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

public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -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);
     }

public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java

@@ -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.

public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java

@@ -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());

public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java

@@ -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) {

public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java

@@ -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());
 

public/java/src/org/broadinstitute/sting/gatk/samples/Sample.java

@@ -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";
+    final private String familyID, paternalID, maternalID;
-    private final static String FATHER = "father";
+    final private Sample.Gender gender;
-    private final static String GENDER = "gender";
+    final private double quantitativePhenotype;
-    private final static String POPULATION = "population";
+    final private Sample.Affection affection;
-    private final static String FAMILY = "familyId";
+    final private String population;
-    private final static String AFFECTION = "affection";
+    final private String ID;
-    private final static String QUANT_TRAIT = "quantTrait";
+    final private SampleDataSource dataSource;
-
-    private final String id;
-
-    private boolean hasSampleFileEntry = false; // true if this sample has an entry in a sample file
 
     private boolean hasSAMFileEntry = false; // true if this sample has an entry in the SAM file
-
+    private Map<String, Object> properties = new HashMap<String, Object>();
-    private HashMap<String, Object> properties = new HashMap<String, Object>();
-
-    private HashMap<String, Sample> relationships = new HashMap<String, Sample>();
 
     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) {
+    public Sample(final String ID, final SampleDataSource dataSource,
-/*        if (id == null) {
+                  final String familyID, final String paternalID, final String maternalID,
-            throw new StingException("Error creating sample: sample ID cannot be null");
+                  final Gender gender, final double quantitativePhenotype, final Affection affection,
-        }*/
+                  final String population) {
-        this.id = id;
+        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() {
+    public Sample(String id, SampleDataSource dataSource) {
-        return this.id;
+        this(id, dataSource,
-    }
+                null, null, null,
-
+                Gender.UNKNOWN, UNSET_QUANTITIATIVE_TRAIT_VALUE, Affection.UNKNOWN, null);
-    public Map<String, Object> getProperties() {
-        return properties;
-    }
-
-    @Deprecated
-    public void setSampleFileEntry(boolean value) {
-        this.hasSampleFileEntry = value;
     }
 
     @Deprecated
@@ -79,58 +75,39 @@ public class Sample implements java.io.Serializable {
         this.hasSAMFileEntry = value;
     }
 
-    /**
+    // -------------------------------------------------------------------------------------
-     * Get one property
+    //
-     * @param key key of property
+    // standard property getters
-     * @return value of property as generic object
+    //
-     */
+    // -------------------------------------------------------------------------------------
-    public Object getProperty(String key) {
+
-        return properties.get(key);
+    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)) {
+    public String getFamilyID() {
-            throw new StingException("The same key cannot exist as a property and a relationship");
+        return familyID;
-        }
-
-        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 getPaternalID() {
-     * Get one relationship
+        return paternalID;
-     * @param key of relationship
-     * @return Sample object that this relationship points to
-     */
-    public Sample getRelationship(String key) {
-        return relationships.get(key);
     }
 
-    /**
+    public String getMaternalID() {
-     * Set one relationship
+        return maternalID;
-     * If already set, it is overwritten
+    }
-     * @param key key of the relationship
+
-     * @param value Sample object this relationship points to
+    public Affection getAffection() {
-     */
+        return affection;
-    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");
+    public boolean hasQuantitativeTrait() {
-        }
+        return affection == Affection.QUANTITATIVE;
-        relationships.put(key, value);
+    }
+
+    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();
     }
 }

public/java/src/org/broadinstitute/sting/gatk/samples/SampleDataSource.java

@@ -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);
+                Sample newSample = new Sample(sampleName, this);
-                newSample.setSAMFileEntry(true);
                 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);
-    }
-
 }

public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java

@@ -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.

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

@@ -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;

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

@@ -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 {

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

@@ -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);
                         }
                     }
                 }

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

@@ -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;
 

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

@@ -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;
     }
 

public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java

@@ -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();
+        sampleMom = sample.getMother().getID();
-        sampleDad = sample.getFather().getId();
+        sampleDad = sample.getFather().getID();
-        sampleChild = sample.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();
+                sampleMom = sample.getMother().getID();
-                sampleDad = sample.getFather().getId();
+                sampleDad = sample.getFather().getID();
-                sampleChild = sample.getId();
+                sampleChild = sample.getID();
                 minGenotypeQuality = minGenotypeQualityP;
                 gotSampleInformation = true;
                 break; // we can only deal with one trio information

public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java

@@ -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 {

public/java/src/org/broadinstitute/sting/utils/pileup/PileupElementTracker.java

@@ -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();
     }
 

public/java/test/org/broadinstitute/sting/gatk/samples/SampleDataSourceUnitTest.java

@@ -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"));
     }

public/java/test/org/broadinstitute/sting/gatk/samples/SampleUnitTest.java

@@ -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

public/java/test/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java

@@ -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");