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Phase I of my promise to Mark: fleshed out integration tests for Indel Realigner 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5297 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-02-23 21:05:20 +00:00
parent 75bd0129e7
commit c59c8b9872
2 changed files with 80 additions and 21 deletions
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3
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
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@ -13,8 +13,7 @@ import java.util.Map;
// Note that this class also serves as an integration test for the VariantAnnotator! //
// ********************************************************************************** //
public class
UnifiedGenotyperIntegrationTest extends WalkerTest {
public class UnifiedGenotyperIntegrationTest extends WalkerTest {
private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER";

98
java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
View File

@ -4,36 +4,96 @@ import org.broadinstitute.sting.WalkerTest;
import org.testng.annotations.Test;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
public class IndelRealignerIntegrationTest extends WalkerTest {
private static final String mainTestBam = validationDataLocation + "indelRealignerTest.pilot1.ceu.bam";
private static final String mainTestIntervals = validationDataLocation + "indelRealignerTest.pilot1.ceu.intervals";
private static final String knownIndels = validationDataLocation + "indelRealignerTest.pilot1.ceu.vcf";
private static final String baseCommandPrefix = "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + mainTestBam + " -targetIntervals " + mainTestIntervals + " -compress 0 -L 20:49,500-55,500 --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe ";
private static final String baseCommand = baseCommandPrefix + "-o %s ";
@Test
public void testRealignerLod5() {
String[] md5s = {"a377de4e2eb4df8ef79590e4131afe35", "c4ef635f2597b12b93a73199f07e509b"};
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -LOD 5 -maxConsensuses 100 -greedy 100 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -o %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
2,
Arrays.asList(md5s));
executeTest("test realigner lod5", spec);
public void testDefaults() {
String md5 = "20ff8b76d834a8aaca46405e8328d258";
WalkerTestSpec spec1 = new WalkerTestSpec(
baseCommand,
1,
Arrays.asList(md5));
executeTest("test realigner defaults", spec1);
WalkerTestSpec spec2 = new WalkerTestSpec(
baseCommand + "-B:indels,vcf " + knownIndels,
1,
Arrays.asList(md5));
executeTest("test realigner defaults with VCF", spec2);
WalkerTestSpec spec3 = new WalkerTestSpec(
baseCommand + "-D " + GATKDataLocation + "dbsnp_129_b36.rod",
1,
Arrays.asList(md5));
executeTest("realigner defaults with dbsnp", spec3);
}
@Test
public void testRealignerLod50() {
String[] md5s = {"a377de4e2eb4df8ef79590e4131afe35", "3735a510513b6fa4161d92155e026283"};
public void testStats() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -LOD 50 -maxConsensuses 100 -greedy 100 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -o %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
2,
Arrays.asList(md5s));
executeTest("test realigner lod50", spec);
baseCommandPrefix + "-stats %s -o /dev/null",
1,
Arrays.asList("ed5a207ddf5bdda4bb76899fb3eae35c"));
executeTest("realigner stats", spec);
}
@Test
public void testRealignerKnownsOnly() {
String[] md5s = {"654cb0c845c3f25af6a3f8911ac06a73", "74652bd8240291293ec921f8ecfa1622"};
public void testLods() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "-LOD 60", "20ff8b76d834a8aaca46405e8328d258" );
e.put( "-LOD 1", "39862f48d9eaaf841ca4a0d2c05c4187" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + entry.getKey(),
1,
Arrays.asList(entry.getValue()));
executeTest(String.format("realigner [%s]", entry.getKey()), spec);
}
}
@Test
public void testKnownsOnly() {
WalkerTestSpec spec1 = new WalkerTestSpec(
baseCommand + "-knownsOnly -B:indels,vcf " + knownIndels,
1,
Arrays.asList("1218d3c8fbd50581af5815938d6c0070"));
executeTest("realigner known indels only from VCF", spec1);
WalkerTestSpec spec2 = new WalkerTestSpec(
baseCommand + "-knownsOnly -D " + GATKDataLocation + "dbsnp_129_b36.rod",
1,
Arrays.asList("848740b201adc5c45bf82384c1f19d4d"));
executeTest("realigner known indels only from dbsnp", spec2);
}
@Test
public void testNoTags() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -LOD 1.0 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10076000 -compress 1 -targetIntervals " + validationDataLocation + "NA12878.indels.intervals -B:knownIndels,VCF " + validationDataLocation + "NA12878.indels.vcf4 -o %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe -knownsOnly",
2,
Arrays.asList(md5s));
executeTest("test realigner known indels only", spec);
baseCommand + "--noOriginalAlignmentTags",
1,
Arrays.asList("00e009c97905f4fa89e3102261a1fd57"));
executeTest("realigner no output tags", spec);
}
@Test
public void testLongRun() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10,000,000-11,000,000 -targetIntervals " + validationDataLocation + "indelRealignerTest.NA12878.chrom1.intervals -compress 0 --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe -o %s",
1,
Arrays.asList(""));
executeTest("realigner long run", spec);
}
}