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Joint Estimate is now the default calculation model. 

Reworked all of the integration tests so that they're now more comprehensive, cover more of what we wan to test, and don't take forever to run.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2376 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-16 19:41:02 +00:00
parent bf76019f22
commit b626fc0684
2 changed files with 88 additions and 178 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
View File

@ -32,8 +32,8 @@ import org.broadinstitute.sting.utils.genotype.GenotypeWriterFactory;
public class UnifiedArgumentCollection {
// control the various models to be used
@Argument(fullName = "genotype_model", shortName = "gm", doc = "Genotype calculation model to employ -- EM_POINT_ESTIMATE is currently the default, while JOINT_ESTIMATE and POOLED are under development.", required = false)
public GenotypeCalculationModel.Model genotypeModel = GenotypeCalculationModel.Model.EM_POINT_ESTIMATE;
@Argument(fullName = "genotype_model", shortName = "gm", doc = "Genotype calculation model to employ -- JOINT_ESTIMATE is currently the default, while POOLED and EM_POINT_ESTIMATE are available.", required = false)
public GenotypeCalculationModel.Model genotypeModel = GenotypeCalculationModel.Model.JOINT_ESTIMATE;
@Argument(fullName = "base_model", shortName = "bm", doc = "Base substitution model to employ -- EMPIRICAL is the recommended default, but it's possible to select the ONE_STATE and THREE_STATE models for comparison purposes", required = false)
public BaseMismatchModel baseModel = BaseMismatchModel.EMPIRICAL;

262
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -12,35 +12,10 @@ import java.util.Map;
// ********************************************************************************** //
public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public static String baseTestString() {
return "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s";
}
public static String testGeliLod5() {
return baseTestString() + " --variant_output_format GELI -confidence 50";
}
private static String OneMb1StateMD5 = "c664bd887b89e9ebc0b4b569ad8eb128";
private static String OneMb3StateMD5 = "9c68f6e900d081023ea97ec467a95bd8";
private static String OneMbEmpiricalMD5 = "0b891eefeb2a2bfe707a8a0838b6d049";
// private static String oneMbMD5(BaseMismatchModel m) {
// switch (m) {
// case ONE_STATE: return OneMb1StateMD5;
// case THREE_STATE: return OneMb3StateMD5;
// case EMPIRICAL: return OneMbEmpiricalMD5;
// default: throw new RuntimeException("Unexpected BaseMismatchModel " + m);
// }
// }
// Uncomment to not check outputs against expectations
//protected boolean parameterize() {
// return true;
//}
// --------------------------------------------------------------------------------------------------------------
//
// testing multi-sample calling
// testing point estimate model
//
// --------------------------------------------------------------------------------------------------------------
@Test
@ -101,29 +76,96 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
executeTest("testSingleSamplePilot2 - Joint Estimate", spec);
}
// --------------------------------------------------------------------------------------------------------------
//
// testing parameters
//
// --------------------------------------------------------------------------------------------------------------
@Test
public void testGenotypeModeJoint() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -genotype -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,001,000 -bm empirical -gm JOINT_ESTIMATE -confidence 70", 1,
Arrays.asList("7e8422f8008a4fe24ea1f5c2913b5d31"));
executeTest("testGenotypeMode - Joint Estimate", spec);
public void testParameter() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "-genotype", "dc908834d97bde696b6bdccf756c9ab6" );
e.put( "-all_bases", "484d424cbcd646b3c5d823cad43f4f5f" );
e.put( "--min_base_quality_score 10", "45e336766e94f05e6ac44d1e50473e18" );
e.put( "--min_mapping_quality_score 10", "de417c1156483ab87b0f8a25f10d4d87" );
e.put( "--max_mismatches_in_40bp_window 5", "05132003c73e10fbdab2af14af677764" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30 " + entry.getKey(), 1,
