zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output. 

JavaCommandLineFunctions can now specify the classpath+mainclass as an alternative to specifying a path to an executable jar.
JCLF by default pass on the current classpath and only require the mainclass be specified by the developer extending the JCLF, relieving the QScript author from having to explicitly specify the jar.
Like the Picard MergeSamFiles, GATK engine by default is now run from the current classpath. The GATK can still be overridden via .jarFile or .javaClasspath.
Walkers from the GATK package are now also embedded into the Queue package.
Updated AnalyzeCovariates to make it easier to guess the main class, AnalyzeCovariates instead of AnalyzeCovariatesCLP.
Removed the GATK jar argument from the example QScripts.
Removed one of the most FAQ when getting started with Scala/Queue, the use of Option[_] in QScripts:
1) Fixed mistaken assumption with java enums. In java enums can be null so they don't need nullable wrappers.
2) Added syntactic sugar for Nullable primitives to the QScript trait. Any variable defined as Option[Int] can just be assigned an Int value or None, ex: myFunc.memoryLimit = 3
Removed other unused code.
Re-fixed dry run function ordering.
Re-ordered the QCommandline companion object so that IntelliJ doesn't complain about missing main methods.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5504 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2011-03-24 14:03:51 +00:00
parent 18271aa1f4
commit f3e94ef2be
66 changed files with 800 additions and 799 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

17
analysis/depristo/distributedGATK/distributedGATKPerformance.scala
View File

@ -1,4 +1,3 @@
import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction
import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.queue.QScript
@ -40,7 +39,7 @@ class DistributedGATKPerformance extends QScript {
@Argument(shortName="trackerDir", doc="root directory for distributed tracker files", required=false) @Argument(shortName="trackerDir", doc="root directory for distributed tracker files", required=false)
var trackerDir: String = "" // "/humgen/gsa-scr1/depristo/tmp/" var trackerDir: String = "" // "/humgen/gsa-scr1/depristo/tmp/"
trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "DEBUG"; jarFile = gatkJarFile; memoryLimit = Some(2); } trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "DEBUG"; jarFile = gatkJarFile; memoryLimit = 2; }
class Target( class Target(
val baseName: String, val baseName: String,
@ -154,9 +153,9 @@ class DistributedGATKPerformance extends QScript {
def addUG(ug: UnifiedGenotyper) = { def addUG(ug: UnifiedGenotyper) = {
if ( ! long ) if ( ! long )
ug.jobLimitSeconds = Some(60 * 60 * 4) ug.jobLimitSeconds = 60 * 60 * 4
if ( limitTo30Min ) if ( limitTo30Min )
ug.jobLimitSeconds = Some(60 * 30) ug.jobLimitSeconds = 60 * 30
add(ug); add(ug);
} }
@ -171,7 +170,7 @@ class DistributedGATKPerformance extends QScript {
var ug: UnifiedGenotyper = new UnifiedGenotyper(target, aname + ".part" + part) var ug: UnifiedGenotyper = new UnifiedGenotyper(target, aname + ".part" + part)
ug.intervalsString ++= getTargetInterval(target) ug.intervalsString ++= getTargetInterval(target)
ug.processingTracker = new File(trackerDir + target.name + "." + aname + ".distributed.txt") ug.processingTracker = new File(trackerDir + target.name + "." + aname + ".distributed.txt")
ug.processingTrackerID = Some(part) ug.processingTrackerID = part
if ( part == 1 ) if ( part == 1 )
ug.performanceLog = new File("%s.%s.pf.log".format(target.name, aname)) ug.performanceLog = new File("%s.%s.pf.log".format(target.name, aname))
ug.processingTrackerStatusFile = new File("%s.%s.%d.ptstatus.log".format(target.name, aname, part)) ug.processingTrackerStatusFile = new File("%s.%s.%d.ptstatus.log".format(target.name, aname, part))
@ -186,12 +185,12 @@ class DistributedGATKPerformance extends QScript {
// 1.) Call SNPs with UG // 1.) Call SNPs with UG
class UnifiedGenotyper(t: Target, aname: String) extends org.broadinstitute.sting.queue.extensions.gatk.UnifiedGenotyper with UNIVERSAL_GATK_ARGS { class UnifiedGenotyper(t: Target, aname: String) extends org.broadinstitute.sting.queue.extensions.gatk.UnifiedGenotyper with UNIVERSAL_GATK_ARGS {
this.reference_sequence = t.reference this.reference_sequence = t.reference
this.dcov = Some( if ( t.isLowpass ) { 50 } else { 250 } ) this.dcov = if ( t.isLowpass ) { 50 } else { 250 }
this.stand_call_conf = Some( if ( t.isLowpass ) { 4.0 } else { 30.0 } ) this.stand_call_conf = if ( t.isLowpass ) { 4.0 } else { 30.0 }
this.stand_emit_conf = Some( if ( t.isLowpass ) { 4.0 } else { 30.0 } ) this.stand_emit_conf = if ( t.isLowpass ) { 4.0 } else { 30.0 }
this.input_file :+= t.bamList this.input_file :+= t.bamList
this.out = t.rawVCF(aname) this.out = t.rawVCF(aname)
this.baq = Some( if (t.useBAQ) {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.RECALCULATE} else {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF}) this.baq = if (t.useBAQ) {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.RECALCULATE} else {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF}
this.analysisName = t.name + "_UG." + aname this.analysisName = t.name + "_UG." + aname
if (t.dbsnpFile.endsWith(".rod")) if (t.dbsnpFile.endsWith(".rod"))
this.DBSNP = new File(t.dbsnpFile) this.DBSNP = new File(t.dbsnpFile)

16
java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
View File

@ -48,7 +48,7 @@ import java.io.*;
* Create collapsed versions of the recal csv file and call R scripts to plot residual error versus the various covariates. * Create collapsed versions of the recal csv file and call R scripts to plot residual error versus the various covariates.
*/ */
class AnalyzeCovariatesCLP extends CommandLineProgram { public class AnalyzeCovariates extends CommandLineProgram {
///////////////////////////// /////////////////////////////
// Command Line Arguments // Command Line Arguments
@ -311,12 +311,14 @@ class AnalyzeCovariatesCLP extends CommandLineProgram {
} }
} }
} }
}
public class AnalyzeCovariates { public static void main(String args[]) {
public static void main(String args[]) throws Exception { try {
AnalyzeCovariatesCLP clp = new AnalyzeCovariatesCLP(); AnalyzeCovariates clp = new AnalyzeCovariates();
CommandLineProgram.start( clp, args ); start(clp, args);
System.exit(0); System.exit(CommandLineProgram.result);
} catch (Exception e) {
exitSystemWithError(e);
}
} }
} }

5
java/src/org/broadinstitute/sting/queue/function/scattergather/Gather.java → java/src/org/broadinstitute/sting/commandline/Gather.java
View File

@ -22,13 +22,12 @@
* OTHER DEALINGS IN THE SOFTWARE. * OTHER DEALINGS IN THE SOFTWARE.
*/ */
package org.broadinstitute.sting.queue.function.scattergather; package org.broadinstitute.sting.commandline;
import java.lang.annotation.*; import java.lang.annotation.*;
/** /**
* Specifies the class type of the CommandLineFunction to gather an @Output * Specifies the class type to gather an @Output
* Written in java because scala doesn't support RetentionPolicy.RUNTIME
*/ */
@Documented @Documented
@Inherited @Inherited

25
scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamEmbeddedFunction.scala → java/src/org/broadinstitute/sting/commandline/Gatherer.java
View File

@ -22,16 +22,25 @@
* OTHER DEALINGS IN THE SOFTWARE. * OTHER DEALINGS IN THE SOFTWARE.
*/ */
package org.broadinstitute.sting.queue.extensions.picard package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.queue.function.EmbeddedCommandLineFunction import java.io.File;
import java.util.List;
/** /**
* Wraps a Picard embedded class that operates on BAM files. * Combines a list of files into a single output.
* See http://picard.sourceforge.net/ for more info.
*
* Since the command lines take slightly different arguments
* some values are optional.
*/ */
trait PicardBamEmbeddedFunction extends EmbeddedCommandLineFunction with PicardBamFunction { public abstract class Gatherer {
/**
* Gathers a list of files into a single output.
* @param inputs Files to combine.
* @param output Path to output file.
*/
public abstract void gather(List<File> inputs, File output);
/**
* Returns true if the caller should wait for the input files to propagate over NFS before running gather().
* @return true if the caller should wait for the input files to propagate over NFS before running gather().
*/
public boolean waitForInputs() { return true; }
} }

207
java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.java
View File

@ -1,207 +0,0 @@
/*
* Copyright (c) 2010 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.playground.analyzeconcordance;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.text.XReadLines;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.PathUtils;
import org.broadinstitute.sting.playground.utils.ProcessUtils;
import org.apache.log4j.Logger;
import java.io.*;
import java.util.*;
/**
* Compares results of VariantEval across a population or a case/control group.
*/
public class AnalyzeConcordance extends CommandLineProgram {
@Argument(fullName = "group_name", shortName = "groupName", doc = "The name of the group which will be prefixed output files", required = false)
private String baseName = "analyze_concordance";
@Argument(fullName = "eval_list", shortName = "evalList", doc = "The input list of unfiltered eval files to analyze", required = true)
private String evalListFile = null;
@Argument(fullName = "filtered_eval_list", shortName = "filteredEvalList", doc = "The input list of filtered eval files to analyze", required = false)
private String filteredEvalListFile = null;
@Argument(fullName = "output_dir", shortName = "outputDir", doc = "The directory in which to output all the plots and intermediate data files", required = false)
private String outputDir = "analyzeConcordance";
@Argument(fullName = "path_to_Rscript", shortName = "Rscript", doc = "The path to your implementation of Rscript", required = false)
private String pathToRscript = "env Rscript";
@Argument(fullName = "path_to_resources", shortName = "resources", doc = "Path to resources folder holding the Sting analyze concordance R scripts", required = false)
private String pathToResources = "R" + File.separator + "analyzeConcordance";
private enum EvalFilterType {
UNFILTERED, FILTERED
}
private static final AnalyzeConcordanceField[] ANALYZE_CONCORDANCE_FIELDS = AnalyzeConcordanceField.values();
private String evalDataFile;
private List<String[]> data = new ArrayList<String[]>();
private static Logger logger = Logger.getLogger(AnalyzeConcordance.class);
protected int execute() {
int result;
try {
createOutputDirectory();
// initialize all the data from the csv file and allocate the list of covariates
logger.info("Reading in input csv file...");
initializeData();
logger.info("...Done!");
// output data tables for Rscript to read in
logger.info("Writing out intermediate tables for R...");
writeDataTables();
logger.info("...Done!");
// perform the analysis using Rscript and output the plots
logger.info("Calling analysis R scripts and writing out figures...");
result = callRScripts();
logger.info("...Done!");
// perform the analysis using Rscript and output the plots
logger.info("Generating html report...");
generateHtmlReport();
logger.info("...Done!");
} catch (Exception e) {
throw new ReviewedStingException("Error analyzing concordance", e);
}
return result;
}
private void createOutputDirectory() {
// create the output directory where all the data tables and plots will go
File outputDir = new File(this.outputDir);
if (!outputDir.exists() && !outputDir.mkdirs()) {
throw new ReviewedStingException("Couldn't create directory: " + this.outputDir);
}
}
private void initializeData() throws FileNotFoundException {
// add the column headers to the data
addHeader();
// read the list of unfiltered eval files
addEvalListFile(EvalFilterType.UNFILTERED, new File(evalListFile));
// if provided, read the list of filtered eval files
if (filteredEvalListFile != null) {
addEvalListFile(EvalFilterType.FILTERED, new File(filteredEvalListFile));
}
}
private void addHeader() {
String[] headers = new String[ANALYZE_CONCORDANCE_FIELDS.length + 2];
int column = 0;
headers[column++] = "eval_id";
headers[column++] = "filter_type";
for (AnalyzeConcordanceField field : ANALYZE_CONCORDANCE_FIELDS) {
headers[column++] = field.getColumnHeader();
}
data.add(headers);
}
private void addEvalListFile(EvalFilterType filterType, File evalListFile) throws FileNotFoundException {
for (String line : new XReadLines(evalListFile)) {
String[] parts = line.split("\t");
addEvalFile(parts[0], filterType, new File(parts[1]));
}
}
private void addEvalFile(String evalID, EvalFilterType filterType, File evalFile) throws FileNotFoundException {
SortedMap<AnalyzeConcordanceField, String> fieldValues = new TreeMap<AnalyzeConcordanceField, String>();
for (String line : new XReadLines(evalFile)) {
for (AnalyzeConcordanceField field : ANALYZE_CONCORDANCE_FIELDS) {
String value = field.parseLine(line);
if (value != null) {
fieldValues.put(field, value);
break; // continue to the next line.
}
}
}
String[] values = new String[ANALYZE_CONCORDANCE_FIELDS.length + 2];
int column = 0;
values[column++] = evalID;
values[column++] = filterType.toString().toLowerCase();
// get all the values, including null if for some reason a value wasn't found
for (AnalyzeConcordanceField field : ANALYZE_CONCORDANCE_FIELDS) {
values[column++] = fieldValues.get(field);
}
data.add(values);
}
private void writeDataTables() throws FileNotFoundException {
evalDataFile = baseName + ".eval_data.tsv";
// Create a PrintStream
PrintStream output = new PrintStream(new File(outputDir, evalDataFile));
for (String[] line : data) {
output.println(Utils.join("\t", line));
}
output.close();
}
private int callRScripts() {
String command = pathToRscript + " "
+ new File(pathToResources, "analyzeConcordance.R") + " "
+ new File(outputDir, baseName) + " "
+ new File(outputDir, evalDataFile);
return ProcessUtils.runCommandAndWait(command);
}
private void generateHtmlReport() throws FileNotFoundException {
// TODO: Enhance the reports
PrintStream output = new PrintStream(new File(outputDir, "report.html"));
output.println("<html><body>");
for (File pngFile : new File(outputDir).listFiles(new PathUtils.ExtensionFilter("png"))) {
output.println("<div><img src=\"" + pngFile.getName() + "\"/></div>");
}
output.println("</body></html>");
output.close();
}
public static void main(String[] argv) {
try {
AnalyzeConcordance instance = new AnalyzeConcordance();
start(instance, argv);
System.exit(CommandLineProgram.result);
} catch (Exception e) {
exitSystemWithError(e);
}
}
}

41
java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordanceField.java
View File

@ -1,41 +0,0 @@
package org.broadinstitute.sting.playground.analyzeconcordance;
import java.util.regex.Pattern;
import java.util.regex.Matcher;
/**
* Created by IntelliJ IDEA.
* User: kshakir
* Date: Feb 11, 2010
*/
public enum AnalyzeConcordanceField {
N_BASES_COVERED("all_bases", "all,summary,variant_counts", "n bases covered"),
ALL_DBSNP_RATE("all_dbsnp", "all,summary,db_coverage", "dbsnp_rate"),
ALL_VARIANT_COUNT("all_variants", "all,summary,variant_counts", "variants"),
ALL_TITV_RATIO("all_titv", "all,summary,transitions_transversions", "ratio"),
KNOWN_VARIANT_COUNT("known_variants", "known,summary,variant_counts", "variants"),
KNOWN_TITV_RATIO("known_titv", "known,summary,transitions_transversions", "ratio"),
NOVEL_VARIANT_COUNT("novel_variants", "novel,summary,variant_counts", "variants"),
NOVEL_TITV_RATIO("novel_titv", "novel,summary,transitions_transversions", "ratio");
private String columnHeader;
private Pattern pattern;
private AnalyzeConcordanceField(String columnHeader, String evalHeader, String analysis) {
this.columnHeader = columnHeader;
String lineRegex = evalHeader + " {2,}" + analysis + " {2,}([0-9.]+).*";
this.pattern = Pattern.compile(lineRegex);
}
public String getColumnHeader() {
return this.columnHeader;
}
public String parseLine(String line) {
Matcher matcher = this.pattern.matcher(line);
if (!matcher.matches())
return null;
return matcher.group(1);
}
}

22
java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
View File

@ -111,15 +111,19 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
public static List<? extends ArgumentField> getArgumentFields(ParsingEngine parsingEngine,Class<?> classType) { public static List<? extends ArgumentField> getArgumentFields(ParsingEngine parsingEngine,Class<?> classType) {
List<ArgumentField> argumentFields = new ArrayList<ArgumentField>(); List<ArgumentField> argumentFields = new ArrayList<ArgumentField>();
for (ArgumentSource argumentSource: parsingEngine.extractArgumentSources(classType)) for (ArgumentSource argumentSource: parsingEngine.extractArgumentSources(classType))
if (!argumentSource.isDeprecated()) if (!argumentSource.isDeprecated()) {
Class<?> gatherer = null;
if (argumentSource.field.isAnnotationPresent(Gather.class))
gatherer = argumentSource.field.getAnnotation(Gather.class).value();
for (ArgumentDefinition argumentDefinition: argumentSource.createArgumentDefinitions()) for (ArgumentDefinition argumentDefinition: argumentSource.createArgumentDefinitions())
argumentFields.addAll(getArgumentFields(argumentDefinition)); argumentFields.addAll(getArgumentFields(argumentDefinition, gatherer));
}
return argumentFields; return argumentFields;
} }
private static final List<String> intervalFields = Arrays.asList("intervals", "excludeIntervals", "targetIntervals"); private static final List<String> intervalFields = Arrays.asList("intervals", "excludeIntervals", "targetIntervals");
private static List<? extends ArgumentField> getArgumentFields(ArgumentDefinition argumentDefinition) { private static List<? extends ArgumentField> getArgumentFields(ArgumentDefinition argumentDefinition, Class<?> gatherer) {
if (intervalFields.contains(argumentDefinition.fullName) && argumentDefinition.ioType == ArgumentIOType.INPUT) { if (intervalFields.contains(argumentDefinition.fullName) && argumentDefinition.ioType == ArgumentIOType.INPUT) {
return Arrays.asList( return Arrays.asList(
new IntervalFileArgumentField(argumentDefinition), new IntervalFileArgumentField(argumentDefinition),
@ -138,7 +142,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
return Collections.singletonList(new InputArgumentField(argumentDefinition)); return Collections.singletonList(new InputArgumentField(argumentDefinition));
} else if (argumentDefinition.ioType == ArgumentIOType.OUTPUT) { } else if (argumentDefinition.ioType == ArgumentIOType.OUTPUT) {
return Collections.singletonList(new OutputArgumentField(argumentDefinition)); return Collections.singletonList(new OutputArgumentField(argumentDefinition, gatherer));
} else if (argumentDefinition.isFlag) { } else if (argumentDefinition.isFlag) {
return Collections.singletonList(new FlagArgumentField(argumentDefinition)); return Collections.singletonList(new FlagArgumentField(argumentDefinition));
@ -224,8 +228,10 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
// if (argumentDefinition.ioType == ArgumentIOType.OUTPUT) // if (argumentDefinition.ioType == ArgumentIOType.OUTPUT)
// Map all outputs to files. // Map all outputs to files.
private static class OutputArgumentField extends ArgumentDefinitionField { private static class OutputArgumentField extends ArgumentDefinitionField {
public OutputArgumentField(ArgumentDefinition argumentDefinition) { private final Class<?> gatherer;
public OutputArgumentField(ArgumentDefinition argumentDefinition, Class<?> gatherer) {
super(argumentDefinition); super(argumentDefinition);
this.gatherer = gatherer;
} }
@Override protected Class<?> getInnerType() { return File.class; } @Override protected Class<?> getInnerType() { return File.class; }
@ -235,7 +241,9 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
@Override public boolean isGather() { return true; } @Override public boolean isGather() { return true; }
@Override protected String getGatherAnnotation() { @Override protected String getGatherAnnotation() {
String gather; String gather;
if (SAMFileWriter.class.isAssignableFrom(argumentDefinition.argumentType)) if (gatherer != null)
gather = "@Gather(classOf[" + gatherer.getName() + "])%n";
else if (SAMFileWriter.class.isAssignableFrom(argumentDefinition.argumentType))
gather = "@Gather(classOf[BamGatherFunction])%n"; gather = "@Gather(classOf[BamGatherFunction])%n";
else if (VCFWriter.class.isAssignableFrom(argumentDefinition.argumentType)) else if (VCFWriter.class.isAssignableFrom(argumentDefinition.argumentType))
gather = "@Gather(classOf[VcfGatherFunction])%n"; gather = "@Gather(classOf[VcfGatherFunction])%n";
@ -272,7 +280,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
} }
// if (!argumentDefinition.required && useOption(argumentDefinition.argumentType)) // if (!argumentDefinition.required && useOption(argumentDefinition.argumentType))
// Any optional arguments that are primitives / enums are wrapped in options. // Any optional arguments that are primitives are wrapped in options.
private static class OptionedArgumentField extends ArgumentDefinitionField { private static class OptionedArgumentField extends ArgumentDefinitionField {
private final boolean useFormatter; private final boolean useFormatter;

2
java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java
View File

@ -217,7 +217,7 @@ public abstract class ArgumentField {
* @return true if option should be used. * @return true if option should be used.
*/ */
protected static boolean useOption(Class<?> argType) { protected static boolean useOption(Class<?> argType) {
return (argType.isPrimitive()) || (Number.class.isAssignableFrom(argType)) || (argType.isEnum()); return (argType.isPrimitive()) || (Number.class.isAssignableFrom(argType));
} }
/** /**

7
java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
View File

@ -140,9 +140,10 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
continue; continue;
String clpClassName = clpManager.getName(clp); String clpClassName = clpManager.getName(clp);
String clpConstructor = String.format("analysisName = \"%s\"%njavaMainClass = \"%s\"%n", clpClassName, clp.getName());
writeClass("org.broadinstitute.sting.queue.function.JarCommandLineFunction", clpClassName, writeClass("org.broadinstitute.sting.queue.function.JavaCommandLineFunction", clpClassName,
false, "", ArgumentDefinitionField.getArgumentFields(parser,clp), dependents); false, clpConstructor, ArgumentDefinitionField.getArgumentFields(parser,clp), dependents);
if (clp == CommandLineGATK.class) { if (clp == CommandLineGATK.class) {
for (Entry<String, Collection<Class<? extends Walker>>> walkersByPackage: walkerManager.getWalkerNamesByPackage(false).entrySet()) { for (Entry<String, Collection<Class<? extends Walker>>> walkersByPackage: walkerManager.getWalkerNamesByPackage(false).entrySet()) {
@ -359,7 +360,7 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
baseClass += " with ScatterGatherableFunction"; baseClass += " with ScatterGatherableFunction";
} }
if (isGather) if (isGather)
importSet.add("import org.broadinstitute.sting.queue.function.scattergather.Gather"); importSet.add("import org.broadinstitute.sting.commandline.Gather");
// Sort the imports so that the are always in the same order. // Sort the imports so that the are always in the same order.
List<String> sortedImports = new ArrayList<String>(importSet); List<String> sortedImports = new ArrayList<String>(importSet);

18
packages/AnalyzeConcordance.xml
View File

@ -1,18 +0,0 @@
<?xml version="1.0" encoding="UTF-8"?>
<!--
Currently built via:
ant playground package -Dexecutable=AnalyzeConcordance
-->
<package name="AnalyzeConcordance">
<executable name="AnalyzeConcordance">
<main-class name="org.broadinstitute.sting.playground.analyzeconcordance.AnalyzeConcordance" />
<resource-bundle file="StingText.properties" />
<dependencies>
<class name="org.broadinstitute.sting.playground.analyzeconcordance.AnalyzeConcordance" />
</dependencies>
</executable>
<resources>
<!-- Supplemental scripts for graph generation, etc. -->
<file name="R/analyzeConcordance/analyzeConcordance.R" />
</resources>
</package>

