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Further cleanup of Sample 

-- Cleaned up interface functions in GAE
-- Added Walker.getSampleDB() function which is an easier option for tools to get the samples db
This commit is contained in:
Mark DePristo 2011-09-29 10:34:51 -04:00
parent e76f381628
commit 2a0cd556d3
19 changed files with 140 additions and 278 deletions
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133
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
View File

@ -1034,123 +1034,16 @@ public class GenomeAnalysisEngine {
return readsDataSource == null ? null : readsDataSource.getCumulativeReadMetrics();
}
public SampleDataSource getSampleMetadata() {
// -------------------------------------------------------------------------------------
//
// code for working with Samples database
//
// -------------------------------------------------------------------------------------
public SampleDataSource getSampleDB() {
return this.sampleDataSource;
}
/**
* Get a sample by its ID
* If an alias is passed in, return the main sample object
* @param id sample id
* @return sample Object with this ID
*/
public Sample getSampleById(String id) {
return sampleDataSource.getSampleById(id);
}
/**
* Get the sample for a given read group
* Must first look up ID for read group
* @param readGroup of sample
* @return sample object with ID from the read group
*/
public Sample getSampleByReadGroup(SAMReadGroupRecord readGroup) {
return sampleDataSource.getSampleByReadGroup(readGroup);
}
/**
* Get a sample for a given read
* Must first look up read group, and then sample ID for that read group
* @param read of sample
* @return sample object of this read
*/
public Sample getSampleByRead(SAMRecord read) {
return getSampleByReadGroup(read.getReadGroup());
}
/**
* Get number of sample objects
* @return size of samples map
*/
public int sampleCount() {
return sampleDataSource.sampleCount();
}
/**
* Return all samples with a given family ID
* Note that this isn't terribly efficient (linear) - it may be worth adding a new family ID data structure for this
* @param familyId family ID
* @return Samples with the given family ID
*/
public Set<Sample> getFamily(String familyId) {
return sampleDataSource.getFamily(familyId);
}
/**
* Returns all children of a given sample
* See note on the efficiency of getFamily() - since this depends on getFamily() it's also not efficient
* @param sample parent sample
* @return children of the given sample
*/
public Set<Sample> getChildren(Sample sample) {
return sampleDataSource.getChildren(sample);
}
/**
* Gets all the samples
* @return
*/
public Collection<Sample> getSamples() {
return sampleDataSource.getSamples();
}
/**
* Takes a list of sample names and returns their corresponding sample objects
*
* @param sampleNameList List of sample names
* @return Corresponding set of samples
*/
public Set<Sample> getSamples(Collection<String> sampleNameList) {
return sampleDataSource.getSamples(sampleNameList);
}
/**
* Returns a set of samples that have any value (which could be null) for a given property
* @param key Property key
* @return Set of samples with the property
*/
public Set<Sample> getSamplesWithProperty(String key) {
return sampleDataSource.getSamplesWithProperty(key);
}
/**
* Returns a set of samples that have a property with a certain value
* Value must be a string for now - could add a similar method for matching any objects in the future
*
* @param key Property key
* @param value String property value
* @return Set of samples that match key and value
*/
public Set<Sample> getSamplesWithProperty(String key, String value) {
return sampleDataSource.getSamplesWithProperty(key, value);
}
/**
* Returns a set of sample objects for the sample names in a variant context
*
* @param context Any variant context
* @return a set of the sample objects
*/
public Set<Sample> getSamplesByVariantContext(VariantContext context) {
Set<Sample> samples = new HashSet<Sample>();
for (String sampleName : context.getSampleNames()) {
samples.add(sampleDataSource.getOrCreateSample(sampleName));
}
return samples;
}
/**
* Returns all samples that were referenced in the SAM file
*/
@ -1158,18 +1051,6 @@ public class GenomeAnalysisEngine {
return sampleDataSource.getSAMFileSamples();
}
/**
* Return a subcontext restricted to samples with a given property key/value
* Gets the sample names from key/value and relies on VariantContext.subContextFromGenotypes for the filtering
* @param context VariantContext to filter
* @param key property key
* @param value property value (must be string)
* @return subcontext
*/
public VariantContext subContextFromSampleProperty(VariantContext context, String key, String value) {
return sampleDataSource.subContextFromSampleProperty(context, key, value);
}
public Map<String,String> getApproximateCommandLineArguments(Object... argumentProviders) {
return CommandLineUtils.getApproximateCommandLineArguments(parsingEngine,argumentProviders);
}

