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Initial changes to the SSG to output GLF by default 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1231 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-07-14 08:46:04 +00:00
parent 0f6bfaaf73
commit 36819ed908
14 changed files with 508 additions and 248 deletions
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219
java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
View File

@ -2,57 +2,61 @@ package org.broadinstitute.sting.playground.gatk.walkers;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceRecord;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.ReadFilters;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
import org.broadinstitute.sting.playground.utils.AlleleMetrics;
import org.broadinstitute.sting.playground.utils.GenotypeLikelihoods;
import org.broadinstitute.sting.playground.utils.IndelLikelihood;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.BasicPileup;
import org.broadinstitute.sting.utils.ReadBackedPileup;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.genotype.GenotypeWriter;
import org.broadinstitute.sting.utils.genotype.GenotypeWriterFactory;
import org.broadinstitute.sting.utils.genotype.LikelihoodObject;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.PrintStream;
import java.io.FileNotFoundException;
import java.util.List;
@ReadFilters(ZeroMappingQualityReadFilter.class)
public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate, String> {
// Control output settings
@Argument(fullName="variants_out", shortName="varout", doc="File to which variants should be written", required=true) public File VARIANTS_FILE;
@Argument(fullName="metrics_out", shortName="metout", doc="File to which metrics should be written", required=false) public File METRICS_FILE = new File("/dev/stderr");
@Argument(fullName = "variants_out", shortName = "varout", doc = "File to which variants should be written", required = true) public File VARIANTS_FILE;
@Argument(fullName = "metrics_out", shortName = "metout", doc = "File to which metrics should be written", required = false) public File METRICS_FILE = new File("/dev/stderr");
@Argument(fullName = "variant_output_format", shortName = "vf", doc = "File to which metrics should be written", required = false) public GenotypeWriterFactory.GENOTYPE_FORMAT VAR_FORMAT = GenotypeWriterFactory.GENOTYPE_FORMAT.GLF;
// Control what goes into the variants file and what format that file should have
@Argument(fullName="lod_threshold", shortName="lod", doc="The lod threshold on which variants should be filtered", required=false) public Double LOD_THRESHOLD = 5.0;
@Argument(fullName="format_geli", shortName="geli", doc="Output variant calls in Geli/Picard format", required=false) public boolean GELI_OUTPUT_FORMAT = false;
@Argument(fullName = "lod_threshold", shortName = "lod", doc = "The lod threshold on which variants should be filtered", required = false)public Double LOD_THRESHOLD = Double.MIN_VALUE;
// Control periodic reporting features
@Argument(fullName="metrics_interval", shortName="metint", doc="Number of loci to process between metrics reports", required=false) public Integer METRICS_INTERVAL = 50000;
@Argument(fullName="suppress_metrics", shortName="printmets", doc="If specified, don't display metrics", required=false) public Boolean SUPPRESS_METRICS = false;
@Argument(fullName = "metrics_interval", shortName = "metint", doc = "Number of loci to process between metrics reports", required = false) public Integer METRICS_INTERVAL = 50000;
@Argument(fullName = "suppress_metrics", shortName = "printmets", doc = "If specified, don't display metrics", required = false) public Boolean SUPPRESS_METRICS = false;
// Control what features we use in calling variants
@Argument(fullName="ignore_secondary_bases", shortName="nosb", doc="Ignore secondary base examination", required=false) public Boolean IGNORE_SECONDARY_BASES = false;
@Argument(fullName="call_indels", shortName="indels", doc="Call indels as well as point mutations", required=false) public Boolean CALL_INDELS = false;
@Argument(fullName = "ignore_secondary_bases", shortName = "nosb", doc = "Ignore secondary base examination", required = false) public Boolean IGNORE_SECONDARY_BASES = false;
@Argument(fullName = "call_indels", shortName = "indels", doc = "Call indels as well as point mutations", required = false) public Boolean CALL_INDELS = false;
// Control how the genotype hypotheses are weighed
@Argument(fullName="priors_any_locus", shortName="plocus", doc="Comma-separated prior likelihoods for any locus (homref,het,homvar)", required=false) public String PRIORS_ANY_LOCUS = "0.999,1e-3,1e-5";
@Argument(fullName="priors_hapmap", shortName="phapmap", doc="Comma-separated prior likelihoods for Hapmap loci (homref,het,homvar)", required=false) public String PRIORS_HAPMAP = "0.999,1e-3,1e-5";
@Argument(fullName="priors_dbsnp", shortName="pdbsnp", doc="Comma-separated prior likelihoods for dbSNP loci (homref,het,homvar)", required=false) public String PRIORS_DBSNP = "0.999,1e-3,1e-5";
@Argument(fullName="priors_2nd_on", shortName="p2ndon", doc="Comma-separated prior likelihoods for the secondary bases of primary on-genotype bases (AA,AC,AG,AT,CC,CG,CT,GG,GT,TT)", required=false) public String PRIORS_2ND_ON = "0.000,0.302,0.366,0.142,0.000,0.548,0.370,0.000,0.319,0.000";
@Argument(fullName="priors_2nd_off", shortName="p2ndoff", doc="Comma-separated prior likelihoods for the secondary bases of primary off-genotype bases (AA,AC,AG,AT,CC,CG,CT,GG,GT,TT)", required=false) public String PRIORS_2ND_OFF = "0.480,0.769,0.744,0.538,0.575,0.727,0.768,0.589,0.762,0.505";
@Argument(fullName = "priors_any_locus", shortName = "plocus", doc = "Comma-separated prior likelihoods for any locus (homref,het,homvar)", required = false) public String PRIORS_ANY_LOCUS = "0.999,1e-3,1e-5";
@Argument(fullName = "priors_hapmap", shortName = "phapmap", doc = "Comma-separated prior likelihoods for Hapmap loci (homref,het,homvar)", required = false) public String PRIORS_HAPMAP = "0.999,1e-3,1e-5";
@Argument(fullName = "priors_dbsnp", shortName = "pdbsnp", doc = "Comma-separated prior likelihoods for dbSNP loci (homref,het,homvar)", required = false) public String PRIORS_DBSNP = "0.999,1e-3,1e-5";
