- Depth annotation now includes MQ0 reads
- Removed MQ0 annotation - Updated RMS MQ annotation to use new pileup - UG now outputs all of its arguments as key/value pairs in the header (for VCF) - Cleaned up VCFGenotypeWriterAdapter interface a bit git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2288 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks
parent
e8822a3fb4
commit
717eb1de96
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@ -15,7 +15,7 @@ public class DepthOfCoverage extends StandardVariantAnnotation {
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public String getKeyName() { return VCFRecord.DEPTH_KEY; }
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public String getDescription() { return getKeyName() + ",1,Integer,\"Total Depth\""; }
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public String getDescription() { return getKeyName() + ",1,Integer,\"Total Depth (including MQ0 reads)\""; }
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public boolean useZeroQualityReads() { return false; }
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public boolean useZeroQualityReads() { return true; }
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}
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@ -1,28 +0,0 @@
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package org.broadinstitute.sting.gatk.walkers.annotator;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
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import org.broadinstitute.sting.utils.genotype.Variation;
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import net.sf.samtools.SAMRecord;
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import java.util.List;
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public class MappingQualityZero extends StandardVariantAnnotation {
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public String annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation) {
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List<SAMRecord> reads = pileup.getReads();
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int MQ0Count = 0;
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for (int i=0; i < reads.size(); i++) {
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if ( reads.get(i).getMappingQuality() == 0 )
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MQ0Count++;
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}
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return String.format("%d", MQ0Count);
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}
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public String getKeyName() { return "MQ0"; }
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public String getDescription() { return "MQ0,1,Integer,\"Total Mapping Quality Zero Reads\""; }
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public boolean useZeroQualityReads() { return true; }
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}
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@ -3,21 +3,18 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.utils.MathUtils;
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import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
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import org.broadinstitute.sting.utils.pileup.PileupElement;
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import org.broadinstitute.sting.utils.genotype.Variation;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
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import net.sf.samtools.SAMRecord;
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import java.util.List;
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public class RMSMappingQuality extends StandardVariantAnnotation {
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public String annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation) {
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List<SAMRecord> reads = pileup.getReads();
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int[] qualities = new int[reads.size()];
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for (int i=0; i < reads.size(); i++)
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qualities[i] = reads.get(i).getMappingQuality();
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int[] qualities = new int[pileup.size()];
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int index = 0;
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for (PileupElement p : pileup )
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qualities[index++] = p.getRead().getMappingQuality();
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double rms = MathUtils.rms(qualities);
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return String.format("%.2f", rms);
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}
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@ -134,31 +134,53 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
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samples.clear();
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// get the optional header fields
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Set<String> headerInfo = getHeaderInfo();
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// create the output writer stream
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if ( VARIANTS_FILE != null )
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writer = GenotypeWriterFactory.create(UAC.VAR_FORMAT, GenomeAnalysisEngine.instance.getSAMFileHeader(), VARIANTS_FILE,
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samples,
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headerInfo);
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else
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writer = GenotypeWriterFactory.create(UAC.VAR_FORMAT, GenomeAnalysisEngine.instance.getSAMFileHeader(), out,
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samples,
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headerInfo);
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callsMetrics = new CallMetrics();
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}
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private Set<String> getHeaderInfo() {
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Set<String> headerInfo = new HashSet<String>();
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headerInfo.add("source=UnifiedGenotyper");
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headerInfo.add("reference=" + getToolkit().getArguments().referenceFile.getName());
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if ( UAC.ALL_ANNOTATIONS )
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headerInfo.addAll(VariantAnnotator.getAllVCFAnnotationDescriptions());
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else
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headerInfo.addAll(VariantAnnotator.getVCFAnnotationDescriptions());
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headerInfo.add("INFO=AF,1,Float,\"Allele Frequency\"");
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headerInfo.add("INFO=NS,1,Integer,\"Number of Samples With Data\"");
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if ( !UAC.NO_SLOD )
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headerInfo.add("INFO=SB,1,Float,\"Strand Bias\"");
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// create the output writer stream
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if ( VARIANTS_FILE != null )
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writer = GenotypeWriterFactory.create(UAC.VAR_FORMAT, GenomeAnalysisEngine.instance.getSAMFileHeader(), VARIANTS_FILE,
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"UnifiedGenotyper",
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this.getToolkit().getArguments().referenceFile.getName(),
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samples,
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headerInfo);
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else
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writer = GenotypeWriterFactory.create(UAC.VAR_FORMAT, GenomeAnalysisEngine.instance.getSAMFileHeader(), out,
