mixture model.", required=false)
public double QUAL_THRESHOLD = 80.0;
@Argument(fullName="shrinkage", shortName="shrinkage", doc="The shrinkage parameter in variational Bayes algorithm.", required=false)

49
public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java
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@ -31,29 +31,70 @@ import java.io.*;
import java.util.Set;
/**
*
* Extend this class to provide a documentation handler for GATKdocs
*/
public abstract class DocumentedGATKFeatureHandler {
private GATKDoclet doclet;
/**
* @return the javadoc RootDoc of this javadoc run
*/
protected RootDoc getRootDoc() {
return this.doclet.rootDoc;
}
/** Set the master doclet driving this handler */
public void setDoclet(GATKDoclet doclet) {
this.doclet = doclet;
}
/**
* @return the GATKDoclet driving this documentation run
*/
public GATKDoclet getDoclet() {
return doclet;
}
public boolean shouldBeProcessed(ClassDoc doc) { return true; }
/**
* Should return false iff this handler wants GATKDoclet to skip documenting
* this ClassDoc.
* @param doc that is being considered for inclusion in the docs
* @return true if the doclet should document ClassDoc doc
*/
public boolean includeInDocs(ClassDoc doc) { return true; }
public String getDestinationFilename(ClassDoc doc) {
return HelpUtils.getClassName(doc).replace(".", "_") + ".html";
/**
* Return the flat filename (no paths) that the handler would like the Doclet to
* write out the documentation for ClassDoc doc and its associated Class clazz
* @param doc
* @param clazz
* @return
*/
public String getDestinationFilename(ClassDoc doc, Class clazz) {
return GATKDoclet.htmlFilenameForClass(clazz);
}
/**
* Return the name of the FreeMarker template we will use to process ClassDoc doc.
*
* Note this is a flat filename relative to settings/helpTemplates in the GATK source tree
* @param doc
* @return
* @throws IOException
*/
public abstract String getTemplateName(ClassDoc doc) throws IOException;
/**
* Actually generate the documentation map associated with toProcess
*
* Can use all to provide references and rootDoc for additional information, if necessary.
* Implementing methods should end with a call to setHandlerContext on toProcess, as in:
*
* toProcess.setHandlerContent(summary, rootMap);
*
* @param rootDoc
* @param toProcess
* @param all
*/
public abstract void processOne(RootDoc rootDoc, GATKDocWorkUnit toProcess, Set<GATKDocWorkUnit> all);
}

48
public/java/src/org/broadinstitute/sting/utils/help/GATKDocWorkUnit.java
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@ -30,19 +30,29 @@ import java.util.HashMap;
import java.util.Map;
/**
* Created by IntelliJ IDEA.
* User: depristo
* Date: 7/24/11
* Time: 7:59 PM
* To change this template use File | Settings | File Templates.
*/
public class GATKDocWorkUnit implements Comparable<GATKDocWorkUnit> {
// known at the start
final String name, filename, group;
final DocumentedGATKFeatureHandler handler;
final ClassDoc classDoc;
* Simple collection of all relevant information about something the GATKDoclet can document
*
* Created by IntelliJ IDEA.
* User: depristo
* Date: 7/24/11
* Time: 7:59 PM
*/
class GATKDocWorkUnit implements Comparable<GATKDocWorkUnit> {
/** The class that's being documented */
final Class clazz;
/** The name of the thing we are documenting */
final String name;
/** the filename where we will be writing the docs for this class */
final String filename;
/** The name of the documentation group (e.g., walkers, read filters) class belongs to */
final String group;
/** The documentation handler for this class */
final DocumentedGATKFeatureHandler handler;
/** The javadoc documentation for clazz */
final ClassDoc classDoc;
/** The annotation that lead to this Class being in GATKDoc */
final DocumentedGATKFeature annotation;
/** When was this walker built, and what's the absolute version number */
final String buildTimestamp, absoluteVersion;
// set by the handler
@ -64,12 +74,21 @@ public class GATKDocWorkUnit implements Comparable<GATKDocWorkUnit> {
this.absoluteVersion = absoluteVersion;
}
/**
* Called by the GATKDoclet to set handler provided context for this work unit
* @param summary
* @param forTemplate
*/
public void setHandlerContent(String summary, Map<String, Object> forTemplate) {
this.summary = summary;
this.forTemplate = forTemplate;
}
public Map<String, String> toMap() {
/**
* Return a String -> String map suitable for FreeMarker to create an index to this WorkUnit
* @return
*/
public Map<String, String> indexDataMap() {
Map<String, String> data = new HashMap<String, String>();
data.put("name", name);
data.put("summary", summary);
@ -78,6 +97,11 @@ public class GATKDocWorkUnit implements Comparable<GATKDocWorkUnit> {
return data;
}
/**
* Sort in order of the name of this WorkUnit
* @param other
* @return
*/
public int compareTo(GATKDocWorkUnit other) {
return this.name.compareTo(other.name);
}