@Argument(fullName = "priors_2nd_on", shortName = "p2ndon", doc = "Comma-separated prior likelihoods for the secondary bases of primary on-genotype bases (AA,AC,AG,AT,CC,CG,CT,GG,GT,TT)", required = false) public String PRIORS_2ND_ON = "0.000,0.302,0.366,0.142,0.000,0.548,0.370,0.000,0.319,0.000";
@Argument(fullName = "priors_2nd_off", shortName = "p2ndoff", doc = "Comma-separated prior likelihoods for the secondary bases of primary off-genotype bases (AA,AC,AG,AT,CC,CG,CT,GG,GT,TT)", required = false) public String PRIORS_2ND_OFF = "0.480,0.769,0.744,0.538,0.575,0.727,0.768,0.589,0.762,0.505";
// Control various sample-level settings
@Argument(fullName="sample_name_regex", shortName="sample_name_regex", doc="Replaces the sample name specified in the BAM read group with the value supplied here", required=false) public String SAMPLE_NAME_REGEX = null;
@Argument(fullName = "sample_name_regex", shortName = "sample_name_regex", doc = "Replaces the sample name specified in the BAM read group with the value supplied here", required = false) public String SAMPLE_NAME_REGEX = null;
public AlleleMetrics metricsOut;
public PrintStream variantsOut;
public PrintStream variantsOut;
public String sampleName;
private GenotypeWriter mGenotypeWriter;
public double[] plocus;
public double[] phapmap;
@ -65,14 +69,17 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
*
* @return true
*/
public boolean requiresReads() { return true; }
public boolean requiresReads() {
return true;
}
/**
* Filter out loci to ignore (at an ambiguous base in the reference or a locus with zero coverage).
*
* @param tracker the meta data tracker
* @param ref the reference base
* @param context contextual information around the locus
* @param tracker the meta data tracker
* @param ref the reference base
* @param context contextual information around the locus
*
* @return true if we should look at this locus, false otherwise
*/
public boolean filter(RefMetaDataTracker tracker, char ref, LocusContext context) {
@ -82,7 +89,8 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
/**
* Convert an array string (value1,value2,...,valueN) to a double array
*
* @param priorsString the array string of priors
* @param priorsString the array string of priors
*
* @return the same array, but each value is now a double
*/
private double[] priorsArray(String priorsString) {
@ -96,44 +104,55 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
return pdbls;
}
/**
* Initialize the walker with some sensible defaults
*/
/** Initialize the walker with some sensible defaults */
public void initialize() {
metricsOut = new AlleleMetrics(METRICS_FILE, LOD_THRESHOLD);
try {
variantsOut = new PrintStream(VARIANTS_FILE);
} catch (FileNotFoundException e) {
err.format("Unable to open file '%s'. Perhaps the parent directory does not exist or is read-only.\n", VARIANTS_FILE.getAbsolutePath());
System.exit(-1);
}
String header = GELI_OUTPUT_FORMAT ? AlleleFrequencyEstimate.geliHeaderString() : AlleleFrequencyEstimate.asTabularStringHeader();
variantsOut.println(header);
if (this.VAR_FORMAT == GenotypeWriterFactory.GENOTYPE_FORMAT.GLF) {
GenotypeLikelihoods.toGLFGenotypePattern();
mGenotypeWriter = GenotypeWriterFactory.create(GenotypeWriterFactory.GENOTYPE_FORMAT.GLF, GenomeAnalysisEngine.instance.getEngine().getSAMHeader(), VARIANTS_FILE);
} else {
try {
variantsOut = new PrintStream(VARIANTS_FILE);
} catch (FileNotFoundException e) {
err.format("Unable to open file '%s'. Perhaps the parent directory does not exist or is read-only.\n", VARIANTS_FILE.getAbsolutePath());
System.exit(-1);
}
if (this.VAR_FORMAT == GenotypeWriterFactory.GENOTYPE_FORMAT.GELI) {
variantsOut.println(AlleleFrequencyEstimate.geliHeaderString());
} else if (this.VAR_FORMAT == GenotypeWriterFactory.GENOTYPE_FORMAT.TABULAR) {
variantsOut.println(AlleleFrequencyEstimate.asTabularStringHeader());
} else {
throw new StingException("Unsupported single sample genotyper output format: " + this.VAR_FORMAT.toString());
}
}
plocus = priorsArray(PRIORS_ANY_LOCUS);
phapmap = priorsArray(PRIORS_HAPMAP);
pdbsnp = priorsArray(PRIORS_DBSNP);
p2ndon = priorsArray(PRIORS_2ND_ON);
p2ndoff = priorsArray(PRIORS_2ND_OFF);
}
}
/**
* Compute the AlleleFrequencyEstimate at a given locus.
*
* @param tracker the meta data tracker
* @param ref the reference base
* @param context contextual information around the locus
* @param tracker the meta data tracker
* @param ref the reference base
* @param context contextual information around the locus
*
* @return an AlleleFrequencyEstimate object
*/
public AlleleFrequencyEstimate map(RefMetaDataTracker tracker, char ref, LocusContext context) {
rationalizeSampleName(context.getReads().get(0));
AlleleFrequencyEstimate freq = getAlleleFrequency(tracker, Character.toUpperCase(ref), context, sampleName);
if (freq != null) { metricsOut.nextPosition(freq, tracker); }
if (!SUPPRESS_METRICS) { metricsOut.printMetricsAtLocusIntervals(METRICS_INTERVAL); }
if (freq != null) {
metricsOut.nextPosition(freq, tracker);
}
if (!SUPPRESS_METRICS) {
metricsOut.printMetricsAtLocusIntervals(METRICS_INTERVAL);
}
return freq;
}
@ -141,18 +160,22 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
/**
* Sometimes the sample names in the BAM files get screwed up. Fix it here if we can.
*
* @param read a read from the pileup (assuming all the reads have the same sample name)
* @param read a read from the pileup (assuming all the reads have the same sample name)
*
* @return a repaired sample name
*/
private String rationalizeSampleName(SAMRecord read) {
String RG = (String)(read.getAttribute("RG"));
String RG = (String) (read.getAttribute("RG"));
SAMReadGroupRecord read_group_record = read.getHeader().getReadGroup(RG);
if (read_group_record != null) {
String localSampleName = read.getHeader().getReadGroup(RG).getSample();
if (SAMPLE_NAME_REGEX != null) { localSampleName = localSampleName.replaceAll(SAMPLE_NAME_REGEX, "$1"); }
if (sampleName == null) { sampleName = localSampleName; }
else {
if (SAMPLE_NAME_REGEX != null) {
localSampleName = localSampleName.replaceAll(SAMPLE_NAME_REGEX, "$1");
}
if (sampleName == null) {
sampleName = localSampleName;
} else {
if (!sampleName.equals(localSampleName)) {
throw new StingException(String.format("Samples appear to have been mixed up: expected '%s' but found '%s'.", sampleName, localSampleName));
}
@ -165,10 +188,11 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
/**
* Compute the allele frequency of the underlying genotype at the given locus.
*
