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Update integration tests to reflect new FT header line standard and new DiagnoseTargets field names

This commit is contained in:
Mark DePristo 2012-06-27 18:19:13 -04:00
parent 64d7e93209
commit 064cc56335
7 changed files with 69 additions and 58 deletions
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7
public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargetsIntegrationTest.java
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@ -36,18 +36,19 @@ public class DiagnoseTargetsIntegrationTest extends WalkerTest {
final String L = validationDataLocation + "DT-itest.interval_list"; final String L = validationDataLocation + "DT-itest.interval_list";
private void DTTest(String testName, String args, String md5) { private void DTTest(String testName, String args, String md5) {
String base = String.format("-T DiagnoseTargets -R %s -L %s", REF, L) + " -o %s "; String base = String.format("-T DiagnoseTargets --no_cmdline_in_header -R %s -L %s", REF, L) + " -o %s ";
WalkerTestSpec spec = new WalkerTestSpec(base + args, Arrays.asList(md5)); WalkerTestSpec spec = new WalkerTestSpec(base + args, Arrays.asList(md5));
spec.disableShadowBCF();
executeTest(testName, spec); executeTest(testName, spec);
} }
@Test(enabled = true) @Test(enabled = true)
public void testSingleSample() { public void testSingleSample() {
DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "2df47009571fe83ead779c94be97fe96"); DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "ef71a569a48697c89e642cdda7bfb766");
} }
@Test(enabled = true) @Test(enabled = true)
public void testMultiSample() { public void testMultiSample() {
DTTest("testMultiSample ", "-I " + multiSample, "6f0c070b9671e1d007ce6374c3183014"); DTTest("testMultiSample ", "-I " + multiSample, "1e6e15156e01e736274898fdac77d911");
} }
} }

4
public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
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@ -80,7 +80,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testGenotypeFilters1() { public void testGenotypeFilters1() {
WalkerTestSpec spec1 = new WalkerTestSpec( WalkerTestSpec spec1 = new WalkerTestSpec(
baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("060e9e7b6faf8b2f7b3291594eb6b39c")); Arrays.asList("c5ed9dd3975b3602293bb484b4fda5f4"));
executeTest("test genotype filter #1", spec1); executeTest("test genotype filter #1", spec1);
} }
@ -88,7 +88,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testGenotypeFilters2() { public void testGenotypeFilters2() {
WalkerTestSpec spec2 = new WalkerTestSpec( WalkerTestSpec spec2 = new WalkerTestSpec(
baseTestString() + " -G_filter 'isHomVar == 1' -G_filterName foo --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, baseTestString() + " -G_filter 'isHomVar == 1' -G_filterName foo --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("00f90028a8c0d56772c47f039816b585")); Arrays.asList("979ccdf484259117aa31305701075602"));
executeTest("test genotype filter #2", spec2); executeTest("test genotype filter #2", spec2);
} }

6
public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
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@ -7,10 +7,6 @@ import org.testng.annotations.DataProvider;
import java.util.*; import java.util.*;
public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
static HashMap<String, String> clusterFiles = new HashMap<String, String>();
static HashMap<String, String> tranchesFiles = new HashMap<String, String>();
static HashMap<String, String> inputVCFFiles = new HashMap<String, String>();
private static class VRTest { private static class VRTest {
String inVCF; String inVCF;
String tranchesMD5; String tranchesMD5;
@ -77,7 +73,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
VRTest indel = new VRTest("combined.phase1.chr20.raw.indels.sites.vcf", VRTest indel = new VRTest("combined.phase1.chr20.raw.indels.sites.vcf",
"da4458d05f6396f5c4ab96f274e5ccdc", // tranches "da4458d05f6396f5c4ab96f274e5ccdc", // tranches