9
public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java
View File

@ -26,7 +26,6 @@
package org.broadinstitute.sting.gatk.contexts;
import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.gatk.samples.Sample;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -76,14 +75,6 @@ public class AlignmentContextUtils {
return splitContextBySampleName(context, null);
}
public static Map<Sample, AlignmentContext> splitContextBySample(AlignmentContext context) {
Map<Sample, AlignmentContext> m = new HashMap<Sample, AlignmentContext>();
for ( Map.Entry<String, AlignmentContext> entry : splitContextBySampleName(context, null).entrySet() ) {
m.put(new Sample(entry.getKey()), entry.getValue());
}
return m;
}
/**
* Splits the given AlignmentContext into a StratifiedAlignmentContext per sample, but referencd by sample name instead
* of sample object.

2
public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
View File

@ -56,7 +56,7 @@ public class LinearMicroScheduler extends MicroScheduler {
traversalEngine.startTimersIfNecessary();
if(shard.getShardType() == Shard.ShardType.LOCUS) {
LocusWalker lWalker = (LocusWalker)walker;
WindowMaker windowMaker = new WindowMaker(shard, engine.getGenomeLocParser(), getReadIterator(shard), shard.getGenomeLocs(), engine.getSampleMetadata());
WindowMaker windowMaker = new WindowMaker(shard, engine.getGenomeLocParser(), getReadIterator(shard), shard.getGenomeLocs(), engine.getSampleDB());
for(WindowMaker.WindowMakerIterator iterator: windowMaker) {
ShardDataProvider dataProvider = new LocusShardDataProvider(shard,iterator.getSourceInfo(),engine.getGenomeLocParser(),iterator.getLocus(),iterator,reference,rods);
Object result = traversalEngine.traverse(walker, dataProvider, accumulator.getReduceInit());

2
public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
View File

@ -62,7 +62,7 @@ public class ShardTraverser implements Callable {
Object accumulator = walker.reduceInit();
LocusWalker lWalker = (LocusWalker)walker;
WindowMaker windowMaker = new WindowMaker(shard,microScheduler.getEngine().getGenomeLocParser(),microScheduler.getReadIterator(shard),shard.getGenomeLocs(), microScheduler.engine.getSampleMetadata()); // todo: microScheduler.engine is protected - is it okay to user it here?
WindowMaker windowMaker = new WindowMaker(shard,microScheduler.getEngine().getGenomeLocParser(),microScheduler.getReadIterator(shard),shard.getGenomeLocs(), microScheduler.engine.getSampleDB()); // todo: microScheduler.engine is protected - is it okay to user it here?
ShardDataProvider dataProvider = null;
for(WindowMaker.WindowMakerIterator iterator: windowMaker) {

4
public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
View File

@ -542,7 +542,7 @@ public class LocusIteratorByState extends LocusIterator {
Map<String,ReadSelector> readSelectors = new HashMap<String,ReadSelector>();
for(Sample sample: samples) {
readStatesBySample.put(sample,new PerSampleReadStateManager());
readSelectors.put(sample.getId(),downsamplingMethod.type == DownsampleType.BY_SAMPLE ? new NRandomReadSelector(null,targetCoverage) : new AllReadsSelector());
readSelectors.put(sample.getID(),downsamplingMethod.type == DownsampleType.BY_SAMPLE ? new NRandomReadSelector(null,targetCoverage) : new AllReadsSelector());
}
samplePartitioner = new SamplePartitioner(readSelectors);
@ -640,7 +640,7 @@ public class LocusIteratorByState extends LocusIterator {
samplePartitioner.complete();
for(Sample sample: samples) {
ReadSelector aggregator = samplePartitioner.getSelectedReads(sample.getId());
ReadSelector aggregator = samplePartitioner.getSelectedReads(sample.getID());
Collection<SAMRecord> newReads = new ArrayList<SAMRecord>(aggregator.getSelectedReads());