* @param tracker the meta data tracker
* @param ref the reference base
* @param context contextual information around the locus
* @param sample_name the name of the sample
* @param tracker the meta data tracker
* @param ref the reference base
* @param context contextual information around the locus
* @param sample_name the name of the sample
*
* @return the allele frequency estimate
*/
private AlleleFrequencyEstimate getAlleleFrequency(RefMetaDataTracker tracker, char ref, LocusContext context, String sample_name) {
@ -177,7 +201,7 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
List<SAMRecord> reads = context.getReads();
List<Integer> offsets = context.getOffsets();
// Handle indels, but don't do anything with the result yet.
// Handle indels, but don't do anything with the result yet.
IndelLikelihood I = (CALL_INDELS) ? callIndel(context, reads, offsets) : null;
// Handle single-base polymorphisms.
@ -189,11 +213,12 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
/**
* Calls the underlying, single locus genotype of the sample
*
* @param tracker the meta data tracker
* @param ref the reference base
* @param pileup the pileup object for the given locus
* @param reads the reads that overlap this locus
* @param offsets the offsets per read that identify the base at this locus
* @param tracker the meta data tracker
* @param ref the reference base
* @param pileup the pileup object for the given locus
* @param reads the reads that overlap this locus
* @param offsets the offsets per read that identify the base at this locus
*
* @return the likelihoods per genotype
*/
private GenotypeLikelihoods callGenotype(RefMetaDataTracker tracker, char ref, ReadBackedPileup pileup, List<SAMRecord> reads, List<Integer> offsets) {
@ -207,17 +232,17 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
G = new GenotypeLikelihoods(plocus[0], plocus[1], plocus[2], p2ndon, p2ndoff);
}
for ( int i = 0; i < reads.size(); i++ ) {
for (int i = 0; i < reads.size(); i++) {
SAMRecord read = reads.get(i);
int offset = offsets.get(i);
G.add(ref, read.getReadString().charAt(offset), read.getBaseQualities()[offset]);
}
G.ApplyPrior(ref, this.alt_allele, this.allele_frequency_prior);
if (!IGNORE_SECONDARY_BASES && pileup.getBases().length() < 750) {
G.applySecondBaseDistributionPrior(pileup.getBases(), pileup.getSecondaryBasePileup());
if (this.VAR_FORMAT != GenotypeWriterFactory.GENOTYPE_FORMAT.GLF) {
G.ApplyPrior(ref, this.alt_allele, this.allele_frequency_prior);
if (!IGNORE_SECONDARY_BASES && pileup.getBases().length() < 750) {
G.applySecondBaseDistributionPrior(pileup.getBases(), pileup.getSecondaryBasePileup());
}
}
return G;
}
@ -225,16 +250,17 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
/**
* Compute the likelihood of an indel at this locus.
*
* @param context contextual information around the locus
* @param reads the reads that overlap this locus
* @param offsets the offsets per read that identify the base at this locus
* @param context contextual information around the locus
* @param reads the reads that overlap this locus
* @param offsets the offsets per read that identify the base at this locus
*
* @return the likelihood of the indel at this location
*/
private IndelLikelihood callIndel(LocusContext context, List<SAMRecord> reads, List<Integer> offsets) {
String[] indels = BasicPileup.indelPileup(reads, offsets);
IndelLikelihood indelCall = new IndelLikelihood(indels, 1e-4);
if (! indelCall.getType().equals("ref")) {
if (!indelCall.getType().equals("ref")) {
System.out.printf("INDEL %s %s\n", context.getLocation(), indelCall);
}
@ -244,7 +270,8 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
/**
* Determine whether we're at a Hapmap site
*
* @param tracker the meta data tracker
* @param tracker the meta data tracker
*
* @return true if we're at a Hapmap site, false if otherwise
*/
private boolean isHapmapSite(RefMetaDataTracker tracker) {
@ -254,7 +281,8 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
/**
* Determine whether we're at a dbSNP site
*
* @param tracker the meta data tracker
* @param tracker the meta data tracker
*
* @return true if we're at a dbSNP site, false if otherwise
*/
private boolean isDbSNPSite(RefMetaDataTracker tracker) {
@ -262,17 +290,17 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
}
double allele_frequency_prior = -1;
char alt_allele;
char alt_allele;
/**
* Accessor for PoolCaller to set the allele frequency prior for this sample.
*
* @param freq the allele frequency
* @param alt the alternate allele
* @param freq the allele frequency
* @param alt the alternate allele
*/
public void setAlleleFrequencyPrior(double freq, char alt) {
this.allele_frequency_prior = freq;
this.alt_allele = alt;
this.alt_allele = alt;
}
/**
@ -287,23 +315,34 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
/**
* If we've found a LOD >= 5 variant, output it to disk.
*
* @param alleleFreq an AlleleFrequencyEstimage object for the variant.
* @param sum accumulator for the reduce.
* @param alleleFreq an AlleleFrequencyEstimage object for the variant.
* @param sum accumulator for the reduce.
*
* @return an empty string
*/
public String reduce(AlleleFrequencyEstimate alleleFreq, String sum) {
if (alleleFreq != null && alleleFreq.lodVsRef >= LOD_THRESHOLD) {
String line = GELI_OUTPUT_FORMAT ? alleleFreq.asGeliString() : alleleFreq.asTabularString();
variantsOut.println(line);
if (this.VAR_FORMAT == GenotypeWriterFactory.GENOTYPE_FORMAT.GELI) {
variantsOut.println(alleleFreq.asGeliString());
} else if (this.VAR_FORMAT == GenotypeWriterFactory.GENOTYPE_FORMAT.TABULAR) {
variantsOut.println(alleleFreq.asTabularString());
} else if (this.VAR_FORMAT == GenotypeWriterFactory.GENOTYPE_FORMAT.GLF) {
SAMSequenceRecord rec = GenomeLocParser.getContigInfo(alleleFreq.location.getContig());
LikelihoodObject obj = new LikelihoodObject(alleleFreq.posteriors, LikelihoodObject.LIKELIHOOD_TYPE.LOG);
obj.setLikelihoodType(LikelihoodObject.LIKELIHOOD_TYPE.NEGITIVE_LOG);
this.mGenotypeWriter.addGenotypeCall(rec,(int)alleleFreq.location.getStart(),0.0f,alleleFreq.ref,alleleFreq.depth,obj);
}
}
return "";
}
/**
* Close the variant file.
*/
public void onTraversalDone() {
variantsOut.close();
}
return "";
}
/** Close the variant file. */
public void onTraversalDone() {
if (this.VAR_FORMAT == GenotypeWriterFactory.GENOTYPE_FORMAT.GLF) {
mGenotypeWriter.close();
} else {
this.variantsOut.close();
}
}
}

