Reorganization of Sample

-- Moved Gender and Afflication to separate public enums
-- PedReader 90% implemented
-- Improve interface cleanup to XReadLines and UserException

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

@@ -0,0 +1,46 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.samples;
+
+/**
+ * Categorical sample trait for association and analysis
+ *
+ * Samples can have unknown status, be affected or unaffected by the
+ * categorical trait, or they can be marked as actually having a
+ * quantitative trait value (stored in an associated value in the Sample class)
+ *
+ * @author Mark DePristo
+ * @since Sept. 2011
+ */
+public enum Affection {
+    /** Status is unknown */
+    UNKNOWN,
+    /** Suffers from the disease */
+    AFFECTED,
+    /** Unaffected by the disease */
+    UNAFFECTED,
+    /** A quantitative trait: value of the trait is stored elsewhere */
+    QUANTITATIVE
+}

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

@@ -0,0 +1,34 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.samples;
+
+/**
+* ENUM of possible human genders: male, female, or unknown
+*/
+public enum Gender {
+    MALE,
+    FEMALE,
+    UNKNOWN
+}

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

@@ -32,6 +32,8 @@ import org.broadinstitute.sting.utils.text.XReadLines;
 
 import java.io.File;
 import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.Reader;
 import java.util.*;
 
 /**
@@ -115,10 +117,6 @@ public class PedReader {
     final static private Set<String> CATAGORICAL_TRAIT_VALUES = new HashSet<String>(Arrays.asList("-9", "0", "1", "2"));
     final static private String commentMarker = "#";
 
-    private final File source;
-    private final List<PedRecord> records;
-
-
     public enum MissingPedFields {
         NO_FAMILY_ID,
         NO_PARENTS,
@@ -127,8 +125,8 @@ public class PedReader {
     }
 
     // phenotype
-    private final static String PHENOTYPE_MISSING_VALUE = "-9";
+    private final static String MISSING_VALUE1 = "-9";
-    private final static String PHENOTYPE_MISSING_VALUE_SECONDARY = "0";
+    private final static String MISSING_VALUE2 = "0";
     private final static String PHENOTYPE_UNAFFECTED = "1";
     private final static String PHENOTYPE_AFFECTED = "2";
 
@@ -137,14 +135,15 @@ public class PedReader {
     private final static String SEX_FEMALE = "2";
     // other=unknown
 
-    public PedReader(File source, EnumSet<MissingPedFields> missingFields) throws FileNotFoundException {
+    public PedReader() { }
-        this.source = source;
+
-        List<String> lines = new XReadLines(source).readLines();
+    public final List<Sample> parse(File source, EnumSet<MissingPedFields> missingFields, SampleDataSource sampleDB) throws FileNotFoundException  {
-        this.records = parsePedLines(lines, missingFields);
+        logger.info("Reading PED file " + source + " with missing fields: " + missingFields);
+        return parse(new FileReader(source), missingFields, sampleDB);
     }
 
-    private final List<PedRecord> parsePedLines(final List<String> lines, EnumSet<MissingPedFields> missingFields) {
+    public final List<Sample> parse(Reader reader, EnumSet<MissingPedFields> missingFields, SampleDataSource sampleDB) {
-        logger.info("Reading PED file " + source + " with missing fields: " + missingFields);
+        final List<String> lines = new XReadLines(reader).readLines();
 
         // What are the record offsets?
         final int familyPos = missingFields.contains(MissingPedFields.NO_FAMILY_ID) ? -1 : 0;
@@ -153,7 +152,7 @@ public class PedReader {
         final int maternalPos = missingFields.contains(MissingPedFields.NO_PARENTS) ? -1 : paternalPos + 1;
         final int sexPos = missingFields.contains(MissingPedFields.NO_SEX) ? -1 : Math.max(maternalPos, samplePos) + 1;
         final int phenotypePos = missingFields.contains(MissingPedFields.NO_PHENOTYPE) ? -1 : Math.max(sexPos, Math.max(maternalPos, samplePos)) + 1;
-        final int nExpectedFields = MathUtils.arrayMaxInt(Arrays.asList(samplePos, paternalPos, maternalPos, sexPos, phenotypePos));
+        final int nExpectedFields = MathUtils.arrayMaxInt(Arrays.asList(samplePos, paternalPos, maternalPos, sexPos, phenotypePos)) + 1;
 
