Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1530 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo
parent
3c2ae55859
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a08c68362e
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@ -56,7 +56,7 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
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if (Types.containsKey(boundName)) {
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throw new RuntimeException(String.format("GATK BUG: adding ROD module %s that is already bound", boundName));
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}
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System.out.printf("* Adding rod class %s%n", name);
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logger.info(String.format("* Adding rod class %s%n", name));
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Types.put(boundName, new RODBinding(name, rodType));
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}
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@ -297,10 +297,15 @@ public abstract class GenotypeLikelihoods implements Cloneable {
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//
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//
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// -----------------------------------------------------------------------------------------------------------------
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final static GenotypeLikelihoods[][][][][] CACHE =
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static GenotypeLikelihoods[][][][][] CACHE =
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new GenotypeLikelihoods[EmpiricalSubstitutionGenotypeLikelihoods.SequencerPlatform.values().length][BaseUtils.BASES.length][QualityUtils.MAX_QUAL_SCORE][MAX_PLOIDY][2];
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static int cacheSize = 0;
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public static void clearCache() {
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CACHE = new GenotypeLikelihoods[EmpiricalSubstitutionGenotypeLikelihoods.SequencerPlatform.values().length][BaseUtils.BASES.length][QualityUtils.MAX_QUAL_SCORE][MAX_PLOIDY][2];
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cacheSize = 0;
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}
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private GenotypeLikelihoods getSetCache( char observedBase, byte qualityScore, int ploidy,
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SAMRecord read, int offset, GenotypeLikelihoods val ) {
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@ -103,7 +103,7 @@ public class SSGenotypeCall implements Genotype, ReadBacked, GenotypesBacked, Li
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* @return get the one minus error value
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*/
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@Override
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public double getLog10PError() {
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public double getNegLog10PError() {
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getBestGenotype();
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getAltGenotype();
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return Math.abs(mGenotypeLikelihoods.getPosterior(mGenotype) - mGenotypeLikelihoods.getPosterior(mCompareTo));
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@ -16,7 +16,7 @@ import org.broadinstitute.sting.utils.genotype.GenotypeWriterFactory;
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import java.io.File;
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@ReadFilters(ZeroMappingQualityReadFilter.class)
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public class SingleSampleGenotyper extends LocusWalker<SSGenotypeCall, GenotypeWriter> {
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public class SingleSampleGenotyper extends LocusWalker<SSGenotypeCall, SingleSampleGenotyper.CallResult> {
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// Control output settings
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@Argument(fullName = "variants_out", shortName = "varout", doc = "File to which variants should be written", required = false)
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public File VARIANTS_FILE = null;
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@ -26,7 +26,7 @@ public class SingleSampleGenotyper extends LocusWalker<SSGenotypeCall, GenotypeW
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// Control what goes into the variants file and what format that file should have
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@Argument(fullName = "lod_threshold", shortName = "lod", doc = "The lod threshold on which variants should be filtered", required = false)
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public Double LOD_THRESHOLD = Double.MIN_VALUE;
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public double LOD_THRESHOLD = Double.MIN_VALUE;
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@Argument(fullName = "genotype", shortName = "genotype", doc = "Should we output confident genotypes or just the variants?", required = false)
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public boolean GENOTYPE = false;
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@ -44,6 +44,22 @@ public class SingleSampleGenotyper extends LocusWalker<SSGenotypeCall, GenotypeW
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@Argument(fullName = "platform", shortName = "pl", doc = "Causes the genotyper to assume that reads without PL header TAG are this platform. Defaults to null, indicating that the system will throw a runtime exception when such reads are detected", required = false)
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public EmpiricalSubstitutionGenotypeLikelihoods.SequencerPlatform defaultPlatform = null;
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public class CallResult {
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long nConfidentCalls = 0;
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long nNonConfidentCalls = 0;
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long nCalledBases = 0;
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GenotypeWriter writer;
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CallResult(GenotypeWriter writer) {
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this.writer = writer;
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}
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public String toString() {
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return String.format("SSG: %d confident and %d non-confident calls were made at %d bases",
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nConfidentCalls, nNonConfidentCalls, nCalledBases);
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}
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}
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/**
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* Filter out loci to ignore (at an ambiguous base in the reference or a locus with zero coverage).