59
java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java
View File

@ -1,26 +1,12 @@
package org.broadinstitute.sting.playground.utils;
import org.broadinstitute.sting.playground.gatk.walkers.AlleleFrequencyWalker;
import java.util.Arrays;
import java.lang.Math;
import org.broadinstitute.sting.utils.GenomeLoc;
import java.util.Arrays;
public class AlleleFrequencyEstimate {
/*
static
{
boolean assertsEnabled = false;
assert assertsEnabled = true; // Intentional side effect!!!
if (!assertsEnabled)
{
System.err.printf("\n\n\nERROR: You must run with asserts enabled. \"java -ea\".\n\n\n");
throw new RuntimeException("Asserts must be enabled!");
}
}
*/
//AlleleFrequencyEstimate();
public GenomeLoc location;
public char ref;
public char alt;
@ -34,7 +20,7 @@ public class AlleleFrequencyEstimate {
public int depth;
public String notes;
public String bases;
public double[][] quals;
//public double[][] quals;
public double[] posteriors;
public String sample_name;
public int n_ref;
@ -48,43 +34,6 @@ public class AlleleFrequencyEstimate {
public AlleleFrequencyEstimate(GenomeLoc location, char ref, char alt, int N, double qhat, double qstar, double lodVsRef, double lodVsNextBest, double pBest, double pRef, int depth, String bases, double[][] quals, double[] posteriors, String sample_name)
{
/*
if( Double.isNaN(lodVsRef)) { System.out.printf("%s: lodVsRef is NaN\n", location.toString()); }
if( Double.isNaN(lodVsNextBest)) { System.out.printf("%s lodVsNextBest is NaN\n", location.toString()); }
if( Double.isNaN(qhat)) { System.out.printf("%s qhat is NaN\n", location.toString()); }
if( Double.isNaN(qstar)) { System.out.printf("%s qstar is NaN\n", location.toString()); }
if( Double.isNaN(pBest)) { System.out.printf("%s pBest is NaN\n", location.toString()); }
if( Double.isNaN(pRef)) { System.out.printf("%s pRef is NaN (%c %s)\n", location.toString(), ref, bases); }
if( Double.isInfinite(lodVsRef))
{
System.out.printf("lodVsRef is Infinite: %s %c %s\n", location.toString(), ref, bases);
for (int i = 0; i < posteriors.length; i++)
{
System.out.printf("POSTERIOR %d %f\n", i, posteriors[i]);
}
}
if( Double.isInfinite(lodVsNextBest)) { System.out.printf("lodVsNextBest is Infinite\n"); }
if( Double.isInfinite(qhat)) { System.out.printf("qhat is Infinite\n"); }
if( Double.isInfinite(qstar)) { System.out.printf("qstar is Infinite\n"); }
if( Double.isInfinite(pBest)) { System.out.printf("pBest is Infinite\n"); }
if( Double.isInfinite(pRef)) { System.out.printf("pRef is Infinite\n"); }
assert(! Double.isNaN(lodVsRef));
assert(! Double.isNaN(lodVsNextBest));
assert(! Double.isNaN(qhat));
assert(! Double.isNaN(qstar));
assert(! Double.isNaN(pBest));
assert(! Double.isNaN(pRef));
assert(! Double.isInfinite(lodVsRef));
assert(! Double.isInfinite(lodVsNextBest));
assert(! Double.isInfinite(qhat));
assert(! Double.isInfinite(qstar));
assert(! Double.isInfinite(pBest));
assert(! Double.isInfinite(pRef));
*/
this.location = location;
this.ref = ref;
this.alt = alt;
@ -98,7 +47,7 @@ public class AlleleFrequencyEstimate {
this.depth = depth;
this.notes = "";
this.bases = bases;
this.quals = quals;
//this.quals = quals;
this.posteriors = posteriors;
this.sample_name = sample_name;
}

40
java/src/org/broadinstitute/sting/playground/utils/GenotypeLikelihoods.java
View File

@ -37,7 +37,19 @@ public class GenotypeLikelihoods {
}
public double[] likelihoods;
public String[] genotypes;
public static String[] genotypes = new String[10];
static {
genotypes[0] = "AA";
genotypes[1] = "AC";
genotypes[2] = "AG";
genotypes[3] = "AT";
genotypes[4] = "CC";
genotypes[5] = "CG";
genotypes[6] = "CT";
genotypes[7] = "GG";
genotypes[8] = "GT";
genotypes[9] = "TT";
}
public int coverage;
// The genotype priors;
@ -75,21 +87,12 @@ public class GenotypeLikelihoods {
this.priorHomVar = priorHomVar;
likelihoods = new double[10];
genotypes = new String[10];
coverage = 0;
for (int i = 0; i < likelihoods.length; i++) { likelihoods[i] = Math.log10(0.1); }
genotypes[0] = "AA";
genotypes[1] = "AC";
genotypes[2] = "AG";
genotypes[3] = "AT";
genotypes[4] = "CC";
genotypes[5] = "CG";
genotypes[6] = "CT";
genotypes[7] = "GG";
genotypes[8] = "GT";
genotypes[9] = "TT";
for (int genotypeIndex = 0; genotypeIndex < 10; genotypeIndex++) {
onNextBestBasePriors.put(genotypes[genotypeIndex], p2ndon[genotypeIndex]);
@ -405,4 +408,17 @@ public class GenotypeLikelihoods {
public void addIndelLikelihood(IndelLikelihood indel_likelihood) { this.indel_likelihood = indel_likelihood; }
public IndelLikelihood getIndelLikelihood() { return this.indel_likelihood; }
// TODO: this is bad, but the formats disagree now.
public static void toGLFGenotypePattern() {
genotypes[0] = "AA";
genotypes[1] = "AT";
genotypes[2] = "AC";
genotypes[3] = "AG";
genotypes[4] = "CC";
genotypes[5] = "CT";
genotypes[6] = "CG";
genotypes[7] = "GG";
genotypes[8] = "GT";
genotypes[9] = "TT";
}
}

14
java/src/org/broadinstitute/sting/utils/genotype/GeliAdapter.java
View File

@ -2,6 +2,7 @@ package org.broadinstitute.sting.utils.genotype;
import edu.mit.broad.picard.genotype.geli.GeliFileWriter;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMSequenceRecord;
import java.io.File;
@ -56,18 +57,16 @@ public class GeliAdapter implements GenotypeWriter {
/**
* add a single point genotype call to the
* add a single point genotype call to the genotype likelihood file
*
* @param contigName the name of the contig you're calling in
* @param contigLength the contig length
* @param contig the contig you're calling in
* @param position the position on the contig
* @param referenceBase the reference base
* @param readDepth the read depth at the specified position
* @param likelihoods the likelihoods of each of the possible alleles
*/
@Override
public void addGenotypeCall(String contigName,
int contigLength,
public void addGenotypeCall(SAMSequenceRecord contig,
int position,
float rmsMapQuals,
char referenceBase,
@ -79,8 +78,7 @@ public class GeliAdapter implements GenotypeWriter {
/**
* add a variable length call to the genotyper
*
* @param contigName the name of the contig you're calling in
* @param contigLength the contig length
* @param contig the contig you're calling in
* @param position the position on the genome
* @param rmsMapQuals the root mean square of the mapping qualities
* @param readDepth the read depth
@ -90,7 +88,7 @@ public class GeliAdapter implements GenotypeWriter {
* @param hetLikelihood the heterozygous likelihood
*/
@Override
public void addVariableLengthCall(String contigName, int contigLength, int position, float rmsMapQuals, int readDepth, char refBase, IndelLikelihood firstHomZyg, IndelLikelihood secondHomZyg, byte hetLikelihood) {
public void addVariableLengthCall(SAMSequenceRecord contig, int position, float rmsMapQuals, int readDepth, char refBase, IndelLikelihood firstHomZyg, IndelLikelihood secondHomZyg, byte hetLikelihood) {
throw new UnsupportedOperationException("Geli format does not support variable length allele calls");
}