         // go through once and determine properties
         int lineNo = 1;
@@ -164,7 +163,7 @@ public class PedReader {
             String[] parts = line.split("\\W+");
 
             if ( parts.length != nExpectedFields )
-                throw new UserException.MalformedFile(source, "Bad PED line " + lineNo + ": wrong number of fields");
+                throw new UserException.MalformedFile(reader.toString(), "Bad PED line " + lineNo + ": wrong number of fields");
 
             if ( phenotypePos != -1 ) {
                 isQT = isQT || CATAGORICAL_TRAIT_VALUES.contains(parts[phenotypePos]);
@@ -177,75 +176,55 @@ public class PedReader {
 
         // now go through and parse each record
         lineNo = 1;
-        final List<PedRecord> recs = new ArrayList<PedRecord>(splits.size());
+        final List<Sample> samples = new ArrayList<Sample>(splits.size());
         for ( final String[] parts : splits ) {
             String familyID = null, individualID, paternalID = null, maternalID = null;
-            Sample.Gender sex = Sample.Gender.UNKNOWN;
+            Gender sex = Gender.UNKNOWN;
-            double quantitativePhenotype = Sample.UNSET_QUANTITIATIVE_TRAIT_VALUE;
+            double quantitativePhenotype = Sample.UNSET_QT;
-            Sample.Affection affection = Sample.Affection.UNKNOWN;
+            Affection affection = Affection.UNKNOWN;
 
-            if ( familyPos != -1 ) familyID = parts[familyPos];
+            if ( familyPos != -1 ) familyID = maybeMissing(parts[familyPos]);
             individualID = parts[samplePos];
-            if ( paternalPos != -1 ) paternalID = parts[paternalPos];
+            if ( paternalPos != -1 ) paternalID = maybeMissing(parts[paternalPos]);
-            if ( maternalPos != -1 ) maternalID = parts[maternalPos];
+            if ( maternalPos != -1 ) maternalID = maybeMissing(parts[maternalPos]);
 
             if ( sexPos != -1 ) {
-                if ( parts[sexPos].equals(SEX_MALE) ) sex = Sample.Gender.MALE;
+                if ( parts[sexPos].equals(SEX_MALE) ) sex = Gender.MALE;
-                else if ( parts[sexPos].equals(SEX_FEMALE) ) sex = Sample.Gender.FEMALE;
+                else if ( parts[sexPos].equals(SEX_FEMALE) ) sex = Gender.FEMALE;
-                else sex = Sample.Gender.UNKNOWN;
+                else sex = Gender.UNKNOWN;
             }
 
             if ( phenotypePos != -1 ) {
                 if ( isQT ) {
-                    if ( parts[phenotypePos].equals(PHENOTYPE_MISSING_VALUE) )
+                    if ( parts[phenotypePos].equals(MISSING_VALUE1) )
-                        affection = Sample.Affection.UNKNOWN;
+                        affection = Affection.UNKNOWN;
                     else {
-                        affection = Sample.Affection.QUANTITATIVE;
+                        affection = Affection.QUANTITATIVE;
                         quantitativePhenotype = Double.valueOf(parts[phenotypePos]);
                     }
                 } else {
-                    if ( parts[phenotypePos].equals(PHENOTYPE_MISSING_VALUE) ) affection = Sample.Affection.UNKNOWN;
+                    if ( parts[phenotypePos].equals(MISSING_VALUE1) ) affection = Affection.UNKNOWN;
-                    else if ( parts[phenotypePos].equals(PHENOTYPE_MISSING_VALUE_SECONDARY) ) affection = Sample.Affection.UNKNOWN;
+                    else if ( parts[phenotypePos].equals(MISSING_VALUE2) ) affection = Affection.UNKNOWN;
-                    else if ( parts[phenotypePos].equals(PHENOTYPE_UNAFFECTED) ) affection = Sample.Affection.UNAFFECTED;
+                    else if ( parts[phenotypePos].equals(PHENOTYPE_UNAFFECTED) ) affection = Affection.UNAFFECTED;
-                    else if ( parts[phenotypePos].equals(PHENOTYPE_AFFECTED) ) affection = Sample.Affection.AFFECTED;
+                    else if ( parts[phenotypePos].equals(PHENOTYPE_AFFECTED) ) affection = Affection.AFFECTED;
                     else throw new ReviewedStingException("Unexpected phenotype type " + parts[phenotypePos] + " at line " + lineNo);
                 }
             }
 
