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Throw a GVCFIndexException when the user doesn't specify the optimal indexing strategy

This commit is contained in:
Joel Thibault 2013-12-03 16:36:23 -05:00
parent 8571a641bf
commit 5fe0531b4d
4 changed files with 59 additions and 4 deletions
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11
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -92,6 +92,7 @@ import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.pairhmm.PairHMM;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variant.GATKVCFIndexType;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.variantcontext.*;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
@ -536,6 +537,10 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
ReferenceConfidenceModel referenceConfidenceModel = null;
// as determined experimentally Nov-Dec 2013
protected final static GATKVCFIndexType OPTIMAL_GVCF_INDEX_TYPE = GATKVCFIndexType.LINEAR;
protected final static int OPTIMAL_GVCF_INDEX_PARAMETER = 128000;
//---------------------------------------------------------------------------------------------------------------
//
// initialize
@ -601,6 +606,12 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
if ( samples.size() != 1 ) throw new UserException.BadArgumentValue("emitRefConfidence", "Can only be used in single sample mode currently");
headerInfo.addAll(referenceConfidenceModel.getVCFHeaderLines());
if ( emitReferenceConfidence == ReferenceConfidenceMode.GVCF ) {
// a kluge to enforce the use of this indexing strategy
if (getToolkit().getArguments().variant_index_type != OPTIMAL_GVCF_INDEX_TYPE ||
getToolkit().getArguments().variant_index_parameter != OPTIMAL_GVCF_INDEX_PARAMETER) {
throw new UserException.GVCFIndexException(OPTIMAL_GVCF_INDEX_TYPE, OPTIMAL_GVCF_INDEX_PARAMETER);
}
try {
vcfWriter = new GVCFWriter(vcfWriter, GVCFGQBands);
} catch ( IllegalArgumentException e ) {

42
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
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@ -47,6 +47,8 @@
package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variant.GATKVCFIndexType;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
@ -79,8 +81,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
*/
@Test(dataProvider = "MyDataProvider")
public void testHCWithGVCF(String bam, HaplotypeCaller.ReferenceConfidenceMode mode, String intervals, String md5) {
final String commandLine = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R %s -I %s %s -ERC %s --no_cmdline_in_header",
b37KGReference, bam, intervals, mode);
final String commandLine = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R %s -I %s %s -ERC %s --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
b37KGReference, bam, intervals, mode, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
final String name = "testHCWithGVCF bam=" + bam + " intervals= " + intervals + " gvcf= " + mode;
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(md5));
executeTest(name, spec);
@ -88,10 +90,42 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
@Test
public void testERCRegionWithNoCalledHaplotypes() {
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF",
b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001");
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF -variant_index_type %s -variant_index_parameter %d",
b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001", HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(""));
spec.disableShadowBCF();
executeTest("testERCRegionWithNoCalledHaplotypes", spec);
}
@Test()
public void testMissingGVCFIndexException() {
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF",
b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001");
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", 1, UserException.GVCFIndexException.class);
spec.disableShadowBCF();
executeTest("testMissingGVCFIndexingStrategyException", spec);
}
@Test()
public void testWrongParameterGVCFIndexException() {
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF -variant_index_type %s -variant_index_parameter %d",
b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001", HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER + 1);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", 1, UserException.GVCFIndexException.class);
spec.disableShadowBCF();
executeTest("testMissingGVCFIndexingStrategyException", spec);
}
@Test()
public void testWrongTypeGVCFIndexException() {
// ensure non-optimal, if optimal changes
GATKVCFIndexType type = GATKVCFIndexType.DYNAMIC_SEEK;
if (HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE == GATKVCFIndexType.DYNAMIC_SEEK)
type = GATKVCFIndexType.DYNAMIC_SIZE;
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF -variant_index_type %s -variant_index_parameter %d",
b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001", type, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", 1, UserException.GVCFIndexException.class);
spec.disableShadowBCF();
executeTest("testMissingGVCFIndexingStrategyException", spec);
}
}

9
public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
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@ -33,6 +33,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variant.GATKVCFIndexType;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.io.File;
@ -455,6 +456,14 @@ public class UserException extends ReviewedStingException {
}
}
public static class GVCFIndexException extends UserException {
public GVCFIndexException (GATKVCFIndexType indexType, int indexParameter) {
super(String.format("GVCF output requires a specific indexing strategy. Please re-run including the arguments " +
"-variant_index_type %s -variant_index_parameter %d.",
indexType, indexParameter));
}
}
/**
* A special exception that happens only in the case where
* the filesystem, by design or configuration, is completely unable

1
public/java/test/org/broadinstitute/sting/WalkerTest.java
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@ -201,6 +201,7 @@ public class WalkerTest extends BaseTest {
this.testClass = getCallingTestClass();
}
// @Test(expectedExceptions) doesn't work in integration tests, so use this instead
public WalkerTestSpec(String args, int nOutputFiles, Class expectedException) {
this.args = args;
this.nOutputFiles = nOutputFiles;