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Bug fix in VariantRecalibrator. Only add sample names from the input rod bindings, not from all rod bindings. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4194 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-09-02 21:12:09 +00:00
parent 3a4844ebde
commit 0bb05fb472
3 changed files with 17 additions and 16 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
View File

@ -163,7 +163,7 @@ public class ApplyVariantCuts extends RodWalker<Integer, Integer> {
final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
hInfo.add(new VCFInfoHeaderLine("OQ", 1, VCFHeaderLineType.Float, "The original variant quality score"));
hInfo.add(new VCFHeaderLine("source", "VariantOptimizer"));
hInfo.add(new VCFHeaderLine("source", "ApplyVariantCuts"));
final TreeSet<String> samples = new TreeSet<String>();
samples.addAll(SampleUtils.getSampleListWithVCFHeader(getToolkit(), null));

23
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
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@ -146,17 +146,6 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
throw new StingException( "Variant Optimization Model is unrecognized. Implemented options are GAUSSIAN_MIXTURE_MODEL and K_NEAREST_NEIGHBORS" );
}
// setup the header fields
final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
final TreeSet<String> samples = new TreeSet<String>();
hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
hInfo.add(new VCFInfoHeaderLine("OQ", 1, VCFHeaderLineType.Float, "The original variant quality score"));
hInfo.add(new VCFHeaderLine("source", "VariantOptimizer"));
samples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit()));
final VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
vcfWriter.writeHeader(vcfHeader);
boolean foundDBSNP = false;
for( ReferenceOrderedDataSource d : this.getToolkit().getRodDataSources() ) {
if( d.getName().startsWith("input") ) {
@ -180,6 +169,18 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
throw new StingException("dbSNP track is required. This calculation is critically dependent on being able to distinguish known and novel sites.");
}
// setup the header fields
final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
final TreeSet<String> samples = new TreeSet<String>();
hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames));
hInfo.add(new VCFInfoHeaderLine("OQ", 1, VCFHeaderLineType.Float, "The original variant quality score"));
hInfo.add(new VCFHeaderLine("source", "VariantRecalibrator"));
samples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit()));
final VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
vcfWriter.writeHeader(vcfHeader);
// Set up default values for the FDR tranches if necessary
if( FDR_TRANCHES == null ) {
FDR_TRANCHES = new Double[5];

8
java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
View File

@ -43,9 +43,9 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
public void testVariantRecalibrator() {
HashMap<String, List<String>> e = new HashMap<String, List<String>>();
e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf",
Arrays.asList("ad0868adddb2e837b4fc08f140e4d9c3", "937080353c7e03e11f8a70fc0004bf76","5b89fa5a4edf0080d64230d4103d2b8d")); // Each test checks the md5 of three output files
Arrays.asList("9c25a88c9fa48d7373029d2bfb40ad54", "937080353c7e03e11f8a70fc0004bf76","5b89fa5a4edf0080d64230d4103d2b8d")); // Each test checks the md5 of three output files
e.put( validationDataLocation + "lowpass.N3.chr1.raw.0.vcf",
Arrays.asList("054d3228acfd6b02d24bfcf2fbd280a0", "f7c5c6cff9dd5280b25e24e0591e4cb0","1de1473db5720b882edf1381fa3dd039")); // Each test checks the md5 of three output files
Arrays.asList("074462f829ff553584e9b5e330be6d4b", "f7c5c6cff9dd5280b25e24e0591e4cb0","1de1473db5720b882edf1381fa3dd039")); // Each test checks the md5 of three output files
for ( Map.Entry<String, List<String>> entry : e.entrySet() ) {
String vcf = entry.getKey();
@ -81,8 +81,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testApplyVariantCuts() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "841deca1cb30a5a081cfbaa6f663e22a" );
e.put( validationDataLocation + "lowpass.N3.chr1.raw.0.vcf", "6234259e75fd7c1db31566dde1c55a82" );
e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "5b00a80b2a8fd078d6c2aa16924920e4" );
e.put( validationDataLocation + "lowpass.N3.chr1.raw.0.vcf", "d785380792da88f8d64fe1cf1133eeb0" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String vcf = entry.getKey();