From 6313c465fbbc72ce4887da581bc53c8f832a383d Mon Sep 17 00:00:00 2001 From: aaron Date: Thu, 20 Aug 2009 21:56:29 +0000 Subject: [PATCH] we want the RMS of the reads qualities not the RMS of the RMS of the read qualities. Also the VCF version tag seems to be standardized as VCR. Updated the VCF code. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1447 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/genotyper/SSGGenotypeCall.java | 2 +- .../broadinstitute/sting/utils/genotype/vcf/VCFHeader.java | 2 +- .../sting/utils/genotype/vcf/VCFValidator.java | 7 ++++--- .../sting/utils/genotype/vcf/VCFHeaderTest.java | 2 +- .../sting/utils/genotype/vcf/VCFWriterTest.java | 2 +- 5 files changed, 8 insertions(+), 7 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SSGGenotypeCall.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SSGGenotypeCall.java index 5ec7059cd..c71c66385 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SSGGenotypeCall.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SSGGenotypeCall.java @@ -50,7 +50,7 @@ public class SSGGenotypeCall implements GenotypeCall, GenotypeOutput { calculateBestNext(discoveryMode, genotypes, likelihoods, refStr); this.readDepth = pileup.getReads().size(); - rmsMapping = Math.sqrt(calculateRMS(pileup) / readDepth); + rmsMapping = calculateRMS(pileup); } diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFHeader.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFHeader.java index cc0682b14..f75e2f6d9 100644 --- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFHeader.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFHeader.java @@ -41,7 +41,7 @@ public class VCFHeader { private boolean hasGenotypingData = false; /** the current vcf version we support. */ - private static final String VCF_VERSION = "VCFv3.2"; + private static final String VCF_VERSION = "VCRv3.2"; /** * create a VCF header, given a list of meta data and auxillary tags diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFValidator.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFValidator.java index 13c3ee8e8..30b875072 100644 --- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFValidator.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFValidator.java @@ -17,7 +17,7 @@ import java.util.TreeMap; */ public class VCFValidator { - private static final String VCF_VERSION = "VCFv3.2"; + private static final String VCF_VERSION = "VCRv3.2"; /** * about as simple as things come right now. We open the file, process all the entries in the file, @@ -114,9 +114,10 @@ public class VCFValidator { public static void printUsage() { System.err.println("VCF validator (VCF Version " + VCF_VERSION + ")"); System.err.println("Usage:"); - System.err.println("vcfvalidator <-A> "); + System.err.println("vcfvalidator <-A> "); System.err.println(""); - System.err.println("\t-A\tTell the validator to attempt to catch all the problems, and not stop at the first. Some may be too fatal to continue."); + System.err.println("\t<-A>\tTell the validator to attempt to catch all the problems, and not stop at the first. Some may be too fatal to continue."); + System.err.println("\t\tThe vcf file. Required."); System.err.println(""); } diff --git a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderTest.java b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderTest.java index b99a865d4..fb94d085c 100644 --- a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderTest.java +++ b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderTest.java @@ -29,7 +29,7 @@ public class VCFHeaderTest extends BaseTest { for (VCFHeader.HEADER_FIELDS field : VCFHeader.HEADER_FIELDS.values()) { headerFields.add(field); } - metaData.put("format","VCFv3.2"); + metaData.put("format","VCRv3.2"); metaData.put("two","2"); additionalColumns.add("extra1"); additionalColumns.add("extra2"); diff --git a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterTest.java b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterTest.java index 72b15f5dc..1ab7a8c4d 100644 --- a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterTest.java +++ b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterTest.java @@ -49,7 +49,7 @@ public class VCFWriterTest extends BaseTest { for (VCFHeader.HEADER_FIELDS field : VCFHeader.HEADER_FIELDS.values()) { headerFields.add(field); } - metaData.put("format", "VCFv3.2"); // required + metaData.put("format", "VCRv3.2"); // required metaData.put("two", "2"); additionalColumns.add("FORMAT"); additionalColumns.add("extra1");