-            recs.add(new PedRecord(familyID, individualID, paternalID, maternalID, sex, quantitativePhenotype, affection));
+            final Sample s = new Sample(familyID, sampleDB, individualID, paternalID, maternalID, sex, affection, quantitativePhenotype);
-
+            samples.add(s);
+            sampleDB.addSample(s);
             lineNo++;
         }
 
-        return Collections.unmodifiableList(recs);
+        sampleDB.validate(samples);
+        return samples;
     }
 
-    public List<PedRecord> getRecords() {
+    private final static String maybeMissing(final String string) {
-        return records;
+        if ( string.equals(MISSING_VALUE1) || string.equals(MISSING_VALUE2) )
-    }
+            return null;
-
+        else
-    public void fillSampleDB(SampleDataSource db) {
+            return string;
-        for ( final PedRecord rec : getRecords() ) {
-        }
-    }
-}
-
-class PedRecord {
-    final String familyID, individualID, paternalID, maternalID;
-    final Sample.Gender sex;
-    final double quantitativePhenotype;
-    final Sample.Affection affection;
-
-    PedRecord(final String familyID, final String individualID,
-              final String paternalID, final String maternalID,
-              final Sample.Gender sex,
-              final double quantitativePhenotype, final Sample.Affection affection) {
-        this.familyID = familyID;
-        this.individualID = individualID;
-        this.paternalID = paternalID;
-        this.maternalID = maternalID;
-        this.sex = sex;
-        this.quantitativePhenotype = quantitativePhenotype;
-        this.affection = affection;
     }
 }

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

@@ -10,37 +10,18 @@ import java.util.Map;
  */
 public class Sample implements java.io.Serializable {
     final private String familyID, paternalID, maternalID;
-    final private Sample.Gender gender;
+    final private Gender gender;
     final private double quantitativePhenotype;
-    final private Sample.Affection affection;
+    final private Affection affection;
     final private String ID;
     final private SampleDataSource dataSource;
+    final private Map<String, Object> properties = new HashMap<String, Object>();
 
-    // todo -- conditionally add the property map -- should be empty by default
+    public final static double UNSET_QT = Double.NaN;
-    private final Map<String, Object> properties = new HashMap<String, Object>();
-
-    public enum Gender {
-        MALE,
-        FEMALE,
-        UNKNOWN
-    }
-
-    public enum Affection {
-        /** Status is unknown */
-        UNKNOWN,
-        /** Suffers from the disease */
-        AFFECTED,
-        /** Unaffected by the disease */
-        UNAFFECTED,
-        /** A quantitative trait: value of the trait is stored elsewhere */
-        QUANTITATIVE
-    }
-
-    public final static double UNSET_QUANTITIATIVE_TRAIT_VALUE = Double.NaN;
 
     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 Gender gender, final Affection affection, final double quantitativePhenotype) {
         this.familyID = familyID;
         this.paternalID = paternalID;
         this.maternalID = maternalID;
@@ -51,20 +32,31 @@ public class Sample implements java.io.Serializable {
         this.dataSource = dataSource;
     }
 
-    public Sample(final String ID, final SampleDataSource dataSource,
+    protected Sample(final String ID,
-                  final String familyID, final String paternalID, final String maternalID, final Gender gender) {
+                     final String familyID, final String paternalID, final String maternalID,
-        this(ID, dataSource, familyID, paternalID, maternalID, gender,
+                     final Gender gender, final Affection affection, final double quantitativePhenotype) {
-                UNSET_QUANTITIATIVE_TRAIT_VALUE, Affection.UNKNOWN);
+        this(ID, null, familyID, paternalID, maternalID, gender, affection, quantitativePhenotype);
     }
 
