From 90212c643b5b5f60e112d1035b620e89e9ecbfa6 Mon Sep 17 00:00:00 2001 From: chartl Date: Wed, 18 Nov 2009 20:53:32 +0000 Subject: [PATCH] more effective & efficient test for SecondBaseSkew git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2075 348d0f76-0448-11de-a6fe-93d51630548a --- .../SecondBaseSkewIntegrationTest.java | 32 ++++++++++++++++++- .../VariantAnnotatorIntegrationTest.java | 15 ++------- 2 files changed, 34 insertions(+), 13 deletions(-) diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java index e97d17a1e..2e47328d8 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java @@ -16,7 +16,7 @@ public class SecondBaseSkewIntegrationTest extends WalkerTest { @Test public void secondBaseSkewTest() { - for ( int test = 1; test <= 1; test ++ ) { + for ( int test = 1; test <= 2; test ++ ) { String bamFilePath = VariantAnnotatorIntegrationTest.validationDataPath()+VariantAnnotatorIntegrationTest.secondBaseTestFile(test)+".a2b.recal.annotation_subset.bam"; String callFile = VariantAnnotatorIntegrationTest.validationDataPath()+VariantAnnotatorIntegrationTest.secondBaseTestFile(test)+".a2b.ssg1b.geli.calls"; String args = VariantAnnotatorIntegrationTest.secondBaseTestString()+" -I "+bamFilePath+" -B variant,Variants,"+callFile+" "+VariantAnnotatorIntegrationTest.secondBaseTestInterval(test)+" -sample variant"; @@ -25,4 +25,34 @@ public class SecondBaseSkewIntegrationTest extends WalkerTest { } } + @Test + public void testOnE2File() { + String test_args = "-T VariantAnnotator -A SecondBaseSkew " + +"-R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta " + +"-I /humgen/gsa-scr1/GATK_Data/Validation_Data/FHSP_pool3_2bannot.bam " + +"-B variant,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_pilot_pool3_raw_calls.geli " + +"-vcf %s -sample variant -L /humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_test_intervals.interval_list"; + + String md5_for_this_test = "6a71095e1cfade39d909b35f6c99d1ca"; + + WalkerTestSpec spec = new WalkerTestSpec(test_args,1, Arrays.asList(md5_for_this_test)); + executeTest("Testing on E2 annotated but not Q2 annotated file ",spec); + + + } + + @Test + public void testOnUnannotatedFile() { + String test_args = "-T VariantAnnotator -A SecondBaseSkew " + +"-R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta " + +"-I /humgen/gsa-scr1/GATK_Data/Validation_Data/FHSP_pool3_test.bam " + +"-B variant,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_pilot_pool3_raw_calls.geli " + +"-vcf %s -sample variant -L /humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_test_intervals.interval_list"; + + String md5_for_this_test = "f105fd8a7ae7026a55107b86e768553a"; + + WalkerTestSpec spec = new WalkerTestSpec(test_args,1, Arrays.asList(md5_for_this_test)); + executeTest("Testing on bam file without 2bb annotations ",spec); + } + } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index 1c40eb13a..2e6a1c34e 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -19,10 +19,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public static String secondBaseTestFile( int testNo ) { switch ( testNo ) { case 1: return "NA12891"; - case 2: return "NA12842"; - case 3: return "NA18510"; - case 4: return "NA18960"; - case 5: return "NA20762"; + case 2: return "NA20762"; default: throw new StingException("Impossible test has been run: secondbasetest number "+ testNo); } } @@ -30,10 +27,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public static String secondBaseTestInterval ( int testNo ) { switch ( testNo ) { case 1: return "-L chr1:14,000,000-18,000,000"; - case 2: return "-L chr2:10,000,000-18,000,000"; - case 3: return "-L chr1:10,000,000-20,000,000"; - case 4: return "-L chr1:10,000,000-15,000,000 -L chr2:5,000,000-12,000,000 -L chr3:4,000,000-14,000,000"; - case 5: return "-L chr20 -L chr21 -L chr22"; + case 2: return "-L chr22:20660081-20660083 -L chr22:29198100-29198104 -L chr22:29821330-29821334"; default: throw new StingException("Impossible test has been run: secondbasetest number "+testNo); } } @@ -41,10 +35,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public static String secondBaseTestmd5( int testNo ) { switch ( testNo ) { case 1: return "48adec9c7fa6d3f5f5647b8eababd4e3"; - case 2: return "2b62ad3444bd16a9809ed2df5d6c66ca"; - case 3: return "90a24b6103c3d7b40ab41204be33005d"; - case 4: return "cc62790f15fb070a59b04cdb94fdd0e9"; - case 5: return "10cffb288bcd0bc992a2603ff0a0e02e"; + case 2: return "3a53d945b38e1fc87a801f23115222fe"; default: throw new StingException("Impossible test has been run: secondbasetest number "+testNo); } }