Arrays.asList(entry.getValue()));
executeTest(String.format("testParameter[%s]", entry.getKey()), spec);
}
}
@Test
public void testAllBasesModeJoint() {
public void testConfidence() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -all_bases -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,001,000 -bm empirical -gm JOINT_ESTIMATE -confidence 70", 1,
Arrays.asList("aedd59f9f2cae7fb07a53812b680852b"));
executeTest("testAllBasesMode - Joint Estimate", spec);
"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -bm empirical -gm JOINT_ESTIMATE -confidence 10 ", 1,
Arrays.asList("ea154d6ab6bbaf40da0dac5162b7e9fd"));
executeTest("testConfidence", spec);
}
//@Test
//public void testGLF() {
// WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
// "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,050,000 -bm empirical -gm JOINT_ESTIMATE -confidence 10", 1,
// Arrays.asList("a95b871bc0bc984f66815b20db7467fe"));
// executeTest("testGLF", spec);
//}
// --------------------------------------------------------------------------------------------------------------
//
// testing other output formats
//
// --------------------------------------------------------------------------------------------------------------
@Test
public void testOtherFormat() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "GLF", "8c72131dfb2b830efb9938a582672a3e" );
e.put( "GELI", "e9e00bdb32ce63420988956c1a9b805f" );
e.put( "GELI_BINARY", "46162567eac3a5004f5f9b4c93d1b8d3" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30 -vf " + entry.getKey(), 1,
Arrays.asList(entry.getValue()));
executeTest(String.format("testOtherFormat[%s]", entry.getKey()), spec);
}
}
// --------------------------------------------------------------------------------------------------------------
//
// testing heterozygosity
//
// --------------------------------------------------------------------------------------------------------------
@Test
public void testHeterozyosity() {
HashMap<Double, String> e = new HashMap<Double, String>();
e.put( 0.01, "ae0134840e0c9fa295b23ecf4ba3e768" );
e.put( 1.0 / 1850, "71ddcf22f4c0538d03508b720d01d3fe" );
for ( Map.Entry<Double, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30 --heterozygosity " + entry.getKey(), 1,
Arrays.asList(entry.getValue()));
executeTest(String.format("testHeterozyosity[%s]", entry.getKey()), spec);
}
}
// --------------------------------------------------------------------------------------------------------------
//
// testing other base calling models
//
// --------------------------------------------------------------------------------------------------------------
@Test
public void testOtherBaseCallModel() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "one_state", "ab71d814e897d7f1440af8f02365b4fa" );
e.put( "three_state", "ce55849c55c58c59773200b2a88db0ee" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -gm JOINT_ESTIMATE -confidence 30 -bm " + entry.getKey(), 1,
Arrays.asList(entry.getValue()));
executeTest(String.format("testOtherBaseCallModel[%s]", entry.getKey()), spec);
}
}
// --------------------------------------------------------------------------------------------------------------
//
@ -139,143 +181,11 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -varout %s" +
" -L 1:10,000,000-10,100,000" +
" -bm empirical" +
" -gm JOINT_ESTIMATE" +
" -vf GELI",
1,
Arrays.asList("eaca4b2323714dbd7c3ed379ce1843ba"));
Arrays.asList("64ffb4ef633ad4c2ff6afbc75450f743"));
executeTest(String.format("testMultiTechnologies"), spec);
}
// --------------------------------------------------------------------------------------------------------------
//
// testing the cache
//
// --------------------------------------------------------------------------------------------------------------
/*
@Test
public void testCache() {
for ( BaseMismatchModel model : BaseMismatchModel.values() ) {
// calculated the expected value without the cache enabled
WalkerTest.WalkerTestSpec withoutCacheSpec = new WalkerTest.WalkerTestSpec(
testGeliLod5() + " -L 1:10,000,000-10,100,000 --disableCache -m " + model.toString(), 1,
Arrays.asList(""));
List<String> withoutCache = executeTest("empirical1MbTest", withoutCacheSpec ).getSecond();
WalkerTest.WalkerTestSpec withCacheSpec = new WalkerTest.WalkerTestSpec(