-    public Sample(final String ID, final SampleDataSource dataSource, final double quantitativePhenotype, final Affection affection) {
+    protected Sample(final String ID,
-        this(ID, dataSource, null, null, null, Gender.UNKNOWN, quantitativePhenotype, affection);
+                     final String familyID, final String paternalID, final String maternalID,
+                     final Gender gender, final Affection affection) {
+        this(ID, null, familyID, paternalID, maternalID, gender, affection, UNSET_QT);
+    }
+
+
+    public Sample(final String ID, final SampleDataSource dataSource,
+                  final String familyID, final String paternalID, final String maternalID, final Gender gender) {
+        this(ID, dataSource, familyID, paternalID, maternalID, gender, Affection.UNKNOWN, UNSET_QT);
+    }
+
+    public Sample(final String ID, final SampleDataSource dataSource, final Affection affection, final double quantitativePhenotype) {
+        this(ID, dataSource, null, null, null, Gender.UNKNOWN, affection, quantitativePhenotype);
     }
 
     public Sample(String id, SampleDataSource dataSource) {
-        this(id, dataSource,
+        this(id, dataSource, null, null, null,
-                null, null, null,
+                Gender.UNKNOWN, Affection.UNKNOWN, UNSET_QT);
-                Gender.UNKNOWN, UNSET_QUANTITIATIVE_TRAIT_VALUE, Affection.UNKNOWN);
     }
 
     // -------------------------------------------------------------------------------------
@@ -77,7 +69,6 @@ public class Sample implements java.io.Serializable {
         return ID;
     }
 
-
     public String getFamilyID() {
         return familyID;
     }
@@ -157,21 +148,4 @@ public class Sample implements java.io.Serializable {
     public boolean hasExtraProperty(String key) {
         return properties.containsKey(key);
     }
-
-//    @Override
-//    public boolean equals(Object o) {
-//        if (this == o) return true;
-//        if (o == null || getClass() != o.getClass()) return false;
-//
-//        Sample sample = (Sample) o;
-//        if (ID != null ? !ID.equals(sample.ID) : sample.ID != null) return false;
-//        if (properties != null ? !properties.equals(sample.properties) : sample.properties != null) return false;
-//
-//        return true;
-//    }
-//
-//    @Override
-//    public int hashCode() {
-//        return ID != null ? ID.hashCode() : "".hashCode();
-//    }
 }

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

@@ -55,7 +55,7 @@ public class SampleDataSource {
     /**
      * Hallucinates sample objects for all the samples in the SAM file and stores them
      */
-    public SampleDataSource addSamples(SAMFileHeader header) {
+    protected SampleDataSource addSamples(SAMFileHeader header) {
         for (String sampleName : SampleUtils.getSAMFileSamples(header)) {
             if (getSample(sampleName) == null) {
                 Sample newSample = new Sample(sampleName, this);
@@ -65,7 +65,7 @@ public class SampleDataSource {
         return this;
     }
 
-    public SampleDataSource addSamples(final List<File> sampleFiles) {
+    protected SampleDataSource addSamples(final List<File> sampleFiles) {
         // add files consecutively
         for (File file : sampleFiles) {
             addSamples(file);
@@ -77,7 +77,7 @@ public class SampleDataSource {
      * Parse one sample file and integrate it with samples that are already there
      * Fail quickly if we find any errors in the file
      */
-    public SampleDataSource addSamples(File sampleFile) {
+    protected SampleDataSource addSamples(File sampleFile) {
         return this;
     }
 
@@ -85,7 +85,7 @@ public class SampleDataSource {
      * Add a sample to the collection
      * @param sample to be added
      */
-    private SampleDataSource addSample(Sample sample) {
+    protected SampleDataSource addSample(Sample sample) {
         samples.put(sample.getID(), sample);
         return this;
     }
@@ -138,8 +138,6 @@ public class SampleDataSource {
     //
     // --------------------------------------------------------------------------------
 
-
-
     /**
      * Get number of sample objects
      * @return size of samples map
@@ -209,4 +207,18 @@ public class SampleDataSource {
         }
         return samples;
     }
+
+    // --------------------------------------------------------------------------------
+    //
+    // Validation
+    //
+    // --------------------------------------------------------------------------------
+
+    public final void validate() {
+        validate(getSamples());
+    }
+
+    public final void validate(Collection<Sample> samplesToCheck) {
+
+    }
 }

