Single positional arguments are now treated as names unless they actually match a tribble feature
This commit is contained in:
Mark DePristo
parent
f8a56bc64b
commit
80924d24de
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@ -317,39 +317,46 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
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String tribbleType = null;
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Tags tags = getArgumentTags(matches);
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// must have one or two tag values here
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if ( tags.getPositionalTags().size() == 2 ) { // -X:name,type style
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if ( tags.getPositionalTags().size() > 2 ) {
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throw new UserException.CommandLineException(
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String.format("Unexpected number of positional tags for argument %s : %s. " +
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"Rod bindings only suport -X:type and -X:name,type argument styles",
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value, source.field.getName()));
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} if ( tags.getPositionalTags().size() == 2 ) {
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// -X:name,type style
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name = tags.getPositionalTags().get(0);
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tribbleType = tags.getPositionalTags().get(1);
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} else {
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if ( tags.getPositionalTags().size() == 1 ) {
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// -X:type style is a type when we cannot determine the type dynamically
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tribbleType = tags.getPositionalTags().get(0);
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// case with 0 or 1 positional tags
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FeatureManager manager = new FeatureManager();
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// -X:type style is a type when we cannot determine the type dynamically
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String tag1 = tags.getPositionalTags().size() == 1 ? tags.getPositionalTags().get(0) : null;
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if ( tag1 != null ) {
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if ( manager.getByName(tag1) != null ) // this a type
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tribbleType = tag1;
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else
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name = tag1;
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}
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// try to determine the file type dynamically
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FeatureManager manager = new FeatureManager();
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File file = new File(value);
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if ( file.canRead() && file.isFile() ) {
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FeatureManager.FeatureDescriptor featureDescriptor = manager.getByFiletype(file);
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if ( featureDescriptor != null ) {
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tribbleType = featureDescriptor.getName();
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logger.warn("Dynamically determined type of " + file + " to be " + tribbleType);
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if ( tags.getPositionalTags().size() == 1 ) {
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// -X:type style is a name when we can determine the type dynamically
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name = tags.getPositionalTags().get(0);
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if ( tribbleType == null ) {
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// try to determine the file type dynamically
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File file = new File(value);
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if ( file.canRead() && file.isFile() ) {
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FeatureManager.FeatureDescriptor featureDescriptor = manager.getByFiletype(file);
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if ( featureDescriptor != null ) {
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tribbleType = featureDescriptor.getName();
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logger.warn("Dynamically determined type of " + file + " to be " + tribbleType);
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}
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}
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}
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// now, if we haven't found a type
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if ( tribbleType == null )
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throw new UserException.CommandLineException(
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String.format("Unexpected number of positional tags for argument %s : %s. " +
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"Rod bindings only suport -X:type and -X:name,type argument styles",
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value, source.field.getName()));
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}
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if ( tribbleType == null ) // error handling
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throw new UserException.CommandLineException(
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String.format("Could not parse argument %s with value %s",
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defaultDefinition.fullName, value));
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Constructor ctor = (makeRawTypeIfNecessary(type)).getConstructor(Class.class, String.class, String.class, String.class, Tags.class);
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Class parameterType = getParameterizedTypeClass(type);
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RodBinding result = (RodBinding)ctor.newInstance(parameterType, name, value, tribbleType, tags);
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@ -24,26 +24,16 @@
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package org.broadinstitute.sting.gatk;
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import org.broad.tribble.Feature;
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import org.broadinstitute.sting.WalkerTest;
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import org.broadinstitute.sting.commandline.Input;
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import org.broadinstitute.sting.commandline.RodBinding;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.testng.Assert;
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import org.testng.annotations.Test;
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import java.util.List;
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/**
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*
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*/
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public class EngineFeaturesIntegrationTest extends WalkerTest {
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private void testBadRODBindingInput(String type, String name, Class c) {
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WalkerTestSpec spec = new WalkerTestSpec("-T SelectVariants -L 1:1 --variants:" + type + " "
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WalkerTestSpec spec = new WalkerTestSpec("-T SelectVariants -L 1:1 --variants:variants," + type + " "
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+ b37dbSNP132 + " -R " + b37KGReference + " -o %s",
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1, c);
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executeTest(name, spec);
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@ -64,27 +54,4 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
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@Test() private void testBadRODBindingInputTypeUnknownType() {
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testBadRODBindingInput("bedXXX", "Unknown input to VCF expecting walker", UserException.UnknownTribbleType.class);
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}
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}
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//class TestRodBindings extends RodWalker<Integer, Integer> {
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// @Input(fullName="req", required=true)
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// public RodBinding<Feature> required;
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//
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// @Input(fullName="optional", required=false)
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// public RodBinding<Feature> optional = RodBinding.makeUnbound(Feature.class);
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//
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// @Input(fullName="rodList", shortName="RL", doc="A list of ROD types that we will convert to a table", required=true)
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// public List<RodBinding<Feature>> variantsList;
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//
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// public void initialize() {
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// // bound values
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// Assert.assertEquals(required.isBound(), true);
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//
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//
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// System.exit(0);
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// }
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//
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// public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { return 0; }
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// public Integer reduceInit() { return 0; }
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// public Integer reduce(Integer counter, Integer sum) { return counter + sum; }
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//}
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}
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@ -11,7 +11,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
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return "-T ReadBackedPhasing" +
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" -R " + reference +
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" -I " + validationDataLocation + reads +
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" -B:variant,VCF " + validationDataLocation + VCF +
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" --variants " + validationDataLocation + VCF +
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" --cacheWindowSize " + cacheWindowSize +
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" --maxPhaseSites " + maxPhaseSites +
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" --phaseQualityThresh " + phaseQualityThresh +
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@ -72,7 +72,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
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public void combinePLs(String file1, String file2, String md5) {
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WalkerTestSpec spec = new WalkerTestSpec(
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"-T CombineVariants -NO_HEADER -o %s -R " + b36KGReference + " -priority v1,v2 -B:v1,VCF " + validationDataLocation + file1 + " -B:v2,VCF " + validationDataLocation + file2,
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"-T CombineVariants -NO_HEADER -o %s -R " + b36KGReference + " -priority v1,v2 -V:v1 " + validationDataLocation + file1 + " -V:v2 " + validationDataLocation + file2,
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1,
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Arrays.asList(md5));
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executeTest("combine PLs 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec);
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@ -17,11 +17,11 @@ public class VCFIntegrationTest extends WalkerTest {
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String baseCommand = "-R " + b37KGReference + " -NO_HEADER -o %s ";
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String test1 = baseCommand + "-T VariantAnnotator --variants:vcf " + testVCF + " -BTI variants";
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String test1 = baseCommand + "-T VariantAnnotator --variants " + testVCF + " -BTI variants";
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WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList(md5ofInputVCF));
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List<File> result = executeTest("Test Variant Annotator with no changes", spec1).getFirst();
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String test2 = baseCommand + "-T VariantsToVCF --variants:vcf " + result.get(0).getAbsolutePath();
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String test2 = baseCommand + "-T VariantsToVCF --variants " + result.get(0).getAbsolutePath();
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WalkerTestSpec spec2 = new WalkerTestSpec(test2, 1, Arrays.asList(md5ofInputVCF));
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executeTest("Test Variants To VCF from new output", spec2);
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}
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