49
packages/GATKEngine.xml 100644
View File

@ -0,0 +1,49 @@
<?xml version="1.0" encoding="UTF-8"?>
<!--
~ 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 name="GATKEngine">
<executable name="GATKEngine">
<dependencies>
<!-- Core walkers -->
<package name="org.broadinstitute.sting.gatk.walkers.**" />
<!-- All non-oneoff GATK-specific RODs -->
<package name="org.broadinstitute.sting.gatk.refdata.**" />
<!-- Filters -->
<package name="org.broadinstitute.sting.gatk.filters" />
<!-- Tribble codecs -->
<package name="org.broad.tribble.*" />
<!-- Workaround - depend on the logger impl required by JEXL -->
<package name="org.apache.commons.logging.impl" />
</dependencies>
</executable>
<resources>
<!-- Sample reads and reference files -->
<file name="testdata/exampleBAM.bam" />
<file name="testdata/exampleBAM.bam.bai" />
<file name="testdata/exampleFASTA.fasta" />
<file name="testdata/exampleFASTA.fasta.fai" />
<file name="testdata/exampleFASTA.dict" />
</resources>
</package>

21
packages/GenomeAnalysisTK.xml
View File

@ -4,18 +4,9 @@
<executable name="GenomeAnalysisTK"> <executable name="GenomeAnalysisTK">
<main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" /> <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
<resource-bundle file="StingText.properties" /> <resource-bundle file="StingText.properties" />
<dependencies> <modules>
<!-- Core walkers --> <module file="GATKEngine.xml"/>
<package name="org.broadinstitute.sting.gatk.walkers.**" /> </modules>
<!-- All non-oneoff GATK-specific RODs -->
<package name="org.broadinstitute.sting.gatk.refdata.**" />
<!-- Filters -->
<package name="org.broadinstitute.sting.gatk.filters" />
<!-- Tribble codecs -->
<package name="org.broad.tribble.*" />
<!-- Workaround - depend on the logger impl required by JEXL -->
<package name="org.apache.commons.logging.impl" />
</dependencies>
</executable> </executable>
<modules> <modules>
<module file="AnalyzeCovariates.xml"/> <module file="AnalyzeCovariates.xml"/>
@ -28,12 +19,6 @@
<file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java" /> <file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java" />
<file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java" /> <file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java" />
<file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java" /> <file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java" />
<!-- Sample reads and reference files -->
<file name="testdata/exampleBAM.bam" />
<file name="testdata/exampleBAM.bam.bai" />
<file name="testdata/exampleFASTA.fasta" />
<file name="testdata/exampleFASTA.fasta.fai" />
<file name="testdata/exampleFASTA.dict" />
</resources> </resources>
<release> <release>
<executable directory="/humgen/gsa-hpprojects/GATK/bin" symlink="current" /> <executable directory="/humgen/gsa-hpprojects/GATK/bin" symlink="current" />

28
packages/Queue.xml
View File

@ -1,4 +1,28 @@
<?xml version="1.0" encoding="UTF-8"?> <?xml version="1.0" encoding="UTF-8"?>
<!--
~ 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 name="Queue"> <package name="Queue">
<version file="StingText.properties" property="org.broadinstitute.sting.queue.version" /> <version file="StingText.properties" property="org.broadinstitute.sting.queue.version" />
<executable name="Queue"> <executable name="Queue">
@ -21,6 +45,10 @@
<!-- JNA, including embedded native libraries --> <!-- JNA, including embedded native libraries -->
<dir name="com/sun/jna" /> <dir name="com/sun/jna" />
</dependencies> </dependencies>
<modules>
<module file="GenomeAnalysisTK.xml"/>
<module file="AnalyzeCovariates.xml"/>
</modules>
</executable> </executable>
<release> <release>
<executable directory="/humgen/gsa-hpprojects/Queue/bin" symlink="current" /> <executable directory="/humgen/gsa-hpprojects/Queue/bin" symlink="current" />

28
scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
View File

@ -185,8 +185,8 @@ class MethodsDevelopmentCallingPipeline extends QScript {
trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { trait UNIVERSAL_GATK_ARGS extends CommandLineGATK {
logging_level = "INFO"; logging_level = "INFO";
jarFile = gatkJarFile; jarFile = gatkJarFile;
memoryLimit = Some(4); memoryLimit = 4;
phone_home = Some(if ( LOCAL_ET ) GATKRunReport.PhoneHomeOption.STANDARD else GATKRunReport.PhoneHomeOption.AWS_S3) phone_home = if ( LOCAL_ET ) GATKRunReport.PhoneHomeOption.STANDARD else GATKRunReport.PhoneHomeOption.AWS_S3
} }
def bai(bam: File) = new File(bam + ".bai") def bai(bam: File) = new File(bam + ".bai")
@ -197,9 +197,9 @@ class MethodsDevelopmentCallingPipeline extends QScript {
this.reference_sequence = t.reference this.reference_sequence = t.reference
this.intervalsString ++= List(t.intervals) this.intervalsString ++= List(t.intervals)
this.scatterCount = 63 // the smallest interval list has 63 intervals, one for each Mb on chr20 this.scatterCount = 63 // the smallest interval list has 63 intervals, one for each Mb on chr20
this.dcov = Some( if ( t.isLowpass ) { 50 } else { 250 } ) this.dcov = if ( t.isLowpass ) { 50 } else { 250 }
this.stand_call_conf = Some( if ( t.isLowpass ) { 4.0 } else { 30.0 } ) this.stand_call_conf = if ( t.isLowpass ) { 4.0 } else { 30.0 }
this.stand_emit_conf = Some( if ( t.isLowpass ) { 4.0 } else { 30.0 } ) this.stand_emit_conf = if ( t.isLowpass ) { 4.0 } else { 30.0 }
this.input_file :+= t.bamList this.input_file :+= t.bamList
if (t.dbsnpFile.endsWith(".rod")) if (t.dbsnpFile.endsWith(".rod"))
this.DBSNP = new File(t.dbsnpFile) this.DBSNP = new File(t.dbsnpFile)
@ -210,11 +210,11 @@ class MethodsDevelopmentCallingPipeline extends QScript {
// 1a.) Call SNPs with UG // 1a.) Call SNPs with UG
class snpCall (t: Target) extends GenotyperBase(t) { class snpCall (t: Target) extends GenotyperBase(t) {
if (minimumBaseQuality >= 0) if (minimumBaseQuality >= 0)
this.min_base_quality_score = Some(minimumBaseQuality) this.min_base_quality_score = minimumBaseQuality
if (qscript.deletions >= 0) if (qscript.deletions >= 0)
this.max_deletion_fraction = Some(qscript.deletions) this.max_deletion_fraction = qscript.deletions
this.out = t.rawVCF this.out = t.rawVCF
this.baq = Some( if (noBAQ) {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF} else {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY}) this.baq = if (noBAQ) {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF} else {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY}
this.analysisName = t.name + "_UGs" this.analysisName = t.name + "_UGs"
this.jobName = queueLogDir + t.name + ".snpcall" this.jobName = queueLogDir + t.name + ".snpcall"
} }
@ -222,8 +222,8 @@ class MethodsDevelopmentCallingPipeline extends QScript {
// 1b.) Call Indels with UG // 1b.) Call Indels with UG
class indelCall (t: Target) extends GenotyperBase(t) { class indelCall (t: Target) extends GenotyperBase(t) {
this.out = t.rawIndelVCF this.out = t.rawIndelVCF
this.glm = Some(org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.DINDEL) this.glm = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.DINDEL
this.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF) this.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF
this.analysisName = t.name + "_UGi" this.analysisName = t.name + "_UGi"
this.jobName = queueLogDir + t.name + ".indelcall" this.jobName = queueLogDir + t.name + ".indelcall"
} }
@ -248,7 +248,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
// 3.) Variant Quality Score Recalibration - Generate Recalibration table // 3.) Variant Quality Score Recalibration - Generate Recalibration table
class VQSR(t: Target, goldStandard: Boolean) extends ContrastiveRecalibrator with UNIVERSAL_GATK_ARGS { class VQSR(t: Target, goldStandard: Boolean) extends ContrastiveRecalibrator with UNIVERSAL_GATK_ARGS {
this.memoryLimit = Some(6) this.memoryLimit = 6
this.reference_sequence = t.reference this.reference_sequence = t.reference
this.intervalsString ++= List(t.intervals) this.intervalsString ++= List(t.intervals)
this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.rawVCF } ) this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.rawVCF } )
@ -272,13 +272,13 @@ class MethodsDevelopmentCallingPipeline extends QScript {
// 4.) Apply the recalibration table to the appropriate tranches // 4.) Apply the recalibration table to the appropriate tranches
class applyVQSR (t: Target, goldStandard: Boolean) extends ApplyRecalibration with UNIVERSAL_GATK_ARGS { class applyVQSR (t: Target, goldStandard: Boolean) extends ApplyRecalibration with UNIVERSAL_GATK_ARGS {
this.memoryLimit = Some(4) this.memoryLimit = 4
this.reference_sequence = t.reference this.reference_sequence = t.reference
this.intervalsString ++= List(t.intervals) this.intervalsString ++= List(t.intervals)
this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.rawVCF } ) this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.rawVCF } )
this.tranches_file = if ( goldStandard ) { t.goldStandardTranchesFile } else { t.tranchesFile} this.tranches_file = if ( goldStandard ) { t.goldStandardTranchesFile } else { t.tranchesFile}
this.recal_file = if ( goldStandard ) { t.goldStandardRecalFile } else { t.recalFile } this.recal_file = if ( goldStandard ) { t.goldStandardRecalFile } else { t.recalFile }
this.fdr_filter_level = Some(2.0) this.fdr_filter_level = 2.0
this.out = t.recalibratedVCF this.out = t.recalibratedVCF
this.analysisName = t.name + "_AVQSR" this.analysisName = t.name + "_AVQSR"
this.jobName = queueLogDir + t.name + ".applyVQSR" this.jobName = queueLogDir + t.name + ".applyVQSR"
@ -293,7 +293,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
this.intervalsString ++= List(t.intervals) this.intervalsString ++= List(t.intervals)
this.out = t.cutVCF this.out = t.cutVCF
this.tranchesFile = t.tranchesFile this.tranchesFile = t.tranchesFile
this.fdr_filter_level = Some(t.trancheTarget) this.fdr_filter_level = t.trancheTarget
if (t.dbsnpFile.endsWith(".rod")) if (t.dbsnpFile.endsWith(".rod"))
this.DBSNP = new File(t.dbsnpFile) this.DBSNP = new File(t.dbsnpFile)
else if (t.dbsnpFile.endsWith(".vcf")) else if (t.dbsnpFile.endsWith(".vcf"))

2
scala/qscript/core/StandardVariantEvaluation.scala
View File

@ -65,7 +65,7 @@ class StandardVariantEvaluation extends QScript {
this.jarFile = gatkJarFile; this.jarFile = gatkJarFile;
this.intervalsString = List(TARGET_INTERVAL); this.intervalsString = List(TARGET_INTERVAL);
this.reference_sequence = referenceFile; this.reference_sequence = referenceFile;
this.memoryLimit = Some(2) this.memoryLimit = 2
} }
def initializeStandardDataFiles() = { def initializeStandardDataFiles() = {

6
scala/qscript/examples/ExampleCountLoci.scala
View File

@ -5,9 +5,6 @@ import org.broadinstitute.sting.queue.extensions.gatk._
* An introductory pipeline with integration tests testing the MD5 of the @Output. * An introductory pipeline with integration tests testing the MD5 of the @Output.
*/ */
class ExampleCountLoci extends QScript { class ExampleCountLoci extends QScript {
@Input(doc="The path to the GenomeAnalysisTK.jar file.", shortName="gatk")
var gatkJar: File = null
@Input(doc="The reference file for the bam files.", shortName="R") @Input(doc="The reference file for the bam files.", shortName="R")
var referenceFile: File = null var referenceFile: File = null
@ -22,12 +19,11 @@ class ExampleCountLoci extends QScript {
def script = { def script = {
val countLoci = new CountLoci val countLoci = new CountLoci
countLoci.jarFile = gatkJar
countLoci.reference_sequence = referenceFile countLoci.reference_sequence = referenceFile
countLoci.input_file = bamFiles countLoci.input_file = bamFiles
countLoci.intervalsString = intervals countLoci.intervalsString = intervals
countLoci.out = out countLoci.out = out
countLoci.memoryLimit = Some(1) countLoci.memoryLimit = 1
add(countLoci) add(countLoci)
} }
} }

7
scala/qscript/examples/ExampleCountReads.scala
View File

@ -7,9 +7,6 @@ import org.broadinstitute.sting.queue.extensions.gatk._
* All bams must have the same reference. * All bams must have the same reference.
*/ */
class ExampleCountReads extends QScript { class ExampleCountReads extends QScript {
@Input(doc="The path to the GenomeAnalysisTK.jar file.", shortName="gatk")
var gatkJar: File = null
@Input(doc="The reference file for the bam files.", shortName="R") @Input(doc="The reference file for the bam files.", shortName="R")
var referenceFile: File = null var referenceFile: File = null
@ -33,9 +30,6 @@ class ExampleCountReads extends QScript {
// The names of walkers are the same as you would use for '-T <WalkerName>' // The names of walkers are the same as you would use for '-T <WalkerName>'
val jointCountReads = new CountReads val jointCountReads = new CountReads
// Set the GATK jar file for this command.
jointCountReads.jarFile = gatkJar
// Each field in the extensions is based off of the full form of the arguments. // Each field in the extensions is based off of the full form of the arguments.
// To get the list of arguments and their descriptions run // To get the list of arguments and their descriptions run
// java -jar <path to GenomeAnalysisTK.jar> -T <WalkerName> -help // java -jar <path to GenomeAnalysisTK.jar> -T <WalkerName> -help
@ -52,7 +46,6 @@ class ExampleCountReads extends QScript {
if (bamFiles.size > 1) { if (bamFiles.size > 1) {
for (bamFile <- bamFiles) { for (bamFile <- bamFiles) {
val singleCountReads = new CountReads val singleCountReads = new CountReads
singleCountReads.jarFile = gatkJar
singleCountReads.reference_sequence = referenceFile singleCountReads.reference_sequence = referenceFile
// ':+' is the scala List append operator // ':+' is the scala List append operator
singleCountReads.input_file :+= bamFile singleCountReads.input_file :+= bamFile

23
scala/qscript/examples/ExampleCustomWalker.scala
View File

@ -2,17 +2,11 @@ import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.gatk._
/** /**
* A pipeline for Queue that runs a custom walker outside of the GATK jar. * A pipeline for Queue that runs a custom walker on the classpath.
* NOTE: This code is an unsupported example for soliciting feedback on how to improve Queue. * NOTE: This code is an unsupported example for soliciting feedback on how to improve Queue.
* Future syntax will simplify running the GATK so please expect the syntax below to change significantly. * Future syntax will simplify running the GATK so please expect the syntax below to change significantly.
*/ */
class ExampleCustomWalker extends QScript { class ExampleCustomWalker extends QScript {
// The full packaged jar should be used.
// You can build this jar via 'ant package' and then find it under
// 'Sting/dist/packages/GenomeAnalysisTK-*/GenomeAnalysisTK.jar'
@Input(doc="The path to the packaged GenomeAnalysisTK.jar file.", shortName="gatk")
var gatkJar: File = null
@Input(doc="The reference file for the bam files.", shortName="R") @Input(doc="The reference file for the bam files.", shortName="R")
var referenceFile: File = null var referenceFile: File = null
@ -29,15 +23,18 @@ class ExampleCustomWalker extends QScript {
* In script, you create and then add() functions to the pipeline. * In script, you create and then add() functions to the pipeline.
*/ */
def script = { def script = {
val myClasses = "myClassDir"
val customWalker = new CommandLineGATK { val customWalker = new CommandLineGATK {
// Set the name of your walker, for example this will be passed as -T MyCustomWalker // Set the name of your walker, for example this will be passed as -T MyCustomWalker
this.analysis_type = "MyCustomWalker" this.analysis_type = "MyCustomWalker"
// NOTE: At this time, you still need to specify the GATK jar or the pipeline won't validate.
this.jarFile = gatkJar // If your walker is already on the classpath you shouldn't need to do anything else
override def javaExecutable = "org.broadinstitute.sting.gatk.CommandLineGATK"
override def javaOpts = "%s -cp %s:%s".format(super.javaOpts, gatkJar, myClasses) // If your walker is in a GATK jar that is for some reason NOT on the classpath
// nor referenced in the Queue.jar's, specify the jar file here
//this.jarFile = "myGATK.jar"
// If your walker needs a custom classpath, specify it here
//this.javaClasspath = List("myClasses")
} }
customWalker.reference_sequence = referenceFile customWalker.reference_sequence = referenceFile

8
scala/qscript/examples/ExampleUnifiedGenotyper.scala
View File

@ -15,9 +15,6 @@ class ExampleUnifiedGenotyper extends QScript {
// Required arguments. All initialized to empty values. // Required arguments. All initialized to empty values.
@Input(doc="The path to the GenomeAnalysisTK.jar file.", shortName="gatk")
var gatkJar: File = null // The command line must pass the gatk jar to this script via -gatk.
@Input(doc="The reference file for the bam files.", shortName="R") @Input(doc="The reference file for the bam files.", shortName="R")
var referenceFile: File = _ // _ is scala shorthand for null var referenceFile: File = _ // _ is scala shorthand for null
@ -39,12 +36,11 @@ class ExampleUnifiedGenotyper extends QScript {
// This trait allows us set the variables below in one place, // This trait allows us set the variables below in one place,
// and then reuse this trait on each CommandLineGATK function below. // and then reuse this trait on each CommandLineGATK function below.
trait UnifiedGenotyperArguments extends CommandLineGATK { trait UnifiedGenotyperArguments extends CommandLineGATK {
this.jarFile = qscript.gatkJar
this.reference_sequence = qscript.referenceFile this.reference_sequence = qscript.referenceFile
this.intervals = List(qscript.intervals) this.intervals = List(qscript.intervals)
// Some() is how you set the value for an scala Option. // is how you set the value for an scala Option.
// Set the memory limit to 2 gigabytes on each command. // Set the memory limit to 2 gigabytes on each command.
this.memoryLimit = Some(2) this.memoryLimit = 2
} }

22
scala/qscript/oneoffs/carneiro/dataProcessing.scala
View File

@ -1,5 +1,5 @@
import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction import org.broadinstitute.sting.queue.extensions.picard.PicardBamFunction
import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.function.ListWriterFunction import org.broadinstitute.sting.queue.function.ListWriterFunction
import scala.io.Source import scala.io.Source
@ -55,7 +55,7 @@ class dataProcessing extends QScript {
trait CommandLineGATKArgs extends CommandLineGATK { trait CommandLineGATKArgs extends CommandLineGATK {
this.jarFile = qscript.GATKjar this.jarFile = qscript.GATKjar
this.reference_sequence = qscript.reference this.reference_sequence = qscript.reference
this.memoryLimit = Some(4) this.memoryLimit = 4
this.isIntermediate = true this.isIntermediate = true
} }
@ -127,7 +127,7 @@ class dataProcessing extends QScript {
class TargetBase (outIntervals: String) extends RealignerTargetCreator with CommandLineGATKArgs { class TargetBase (outIntervals: String) extends RealignerTargetCreator with CommandLineGATKArgs {
this.out = new File(outIntervals) this.out = new File(outIntervals)
this.mismatchFraction = Some(0.0) this.mismatchFraction = 0.0
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP) this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
this.rodBind :+= RodBind("indels", "VCF", indels) this.rodBind :+= RodBind("indels", "VCF", indels)
@ -139,7 +139,7 @@ class dataProcessing extends QScript {
class allTargets (inBams: String, outIntervals: String) extends TargetBase(outIntervals) { class allTargets (inBams: String, outIntervals: String) extends TargetBase(outIntervals) {
this.input_file :+= new File(inBams) this.input_file :+= new File(inBams)
this.memoryLimit = Some(6) this.memoryLimit = 6
this.jobName = queueLogDir + outIntervals + ".atarget" this.jobName = queueLogDir + outIntervals + ".atarget"
} }
@ -151,16 +151,16 @@ class dataProcessing extends QScript {
this.rodBind :+= RodBind("indels", "VCF", qscript.indels) this.rodBind :+= RodBind("indels", "VCF", qscript.indels)
this.useOnlyKnownIndels = knownsOnly this.useOnlyKnownIndels = knownsOnly
this.doNotUseSW = true this.doNotUseSW = true
this.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY) this.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY
this.compress = Some(0) this.compress = 0
this.U = Some(org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION) // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly! this.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly!
this.isIntermediate = intermediate this.isIntermediate = intermediate
this.jobName = queueLogDir + outBam + ".clean" this.jobName = queueLogDir + outBam + ".clean"
if (!intermediate && !qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString) if (!intermediate && !qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
if (!intermediate && qscript.intervals != null) this.intervals :+= qscript.intervals if (!intermediate && qscript.intervals != null) this.intervals :+= qscript.intervals
} }
class dedup (inBam: String, outBam: String, metricsFile: String) extends PicardBamJarFunction { class dedup (inBam: String, outBam: String, metricsFile: String) extends PicardBamFunction {
@Input(doc="fixed bam") var clean: File = new File(inBam) @Input(doc="fixed bam") var clean: File = new File(inBam)
@Output(doc="deduped bam") var deduped: File = new File(outBam) @Output(doc="deduped bam") var deduped: File = new File(outBam)
@Output(doc="deduped bam index") var dedupedIndex: File = new File(outBam + ".bai") @Output(doc="deduped bam index") var dedupedIndex: File = new File(outBam + ".bai")
@ -169,7 +169,7 @@ class dataProcessing extends QScript {
override def outputBam = deduped override def outputBam = deduped
override def commandLine = super.commandLine + " M=" + metricsFile + " CREATE_INDEX=true" override def commandLine = super.commandLine + " M=" + metricsFile + " CREATE_INDEX=true"
sortOrder = null sortOrder = null
this.memoryLimit = Some(6) this.memoryLimit = 6
this.jarFile = qscript.dedupJar this.jarFile = qscript.dedupJar
this.isIntermediate = true this.isIntermediate = true
this.jobName = queueLogDir + outBam + ".dedup" this.jobName = queueLogDir + outBam + ".dedup"
@ -188,8 +188,8 @@ class dataProcessing extends QScript {
this.input_file :+= new File (inBam) this.input_file :+= new File (inBam)
this.recal_file = new File(inRecalFile) this.recal_file = new File(inRecalFile)
this.out = new File(outBam) this.out = new File(outBam)
this.U = Some(org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION) // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly! this.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly!
this.index_output_bam_on_the_fly = Some(true) this.index_output_bam_on_the_fly = true
this.jobName = queueLogDir + outBam + ".recalibration" this.jobName = queueLogDir + outBam + ".recalibration"
} }