15
java/src/org/broadinstitute/sting/utils/genotype/GenotypeWriter.java
View File

@ -1,5 +1,7 @@
package org.broadinstitute.sting.utils.genotype;
import net.sf.samtools.SAMSequenceRecord;
/*
* Copyright (c) 2009 The Broad Institute
*
@ -33,18 +35,17 @@ package org.broadinstitute.sting.utils.genotype;
* The interface for storing genotype calls.
*/
public interface GenotypeWriter {
/**
* add a single point genotype call to the
*
* @param contigName the name of the contig you're calling in
* @param contigLength the contig length
* @param contig the contig you're calling in
* @param position the position on the contig
* @param referenceBase the reference base
* @param readDepth the read depth at the specified position
* @param likelihoods the likelihoods of each of the possible alleles
*/
public void addGenotypeCall(String contigName,
int contigLength,
public void addGenotypeCall(SAMSequenceRecord contig,
int position,
float rmsMapQuals,
char referenceBase,
@ -54,8 +55,7 @@ public interface GenotypeWriter {
/**
* add a variable length call to the genotyper
*
* @param contigName the name of the contig you're calling in
* @param contigLength the contig length
* @param contig the contig you're calling in
* @param position the position on the genome
* @param rmsMapQuals the root mean square of the mapping qualities
* @param readDepth the read depth
@ -64,8 +64,7 @@ public interface GenotypeWriter {
* @param secondHomZyg the second homozygous indel (if present, null if not)
* @param hetLikelihood the heterozygous likelihood
*/
public void addVariableLengthCall(String contigName,
int contigLength,
public void addVariableLengthCall(SAMSequenceRecord contig,
int position,
float rmsMapQuals,
int readDepth,

38
java/src/org/broadinstitute/sting/utils/genotype/GenotypeWriterFactory.java 100644
View File

@ -0,0 +1,38 @@
package org.broadinstitute.sting.utils.genotype;
import net.sf.samtools.SAMFileHeader;
import org.broadinstitute.sting.utils.genotype.glf.GLFWriter;
import java.io.File;
/**
* @author aaron
* <p/>
* Class GenotypeWriterFactory
* <p/>
* A descriptions should go here. Blame aaron if it's missing.
*/
public class GenotypeWriterFactory {
/** available genotype writers */
public enum GENOTYPE_FORMAT {
GELI, GLF, GFF, TABULAR;
}
/**
* create a genotype writer
* @param format the format
* @param header the sam file header
* @param destination the destination file
* @return the genotype writer object
*/
public static GenotypeWriter create(GENOTYPE_FORMAT format, SAMFileHeader header, File destination) {
switch (format) {
case GLF:
return new GLFWriter(header.toString(), destination);
case GELI:
return new GeliAdapter(destination, header);
}
return null;
}
}

