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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
This commit is contained in:
aaron 2009-08-20 21:56:29 +00:00
parent 6c0adc9145
commit 6313c465fb
5 changed files with 8 additions and 7 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SSGGenotypeCall.java
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@ -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);
}

2
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFHeader.java
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@ -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

7
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFValidator.java
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@ -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> <fille.vcf>");
System.err.println("vcfvalidator <-A> <file.vcf>");
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<file.vcf>\tThe vcf file. Required.");
System.err.println("");
}

2
java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderTest.java
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@ -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");

2
java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterTest.java
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@ -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");