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

@@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgume
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.samples.Sample;
+import org.broadinstitute.sting.gatk.samples.Gender;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VQSRCalibrationCurve;
 import org.broadinstitute.sting.utils.GenomeLoc;
@@ -248,7 +248,7 @@ 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 && getSample(sample).getGender() == Sample.Gender.MALE;
+            boolean isMaleOnChrX = CHECK_IS_MALE_ON_CHR_X && getSample(sample).getGender() == Gender.MALE;
 
             Genotype genotype;
             boolean isValidation;

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

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.qc;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.samples.Gender;
 import org.broadinstitute.sting.gatk.samples.Sample;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
@@ -41,7 +42,7 @@ import org.broadinstitute.sting.gatk.walkers.Requires;
 public class CountMalesWalker extends ReadWalker<Integer, Integer> {
     public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker tracker) {
         Sample sample = getSampleDB().getSample(read);
-        return sample.getGender() == Sample.Gender.MALE ? 1 : 0;
+        return sample.getGender() == Gender.MALE ? 1 : 0;
     }
 
     public Integer reduceInit() { return 0; }

public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java

@@ -215,6 +215,10 @@ public class UserException extends ReviewedStingException {
             super(String.format("File %s is malformed: %s caused by %s", f.getAbsolutePath(), message, e.getMessage()));
         }
 
+        public MalformedFile(String name, String message) {
+            super(String.format("File associated with name %s is malformed: %s", name, message));
+        }
+
         public MalformedFile(String name, String message, Exception e) {
             super(String.format("File associated with name %s is malformed: %s caused by %s", name, message, e.getMessage()));
         }

public/java/src/org/broadinstitute/sting/utils/text/XReadLines.java

@@ -99,9 +99,9 @@ public class XReadLines implements Iterator<String>, Iterable<String> {
      *
      * @param reader
      */
-    public XReadLines(final BufferedReader reader, final boolean trimWhitespace) {
+    public XReadLines(final Reader reader, final boolean trimWhitespace) {
         try {
-            this.in = reader;
+            this.in = new BufferedReader(reader);
             nextline = readNextLine();
             this.trimWhitespace = trimWhitespace;
         } catch(IOException e) {
@@ -109,7 +109,7 @@ public class XReadLines implements Iterator<String>, Iterable<String> {
         }
     }
 
-    public XReadLines(final BufferedReader reader) throws FileNotFoundException {
+    public XReadLines(final Reader reader) {
         this(reader, true);
     }
 

public/java/test/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java

@@ -40,6 +40,7 @@ import org.broadinstitute.sting.gatk.iterators.LocusIteratorByState;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.baq.BAQ;
 
+import java.io.File;
 import java.util.Collections;
 import java.util.Iterator;
 
@@ -85,8 +86,6 @@ public class DownsamplerBenchmark extends ReadProcessingBenchmark {
                                                                (byte)0);
 
             GenomeLocParser genomeLocParser = new GenomeLocParser(reader.getFileHeader().getSequenceDictionary());
-            SampleDataSource sampleDataSource = new SampleDataSource().addSamples(reader.getFileHeader());
-
             // Filter unmapped reads.  TODO: is this always strictly necessary?  Who in the GATK normally filters these out?
             Iterator<SAMRecord> readIterator = new FilteringIterator(reader.iterator(),new UnmappedReadFilter());
             LocusIteratorByState locusIteratorByState = new LocusIteratorByState(readIterator,readProperties,genomeLocParser, LocusIteratorByState.sampleListForSAMWithoutReadGroups());