"a04a9001f62eff43d363f4d63769f3ee", // recal file "a04a9001f62eff43d363f4d63769f3ee", // recal file
"05e88052e0798f1c1e83f0a8938bce56"); // cut VCF "b9936d2432d3c85b2d8b5b7aa17d0950"); // cut VCF
@DataProvider(name = "VRIndelTest") @DataProvider(name = "VRIndelTest")
public Object[][] createData2() { public Object[][] createData2() {

2
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
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@ -60,7 +60,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
" --no_cmdline_in_header " + " --no_cmdline_in_header " +
" -o %s", " -o %s",
1, 1,
Arrays.asList("2cdcd9e140eb1b6da7e365e37dd7d859") Arrays.asList("283f434b3efbebb8e10ed6347f97d104")
); );
executeTest("testSimpleVCFStreaming", spec); executeTest("testSimpleVCFStreaming", spec);

3
public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2EncoderDecoderUnitTest.java
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@ -480,7 +480,8 @@ public class BCF2EncoderDecoderUnitTest extends BaseTest {
final byte typeDescriptor = decoder.readTypeDescriptor(); final byte typeDescriptor = decoder.readTypeDescriptor();
// read the int[] with the low-level version // read the int[] with the low-level version
final int[] decoded = decoder.decodeIntArray(typeDescriptor); final int size = decoder.decodeNumberOfElements(typeDescriptor);
final int[] decoded = decoder.decodeIntArray(typeDescriptor, size);
if ( isMissing(ints) ) { if ( isMissing(ints) ) {
// we expect that the result is null in this case // we expect that the result is null in this case

2
public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
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@ -34,7 +34,7 @@ public class VCFIntegrationTest extends WalkerTest {
String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s "; String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
String test1 = baseCommand + "-T SelectVariants -V " + testVCF; String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("355b029487c3b4c499140d71310ca37e")); WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("13329ba7360a8beb3afc02569e5a20c4"));
executeTest("Test reading and writing breakpoint VCF", spec1); executeTest("Test reading and writing breakpoint VCF", spec1);
} }

103
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java
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@ -56,18 +56,23 @@ public class VariantContextTestProvider {
final private static boolean ENABLE_VARARRAY_TESTS = true; final private static boolean ENABLE_VARARRAY_TESTS = true;
final private static boolean ENABLE_PLOIDY_TESTS = true; final private static boolean ENABLE_PLOIDY_TESTS = true;
final private static boolean ENABLE_PL_TESTS = true; final private static boolean ENABLE_PL_TESTS = true;
final private static boolean ENABLE_SYMBOLIC_ALLELE_TESTS = false;
final private static boolean ENABLE_SOURCE_VCF_TESTS = true; final private static boolean ENABLE_SOURCE_VCF_TESTS = true;
final private static boolean ENABLE_VARIABLE_LENGTH_GENOTYPE_STRING_TESTS = true; final private static boolean ENABLE_VARIABLE_LENGTH_GENOTYPE_STRING_TESTS = true;
final private static List<Integer> TWENTY_INTS = Arrays.asList(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20);
private static VCFHeader syntheticHeader; private static VCFHeader syntheticHeader;
final static List<VariantContextTestData> TEST_DATAs = new ArrayList<VariantContextTestData>(); final static List<VariantContextTestData> TEST_DATAs = new ArrayList<VariantContextTestData>();
private static VariantContext ROOT; private static VariantContext ROOT;
private final static List<File> testSourceVCFs = Arrays.asList( private final static List<File> testSourceVCFs = new ArrayList<File>();
new File(BaseTest.privateTestDir + "ILLUMINA.wex.broad_phase2_baseline.20111114.both.exome.genotypes.1000.vcf"), static {
new File(BaseTest.privateTestDir + "ex2.vcf"), testSourceVCFs.add(new File(BaseTest.privateTestDir + "ILLUMINA.wex.broad_phase2_baseline.20111114.both.exome.genotypes.1000.vcf"));
