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Change GC Content value type from Integer to Float

This commit is contained in:
Ron Levine 2015-02-24 13:06:28 -05:00
parent f3a57a6b07
commit 44e5965a4b
3 changed files with 19 additions and 2 deletions
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3
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GCContent.java
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@ -61,6 +61,7 @@ import org.broadinstitute.gatk.utils.BaseUtils;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.gatk.utils.variant.GATKVCFConstants;
import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines;
import java.util.Arrays;
import java.util.HashMap;
@ -92,7 +93,7 @@ public class GCContent extends InfoFieldAnnotation {
public List<String> getKeyNames() { return Arrays.asList(GATKVCFConstants.GC_CONTENT_KEY); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(GATKVCFHeaderLines.getInfoLine(getKeyNames().get(0)));}
public boolean useZeroQualityReads() { return false; }

16
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java
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@ -54,9 +54,12 @@ package org.broadinstitute.gatk.tools.walkers.annotator;
import htsjdk.tribble.readers.LineIterator;
import htsjdk.tribble.readers.PositionalBufferedStream;
import htsjdk.variant.variantcontext.Genotype;
import htsjdk.variant.vcf.VCFHeader;
import htsjdk.variant.vcf.VCFHeaderLine;
import org.broadinstitute.gatk.engine.walkers.WalkerTest;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFCodec;
import org.broadinstitute.gatk.utils.variant.GATKVCFConstants;
import org.testng.Assert;
import org.testng.annotations.Test;
@ -162,6 +165,19 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
Assert.assertTrue(FileUtils.readFileToString(file).contains("Annotation will not be calculated, must be called from HaplotyepCaller"));
}
@Test
public void testAskingGCContent() throws IOException{
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000 -A GCContent", 1,
Arrays.asList("02f634fd978cf2a66738704581508569"));
final File outputVCF = executeTest("test file has annotations, adding GCContent annotation", spec).getFirst().get(0);
final VCFCodec codec = new VCFCodec();
final VCFHeader header = (VCFHeader) codec.readActualHeader(codec.makeSourceFromStream(new FileInputStream(outputVCF)));
final VCFHeaderLine infoLineGC = header.getInfoHeaderLine(GATKVCFConstants.GC_CONTENT_KEY);
// GC content must be a Float type
Assert.assertTrue(infoLineGC.toString().contains("Type=Float"));
}
@Test
public void testOverwritingHeader() {
WalkerTestSpec spec = new WalkerTestSpec(

2
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java
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@ -100,7 +100,7 @@ public class GATKVCFHeaderLines {
addInfoLine(new VCFInfoHeaderLine(BASE_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"));
addInfoLine(new VCFInfoHeaderLine(CLIPPING_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, "Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases"));
addInfoLine(new VCFInfoHeaderLine(FISHER_STRAND_KEY, 1, VCFHeaderLineType.Float, "Phred-scaled p-value using Fisher's exact test to detect strand bias"));
addInfoLine(new VCFInfoHeaderLine(GC_CONTENT_KEY, 1, VCFHeaderLineType.Integer, "GC content around the variant (see docs for window size details)"));
addInfoLine(new VCFInfoHeaderLine(GC_CONTENT_KEY, 1, VCFHeaderLineType.Float, "GC content around the variant (see docs for window size details)"));
addInfoLine(new VCFInfoHeaderLine(NOCALL_CHROM_KEY, 1, VCFHeaderLineType.Integer, "Number of no-called samples"));
addInfoLine(new VCFInfoHeaderLine(GQ_MEAN_KEY, 1, VCFHeaderLineType.Float, "Mean of all GQ values"));
addInfoLine(new VCFInfoHeaderLine(GQ_STDEV_KEY, 1, VCFHeaderLineType.Float, "Standard deviation of all GQ values"));