171
public/java/src/org/broadinstitute/sting/gatk/samples/Sample.java
View File

@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.samples;
import org.broadinstitute.sting.utils.exceptions.StingException;
import java.util.Collections;
import java.util.HashMap;
import java.util.Map;
@ -13,23 +14,16 @@ import java.util.Map;
* Time: 3:31:38 PM
*/
public class Sample implements java.io.Serializable {
private final static String MOTHER = "mother";
private final static String FATHER = "father";
private final static String GENDER = "gender";
private final static String POPULATION = "population";
private final static String FAMILY = "familyId";
private final static String AFFECTION = "affection";
private final static String QUANT_TRAIT = "quantTrait";
private final String id;
private boolean hasSampleFileEntry = false; // true if this sample has an entry in a sample file
final private String familyID, paternalID, maternalID;
final private Sample.Gender gender;
final private double quantitativePhenotype;
final private Sample.Affection affection;
final private String population;
final private String ID;
final private SampleDataSource dataSource;
private boolean hasSAMFileEntry = false; // true if this sample has an entry in the SAM file
private HashMap<String, Object> properties = new HashMap<String, Object>();
private HashMap<String, Sample> relationships = new HashMap<String, Sample>();
private Map<String, Object> properties = new HashMap<String, Object>();
public enum Gender {
MALE,
@ -47,26 +41,28 @@ public class Sample implements java.io.Serializable {
/** A quantitative trait: value of the trait is stored elsewhere */
QUANTITATIVE
}
public final static double UNSET_QUANTITIATIVE_TRAIT_VALUE = Double.NaN;
public Sample(String id) {
/* if (id == null) {
throw new StingException("Error creating sample: sample ID cannot be null");
}*/
this.id = id;
public Sample(final String ID, final SampleDataSource dataSource,
final String familyID, final String paternalID, final String maternalID,
final Gender gender, final double quantitativePhenotype, final Affection affection,
final String population) {
this.familyID = familyID;
this.paternalID = paternalID;
this.maternalID = maternalID;
this.gender = gender;
this.quantitativePhenotype = quantitativePhenotype;
this.affection = affection;
this.population = population;
this.ID = ID;
this.dataSource = dataSource;
}
public String getId() {
return this.id;
}
public Map<String, Object> getProperties() {
return properties;
}
@Deprecated
public void setSampleFileEntry(boolean value) {
this.hasSampleFileEntry = value;
public Sample(String id, SampleDataSource dataSource) {
this(id, dataSource,
null, null, null,
Gender.UNKNOWN, UNSET_QUANTITIATIVE_TRAIT_VALUE, Affection.UNKNOWN, null);
}
@Deprecated
@ -79,58 +75,39 @@ public class Sample implements java.io.Serializable {
this.hasSAMFileEntry = value;
}
/**
* Get one property
* @param key key of property
* @return value of property as generic object
*/
public Object getProperty(String key) {
return properties.get(key);
// -------------------------------------------------------------------------------------
//
// standard property getters
//
// -------------------------------------------------------------------------------------
public String getID() {
return ID;
}
/**
* Set a property
* If property already exists, it is overwritten
* @param key key of property
* @param value object to be stored in properties array
*/
public void setProperty(String key, Object value) {
if (relationships.containsKey(key)) {
throw new StingException("The same key cannot exist as a property and a relationship");
}
if (key.equals(GENDER) && value.getClass() != Gender.class) {
throw new StingException("'gender' property must be of type Sample.Gender");
}
if (key.equals(POPULATION) && value.getClass() != String.class) {
throw new StingException("'population' property must be of type String");