144
java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java
View File

@ -1,12 +1,12 @@
package org.broadinstitute.sting.utils.genotype;
import edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods;
import edu.mit.broad.picard.genotype.DiploidGenotype;
import edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods;
import net.sf.samtools.SAMFileHeader;
import org.broadinstitute.sting.utils.StingException;
import java.util.HashMap;
import net.sf.samtools.SAMFileHeader;
/*
* Copyright (c) 2009 The Broad Institute
@ -35,43 +35,52 @@ import net.sf.samtools.SAMFileHeader;
/**
* @author aaron
*
* Class LikelyhoodObject
*
* An object used to store likelyhood information for genotypes. Genotype
* likelihoods are assumed to be infinite (negitive log likelihood), unless set.
* This allows the consumer to make an empty LikelihoodObject, and just set
* those values which have associated likelihood values.
*
* <p/>
* Class LikelyhoodObject
* <p/>
* An object used to store likelyhood information for genotypes. Genotype
* likelihoods are assumed to be infinite (negitive log likelihood), unless set.
* This allows the consumer to make an empty LikelihoodObject, and just set
* those values which have associated likelihood values.
*/
public class LikelihoodObject {
// our possible genotypes, in order according to GLFv3
public enum GENOTYPE {
AA, AT, AC, AG, CC, CT, CG, GG, GT, TT
}
// our pileup of bases
//final private String basePileup;
// possible types of likihoods to store
public enum LIKELIHOOD_TYPE {
NEGITIVE_LOG, LOG, RAW;
}
// our qhet and qstar values; wait, what?
// TODO: are these really needed here? We have them to support the tabular output format only.
//private double qhat;
//private double qstar;
// our liklihood storage type
protected LIKELIHOOD_TYPE mLikelihoodType = LIKELIHOOD_TYPE.NEGITIVE_LOG;
// default the bestGenotype likelihood to the allele AA
// default the bestGenotype likelihoods to the allele AA
protected GENOTYPE bestGenotype = GENOTYPE.AA;
// how many genotypes we're storing
public static final int genoTypeCount = GENOTYPE.values().length;
// the associated negitive log likelihoods for each genotype
protected final HashMap<GENOTYPE, Double> likelihood = new HashMap<GENOTYPE, Double>();
protected final HashMap<GENOTYPE, Double> likelihoods = new HashMap<GENOTYPE, Double>();
/** create a blank likelihood object */
public LikelihoodObject() {
for (GENOTYPE type : GENOTYPE.values()) {
likelihood.put(type, Double.MAX_VALUE);
likelihoods.put(type, Double.MAX_VALUE);
}
}
@ -82,15 +91,18 @@ public class LikelihoodObject {
*
* @param lk the likelihood object
*/
public LikelihoodObject( GenotypeLikelihoods lk ) {
public LikelihoodObject(GenotypeLikelihoods lk) {
mLikelihoodType = LIKELIHOOD_TYPE.LOG;
Double minValue = Double.MAX_VALUE;
for (GENOTYPE type : GENOTYPE.values()) {
byte[] bases = new byte[2];
bases[0] = (byte) type.toString().charAt(0);
bases[1] = (byte) type.toString().charAt(1);
double val = -1.0d * lk.getLikelihood(DiploidGenotype.fromBases(bases));
likelihood.put(type, val);
if (val < minValue) { bestGenotype = type; }
likelihoods.put(type, val);
if (val < minValue) {
bestGenotype = type;
}
}
}
@ -98,18 +110,28 @@ public class LikelihoodObject {
* create a likelyhood object, given an array of genotype scores in GLFv3 ordering
*
* @param values an array of int's from 0 to 255, representing the negitive log likelihoods.
* @param type the likelihood storage type
*/
public LikelihoodObject( double[] values ) {
public LikelihoodObject(double[] values, LIKELIHOOD_TYPE type) {
mLikelihoodType = type;
if (values.length != GENOTYPE.values().length) {
throw new IllegalArgumentException("invalid array passed to LikelihoodObject, should be size " + GENOTYPE.values().length);
}
findBestLikelihood(values);
}
/**
* find the best likelihood
* @param values
*/
private void findBestLikelihood(double[] values) {
int index = 0;
double lowestScore = Double.MAX_VALUE;
for (GENOTYPE type : GENOTYPE.values()) {
likelihood.put(type, values[index]);
for (GENOTYPE t : GENOTYPE.values()) {
likelihoods.put(t, values[index]);
if (values[index] < lowestScore) {
lowestScore = values[index];
bestGenotype = type;
bestGenotype = t;
}
++index;
}
@ -119,11 +141,11 @@ public class LikelihoodObject {
* set the likelihood, given it's probability and the genotype
*
* @param type the genotype
* @param lh the likelihood as a double between 0 and 1, which is converted to a byte
* @param lh the likelihood as a double
*/
public void setLikelihood( GENOTYPE type, double lh ) {
likelihood.put(type, lh);
if (lh < likelihood.get(this.bestGenotype)) {
public void setLikelihood(GENOTYPE type, double lh) {
likelihoods.put(type, lh);
if (lh < likelihoods.get(this.bestGenotype)) {
this.bestGenotype = type;
}
}
@ -135,7 +157,7 @@ public class LikelihoodObject {
* @return the min value
*/
public double getBestLikelihood() {
return likelihood.get(this.bestGenotype);
return likelihoods.get(this.bestGenotype);
}
/**
@ -149,7 +171,7 @@ public class LikelihoodObject {
short ret[] = new short[GENOTYPE.values().length];
int index = 0;
for (GENOTYPE type : GENOTYPE.values()) {
ret[index] = ( likelihood.get(type).intValue() > 254 ) ? 255 : (short) likelihood.get(type).intValue();
ret[index] = (likelihoods.get(type).intValue() > 254) ? 255 : (short) likelihoods.get(type).intValue();
++index;
}
return ret;
@ -166,7 +188,8 @@ public class LikelihoodObject {
double[] ft = new double[10];
int index = 0;
for (GENOTYPE T : GENOTYPE.values()) {
ft[index] = this.likelihood.get(T).floatValue();
ft[index] = this.likelihoods.get(T).doubleValue();
index++;
}
return ft;
}
@ -177,16 +200,16 @@ public class LikelihoodObject {
*
* @return a GenotypeLikelihoods object representing our data
*/
public GenotypeLikelihoods convert( SAMFileHeader samHeader, int seqIndex, int seqPosition, byte refBase ) {
public GenotypeLikelihoods convert(SAMFileHeader samHeader, int seqIndex, int seqPosition, byte refBase) {
double[] ft = toDoubleArray();
float[] db = new float[ft.length];
int index = 0;
if (this.mLikelihoodType == LIKELIHOOD_TYPE.NEGITIVE_LOG) {
for (;index < ft.length; index++) {
db[index] = ((float)ft[index] * -1.0f);
for (; index < ft.length; index++) {
db[index] = ((float) ft[index] * -1.0f);
}
} else if (this.mLikelihoodType == LIKELIHOOD_TYPE.RAW) {
for (;index < ft.length; index++) {
for (; index < ft.length; index++) {
db[index] = (float) Math.log(ft[index]);
}
}
@ -195,18 +218,45 @@ public class LikelihoodObject {
/**
* getter for the likelihood type
*
* @return our likelihood storage type
*/
public LIKELIHOOD_TYPE getLikelihoodType() {
public LIKELIHOOD_TYPE getLikelihoodType() {
return mLikelihoodType;
}
/**
* validate a genotype score
*
* @param score the score to validate
*/
public void validateScore(double score) {
int x = 0;
switch (mLikelihoodType) {
case NEGITIVE_LOG:
if (score < 0)
throw new StingException("Likelikhood score of " + score + " is invalid, for NEGITIVE_LOG it must be greater than or equal to 0");
break;
case LOG:
if (score > 0)
throw new StingException("Likelikhood score of " + score + " is invalid, for LOG it must be less than or equal to 0");
break;
case RAW:
if (score < 0 || score > 1)
throw new StingException("Likelikhood score of " + score + " is invalid, for RAW it must be [0,1]");
break;
}
}
/**
* set our likelihood storage type, and adjust our current likelihood values to reflect
* the new setting.
* the new setting.
*
* @param likelihood the type to set the values to.
*/
public void setLikelihoodType( LIKELIHOOD_TYPE likelihood ) {
public void setLikelihoodType(LIKELIHOOD_TYPE likelihood) {
if (likelihood == mLikelihoodType)
return;
if (mLikelihoodType == LIKELIHOOD_TYPE.RAW) {
@ -214,25 +264,27 @@ public class LikelihoodObject {
if (likelihood == LIKELIHOOD_TYPE.NEGITIVE_LOG) {
mult = -1.0;
}
for (Double d : this.likelihood.values()) {
d = mult * Math.log(d);
// one of us in log, the other negitive log, it doesn't matter which
for (GENOTYPE g : likelihoods.keySet()) {
likelihoods.put(g, -1.0 * Math.log(likelihoods.get(g)));
}
}
else if (likelihood == LIKELIHOOD_TYPE.RAW) {
} else if (likelihood == LIKELIHOOD_TYPE.RAW) {
double mult = 1.0;
if (mLikelihoodType == LIKELIHOOD_TYPE.NEGITIVE_LOG) {
mult = -1.0;
}
for (Double d : this.likelihood.values()) {
d = Math.pow(d*mult,10);
}
}
else {
// one of us in log, the other negitive log, it doesn't matter which
for (Double d : this.likelihood.values()) {
d = -1.0 * Math.log(d);
for (GENOTYPE g : likelihoods.keySet()) {
likelihoods.put(g, Math.pow(likelihoods.get(g) * mult, 10));
}
} else {
// one of us in log, the other negitive log, it doesn't matter which
for (GENOTYPE g : likelihoods.keySet()) {
likelihoods.put(g, -1.0 * likelihoods.get(g));
}
}
this.mLikelihoodType = likelihood;
}
}

99
java/src/org/broadinstitute/sting/utils/genotype/TabularLFWriter.java 100644
View File