22
scala/qscript/oneoffs/carneiro/dataProcessingV2.scala
View File

@ -1,7 +1,7 @@
package oneoffs.carneiro package oneoffs.carneiro
import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction import org.broadinstitute.sting.queue.extensions.picard.PicardBamFunction
import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.function.ListWriterFunction import org.broadinstitute.sting.queue.function.ListWriterFunction
@ -173,11 +173,11 @@ class dataProcessingV2 extends QScript {
trait CommandLineGATKArgs extends CommandLineGATK { trait CommandLineGATKArgs extends CommandLineGATK {
this.jarFile = qscript.GATKjar this.jarFile = qscript.GATKjar
this.reference_sequence = qscript.reference this.reference_sequence = qscript.reference
this.memoryLimit = Some(4) this.memoryLimit = 4
this.isIntermediate = true this.isIntermediate = true
} }
case class joinBams (inBams: List[File], outBam: File) extends PicardBamJarFunction { case class joinBams (inBams: List[File], outBam: File) extends PicardBamFunction {
@Input(doc="input bam list") var join = inBams @Input(doc="input bam list") var join = inBams
@Output(doc="joined bam") var joined = outBam @Output(doc="joined bam") var joined = outBam
@Output(doc="joined bam index") var joinedIndex = new File(outBam + "bai") @Output(doc="joined bam index") var joinedIndex = new File(outBam + "bai")
@ -194,7 +194,7 @@ class dataProcessingV2 extends QScript {
if (!knownsOnly) if (!knownsOnly)
this.input_file :+= inBams this.input_file :+= inBams
this.out = outIntervals this.out = outIntervals
this.mismatchFraction = Some(0.0) this.mismatchFraction = 0.0
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP) this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
this.rodBind :+= RodBind("indels", "VCF", indels) this.rodBind :+= RodBind("indels", "VCF", indels)
this.scatterCount = nContigs this.scatterCount = nContigs
@ -210,14 +210,14 @@ class dataProcessingV2 extends QScript {
this.rodBind :+= RodBind("indels", "VCF", qscript.indels) this.rodBind :+= RodBind("indels", "VCF", qscript.indels)
this.useOnlyKnownIndels = knownsOnly this.useOnlyKnownIndels = knownsOnly
this.doNotUseSW = useSW this.doNotUseSW = useSW
this.compress = Some(0) this.compress = 0
this.U = Some(org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION) // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly! this.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly!
this.scatterCount = nContigs this.scatterCount = nContigs
this.analysisName = queueLogDir + outBam + ".clean" this.analysisName = queueLogDir + outBam + ".clean"
this.jobName = queueLogDir + outBam + ".clean" this.jobName = queueLogDir + outBam + ".clean"
} }
case class dedup (inBam: File, outBam: File, metricsFile: File) extends PicardBamJarFunction { case class dedup (inBam: File, outBam: File, metricsFile: File) extends PicardBamFunction {
@Input(doc="fixed bam") var clean = inBam @Input(doc="fixed bam") var clean = inBam
@Output(doc="deduped bam") var deduped = outBam @Output(doc="deduped bam") var deduped = outBam
@Output(doc="deduped bam index") var dedupedIndex = new File(outBam + ".bai") @Output(doc="deduped bam index") var dedupedIndex = new File(outBam + ".bai")
@ -226,7 +226,7 @@ class dataProcessingV2 extends QScript {
override def outputBam = deduped override def outputBam = deduped
override def commandLine = super.commandLine + " M=" + metricsFile + " CREATE_INDEX=true" override def commandLine = super.commandLine + " M=" + metricsFile + " CREATE_INDEX=true"
sortOrder = null sortOrder = null
this.memoryLimit = Some(6) this.memoryLimit = 6
this.jarFile = qscript.dedupJar this.jarFile = qscript.dedupJar
this.analysisName = queueLogDir + outBam + ".dedup" this.analysisName = queueLogDir + outBam + ".dedup"
this.jobName = queueLogDir + outBam + ".dedup" this.jobName = queueLogDir + outBam + ".dedup"
@ -246,12 +246,12 @@ class dataProcessingV2 extends QScript {
@Output(doc="recalibrated bam index") var recalIndex = new File(outBam + ".bai") @Output(doc="recalibrated bam index") var recalIndex = new File(outBam + ".bai")
this.input_file :+= inBam this.input_file :+= inBam
this.recal_file = inRecalFile this.recal_file = inRecalFile
this.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY) this.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY
this.out = outBam this.out = outBam
if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString) if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
else if (qscript.intervals != null) this.intervals :+= qscript.intervals else if (qscript.intervals != null) this.intervals :+= qscript.intervals
this.U = Some(org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION) // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly! this.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly!
this.index_output_bam_on_the_fly = Some(true) this.index_output_bam_on_the_fly = true
this.analysisName = queueLogDir + outBam + ".recalibration" this.analysisName = queueLogDir + outBam + ".recalibration"
this.jobName = queueLogDir + outBam + ".recalibration" this.jobName = queueLogDir + outBam + ".recalibration"

10
scala/qscript/oneoffs/carneiro/justClean.scala
View File

@ -42,10 +42,10 @@ class justClean extends QScript {
target.input_file :+= input target.input_file :+= input
target.out = tIntervals target.out = tIntervals
target.reference_sequence = reference target.reference_sequence = reference
target.mismatchFraction = Some(0.0) target.mismatchFraction = 0.0
target.rodBind :+= RodBind("dbsnp", "VCF", dbSNP) target.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
target.rodBind :+= RodBind("indels", "VCF", indels) target.rodBind :+= RodBind("indels", "VCF", indels)
target.memoryLimit = Some(6) target.memoryLimit = 6
target.jobName = queueLogDir + tIntervals + ".atarget" target.jobName = queueLogDir + tIntervals + ".atarget"
target.jarFile = GATKjar target.jarFile = GATKjar
target.scatterCount = 84 target.scatterCount = 84
@ -60,11 +60,11 @@ class justClean extends QScript {
clean.rodBind :+= RodBind("dbsnp", "VCF", dbSNP) clean.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
clean.rodBind :+= RodBind("indels", "VCF", indels) clean.rodBind :+= RodBind("indels", "VCF", indels)
clean.doNotUseSW = true clean.doNotUseSW = true
clean.compress = Some(0) clean.compress = 0
clean.U = Some(org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION) // todo -- update clean with the last consensus between Tim, Matt and Eric. This is ugly! clean.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION // todo -- update clean with the last consensus between Tim, Matt and Eric. This is ugly!
clean.jobName = queueLogDir + outBam + ".clean" clean.jobName = queueLogDir + outBam + ".clean"
clean.jarFile = GATKjar clean.jarFile = GATKjar
clean.memoryLimit = Some(12) clean.memoryLimit = 12
clean.scatterCount = 84 clean.scatterCount = 84
add(clean); add(clean);

20
scala/qscript/oneoffs/carneiro/pbCalling.scala
View File

@ -158,20 +158,20 @@ class pbCalling extends QScript {
this.reference_sequence = t.reference this.reference_sequence = t.reference
this.intervalsString ++= List(t.intervals) this.intervalsString ++= List(t.intervals)
this.scatterCount = 63 // the smallest interval list has 63 intervals, one for each Mb on chr20 this.scatterCount = 63 // the smallest interval list has 63 intervals, one for each Mb on chr20
this.dcov = Some( if ( t.isLowpass ) { 50 } else { 250 } ) this.dcov = if ( t.isLowpass ) { 50 } else { 250 }
this.stand_call_conf = Some( if ( t.isLowpass ) { 4.0 } else { 30.0 } ) this.stand_call_conf = if ( t.isLowpass ) { 4.0 } else { 30.0 }
this.stand_emit_conf = Some( if ( t.isLowpass ) { 4.0 } else { 30.0 } ) this.stand_emit_conf = if ( t.isLowpass ) { 4.0 } else { 30.0 }
this.input_file :+= t.bamList this.input_file :+= t.bamList
this.out = t.rawVCF this.out = t.rawVCF
this.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY) this.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY
this.analysisName = t.name + "_UG" this.analysisName = t.name + "_UG"
if (t.dbsnpFile.endsWith(".rod")) if (t.dbsnpFile.endsWith(".rod"))
this.DBSNP = new File(t.dbsnpFile) this.DBSNP = new File(t.dbsnpFile)
else if (t.dbsnpFile.endsWith(".vcf")) else if (t.dbsnpFile.endsWith(".vcf"))
this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile) this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
// Ridiculous workaround to get pacbio data to run.. never commit this! // Ridiculous workaround to get pacbio data to run.. never commit this!
this.deletions = Some(0.5) this.deletions = 0.5
this.mbq = Some(10) this.mbq = 10
} }
// 2.) Filter SNPs // 2.) Filter SNPs
@ -188,7 +188,7 @@ class pbCalling extends QScript {
} }
class VQSR(t: Target, goldStandard: Boolean) extends ContrastiveRecalibrator { class VQSR(t: Target, goldStandard: Boolean) extends ContrastiveRecalibrator {
this.memoryLimit = Some(6) this.memoryLimit = 6
this.intervalsString ++= List(t.intervals) this.intervalsString ++= List(t.intervals)
this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.filteredVCF } ) this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.filteredVCF } )
this.rodBind :+= RodBind("hapmap", "VCF", t.hapmapFile) this.rodBind :+= RodBind("hapmap", "VCF", t.hapmapFile)
@ -208,12 +208,12 @@ class pbCalling extends QScript {
} }
class applyVQSR (t: Target, goldStandard: Boolean) extends ApplyRecalibration { class applyVQSR (t: Target, goldStandard: Boolean) extends ApplyRecalibration {
this.memoryLimit = Some(4) this.memoryLimit = 4
this.intervalsString ++= List(t.intervals) this.intervalsString ++= List(t.intervals)
this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.filteredVCF } ) this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.filteredVCF } )
this.tranches_file = if ( goldStandard ) { t.goldStandardTranchesFile } else { t.tranchesFile} this.tranches_file = if ( goldStandard ) { t.goldStandardTranchesFile } else { t.tranchesFile}
this.recal_file = if ( goldStandard ) { t.goldStandardRecalFile } else { t.recalFile } this.recal_file = if ( goldStandard ) { t.goldStandardRecalFile } else { t.recalFile }
this.fdr_filter_level = Some(2.0) this.fdr_filter_level = 2.0
this.out = t.recalibratedVCF this.out = t.recalibratedVCF
} }
@ -226,7 +226,7 @@ class pbCalling extends QScript {
this.intervalsString ++= List(t.intervals) this.intervalsString ++= List(t.intervals)
this.out = t.cutVCF this.out = t.cutVCF
this.tranchesFile = t.tranchesFile this.tranchesFile = t.tranchesFile
this.fdr_filter_level = Some(1.0) this.fdr_filter_level = 1.0
if (t.dbsnpFile.endsWith(".rod")) if (t.dbsnpFile.endsWith(".rod"))
this.DBSNP = new File(t.dbsnpFile) this.DBSNP = new File(t.dbsnpFile)
else if (t.dbsnpFile.endsWith(".vcf")) else if (t.dbsnpFile.endsWith(".vcf"))

36
scala/qscript/oneoffs/chartl/BootstrapCalls.q
View File

@ -37,14 +37,14 @@ class BootstrapCalls extends QScript {
trait UGArgs extends UnifiedGenotyper { trait UGArgs extends UnifiedGenotyper {
this.input_file = bams this.input_file = bams
this.reference_sequence = reference this.reference_sequence = reference
this.dcov = Some(downsamplingLevel) this.dcov = downsamplingLevel
this.intervals :+= intervalFile this.intervals :+= intervalFile
this.stand_call_conf = Some(standCallConf) this.stand_call_conf = standCallConf
this.stand_emit_conf = Some(standCallConf) this.stand_emit_conf = standCallConf
this.rodBind :+= new RodBind("dbsnp","vcf",dbsnp) this.rodBind :+= new RodBind("dbsnp","vcf",dbsnp)
this.scatterCount = 20 this.scatterCount = 20
this.jarFile = sting this.jarFile = sting
this.memoryLimit = Some(4) this.memoryLimit = 4
} }
val bootstrapBase = swapExt(bootstrapMergedOut,".vcf",".boot%d.vcf").getAbsolutePath val bootstrapBase = swapExt(bootstrapMergedOut,".vcf",".boot%d.vcf").getAbsolutePath
@ -63,7 +63,7 @@ class BootstrapCalls extends QScript {
this.intervals :+= intervalFile this.intervals :+= intervalFile
this.scatterCount = 40 this.scatterCount = 40
this.jarFile = sting this.jarFile = sting
this.memoryLimit = Some(4) this.memoryLimit = 4
this.rodBind ++= calls.map(u => u.out).zipWithIndex.map(u => new RodBind("bootstrap_%d".format(u._2),"vcf",u._1)) this.rodBind ++= calls.map(u => u.out).zipWithIndex.map(u => new RodBind("bootstrap_%d".format(u._2),"vcf",u._1))
this.out = bootstrapMergedOut this.out = bootstrapMergedOut
} }
@ -81,11 +81,11 @@ class BootstrapCalls extends QScript {
this.rodBind :+= new RodBind("truth1kg","vcf", new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/1212samples.b37.sites.vcf")) this.rodBind :+= new RodBind("truth1kg","vcf", new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/1212samples.b37.sites.vcf"))
this.cluster_file = swapExt(bootstrapMergedOut,"vcf","cluster") this.cluster_file = swapExt(bootstrapMergedOut,"vcf","cluster")
this.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun") this.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
this.qual = Some(100) this.qual = 100
this.std = Some(3.5) this.std = 3.5
this.mG = Some(8) this.mG = 8
this.trustAllPolymorphic = true this.trustAllPolymorphic = true
this.memoryLimit = Some(8) this.memoryLimit = 8
this.jarFile = sting this.jarFile = sting
} }
@ -102,11 +102,11 @@ class BootstrapCalls extends QScript {
this.rodBind :+= new RodBind("truthHapMap","vcf",new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf")) this.rodBind :+= new RodBind("truthHapMap","vcf",new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf"))
this.rodBind :+= new RodBind("truth1kg","vcf", new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/1212samples.b37.sites.vcf")) this.rodBind :+= new RodBind("truth1kg","vcf", new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/1212samples.b37.sites.vcf"))
this.cluster_file = swapExt(bootstrapMergedOut,"vcf","cluster") this.cluster_file = swapExt(bootstrapMergedOut,"vcf","cluster")
this.sm = Some(org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.SelectionMetricType.TRUTH_SENSITIVITY) this.sm = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.SelectionMetricType.TRUTH_SENSITIVITY
this.tranche ++= List("0.1", "0.5", "0.7", "1.0", "3.0", "5.0", "10.0", "100.0") this.tranche ++= List("0.1", "0.5", "0.7", "1.0", "3.0", "5.0", "10.0", "100.0")
this.trustAllPolymorphic = true this.trustAllPolymorphic = true
this.tranchesFile = swapExt(bootstrapMergedOut,"vcf","tranche") this.tranchesFile = swapExt(bootstrapMergedOut,"vcf","tranche")
this.memoryLimit=Some(8) this.memoryLimit=8
this.jarFile = sting this.jarFile = sting
this.rodBind :+= new RodBind("dbsnp","vcf",dbsnp) this.rodBind :+= new RodBind("dbsnp","vcf",dbsnp)
} }
@ -119,10 +119,10 @@ class BootstrapCalls extends QScript {
this.intervals :+= intervalFile this.intervals :+= intervalFile
this.rodBind :+= new RodBind("input","vcf",recal.out) this.rodBind :+= new RodBind("input","vcf",recal.out)
this.tranchesFile = recal.tranchesFile this.tranchesFile = recal.tranchesFile
this.fdr_filter_level = Some(1.0) this.fdr_filter_level = 1.0
this.out = swapExt(bootstrapMergedOut,".vcf",".recal.cut.vcf") this.out = swapExt(bootstrapMergedOut,".vcf",".recal.cut.vcf")
this.jarFile = sting this.jarFile = sting
this.memoryLimit = Some(4) this.memoryLimit = 4
this.scatterCount = 5 this.scatterCount = 5
} }
@ -149,12 +149,12 @@ class BootstrapCalls extends QScript {
this.intervals :+= intervalFile this.intervals :+= intervalFile
this.rodBind :+= new RodBind("loCov","vcf",rm.noheadvcf) this.rodBind :+= new RodBind("loCov","vcf",rm.noheadvcf)
this.rodBind :+= new RodBind("hiCov","vcf",new File("/humgen/gsa-pipeline/PVQF4/all_batches_v001/batch_001/SnpCalls/ESPGO_Gabriel_NHLBI_EOMI_setone_EOMI_Project.cleaned.annotated.handfiltered.vcf")) this.rodBind :+= new RodBind("hiCov","vcf",new File("/humgen/gsa-pipeline/PVQF4/all_batches_v001/batch_001/SnpCalls/ESPGO_Gabriel_NHLBI_EOMI_setone_EOMI_Project.cleaned.annotated.handfiltered.vcf"))
this.variantMergeOptions = Some(VariantMergeType.UNION) this.variantMergeOptions = VariantMergeType.UNION
this.genotypeMergeOptions = Some(GenotypeMergeType.PRIORITIZE) this.genotypeMergeOptions = GenotypeMergeType.PRIORITIZE
this.priority = "hiCov,loCov" this.priority = "hiCov,loCov"
this.out = swapExt(bootstrapMergedOut,".vcf",".merged.combined.vcf") this.out = swapExt(bootstrapMergedOut,".vcf",".merged.combined.vcf")
this.jarFile = sting this.jarFile = sting
this.memoryLimit = Some(6) this.memoryLimit = 6
} }
var combine : CombineVariants = new CombineVariants with CombineArgs var combine : CombineVariants = new CombineVariants with CombineArgs
@ -175,8 +175,8 @@ class BootstrapCalls extends QScript {
"\"set == 'hiCov'\"","\"set == 'FilteredInAll'\"") "\"set == 'hiCov'\"","\"set == 'FilteredInAll'\"")
this.EV = List("TiTvVariantEvaluator","CountVariants","CompOverlap") this.EV = List("TiTvVariantEvaluator","CountVariants","CompOverlap")
this.out = swapExt(bootstrapMergedOut,".vcf",".merged.combined.eval") this.out = swapExt(bootstrapMergedOut,".vcf",".merged.combined.eval")
this.nt = Some(8) this.nt = 8
this.memoryLimit = Some(12) this.memoryLimit = 12
} }
var eval : VariantEval = new VariantEval with EvalArgs var eval : VariantEval = new VariantEval with EvalArgs

7
scala/qscript/oneoffs/chartl/RefineGenotypesAndMerge.q
View File

@ -3,7 +3,6 @@ import net.sf.picard.reference.FastaSequenceFile
import org.broadinstitute.sting.datasources.pipeline.Pipeline import org.broadinstitute.sting.datasources.pipeline.Pipeline
import org.broadinstitute.sting.gatk.DownsampleType import org.broadinstitute.sting.gatk.DownsampleType
import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
import org.broadinstitute.sting.queue.extensions.samtools._ import org.broadinstitute.sting.queue.extensions.samtools._
import org.broadinstitute.sting.queue.{QException, QScript} import org.broadinstitute.sting.queue.{QException, QScript}
import collection.JavaConversions._ import collection.JavaConversions._
@ -69,7 +68,7 @@ class RefineGenotypesAndMerge extends QScript {
refine.beagleInput = beagleInput.out refine.beagleInput = beagleInput.out
refine.beagleOutputBase = beagleBase refine.beagleOutputBase = beagleBase
refine.beagleMemoryGigs = 6 refine.beagleMemoryGigs = 6
refine.memoryLimit = Some(6) refine.memoryLimit = 6
refine.freezeOutputs refine.freezeOutputs
var unzipPhased = new GunzipFile(refine.beaglePhasedFile,swapExt(refine.beaglePhasedFile,".gz",".bgl")) var unzipPhased = new GunzipFile(refine.beaglePhasedFile,swapExt(refine.beaglePhasedFile,".gz",".bgl"))
@ -94,8 +93,8 @@ class RefineGenotypesAndMerge extends QScript {
def mergeVCFs(vcfs: List[File], outputVCF: File) : CombineVariants = { def mergeVCFs(vcfs: List[File], outputVCF: File) : CombineVariants = {
var cv = new CombineVariants with GATKArgs var cv = new CombineVariants with GATKArgs
cv.out = outputVCF cv.out = outputVCF
cv.genotypemergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.GenotypeMergeType.UNSORTED) cv.genotypemergeoption = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.GenotypeMergeType.UNSORTED
cv.variantmergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION) cv.variantmergeoption = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION
cv.priority = (vcfs.foldLeft[List[String]](Nil)( (bNames,vcf) => bNames ::: List[String](swapExt(vcf,".vcf","").getName))).mkString(",") cv.priority = (vcfs.foldLeft[List[String]](Nil)( (bNames,vcf) => bNames ::: List[String](swapExt(vcf,".vcf","").getName))).mkString(",")
cv.rodBind = vcfs.foldLeft[List[RodBind]](Nil)( (rods,vcf) => rods ::: List[RodBind](new RodBind(swapExt(vcf,".vcf","").getName,"VCF",vcf))) cv.rodBind = vcfs.foldLeft[List[RodBind]](Nil)( (rods,vcf) => rods ::: List[RodBind](new RodBind(swapExt(vcf,".vcf","").getName,"VCF",vcf)))

14
scala/qscript/oneoffs/chartl/expanded_targets.q
View File

@ -39,14 +39,14 @@ class expanded_targets extends QScript {
rtc.out = swapExt(userDir,u,".bam",".clean.targets.interval_list") rtc.out = swapExt(userDir,u,".bam",".clean.targets.interval_list")
rtc.input_file :+= u.getAbsoluteFile rtc.input_file :+= u.getAbsoluteFile
rtc.intervals :+= cleanIntervals.outList rtc.intervals :+= cleanIntervals.outList
rtc.memoryLimit = Some(6) rtc.memoryLimit = 6
rtc rtc
}) })
val clean : List[IndelRealigner] = realign.map( u => { val clean : List[IndelRealigner] = realign.map( u => {
var cleaner : IndelRealigner = new IndelRealigner with GATKArgs var cleaner : IndelRealigner = new IndelRealigner with GATKArgs
cleaner.targetIntervals = u.out cleaner.targetIntervals = u.out
cleaner.input_file = u.input_file cleaner.input_file = u.input_file
cleaner.memoryLimit = Some(6) cleaner.memoryLimit = 6
cleaner.out = new File(userDir+"/"+swapExt(u.out,".bam",".expanded.targets.bam").getName) cleaner.out = new File(userDir+"/"+swapExt(u.out,".bam",".expanded.targets.bam").getName)
cleaner.intervals :+= cleanIntervals.outList cleaner.intervals :+= cleanIntervals.outList
cleaner cleaner
@ -71,10 +71,10 @@ class expanded_targets extends QScript {
var call : UnifiedGenotyper = new UnifiedGenotyper with GATKArgs var call : UnifiedGenotyper = new UnifiedGenotyper with GATKArgs
call.input_file = bams call.input_file = bams
call.out = swapExt(iList,".interval_list",".raw.vcf") call.out = swapExt(iList,".interval_list",".raw.vcf")
call.trig_emit_conf = Some(0.0) call.trig_emit_conf = 0.0
call.rodBind :+= new RodBind("trigger","vcf",thisTrigger) call.rodBind :+= new RodBind("trigger","vcf",thisTrigger)
call.scatterCount = 10 call.scatterCount = 10
call.memoryLimit = Some(6) call.memoryLimit = 6
var filter : VariantFiltration = new VariantFiltration with GATKArgs var filter : VariantFiltration = new VariantFiltration with GATKArgs
filter.rodBind :+= new RodBind("variant","vcf",call.out) filter.rodBind :+= new RodBind("variant","vcf",call.out)
filter.filterExpression :+= "\"QD<5.0\"" filter.filterExpression :+= "\"QD<5.0\""
@ -87,7 +87,7 @@ class expanded_targets extends QScript {
callHiseq.input_file = List(new File("/seq/picard_aggregation/EXT1/NA12878/v3/NA12878.bam")) callHiseq.input_file = List(new File("/seq/picard_aggregation/EXT1/NA12878/v3/NA12878.bam"))
callHiseq.rodBind :+= new RodBind("trigger","vcf",filter.out) callHiseq.rodBind :+= new RodBind("trigger","vcf",filter.out)
callHiseq.out = swapExt(iList,".interval_list",".hiSeq.genotypes.vcf") callHiseq.out = swapExt(iList,".interval_list",".hiSeq.genotypes.vcf")
callHiseq.trig_emit_conf = Some(0.0) callHiseq.trig_emit_conf = 0.0
callHiseq.scatterCount = 5 callHiseq.scatterCount = 5
add(call,filter,callHiseq) add(call,filter,callHiseq)
@ -98,8 +98,8 @@ class expanded_targets extends QScript {
eval.rodBind :+= new RodBind("compHiSeq_atSites","vcf",callHiseq.out) eval.rodBind :+= new RodBind("compHiSeq_atSites","vcf",callHiseq.out)
eval.rodBind :+= new RodBind("compOMNI","vcf",new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/764samples.deduped.b37.annot.vcf")) eval.rodBind :+= new RodBind("compOMNI","vcf",new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/764samples.deduped.b37.annot.vcf"))
eval.out = swapExt(iList,".interval_list",".eval") eval.out = swapExt(iList,".interval_list",".eval")
eval.reportType = Option(org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.CSV) eval.reportType = org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.CSV
eval.memoryLimit = Some(4) eval.memoryLimit = 4
add(eval) add(eval)
eval.out eval.out