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

@@ -0,0 +1,201 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.samples;
+
+import org.apache.log4j.Logger;
+import org.broadinstitute.sting.BaseTest;
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.io.StringReader;
+import java.util.Arrays;
+import java.util.EnumSet;
+import java.util.List;
+
+/**
+ * UnitTest for PedReader
+ *
+ * @author Mark DePristo
+ * @since 2011
+ */
+public class PedReaderUnitTest extends BaseTest {
+    private static Logger logger = Logger.getLogger(PedReaderUnitTest.class);
+
+    private class PedReaderTest extends TestDataProvider {
+        public String fileContents;
+        public List<Sample> expectedSamples;
+
+        private PedReaderTest(final String name, final List<Sample> expectedSamples, final String fileContents) {
+            super(PedReaderTest.class, name);
+            this.fileContents = fileContents;
+            this.expectedSamples = expectedSamples;
+        }
+    }
+
+//     Family ID
+//     Individual ID
+//     Paternal ID
+//     Maternal ID
+//     Sex (1=male; 2=female; other=unknown)
+//     Phenotype
+//
+//     -9 missing
+//     0 missing
+//     1 unaffected
+//     2 affected
+
+    @DataProvider(name = "readerTest")
+    public Object[][] createPEDFiles() {
+        new PedReaderTest("singleRecordMale",
+                Arrays.asList(new Sample("kid", "fam1", null, null, Gender.MALE, Affection.UNAFFECTED)),
+                "fam1 kid 0 0 1 1");
+
+        new PedReaderTest("singleRecordFemale",
+                Arrays.asList(new Sample("kid", "fam1", null, null, Gender.FEMALE, Affection.UNAFFECTED)),
+                "fam1 kid 0 0 2 1");
+
+        new PedReaderTest("singleRecordMissingGender",
+                Arrays.asList(new Sample("kid", "fam1", null, null, Gender.UNKNOWN, Affection.UNKNOWN)),
+                "fam1 kid 0 0 0 0");
+
+        // Affection
+        new PedReaderTest("singleRecordAffected",
+                Arrays.asList(new Sample("kid", "fam1", null, null, Gender.MALE, Affection.AFFECTED)),
+                "fam1 kid 0 0 1 2");
+
+        new PedReaderTest("singleRecordUnaffected",
+                Arrays.asList(new Sample("kid", "fam1", null, null, Gender.MALE, Affection.UNAFFECTED)),
+                "fam1 kid 0 0 1 1");
+
+        new PedReaderTest("singleRecordMissingAffection-9",
+                Arrays.asList(new Sample("kid", "fam1", null, null, Gender.MALE, Affection.UNKNOWN)),
+                "fam1 kid 0 0 1 -9");
+
+        new PedReaderTest("singleRecordMissingAffection0",
+                Arrays.asList(new Sample("kid", "fam1", null, null, Gender.MALE, Affection.UNKNOWN)),
+                "fam1 kid 0 0 1 0");
+
+        new PedReaderTest("multipleUnrelated",
+                Arrays.asList(
+                    new Sample("s1", "fam1", null, null, Gender.MALE,   Affection.AFFECTED),
+                    new Sample("s2", "fam2", null, null, Gender.FEMALE, Affection.UNAFFECTED)),
+                String.format("%s\n%s",
+                        "fam1 s1 0 0 1 1",
+                        "fam2 s2 0 0 2 2"));
+
+        new PedReaderTest("explicitTrio",
+                Arrays.asList(
+                    new Sample("kid", "fam1", "dad", "mom", Gender.MALE,   Affection.AFFECTED),
+                    new Sample("dad", "fam1", null, null,   Gender.MALE,   Affection.UNAFFECTED),
+                    new Sample("mom", "fam1", null, null,   Gender.FEMALE, Affection.AFFECTED)),
+                String.format("%s\n%s\n%s",
+                        "fam1 kid dad mom 1 2",
+                        "fam1 dad 0   0   1 1",
+                        "fam1 mom 0   0   2 2"));
+
+        new PedReaderTest("implicitTrio",
+                Arrays.asList(
+                    new Sample("kid", "fam1", "dad", "mom", Gender.MALE,   Affection.AFFECTED),
+                    new Sample("dad", "fam1", null, null,   Gender.MALE,   Affection.UNKNOWN),
+                    new Sample("mom", "fam1", null, null,   Gender.FEMALE, Affection.UNKNOWN)),
+                "fam1 kid dad mom 1 1");
+
+        new PedReaderTest("partialTrio",