new File(BaseTest.privateTestDir + "dbsnp_135.b37.1000.vcf") testSourceVCFs.add(new File(BaseTest.privateTestDir + "ex2.vcf"));
); testSourceVCFs.add(new File(BaseTest.privateTestDir + "dbsnp_135.b37.1000.vcf"));
if ( ENABLE_SYMBOLIC_ALLELE_TESTS )
testSourceVCFs.add(new File(BaseTest.privateTestDir + "diagnosis_targets_testfile.vcf"));
}
public abstract static class VariantContextIOTest { public abstract static class VariantContextIOTest {
public String toString() { public String toString() {
@ -245,7 +250,7 @@ public class VariantContextTestProvider {
add(builder().attribute("INT3", Arrays.asList(1000, 2000, 3000))); add(builder().attribute("INT3", Arrays.asList(1000, 2000, 3000)));
add(builder().attribute("INT3", Arrays.asList(100000, 200000, 300000))); add(builder().attribute("INT3", Arrays.asList(100000, 200000, 300000)));
add(builder().attribute("INT3", null)); add(builder().attribute("INT3", null));
add(builder().attribute("INT20", Arrays.asList(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20))); add(builder().attribute("INT20", TWENTY_INTS));
add(builder().attribute("FLOAT1", 1.0)); add(builder().attribute("FLOAT1", 1.0));
add(builder().attribute("FLOAT1", 100.0)); add(builder().attribute("FLOAT1", 100.0));
@ -449,6 +454,11 @@ public class VariantContextTestProvider {
attr("g1", ref, "INT3", 1, 2, 3), attr("g1", ref, "INT3", 1, 2, 3),
attr("g2", ref, "INT3")); attr("g2", ref, "INT3"));
addGenotypeTests(site,
attr("g1", ref, "INT20", TWENTY_INTS),
attr("g2", ref, "INT20", TWENTY_INTS));
if (ENABLE_VARARRAY_TESTS) { if (ENABLE_VARARRAY_TESTS) {
addGenotypeTests(site, addGenotypeTests(site,
attr("g1", ref, "INT.VAR", 1, 2, 3), attr("g1", ref, "INT.VAR", 1, 2, 3),
@ -693,20 +703,23 @@ public class VariantContextTestProvider {
* @param expected * @param expected
*/ */
public static void assertEquals( final VariantContext actual, final VariantContext expected ) { public static void assertEquals( final VariantContext actual, final VariantContext expected ) {
Assert.assertNotNull(actual); Assert.assertNotNull(actual, "VariantContext expected not null");
Assert.assertEquals(actual.getChr(), expected.getChr()); Assert.assertEquals(actual.getChr(), expected.getChr(), "chr");
Assert.assertEquals(actual.getStart(), expected.getStart()); Assert.assertEquals(actual.getStart(), expected.getStart(), "start");
Assert.assertEquals(actual.getEnd(), expected.getEnd()); Assert.assertEquals(actual.getEnd(), expected.getEnd(), "end");
Assert.assertEquals(actual.getID(), expected.getID()); Assert.assertEquals(actual.getID(), expected.getID(), "id");
Assert.assertEquals(actual.getAlleles(), expected.getAlleles()); Assert.assertEquals(actual.getAlleles(), expected.getAlleles(), "alleles");
assertAttributesEquals(actual.getAttributes(), expected.getAttributes()); assertAttributesEquals(actual.getAttributes(), expected.getAttributes());
Assert.assertEquals(actual.getFilters(), expected.getFilters()); Assert.assertEquals(actual.getFilters(), expected.getFilters(), "filters");
BaseTest.assertEqualsDoubleSmart(actual.getPhredScaledQual(), expected.getPhredScaledQual()); BaseTest.assertEqualsDoubleSmart(actual.getPhredScaledQual(), expected.getPhredScaledQual());
Assert.assertEquals(actual.hasGenotypes(), expected.hasGenotypes()); Assert.assertEquals(actual.hasGenotypes(), expected.hasGenotypes(), "hasGenotypes");
if ( expected.hasGenotypes() ) { if ( expected.hasGenotypes() ) {
Assert.assertEquals(actual.getSampleNames(), expected.getSampleNames()); final Set<String> actualSampleSet = new HashSet<String>(actual.getSampleNames());
final Set<String> expectedSampleSet = new HashSet<String>(expected.getSampleNames());
Assert.assertTrue(actualSampleSet.equals(expectedSampleSet), "sample names"); // note this is necessary due to testng bug for set comps
Assert.assertEquals(actual.getSampleNamesOrderedByName(), expected.getSampleNamesOrderedByName(), "sample names");
final Set<String> samples = expected.getSampleNames(); final Set<String> samples = expected.getSampleNames();
for ( final String sample : samples ) { for ( final String sample : samples ) {