testGeliLod5() + " -L 1:10,000,000-10,100,000 -bm " + model.toString(), 1,
withoutCache);
executeTest(String.format("testCache[%s]", model), withCacheSpec );
}
}
*/
// --------------------------------------------------------------------------------------------------------------
//
// testing genotype mode
//
// --------------------------------------------------------------------------------------------------------------
@Test
public void genotypeTest() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
testGeliLod5() + " -L 1:10,000,000-10,100,000 -bm empirical --genotype", 1,
Arrays.asList("f9bdd9a8864467dbc4e5356bb8801a33"));
executeTest("genotypeTest", spec);
}
// --------------------------------------------------------------------------------------------------------------
//
// basic base calling models
//
// --------------------------------------------------------------------------------------------------------------
@Test
public void oneState100bpTest() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( testGeliLod5() + " -L 1:10,000,000-10,000,100 -bm one_state", 1, Arrays.asList("3cd402d889c015be4a318123468f4262"));
executeTest("oneState100bpTest", spec);
}
@Test
public void oneState1MbTest() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
testGeliLod5() + " -L 1:10,000,000-11,000,000 -bm one_state",
1, Arrays.asList(OneMb1StateMD5));
executeTest("oneState1MbTest", spec);
}
@Test
public void threeState1MbTest() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
testGeliLod5() + " -L 1:10,000,000-11,000,000 -bm three_state", 1,
Arrays.asList(OneMb3StateMD5));
executeTest("threeState1MbTest", spec);
}
@Test
public void empirical1MbTest() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
testGeliLod5() + " -L 1:10,000,000-11,000,000 -bm empirical", 1,
Arrays.asList(OneMbEmpiricalMD5));
executeTest("empirical1MbTest", spec);
}
// --------------------------------------------------------------------------------------------------------------
//
// testing output formats
//
// --------------------------------------------------------------------------------------------------------------
//@Argument(fullName = "variant_output_format", shortName = "vf", doc = "File format to be used", required = false)
//public GenotypeWriterFactory.GENOTYPE_FORMAT VAR_FORMAT = GenotypeWriterFactory.GENOTYPE_FORMAT.GELI;
// --------------------------------------------------------------------------------------------------------------
//
// testing LOD thresholding
//
// --------------------------------------------------------------------------------------------------------------
@Test
public void testLOD() {
HashMap<Double, String> e = new HashMap<Double, String>();
e.put( 100.0, "6eec841b28fae433015b3d85608e03f7" );
e.put( 30.0, "1b3365f41bbf6867516699afe9efc5f8" );
for ( Map.Entry<Double, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseTestString() + " --variant_output_format GELI -L 1:10,000,000-11,000,000 -bm EMPIRICAL -confidence " + entry.getKey(), 1,
Arrays.asList(entry.getValue()));
executeTest("testLOD", spec);
}
}
// --------------------------------------------------------------------------------------------------------------
//
// testing hetero setting
//
// --------------------------------------------------------------------------------------------------------------
@Test
public void testHeterozyosity() {
HashMap<Double, String> e = new HashMap<Double, String>();
e.put( 0.01, "601c48fc350083d14534ba5c3093edb9" );
e.put( 0.0001, "bd03f7307314e45951d4d3e85fe63d16" );
e.put( 1.0 / 1850, "662d479f1cd54480da1d0e66c81259b0" );
for ( Map.Entry<Double, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
testGeliLod5() + " -L 1:10,000,000-11,000,000 -bm EMPIRICAL --heterozygosity " + entry.getKey(), 1,
Arrays.asList(entry.getValue()));
executeTest(String.format("testHeterozyosity[%s]", entry.getKey()), spec);
}
}
/**
* test the output of a binary geli file
*/
@Test
public void empirical1MbTestBinaryGeli() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseTestString() + " -L 1:10,000,000-11,000,000 -bm empirical --variant_output_format GELI_BINARY -confidence 50", 1,
Arrays.asList("b1027cf309c9ab7572528ce986e2c2d4"));
executeTest("empirical1MbTestBinaryGeli", spec);
}
}