}
properties.put(key, value);
public String getFamilyID() {
return familyID;
}
/**
* Get one relationship
* @param key of relationship
* @return Sample object that this relationship points to
*/
public Sample getRelationship(String key) {
return relationships.get(key);
public String getPaternalID() {
return paternalID;
}
/**
* Set one relationship
* If already set, it is overwritten
* @param key key of the relationship
* @param value Sample object this relationship points to
*/
public void setRelationship(String key, Sample value) {
if (properties.containsKey(key)) {
throw new StingException("The same key cannot exist as a property and a relationship");
}
relationships.put(key, value);
public String getMaternalID() {
return maternalID;
}
public Affection getAffection() {
return affection;
}
public boolean hasQuantitativeTrait() {
return affection == Affection.QUANTITATIVE;
}
public double getQuantitativePhenotype() {
return quantitativePhenotype;
}
/**
@ -138,7 +115,7 @@ public class Sample implements java.io.Serializable {
* @return sample object with relationship mother, if exists, or null
*/
public Sample getMother() {
return getRelationship(MOTHER);
return dataSource.getSampleById(maternalID);
}
/**
@ -146,7 +123,7 @@ public class Sample implements java.io.Serializable {
* @return sample object with relationship father, if exists, or null
*/
public Sample getFather() {
return getRelationship(FATHER);
return dataSource.getSampleById(paternalID);
}
/**
@ -154,29 +131,48 @@ public class Sample implements java.io.Serializable {
* @return property of key "gender" - must be of type Gender
*/
public Gender getGender() {
return (Gender) properties.get(GENDER);
return gender;
}
public String getPopulation() {
return (String) properties.get(POPULATION);
return population;
}
public String getFamilyId() {
return (String) properties.get(FAMILY);
return familyID;
}
/**
* @return True if sample is male, false if female, unknown, or null
*/
public boolean isMale() {
return properties.get(GENDER) == Gender.MALE;
return getGender() == Gender.MALE;
}
/**
* @return True if sample is female, false if male, unknown or null
*/
public boolean isFemale() {
return properties.get(GENDER) == Gender.MALE;
return getGender() == Gender.MALE;
}
// -------------------------------------------------------------------------------------
//
// code for working with additional -- none standard -- properites
//
// -------------------------------------------------------------------------------------
public Map<String, Object> getExtraProperties() {
return Collections.unmodifiableMap(properties);
}
/**
* Get one property
* @param key key of property
* @return value of property as generic object
*/
public Object getExtraPropertyValue(final String key) {
return properties.get(key);
}
/**
@ -184,7 +180,7 @@ public class Sample implements java.io.Serializable {
* @param key property key
* @return true if sample has this property (even if its value is null)
*/
public boolean hasProperty(String key) {
public boolean hasExtraProperty(String key) {
return properties.containsKey(key);
}
@ -196,17 +192,14 @@ public class Sample implements java.io.Serializable {
Sample sample = (Sample) o;
if (hasSAMFileEntry != sample.hasSAMFileEntry) return false;
if (hasSampleFileEntry != sample.hasSampleFileEntry) return false;
if (id != null ? !id.equals(sample.id) : sample.id != null) return false;
if (ID != null ? !ID.equals(sample.ID) : sample.ID != null) return false;
if (properties != null ? !properties.equals(sample.properties) : sample.properties != null) return false;
if (relationships != null ? !relationships.equals(sample.relationships) : sample.relationships != null)
return false;
return true;
}
@Override
public int hashCode() {
return id != null ? id.hashCode() : "".hashCode();
return ID != null ? ID.hashCode() : "".hashCode();
}
}

