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Removed ability of users to specify annotations to recompute, cleanups. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3501 348d0f76-0448-11de-a6fe-93d51630548a
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delangel 2010-06-08 19:17:59 +00:00
parent 4d1a6b3d99
commit de134c226d
1 changed files with 9 additions and 46 deletions
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55
java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
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@ -29,7 +29,6 @@ import org.broad.tribble.vcf.*;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -38,8 +37,6 @@ import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.genotype.vcf.VCFReader;
@ -65,15 +62,6 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
@Argument(fullName="output_file", shortName="output", doc="VCF file to which output should be written", required=true)
private String OUTPUT_FILE = null;
@Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to apply to variant calls", required=false)
protected String[] annotationsToUse = {"AlleleBalance"};
@Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", required=false)
protected String[] annotationClassesToUse = {};
@Argument(fullName="useAllAnnotations", shortName="all", doc="Use all possible annotations (not for the faint of heart)", required=false)
protected Boolean USE_ALL_ANNOTATIONS = false;
public static final String INPUT_ROD_NAME = "inputvcf";
@ -82,8 +70,6 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
protected static BeagleFileReader likeReader = null;
protected static BeagleFileReader r2Reader = null;
private VariantAnnotatorEngine engine;
protected static String line = null;
protected HashMap<String,BeagleSampleRecord> beagleSampleRecords;
@ -95,10 +81,6 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
private final double MAX_GENOTYPE_QUALITY = 6.0;
public void initialize() {
if ( USE_ALL_ANNOTATIONS )
engine = new VariantAnnotatorEngine(getToolkit());
else
engine = new VariantAnnotatorEngine(getToolkit(), annotationClassesToUse, annotationsToUse);
// setup the header fields
@ -106,7 +88,6 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
hInfo.add(new VCFInfoHeaderLine("R2", 1, VCFInfoHeaderLine.INFO_TYPE.Float, "r2 Value reported by Beable on each site"));
hInfo.add(new VCFHeaderLine("source", "BeagleImputation"));
hInfo.addAll(engine.getVCFAnnotationDescriptions());
final List<ReferenceOrderedDataSource> dataSources = this.getToolkit().getRodDataSources();
@ -441,37 +422,19 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
altAlleleCountString.append(filteredVC.getChromosomeCount(allele));
}
VCFRecord vcf = VariantContextAdaptors.toVCF(filteredVC, ref.getBase());
// if the reference base is not ambiguous, we can annotate
Collection<VariantContext> annotatedVCs = Arrays.asList(filteredVC);
Map<String, StratifiedAlignmentContext> stratifiedContexts;
if ( BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1 ) {
if ( ! context.hasExtendedEventPileup() ) {
stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(context.getBasePileup());
} else {
stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(context.getExtendedEventPileup());
}
if ( stratifiedContexts != null ) {
annotatedVCs = engine.annotateContext(tracker, ref, stratifiedContexts, filteredVC);
if ( filteredVC.getChromosomeCount() > 0 ) {
vcf.addInfoField(VCFRecord.ALLELE_NUMBER_KEY, String.format("%d", filteredVC.getChromosomeCount()));
if ( altAlleleCountString.length() > 0 ) {
vcf.addInfoField(VCFRecord.ALLELE_COUNT_KEY, altAlleleCountString.toString());
vcf.addInfoField(VCFRecord.ALLELE_FREQUENCY_KEY, String.format("%4.2f",
Double.valueOf(altAlleleCountString.toString())/(filteredVC.getChromosomeCount())));
}
}
for(VariantContext annotatedVC : annotatedVCs ) {
VCFRecord vcf = VariantContextAdaptors.toVCF(filteredVC, ref.getBase());
if ( annotatedVC.getChromosomeCount() > 0 ) {
vcf.addInfoField(VCFRecord.ALLELE_NUMBER_KEY, String.format("%d", annotatedVC.getChromosomeCount()));
if ( altAlleleCountString.length() > 0 ) {
vcf.addInfoField(VCFRecord.ALLELE_COUNT_KEY, altAlleleCountString.toString());
vcf.addInfoField(VCFRecord.ALLELE_FREQUENCY_KEY, String.format("%4.2f",
Double.valueOf(altAlleleCountString.toString())/(annotatedVC.getChromosomeCount())));
}
}
vcf.addInfoField("R2", (bglRecord.getR2Value()).toString() );
vcfWriter.addRecord(vcf);
}
vcf.addInfoField("R2", (bglRecord.getR2Value()).toString() );
vcfWriter.addRecord(vcf);
}
return 1;