zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Bug fix: call RodBinding.resetNameCounter() in new ParsingEngine() so that we don't magically misnumber arguments in the integration tests where the GATK is only instantiated once.

This commit is contained in:
Mark DePristo 2011-08-04 12:06:10 -04:00
parent 490ca475fc
commit f0d798d47c
3 changed files with 2 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
View File

@ -91,6 +91,7 @@ public class ParsingEngine {
protected static Logger logger = Logger.getLogger(ParsingEngine.class);
public ParsingEngine( CommandLineProgram clp ) {
RodBinding.resetNameCounter();
parsingMethods.add( ParsingMethod.FullNameParsingMethod );
parsingMethods.add( ParsingMethod.ShortNameParsingMethod );

1
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
View File

@ -31,7 +31,6 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@DataProvider(name = "cctestdata")
public Object[][] createCCTestData() {
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" );

2
public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
View File

@ -17,7 +17,7 @@ public class VCFIntegrationTest extends WalkerTest {
String baseCommand = "-R " + b37KGReference + " -NO_HEADER -o %s ";
String test1 = baseCommand + "-T VariantAnnotator -BTI variants --variants:vcf " + testVCF;
String test1 = baseCommand + "-T VariantAnnotator --variants:vcf " + testVCF + " -BTI variants";
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList(md5ofInputVCF));
List<File> result = executeTest("Test Variant Annotator with no changes", spec1).getFirst();