From 886c44303ace3426a5d384d484ff6aee5af02c71 Mon Sep 17 00:00:00 2001 From: chartl Date: Wed, 2 Dec 2009 05:37:15 +0000 Subject: [PATCH] -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 --- ...ionTableCalculatorJavaIntegrationTest.java | 91 ------------------- 1 file changed, 91 deletions(-) delete mode 100644 java/test/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaIntegrationTest.java diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaIntegrationTest.java deleted file mode 100644 index 452ecee86..000000000 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaIntegrationTest.java +++ /dev/null @@ -1,91 +0,0 @@ -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); - } -}