diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java index 0e76489b7..735ce15e7 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java @@ -21,7 +21,6 @@ import org.broadinstitute.sting.utils.genotype.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.genotype.vcf.VCFUtils; import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter; -import java.io.File; import java.util.*; @@ -33,8 +32,6 @@ import java.util.*; @Reference(window=@Window(start=-50,stop=50)) @By(DataSource.REFERENCE) public class VariantAnnotator extends LocusWalker { - @Argument(fullName="vcfOutput", shortName="vcf", doc="VCF file to which all variants should be written with annotations", required=true) - protected File VCF_OUT; @Argument(fullName="sampleName", shortName="sample", doc="The sample (NA-ID) corresponding to the variant input (for non-VCF input only)", required=false) protected String sampleName = null; @@ -111,7 +108,7 @@ public class VariantAnnotator extends LocusWalker { hInfo.add(new VCFHeaderLine("annotatorReference", getToolkit().getArguments().referenceFile.getName())); hInfo.addAll(engine.getVCFAnnotationDescriptions()); - vcfWriter = new VCFWriter(VCF_OUT); + vcfWriter = new VCFWriter(out); VCFHeader vcfHeader = new VCFHeader(hInfo, samples); vcfWriter.writeHeader(vcfHeader); } @@ -154,7 +151,7 @@ public class VariantAnnotator extends LocusWalker { return 0; // if the reference base is not ambiguous, we can annotate - Collection annotatedVCs = Arrays.asList( new VariantContext[] { vc } ); + Collection annotatedVCs = Arrays.asList(vc); if ( BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1 ) { Map stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(context.getBasePileup()); if ( stratifiedContexts != null ) { @@ -188,8 +185,7 @@ public class VariantAnnotator extends LocusWalker { * @param result the number of loci seen. */ public void onTraversalDone(Integer result) { - out.printf("Processed %d loci.\n", result); - + logger.info("Processed " + result + " loci.\n"); vcfWriter.close(); } } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java index d8f1cf176..7db037036 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java @@ -28,8 +28,6 @@ import java.util.*; */ @Reference(window=@Window(start=0,stop=40)) public class SequenomValidationConverter extends RodWalker { - @Argument(fullName="outputVCF", shortName="vcf", doc="The VCF file to write results", required=true) - protected File vcfFile = null; @Argument(fullName="maxHardy", doc="Maximum phred-scaled Hardy-Weinberg violation pvalue to consider an assay valid [default:20]", required=false) protected double maxHardy = 20.0; @Argument(fullName="maxNoCall", doc="Maximum no-call rate (as a fraction) to consider an assay valid [default:0.05]", required=false) @@ -106,7 +104,7 @@ public class SequenomValidationConverter extends RodWalker { if ( sampleNames == null ) sampleNames = new TreeSet(); - VCFWriter vcfWriter = new VCFWriter(vcfFile); + VCFWriter vcfWriter = new VCFWriter(out); // set up the info and filter headers Set hInfo = new HashSet(); 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 ba6162a4e..a0fcc2274 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java @@ -33,7 +33,7 @@ public class SecondBaseSkewIntegrationTest extends WalkerTest { +"-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta " +"-I " + validationDataLocation + "FHSP_pool3_2bannot.bam " +"-B variant,Variants," + validationDataLocation + "FHS_pilot_pool3_raw_calls.geli " - +"-vcf %s -sample variant -L " + validationDataLocation + "FHS_test_intervals.interval_list"; + +"-o %s -sample variant -L " + validationDataLocation + "FHS_test_intervals.interval_list"; String md5_for_this_test = "c1116b3196cc9f553ae2442a4063bc5e"; @@ -49,7 +49,7 @@ public class SecondBaseSkewIntegrationTest extends WalkerTest { +"-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta " +"-I " + validationDataLocation + "FHSP_pool3_test.bam " +"-B variant,Variants," + validationDataLocation + "FHS_pilot_pool3_raw_calls.geli " - +"-vcf %s -sample variant -L " + validationDataLocation + "FHS_test_intervals.interval_list"; + +"-o %s -sample variant -L " + validationDataLocation + "FHS_test_intervals.interval_list"; String md5_for_this_test = "a297259694ac88f769a45bce96a08e51"; @@ -62,7 +62,7 @@ public class SecondBaseSkewIntegrationTest extends WalkerTest { String test_args = "-T VariantAnnotator -I " + validationDataLocation + "FHS_Pileup_Test.bam" + " -R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -A SecondBaseSkew" + " -sample variant -B variant,VCF," + validationDataLocation + "FHS_pileup_test_chr15.vcf" - + " -vcf %s -L chr15:46347148"; + + " -o %s -L chr15:46347148"; String expected_md5 = "465f92e689110afeb308c201cb6e8c5a"; WalkerTestSpec spec = new WalkerTestSpec(test_args,1,Arrays.asList(expected_md5)); executeTest("Testing on locus with many indels", 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 af218dee6..d1ec4e681 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -41,7 +41,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { } public static String baseTestString() { - return "-T VariantAnnotator -R " + oneKGLocation + "reference/human_b36_both.fasta -vcf %s"; + return "-T VariantAnnotator -R " + oneKGLocation + "reference/human_b36_both.fasta -o %s"; } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverterIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverterIntegrationTest.java index 5d4325375..a69d862b3 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverterIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverterIntegrationTest.java @@ -9,7 +9,7 @@ public class SequenomValidationConverterIntegrationTest extends WalkerTest { @Test public void testSNPs() { String testPedFile = validationDataLocation + "Sequenom_Test_File.txt"; - String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -T SequenomValidationConverter -B input,Plink,"+testPedFile+" -vcf %s"; + String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -T SequenomValidationConverter -B input,Plink,"+testPedFile+" -o %s"; WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1, Arrays.asList("d19f28fdbe3e731522a52c5329777a9f")); executeTest("Test SNPs", spec); @@ -18,7 +18,7 @@ public class SequenomValidationConverterIntegrationTest extends WalkerTest { @Test public void testIndels() { String testPedFile = validationDataLocation + "pilot2_indel_validation.renamed.ped"; - String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -T SequenomValidationConverter -B input,Plink,"+testPedFile+" -vcf %s"; + String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -T SequenomValidationConverter -B input,Plink,"+testPedFile+" -o %s"; WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1, Arrays.asList("257fcd5e345f2853813e37b88fbc707c")); executeTest("Test Indels", spec);