37
public/java/src/org/broadinstitute/sting/gatk/samples/SampleDataSource.java
View File

@ -46,12 +46,6 @@ public class SampleDataSource {
*/
private HashMap<String, String> sampleAliases = new HashMap<String, String>();
/**
* While loading sample files, we must be aware of "special" properties and relationships that are always allowed
*/
public static final String[] specialProperties = new String[] {"familyId", "population", "gender"};
public static final String[] specialRelationships = new String[] {"mother", "father"};
/**
* Constructor takes both a SAM header and sample files because the two must be integrated.
* @param header SAMFileHeader that has been created for this analysis
@ -63,8 +57,7 @@ public class SampleDataSource {
// create empty sample object for each sample referenced in the SAM header
for (String sampleName : SampleUtils.getSAMFileSamples(header)) {
if (!hasSample(sampleName)) {
Sample newSample = new Sample(sampleName);
newSample.setSAMFileEntry(true);
Sample newSample = new Sample(sampleName, this);
samples.put(sampleName, newSample);
}
}
@ -78,7 +71,7 @@ public class SampleDataSource {
}
public SampleDataSource() {
samples.put(null, new Sample(null));
samples.put(null, new Sample(null, this));
}
/**
@ -87,7 +80,7 @@ public class SampleDataSource {
public void addSamplesFromSAMHeader(SAMFileHeader header) {
for (String sampleName : SampleUtils.getSAMFileSamples(header)) {
if (!hasSample(sampleName)) {
Sample newSample = new Sample(sampleName);
Sample newSample = new Sample(sampleName, this);
newSample.setSAMFileEntry(true);
samples.put(sampleName, newSample);
}
@ -151,9 +144,9 @@ public class SampleDataSource {
//
// try {
// // step 1: add the sample if it doesn't already exist
// Sample sample = getSampleById(sampleParser.getId());
// Sample sample = getSampleById(sampleParser.getID());
// if (sample == null) {
// sample = new Sample(sampleParser.getId());
// sample = new Sample(sampleParser.getID());
// }
// addSample(sample);
// sample.setSampleFileEntry(true);
@ -207,7 +200,7 @@ public class SampleDataSource {
//
// // next check that there isn't already a conflicting property there
// if (sample.getRelationship(relationship) != null) {
// if (sample.getRelationship(relationship).getId() != sampleParser.getProperties().get(relationship)) {
// if (sample.getRelationship(relationship).getID() != sampleParser.getProperties().get(relationship)) {
// throw new StingException(relationship + " is a conflicting relationship!");
// }
// // if the relationship is already set - and consistent with what we're reading now - no need to continue
@ -222,7 +215,7 @@ public class SampleDataSource {
// }
// } catch (Exception e) {
// throw new StingException("An error occurred while loading this sample from the sample file: " +
// sampleParser.getId(), e);
// sampleParser.getID(), e);
// }
// }
// }
@ -377,7 +370,7 @@ public class SampleDataSource {
* @param sample to be added
*/
private void addSample(Sample sample) {
samples.put(sample.getId(), sample);
samples.put(sample.getID(), sample);
}
/**
@ -496,7 +489,7 @@ public class SampleDataSource {
public Set<Sample> getSamplesWithProperty(String key) {
HashSet<Sample> toReturn = new HashSet<Sample>();
for (Sample s : samples.values()) {
if (s.hasProperty(key))
if (s.hasExtraProperty(key))
toReturn.add(s);
}
return toReturn;
@ -513,7 +506,7 @@ public class SampleDataSource {
public Set<Sample> getSamplesWithProperty(String key, String value) {
Set<Sample> toReturn = getSamplesWithProperty(key);
for (Sample s : toReturn) {
if (!s.getProperty(key).equals(value))
if (!s.getExtraPropertyValue(key).equals(value))
toReturn.remove(s);
}
return toReturn;
@ -522,7 +515,7 @@ public class SampleDataSource {
public Sample getOrCreateSample(String id) {
Sample sample = getSampleById(id);
if (sample == null) {
sample = new Sample(id);
sample = new Sample(id, this);
addSample(sample);
}
return sample;
@ -568,16 +561,10 @@ public class SampleDataSource {
Set<String> samplesWithProperty = new HashSet<String>();
for (String sampleName : context.getSampleNames()) {
Sample s = samples.get(sampleName);
if (s != null && s.hasProperty(key) && s.getProperty(key).equals(value))
if (s != null && s.hasExtraProperty(key) && s.getExtraPropertyValue(key).equals(value))
samplesWithProperty.add(sampleName);
}
Map<String, Genotype> genotypes = context.getGenotypes(samplesWithProperty);
return context.subContextFromGenotypes(genotypes.values());
}
public static SampleDataSource createEmptyDataSource() {
SAMFileHeader header = new SAMFileHeader();
return new SampleDataSource(header, null);
}
}

10
public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
View File

@ -30,6 +30,8 @@ import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.filters.MalformedReadFilter;
import org.broadinstitute.sting.gatk.samples.Sample;
import org.broadinstitute.sting.gatk.samples.SampleDataSource;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.collections.Pair;
@ -87,6 +89,14 @@ public abstract class Walker<MapType, ReduceType> {
return getToolkit().getMasterSequenceDictionary();
}
protected SampleDataSource getSampleDB() {
return getToolkit().getSampleDB();
}
protected Sample getSampleByID(final String id) {
return getToolkit().getSampleDB().getSampleById(id);
}
/**
* (conceptual static) method that states whether you want to see reads piling up at a locus
* that contain a deletion at the locus.