10
scala/qscript/oneoffs/chartl/old/private_mutations_old.q
View File

@ -165,8 +165,8 @@ class private_mutations_old extends QScript {
getVennExS.intervals :+= exome_single.out_list getVennExS.intervals :+= exome_single.out_list
getVennExS.reference_sequence = new File("/humgen/1kg/reference/human_g1k_v37.fasta") getVennExS.reference_sequence = new File("/humgen/1kg/reference/human_g1k_v37.fasta")
getVennExS.jarFile = new File("/humgen/gsa-scr1/chartl/sting/dist/GenomeAnalysisTK.jar") getVennExS.jarFile = new File("/humgen/gsa-scr1/chartl/sting/dist/GenomeAnalysisTK.jar")
getVennExS.genotypeMergeOptions = Some(VariantContextUtils.GenotypeMergeType.UNIQUIFY) getVennExS.genotypeMergeOptions = VariantContextUtils.GenotypeMergeType.UNIQUIFY
getVennExS.variantMergeOptions = Some(VariantContextUtils.VariantMergeType.UNION) getVennExS.variantMergeOptions = VariantContextUtils.VariantMergeType.UNION
getVennExS.out = new File(VCF_DIR + "g1k_exome_plus_lowpass.singlesample.merged.exome.sites.vcf") getVennExS.out = new File(VCF_DIR + "g1k_exome_plus_lowpass.singlesample.merged.exome.sites.vcf")
//add(getVennExS) //add(getVennExS)
@ -178,8 +178,8 @@ class private_mutations_old extends QScript {
getVennLPS.intervals :+= lowpass_single.out_list getVennLPS.intervals :+= lowpass_single.out_list
getVennLPS.reference_sequence = new File("/humgen/1kg/reference/human_g1k_v37.fasta") getVennLPS.reference_sequence = new File("/humgen/1kg/reference/human_g1k_v37.fasta")
getVennLPS.jarFile = new File("/humgen/gsa-scr1/chartl/sting/dist/GenomeAnalysisTK.jar") getVennLPS.jarFile = new File("/humgen/gsa-scr1/chartl/sting/dist/GenomeAnalysisTK.jar")
getVennLPS.genotypeMergeOptions = Some(VariantContextUtils.GenotypeMergeType.UNIQUIFY) getVennLPS.genotypeMergeOptions = VariantContextUtils.GenotypeMergeType.UNIQUIFY
getVennLPS.variantMergeOptions = Some(VariantContextUtils.VariantMergeType.UNION) getVennLPS.variantMergeOptions = VariantContextUtils.VariantMergeType.UNION
getVennLPS.out = new File(VCF_DIR + "g1k_exome_plus_lowpass.singlesample.merged.lowpass.sites.vcf") getVennLPS.out = new File(VCF_DIR + "g1k_exome_plus_lowpass.singlesample.merged.lowpass.sites.vcf")
add(getVennLPS) add(getVennLPS)
@ -397,7 +397,7 @@ class private_mutations_old extends QScript {
genotype.intervals :+= sites.out_list genotype.intervals :+= sites.out_list
genotype.out = new File(VCF_DIR+"g1k_lowpass.%s.exome_sites.vcf".format(s)) genotype.out = new File(VCF_DIR+"g1k_lowpass.%s.exome_sites.vcf".format(s))
genotype.input_file :+= bamList.outList genotype.input_file :+= bamList.outList
genotype.memoryLimit = Some(3) genotype.memoryLimit = 3
genotype.output_all_callable_bases = true genotype.output_all_callable_bases = true
add(genotype) add(genotype)

29
scala/qscript/oneoffs/chartl/omni_qc.q
View File

@ -5,7 +5,6 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils
import org.broadinstitute.sting.gatk.DownsampleType import org.broadinstitute.sting.gatk.DownsampleType
import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeCalculationModel.Model import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeCalculationModel.Model
import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
import org.broadinstitute.sting.queue.extensions.samtools._ import org.broadinstitute.sting.queue.extensions.samtools._
import org.broadinstitute.sting.queue.{QException, QScript} import org.broadinstitute.sting.queue.{QException, QScript}
import collection.JavaConversions._ import collection.JavaConversions._
@ -201,7 +200,7 @@ class omni_qc extends QScript {
eval1KG_exclude.evalModule :+= "GenotypeConcordance" eval1KG_exclude.evalModule :+= "GenotypeConcordance"
eval1KG_exclude.evalModule :+= "SimpleMetricsBySample" eval1KG_exclude.evalModule :+= "SimpleMetricsBySample"
eval1KG_exclude.reference_sequence = b36_ref eval1KG_exclude.reference_sequence = b36_ref
eval1KG_exclude.reportType = Some(VE2TemplateType.CSV) eval1KG_exclude.reportType = VE2TemplateType.CSV
eval1KG_exclude.intervalsString :+= pilot3_interval_list eval1KG_exclude.intervalsString :+= pilot3_interval_list
eval1KG_exclude.out = new File(eval_dir+"%s_vs_%s.%s".format("OMNI_764","Pilot3","exclude.mixups.eval.csv")) eval1KG_exclude.out = new File(eval_dir+"%s_vs_%s.%s".format("OMNI_764","Pilot3","exclude.mixups.eval.csv"))
@ -222,7 +221,7 @@ class omni_qc extends QScript {
combine.rodBind :+= new RodBind("CEU","VCF",gunzip_p1_ceu.outFile) combine.rodBind :+= new RodBind("CEU","VCF",gunzip_p1_ceu.outFile)
combine.rodBind :+= new RodBind("ASN","VCF",gunzip_p1_chb.outFile) combine.rodBind :+= new RodBind("ASN","VCF",gunzip_p1_chb.outFile)
combine.rodBind :+= new RodBind("YRI","VCF",gunzip_p1_yri.outFile) combine.rodBind :+= new RodBind("YRI","VCF",gunzip_p1_yri.outFile)
combine.genotypeMergeOptions = Some(VariantContextUtils.GenotypeMergeType.UNIQUIFY) combine.genotypeMergeOptions = VariantContextUtils.GenotypeMergeType.UNIQUIFY
combine.priority = "%s,%s,%s".format("CEU","ASN","YRI") combine.priority = "%s,%s,%s".format("CEU","ASN","YRI")
combine.out = new File(vcf_dir+"Pilot1_Populations_Combined.vcf") combine.out = new File(vcf_dir+"Pilot1_Populations_Combined.vcf")
@ -257,7 +256,7 @@ class omni_qc extends QScript {
vEval.evalModule :+= "SimpleMetricsBySample" vEval.evalModule :+= "SimpleMetricsBySample"
vEval.intervalsString :+= intervals vEval.intervalsString :+= intervals
vEval.reference_sequence = reference vEval.reference_sequence = reference
vEval.reportType = Some(VE2TemplateType.CSV) vEval.reportType = VE2TemplateType.CSV
vEval.out = new File(eval_dir+base+".eval.csv") vEval.out = new File(eval_dir+base+".eval.csv")
@ -318,8 +317,8 @@ class omni_qc extends QScript {
panelCombine.priority = if ( panelCombine.priority.equals("") ) p else panelCombine.priority + "," + p panelCombine.priority = if ( panelCombine.priority.equals("") ) p else panelCombine.priority + "," + p
} }
panelCombine.out = OMNI_b36_panel_vcf panelCombine.out = OMNI_b36_panel_vcf
panelCombine.genotypeMergeOptions = Some(VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE) panelCombine.genotypeMergeOptions = VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE
panelCombine.variantMergeOptions = Some(VariantContextUtils.VariantMergeType.UNION) panelCombine.variantMergeOptions = VariantContextUtils.VariantMergeType.UNION
panelCombine.setKey = "panel" panelCombine.setKey = "panel"
add(panelCombine) add(panelCombine)
@ -348,7 +347,7 @@ class omni_qc extends QScript {
eval.rodBind :+= new RodBind("comp%s".format(cBase),"VCF",compVCF) eval.rodBind :+= new RodBind("comp%s".format(cBase),"VCF",compVCF)
eval.noStandard = true eval.noStandard = true
eval.E :+= "AlleleFrequencyComparison" eval.E :+= "AlleleFrequencyComparison"
eval.reportType = Some(VE2TemplateType.CSV) eval.reportType = VE2TemplateType.CSV
eval.out = new File(eval_dir+"%s_vs_%s_allele_frequency.eval".format(eBase,cBase)) eval.out = new File(eval_dir+"%s_vs_%s_allele_frequency.eval".format(eBase,cBase))
add(eval) add(eval)
@ -358,7 +357,7 @@ class omni_qc extends QScript {
combine.rodBind :+= new RodBind(eBase,"VCF",evalVCF) combine.rodBind :+= new RodBind(eBase,"VCF",evalVCF)
combine.rodBind :+= new RodBind(cBase,"VCF",compVCF) combine.rodBind :+= new RodBind(cBase,"VCF",compVCF)
combine.out = new File(vcf_dir+"%s_plus_%s.vcf".format(eBase,cBase)) combine.out = new File(vcf_dir+"%s_plus_%s.vcf".format(eBase,cBase))
combine.genotypeMergeOptions = Some(VariantContextUtils.GenotypeMergeType.UNIQUIFY) combine.genotypeMergeOptions = VariantContextUtils.GenotypeMergeType.UNIQUIFY
combine.priority = "%s,%s".format(eBase,cBase) combine.priority = "%s,%s".format(eBase,cBase)
//add(combine) //add(combine)
@ -386,8 +385,8 @@ class omni_qc extends QScript {
combine.priority = "%s%s".format("beagle",c) combine.priority = "%s%s".format("beagle",c)
} }
} }
combine.genotypeMergeOptions = Some(VariantContextUtils.GenotypeMergeType.PRIORITIZE) combine.genotypeMergeOptions = VariantContextUtils.GenotypeMergeType.PRIORITIZE
combine.variantMergeOptions = Some(VariantContextUtils.VariantMergeType.UNION) combine.variantMergeOptions = VariantContextUtils.VariantMergeType.UNION
combine.out = swapExt(pilot1_with_na12878_vcf,".vcf",".beagle_refined_with_omni.vcf") combine.out = swapExt(pilot1_with_na12878_vcf,".vcf",".beagle_refined_with_omni.vcf")
@ -408,7 +407,7 @@ class omni_qc extends QScript {
eval.E :+= "GenotypeConcordance" eval.E :+= "GenotypeConcordance"
eval.out = new File(eval_dir+"NA12878.lowpass.beagle.vs.HiSeq.eval") eval.out = new File(eval_dir+"NA12878.lowpass.beagle.vs.HiSeq.eval")
eval.excludeIntervals :+= new File(pilot1_interval_list) eval.excludeIntervals :+= new File(pilot1_interval_list)
eval.reportType = Some(VE2TemplateType.CSV) eval.reportType = VE2TemplateType.CSV
add(eval) add(eval)
@ -420,7 +419,7 @@ class omni_qc extends QScript {
eval2.sample :+= "NA12878" eval2.sample :+= "NA12878"
eval2.out = new File(eval_dir+"NA12878.lowpass.nochip.vs.Hiseq.eval") eval2.out = new File(eval_dir+"NA12878.lowpass.nochip.vs.Hiseq.eval")
eval2.excludeIntervals :+= new File(pilot1_interval_list) eval2.excludeIntervals :+= new File(pilot1_interval_list)
eval2.reportType = Some(VE2TemplateType.CSV) eval2.reportType = VE2TemplateType.CSV
add(eval2) add(eval2)
@ -432,7 +431,7 @@ class omni_qc extends QScript {
eval3.sample :+= "NA12878" eval3.sample :+= "NA12878"
eval3.out = new File(eval_dir+"NA12878.lowpass.nochip.norefined.vs.Hiseq.eval") eval3.out = new File(eval_dir+"NA12878.lowpass.nochip.norefined.vs.Hiseq.eval")
eval3.excludeIntervals :+= new File(pilot1_interval_list) eval3.excludeIntervals :+= new File(pilot1_interval_list)
eval3.reportType = Some(VE2TemplateType.CSV) eval3.reportType = VE2TemplateType.CSV
add(eval3) add(eval3)
} }
@ -443,7 +442,7 @@ class omni_qc extends QScript {
beagleInput.intervalsString :+= chr beagleInput.intervalsString :+= chr
beagleInput.variantVCF = pilot1_with_na12878_vcf beagleInput.variantVCF = pilot1_with_na12878_vcf
beagleInput.rodBind :+= new RodBind("validation","VCF",omnivcf) beagleInput.rodBind :+= new RodBind("validation","VCF",omnivcf)
beagleInput.validation_genotype_ptrue = Some(0.99) beagleInput.validation_genotype_ptrue = 0.99
beagleInput.out = new File(scratch_dir+"/"+swapExt(beagleInput.variantVCF.getName,".vcf",".%s.beagle".format(chr))) beagleInput.out = new File(scratch_dir+"/"+swapExt(beagleInput.variantVCF.getName,".vcf",".%s.beagle".format(chr)))
println (beagleInput.out.getAbsolutePath) println (beagleInput.out.getAbsolutePath)
@ -451,7 +450,7 @@ class omni_qc extends QScript {
runBeagle.beagleInput = beagleInput.out runBeagle.beagleInput = beagleInput.out
runBeagle.beagleOutputBase = "Pilot1_NA12878_Beagle_with_OMNI_chr%s".format(chr) runBeagle.beagleOutputBase = "Pilot1_NA12878_Beagle_with_OMNI_chr%s".format(chr)
runBeagle.beagleMemoryGigs = 6 runBeagle.beagleMemoryGigs = 6
runBeagle.memoryLimit = Some(6) runBeagle.memoryLimit = 6
runBeagle.beagleOutputDir = "" runBeagle.beagleOutputDir = ""
runBeagle.freezeOutputs runBeagle.freezeOutputs

6
scala/qscript/oneoffs/chartl/private_mutations.q
View File

@ -61,7 +61,7 @@ class private_mutations extends QScript {
eval_all.noStandard = true eval_all.noStandard = true
eval_all.E :+= "ACTransitionTable" eval_all.E :+= "ACTransitionTable"
eval_all.out = swapExt(finalMergedVCF,".vcf",".perm.csv") eval_all.out = swapExt(finalMergedVCF,".vcf",".perm.csv")
eval_all.reportType = Some(org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.CSV) eval_all.reportType = org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.CSV
add(eval_all) add(eval_all)
@ -70,7 +70,7 @@ class private_mutations extends QScript {
eval_afr.rodBind :+= new RodBind("compEUR","VCF",extract_eur.outputVCF) eval_afr.rodBind :+= new RodBind("compEUR","VCF",extract_eur.outputVCF)
eval_afr.E :+= "ACTransitionTable" eval_afr.E :+= "ACTransitionTable"
eval_afr.out = swapExt(extract_afr.outputVCF,".vcf",".perm.csv") eval_afr.out = swapExt(extract_afr.outputVCF,".vcf",".perm.csv")
eval_afr.reportType = Some(org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.CSV) eval_afr.reportType = org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.CSV
eval_afr.noStandard = true eval_afr.noStandard = true
add(eval_afr) add(eval_afr)
@ -80,7 +80,7 @@ class private_mutations extends QScript {
eval_eur.rodBind :+= new RodBind("evalEUR","VCF",extract_eur.outputVCF) eval_eur.rodBind :+= new RodBind("evalEUR","VCF",extract_eur.outputVCF)
eval_eur.E :+= "ACTransitionTable" eval_eur.E :+= "ACTransitionTable"
eval_eur.out = swapExt(extract_eur.outputVCF,".vcf",".perm.csv") eval_eur.out = swapExt(extract_eur.outputVCF,".vcf",".perm.csv")
eval_eur.reportType = Some(org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.CSV) eval_eur.reportType = org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.CSV
eval_eur.noStandard = true eval_eur.noStandard = true
add(eval_eur) add(eval_eur)

29
scala/qscript/oneoffs/delangel/Phase1IndelCalling.scala
View File

@ -4,7 +4,6 @@ import org.broadinstitute.sting.datasources.pipeline.Pipeline
import org.broadinstitute.sting.gatk.DownsampleType import org.broadinstitute.sting.gatk.DownsampleType
import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel
import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
import org.broadinstitute.sting.queue.extensions.samtools._ import org.broadinstitute.sting.queue.extensions.samtools._
import org.broadinstitute.sting.queue.function.scattergather.{GatherFunction, CloneFunction, ScatterFunction} import org.broadinstitute.sting.queue.function.scattergather.{GatherFunction, CloneFunction, ScatterFunction}
import org.broadinstitute.sting.queue.{QException, QScript} import org.broadinstitute.sting.queue.{QException, QScript}
@ -55,7 +54,7 @@ class Phase1Calling extends QScript {
trait CommandLineGATKArgs extends CommandLineGATK { trait CommandLineGATKArgs extends CommandLineGATK {
this.jarFile = qscript.gatkJar this.jarFile = qscript.gatkJar
this.reference_sequence = qscript.reference this.reference_sequence = qscript.reference
this.memoryLimit = Some(3) this.memoryLimit = 3
this.jobTempDir = qscript.tmpDir this.jobTempDir = qscript.tmpDir
this.jobQueue = "gsa"; this.jobQueue = "gsa";
@ -102,15 +101,15 @@ class Phase1Calling extends QScript {
} }
call.dcov = Some( 50 ) call.dcov = 50
call.stand_call_conf = Some( 4.0 ) call.stand_call_conf = 4.0
call.stand_emit_conf = Some( 4.0 ) call.stand_emit_conf = 4.0
call.input_file :+= bamList call.input_file :+= bamList
call.out = rawCalls call.out = rawCalls
call.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF) call.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF
call.analysisName = baseName + "_UG" call.analysisName = baseName + "_UG"
call.rodBind :+= RodBind("dbsnp", "VCF", qscript.dbSNPIndels) call.rodBind :+= RodBind("dbsnp", "VCF", qscript.dbSNPIndels)
call.glm = Some(GenotypeLikelihoodsCalculationModel.Model.DINDEL) call.glm = GenotypeLikelihoodsCalculationModel.Model.DINDEL
var filter = new VariantFiltration with CommandLineGATKArgs var filter = new VariantFiltration with CommandLineGATKArgs
@ -132,9 +131,9 @@ class Phase1Calling extends QScript {
gvc.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun") gvc.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
gvc.analysisName = baseName + "_GVC" gvc.analysisName = baseName + "_GVC"
gvc.intervalsString ++= List(qscript.intervals) gvc.intervalsString ++= List(qscript.intervals)
//gvc.qual = Some(100) // clustering parameters to be updated soon pending new experimentation results //gvc.qual = 100 // clustering parameters to be updated soon pending new experimentation results
//gvc.std = Some(4.5) //gvc.std = 4.5
//gvc.mG = Some(6) //gvc.mG = 6
/* /*
var vr = new VariantRecalibrator with CommandLineGATKArgs var vr = new VariantRecalibrator with CommandLineGATKArgs
vr.rodBind :+= RodBind("1kg", "VCF", qscript.omni) vr.rodBind :+= RodBind("1kg", "VCF", qscript.omni)
@ -146,13 +145,13 @@ class Phase1Calling extends QScript {
vr.analysisName = baseName + "_VR" vr.analysisName = baseName + "_VR"
vr.intervalsString ++= List(qscript.intervals) vr.intervalsString ++= List(qscript.intervals)
vr.ignoreFilter ++= List("HARD_TO_VALIDATE") vr.ignoreFilter ++= List("HARD_TO_VALIDATE")
vr.target_titv = Some(2.3) vr.target_titv = 2.3
vr.sm = Some(org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.SelectionMetricType.TRUTH_SENSITIVITY) vr.sm = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.SelectionMetricType.TRUTH_SENSITIVITY
vr.tranche ++= List("0.1", "1.0", "2.0", "3.0", "5.0", "10.0", "100.0") vr.tranche ++= List("0.1", "1.0", "2.0", "3.0", "5.0", "10.0", "100.0")
vr.out = recalibratedCalls vr.out = recalibratedCalls
vr.priorDBSNP = Some(10.0) vr.priorDBSNP = 10.0
vr.priorHapMap = Some(12.0) vr.priorHapMap = 12.0
vr.prior1KG = Some(12.0) vr.prior1KG = 12.0
vr.tranchesFile = tranchesFile vr.tranchesFile = tranchesFile
add(call, filter, gvc, vr) */ add(call, filter, gvc, vr) */

12
scala/qscript/oneoffs/depristo/1kg_table1.scala
View File

@ -127,10 +127,10 @@ class VariantEval(vcfIn: String, evalOut: String, vcfType: String = "VCF") exten
this.rodBind :+= RodBind("eval", vcfType, vcfFile) this.rodBind :+= RodBind("eval", vcfType, vcfFile)
this.out = new File(evalOut) this.out = new File(evalOut)
this.DBSNP = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_b36.rod") this.DBSNP = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_b36.rod")
this.reportType = Some(VE2TemplateType.Grep) this.reportType = VE2TemplateType.Grep
this.noStandard = true; this.noStandard = true;
this.evalModule :+= "CompOverlap" this.evalModule :+= "CompOverlap"
this.memoryLimit = Some(3) this.memoryLimit = 3
override def dotString = "VariantEval: " + vcfFile.getName override def dotString = "VariantEval: " + vcfFile.getName
} }
@ -147,8 +147,8 @@ class StatPop(target: Target) extends CommandLineFunction {
class Combine(vcfsInArg: List[String], vcfOutPath: String) extends org.broadinstitute.sting.queue.extensions.gatk.CombineVariants with UNIVERSAL_GATK_ARGS { class Combine(vcfsInArg: List[String], vcfOutPath: String) extends org.broadinstitute.sting.queue.extensions.gatk.CombineVariants with UNIVERSAL_GATK_ARGS {
val vcfs = vcfsInArg.map((x: String) => new File(x)) val vcfs = vcfsInArg.map((x: String) => new File(x))
val vcfFile = new File(vcfOutPath) val vcfFile = new File(vcfOutPath)
this.variantmergeoption = Some(VariantMergeType.UNION) this.variantmergeoption = VariantMergeType.UNION
this.genotypemergeoption = Some(GenotypeMergeType.PRIORITIZE) this.genotypemergeoption = GenotypeMergeType.PRIORITIZE
this.out = vcfFile this.out = vcfFile
this.rodBind ++= vcfs.map( input => RodBind(input.getName,"VCF",input) ) this.rodBind ++= vcfs.map( input => RodBind(input.getName,"VCF",input) )
this.rod_priority_list = vcfs.map( _.getName ).mkString(",") this.rod_priority_list = vcfs.map( _.getName ).mkString(",")
@ -164,8 +164,8 @@ class DepthOfCoverage(bam: String, docOutPath: String, interval: String) extends
val bamFile = new File(bam) val bamFile = new File(bam)
this.omitIntervalStatistics = true this.omitIntervalStatistics = true
this.omitDepthOutputAtEachBase = true this.omitDepthOutputAtEachBase = true
this.minBaseQuality = Some(0) this.minBaseQuality = 0
this.minMappingQuality = Some(0) this.minMappingQuality = 0
this.out = new File(docOutPath) this.out = new File(docOutPath)
this.input_file :+= bamFile this.input_file :+= bamFile
if (interval != null) { if (interval != null) {

