From d8f1ebf8c69b1d1ca94f6517a857c4d040bb4737 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Wed, 3 Aug 2011 20:06:00 -0400 Subject: [PATCH] Parameterized RecalibrationWalkers with clean unstable database --- .../RecalibrationWalkersIntegrationTest.java | 43 +++++++++++-------- 1 file changed, 25 insertions(+), 18 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java index 97748cf7f..ecef7ca90 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java @@ -13,7 +13,6 @@ import java.io.File; public class RecalibrationWalkersIntegrationTest extends WalkerTest { static HashMap paramsFiles = new HashMap(); - static HashMap paramsFilesNoReadGroupTest = new HashMap(); static HashMap paramsFilesSolidIndels = new HashMap(); private static final class CCTest extends TestDataProvider { @@ -24,15 +23,19 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { this.file = file; this.md5 = md5; } + + public String toString() { + return "CCTest: " + file; + } } @DataProvider(name = "cctestdata") public Object[][] createCCTestData() { - new CCTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "" ); - new CCTest( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", ""); - new CCTest( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "" ); - new CCTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "" ); + new CCTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "5a52b00d9794d27af723bcf93366681e" ); + new CCTest( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "17d4b8001c982a70185e344929cf3941"); + new CCTest( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "714e65d6cb51ae32221a77ce84cbbcdc" ); + new CCTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "64e9f17a1cf6fc04c1f2717c2d2eca67" ); return CCTest.getTests(CCTest.class); } @@ -78,14 +81,18 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { this.file = file; this.md5 = md5; } + + public String toString() { + return "TRTest: " + file; + } } @DataProvider(name = "trtestdata") public Object[][] createTRTestData() { - new TRTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "" ); - new TRTest( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", ""); - new TRTest( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "" ); - new TRTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "" ); + new TRTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "2864f231fab7030377f3c8826796e48f" ); + new TRTest( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "c164dd635721ba6df3f06dac1877c32d"); + new TRTest( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "74314e5562c1a65547bb0edaacffe602" ); + new TRTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "2a37c6001826bfabf87063b1dfcf594f" ); return TRTest.getTests(TRTest.class); } @@ -115,7 +122,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testCountCovariatesUseOriginalQuals() { HashMap e = new HashMap(); - e.put( validationDataLocation + "originalQuals.1kg.chr1.1-1K.bam", ""); + e.put( validationDataLocation + "originalQuals.1kg.chr1.1-1K.bam", "278846c55d97bd9812b758468a83f559"); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -139,7 +146,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testTableRecalibratorMaxQ70() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "" ); + e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "2864f231fab7030377f3c8826796e48f" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -168,7 +175,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testCountCovariatesSolidIndelsRemoveRefBias() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "" ); + e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "8379f24cf5312587a1f92c162ecc220f" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -194,7 +201,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testTableRecalibratorSolidIndelsRemoveRefBias() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "" ); + e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "7d5edb75b176e4151de225f699719ee4" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -222,7 +229,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testCountCovariatesVCF() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", ""); + e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "170f0c3cc4b8d72c539136effeec9a16"); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -246,7 +253,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testCountCovariatesBED() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", ""); + e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "b460478d9683e827784e42bc352db8bb"); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -270,7 +277,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testCountCovariatesVCFPlusDBsnp() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", ""); + e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "9131d96f39badbf9753653f55b148012"); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -298,7 +305,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testCountCovariatesNoIndex() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "" ); + e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "8993d32df5cb66c7149f59eccbd57f4c" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -324,7 +331,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testTableRecalibratorNoIndex() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "" ); + e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "5f913c98ca99754902e9d34f99df468f" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey();