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Fixing syntax of BQSR and UG performance tests.

This commit is contained in:
Ryan Poplin 2011-08-11 17:04:09 -04:00
parent 902eb0c61e
commit f1d1252be2
3 changed files with 6 additions and 5 deletions
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1
public/java/test/org/broadinstitute/sting/BaseTest.java
View File

@ -67,6 +67,7 @@ public abstract class BaseTest {
public static final String b36dbSNP129 = dbsnpDataLocation + "dbsnp_129_b36.vcf";
public static final String b37dbSNP129 = dbsnpDataLocation + "dbsnp_129_b37.vcf";
public static final String b37dbSNP132 = dbsnpDataLocation + "dbsnp_132_b37.vcf";
public static final String hg18dbSNP132 = dbsnpDataLocation + "dbsnp_132.hg18.vcf";
public static final String hapmapDataLocation = comparisonDataLocation + "Validated/HapMap/3.3/";
public static final String b37hapmapGenotypes = hapmapDataLocation + "genotypes_r27_nr.b37_fwd.vcf";

6
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java
View File

@ -15,7 +15,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
" -glm BOTH" +
" -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
" -L chr1:1-50,000,000" +
" --dbsnp:VCF " + b36dbSNP129 +
" --dbsnp:VCF " + hg18dbSNP132 +
" -o /dev/null",
0,
new ArrayList<String>(0));
@ -30,7 +30,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
" -glm BOTH" +
" -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
" -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +
" --dbsnp:vcf " + b36dbSNP129 +
" --dbsnp:vcf " + hg18dbSNP132 +
" -o /dev/null",
0,
new ArrayList<String>(0));
@ -46,7 +46,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
" -glm BOTH" +
" -L chr1:1-50,000,000" +
" -nt 10" +
" --dbsnp:vcf " + b36dbSNP129 +
" --dbsnp:vcf " + hg18dbSNP132 +
" -o /dev/null",
0,
new ArrayList<String>(0));

4
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
View File

@ -16,7 +16,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
" -L chr1:1-50,000,000" +
" -standard" +
" -OQ" +
" -B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
" -knownSites " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
" -recalFile /dev/null" + moreArgs,
0,
new ArrayList<String>(0));
@ -31,7 +31,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
" -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +
" -standard" +
" -OQ" +
" -B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
" -knownSites " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
" -recalFile /dev/null" + moreArgs,
0,
new ArrayList<String>(0));