22
scala/qscript/oneoffs/depristo/CleaningTest.scala
View File

@ -4,8 +4,8 @@ package oneoffs.depristo
import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.queue.QScript
import collection.JavaConversions._ import collection.JavaConversions._
import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction import org.broadinstitute.sting.queue.extensions.picard.PicardBamFunction
import org.broadinstitute.sting.queue.function.JarCommandLineFunction import org.broadinstitute.sting.queue.function.JavaCommandLineFunction
class CleaningTest extends QScript { class CleaningTest extends QScript {
@ -45,7 +45,7 @@ class CleaningTest extends QScript {
trait CommandLineGATKArgs extends CommandLineGATK { trait CommandLineGATKArgs extends CommandLineGATK {
this.jarFile = qscript.gatkJar this.jarFile = qscript.gatkJar
this.reference_sequence = qscript.reference this.reference_sequence = qscript.reference
this.memoryLimit = Some(4) this.memoryLimit = 4
this.jobTempDir = qscript.tmpDir this.jobTempDir = qscript.tmpDir
} }
@ -62,7 +62,7 @@ class CleaningTest extends QScript {
target.input_file :+= bamList target.input_file :+= bamList
target.intervalsString :+= interval target.intervalsString :+= interval
target.out = targetIntervals target.out = targetIntervals
target.mismatchFraction = Some(0.0) target.mismatchFraction = 0.0
target.rodBind :+= RodBind("dbsnp", "VCF", qscript.dbSNP) target.rodBind :+= RodBind("dbsnp", "VCF", qscript.dbSNP)
target.rodBind :+= RodBind("indels3", "VCF", qscript.dindelEURCalls) target.rodBind :+= RodBind("indels3", "VCF", qscript.dindelEURCalls)
//target.jobName = baseName + ".target" //target.jobName = baseName + ".target"
@ -79,7 +79,7 @@ class CleaningTest extends QScript {
clean.out = if ( cm ) cleanedBam else new File(cleanedBam + ".intermediate.bam") clean.out = if ( cm ) cleanedBam else new File(cleanedBam + ".intermediate.bam")
clean.doNotUseSW = true clean.doNotUseSW = true
clean.constrainMovement = cm clean.constrainMovement = cm
clean.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF) clean.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF
clean.rodBind :+= RodBind("dbsnp", "VCF", qscript.dbSNP) clean.rodBind :+= RodBind("dbsnp", "VCF", qscript.dbSNP)
clean.rodBind :+= RodBind("indels3", "VCF", qscript.dindelEURCalls) clean.rodBind :+= RodBind("indels3", "VCF", qscript.dindelEURCalls)
//clean.sortInCoordinateOrderEvenThoughItIsHighlyUnsafe = true //clean.sortInCoordinateOrderEvenThoughItIsHighlyUnsafe = true
@ -90,7 +90,7 @@ class CleaningTest extends QScript {
if ( ! cm ) { if ( ! cm ) {
// Explicitly run fix mates if the function won't be scattered. // Explicitly run fix mates if the function won't be scattered.
val fixMates = new PicardBamJarFunction { val fixMates = new PicardBamFunction {
// Declare inputs/outputs for dependency tracking. // Declare inputs/outputs for dependency tracking.
@Input(doc="unfixed bam") var unfixed: File = _ @Input(doc="unfixed bam") var unfixed: File = _
@Output(doc="fixed bam") var fixed: File = _ @Output(doc="fixed bam") var fixed: File = _
@ -99,7 +99,7 @@ class CleaningTest extends QScript {
} }
//fixMates.jobOutputFile = new File(".queue/logs/Cleaning/%s/FixMates.out".format(sampleId)) //fixMates.jobOutputFile = new File(".queue/logs/Cleaning/%s/FixMates.out".format(sampleId))
fixMates.memoryLimit = Some(4) fixMates.memoryLimit = 4
fixMates.jarFile = qscript.picardFixMatesJar fixMates.jarFile = qscript.picardFixMatesJar
fixMates.unfixed = clean.out fixMates.unfixed = clean.out
fixMates.fixed = cleanedBam fixMates.fixed = cleanedBam
@ -110,7 +110,7 @@ class CleaningTest extends QScript {
add(fixMates) add(fixMates)
} }
val validate = new JarCommandLineFunction { val validate = new JavaCommandLineFunction {
// Declare inputs/outputs for dependency tracking. // Declare inputs/outputs for dependency tracking.
@Input(doc="unfixed bam") var unfixed: File = _ @Input(doc="unfixed bam") var unfixed: File = _
def inputBams = List(unfixed) def inputBams = List(unfixed)
@ -119,12 +119,12 @@ class CleaningTest extends QScript {
} }
//fixMates.jobOutputFile = new File(".queue/logs/Cleaning/%s/FixMates.out".format(sampleId)) //fixMates.jobOutputFile = new File(".queue/logs/Cleaning/%s/FixMates.out".format(sampleId))
validate.memoryLimit = Some(2) validate.memoryLimit = 2
validate.jarFile = qscript.picardValidateJar validate.jarFile = qscript.picardValidateJar
validate.unfixed = cleanedBam validate.unfixed = cleanedBam
add(validate) add(validate)
val toQueryName = new PicardBamJarFunction { val toQueryName = new PicardBamFunction {
// Declare inputs/outputs for dependency tracking. // Declare inputs/outputs for dependency tracking.
@Input(doc="coordiante bam") var cobam: File = _ @Input(doc="coordiante bam") var cobam: File = _
@Output(doc="query bam") var qnbam: File = _ @Output(doc="query bam") var qnbam: File = _
@ -133,7 +133,7 @@ class CleaningTest extends QScript {
} }
//fixMates.jobOutputFile = new File(".queue/logs/Cleaning/%s/FixMates.out".format(sampleId)) //fixMates.jobOutputFile = new File(".queue/logs/Cleaning/%s/FixMates.out".format(sampleId))
toQueryName.memoryLimit = Some(4) toQueryName.memoryLimit = 4
toQueryName.jarFile = qscript.picardSortSamJar toQueryName.jarFile = qscript.picardSortSamJar
toQueryName.cobam = cleanedBam toQueryName.cobam = cleanedBam
toQueryName.qnbam = new File(cleanedBam.getAbsolutePath + ".qn.bam") toQueryName.qnbam = new File(cleanedBam.getAbsolutePath + ".qn.bam")

14
scala/qscript/oneoffs/depristo/RefineGenotypesWithBeagle.q
View File

@ -36,7 +36,7 @@ class RefineGenotypesWithBeagle extends QScript {
trait GATKArgs extends CommandLineGATK { trait GATKArgs extends CommandLineGATK {
this.reference_sequence = qscript.reference this.reference_sequence = qscript.reference
this.jarFile = qscript.gatkJarFile this.jarFile = qscript.gatkJarFile
this.memoryLimit = Some(2) this.memoryLimit = 2
} }
// -------------------------------------------------------------------------------- // --------------------------------------------------------------------------------
@ -48,9 +48,9 @@ class RefineGenotypesWithBeagle extends QScript {
class GenotypeBAMAtSites(@Input bam: File, @Input sitesVCF: File, @Output genotypesVCF: File) extends UnifiedGenotyper with GATKArgs { class GenotypeBAMAtSites(@Input bam: File, @Input sitesVCF: File, @Output genotypesVCF: File) extends UnifiedGenotyper with GATKArgs {
this.input_file = List(bam) this.input_file = List(bam)
this.o = genotypesVCF this.o = genotypesVCF
this.stand_call_conf = Some(0.0) this.stand_call_conf = 0.0
this.out_mode = Some(org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES) this.out_mode = org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES
this.gt_mode = Some(org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) this.gt_mode = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES
this.rodBind :+= new RodBind("alleles","VCF",sitesVCF) this.rodBind :+= new RodBind("alleles","VCF",sitesVCF)
// we only want chromosome counts annotations // we only want chromosome counts annotations
@ -62,7 +62,7 @@ class RefineGenotypesWithBeagle extends QScript {
// make sure we have the right intervals // make sure we have the right intervals
if ( interval != null ) { if ( interval != null ) {
this.intervalsString = List(interval) this.intervalsString = List(interval)
this.BTIMR = Some(org.broadinstitute.sting.utils.interval.IntervalSetRule.INTERSECTION) this.BTIMR = org.broadinstitute.sting.utils.interval.IntervalSetRule.INTERSECTION
} }
} }
@ -73,7 +73,7 @@ class RefineGenotypesWithBeagle extends QScript {
// -------------------------------------------------------------------------------- // --------------------------------------------------------------------------------
class BeagleCommand(outputBase: String) extends CommandLineFunction { class BeagleCommand(outputBase: String) extends CommandLineFunction {
this.memoryLimit = Some(BEAGLE_MEM_IN_GB) this.memoryLimit = BEAGLE_MEM_IN_GB
// Note: These get set // Note: These get set
@Output val beaglePhasedFile: File = new File(outputBase +".phased.gz") @Output val beaglePhasedFile: File = new File(outputBase +".phased.gz")
@ -151,7 +151,7 @@ class RefineGenotypesWithBeagle extends QScript {
if ( interval != null ) evalBeagle.intervalsString = List(interval) if ( interval != null ) evalBeagle.intervalsString = List(interval)
evalBeagle.variantVCF = evalVCF evalBeagle.variantVCF = evalVCF
evalBeagle.out = swapExt(outputVCF,".vcf",".unphased.beagle") evalBeagle.out = swapExt(outputVCF,".vcf",".unphased.beagle")
evalBeagle.bs = Some(percentLeftOut) evalBeagle.bs = percentLeftOut
evalBeagle.bsvcf = swapExt(outputVCF,".vcf",".missing.vcf") evalBeagle.bsvcf = swapExt(outputVCF,".vcf",".missing.vcf")
evalBeagle.missing = MISSING_KEY evalBeagle.missing = MISSING_KEY
//evalBeagle.isIntermediate = true //evalBeagle.isIntermediate = true

15
scala/qscript/oneoffs/depristo/VQSRCutByNRS.scala
View File

@ -1,4 +1,3 @@
import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction
import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.queue.QScript
@ -18,7 +17,7 @@ class VQSRCutByNRS extends QScript {
@Argument(fullName = "prefix", doc="Prefix argument", required=false) @Argument(fullName = "prefix", doc="Prefix argument", required=false)
var prefix: String = "" var prefix: String = ""
trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; jarFile = gatkJarFile; memoryLimit = Some(3) } trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; jarFile = gatkJarFile; memoryLimit = 3 }
class Target(val name: String, val reference: File, val rodName: String, val VCF: File, val intervals: Option[String], val titvTarget: Double) { class Target(val name: String, val reference: File, val rodName: String, val VCF: File, val intervals: Option[String], val titvTarget: Double) {
def clusterFile = new File(name + ".clusters") def clusterFile = new File(name + ".clusters")
@ -67,9 +66,9 @@ class GenerateVariantClusters(t: Target) extends org.broadinstitute.sting.queue.
this.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun") this.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
this.analysisName = t.name + "_Cluster" this.analysisName = t.name + "_Cluster"
if ( t.intervals != None ) this.intervalsString ++= List(t.intervals.get) if ( t.intervals != None ) this.intervalsString ++= List(t.intervals.get)
this.qual = Some(300) this.qual = 300
this.std = Some(3.5) this.std = 3.5
this.mG = Some(16) // v2 calls this.mG = 16 // v2 calls
// ignores // ignores
this.ignoreFilter ++= FiltersToIgnore this.ignoreFilter ++= FiltersToIgnore
} }
@ -86,8 +85,8 @@ class VariantRecalibratorBase(t: Target, ans: List[String]) extends org.broadins
if ( t.intervals != None ) this.intervalsString ++= List(t.intervals.get) if ( t.intervals != None ) this.intervalsString ++= List(t.intervals.get)
this.ignoreFilter ++= FiltersToIgnore this.ignoreFilter ++= FiltersToIgnore
this.ignoreFilter ++= List("HARD_TO_VALIDATE") this.ignoreFilter ++= List("HARD_TO_VALIDATE")
this.priorDBSNP = Some(2.0) this.priorDBSNP = 2.0
this.priorHapMap = Some(2.0) this.priorHapMap = 2.0
this.target_titv = t.titvTarget this.target_titv = t.titvTarget
this.use_annotation ++= ans this.use_annotation ++= ans
this.out = new File("/dev/null") this.out = new File("/dev/null")
@ -100,7 +99,7 @@ class VariantRecalibratorTiTv(t: Target, ans: List[String], prefix: String) exte
} }
class VariantRecalibratorNRS(t: Target, ans: List[String], prefix: String) extends VariantRecalibratorBase(t,ans) { class VariantRecalibratorNRS(t: Target, ans: List[String], prefix: String) extends VariantRecalibratorBase(t,ans) {
this.sm = Some(org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.SelectionMetricType.TRUTH_SENSITIVITY) this.sm = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.SelectionMetricType.TRUTH_SENSITIVITY
this.tranche ++= List("50", "25", "10", "5", "2", "1", "0.5", "0.1") this.tranche ++= List("50", "25", "10", "5", "2", "1", "0.5", "0.1")
//this.out = new File(t.name + ".ts.recalibrated.vcf") //this.out = new File(t.name + ".ts.recalibrated.vcf")
this.tranchesFile = new File(t.name + prefix + ".ts.tranches") this.tranchesFile = new File(t.name + prefix + ".ts.tranches")

16
scala/qscript/oneoffs/depristo/manySampleUGPerformance.scala
View File

@ -29,7 +29,7 @@ class ManySampleUGPerformanceTesting extends QScript {
this.intervals = List(new File(TARGET_INTERVAL)); this.intervals = List(new File(TARGET_INTERVAL));
this.reference_sequence = referenceFile; this.reference_sequence = referenceFile;
this.jobQueue = "gsa"; this.jobQueue = "gsa";
this.memoryLimit = Some(4) this.memoryLimit = 4
//this.commandDirectory = new File("results"); //this.commandDirectory = new File("results");
} }
@ -52,11 +52,11 @@ class ManySampleUGPerformanceTesting extends QScript {
// SNP calling // SNP calling
//add(new Call(sublist.list, nSamples, "dynamic_merge")) //add(new Call(sublist.list, nSamples, "dynamic_merge"))
val gt = new Call(bams, nSamples, name); val gt = new Call(bams, nSamples, name);
gt.exactCalculation = Some(org.broadinstitute.sting.gatk.walkers.genotyper.ExactAFCalculationModel.ExactCalculation.N2_GOLD_STANDARD) gt.exactCalculation = org.broadinstitute.sting.gatk.walkers.genotyper.ExactAFCalculationModel.ExactCalculation.N2_GOLD_STANDARD
add(gt) add(gt)
val gtLinear = new Call(bams, nSamples, name + "_linear"); val gtLinear = new Call(bams, nSamples, name + "_linear");
gtLinear.exactCalculation = Some(org.broadinstitute.sting.gatk.walkers.genotyper.ExactAFCalculationModel.ExactCalculation.LINEAR_EXPERIMENTAL) gtLinear.exactCalculation = org.broadinstitute.sting.gatk.walkers.genotyper.ExactAFCalculationModel.ExactCalculation.LINEAR_EXPERIMENTAL
add(gtLinear) add(gtLinear)
// SNP calling -- no annotations // SNP calling -- no annotations
@ -74,24 +74,24 @@ class ManySampleUGPerformanceTesting extends QScript {
} }
class MergeBAMs(bamList: File) extends PrintReads with UNIVERSAL_GATK_ARGS { class MergeBAMs(bamList: File) extends PrintReads with UNIVERSAL_GATK_ARGS {
this.memoryLimit = Some(3) this.memoryLimit = 3
this.input_file :+= bamList this.input_file :+= bamList
this.memoryLimit = Some(16) this.memoryLimit = 16
this.o = new File(MERGED_DIR + "/" + bamList.getName + ".bam") this.o = new File(MERGED_DIR + "/" + bamList.getName + ".bam")
} }
class Call(@Input(doc="foo") bamList: File, n: Int, name: String) extends UnifiedGenotyper with UNIVERSAL_GATK_ARGS { class Call(@Input(doc="foo") bamList: File, n: Int, name: String) extends UnifiedGenotyper with UNIVERSAL_GATK_ARGS {
@Output(doc="foo") var outVCF: File = new File("%s.%d.%s.vcf".format(bamList.getName, n, name)) @Output(doc="foo") var outVCF: File = new File("%s.%d.%s.vcf".format(bamList.getName, n, name))
this.input_file :+= bamList this.input_file :+= bamList
this.stand_call_conf = Option(10.0) this.stand_call_conf = 10.0
this.dcov = Option(DCOV); this.dcov = DCOV;
this.o = outVCF this.o = outVCF
} }
class MyCountLoci(@Input(doc="foo") bamList: File, n: Int, name: String) extends CountLoci with UNIVERSAL_GATK_ARGS { class MyCountLoci(@Input(doc="foo") bamList: File, n: Int, name: String) extends CountLoci with UNIVERSAL_GATK_ARGS {
@Output(doc="foo") var outFile: File = new File("%s.%d.%s.txt".format(bamList.getName, n, name)) @Output(doc="foo") var outFile: File = new File("%s.%d.%s.txt".format(bamList.getName, n, name))
this.input_file :+= bamList this.input_file :+= bamList
this.dcov = Option(DCOV); this.dcov = DCOV;
this.o = outFile this.o = outFile
} }

8
scala/qscript/oneoffs/depristo/resequencingSamples1KG.scala
View File

@ -20,8 +20,8 @@ class resequencingSamples1KG extends QScript {
this.intervals = List(new File(TARGET_INTERVAL)); this.intervals = List(new File(TARGET_INTERVAL));
this.reference_sequence = referenceFile; this.reference_sequence = referenceFile;
this.jobQueue = "gsa"; this.jobQueue = "gsa";
this.et = Option(org.broadinstitute.sting.gatk.phonehome.GATKRunReport.PhoneHomeOption.STANDARD); this.et = org.broadinstitute.sting.gatk.phonehome.GATKRunReport.PhoneHomeOption.STANDARD;
this.dcov = Option(50); this.dcov = 50;
} }
def script = { def script = {
@ -30,10 +30,10 @@ class resequencingSamples1KG extends QScript {
} }
class MyQSample(@Input(doc="foo") bamList: File) extends QSample with UNIVERSAL_GATK_ARGS { class MyQSample(@Input(doc="foo") bamList: File) extends QSample with UNIVERSAL_GATK_ARGS {
this.memoryLimit = Some(4) this.memoryLimit = 4
this.input_file :+= bamList this.input_file :+= bamList
//this.BTI = "genotypes" //this.BTI = "genotypes"
this.nt = Option(10) this.nt = 10
this.rodBind :+= RodBind("genotypes", "VCF", HM3) this.rodBind :+= RodBind("genotypes", "VCF", HM3)
this.o = new File("%s.qsample".format(bamList.getName)) this.o = new File("%s.qsample".format(bamList.getName))
} }

4
scala/qscript/oneoffs/fromer/PhaseSamples.scala
View File

@ -38,7 +38,7 @@ class PhaseSamples extends QScript {
this.intervalsString = List(qscript.intervals) this.intervalsString = List(qscript.intervals)
this.jarFile = qscript.gatkJarFile this.jarFile = qscript.gatkJarFile
this.reference_sequence = qscript.referenceFile this.reference_sequence = qscript.referenceFile
this.memoryLimit = Some(3) this.memoryLimit = 3
this.logging_level = "INFO" this.logging_level = "INFO"
} }
@ -102,7 +102,7 @@ class PhaseSamples extends QScript {
// add the master call: // add the master call:
this.rodBind :+= RodBind("master", "VCF", masterCalls) this.rodBind :+= RodBind("master", "VCF", masterCalls)
this.variantMergeOptions = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.MASTER) this.variantMergeOptions = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.MASTER
this.out = outputPhased this.out = outputPhased
} }

8
scala/qscript/oneoffs/fromer/ReadDepthCNVanalysis.scala
View File

@ -48,7 +48,7 @@ class ReadDepthCNVanalysis extends QScript {
this.intervalsString = List(qscript.intervals) this.intervalsString = List(qscript.intervals)
this.jarFile = qscript.gatkJarFile this.jarFile = qscript.gatkJarFile
this.reference_sequence = qscript.referenceFile this.reference_sequence = qscript.referenceFile
//this.memoryLimit = Some(3) //this.memoryLimit = 3
this.logging_level = "INFO" this.logging_level = "INFO"
} }
@ -98,8 +98,8 @@ class ReadDepthCNVanalysis extends QScript {
this.input_file = t.bams this.input_file = t.bams
this.downsample_to_coverage = Some(MAX_DEPTH) this.downsample_to_coverage = MAX_DEPTH
this.downsampling_type = Some(DownsampleType.BY_SAMPLE) this.downsampling_type = DownsampleType.BY_SAMPLE
this.scatterCount = scatterCountInput this.scatterCount = scatterCountInput
this.scatterClass = classOf[IntervalScatterFunction] this.scatterClass = classOf[IntervalScatterFunction]
@ -132,6 +132,6 @@ class ReadDepthCNVanalysis extends QScript {
def commandLine = command def commandLine = command
// Since loading ALL of the output into the perl script can take significant memory: // Since loading ALL of the output into the perl script can take significant memory:
this.memoryLimit = Some(9) this.memoryLimit = 9
} }
} }

4
scala/qscript/oneoffs/hanna/DoC.scala
View File

@ -35,14 +35,14 @@ class DoC extends QScript {
this.jarFile = DoC.this.gatkJar this.jarFile = DoC.this.gatkJar
this.reference_sequence = DoC.this.referenceFile this.reference_sequence = DoC.this.referenceFile
this.intervalsString = DoC.this.intervalsString this.intervalsString = DoC.this.intervalsString
this.memoryLimit = Some(8) this.memoryLimit = 8
} }
def script = { def script = {
// Create the four function that we can run. // Create the four function that we can run.
val doc = new DepthOfCoverage with DepthOfCoverageArguments val doc = new DepthOfCoverage with DepthOfCoverageArguments
doc.downsampling_type = Some(DownsampleType.NONE) doc.downsampling_type = DownsampleType.NONE
doc.omitLocusTable = true doc.omitLocusTable = true
doc.omitIntervals = true doc.omitIntervals = true
doc.omitSampleSummary = true doc.omitSampleSummary = true

4
scala/qscript/oneoffs/kshakir/UGMemoryTests.scala
View File

@ -35,13 +35,13 @@ class UGMemoryTests extends QScript {
snps.jobOutputFile = new File(dir, "UnifiedGenotyper.out") snps.jobOutputFile = new File(dir, "UnifiedGenotyper.out")
snps.out = new File(dir, "UnifiedGenotyper.vcf") snps.out = new File(dir, "UnifiedGenotyper.vcf")
snps.input_file = squid1Bams.take(numBams/2) ++ squid2Bams.take(numBams/2) snps.input_file = squid1Bams.take(numBams/2) ++ squid2Bams.take(numBams/2)
snps.memoryLimit = Some(memoryLimit) snps.memoryLimit = memoryLimit
snps.jarFile = qscript.gatkJar snps.jarFile = qscript.gatkJar
snps.reference_sequence = pipeline.getProject.getReferenceFile snps.reference_sequence = pipeline.getProject.getReferenceFile
snps.intervals = List(pipeline.getProject.getIntervalList) snps.intervals = List(pipeline.getProject.getIntervalList)
snps.rodBind :+= new RodBind("dbsnp", pipeline.getProject.getGenotypeDbsnpType, pipeline.getProject.getGenotypeDbsnp) snps.rodBind :+= new RodBind("dbsnp", pipeline.getProject.getGenotypeDbsnpType, pipeline.getProject.getGenotypeDbsnp)
snps.downsample_to_coverage = Some(qscript.downsampling_coverage) snps.downsample_to_coverage = qscript.downsampling_coverage
snps.annotation ++= List("AlleleBalance") snps.annotation ++= List("AlleleBalance")
snps.group :+= "Standard" snps.group :+= "Standard"