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*
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@ -59,6 +75,7 @@ public class SingleSampleGenotyper extends LocusWalker<SSGenotypeCall, GenotypeW
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/** Initialize the walker with some sensible defaults */
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public void initialize() {
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GenotypeLikelihoods.clearCache();
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// nothing to do
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}
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@ -111,11 +128,11 @@ public class SingleSampleGenotyper extends LocusWalker<SSGenotypeCall, GenotypeW
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*
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* @return an empty string
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*/
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public GenotypeWriter reduceInit() {
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public CallResult reduceInit() {
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if ( VARIANTS_FILE != null )
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return GenotypeWriterFactory.create(VAR_FORMAT, GenomeAnalysisEngine.instance.getSAMFileHeader(), VARIANTS_FILE);
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return new CallResult(GenotypeWriterFactory.create(VAR_FORMAT, GenomeAnalysisEngine.instance.getSAMFileHeader(), VARIANTS_FILE));
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else
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return GenotypeWriterFactory.create(VAR_FORMAT, GenomeAnalysisEngine.instance.getSAMFileHeader(), out);
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return new CallResult(GenotypeWriterFactory.create(VAR_FORMAT, GenomeAnalysisEngine.instance.getSAMFileHeader(), out));
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}
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/**
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@ -126,18 +143,24 @@ public class SingleSampleGenotyper extends LocusWalker<SSGenotypeCall, GenotypeW
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*
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* @return an empty string
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*/
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public GenotypeWriter reduce(SSGenotypeCall call, GenotypeWriter sum) {
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public CallResult reduce(SSGenotypeCall call, CallResult sum) {
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sum.nCalledBases++;
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if (call != null && (GENOTYPE || call.isVariant(call.getReference()))) {
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if (call.getLog10PError() >= LOD_THRESHOLD) {
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sum.addGenotypeCall(call);
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if (call.getNegLog10PError() >= LOD_THRESHOLD) {
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sum.nConfidentCalls++;
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//System.out.printf("Call %s%n", call);
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sum.writer.addGenotypeCall(call);
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} else {
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sum.nNonConfidentCalls++;
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}
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}
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return sum;
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}
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/** Close the variant file. */
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public void onTraversalDone(GenotypeWriter sum) {
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sum.close();
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public void onTraversalDone(CallResult sum) {
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sum.writer.close();
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}
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}
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@ -251,7 +251,7 @@ public class ArtificialPoolContext {
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public String genotypeAndConfidenceToString(int group, String spacer) {
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Genotype call = this.getGenotype(group);
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return (call.getBases() + spacer + call.getLog10PError()); // TODO: fix me
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return (call.getBases() + spacer + call.getNegLog10PError()); // TODO: fix me
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}
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public Genotype getGenotype(int group) {
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@ -15,7 +15,7 @@ public interface Genotype {
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*
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* @return the log based error estimate
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*/
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public double getLog10PError();
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public double getNegLog10PError();
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/**
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* get the bases that represent this
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@ -0,0 +1,140 @@
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package org.broadinstitute.sting.gatk.walkers.genotyper;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.utils.genotype.Variant;
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import org.broadinstitute.sting.utils.genotype.GenotypeWriterFactory;
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import org.junit.Test;
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import org.broadinstitute.sting.gatk.GATKArgumentCollection;
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import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
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import org.broadinstitute.sting.gatk.executive.Accumulator;
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import java.io.*;
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import java.util.Arrays;
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import java.util.EnumMap;
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import java.security.MessageDigest;
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import java.math.BigInteger;
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import junit.framework.Assert;
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public class SingleSampleGenotyperTest extends BaseTest {
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private final static double DELTA = 1e-8;
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private static final String oneMB = "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam";
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private static final String fiveMB = "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_15_mb.SLX.bam";
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private static String gatkargs(final String bam) {
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final String GATKArgs =
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"<GATK-argument-collection>\n" +
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" <sam-files class=\"java.util.ArrayList\">\n" +
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" <file>%s</file>\n" +
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" </sam-files>\n" +
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" <reference-file>/broad/1KG/reference/human_b36_both.fasta</reference-file>\n" +
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" <analysis-name>SingleSampleGenotyper</analysis-name>\n" +
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"</GATK-argument-collection>";
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return String.format(GATKArgs, bam);
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}
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private static class ExpectedResult {
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long nCalls;
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String md5sum;
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public ExpectedResult(long calls, String md5) {
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this.nCalls = calls;
