Added a generic method for returning the complete command-line used when calling a walker, to be used in the bam/vcf headers. As requested, every possible engine/walker argument is included. I've added it to the Unified Genotyper output, so people can try it out and let me know what they think. Something that needs to be discussed in group meeting: what happens when we merge VCFs? Do we keep all of the command-lines?
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3969 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks
parent
6e389059cf
commit
594b7912f1
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@ -26,11 +26,10 @@
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package org.broadinstitute.sting.commandline;
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import org.broadinstitute.sting.utils.classloader.JVMUtils;
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import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
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import org.broadinstitute.sting.gatk.walkers.Walker;
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import java.util.Map;
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import java.util.List;
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import java.util.LinkedHashMap;
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import java.util.Collection;
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import java.util.*;
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/**
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* Static utility methods for working with command-line arguments.
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@ -66,4 +65,27 @@ public class CommandLineUtils {
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return commandLineArguments;
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}
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public static String createApproximateCommandLineArgumentString(GenomeAnalysisEngine toolkit, Collection<Object> otherArgumentProviders, Class<? extends Walker> walkerType) {
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StringBuffer sb = new StringBuffer();
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sb.append("analysis_type=");
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sb.append(toolkit.getWalkerName(walkerType));
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ArrayList<Object> allArgumentProviders = new ArrayList<Object>();
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allArgumentProviders.add(toolkit.getArguments());
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allArgumentProviders.addAll(otherArgumentProviders);
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Map<String,String> commandLineArgs = getApproximateCommandLineArguments(allArgumentProviders);
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for ( Map.Entry<String, String> commandLineArg : commandLineArgs.entrySet() ) {
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sb.append(" ");
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sb.append(commandLineArg.getKey());
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sb.append("=");
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sb.append(commandLineArg.getValue());
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}
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return sb.toString();
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}
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}
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@ -39,7 +39,6 @@ import org.broadinstitute.sting.utils.genotype.vcf.*;
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import java.util.*;
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import java.io.PrintStream;
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import java.io.File;
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/**
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@ -56,10 +55,10 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
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public GenotypeWriter writer = null;
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@Argument(fullName = "verbose_mode", shortName = "verbose", doc = "File to print all of the annotated and detailed debugging output", required = false)
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public PrintStream verboseWriter = null;
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protected PrintStream verboseWriter = null;
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@Argument(fullName = "metrics_file", shortName = "metrics", doc = "File to print any relevant callability metrics output", required = false)
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public PrintStream metricsWriter = null;
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protected PrintStream metricsWriter = null;
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@Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to apply to variant calls", required=false)
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protected String[] annotationsToUse = {};
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@ -67,6 +66,10 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
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@Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", required=false)
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protected String[] annotationClassesToUse = { "Standard" };
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@Argument(fullName = "NO_HEADER", shortName = "NO_HEADER", doc = "Don't output the usual VCF header tag with the command line. FOR DEBUGGING PURPOSES ONLY. This option is required in order to pass integration tests.", required = false)
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protected Boolean NO_VCF_HEADER_LINE = false;
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// the calculation arguments
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private UnifiedGenotyperEngine UG_engine = null;
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@ -133,10 +136,6 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
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if ( !(writer instanceof VCFGenotypeWriter) )
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return headerInfo;
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// first, the basic info
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headerInfo.add(new VCFHeaderLine("source", "UnifiedGenotyper"));
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headerInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
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// all annotation fields from VariantAnnotatorEngine
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headerInfo.addAll(annotationEngine.getVCFAnnotationDescriptions());
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@ -155,16 +154,12 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
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headerInfo.add(new VCFFilterHeaderLine(UnifiedGenotyperEngine.LOW_QUAL_FILTER_NAME, "Low quality"));
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// all of the arguments from the argument collection
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Set<Object> args = new HashSet<Object>();
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args.add(UAC);
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args.addAll(getToolkit().getFilters());
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Map<String,String> commandLineArgs = CommandLineUtils.getApproximateCommandLineArguments(args);
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for ( Map.Entry<String, String> commandLineArg : commandLineArgs.entrySet() )
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headerInfo.add(new VCFHeaderLine(String.format("UG_%s", commandLineArg.getKey()), commandLineArg.getValue()));
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// also, the list of input bams
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for ( File file : getToolkit().getArguments().samFiles )
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headerInfo.add(new VCFHeaderLine("UG_bam_file_used", file.getName()));
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if ( !NO_VCF_HEADER_LINE ) {
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Set<Object> args = new HashSet<Object>();
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args.add(UAC);
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headerInfo.add(new VCFHeaderLine("UnifiedGenotyper", "\"" + CommandLineUtils.createApproximateCommandLineArgumentString(getToolkit(), args, getClass()) + "\""));
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}
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return headerInfo;
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}
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@ -13,18 +13,7 @@ import java.util.Map;
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public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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// --------------------------------------------------------------------------------------------------------------
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//
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// testing pooled model
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//
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// --------------------------------------------------------------------------------------------------------------
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// @Test
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// public void testPooled1() {
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// WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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// "-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,000-10,024,000 -bm empirical -gm POOLED -ps 60 -confidence 30", 1,
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// Arrays.asList("c91f44a198cd7222520118726ea806ca"));
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// executeTest("testPooled1", spec);
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// }
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private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER";