4
scala/qscript/oneoffs/kshakir/linearindexbintests/LinearIndexBinTests.scala
View File

@ -49,10 +49,10 @@ class LinearIndexBinTests extends QScript {
countRod.jarFile = qscript.gatkJar countRod.jarFile = qscript.gatkJar
countRod.reference_sequence = reference countRod.reference_sequence = reference
countRod.memoryLimit = Some(memoryLimit) countRod.memoryLimit = memoryLimit
// Some of the BED files don't have a chrM, which makes the GATK angry. Run unsafe. // Some of the BED files don't have a chrM, which makes the GATK angry. Run unsafe.
countRod.U = Some(org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.ALL) countRod.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.ALL
for ((rodFile, index) <- rodFiles.zipWithIndex) { for ((rodFile, index) <- rodFiles.zipWithIndex) {
val rodType = rodFile.getName.split("\\.").last val rodType = rodFile.getName.split("\\.").last

31
scala/qscript/oneoffs/rpoplin/ASHGcalling.scala
View File

@ -3,7 +3,6 @@ import org.broadinstitute.sting.datasources.pipeline.Pipeline
import org.broadinstitute.sting.gatk.DownsampleType import org.broadinstitute.sting.gatk.DownsampleType
import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeCalculationModel.Model import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeCalculationModel.Model
import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
import org.broadinstitute.sting.queue.extensions.samtools._ import org.broadinstitute.sting.queue.extensions.samtools._
import org.broadinstitute.sting.queue.{QException, QScript} import org.broadinstitute.sting.queue.{QException, QScript}
import collection.JavaConversions._ import collection.JavaConversions._
@ -42,7 +41,7 @@ class ASHGcalling extends QScript {
trait CommandLineGATKArgs extends CommandLineGATK { trait CommandLineGATKArgs extends CommandLineGATK {
this.jarFile = qscript.gatkJar this.jarFile = qscript.gatkJar
this.reference_sequence = qscript.reference this.reference_sequence = qscript.reference
this.memoryLimit = Some(2) this.memoryLimit = 2
this.DBSNP = qscript.dbSNP this.DBSNP = qscript.dbSNP
this.jobTempDir = qscript.tmpDir this.jobTempDir = qscript.tmpDir
} }
@ -84,8 +83,8 @@ class ASHGcalling extends QScript {
combineVariants = new CombineVariants with CommandLineGATKArgs combineVariants = new CombineVariants with CommandLineGATKArgs
combineVariants.rodBind = vcfChunks combineVariants.rodBind = vcfChunks
combineVariants.out = new TaggedFile(qscript.baseName + ".chr" + qscript.chr.toString + ".filtered.vcf", "vcf") combineVariants.out = new TaggedFile(qscript.baseName + ".chr" + qscript.chr.toString + ".filtered.vcf", "vcf")
combineVariants.variantmergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION) combineVariants.variantmergeoption = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION
combineVariants.genotypemergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.GenotypeMergeType.UNSORTED) combineVariants.genotypemergeoption = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.GenotypeMergeType.UNSORTED
combineVariants.setKey = "null" combineVariants.setKey = "null"
add(combineVariants) add(combineVariants)
*/ */
@ -104,16 +103,16 @@ class ASHGcalling extends QScript {
// 1.) Clean at known indels // 1.) Clean at known indels
var clean = new IndelRealigner with CommandLineGATKArgs var clean = new IndelRealigner with CommandLineGATKArgs
val cleanedBam = new File(baseTmpName + "cleaned.bam") val cleanedBam = new File(baseTmpName + "cleaned.bam")
clean.memoryLimit = Some(4) clean.memoryLimit = 4
clean.input_file :+= bamList clean.input_file :+= bamList
clean.intervalsString :+= interval clean.intervalsString :+= interval
clean.targetIntervals = qscript.targetIntervals clean.targetIntervals = qscript.targetIntervals
clean.out = cleanedBam clean.out = cleanedBam
clean.rodBind :+= RodBind("indels", "VCF", qscript.dindelCalls) clean.rodBind :+= RodBind("indels", "VCF", qscript.dindelCalls)
clean.knownsOnly = true clean.knownsOnly = true
clean.LOD = Some(1.0) clean.LOD = 1.0
clean.sortInCoordinateOrderEvenThoughItIsHighlyUnsafe = true clean.sortInCoordinateOrderEvenThoughItIsHighlyUnsafe = true
clean.compress = Some(2) clean.compress = 2
clean.jobName = baseName + population + ".clean" clean.jobName = baseName + population + ".clean"
//clean.stripBam = true //clean.stripBam = true
//clean.fileSystemUsage = "indium" //clean.fileSystemUsage = "indium"
@ -121,7 +120,7 @@ class ASHGcalling extends QScript {
// 2.) Apply BAQ calculation // 2.) Apply BAQ calculation
var baq = new SamtoolsBaqFunction var baq = new SamtoolsBaqFunction
val baqedBam = new File(baseTmpName + "cleaned.baq.bam") val baqedBam = new File(baseTmpName + "cleaned.baq.bam")
baq.memoryLimit = Some(4) baq.memoryLimit = 4
baq.in_bam = cleanedBam baq.in_bam = cleanedBam
baq.out_bam = baqedBam baq.out_bam = baqedBam
baq.jobName = baseName + population + ".baq" baq.jobName = baseName + population + ".baq"
@ -154,22 +153,22 @@ class ASHGcalling extends QScript {
} }
// 4.) Call with UGv2 // 4.) Call with UGv2
call.memoryLimit = Some(4) call.memoryLimit = 4
call.intervalsString :+= interval call.intervalsString :+= interval
call.out = rawCalls call.out = rawCalls
call.dcov = Some(50) call.dcov = 50
call.standard_min_confidence_threshold_for_calling = Some(50) call.standard_min_confidence_threshold_for_calling = 50
call.standard_min_confidence_threshold_for_emitting = Some(30) call.standard_min_confidence_threshold_for_emitting = 30
call.min_mapping_quality_score = Some(20) call.min_mapping_quality_score = 20
call.min_base_quality_score = Some(20) call.min_base_quality_score = 20
call.pnrm = Some(org.broadinstitute.sting.playground.gatk.walkers.genotyper.AlleleFrequencyCalculationModel.Model.GRID_SEARCH) call.pnrm = org.broadinstitute.sting.playground.gatk.walkers.genotyper.AlleleFrequencyCalculationModel.Model.GRID_SEARCH
call.jobName = baseName + "call" call.jobName = baseName + "call"
//call.fileSystemUsage = "iodine" //call.fileSystemUsage = "iodine"
// 5b.) Filter near indels and HARD_TO_VALIDATE // 5b.) Filter near indels and HARD_TO_VALIDATE
var filter = new VariantFiltration with CommandLineGATKArgs var filter = new VariantFiltration with CommandLineGATKArgs
val filteredCalls = new File(baseName + "filtered.vcf") val filteredCalls = new File(baseName + "filtered.vcf")
filter.memoryLimit = Some(1) filter.memoryLimit = 1
filter.out = filteredCalls filter.out = filteredCalls
filter.intervalsString :+= interval filter.intervalsString :+= interval
filter.variantVCF = rawCalls filter.variantVCF = rawCalls

27
scala/qscript/oneoffs/rpoplin/Phase1Calling.scala
View File

@ -2,7 +2,6 @@ import net.sf.picard.reference.FastaSequenceFile
import org.broadinstitute.sting.datasources.pipeline.Pipeline import org.broadinstitute.sting.datasources.pipeline.Pipeline
import org.broadinstitute.sting.gatk.DownsampleType import org.broadinstitute.sting.gatk.DownsampleType
import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
import org.broadinstitute.sting.queue.extensions.samtools._ import org.broadinstitute.sting.queue.extensions.samtools._
import org.broadinstitute.sting.queue.{QException, QScript} import org.broadinstitute.sting.queue.{QException, QScript}
import collection.JavaConversions._ import collection.JavaConversions._
@ -51,7 +50,7 @@ class Phase1Calling extends QScript {
trait CommandLineGATKArgs extends CommandLineGATK { trait CommandLineGATKArgs extends CommandLineGATK {
this.jarFile = qscript.gatkJar this.jarFile = qscript.gatkJar
this.reference_sequence = qscript.reference this.reference_sequence = qscript.reference
this.memoryLimit = Some(3) this.memoryLimit = 3
this.jobTempDir = qscript.tmpDir this.jobTempDir = qscript.tmpDir
this.DBSNP = qscript.dbSNP this.DBSNP = qscript.dbSNP
} }
@ -79,12 +78,12 @@ class Phase1Calling extends QScript {
var call = new UnifiedGenotyper with CommandLineGATKArgs var call = new UnifiedGenotyper with CommandLineGATKArgs
call.intervalsString ++= List(qscript.intervals) call.intervalsString ++= List(qscript.intervals)
call.scatterCount = 63 // the smallest interval list has 63 intervals, one for each Mb on chr20 call.scatterCount = 63 // the smallest interval list has 63 intervals, one for each Mb on chr20
call.dcov = Some( 50 ) call.dcov = 50
call.stand_call_conf = Some( 4.0 ) call.stand_call_conf = 4.0
call.stand_emit_conf = Some( 4.0 ) call.stand_emit_conf = 4.0
call.input_file :+= bamList call.input_file :+= bamList
call.out = rawCalls call.out = rawCalls
call.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY) call.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY
call.analysisName = baseName + "_UG" call.analysisName = baseName + "_UG"
var filter = new VariantFiltration with CommandLineGATKArgs var filter = new VariantFiltration with CommandLineGATKArgs
@ -106,9 +105,9 @@ class Phase1Calling extends QScript {
gvc.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun") gvc.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
gvc.analysisName = baseName + "_GVC" gvc.analysisName = baseName + "_GVC"
gvc.intervalsString ++= List(qscript.intervals) gvc.intervalsString ++= List(qscript.intervals)
gvc.qual = Some(100) // clustering parameters to be updated soon pending new experimentation results gvc.qual = 100 // clustering parameters to be updated soon pending new experimentation results
gvc.std = Some(4.5) gvc.std = 4.5
gvc.mG = Some(6) gvc.mG = 6
var vr = new VariantRecalibrator with CommandLineGATKArgs var vr = new VariantRecalibrator with CommandLineGATKArgs
vr.rodBind :+= RodBind("1kg", "VCF", qscript.omni) vr.rodBind :+= RodBind("1kg", "VCF", qscript.omni)
@ -120,13 +119,13 @@ class Phase1Calling extends QScript {
vr.analysisName = baseName + "_VR" vr.analysisName = baseName + "_VR"
vr.intervalsString ++= List(qscript.intervals) vr.intervalsString ++= List(qscript.intervals)
vr.ignoreFilter ++= List("HARD_TO_VALIDATE") vr.ignoreFilter ++= List("HARD_TO_VALIDATE")
vr.target_titv = Some(2.3) vr.target_titv = 2.3
vr.sm = Some(org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.SelectionMetricType.TRUTH_SENSITIVITY) vr.sm = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.SelectionMetricType.TRUTH_SENSITIVITY
vr.tranche ++= List("0.1", "1.0", "2.0", "3.0", "5.0", "10.0", "100.0") vr.tranche ++= List("0.1", "1.0", "2.0", "3.0", "5.0", "10.0", "100.0")
vr.out = recalibratedCalls vr.out = recalibratedCalls
vr.priorDBSNP = Some(10.0) vr.priorDBSNP = 10.0
vr.priorHapMap = Some(12.0) vr.priorHapMap = 12.0
vr.prior1KG = Some(12.0) vr.prior1KG = 12.0
vr.tranchesFile = tranchesFile vr.tranchesFile = tranchesFile
add(call, filter, gvc, vr) add(call, filter, gvc, vr)

11
scala/qscript/oneoffs/rpoplin/Phase1Cleaning.scala
View File

@ -2,7 +2,6 @@ import net.sf.picard.reference.FastaSequenceFile
import org.broadinstitute.sting.datasources.pipeline.Pipeline import org.broadinstitute.sting.datasources.pipeline.Pipeline
import org.broadinstitute.sting.gatk.DownsampleType import org.broadinstitute.sting.gatk.DownsampleType
import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
import org.broadinstitute.sting.queue.extensions.samtools._ import org.broadinstitute.sting.queue.extensions.samtools._
import org.broadinstitute.sting.queue.{QException, QScript} import org.broadinstitute.sting.queue.{QException, QScript}
import collection.JavaConversions._ import collection.JavaConversions._
@ -43,7 +42,7 @@ class Phase1Cleaning extends QScript {
trait CommandLineGATKArgs extends CommandLineGATK { trait CommandLineGATKArgs extends CommandLineGATK {
this.jarFile = qscript.gatkJar this.jarFile = qscript.gatkJar
this.reference_sequence = qscript.reference this.reference_sequence = qscript.reference
this.memoryLimit = Some(2) this.memoryLimit = 2
this.jobTempDir = qscript.tmpDir this.jobTempDir = qscript.tmpDir
} }
@ -62,11 +61,11 @@ class Phase1Cleaning extends QScript {
// 1.) Create cleaning targets // 1.) Create cleaning targets
var target = new RealignerTargetCreator with CommandLineGATKArgs var target = new RealignerTargetCreator with CommandLineGATKArgs
target.memoryLimit = Some(4) target.memoryLimit = 4
target.input_file :+= bamList target.input_file :+= bamList
target.intervalsString :+= interval target.intervalsString :+= interval
target.out = targetIntervals target.out = targetIntervals
target.mismatchFraction = Some(0.0) target.mismatchFraction = 0.0
target.rodBind :+= RodBind("dbsnp", "VCF", qscript.dbSNP) target.rodBind :+= RodBind("dbsnp", "VCF", qscript.dbSNP)
target.rodBind :+= RodBind("indels1", "VCF", qscript.dindelPilotCalls) target.rodBind :+= RodBind("indels1", "VCF", qscript.dindelPilotCalls)
target.rodBind :+= RodBind("indels2", "VCF", qscript.dindelAFRCalls) target.rodBind :+= RodBind("indels2", "VCF", qscript.dindelAFRCalls)
@ -77,13 +76,13 @@ class Phase1Cleaning extends QScript {
// 2.) Clean without SW // 2.) Clean without SW
var clean = new IndelRealigner with CommandLineGATKArgs var clean = new IndelRealigner with CommandLineGATKArgs
val cleanedBam = new File(baseTmpName + "cleaned.bam") val cleanedBam = new File(baseTmpName + "cleaned.bam")
clean.memoryLimit = Some(4) clean.memoryLimit = 4
clean.input_file :+= bamList clean.input_file :+= bamList
clean.intervalsString :+= interval clean.intervalsString :+= interval
clean.targetIntervals = targetIntervals clean.targetIntervals = targetIntervals
clean.out = cleanedBam clean.out = cleanedBam
clean.doNotUseSW = true clean.doNotUseSW = true
clean.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.RECALCULATE) clean.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.RECALCULATE
clean.rodBind :+= RodBind("dbsnp", "VCF", qscript.dbSNP) clean.rodBind :+= RodBind("dbsnp", "VCF", qscript.dbSNP)
clean.rodBind :+= RodBind("indels1", "VCF", qscript.dindelPilotCalls) clean.rodBind :+= RodBind("indels1", "VCF", qscript.dindelPilotCalls)
clean.rodBind :+= RodBind("indels2", "VCF", qscript.dindelAFRCalls) clean.rodBind :+= RodBind("indels2", "VCF", qscript.dindelAFRCalls)

19
scala/qscript/oneoffs/rpoplin/VQSR_parameterSearch.scala
View File

@ -1,4 +1,3 @@
import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction
import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.queue.QScript
@ -19,7 +18,7 @@ class VQSR_parameterSearch extends QScript {
@Argument(shortName="skipCalling", doc="If true, skip the calling part of the pipeline and only run VQSR on preset, gold standard VCF files", required=false) @Argument(shortName="skipCalling", doc="If true, skip the calling part of the pipeline and only run VQSR on preset, gold standard VCF files", required=false)
var skipCalling: Boolean = false var skipCalling: Boolean = false
trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; jarFile = gatkJarFile; memoryLimit = Some(2); } trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; jarFile = gatkJarFile; memoryLimit = 2; }
class Target(val baseName: String, val reference: File, val rodName: String, val bamList: File, val goldStandard_VCF: File, val intervals: String, val titvTarget: Double, val isLowpass: Boolean) { class Target(val baseName: String, val reference: File, val rodName: String, val bamList: File, val goldStandard_VCF: File, val intervals: String, val titvTarget: Double, val isLowpass: Boolean) {
def name = qscript.outputDir + baseName def name = qscript.outputDir + baseName
@ -309,12 +308,12 @@ class VQSR_parameterSearch extends QScript {
} }
this.analysisName = name + "_GVC" this.analysisName = name + "_GVC"
this.intervalsString ++= List(t.intervals) this.intervalsString ++= List(t.intervals)
this.qual = Some(t.qualCutoff) this.qual = t.qualCutoff
this.std = Some(t.std) this.std = t.std
this.mG = Some(t.gaussian) this.mG = t.gaussian
this.ignoreFilter ++= FiltersToIgnore this.ignoreFilter ++= FiltersToIgnore
this.dirichlet = Some(t.dirichlet) this.dirichlet = t.dirichlet
this.shrinkage = Some(t.shrinkage) this.shrinkage = t.shrinkage
} }
// 4.) VQSR part2 Calculate new LOD for all input SNPs by evaluating the Gaussian clusters // 4.) VQSR part2 Calculate new LOD for all input SNPs by evaluating the Gaussian clusters
@ -336,8 +335,8 @@ class VQSR_parameterSearch extends QScript {
this.intervalsString ++= List(t.intervals) this.intervalsString ++= List(t.intervals)
this.ignoreFilter ++= FiltersToIgnore this.ignoreFilter ++= FiltersToIgnore
this.ignoreFilter ++= List("HARD_TO_VALIDATE") this.ignoreFilter ++= List("HARD_TO_VALIDATE")
this.target_titv = Some(t.titvTarget) this.target_titv = t.titvTarget
this.backOff = Some(t.backoff) this.backOff = t.backoff
} }
// 4a.) Choose VQSR tranches based on novel ti/tv // 4a.) Choose VQSR tranches based on novel ti/tv
@ -350,7 +349,7 @@ class VQSR_parameterSearch extends QScript {
// 4b.) Choose VQSR tranches based on sensitivity to truth set // 4b.) Choose VQSR tranches based on sensitivity to truth set
class VariantRecalibratorNRS(t: Target, goldStandard: Boolean) extends VariantRecalibratorBase(t, goldStandard) { class VariantRecalibratorNRS(t: Target, goldStandard: Boolean) extends VariantRecalibratorBase(t, goldStandard) {
this.sm = Some(org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.SelectionMetricType.TRUTH_SENSITIVITY) this.sm = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.SelectionMetricType.TRUTH_SENSITIVITY
if(t.trainOmni == 0 ) { if(t.trainOmni == 0 ) {
this.tranche ++= List("1.0") this.tranche ++= List("1.0")
} else { } else {

28
scala/qscript/playground/BatchMerge.q
View File

@ -48,22 +48,22 @@ class batchMergePipeline extends QScript {
trait CalcLikelihoodArgs extends UGCalcLikelihoods { trait CalcLikelihoodArgs extends UGCalcLikelihoods {
this.reference_sequence = batchMerge.ref this.reference_sequence = batchMerge.ref
this.max_mismatches_in_40bp_window = Some(batchMerge.mmb) this.max_mismatches_in_40bp_window = batchMerge.mmb
this.min_base_quality_score = Some(batchMerge.mbq) this.min_base_quality_score = batchMerge.mbq
this.min_mapping_quality_score = Some(batchMerge.mmq) this.min_mapping_quality_score = batchMerge.mmq
if ( batchMerge.baq >= 0 ) { if ( batchMerge.baq >= 0 ) {
this.baqGapOpenPenalty = Some(batchMerge.baq) this.baqGapOpenPenalty = batchMerge.baq
this.baq = Some(BAQ.CalculationMode.CALCULATE_AS_NECESSARY) this.baq = BAQ.CalculationMode.CALCULATE_AS_NECESSARY
} }
this.intervals :+= extractIntervals.listOut this.intervals :+= extractIntervals.listOut
this.alleleVCF = combineVCFs.outVCF this.alleleVCF = combineVCFs.outVCF
this.jarFile = new File(stingDir+"/dist/GenomeAnalysisTK.jar") this.jarFile = new File(stingDir+"/dist/GenomeAnalysisTK.jar")
this.memoryLimit = Some(4) this.memoryLimit = 4
this.scatterCount = 60 this.scatterCount = 60
this.output_mode = Some(UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES) this.output_mode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES
this.genotyping_mode = Some(GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) this.genotyping_mode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES
if ( batchMerge.indelMode ) { if ( batchMerge.indelMode ) {
this.genotype_likelihoods_model = Some(GenotypeLikelihoodsCalculationModel.Model.DINDEL) this.genotype_likelihoods_model = GenotypeLikelihoodsCalculationModel.Model.DINDEL
} }
} }
@ -82,11 +82,11 @@ class batchMergePipeline extends QScript {
this.intervals :+= extractIntervals.listOut this.intervals :+= extractIntervals.listOut
this.jarFile = new File(stingDir+"/dist/GenomeAnalysisTK.jar") this.jarFile = new File(stingDir+"/dist/GenomeAnalysisTK.jar")
this.scatterCount = 30 this.scatterCount = 30
this.memoryLimit = Some(8) this.memoryLimit = 8
this.output_mode = Some(UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES) this.output_mode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES
this.genotyping_mode = Some(GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) this.genotyping_mode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES
if ( batchMerge.indelMode ) { if ( batchMerge.indelMode ) {
this.genotype_likelihoods_model = Some(GenotypeLikelihoodsCalculationModel.Model.DINDEL) this.genotype_likelihoods_model = GenotypeLikelihoodsCalculationModel.Model.DINDEL
} }
} }
@ -100,7 +100,7 @@ class batchMergePipeline extends QScript {
this.intervals :+= extractIntervals.listOut this.intervals :+= extractIntervals.listOut
this.jarFile = new File(batchMerge.stingDir+"/dist/GenomeAnalysisTK.jar") this.jarFile = new File(batchMerge.stingDir+"/dist/GenomeAnalysisTK.jar")
this.scatterCount = 10 this.scatterCount = 10
this.memoryLimit=Some(4) this.memoryLimit=4
} }
var combine : CombineVariants = new CombineVariants with CombineVariantsArgs var combine : CombineVariants = new CombineVariants with CombineVariantsArgs