@ -0,0 +1,99 @@
package org.broadinstitute.sting.utils.genotype;
import net.sf.samtools.SAMSequenceRecord;
import org.broadinstitute.sting.utils.StingException;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.PrintStream;
/**
*
* @author aaron
*
* Class TabularLF
*
* the tabular likelihood format, as an implementation of the genotype interface
*/
public class TabularLFWriter implements GenotypeWriter {
/**
* where to print the tabular genotype likelihood info to
*/
public PrintStream outStream;
/**
* construct, writing to a specified file
* @param writeTo
*/
public TabularLFWriter(File writeTo) {
try {
outStream = new PrintStream(writeTo);
} catch (FileNotFoundException e) {
throw new StingException("Unable to write to specified file: " + writeTo.getName());
}
// print the header out
outStream.println("location sample_name ref alt genotype qhat qstar lodVsRef lodVsNextBest depth bases");
}
/**
* add a single point genotype call to the
*
* @param contig the contig you're calling in
* @param position the position on the contig
* @param referenceBase the reference base
* @param readDepth the read depth at the specified position
* @param likelihoods the likelihoods of each of the possible alleles
*/
@Override
public void addGenotypeCall(SAMSequenceRecord contig, int position, float rmsMapQuals, char referenceBase, int readDepth, LikelihoodObject likelihoods) {
/**return String.format("%s %s %c %c %s %f %f %f %f %d %s",
location,
contig.getSpecies(),
ref,
alt,
genotype(),
qhat,
qstar,
lodVsRef,
lodVsNextBest,
depth,
bases);*/
}
/**
* add a variable length call to the genotyper
*
* @param contig the contig you're calling in
* @param position the position on the genome
* @param rmsMapQuals the root mean square of the mapping qualities
* @param readDepth the read depth
* @param refBase the reference base
* @param firstHomZyg the first homozygous indel
* @param secondHomZyg the second homozygous indel (if present, null if not)
* @param hetLikelihood the heterozygous likelihood
*/
@Override
public void addVariableLengthCall(SAMSequenceRecord contig, int position, float rmsMapQuals, int readDepth, char refBase, IndelLikelihood firstHomZyg, IndelLikelihood secondHomZyg, byte hetLikelihood) {
throw new StingException("TabularLFWriter doesn't support variable length calls");
}
/**
* add a no call to the genotype file, if supported.
*
* @param position
* @param readDepth
*/
@Override
public void addNoCall(int position, int readDepth) {
throw new StingException("TabularLFWriter doesn't support no-calls");
}
/** finish writing, closing any open files. */
@Override
public void close() {
if (this.outStream != null) {
outStream.close();
}
}
}

66
java/src/org/broadinstitute/sting/utils/genotype/gff/GFFWriter.java 100644
View File

@ -0,0 +1,66 @@
package org.broadinstitute.sting.utils.genotype.gff;
import org.broadinstitute.sting.utils.genotype.GenotypeWriter;
import org.broadinstitute.sting.utils.genotype.LikelihoodObject;
import org.broadinstitute.sting.utils.genotype.IndelLikelihood;
import net.sf.samtools.SAMSequenceRecord;
/**
* @author aaron
* <p/>
* Class GFFWriter
* <p/>
* A descriptions should go here. Blame aaron if it's missing.
*/
public class GFFWriter implements GenotypeWriter {
/**
* add a single point genotype call to the file
*
* @param contig the contig you're calling in
* @param position the position on the contig
* @param referenceBase the reference base
* @param readDepth the read depth at the specified position
* @param likelihoods the likelihoods of each of the possible alleles
*/
@Override
public void addGenotypeCall(SAMSequenceRecord contig, int position, float rmsMapQuals, char referenceBase, int readDepth, LikelihoodObject likelihoods) {
//To change body of implemented methods use File | Settings | File Templates.
}
/**
* add a variable length call to the genotype file
*
* @param contig the contig you're calling in
* @param position the position on the genome
* @param rmsMapQuals the root mean square of the mapping qualities
* @param readDepth the read depth
* @param refBase the reference base
* @param firstHomZyg the first homozygous indel
* @param secondHomZyg the second homozygous indel (if present, null if not)
* @param hetLikelihood the heterozygous likelihood
*/
@Override
public void addVariableLengthCall(SAMSequenceRecord contig, int position, float rmsMapQuals, int readDepth, char refBase, IndelLikelihood firstHomZyg, IndelLikelihood secondHomZyg, byte hetLikelihood) {
//To change body of implemented methods use File | Settings | File Templates.
}
/**
* add a no call to the genotype file, if supported.
*
* @param position the position
* @param readDepth the read depth
*/
@Override
public void addNoCall(int position, int readDepth) {
//To change body of implemented methods use File | Settings | File Templates.
}
/** finish writing, closing any open files. */
@Override
public void close() {
//To change body of implemented methods use File | Settings | File Templates.
}
}

3
java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java
View File

@ -194,7 +194,8 @@ abstract class GLFRecord {
short bite = ((short) (this.getRecordType().getReadTypeValue() << 4 | (refBase.getBaseHexValue() & 0x0f)));
out.writeUByte((short) (this.getRecordType().getReadTypeValue() << 4 | (refBase.getBaseHexValue() & 0x0f)));
out.writeUInt(((Long) offset).intValue());
out.writeUInt((new Long(readDepth).intValue()));
int write = ((new Long(readDepth).intValue()) | this.minimumLikelihood << 24);
out.writeUInt(write);
out.writeUByte((short) rmsMapQ);
}