assertEquals(actual.getGenotype(sample), expected.getGenotype(sample)); assertEquals(actual.getGenotype(sample), expected.getGenotype(sample));
@ -715,33 +728,33 @@ public class VariantContextTestProvider {
} }
public static void assertEquals(final Genotype actual, final Genotype expected) { public static void assertEquals(final Genotype actual, final Genotype expected) {
Assert.assertEquals(actual.getSampleName(), expected.getSampleName()); Assert.assertEquals(actual.getSampleName(), expected.getSampleName(), "Genotype names");
Assert.assertEquals(actual.getAlleles(), expected.getAlleles()); Assert.assertEquals(actual.getAlleles(), expected.getAlleles(), "Genotype alleles");
Assert.assertEquals(actual.getGenotypeString(), expected.getGenotypeString()); Assert.assertEquals(actual.getGenotypeString(), expected.getGenotypeString(), "Genotype string");
Assert.assertEquals(actual.getType(), expected.getType()); Assert.assertEquals(actual.getType(), expected.getType(), "Genotype type");
// filters are the same // filters are the same
Assert.assertEquals(actual.getFilters(), expected.getFilters()); Assert.assertEquals(actual.getFilters(), expected.getFilters(), "Genotype fields");
Assert.assertEquals(actual.isFiltered(), expected.isFiltered()); Assert.assertEquals(actual.isFiltered(), expected.isFiltered(), "Genotype isFiltered");
// inline attributes // inline attributes
Assert.assertEquals(actual.getDP(), expected.getDP()); Assert.assertEquals(actual.getDP(), expected.getDP(), "Genotype dp");
Assert.assertEquals(actual.getAD(), expected.getAD()); Assert.assertEquals(actual.getAD(), expected.getAD(), "Genotype ad");
Assert.assertEquals(actual.getGQ(), expected.getGQ()); Assert.assertEquals(actual.getGQ(), expected.getGQ(), "Genotype gq");
Assert.assertEquals(actual.hasPL(), expected.hasPL()); Assert.assertEquals(actual.hasPL(), expected.hasPL(), "Genotype hasPL");
Assert.assertEquals(actual.hasAD(), expected.hasAD()); Assert.assertEquals(actual.hasAD(), expected.hasAD(), "Genotype hasAD");
Assert.assertEquals(actual.hasGQ(), expected.hasGQ()); Assert.assertEquals(actual.hasGQ(), expected.hasGQ(), "Genotype hasGQ");
Assert.assertEquals(actual.hasDP(), expected.hasDP()); Assert.assertEquals(actual.hasDP(), expected.hasDP(), "Genotype hasDP");
Assert.assertEquals(actual.hasLikelihoods(), expected.hasLikelihoods()); Assert.assertEquals(actual.hasLikelihoods(), expected.hasLikelihoods(), "Genotype haslikelihoods");
Assert.assertEquals(actual.getLikelihoodsString(), expected.getLikelihoodsString()); Assert.assertEquals(actual.getLikelihoodsString(), expected.getLikelihoodsString(), "Genotype getlikelihoodsString");
Assert.assertEquals(actual.getLikelihoods(), expected.getLikelihoods()); Assert.assertEquals(actual.getLikelihoods(), expected.getLikelihoods(), "Genotype getLikelihoods");
Assert.assertEquals(actual.getPL(), expected.getPL()); Assert.assertEquals(actual.getPL(), expected.getPL(), "Genotype getPL");
Assert.assertEquals(actual.getPhredScaledQual(), expected.getPhredScaledQual()); Assert.assertEquals(actual.getPhredScaledQual(), expected.getPhredScaledQual(), "Genotype phredScaledQual");
assertAttributesEquals(actual.getExtendedAttributes(), expected.getExtendedAttributes()); assertAttributesEquals(actual.getExtendedAttributes(), expected.getExtendedAttributes());
Assert.assertEquals(actual.isPhased(), expected.isPhased()); Assert.assertEquals(actual.isPhased(), expected.isPhased(), "Genotype isPhased");
Assert.assertEquals(actual.getPloidy(), expected.getPloidy()); Assert.assertEquals(actual.getPloidy(), expected.getPloidy(), "Genotype getPloidy");
} }
private static void assertAttributesEquals(final Map<String, Object> actual, Map<String, Object> expected) { private static void assertAttributesEquals(final Map<String, Object> actual, Map<String, Object> expected) {
@ -753,16 +766,16 @@ public class VariantContextTestProvider {
final Object expectedValue = expected.get(act.getKey()); final Object expectedValue = expected.get(act.getKey());