32
scala/qscript/playground/FullCallingPipeline.q
View File

@ -1,7 +1,7 @@
import org.broadinstitute.sting.commandline.ArgumentSource import org.broadinstitute.sting.commandline.ArgumentSource
import org.broadinstitute.sting.datasources.pipeline.Pipeline import org.broadinstitute.sting.datasources.pipeline.Pipeline
import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.picard.PicardBamEmbeddedFunction import org.broadinstitute.sting.queue.extensions.picard.PicardBamFunction
import org.broadinstitute.sting.queue.extensions.samtools._ import org.broadinstitute.sting.queue.extensions.samtools._
import org.broadinstitute.sting.queue.function.ListWriterFunction import org.broadinstitute.sting.queue.function.ListWriterFunction
import org.broadinstitute.sting.queue.function.scattergather.{GatherFunction, CloneFunction, ScatterFunction} import org.broadinstitute.sting.queue.function.scattergather.{GatherFunction, CloneFunction, ScatterFunction}
@ -42,7 +42,7 @@ class FullCallingPipeline extends QScript {
this.intervals = List(qscript.pipeline.getProject.getIntervalList) this.intervals = List(qscript.pipeline.getProject.getIntervalList)
this.jarFile = qscript.gatkJar this.jarFile = qscript.gatkJar
this.reference_sequence = qscript.pipeline.getProject.getReferenceFile this.reference_sequence = qscript.pipeline.getProject.getReferenceFile
this.memoryLimit = Some(4) this.memoryLimit = 4
} }
@ -77,7 +77,7 @@ class FullCallingPipeline extends QScript {
targetCreator.analysisName = "CreateTargets_"+sampleId targetCreator.analysisName = "CreateTargets_"+sampleId
targetCreator.input_file :+= bam targetCreator.input_file :+= bam
targetCreator.out = indel_targets targetCreator.out = indel_targets
targetCreator.memoryLimit = Some(2) targetCreator.memoryLimit = 2
targetCreator.isIntermediate = true targetCreator.isIntermediate = true
val realigner = new IndelRealigner with CommandLineGATKArgs val realigner = new IndelRealigner with CommandLineGATKArgs
@ -108,8 +108,8 @@ class FullCallingPipeline extends QScript {
case (gather: BamGatherFunction, source: ArgumentSource) => case (gather: BamGatherFunction, source: ArgumentSource) =>
gather.commandDirectory = new File("CleanedBams/IntermediateFiles/%s/ScatterGather/Gather_%s".format(sampleId, source.field.getName)) gather.commandDirectory = new File("CleanedBams/IntermediateFiles/%s/ScatterGather/Gather_%s".format(sampleId, source.field.getName))
gather.jobOutputFile = new File(".queue/logs/Cleaning/%s/FixMates.out".format(sampleId)) gather.jobOutputFile = new File(".queue/logs/Cleaning/%s/FixMates.out".format(sampleId))
gather.memoryLimit = Some(6) gather.memoryLimit = 6
gather.mainClass = picardFixMatesClass gather.javaMainClass = picardFixMatesClass
gather.assumeSorted = None gather.assumeSorted = None
case (gather: GatherFunction, source: ArgumentSource) => case (gather: GatherFunction, source: ArgumentSource) =>
gather.commandDirectory = new File("CleanedBams/IntermediateFiles/%s/ScatterGather/Gather_%s".format(sampleId, source.field.getName)) gather.commandDirectory = new File("CleanedBams/IntermediateFiles/%s/ScatterGather/Gather_%s".format(sampleId, source.field.getName))
@ -122,7 +122,7 @@ class FullCallingPipeline extends QScript {
realigner.isIntermediate = true realigner.isIntermediate = true
// Explicitly run fix mates if the function won't be scattered. // Explicitly run fix mates if the function won't be scattered.
val fixMates = new PicardBamEmbeddedFunction { val fixMates = new PicardBamFunction {
@Input(doc="unfixed bam") var unfixed: File = _ @Input(doc="unfixed bam") var unfixed: File = _
@Output(doc="fixed bam") var fixed: File = _ @Output(doc="fixed bam") var fixed: File = _
def inputBams = List(unfixed) def inputBams = List(unfixed)
@ -130,8 +130,8 @@ class FullCallingPipeline extends QScript {
} }
fixMates.jobOutputFile = new File(".queue/logs/Cleaning/%s/FixMates.out".format(sampleId)) fixMates.jobOutputFile = new File(".queue/logs/Cleaning/%s/FixMates.out".format(sampleId))
fixMates.memoryLimit = Some(6) fixMates.memoryLimit = 6
fixMates.mainClass = picardFixMatesClass fixMates.javaMainClass = picardFixMatesClass
fixMates.unfixed = realigner.out fixMates.unfixed = realigner.out
fixMates.fixed = cleaned_bam fixMates.fixed = cleaned_bam
fixMates.analysisName = "FixMates_"+sampleId fixMates.analysisName = "FixMates_"+sampleId
@ -173,9 +173,9 @@ class FullCallingPipeline extends QScript {
val indels = new UnifiedGenotyper with CommandLineGATKArgs with ExpandedIntervals val indels = new UnifiedGenotyper with CommandLineGATKArgs with ExpandedIntervals
indels.analysisName = base + "_indels" indels.analysisName = base + "_indels"
indels.jobOutputFile = new File(".queue/logs/IndelCalling/UnifiedGenotyper.indels.out") indels.jobOutputFile = new File(".queue/logs/IndelCalling/UnifiedGenotyper.indels.out")
indels.memoryLimit = Some(6) indels.memoryLimit = 6
indels.downsample_to_coverage = Some(600) indels.downsample_to_coverage = 600
indels.genotype_likelihoods_model = Option(org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.DINDEL) indels.genotype_likelihoods_model = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.DINDEL
indels.input_file = bamFiles indels.input_file = bamFiles
indels.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getGenotypeDbsnpType, qscript.pipeline.getProject.getGenotypeDbsnp) indels.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getGenotypeDbsnpType, qscript.pipeline.getProject.getGenotypeDbsnp)
indels.out = new File("IndelCalls", base+".indels.vcf") indels.out = new File("IndelCalls", base+".indels.vcf")
@ -210,8 +210,8 @@ class FullCallingPipeline extends QScript {
val snps = new UnifiedGenotyper with CommandLineGATKArgs with ExpandedIntervals val snps = new UnifiedGenotyper with CommandLineGATKArgs with ExpandedIntervals
snps.analysisName = base+"_snps" snps.analysisName = base+"_snps"
snps.jobOutputFile = new File(".queue/logs/SNPCalling/UnifiedGenotyper.snps.out") snps.jobOutputFile = new File(".queue/logs/SNPCalling/UnifiedGenotyper.snps.out")
snps.memoryLimit = Some(6) snps.memoryLimit = 6
snps.downsample_to_coverage = Some(600) snps.downsample_to_coverage = 600
snps.input_file = bamFiles snps.input_file = bamFiles
snps.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getGenotypeDbsnpType, qscript.pipeline.getProject.getGenotypeDbsnp) snps.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getGenotypeDbsnpType, qscript.pipeline.getProject.getGenotypeDbsnp)
snps.out = new File("SnpCalls", base+".snps.vcf") snps.out = new File("SnpCalls", base+".snps.vcf")
@ -239,8 +239,8 @@ class FullCallingPipeline extends QScript {
filteredSNPs.jobOutputFile = new File(".queue/logs/SNPCalling/VariantFiltration.snps.out") filteredSNPs.jobOutputFile = new File(".queue/logs/SNPCalling/VariantFiltration.snps.out")
filteredSNPs.filterName ++= List("SNPSBFilter","SNPQDFilter","SNPHRunFilter") filteredSNPs.filterName ++= List("SNPSBFilter","SNPQDFilter","SNPHRunFilter")
filteredSNPs.filterExpression ++= List("\"SB>=0.10\"","\"QD<5.0\"","\"HRun>=4\"") filteredSNPs.filterExpression ++= List("\"SB>=0.10\"","\"QD<5.0\"","\"HRun>=4\"")
filteredSNPs.clusterWindowSize = Some(10) filteredSNPs.clusterWindowSize = 10
filteredSNPs.clusterSize = Some(3) filteredSNPs.clusterSize = 3
filteredSNPs.rodBind :+= RodBind("mask", "VCF", filteredIndels.out) filteredSNPs.rodBind :+= RodBind("mask", "VCF", filteredIndels.out)
filteredSNPs.variantVCF = snps.out filteredSNPs.variantVCF = snps.out
filteredSNPs.out = swapExt("SnpCalls",snps.out,".vcf",".filtered.vcf") filteredSNPs.out = swapExt("SnpCalls",snps.out,".vcf",".filtered.vcf")
@ -249,7 +249,7 @@ class FullCallingPipeline extends QScript {
val combineAll = new CombineVariants with CommandLineGATKArgs with ExpandedIntervals val combineAll = new CombineVariants with CommandLineGATKArgs with ExpandedIntervals
combineAll.analysisName = base + "_combineAll" combineAll.analysisName = base + "_combineAll"
combineAll.jobOutputFile = new File(".queue/logs/Combined/CombineVariants.out") combineAll.jobOutputFile = new File(".queue/logs/Combined/CombineVariants.out")
combineAll.variantMergeOptions = Option(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION) combineAll.variantMergeOptions = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION
combineAll.rod_priority_list = "Indels,SNPs" combineAll.rod_priority_list = "Indels,SNPs"
combineAll.rodBind :+= RodBind("Indels", "VCF", filteredIndels.out) combineAll.rodBind :+= RodBind("Indels", "VCF", filteredIndels.out)
combineAll.rodBind :+= RodBind("SNPs", "VCF", filteredSNPs.out) combineAll.rodBind :+= RodBind("SNPs", "VCF", filteredSNPs.out)

6
scala/qscript/playground/MultiFullCallingPipeline.scala
View File

@ -1,5 +1,5 @@
import collection.JavaConversions import collection.JavaConversions
import org.broadinstitute.sting.queue.function.JarCommandLineFunction import org.broadinstitute.sting.queue.function.JavaCommandLineFunction
import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.util.IOUtils import org.broadinstitute.sting.queue.util.IOUtils
import org.broadinstitute.sting.utils.text.XReadLines import org.broadinstitute.sting.utils.text.XReadLines
@ -69,7 +69,7 @@ class MultiFullCallingPipeline extends QScript {
* Runs a yaml in a pipeline only after a previous pipeline * Runs a yaml in a pipeline only after a previous pipeline
* run has produced the passed in output file. * run has produced the passed in output file.
*/ */
class RunPipeline(yamlFile: File, lastOutput: File) extends JarCommandLineFunction { class RunPipeline(yamlFile: File, lastOutput: File) extends JavaCommandLineFunction {
private var yamlName = yamlFile.getName.stripSuffix(".yaml") private var yamlName = yamlFile.getName.stripSuffix(".yaml")
@Input(doc="output file to wait for", required=false) @Input(doc="output file to wait for", required=false)
@ -81,7 +81,7 @@ class MultiFullCallingPipeline extends QScript {
commandDirectory = yamlFile.getParentFile commandDirectory = yamlFile.getParentFile
jobOutputFile = IOUtils.absolute(commandDirectory, yamlName + ".queue.txt") jobOutputFile = IOUtils.absolute(commandDirectory, yamlName + ".queue.txt")
jarFile = queueJar jarFile = queueJar
memoryLimit = Some(1) memoryLimit = 1
override def commandLine = super.commandLine + override def commandLine = super.commandLine +
optional(" -statusTo ", qscript.pipelineStatusTo) + optional(" -statusTo ", qscript.pipelineStatusTo) +

16
scala/qscript/playground/recalibrate.scala
View File

@ -1,4 +1,3 @@
import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction
import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.queue.QScript
@ -23,9 +22,6 @@ class recalibrate extends QScript {
@Argument(shortName = "R", doc="ref") @Argument(shortName = "R", doc="ref")
var referenceFile: File = _ var referenceFile: File = _
@Argument(doc="X", required=false)
var picardMergeSamFilesJar: File = new File("/seq/software/picard/current/bin/MergeSamFiles.jar")
trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; jarFile = gatkJarFile; reference_sequence = referenceFile; } trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; jarFile = gatkJarFile; reference_sequence = referenceFile; }
def script = { def script = {
@ -40,13 +36,11 @@ def script = {
val tableRecal = new TableRecalibrate(bamIn, recalData, recalBam) { useOriginalQualities = true } val tableRecal = new TableRecalibrate(bamIn, recalData, recalBam) { useOriginalQualities = true }
if ( scatter ) { if ( scatter ) {
tableRecal.intervals = List(new File("/humgen/gsa-hpprojects/GATK/data/chromosomes.hg18.interval_list")) tableRecal.intervals = List(new File("/humgen/gsa-hpprojects/GATK/data/chromosomes.hg18.interval_list"))
//tableRecal.scatterClass = classOf[ContigScatterFunction]
tableRecal.setupGatherFunction = { case (f: PicardBamJarFunction, _) => f.jarFile = picardMergeSamFilesJar; f.memoryLimit = Some(4) }
tableRecal.scatterCount = 25 tableRecal.scatterCount = 25
} }
add(tableRecal) add(tableRecal)
add(new Index(recalBam)) add(new Index(recalBam))
add(new CountCovariates(recalBam, recalRecalData) { num_threads = Some(4) }) add(new CountCovariates(recalBam, recalRecalData) { num_threads = 4 })
add(new AnalyzeCovariates(recalData, new File(recalData.getPath() + ".analyzeCovariates"))) add(new AnalyzeCovariates(recalData, new File(recalData.getPath() + ".analyzeCovariates")))
add(new AnalyzeCovariates(recalRecalData, new File(recalRecalData.getPath() + ".analyzeCovariates"))) add(new AnalyzeCovariates(recalRecalData, new File(recalRecalData.getPath() + ".analyzeCovariates")))
} }
@ -65,7 +59,7 @@ class CountCovariates(bamIn: File, recalDataIn: File) extends org.broadinstitute
this.DBSNP = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod") this.DBSNP = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod")
this.logging_level = "INFO" this.logging_level = "INFO"
this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate") this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
this.memoryLimit = Some(3) this.memoryLimit = 3
override def dotString = "CountCovariates: %s [args %s]".format(bamIn.getName, if (this.num_threads.isDefined) "-nt " + this.num_threads else "") override def dotString = "CountCovariates: %s [args %s]".format(bamIn.getName, if (this.num_threads.isDefined) "-nt " + this.num_threads else "")
} }
@ -76,7 +70,7 @@ class TableRecalibrate(bamInArg: File, recalDataIn: File, bamOutArg: File) exten
this.recal_file = recalDataIn this.recal_file = recalDataIn
this.out = bamOutArg this.out = bamOutArg
this.logging_level = "INFO" this.logging_level = "INFO"
this.memoryLimit = Some(2) this.memoryLimit = 2
this.skipUQUpdate = skipUQUpdateArg this.skipUQUpdate = skipUQUpdateArg
override def dotString = "TableRecalibrate: %s => %s".format(bamInArg.getName, bamOutArg.getName, if (this.useOriginalQualities) " -OQ" else "") override def dotString = "TableRecalibrate: %s => %s".format(bamInArg.getName, bamOutArg.getName, if (this.useOriginalQualities) " -OQ" else "")
@ -87,9 +81,9 @@ class AnalyzeCovariates(recalDataIn: File, outputDir: File) extends org.broadin
this.recal_file = recalDataIn this.recal_file = recalDataIn
this.output_dir = outputDir.toString this.output_dir = outputDir.toString
this.path_to_resources = "/home/radon01/depristo/dev/GenomeAnalysisTK/trunk/R/" this.path_to_resources = "/home/radon01/depristo/dev/GenomeAnalysisTK/trunk/R/"
this.ignoreQ = Some(5) this.ignoreQ = 5
this.path_to_Rscript = "/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.7.2/bin/Rscript" this.path_to_Rscript = "/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.7.2/bin/Rscript"
this.memoryLimit = Some(2) this.memoryLimit = 2
override def dotString = "AnalyzeCovariates: %s".format(recalDataIn.getName) override def dotString = "AnalyzeCovariates: %s".format(recalDataIn.getName)
} }

86
scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
View File

@ -1,3 +1,27 @@
/*
* 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.queue package org.broadinstitute.sting.queue
import function.QFunction import function.QFunction
@ -10,6 +34,37 @@ import collection.JavaConversions._
import org.broadinstitute.sting.utils.classloader.PluginManager import org.broadinstitute.sting.utils.classloader.PluginManager
import org.broadinstitute.sting.utils.exceptions.UserException import org.broadinstitute.sting.utils.exceptions.UserException
/**
* Entry point of Queue. Compiles and runs QScripts passed in to the command line.
*/
object QCommandLine {
/**
* Main.
* @param argv Arguments.
*/
def main(argv: Array[String]) {
val qCommandLine = new QCommandLine
Runtime.getRuntime.addShutdownHook(new Thread {
/** Cleanup as the JVM shuts down. */
override def run = {
ProcessController.shutdown()
qCommandLine.shutdown()
}
})
try {
CommandLineProgram.start(qCommandLine, argv);
if (CommandLineProgram.result != 0)
System.exit(CommandLineProgram.result);
} catch {
case e: Exception => CommandLineProgram.exitSystemWithError(e)
} finally {
}
}
}
/** /**
* Entry point of Queue. Compiles and runs QScripts passed in to the command line. * Entry point of Queue. Compiles and runs QScripts passed in to the command line.
*/ */
@ -99,34 +154,3 @@ class QCommandLine extends CommandLineProgram with Logging {
if (qScriptClasses != null) IOUtils.tryDelete(qScriptClasses) if (qScriptClasses != null) IOUtils.tryDelete(qScriptClasses)
} }
} }
/**
* Entry point of Queue. Compiles and runs QScripts passed in to the command line.
*/
object QCommandLine {
/**
* Main.
* @param argv Arguments.
*/
def main(argv: Array[String]) {
val qCommandLine = new QCommandLine
Runtime.getRuntime.addShutdownHook(new Thread {
/** Cleanup as the JVM shuts down. */
override def run = {
ProcessController.shutdown()
qCommandLine.shutdown()
}
})
try {
CommandLineProgram.start(qCommandLine, argv);
if (CommandLineProgram.result != 0)
System.exit(CommandLineProgram.result);
} catch {
case e: Exception => CommandLineProgram.exitSystemWithError(e)
} finally {
}
}
}

7
scala/src/org/broadinstitute/sting/queue/QScript.scala
View File

@ -24,7 +24,7 @@
package org.broadinstitute.sting.queue package org.broadinstitute.sting.queue
import org.broadinstitute.sting.queue.util.Logging import util.{PrimitiveOptionConversions, Logging}
import org.broadinstitute.sting.queue.function.QFunction import org.broadinstitute.sting.queue.function.QFunction
import org.broadinstitute.sting.utils.text.XReadLines import org.broadinstitute.sting.utils.text.XReadLines
import annotation.target.field import annotation.target.field
@ -32,7 +32,8 @@ import annotation.target.field
/** /**
* Defines a Queue pipeline as a collection of CommandLineFunctions. * Defines a Queue pipeline as a collection of CommandLineFunctions.
*/ */
trait QScript extends Logging { trait QScript extends Logging with PrimitiveOptionConversions {
// Type aliases so users don't have to import // Type aliases so users don't have to import
type File = java.io.File type File = java.io.File
type CommandLineFunction = org.broadinstitute.sting.queue.function.CommandLineFunction type CommandLineFunction = org.broadinstitute.sting.queue.function.CommandLineFunction
@ -49,7 +50,7 @@ trait QScript extends Logging {
type Output = org.broadinstitute.sting.commandline.Output @field type Output = org.broadinstitute.sting.commandline.Output @field
type Argument = org.broadinstitute.sting.commandline.Argument @field type Argument = org.broadinstitute.sting.commandline.Argument @field
type ArgumentCollection = org.broadinstitute.sting.commandline.ArgumentCollection @field type ArgumentCollection = org.broadinstitute.sting.commandline.ArgumentCollection @field
type Gather = org.broadinstitute.sting.queue.function.scattergather.Gather @field type Gather = org.broadinstitute.sting.commandline.Gather @field
/** /**
* Builds the CommandLineFunctions that will be used to run this script and adds them to this.functions directly or using the add() utility method. * Builds the CommandLineFunctions that will be used to run this script and adds them to this.functions directly or using the add() utility method.

19
scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
View File

@ -318,7 +318,7 @@ class QGraph extends Logging {
var readyJobs = getReadyJobs() var readyJobs = getReadyJobs()
while (running && readyJobs.size > 0) { while (running && readyJobs.size > 0) {
logger.debug("+++++++") logger.debug("+++++++")
readyJobs.foreach(edge => { foreachFunction(readyJobs.toList, edge => {
if (running) { if (running) {
logEdge(edge) logEdge(edge)
edge.markAsDone edge.markAsDone
@ -870,12 +870,17 @@ class QGraph extends Logging {
* Utility function for running a method over all function edges. * Utility function for running a method over all function edges.
* @param edgeFunction Function to run for each FunctionEdge. * @param edgeFunction Function to run for each FunctionEdge.
*/ */
private def foreachFunction(f: (FunctionEdge) => Unit) = { private def foreachFunction(f: (FunctionEdge) => Unit) {
jobGraph.edgeSet.toList foreachFunction(jobGraph.edgeSet.toList.filter(_.isInstanceOf[FunctionEdge]).asInstanceOf[List[FunctionEdge]], f)
.filter(_.isInstanceOf[FunctionEdge]) }
.asInstanceOf[List[FunctionEdge]]
.sorted(functionOrdering) /**
.foreach(edge => if (running) f(edge)) * Utility function for running a method over a list of function edges.
* @param edegs Edges to traverse.
* @param edgeFunction Function to run for each FunctionEdge.
*/
private def foreachFunction(edges: List[FunctionEdge], f: (FunctionEdge) => Unit) {
edges.sorted(functionOrdering).foreach(edge => if (running) f(edge))
} }
/** /**

45
scala/src/org/broadinstitute/sting/queue/extensions/firehose/ImportSingleValueFunction.scala
View File

@ -1,45 +0,0 @@
package org.broadinstitute.sting.queue.extensions.firehose
import org.broadinstitute.sting.queue.function.JarCommandLineFunction
import org.broadinstitute.sting.commandline.{Input, Argument}
import java.io.File
/**
* Runs the Firehose ImportSingleValue jar file.
*/
class ImportSingleValueFunction extends JarCommandLineFunction {
@Argument(doc="firehose host")
var host: String = _
@Argument(doc="firehose port")
var port: Int = _
@Argument(doc="firehose domain")
var domain: String = _
@Argument(doc="firehose entity type")
var entityType: String = _
@Argument(doc="firehose entity id")
var entityID: String = _
@Argument(doc="firehose annotation type name", shortName="bamFHAnn", required=false)
var annotationTypeName: String = _
@Argument(doc="clean bam firehose security token", shortName="bamFHToken", required=false)
var securityToken: String = _
@Input(doc="imports the path to this file", exclusiveOf="importValueInFile")
var importValue: File = _
@Input(doc="imports the value contained in the file", exclusiveOf="importValue")
var importValueInFile: File = _
override def commandLine = super.commandLine + ("" +
" PORT=%s HOST=%s DOMAIN=%s ENTITY_TYPE=%s" +
" ENTITY_ID=%s ANNOTATION_TYPE_NAME=%s SECURITY_TOKEN=%s" +
"%s%s"
).format(
port, host, domain, entityType, entityID, annotationTypeName, securityToken,
optional(" VALUE=", importValue), optional(" VALUE_FILE=", importValueInFile))
}

30
scala/src/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala
View File

@ -1,13 +1,37 @@
/*
* 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.queue.extensions.gatk package org.broadinstitute.sting.queue.extensions.gatk
import org.broadinstitute.sting.queue.function.scattergather.GatherFunction import org.broadinstitute.sting.queue.function.scattergather.GatherFunction
import org.broadinstitute.sting.queue.extensions.picard.PicardBamEmbeddedFunction import org.broadinstitute.sting.queue.extensions.picard.PicardBamFunction
/** /**
* Merges BAM files using Picards net.sf.picard.sam.MergeSamFiles. * Merges BAM files using Picards net.sf.picard.sam.MergeSamFiles.
*/ */
class BamGatherFunction extends GatherFunction with PicardBamEmbeddedFunction { class BamGatherFunction extends GatherFunction with PicardBamFunction {
this.mainClass = "net.sf.picard.sam.MergeSamFiles" this.javaMainClass = "net.sf.picard.sam.MergeSamFiles"
this.assumeSorted = Some(true) this.assumeSorted = Some(true)
protected def inputBams = gatherParts protected def inputBams = gatherParts
protected def outputBam = originalOutput protected def outputBam = originalOutput