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"UnifiedGenotyper",
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this.getToolkit().getArguments().referenceFile.getName(),
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samples,
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headerInfo);
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headerInfo.add("UG_genotype_model=" + UAC.genotypeModel);
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headerInfo.add("UG_base_model=" + UAC.baseModel);
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headerInfo.add("UG_heterozygosity=" + UAC.heterozygosity);
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headerInfo.add("UG_genotype_mode=" + UAC.GENOTYPE);
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headerInfo.add("UG_all_bases_mode=" + UAC.ALL_BASES);
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headerInfo.add("UG_min_confidence=" + UAC.CONFIDENCE_THRESHOLD);
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headerInfo.add("UG_max_deletion_fraction=" + UAC.MAX_DELETION_FRACTION);
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headerInfo.add("UG_max_coverage=" + UAC.MAX_READS_IN_PILEUP);
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if ( UAC.POOLSIZE > 0 )
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headerInfo.add("UG_poolSize=" + UAC.POOLSIZE);
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if ( UAC.ASSUME_SINGLE_SAMPLE != null )
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headerInfo.add("UG_single_sample=" + UAC.ASSUME_SINGLE_SAMPLE);
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if ( UAC.defaultPlatform != null )
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headerInfo.add("UG_default_platform=" + UAC.defaultPlatform);
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callsMetrics = new CallMetrics();
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return headerInfo;
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}
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/**
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@ -30,8 +30,6 @@ public class GenotypeWriterFactory {
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* @param format the format
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* @param header the sam file header
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* @param destination the destination file
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* @param source the source
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* @param referenceName the ref name
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* @param sampleNames the sample names
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* @param headerInfo the optional header info fields
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* @return the genotype writer object
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@ -39,8 +37,6 @@ public class GenotypeWriterFactory {
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public static GenotypeWriter create(GENOTYPE_FORMAT format,
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SAMFileHeader header,
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File destination,
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String source,
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String referenceName,
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Set<String> sampleNames,
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Set<String> headerInfo) {
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switch (format) {
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@ -51,7 +47,7 @@ public class GenotypeWriterFactory {
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case GELI_BINARY:
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return new GeliAdapter(destination, header);
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case VCF:
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return new VCFGenotypeWriterAdapter(source, referenceName, destination, sampleNames, headerInfo);
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return new VCFGenotypeWriterAdapter(destination, sampleNames, headerInfo);
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default:
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throw new StingException("Genotype writer " + format.toString() + " is not implemented");
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}
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@ -60,8 +56,6 @@ public class GenotypeWriterFactory {
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public static GenotypeWriter create(GENOTYPE_FORMAT format,
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SAMFileHeader header,
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PrintStream destination,
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String source,
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String referenceName,
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Set<String> sampleNames,
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Set<String> headerInfo) {
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switch (format) {
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@ -70,7 +64,7 @@ public class GenotypeWriterFactory {
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case GLF:
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return new GLFWriter(header.toString(), destination);
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case VCF:
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return new VCFGenotypeWriterAdapter(source, referenceName, destination, sampleNames, headerInfo);
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return new VCFGenotypeWriterAdapter(destination, sampleNames, headerInfo);
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default:
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throw new StingException("Genotype writer to " + format.toString() + " to standard output is not implemented");
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}
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@ -19,17 +19,13 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
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// our VCF objects
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private VCFWriter mWriter = null;
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private VCFHeader mHeader = null;
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private String mSource;
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private String mReferenceName;
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private final Set<String> mSampleNames = new LinkedHashSet<String>();
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/** our log, which we want to capture anything from this class */
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protected static Logger logger = Logger.getLogger(VCFGenotypeWriterAdapter.class);
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public VCFGenotypeWriterAdapter(String source, String referenceName, File writeTo, Set<String> sampleNames, Set<String> headerInfo) {
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mReferenceName = referenceName;
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mSource = source;
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public VCFGenotypeWriterAdapter(File writeTo, Set<String> sampleNames, Set<String> headerInfo) {
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mSampleNames.addAll(sampleNames);
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initializeHeader(headerInfo);
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@ -38,9 +34,7 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
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mWriter = new VCFWriter(mHeader, writeTo);
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}
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public VCFGenotypeWriterAdapter(String source, String referenceName, OutputStream writeTo, Set<String> sampleNames, Set<String> headerInfo) {
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mReferenceName = referenceName;
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mSource = source;
