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Removing the Variant Recalibration Performance test because it isn't ready yet. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3460 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-05-28 18:27:25 +00:00
parent 522dd7a5b2
commit 4e268ef6ac
1 changed files with 0 additions and 65 deletions
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65
java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersPerformanceTest.java
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@ -1,65 +0,0 @@
package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;
import java.util.*;
import java.io.File;
public class VariantRecalibrationWalkersPerformanceTest extends WalkerTest {
static HashMap<String, String> paramsFiles = new HashMap<String, String>();
@Test
public void testGenerateVariantClusters() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "b39bde091254e90490b0d7bf9f0ef24a" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String vcf = entry.getKey();
String md5 = entry.getValue();
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + oneKGLocation + "reference/human_b36_both.fasta" +
" --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
" -T GenerateVariantClusters" +
" -B input,VCF," + vcf +
" -nG 6" +
" -nI 5" +
" --ignore_filter GATK_STANDARD" +
" -an QD -an HRun -an SB" +
" -clusterFile /dev/null",
0, // just one output file
new ArrayList<String>(0));
List<File> result = executeTest("testGenerateVariantClusters", spec).getFirst();
paramsFiles.put(vcf, result.get(0).getAbsolutePath());
}
}
@Test
public void testVariantRecalibrator() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "412bdb2eb4ca8f7ee9dfb39cda676c95" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String vcf = entry.getKey();
String md5 = entry.getValue();
String paramsFile = paramsFiles.get(vcf);
System.out.printf("PARAMS FOR %s is %s%n", vcf, paramsFile);
if ( paramsFile != null ) {
File file = createTempFile("cluster",".vcf");
WalkerTestSpec spec = new WalkerTestSpec(
"-R " + oneKGLocation + "reference/human_b36_both.fasta" +
" --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
" -T VariantRecalibrator" +
" -B input,VCF," + vcf +
" --ignore_filter GATK_STANDARD" +
" -output /dev/null" +
" -clusterFile " + validationDataLocation + "clusterFile",
0,
new ArrayList<String>(0));
executeTest("testVariantRecalibrator", spec);
}
}
}
}