From 6e855809e1f9c9e9d0ada9c17d527b9b47130ae3 Mon Sep 17 00:00:00 2001 From: ebanks Date: Wed, 10 Mar 2010 02:31:10 +0000 Subject: [PATCH] Renaming and moving relevant tools into a sequenom directory git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2971 348d0f76-0448-11de-a6fe-93d51630548a --- .../CreateSequenomMask.java | 2 +- .../PickSequenomProbes.java | 2 +- .../SequenomValidationConverter.java} | 4 +-- .../sequenom}/PlinkToVCFIntegrationTest.java | 0 ...nomValidationConverterIntegrationTest.java | 26 +++++++++++++++++++ 5 files changed, 30 insertions(+), 4 deletions(-) rename java/src/org/broadinstitute/sting/gatk/walkers/{fasta => sequenom}/CreateSequenomMask.java (96%) rename java/src/org/broadinstitute/sting/gatk/walkers/{fasta => sequenom}/PickSequenomProbes.java (99%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/variantstovcf/PlinkToVCF.java => gatk/walkers/sequenom/SequenomValidationConverter.java} (98%) rename java/test/org/broadinstitute/sting/{playground/gatk/walkers/variantstovcf => gatk/walkers/sequenom}/PlinkToVCFIntegrationTest.java (100%) create mode 100755 java/test/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverterIntegrationTest.java diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/CreateSequenomMask.java b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java similarity index 96% rename from java/src/org/broadinstitute/sting/gatk/walkers/fasta/CreateSequenomMask.java rename to java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java index 9b4d562db..9eaf0e300 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/CreateSequenomMask.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.walkers.fasta; +package org.broadinstitute.sting.gatk.walkers.sequenom; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java similarity index 99% rename from java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java rename to java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java index 2cab97543..c2ad5b118 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.walkers.fasta; +package org.broadinstitute.sting.gatk.walkers.sequenom; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/PlinkToVCF.java b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/PlinkToVCF.java rename to java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java index f464dfa78..648468ccc 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/PlinkToVCF.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variantstovcf; +package org.broadinstitute.sting.gatk.walkers.sequenom; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; @@ -25,7 +25,7 @@ import java.util.*; * Converts Sequenom files to a VCF annotated with QC metrics (HW-equilibrium, % failed probes) */ @Reference(window=@Window(start=0,stop=40)) -public class PlinkToVCF extends RodWalker { +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) diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/PlinkToVCFIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PlinkToVCFIntegrationTest.java similarity index 100% rename from java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/PlinkToVCFIntegrationTest.java rename to java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PlinkToVCFIntegrationTest.java diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverterIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverterIntegrationTest.java new file mode 100755 index 000000000..d4c73b987 --- /dev/null +++ b/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverterIntegrationTest.java @@ -0,0 +1,26 @@ +package org.broadinstitute.sting.gatk.walkers.sequenom; + +import org.broadinstitute.sting.WalkerTest; +import org.junit.Test; + +import java.util.Arrays; + +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"; + WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1, + Arrays.asList("02dcb683db503599efed0b76daa8fcba")); + executeTest("Test SNPs", spec); + } + + @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"; + WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1, + Arrays.asList("e72c0ab95b279a4d39cc14d40770a801")); + executeTest("Test Indels", spec); + } +}