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public VCFGenotypeWriterAdapter(OutputStream writeTo, Set<String> sampleNames, Set<String> headerInfo) {
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mSampleNames.addAll(sampleNames);
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initializeHeader(headerInfo);
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@ -59,8 +53,6 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
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// setup the header fields
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hInfo.add(VCFHeader.FULL_FORMAT_LINE);
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hInfo.add("source=" + mSource);
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hInfo.add("reference=" + mReferenceName);
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hInfo.addAll(optionalHeaderInfo);
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// setup the sample names
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@ -66,7 +66,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testHasAnnotsAsking1() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -standard -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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Arrays.asList("31ddecd3118bd6aea00bcd0369a1b32f"));
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Arrays.asList("24609ede968a90ebff949791694f70a0"));
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executeTest("test file has annotations, asking for annotations, #1", spec);
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}
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@ -74,7 +74,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testHasAnnotsAsking2() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -standard -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample3.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
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Arrays.asList("553c55f3bcf31a6b1d9a2c1d27fde480"));
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Arrays.asList("9f05c78ef9913259c02f8bda6ec97505"));
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executeTest("test file has annotations, asking for annotations, #2", spec);
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}
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@ -98,7 +98,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testNoAnnotsAsking1() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -standard -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2empty.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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Arrays.asList("fa1071b292fd2e9db5c36410ffd44fdb"));
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Arrays.asList("54811556d642a83fcfa2b359aa275023"));
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executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
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}
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@ -106,7 +106,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testNoAnnotsAsking2() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -standard -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample3empty.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
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Arrays.asList("9d133a91949e477523a039a0a52ac2a8"));
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Arrays.asList("b67282a03c92ae3d24a7b588aa1e61df"));
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executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
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}
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@ -47,7 +47,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testMultiSamplePilot1PointEM() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,400-10,024,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1,
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Arrays.asList("68fcdca40df72b3c703bab846c5f0bbd"));
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Arrays.asList("7c27fc1ad1fedab6944d5f93094ef914"));
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executeTest("testMultiSamplePilot1 - Point Estimate EM", spec);
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}
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@ -55,7 +55,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testMultiSamplePilot2PointEM() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,010,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1,
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Arrays.asList("eb0cd5494ae4c1781bfa00b6c4146993"));
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Arrays.asList("cd08c5e4dbd0cf477efd1204c681c7c6"));
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executeTest("testMultiSamplePilot2 - Point Estimate EM", spec);
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}
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@ -68,7 +68,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testPooled1() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,000-10,024,000 -bm empirical -gm POOLED -ps 60 -confidence 30", 1,
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Arrays.asList("ec1aeb69d7d54a7ced1ce625146d1d59"));
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Arrays.asList("d7579207d2521f36648b2b43be805bc4"));
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executeTest("testPooled1", spec);
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}
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@ -81,7 +81,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testMultiSamplePilot1Joint() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,022,000-10,025,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
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Arrays.asList("e27552dad05ddf17403aaa7176b9cfe2"));
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Arrays.asList("f4e8721a905e42f511967a1cfdb966ec"));
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executeTest("testMultiSamplePilot1 - Joint Estimate", spec);
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}
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@ -89,7 +89,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testMultiSamplePilot2Joint() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,050,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
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Arrays.asList("3618711e41b7e37f47b995d39adbc76b"));
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Arrays.asList("962838ae188b1c07a35ead671019062e"));
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executeTest("testMultiSamplePilot2 - Joint Estimate", spec);
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}
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@ -97,7 +97,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testSingleSamplePilot2Joint() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
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Arrays.asList("2a32add40319ab2de44951624df2be4b"));
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Arrays.asList("a9cf1abecf709de9f158f6ffe57b00e7"));
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executeTest("testSingleSamplePilot2 - Joint Estimate", spec);
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}
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@ -44,7 +44,6 @@
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<class>org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.HomopolymerRun</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.MappingQualityZero</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions</class>
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</dependencies>
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@ -44,7 +44,6 @@
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<class>org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.HomopolymerRun</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.MappingQualityZero</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions</class>
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</dependencies>
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