2
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
View File

@ -247,7 +247,7 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
Map<String,Genotype> preferredGenotypes = preferredVC.getGenotypes();
Map<String,Genotype> otherGenotypes = goodSite(otherVC) ? otherVC.getGenotypes() : null;
for ( String sample : samples ) {
boolean isMaleOnChrX = CHECK_IS_MALE_ON_CHR_X && getToolkit().getSampleById(sample).isMale();
boolean isMaleOnChrX = CHECK_IS_MALE_ON_CHR_X && getSampleByID(sample).isMale();
Genotype genotype;
boolean isValidation;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java
View File

@ -227,9 +227,9 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
@Override
public void initialize() {
if ( getToolkit().getSamples().size() != 2 ) {
if ( getSampleDB().getSamples().size() != 2 ) {
// unbelievably there are actually two samples even when there's just one in the header. God I hate this Samples system
throw new UserException.BadArgumentValue("-I", "CallableLoci only works for a single sample, but multiple samples were found in the provided BAM files: " + getToolkit().getSamples());
throw new UserException.BadArgumentValue("-I", "CallableLoci only works for a single sample, but multiple samples were found in the provided BAM files: " + getSampleDB().getSamples());
}
try {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
View File

@ -1102,7 +1102,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
if (!p.isDeletion()) // IGNORE deletions for now
readBases.putReadBase(p);
}
sampleReadBases.put(sample.getId(), readBases);
sampleReadBases.put(sample.getID(), readBases);
}
}
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociByPopulationWalker.java
View File

@ -25,7 +25,7 @@ public class CountLociByPopulationWalker extends LocusWalker<Integer, Long> impl
for (SAMRecord read : reads) {
// get the sample
Sample sample = getToolkit().getSampleByRead(read);
Sample sample = getSampleDB().getSampleByRead(read);
if (sample == null)
return 1;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMalesWalker.java
View File

@ -16,7 +16,7 @@ import org.broadinstitute.sting.gatk.walkers.Requires;
@Requires({DataSource.READS, DataSource.REFERENCE})
public class CountMalesWalker extends ReadWalker<Integer, Integer> {
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker tracker) {
Sample sample = getToolkit().getSampleByRead(read);
Sample sample = getSampleDB().getSampleByRead(read);
return sample.isMale() ? 1 : 0;
}

14
public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java
View File

@ -88,9 +88,9 @@ public class MendelianViolation {
* @param minGenotypeQualityP - the minimum phred scaled genotype quality score necessary to asses mendelian violation
*/
public MendelianViolation(Sample sample, double minGenotypeQualityP) {
sampleMom = sample.getMother().getId();
sampleDad = sample.getFather().getId();
sampleChild = sample.getId();
sampleMom = sample.getMother().getID();
sampleDad = sample.getFather().getID();
sampleChild = sample.getID();
minGenotypeQuality = minGenotypeQualityP;
}
@ -102,13 +102,13 @@ public class MendelianViolation {
*/
public MendelianViolation(GenomeAnalysisEngine engine, double minGenotypeQualityP) {
boolean gotSampleInformation = false;
Collection<Sample> samples = engine.getSamples();
Collection<Sample> samples = engine.getSampleDB().getSamples();
// Iterate through all samples in the sample_metadata file but we really can only take one.
for (Sample sample : samples) {
if (sample.getMother() != null && sample.getFather() != null) {
sampleMom = sample.getMother().getId();
sampleDad = sample.getFather().getId();
sampleChild = sample.getId();
sampleMom = sample.getMother().getID();
sampleDad = sample.getFather().getID();
sampleChild = sample.getID();
minGenotypeQuality = minGenotypeQualityP;
gotSampleInformation = true;
break; // we can only deal with one trio information

4
public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
View File

@ -555,7 +555,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
PerSamplePileupElementTracker<PE> tracker = (PerSamplePileupElementTracker<PE>)pileupElementTracker;
Collection<String> sampleNames = new HashSet<String>();
for (Sample sample : tracker.getSamples()) {
sampleNames.add(sample.getId());
sampleNames.add(sample.getID());
}
return sampleNames;
}
@ -700,7 +700,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
for(PE p: pileupElementTracker) {
SAMRecord read = p.getRead();
if(sample != null) {
if(read.getReadGroup() != null && sample.getId().equals(read.getReadGroup().getSample()))
if(read.getReadGroup() != null && sample.getID().equals(read.getReadGroup().getSample()))
filteredTracker.add(p);
}
else {