if ( expectedValue instanceof List ) { if ( expectedValue instanceof List ) {
final List<Object> expectedList = (List<Object>)expectedValue; final List<Object> expectedList = (List<Object>)expectedValue;
Assert.assertTrue(actualValue instanceof List); Assert.assertTrue(actualValue instanceof List, act.getKey() + " should be a list but isn't");
final List<Object> actualList = (List<Object>)actualValue; final List<Object> actualList = (List<Object>)actualValue;
Assert.assertEquals(actualList.size(), expectedList.size()); Assert.assertEquals(actualList.size(), expectedList.size(), act.getKey() + " size");
for ( int i = 0; i < expectedList.size(); i++ ) for ( int i = 0; i < expectedList.size(); i++ )
assertAttributesEquals(actualList.get(i), expectedList.get(i)); assertAttributeEquals(act.getKey(), actualList.get(i), expectedList.get(i));
} else } else
assertAttributesEquals(actualValue, expectedValue); assertAttributeEquals(act.getKey(), actualValue, expectedValue);
} else { } else {
// it's ok to have a binding in x -> null that's absent in y // it's ok to have a binding in x -> null that's absent in y
Assert.assertNull(actualValue); Assert.assertNull(actualValue, act.getKey() + " present in one but not in the other");
} }
expectedKeys.remove(act.getKey()); expectedKeys.remove(act.getKey());
} }
@ -771,7 +784,7 @@ public class VariantContextTestProvider {
// and they must all be null // and they must all be null
for ( final String missingExpected : expectedKeys ) { for ( final String missingExpected : expectedKeys ) {
final Object value = expected.get(missingExpected); final Object value = expected.get(missingExpected);
Assert.assertTrue(isMissing(value)); Assert.assertTrue(isMissing(value), "Attribute " + missingExpected + " missing in one but not in other" );
} }
} }
@ -788,12 +801,12 @@ public class VariantContextTestProvider {
return false; return false;
} }
private static void assertAttributesEquals(final Object actual, final Object expected) { private static void assertAttributeEquals(final String key, final Object actual, final Object expected) {
if ( expected instanceof Double ) { if ( expected instanceof Double ) {
// must be very tolerant because doubles are being rounded to 2 sig figs // must be very tolerant because doubles are being rounded to 2 sig figs
BaseTest.assertEqualsDoubleSmart(actual, (Double)expected, 1e-2); BaseTest.assertEqualsDoubleSmart(actual, (Double)expected, 1e-2);
} else } else
Assert.assertEquals(actual, expected); Assert.assertEquals(actual, expected, "Attribute " + key);
} }
public static void addComplexGenotypesTest() { public static void addComplexGenotypesTest() {
@ -863,14 +876,14 @@ public class VariantContextTestProvider {
} }
public static void assertEquals(final VCFHeader actual, final VCFHeader expected) { public static void assertEquals(final VCFHeader actual, final VCFHeader expected) {
Assert.assertEquals(actual.getMetaData().size(), expected.getMetaData().size()); Assert.assertEquals(actual.getMetaData().size(), expected.getMetaData().size(), "No VCF header lines");
// for some reason set.equals() is returning false but all paired elements are .equals(). Perhaps compare to is busted? // for some reason set.equals() is returning false but all paired elements are .equals(). Perhaps compare to is busted?
//Assert.assertEquals(actual.getMetaData(), expected.getMetaData()); //Assert.assertEquals(actual.getMetaData(), expected.getMetaData());
final List<VCFHeaderLine> actualLines = new ArrayList<VCFHeaderLine>(actual.getMetaData()); final List<VCFHeaderLine> actualLines = new ArrayList<VCFHeaderLine>(actual.getMetaData());
final List<VCFHeaderLine> expectedLines = new ArrayList<VCFHeaderLine>(expected.getMetaData()); final List<VCFHeaderLine> expectedLines = new ArrayList<VCFHeaderLine>(expected.getMetaData());
for ( int i = 0; i < actualLines.size(); i++ ) { for ( int i = 0; i < actualLines.size(); i++ ) {
Assert.assertEquals(actualLines.get(i), expectedLines.get(i)); Assert.assertEquals(actualLines.get(i), expectedLines.get(i), "VCF header lines");
} }
} }