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this.md5sum = md5;
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}
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}
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public static EnumMap<BaseMismatchModel, ExpectedResult> expectedOutput = new EnumMap<BaseMismatchModel, ExpectedResult>(BaseMismatchModel.class);
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static {
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expectedOutput.put(BaseMismatchModel.ONE_STATE, new ExpectedResult(983L, "d5404668e76f206055f03d97162ea6d9"));
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expectedOutput.put(BaseMismatchModel.THREE_STATE, new ExpectedResult(1055L, "46fb7b66da3dac341e9c342f751d74cd"));
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expectedOutput.put(BaseMismatchModel.EMPIRICAL, new ExpectedResult(1070L, "ea0be2fd074a6c824a0670ad5b3e0aca"));
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}
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//private static double callingTolerance = 0.2; // I'm willing to tolerate +/- 10% variation in call rate from that expected
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public static long nExpectedCalls(BaseMismatchModel model) {
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return expectedOutput.get(model).nCalls;
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}
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// public static double nExpectedCallsTolerance(long nBasesCalled) {
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// return nExpectedCalls(nBasesCalled) * callingTolerance;
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// }
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public static void assertGoodNumberOfCalls(final String name, BaseMismatchModel model, SingleSampleGenotyper.CallResult calls) {
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Assert.assertEquals(name, nExpectedCalls(model), calls.nConfidentCalls);
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}
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public static void assertMatchingMD5(final String name, BaseMismatchModel model, final File resultsFile ) {
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try {
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byte[] bytesOfMessage = getBytesFromFile(resultsFile);
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byte[] thedigest = MessageDigest.getInstance("MD5").digest(bytesOfMessage);
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BigInteger bigInt = new BigInteger(1, thedigest);
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String filemd5sum = bigInt.toString(16);
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Assert.assertEquals(name + "Mismatching MD5s", expectedOutput.get(model).md5sum, filemd5sum);
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} catch ( Exception e ) {
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throw new RuntimeException("Failed to read bytes from calls file: " + resultsFile);
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}
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}
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public static byte[] getBytesFromFile(File file) throws IOException {
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InputStream is = new FileInputStream(file);
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// Get the size of the file
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long length = file.length();
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if (length > Integer.MAX_VALUE) {
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// File is too large
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}
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// Create the byte array to hold the data
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byte[] bytes = new byte[(int)length];
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// Read in the bytes
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int offset = 0;
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int numRead = 0;
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while (offset < bytes.length
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&& (numRead=is.read(bytes, offset, bytes.length-offset)) >= 0) {
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offset += numRead;
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}
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// Ensure all the bytes have been read in
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if (offset < bytes.length) {
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throw new IOException("Could not completely read file "+file.getName());
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}
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// Close the input stream and return bytes
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is.close();
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return bytes;
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}
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private void oneMBCallTest(BaseMismatchModel model) {
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logger.warn("Executing oneMBCallTest for " + model);
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InputStream stream = new ByteArrayInputStream(gatkargs(oneMB).getBytes());
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GATKArgumentCollection mycoll = GATKArgumentCollection.unmarshal(stream);
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mycoll.intervals = Arrays.asList("1:10,000,000-11,000,000");
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SingleSampleGenotyper SSG = new SingleSampleGenotyper();
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SSG.VAR_FORMAT = GenotypeWriterFactory.GENOTYPE_FORMAT.GELI;
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SSG.LOD_THRESHOLD = 5.0;
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try {
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SSG.VARIANTS_FILE = File.createTempFile("SSGTempTmpCalls.geli.calls", ".tmp" );
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} catch (IOException ex) {
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System.err.println("Cannot create temp file: " + ex.getMessage());
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}
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SSG.baseModel = model;
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GenomeAnalysisEngine engine = new GenomeAnalysisEngine();
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System.out.printf("model is %s, SSG says %s%n", model, SSG.baseModel );
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Accumulator obj = (Accumulator)engine.execute(mycoll, SSG);
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SingleSampleGenotyper.CallResult calls = (SingleSampleGenotyper.CallResult)obj.finishTraversal();
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logger.warn(String.format("SSG(%s): made %d calls at %d bases", SSG.baseModel, calls.nConfidentCalls, calls.nCalledBases));
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assertMatchingMD5("testBasic", model, SSG.VARIANTS_FILE);
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assertGoodNumberOfCalls("testBasic", model, calls);
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}
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@Test public void oneStateOneMBTest() { oneMBCallTest(BaseMismatchModel.ONE_STATE); }
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@Test public void threeStateOneMBTest() { oneMBCallTest(BaseMismatchModel.THREE_STATE); }
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@Test public void empiricalStateOneMBTest() { oneMBCallTest(BaseMismatchModel.EMPIRICAL); }
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}
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@ -0,0 +1,9 @@
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#!/bin/tcsh
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foreach model (ONE_STATE THREE_STATE EMPIRICAL)
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java -Xmx4096m -jar ~/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar -l INFO -L 1:10,000,000-11,000,000 -R /broad/1KG/reference/human_b36_both.fasta -T SingleSampleGenotyper -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout ./$model.geli.calls -lod 5 -m $model
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end
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wc -l *.geli.calls
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md5sum *.geli.calls
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