4
public/java/src/org/broadinstitute/sting/utils/pileup/PileupElementTracker.java
View File

@ -74,7 +74,7 @@ class PerSamplePileupElementTracker<PE extends PileupElement> extends PileupElem
Sample sample = entry.getKey();
AbstractReadBackedPileup<?,PE> pileupBySample = entry.getValue();
pileup.put(sample,pileupBySample.pileupElementTracker);
sampleNames.put(sample.getId(), sample);
sampleNames.put(sample.getID(), sample);
}
}
@ -105,7 +105,7 @@ class PerSamplePileupElementTracker<PE extends PileupElement> extends PileupElem
public void addElements(final Sample sample, PileupElementTracker<PE> elements) {
pileup.put(sample,elements);
sampleNames.put(sample.getId(), sample);
sampleNames.put(sample.getID(), sample);
size += elements.size();
}

8
public/java/test/org/broadinstitute/sting/gatk/samples/SampleDataSourceUnitTest.java
View File

@ -149,8 +149,8 @@ public class SampleDataSourceUnitTest extends BaseTest {
Iterator<Sample> i = ceuSamples.iterator();
ArrayList<String> sampleNames = new ArrayList<String>();
sampleNames.add(i.next().getId());
sampleNames.add(i.next().getId());
sampleNames.add(i.next().getID());
sampleNames.add(i.next().getID());
Assert.assertTrue(sampleNames.contains("sampleA"));
Assert.assertTrue(sampleNames.contains("sampleB"));
}
@ -191,8 +191,8 @@ public class SampleDataSourceUnitTest extends BaseTest {
// make sure both samples are included
Iterator<Sample> i = set.iterator();
ArrayList<String> sampleNames = new ArrayList<String>();
sampleNames.add(i.next().getId());
sampleNames.add(i.next().getId());
sampleNames.add(i.next().getID());
sampleNames.add(i.next().getID());
Assert.assertTrue(sampleNames.contains("NA123"));
Assert.assertTrue(sampleNames.contains("NA456"));
}

2
public/java/test/org/broadinstitute/sting/gatk/samples/SampleUnitTest.java
View File

@ -55,7 +55,7 @@ public class SampleUnitTest extends BaseTest {
*/
@Test()
public void specialGettersTest() {
Assert.assertTrue(sampleC.getId().equals("sampleC"));
Assert.assertTrue(sampleC.getID().equals("sampleC"));
Assert.assertTrue(sampleC.getPopulation().equals("pop1"));
Assert.assertTrue(sampleC.isMale());
Assert.assertFalse(sampleA.isMale()); // sample A doesn't have a gender, so this should be false

6
public/java/test/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java
View File

@ -168,9 +168,9 @@ public class ReadBackedPileupUnitTest {
Sample sample2 = new Sample("sample2");
SAMReadGroupRecord readGroupOne = new SAMReadGroupRecord("rg1");
readGroupOne.setSample(sample1.getId());
readGroupOne.setSample(sample1.getID());
SAMReadGroupRecord readGroupTwo = new SAMReadGroupRecord("rg2");
readGroupTwo.setSample(sample2.getId());
readGroupTwo.setSample(sample2.getID());
SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1,1,1000);
header.addReadGroup(readGroupOne);
@ -191,7 +191,7 @@ public class ReadBackedPileupUnitTest {
Assert.assertEquals(sample1Pileup.size(),1,"Sample 1 pileup has wrong number of elements");
Assert.assertEquals(sample1Pileup.getReads().get(0),read1,"Sample 1 pileup has incorrect read");
ReadBackedPileup sample2Pileup = pileup.getPileupForSampleName(sample2.getId());
ReadBackedPileup sample2Pileup = pileup.getPileupForSampleName(sample2.getID());
Assert.assertEquals(sample2Pileup.size(),1,"Sample 2 pileup has wrong number of elements");
Assert.assertEquals(sample2Pileup.getReads().get(0),read2,"Sample 2 pileup has incorrect read");