zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

UG integration test. This was the old SSG test with MD5s updated. 

I'll need to add some multi-sample tests in a bit...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1791 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-10-08 17:43:58 +00:00
parent b39a307a04
commit df8ea8f437
1 changed files with 190 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

190
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java 100755
View File

@ -0,0 +1,190 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;
import java.util.Arrays;
import java.util.HashMap;
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 -lod 5";
}
private static String OneMb1StateMD5 = "7e3fc1d8427329eb2a3e05a81011749a";
private static String OneMb3StateMD5 = "f5912d5d6585436a77495688f09cf1cc";
private static String OneMbEmpiricalMD5 = "b9b2d9c7eb9a7af416fddd3b77a72efe";
// 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 calls with SLX, 454, and SOLID data
//
// --------------------------------------------------------------------------------------------------------------
@Test
public void testMultiTechnologies() {
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.allTechs.bam" +
" -varout %s" +
" -L 1:10,000,000-10,100,000" +
" -bm empirical",
1,
Arrays.asList("f490a407c9c62d43eb83107e83c858f6"));
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("6a930a8f115495f5319541c21a892d8e"));
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( 10.0, "94c5b48c0c956fcdacbffaa38a80d926" );
e.put( 3.0, "f1f53b944b821f05d5dd1ad8fda2f57b" );
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 -lod " + 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, "953fe510a81e357d0b56feac2a90095d" );
e.put( 0.0001, "ef0f2af7d13f166829d86b15fabc2b81" );
e.put( 1.0 / 1850, "a435c8c966c11f4393a25a9d01c4fc3d" );
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 -lod 5", 1,
Arrays.asList("915abf82a04fcd1842f6865501bae67c"));
executeTest("empirical1MbTestBinaryGeli", spec);
}
}