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more effective & efficient test for SecondBaseSkew 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2075 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-11-18 20:53:32 +00:00
parent 087e01a439
commit 90212c643b
2 changed files with 34 additions and 13 deletions
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32
java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java
View File

@ -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);
}
}

15
java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -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);
}
}