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// --------------------------------------------------------------------------------------------------------------
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//
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@ -34,24 +23,24 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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@Test
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public void testMultiSamplePilot1Joint() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,022,000-10,025,000", 1,
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Arrays.asList("680292498be02796787bc4b2393a003c"));
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baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,022,000-10,025,000", 1,
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Arrays.asList("73d514f53f1630832b3bed65c67fe869"));
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executeTest("testMultiSamplePilot1 - Joint Estimate", spec);
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}
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@Test
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public void testMultiSamplePilot2Joint() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,050,000", 1,
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Arrays.asList("1bf2dc92f97f7bd661e61453b657477a"));
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baseCommand + " -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,050,000", 1,
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Arrays.asList("e21ff78ca74bdaacaea562795a90e979"));
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executeTest("testMultiSamplePilot2 - Joint Estimate", spec);
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}
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@Test
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public void testSingleSamplePilot2Joint() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000", 1,
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Arrays.asList("6cab256a3c984c8938ffe026ed620c36"));
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000", 1,
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Arrays.asList("20878adf2f56687ef03f32e6bac8fb30"));
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executeTest("testSingleSamplePilot2 - Joint Estimate", spec);
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}
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@ -63,20 +52,20 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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@Test
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public void testParallelization() {
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String md5 = "8f464769be0920ee2bdfd72da2193161";
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String md5 = "664f02681a0ff09bdf3269f97284009c";
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WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,075,000", 1,
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,075,000", 1,
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Arrays.asList(md5));
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executeTest("test parallelization (single thread)", spec1);
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WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,075,000 -nt 2", 1,
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,075,000 -nt 2", 1,
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Arrays.asList(md5));
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executeTest("test parallelization (2 threads)", spec2);
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WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,075,000 -nt 4", 1,
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,075,000 -nt 4", 1,
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Arrays.asList(md5));
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executeTest("test parallelization (4 threads)", spec3);
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}
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@ -90,15 +79,15 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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@Test
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public void testParameter() {
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HashMap<String, String> e = new HashMap<String, String>();
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e.put( "-genotype", "e4735f7d20f8d82d359f89824cfafbad" );
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e.put( "-all_bases", "c41acfac9f7908609a8d0ccdcefbd9e4" );
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e.put( "--min_base_quality_score 26", "6fea507d70c1b7b74fb6b553bd8904c2" );
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e.put( "--min_mapping_quality_score 26", "f8b1a0449f0a49c1c5edb70f4e90b5f8" );
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e.put( "--max_mismatches_in_40bp_window 5", "bf29fc94431f7b18fd4c65025294de3c" );
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e.put( "-genotype", "5d3f4a25039959e1758a035b8dc595b7" );
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e.put( "-all_bases", "402740e2e1ef23a246120dde91a42dcd" );
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e.put( "--min_base_quality_score 26", "a6fe67665b1ffe1d53194199b1d28b9a" );
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e.put( "--min_mapping_quality_score 26", "3fcb922f5939221ee73661f83d604050" );
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e.put( "--max_mismatches_in_40bp_window 5", "93a0d181625c2c98c35acd03599f6f8b" );
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for ( Map.Entry<String, String> entry : e.entrySet() ) {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 " + entry.getKey(), 1,
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 " + entry.getKey(), 1,
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Arrays.asList(entry.getValue()));
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executeTest(String.format("testParameter[%s]", entry.getKey()), spec);
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}
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@ -107,13 +96,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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@Test
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public void testConfidence() {
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WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1,
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Arrays.asList("065be668bbea5342c7700017e131eb2a"));
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1,
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Arrays.asList("292ecd223494a2cff64a9cb72b0850d9"));
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executeTest("testConfidence1", spec1);
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WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1,
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Arrays.asList("b58578df1d05926fb7ecd9fecffa9c5e"));
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1,
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Arrays.asList("65e29fad296e3d03312087e7e9168095"));
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executeTest("testConfidence2", spec2);
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}
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@ -131,7 +120,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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for ( Map.Entry<String, String> entry : e.entrySet() ) {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -vf " + entry.getKey(), 1,
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -vf " + entry.getKey(), 1,
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Arrays.asList(entry.getValue()));
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executeTest(String.format("testOtherFormat[%s]", entry.getKey()), spec);
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}
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@ -154,7 +143,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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for ( Map.Entry<Double, String> entry : e.entrySet() ) {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -vf GELI -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 --heterozygosity " + entry.getKey(), 1,
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baseCommand + " -vf GELI -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 --heterozygosity " + entry.getKey(), 1,
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Arrays.asList(entry.getValue()));
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executeTest(String.format("testHeterozyosity[%s]", entry.getKey()), spec);
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}
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@ -174,7 +163,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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for ( Map.Entry<String, String> entry : e.entrySet() ) {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -vf GELI -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm " + entry.getKey(), 1,
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baseCommand + " -vf GELI -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm " + entry.getKey(), 1,
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Arrays.asList(entry.getValue()));
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executeTest(String.format("testOtherBaseCallModel[%s]", entry.getKey()), spec);
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}
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@ -188,8 +177,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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@Test
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public void testMultiTechnologies() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper" +
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" -R " + b36KGReference +
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baseCommand +
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" -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" +
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" -varout %s" +
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" -L 1:10,000,000-10,100,000" +
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