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-Removing BTTJ integration test -- this broke a few revisions ago (2169) and it is unclear whether the resulting change was a correction to something that had previously been incorrect, or a true build-breaker. I'm currently investigating which case this is, but since Bamboo is back up I'm removing this _temporarily_ so that other testing can occur, and will make whatever changes to the test necessary to reflect the truth, then replace the test itself. Additional (and related) pileup tests are upcoming as well. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2210 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-12-02 05:37:15 +00:00
parent b979bd2ced
commit 886c44303a
1 changed files with 0 additions and 91 deletions
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91
java/test/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaIntegrationTest.java
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package org.broadinstitute.sting.playground.gatk.walkers;
import org.junit.Test;
import org.broadinstitute.sting.WalkerTest;
import java.util.Arrays;
/**
* Created by IntelliJ IDEA.
* User: chartl
* Date: Oct 19, 2009
* Time: 1:57:59 PM
* To change this template use File | Settings | File Templates.
*/
public class BaseTransitionTableCalculatorJavaIntegrationTest extends WalkerTest{
// MD5s last computed 10/26 at revision 1897
public static final String OUTPUT_MD5_STANDARD = "bb7f7c8b71a2a19dbbd47699708816b0";
public static final String OUTPUT_MD5_3MISMATCHES = "000bd16dfea8df415e2104fe894aec83";
public static final String OUTPUT_MD5_LOWMAPPINGQUALITY = "db3af69e61e90c59a3ca0ca25605fa67";
public static final String OUTPUT_MD5_LOWQUALITYSCORE = "f990bd4ba5a951b16603131906b74326";
public static final String OUTPUT_MD5_LOWCONFIDENTREFTHRESHOLD = "7c6c2ed2110ee3030fcd060346623fcc";
public static final String OUTPUT_MD5_HIGHCONFIDENTREFTHRESHOLD = "b30efed02e8f6b356e56e5875db40f2c";
public static final String OUTPUT_MD5_ALLARGUMENTS = "3f1901a40e79300da4cbab1488c4839d";
public static final String OUTPUT_MD5_USEREADGROUP = "7422ea018b8dea52398b81502cbe5c38";
public static final String LOCUS = "1:10,000,000-10,200,000";
public static final String BAM_FILE = "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam";
public static final String REFERENCE = "/broad/1KG/reference/human_b36_both.fasta";
@Test
public void testBaseTransitionTableCalculatorJava() {
String args = "-T BaseTransitionTableCalculatorJava -o %s -I "+BAM_FILE+" -L "+LOCUS+" -R "+REFERENCE;
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(args,1,Arrays.asList(OUTPUT_MD5_STANDARD));
executeTest("testBaseTransitionTableCalculatorJava", spec);
}
@Test
public void testBaseTransitionTableCalculatorJavaTreeReduce() {
String args = "-T BaseTransitionTableCalculatorJava -of %s -I "+BAM_FILE+" -L "+LOCUS+" -R "+REFERENCE+" -nt 5";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(args,1,Arrays.asList(OUTPUT_MD5_STANDARD));
executeTest("testBaseTransitionTableCalculatorJava: tree reduce", spec);
}
@Test
public void testBaseTransitionTableCalculatorJavaAdditionalMismatches() {
String args = "-T BaseTransitionTableCalculatorJava -o %s -I "+BAM_FILE+" -L "+LOCUS+" -R "+REFERENCE+" --maxNumMismatches 3";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(args,1,Arrays.asList(OUTPUT_MD5_3MISMATCHES));
executeTest("BaseTransitionTableCalculatorJava: Additional Mismatches",spec);
}
@Test
public void testBaseTransitionCalculatorJavaLowMapingQuality() {
String args = "-T BaseTransitionTableCalculatorJava -o %s -I "+BAM_FILE+" -L "+LOCUS+" -R "+REFERENCE+ " --minMappingQuality 5";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(args,1,Arrays.asList(OUTPUT_MD5_LOWMAPPINGQUALITY));
executeTest("BaseTransitionTableCalculatorJava: Low Mapping Quality",spec);
}
@Test
public void testBaseTransitionCalculatorJavaLowQualityScore() {
String args = "-T BaseTransitionTableCalculatorJava -o %s -I "+BAM_FILE+" -L "+LOCUS+" -R "+REFERENCE+ " --minQualityScore 5";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(args,1,Arrays.asList(OUTPUT_MD5_LOWQUALITYSCORE));
executeTest("BaseTransitionTableCalculatorJava: Low Quality Score",spec);
}
@Test
public void testBaseTransitionCalculatorJavaLowConfidentRefThreshold() {
String args = "-T BaseTransitionTableCalculatorJava -o %s -I "+BAM_FILE+" -L "+LOCUS+" -R "+REFERENCE+ " --confidentRefThreshold 2";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(args,1,Arrays.asList(OUTPUT_MD5_LOWCONFIDENTREFTHRESHOLD));
executeTest("BaseTransitionTableCalculatorJava: Low Ref Threshold",spec);
}
@Test
public void testBaseTransitionCalculatorJavaHighConfidentRefThreshold() {
String args = "-T BaseTransitionTableCalculatorJava -o %s -I "+BAM_FILE+" -L "+LOCUS+" -R "+REFERENCE+ " --confidentRefThreshold 8";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(args,1,Arrays.asList(OUTPUT_MD5_HIGHCONFIDENTREFTHRESHOLD));
executeTest("BaseTransitionTableCalculatorJava: High Ref Threshold",spec);
}
@Test
public void testBaseTransitionCalculatorJavaAllArguments() {
String args = "-T BaseTransitionTableCalculatorJava -o %s -I "+BAM_FILE+" -L "+LOCUS+" -R "+REFERENCE+ " --confidentRefThreshold 2 --minQualityScore 5 --minMappingQuality 5 --maxNumMismatches 3";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(args,1,Arrays.asList(OUTPUT_MD5_ALLARGUMENTS));
executeTest("BaseTransitionTableCalculatorJava: Low Ref Threshold, Low Q Score, Low Mapping Quality, Additional Mismatches",spec);
}
@Test
public void testBaseTransitionTableCalculatorJavaUseReadGroup() {
String args = "-T BaseTransitionTableCalculatorJava -o %s -I "+BAM_FILE+" -L "+LOCUS+" -R "+REFERENCE+" --useReadGroup";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(args,1,Arrays.asList(OUTPUT_MD5_USEREADGROUP));
executeTest("testBaseTransitionTableCalculatorJava: Use read group", spec);
}
}