33
java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java
View File

@ -2,6 +2,7 @@ package org.broadinstitute.sting.utils.genotype.glf;
import net.sf.samtools.util.BinaryCodec;
import net.sf.samtools.util.BlockCompressedOutputStream;
import net.sf.samtools.SAMSequenceRecord;
import org.broadinstitute.sting.utils.genotype.GenotypeWriter;
import org.broadinstitute.sting.utils.genotype.IndelLikelihood;
import org.broadinstitute.sting.utils.genotype.LikelihoodObject;
@ -53,6 +54,9 @@ public class GLFWriter implements GenotypeWriter {
private String referenceSequenceName = null;
private long referenceSequenceLength = 0;
// the last position written
private int lastPos = 0;
/**
* The public constructor for creating a GLF object
*
@ -69,17 +73,15 @@ public class GLFWriter implements GenotypeWriter {
/**
* add a point genotype to the GLF writer
*
* @param contigName the name of the contig you're calling in
* @param contigLength the contig length
* @param contig the name of the contig you're calling in
* @param refBase the reference base, as a char
* @param genomicLoc the location, as an offset from the previous glf record
* @param genomicLoc the location the location on the reference contig
* @param readDepth the read depth at the specified postion
* @param rmsMapQ the root mean square of the mapping quality
* @param lhValues the GenotypeLikelihoods object, representing the genotype likelyhoods
*/
@Override
public void addGenotypeCall(String contigName,
int contigLength,
public void addGenotypeCall(SAMSequenceRecord contig,
int genomicLoc,
float rmsMapQ,
char refBase,
@ -87,23 +89,23 @@ public class GLFWriter implements GenotypeWriter {
LikelihoodObject lhValues) {
// check if we've jumped to a new contig
checkSequence(contigName, contigLength);
checkSequence(contig.getSequenceName(), contig.getSequenceLength());
SinglePointCall call = new SinglePointCall(refBase,
genomicLoc,
genomicLoc - lastPos,
readDepth,
(short) rmsMapQ,
lhValues.toDoubleArray());
lastPos = genomicLoc;
call.write(this.outputBinaryCodec);
}
/**
* add a variable length (indel, deletion, etc) to the genotype writer
*
* @param contigName the name of the contig you're calling in
* @param contigLength the contig length
* @param contig the name of the contig you're calling in
* @param refBase the reference base
* @param genomicLoc the location, as an offset from the previous glf record
* @param genomicLoc the location on the reference contig
* @param readDepth the read depth at the specified postion
* @param rmsMapQ the root mean square of the mapping quality
* @param firstHomZyg the first homozygous call
@ -111,8 +113,7 @@ public class GLFWriter implements GenotypeWriter {
* @param hetLikelihood the negitive log likelihood of the heterozygote, from 0 to 255
*/
@Override
public void addVariableLengthCall(String contigName,
int contigLength,
public void addVariableLengthCall(SAMSequenceRecord contig,
int genomicLoc,
float rmsMapQ,
int readDepth,
@ -122,11 +123,11 @@ public class GLFWriter implements GenotypeWriter {
byte hetLikelihood) {
// check if we've jumped to a new contig
checkSequence(contigName, contigLength);
checkSequence(contig.getSequenceName(), contig.getSequenceLength());
// normalize the two
VariableLengthCall call = new VariableLengthCall(refBase,
genomicLoc,
genomicLoc - lastPos,
readDepth,
(short) rmsMapQ,
firstHomZyg.getLikelihood(),
@ -136,7 +137,7 @@ public class GLFWriter implements GenotypeWriter {
firstHomZyg.getIndelSequence(),
secondHomZyg.getLengthOfIndel(),
secondHomZyg.getIndelSequence());
lastPos = genomicLoc;
call.write(this.outputBinaryCodec);
}

2
java/src/org/broadinstitute/sting/utils/genotype/glf/SinglePointCall.java
View File

@ -37,7 +37,7 @@ import net.sf.samtools.util.BinaryCodec;
*/
class SinglePointCall extends GLFRecord {
// our likelihood object
// our likelihoods object
private double likelihoods[];
/**

6
java/test/org/broadinstitute/sting/utils/genotype/GeliAdapterTest.java
View File

@ -1,6 +1,7 @@
package org.broadinstitute.sting.utils.genotype;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMSequenceRecord;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.junit.Test;
@ -55,8 +56,9 @@ public class GeliAdapterTest extends BaseTest {
File fl = new File("testFile.txt");
SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(2,1,10);
adapter = new GeliAdapter(fl,header);
LikelihoodObject obj = new LikelihoodObject(createFakeLikelihoods());
adapter.addGenotypeCall("chr1",10,100,100,'A',100,obj);
LikelihoodObject obj = new LikelihoodObject(createFakeLikelihoods(), LikelihoodObject.LIKELIHOOD_TYPE.LOG);
SAMSequenceRecord rec = new SAMSequenceRecord("chr1",10);
adapter.addGenotypeCall(rec,100,100,'A',100,obj);
adapter.close();
}

18
java/test/org/broadinstitute/sting/utils/genotype/LikelihoodObjectTest.java
View File

@ -52,7 +52,7 @@ public class LikelihoodObjectTest extends BaseTest {
@Test
public void testBlankConstruction() {
mLO = new LikelihoodObject();
assertTrue(mLO.likelihood.size() == LikelihoodObject.GENOTYPE.values().length);
assertTrue(mLO.likelihoods.size() == LikelihoodObject.GENOTYPE.values().length);
}
@Test
@ -61,12 +61,12 @@ public class LikelihoodObjectTest extends BaseTest {
for (int x = 0; x < 10; x++) {
ray[x] = ( x * 25 );
}
mLO = new LikelihoodObject(ray);
assertTrue(mLO.likelihood.size() == LikelihoodObject.GENOTYPE.values().length);
mLO = new LikelihoodObject(ray,LikelihoodObject.LIKELIHOOD_TYPE.NEGITIVE_LOG);
assertTrue(mLO.likelihoods.size() == LikelihoodObject.GENOTYPE.values().length);
int index = 0;
for (LikelihoodObject.GENOTYPE t : LikelihoodObject.GENOTYPE.values()) {
assertTrue(ray[index] == mLO.likelihood.get(t));
assertTrue(ray[index] == mLO.likelihoods.get(t));
++index;
}
}
@ -77,8 +77,8 @@ public class LikelihoodObjectTest extends BaseTest {
for (int x = 0; x < 10; x++) {
ray[x] = ( x * 25.0 );
}
mLO = new LikelihoodObject(ray);
assertTrue(mLO.likelihood.size() == LikelihoodObject.GENOTYPE.values().length);
mLO = new LikelihoodObject(ray,LikelihoodObject.LIKELIHOOD_TYPE.NEGITIVE_LOG);
assertTrue(mLO.likelihoods.size() == LikelihoodObject.GENOTYPE.values().length);
int index = 0;
short[] ret = mLO.toByteArray();
@ -104,8 +104,8 @@ public class LikelihoodObjectTest extends BaseTest {
ray[x] = ( 240.0 );
}
ray [5] = 0;
mLO = new LikelihoodObject(ray);
assertTrue(mLO.likelihood.size() == LikelihoodObject.GENOTYPE.values().length);
mLO = new LikelihoodObject(ray, LikelihoodObject.LIKELIHOOD_TYPE.NEGITIVE_LOG);
assertTrue(mLO.likelihoods.size() == LikelihoodObject.GENOTYPE.values().length);
short smallest = (short)mLO.getBestLikelihood();
assertTrue(smallest == 0);
int index = 0;
@ -122,7 +122,7 @@ public class LikelihoodObjectTest extends BaseTest {
for (LikelihoodObject.GENOTYPE t : LikelihoodObject.GENOTYPE.values()) {
mLO.setLikelihood(t,128);
}
assertTrue(mLO.likelihood.size() == LikelihoodObject.GENOTYPE.values().length);
assertTrue(mLO.likelihoods.size() == LikelihoodObject.GENOTYPE.values().length);
int index = 0;
short[] ret = mLO.toByteArray();