22
public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java
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@ -42,6 +42,9 @@ 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);
@ -89,6 +92,19 @@ 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>();
@ -101,9 +117,9 @@ public class GATKDoclet {
DocumentedGATKFeature feature = getFeatureForClassDoc(doc);
DocumentedGATKFeatureHandler handler = createHandler(doc, feature);
if ( handler != null && handler.shouldBeProcessed(doc) ) {
if ( handler != null && handler.includeInDocs(doc) ) {
logger.info("Going to generate documentation for class " + doc);
String filename = handler.getDestinationFilename(doc);
String filename = handler.getDestinationFilename(doc, clazz);
GATKDocWorkUnit unit = new GATKDocWorkUnit(doc.name(),
filename, feature.groupName(),
feature, handler, doc, clazz,
@ -220,7 +236,7 @@ public class GATKDoclet {
Set<DocumentedGATKFeature> docFeatures = new HashSet<DocumentedGATKFeature>();
List<Map<String, String>> data = new ArrayList<Map<String, String>>();
for ( GATKDocWorkUnit workUnit : indexData ) {
data.add(workUnit.toMap());
data.add(workUnit.indexDataMap());
docFeatures.add(workUnit.annotation);
}

2
public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
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@ -51,7 +51,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
RootDoc rootDoc;
@Override
public boolean shouldBeProcessed(ClassDoc doc) {
public boolean includeInDocs(ClassDoc doc) {
return true;
// try {
// Class type = HelpUtils.getClassForDoc(doc);

6
public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
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@ -26,9 +26,9 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
}
VRTest lowPass = new VRTest("phase1.projectConsensus.chr20.raw.snps.vcf",
"d33212a84368e821cbedecd4f59756d6", // tranches
"4652dca41222bebdf9d9fda343b2a835", // recal file
"243a397a33a935fcaccd5deb6d16f0c0"); // cut VCF
"0ddd1e0e483d2eaf56004615cea23ec7", // tranches
"58780f63182e139fdbe17f6c18b5b774", // recal file
"f67d844b6252a55452cf4167b77530b1"); // cut VCF
@DataProvider(name = "VRTest")
public Object[][] createData1() {

3
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
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@ -134,6 +134,9 @@ class GATKResourcesBundle extends QScript {
addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/AFR+EUR+ASN+1KG.dindel_august_release_merged_pilot1.20110126.sites.vcf",
"1000G_indels_for_realignment", b37, true, false))
addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Mills_Devine_Indels_2011/ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.sites.vcf",
"indels_mills_devine", b37, true, true))
//
// example call set for wiki tutorial
//

2
public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala
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@ -52,7 +52,7 @@ class ShellJobRunner(val function: CommandLineFunction) extends CommandLineJobRu
updateStatus(RunnerStatus.RUNNING)
job.run()
updateStatus(RunnerStatus.FAILED)
updateStatus(RunnerStatus.DONE)
}
override def checkUnknownStatus() {}