2
scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala
View File

@ -69,7 +69,7 @@ trait GATKScatterFunction extends ScatterFunction {
} }
override def isScatterGatherable = { override def isScatterGatherable = {
if (this.originalGATK.BTI != null && this.originalGATK.BTIMR.isEmpty) if (this.originalGATK.BTI != null && this.originalGATK.BTIMR == null)
throw new IllegalArgumentException("BTI requires BTIMR for use with scatter-gather (recommended: INTERSECTION)") throw new IllegalArgumentException("BTI requires BTIMR for use with scatter-gather (recommended: INTERSECTION)")
this.originalGATK.reference_sequence != null this.originalGATK.reference_sequence != null
} }

22
scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala
View File

@ -25,7 +25,9 @@
package org.broadinstitute.sting.queue.extensions.picard package org.broadinstitute.sting.queue.extensions.picard
import java.io.File import java.io.File
import org.broadinstitute.sting.queue.function.CommandLineFunction import org.broadinstitute.sting.queue.function.JavaCommandLineFunction
import net.sf.samtools.SAMFileReader.ValidationStringency
import net.sf.samtools.SAMFileHeader.SortOrder
/** /**
* Wraps a Picard function that operates on BAM files. * Wraps a Picard function that operates on BAM files.
@ -34,9 +36,9 @@ import org.broadinstitute.sting.queue.function.CommandLineFunction
* Since the various BAM utilities take slightly different arguments * Since the various BAM utilities take slightly different arguments
* some values are optional. * some values are optional.
*/ */
trait PicardBamFunction extends CommandLineFunction { trait PicardBamFunction extends JavaCommandLineFunction {
var validationStringency = "SILENT" var validationStringency: ValidationStringency = ValidationStringency.SILENT
var sortOrder = "coordinate" var sortOrder: SortOrder = SortOrder.coordinate
var compressionLevel: Option[Int] = None var compressionLevel: Option[Int] = None
var maxRecordsInRam: Option[Int] = None var maxRecordsInRam: Option[Int] = None
var assumeSorted: Option[Boolean] = None var assumeSorted: Option[Boolean] = None
@ -45,7 +47,13 @@ trait PicardBamFunction extends CommandLineFunction {
protected def outputBam: File protected def outputBam: File
abstract override def commandLine = super.commandLine + abstract override def commandLine = super.commandLine +
Array(optional(" COMPRESSION_LEVEL=", compressionLevel), optional(" VALIDATION_STRINGENCY=", validationStringency), Array(
optional(" SO=", sortOrder), optional( " MAX_RECORDS_IN_RAM=", maxRecordsInRam), optional(" ASSUME_SORTED=", assumeSorted), repeat(" INPUT=", inputBams),
" OUTPUT=" + outputBam, repeat(" INPUT=", inputBams), " TMP_DIR=" + jobTempDir).mkString " OUTPUT=" + outputBam,
" TMP_DIR=" + jobTempDir,
optional(" COMPRESSION_LEVEL=", compressionLevel),
optional(" VALIDATION_STRINGENCY=", validationStringency),
optional(" SO=", sortOrder),
optional(" MAX_RECORDS_IN_RAM=", maxRecordsInRam),
optional(" ASSUME_SORTED=", assumeSorted)).mkString
} }

45
scala/src/org/broadinstitute/sting/queue/function/EmbeddedCommandLineFunction.scala
View File

@ -1,45 +0,0 @@
/*
* 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.queue.function
import java.io.File
import org.broadinstitute.sting.queue.util.IOUtils
import org.broadinstitute.sting.commandline.Argument
/**
* Defines a command line function that runs java code from inside the existing class path.
*/
trait EmbeddedCommandLineFunction extends JavaCommandLineFunction {
@Argument(doc="Main class to run from the current classpath")
var mainClass: String = null
def javaExecutable = "-cp %s %s".format(EmbeddedCommandLineFunction.classpath, mainClass)
}
object EmbeddedCommandLineFunction {
private val classpath = System.getProperty("java.class.path")
.split(File.pathSeparatorChar).map(path => IOUtils.absolute(new File(path)))
.mkString("\"", "\"" + File.pathSeparator + "\"", "\"")
}

14
scala/src/org/broadinstitute/sting/queue/function/JarCommandLineFunction.scala
View File

@ -1,14 +0,0 @@
package org.broadinstitute.sting.queue.function
import org.broadinstitute.sting.commandline.Argument
import java.io.File
/**
* Defines a command line function that runs from a jar file.
*/
trait JarCommandLineFunction extends JavaCommandLineFunction {
@Argument(doc="jar")
var jarFile: File = _
def javaExecutable = "-jar " + jarFile
}

59
scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala
View File

@ -1,24 +1,74 @@
/*
* 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.queue.function package org.broadinstitute.sting.queue.function
import org.broadinstitute.sting.commandline.Argument
import org.broadinstitute.sting.queue.util.IOUtils
import java.io.File
/** /**
* Defines a command line function that runs java code. * Defines a command line function that runs java code.
*/ */
trait JavaCommandLineFunction extends CommandLineFunction { trait JavaCommandLineFunction extends CommandLineFunction {
@Argument(doc="jar", exclusiveOf="javaMainClass")
var jarFile: File = _
@Argument(doc="Main class to run from javaClasspath", exclusiveOf="jarFile")
var javaMainClass: String = _
/** /**
* Returns the java executable to run. * Class path for the main class.
* Defaults to the current classpath.
*/ */
def javaExecutable: String var javaClasspath: List[String] = Nil
/** /**
* Memory limit for the java executable, or if None will use the default memoryLimit. * Memory limit for the java executable, or if None will use the default memoryLimit.
*/ */
var javaMemoryLimit: Option[Int] = None var javaMemoryLimit: Option[Int] = None
/**
* Returns the java executable to run.
*/
def javaExecutable: String = {
if (jarFile != null)
"-jar " + jarFile
else if (javaMainClass != null)
"-cp \"%s\" %s".format(javaClasspath.mkString(File.pathSeparator), javaMainClass)
else
null
}
override def freezeFieldValues = { override def freezeFieldValues = {
super.freezeFieldValues super.freezeFieldValues
if (javaMemoryLimit.isEmpty && memoryLimit.isDefined) if (javaMemoryLimit.isEmpty && memoryLimit.isDefined)
javaMemoryLimit = memoryLimit javaMemoryLimit = memoryLimit
if (javaMainClass != null && javaClasspath.isEmpty)
javaClasspath = JavaCommandLineFunction.currentClasspath
} }
def javaOpts = "%s -Djava.io.tmpdir=%s" def javaOpts = "%s -Djava.io.tmpdir=%s"
@ -27,3 +77,8 @@ trait JavaCommandLineFunction extends CommandLineFunction {
def commandLine = "java%s %s" def commandLine = "java%s %s"
.format(javaOpts, javaExecutable) .format(javaOpts, javaExecutable)
} }
object JavaCommandLineFunction {
val currentClasspath = System.getProperty("java.class.path")
.split(File.pathSeparatorChar).map(path => IOUtils.absolute(new File(path)).getPath).toList
}

26
scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
View File

@ -1,3 +1,27 @@
/*
* 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.queue.function package org.broadinstitute.sting.queue.function
import java.io.File import java.io.File
@ -5,7 +29,7 @@ import java.lang.annotation.Annotation
import org.broadinstitute.sting.commandline._ import org.broadinstitute.sting.commandline._
import org.broadinstitute.sting.queue.{QException, QSettings} import org.broadinstitute.sting.queue.{QException, QSettings}
import collection.JavaConversions._ import collection.JavaConversions._
import org.broadinstitute.sting.queue.function.scattergather.{Gather, SimpleTextGatherFunction} import org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction
import org.broadinstitute.sting.queue.util.{Logging, CollectionUtils, IOUtils, ReflectionUtils} import org.broadinstitute.sting.queue.util.{Logging, CollectionUtils, IOUtils, ReflectionUtils}
/** /**

20
scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamJarFunction.scala → scala/src/org/broadinstitute/sting/queue/function/scattergather/GathererFunction.scala
View File

@ -22,16 +22,20 @@
* OTHER DEALINGS IN THE SOFTWARE. * OTHER DEALINGS IN THE SOFTWARE.
*/ */
package org.broadinstitute.sting.queue.extensions.picard package org.broadinstitute.sting.queue.function.scattergather
import org.broadinstitute.sting.queue.function.JarCommandLineFunction import org.broadinstitute.sting.commandline.Gatherer
import org.broadinstitute.sting.queue.function.InProcessFunction
import collection.JavaConversions._
/** /**
* Wraps a Picard jar that operates on BAM files. * Runs a Gatherer in process.
* See http://picard.sourceforge.net/ for more info.
*
* Since the jar files take slightly different arguments
* some values are optional.
*/ */
trait PicardBamJarFunction extends JarCommandLineFunction with PicardBamFunction { class GathererFunction(gathererClass: Class[_ <: Gatherer]) extends InProcessFunction with GatherFunction {
def run() {
val gatherer = gathererClass.newInstance
if (gatherer.waitForInputs)
waitForGatherParts
gatherer.gather(this.gatherParts, this.originalOutput)
}
} }

27
scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala
View File

@ -26,7 +26,7 @@ package org.broadinstitute.sting.queue.function.scattergather
import java.io.File import java.io.File
import org.broadinstitute.sting.queue.util._ import org.broadinstitute.sting.queue.util._
import org.broadinstitute.sting.commandline.ArgumentSource import org.broadinstitute.sting.commandline.{Gatherer, Gather, ArgumentSource}
import org.broadinstitute.sting.queue.function.{QFunction, CommandLineFunction} import org.broadinstitute.sting.queue.function.{QFunction, CommandLineFunction}
import org.broadinstitute.sting.queue.QException import org.broadinstitute.sting.queue.QException
@ -240,14 +240,29 @@ trait ScatterGatherableFunction extends CommandLineFunction {
* @return A GatherFunction instantiated from @Gather. * @return A GatherFunction instantiated from @Gather.
*/ */
protected def newGatherFunction(gatherField: ArgumentSource) : GatherFunction = { protected def newGatherFunction(gatherField: ArgumentSource) : GatherFunction = {
var gatherClass: Class[_ <: GatherFunction] = null var gatherClass: Class[_] = null
// Check if there is a function that will return the gather class for this field.
if (this.gatherClass != null) if (this.gatherClass != null)
if (this.gatherClass.isDefinedAt(gatherField)) if (this.gatherClass.isDefinedAt(gatherField))
gatherClass = this.gatherClass(gatherField) gatherClass = this.gatherClass(gatherField)
if (gatherClass == null)
gatherClass = ReflectionUtils.getAnnotation(gatherField.field, classOf[Gather]) // Check for an annotation defining the gather class.
.value.asSubclass(classOf[GatherFunction]) if (gatherClass == null) {
gatherClass.newInstance.asInstanceOf[GatherFunction] if (ReflectionUtils.hasAnnotation(gatherField.field, classOf[Gather])) {
gatherClass = ReflectionUtils.getAnnotation(gatherField.field, classOf[Gather]).value
} else {
throw new QException("Missing @Gather annotation: " + gatherField.field.getName)
}
}
if (classOf[GatherFunction].isAssignableFrom(gatherClass)) {
gatherClass.newInstance.asInstanceOf[GatherFunction]
} else if (classOf[Gatherer].isAssignableFrom(gatherClass)) {
new GathererFunction(gatherClass.asSubclass(classOf[Gatherer]))
} else {
throw new QException("Unsupported @Gather class type: " + gatherClass)
}
} }
/** /**

4
scala/src/org/broadinstitute/sting/queue/pipeline/BamProcessing.scala
View File

@ -2,7 +2,7 @@ package org.broadinstitute.sting.queue.pipeline
import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.gatk._
import java.io.File import java.io.File
import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction import org.broadinstitute.sting.queue.extensions.picard.PicardBamFunction
import org.broadinstitute.sting.queue.function.CommandLineFunction import org.broadinstitute.sting.queue.function.CommandLineFunction
import org.broadinstitute.sting.utils.yaml.YamlUtils import org.broadinstitute.sting.utils.yaml.YamlUtils
import org.broadinstitute.sting.datasources.pipeline.Pipeline import org.broadinstitute.sting.datasources.pipeline.Pipeline
@ -125,7 +125,7 @@ class BamProcessing(attribs: Pipeline, gatkJar: File, fixMatesJar: File) {
return pfm return pfm
} }
class PicardFixMates extends PicardBamJarFunction { class PicardFixMates extends PicardBamFunction {
@Input(doc="input bam files") var bams: List[File] = Nil @Input(doc="input bam files") var bams: List[File] = Nil
@Output(doc="output bam file") var outBam: File = null @Output(doc="output bam file") var outBam: File = null

8
scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala
View File

@ -57,7 +57,7 @@ class VariantCalling(attribs: Pipeline,gatkJar: File) {
ug.input_file = bams ug.input_file = bams
ug.out = output ug.out = output
ug.downsample_to_coverage = Some(300) ug.downsample_to_coverage = Some(300)
ug.dt = Some(DownsampleType.BY_SAMPLE) ug.dt = DownsampleType.BY_SAMPLE
ug.scatterCount = 50 ug.scatterCount = 50
if ( bams.size > 40 ) { if ( bams.size > 40 ) {
@ -105,8 +105,8 @@ class VariantCalling(attribs: Pipeline,gatkJar: File) {
def StandardIndelCombine( igList : List[IndelGenotyperV2], output : File ) : CombineVariants = { def StandardIndelCombine( igList : List[IndelGenotyperV2], output : File ) : CombineVariants = {
var cv = new CombineVariants with StandardCommandLineGATK var cv = new CombineVariants with StandardCommandLineGATK
cv.out = output cv.out = output
cv.genotypemergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.GenotypeMergeType.UNIQUIFY) cv.genotypemergeoption = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.GenotypeMergeType.UNIQUIFY
cv.variantmergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION) cv.variantmergeoption = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION
cv.analysisName = "IndelGenotyper" cv.analysisName = "IndelGenotyper"
cv.priority = (igList.map[String,List[String]](ig => swapExt(ig.out,".vcf","").getAbsolutePath)).mkString(",") cv.priority = (igList.map[String,List[String]](ig => swapExt(ig.out,".vcf","").getAbsolutePath)).mkString(",")
//cv.priority = (igList.foldLeft[List[String]](Nil)( (prLs, ig) => prLs ::: List(swapExt(ig.out,".vcf","").getAbsolutePath))).mkString(",") //cv.priority = (igList.foldLeft[List[String]](Nil)( (prLs, ig) => prLs ::: List(swapExt(ig.out,".vcf","").getAbsolutePath))).mkString(",")
@ -408,7 +408,7 @@ object VariantCalling {
ugTokens.foreach( addEntry(_) ) ugTokens.foreach( addEntry(_) )
myUG.reference_sequence = new File(ugMap("reference_sequence")) myUG.reference_sequence = new File(ugMap("reference_sequence"))
myUG.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.valueOf(ugMap("baq"))) myUG.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.valueOf(ugMap("baq"))
myUG.baqGapOpenPenalty = Some(ugMap("baqGapOpenPenalty").toDouble) myUG.baqGapOpenPenalty = Some(ugMap("baqGapOpenPenalty").toDouble)
myUG.DBSNP = new File(ugMap("DBSNP")) myUG.DBSNP = new File(ugMap("DBSNP"))

139
scala/src/org/broadinstitute/sting/queue/util/PrimitiveOptionConversions.scala 100644
View File

@ -0,0 +1,139 @@
/*
* 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.queue.util
/**
* An importable object that provides automatic primitive to option conversion.
*/
object PrimitiveOptionConversions {
// Conversion from Option
implicit def byteOption2byte(x: Option[Byte]) = x.get
implicit def shortOption2short(x: Option[Short]) = x.get
implicit def charOption2char(x: Option[Char]) = x.get
implicit def intOption2int(x: Option[Int]) = x.get
implicit def longOption2long(x: Option[Long]) = x.get
implicit def floatOption2float(x: Option[Float]) = x.get
implicit def doubleOption2double(x: Option[Double]) = x.get
implicit def booleanOption2boolean(x: Option[Boolean]) = x.get
// Conversion to Option
implicit def byte2byteOption(x: Byte) = Some(x)
implicit def short2shortOption(x: Short) = Some(x)
implicit def char2charOption(x: Char) = Some(x)
implicit def int2intOption(x: Int) = Some(x)
implicit def long2longOption(x: Long) = Some(x)
implicit def float2floatOption(x: Float) = Some(x)
implicit def double2doubleOption(x: Double) = Some(x)
implicit def boolean2booleanOption(x: Boolean) = Some(x)
// Narrowing for constants to byte, short, and float
implicit def int2byteOption(x: Int) = Some(x.toByte)
implicit def int2shortOption(x: Int) = Some(x.toShort)
implicit def double2floatOption(x: Float) = Some(x.toFloat)
// Widening
implicit def byte2shortOption(x: Byte) = Some(x.toShort)
implicit def byte2intOption(x: Byte) = Some(x.toInt)
implicit def byte2longOption(x: Byte) = Some(x.toLong)
implicit def byte2floatOption(x: Byte) = Some(x.toFloat)
implicit def byte2doubleOption(x: Byte) = Some(x.toDouble)
implicit def short2intOption(x: Short) = Some(x.toInt)
implicit def short2longOption(x: Short) = Some(x.toLong)
implicit def short2floatOption(x: Short) = Some(x.toFloat)
implicit def short2doubleOption(x: Short) = Some(x.toDouble)
implicit def char2intOption(x: Char) = Some(x.toInt)
implicit def char2longOption(x: Char) = Some(x.toLong)
implicit def char2floatOption(x: Char) = Some(x.toFloat)
implicit def char2doubleOption(x: Char) = Some(x.toDouble)
implicit def int2longOption(x: Int) = Some(x.toLong)
implicit def int2floatOption(x: Int) = Some(x.toFloat)
implicit def int2doubleOption(x: Int) = Some(x.toDouble)
implicit def long2floatOption(x: Long) = Some(x.toFloat)
implicit def long2doubleOption(x: Long) = Some(x.toDouble)
implicit def float2doubleOption(x: Float) = Some(x.toDouble)
}
/**
* A trait that exposes the above functions to all sub classes as well.
*/
trait PrimitiveOptionConversions {
// How to we import these implicit definitions into the trait so that they are seen by objects extending a trait?
// import PrimitiveOptionConversion._ inside of a trait does not seem to work?
// Declaring them in a trait like this does work but does not seem scala-ish.
implicit def byteOption2byte(x: Option[Byte]) = PrimitiveOptionConversions.byteOption2byte(x)
implicit def shortOption2short(x: Option[Short]) = PrimitiveOptionConversions.shortOption2short(x)
implicit def charOption2char(x: Option[Char]) = PrimitiveOptionConversions.charOption2char(x)
implicit def intOption2int(x: Option[Int]) = PrimitiveOptionConversions.intOption2int(x)
implicit def longOption2long(x: Option[Long]) = PrimitiveOptionConversions.longOption2long(x)
implicit def floatOption2float(x: Option[Float]) = PrimitiveOptionConversions.floatOption2float(x)
implicit def doubleOption2double(x: Option[Double]) = PrimitiveOptionConversions.doubleOption2double(x)
implicit def booleanOption2boolean(x: Option[Boolean]) = PrimitiveOptionConversions.booleanOption2boolean(x)
implicit def byte2byteOption(x: Byte) = PrimitiveOptionConversions.byte2byteOption(x)
implicit def short2shortOption(x: Short) = PrimitiveOptionConversions.short2shortOption(x)
implicit def char2charOption(x: Char) = PrimitiveOptionConversions.char2charOption(x)
implicit def int2intOption(x: Int) = PrimitiveOptionConversions.int2intOption(x)
implicit def long2longOption(x: Long) = PrimitiveOptionConversions.long2longOption(x)
implicit def float2floatOption(x: Float) = PrimitiveOptionConversions.float2floatOption(x)
implicit def double2doubleOption(x: Double) = PrimitiveOptionConversions.double2doubleOption(x)
implicit def boolean2booleanOption(x: Boolean) = PrimitiveOptionConversions.boolean2booleanOption(x)
implicit def int2byteOption(x: Int) = PrimitiveOptionConversions.int2byteOption(x)
implicit def int2shortOption(x: Int) = PrimitiveOptionConversions.int2shortOption(x)
implicit def double2floatOption(x: Float) = PrimitiveOptionConversions.double2floatOption(x)
implicit def byte2shortOption(x: Byte) = PrimitiveOptionConversions.byte2shortOption(x)
implicit def byte2intOption(x: Byte) = PrimitiveOptionConversions.byte2intOption(x)
implicit def byte2longOption(x: Byte) = PrimitiveOptionConversions.byte2longOption(x)
implicit def byte2floatOption(x: Byte) = PrimitiveOptionConversions.byte2floatOption(x)
implicit def byte2doubleOption(x: Byte) = PrimitiveOptionConversions.byte2doubleOption(x)
implicit def short2intOption(x: Short) = PrimitiveOptionConversions.short2intOption(x)
implicit def short2longOption(x: Short) = PrimitiveOptionConversions.short2longOption(x)
implicit def short2floatOption(x: Short) = PrimitiveOptionConversions.short2floatOption(x)
implicit def short2doubleOption(x: Short) = PrimitiveOptionConversions.short2doubleOption(x)
implicit def char2intOption(x: Char) = PrimitiveOptionConversions.char2intOption(x)
implicit def char2longOption(x: Char) = PrimitiveOptionConversions.char2longOption(x)
implicit def char2floatOption(x: Char) = PrimitiveOptionConversions.char2floatOption(x)
implicit def char2doubleOption(x: Char) = PrimitiveOptionConversions.char2doubleOption(x)
implicit def int2longOption(x: Int) = PrimitiveOptionConversions.int2longOption(x)
implicit def int2floatOption(x: Int) = PrimitiveOptionConversions.int2floatOption(x)
implicit def int2doubleOption(x: Int) = PrimitiveOptionConversions.int2doubleOption(x)
implicit def long2floatOption(x: Long) = PrimitiveOptionConversions.long2floatOption(x)
implicit def long2doubleOption(x: Long) = PrimitiveOptionConversions.long2doubleOption(x)
implicit def float2doubleOption(x: Float) = PrimitiveOptionConversions.float2doubleOption(x)
}

28
scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
View File

@ -1,3 +1,27 @@
/*
* 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.queue.pipeline.examples package org.broadinstitute.sting.queue.pipeline.examples
import org.testng.annotations.Test import org.testng.annotations.Test
@ -10,8 +34,8 @@ class ExampleCountLociPipelineTest {
var testOut = "count.out" var testOut = "count.out"
val spec = new PipelineTestSpec val spec = new PipelineTestSpec
spec.name = "countloci" spec.name = "countloci"
spec.args = "-S scala/qscript/examples/ExampleCountLoci.scala -gatk %s -R %s -I %s -o %s".format( spec.args = "-S scala/qscript/examples/ExampleCountLoci.scala -R %s -I %s -o %s".format(
PipelineTest.currentGATK, BaseTest.hg18Reference, BaseTest.validationDataLocation + "small_bam_for_countloci.bam", testOut BaseTest.hg18Reference, BaseTest.validationDataLocation + "small_bam_for_countloci.bam", testOut
) )
spec.fileMD5s += testOut -> "67823e4722495eb10a5e4c42c267b3a6" spec.fileMD5s += testOut -> "67823e4722495eb10a5e4c42c267b3a6"
PipelineTest.executeTest(spec) PipelineTest.executeTest(spec)