+                Arrays.asList(
+                    new Sample("kid", "fam1", "dad", "mom", Gender.MALE,   Affection.AFFECTED),
+                    new Sample("dad", "fam1", null, null,   Gender.MALE,   Affection.UNAFFECTED),
+                    new Sample("mom", "fam1", null, null,   Gender.FEMALE, Affection.UNKNOWN)),
+                String.format("%s\n%s",
+                        "fam1 kid dad mom 1 2",
+                        "fam1 dad 0   0   1 1"));
+
+        new PedReaderTest("bigPedigree",
+                Arrays.asList(
+                    new Sample("kid", "fam1", "dad",       "mom",      Gender.MALE,   Affection.AFFECTED),
+                    new Sample("dad", "fam1", "granddad1", "grandma1", Gender.MALE,   Affection.UNAFFECTED),
+                    new Sample("granddad1", "fam1", null, null,        Gender.MALE,   Affection.UNKNOWN),
+                    new Sample("grandma1",  "fam1", null, null,        Gender.FEMALE,   Affection.UNKNOWN),
+                    new Sample("mom", "fam1", "granddad2", "grandma2", Gender.FEMALE, Affection.AFFECTED),
+                    new Sample("granddad2", "fam1", null, null,        Gender.MALE,   Affection.UNKNOWN),
+                    new Sample("grandma2",  "fam1", null, null,        Gender.FEMALE,   Affection.UNKNOWN)),
+                String.format("%s\n%s\n%s",
+                        "fam1 kid dad       mom      1 2",
+                        "fam1 dad granddad1 grandma1 1 1",
+                        "fam1 mom granddad2 grandma2 2 2"));
+
+        // Quantitative trait
+        new PedReaderTest("QuantitativeTrait",
+                Arrays.asList(
+                    new Sample("s1", "fam1", null, null, Gender.MALE,   Affection.QUANTITATIVE, 1.0),
+                    new Sample("s2", "fam2", null, null, Gender.FEMALE, Affection.QUANTITATIVE, 10.0)),
+                String.format("%s\n%s",
+                        "fam1 s1 0 0 1 1",
+                        "fam2 s2 0 0 2 10.0"));
+
+        new PedReaderTest("QuantitativeTraitWithMissing",
+                Arrays.asList(
+                    new Sample("s1", "fam1", null, null, Gender.MALE,   Affection.UNKNOWN, Sample.UNSET_QT),
+                    new Sample("s2", "fam2", null, null, Gender.FEMALE, Affection.QUANTITATIVE, 10.0)),
+                String.format("%s\n%s",
+                        "fam1 s1 0 0 1 -9",
+                        "fam2 s2 0 0 2 10.0"));
+
+        new PedReaderTest("QuantitativeTraitOnlyInts",
+                Arrays.asList(
+                    new Sample("s1", "fam1", null, null, Gender.MALE,   Affection.QUANTITATIVE, 1.0),
+                    new Sample("s2", "fam2", null, null, Gender.FEMALE, Affection.QUANTITATIVE, 10.0)),
+                String.format("%s\n%s",
+                        "fam1 s1 0 0 1 1",
+                        "fam2 s2 0 0 2 10"));
+
+        return PedReaderTest.getTests(PedReaderTest.class);
+    }
+
+    private static final void runTest(PedReaderTest test, String myFileContents, EnumSet<PedReader.MissingPedFields> missing) {
+        logger.warn("Test " + test);
+        PedReader reader = new PedReader();
+        SampleDataSource sampleDB = new SampleDataSource();
+        List<Sample> readSamples = reader.parse(new StringReader(myFileContents), missing, sampleDB);
+        Assert.assertEquals(test.expectedSamples, readSamples, "Parsed incorrect number of samples");
+    }
+
+    @Test(enabled = true, dataProvider = "readerTest")
+    public void testPedReader(PedReaderTest test) {
+        runTest(test, test.fileContents, EnumSet.noneOf(PedReader.MissingPedFields.class));
+    }
+
+    @Test(enabled = true, dataProvider = "readerTest", dependsOnMethods = "testPedReader")
+    public void testPedReaderWithComments(PedReaderTest test) {
+        runTest(test, "#comment\n" + test.fileContents, EnumSet.noneOf(PedReader.MissingPedFields.class));
+    }
+
+    @Test(enabled = true, dataProvider = "readerTest", dependsOnMethods = "testPedReader")
+    public void testPedReaderWithMissing(PedReaderTest test) {
+        // todo -- test MISSING by splicing strings
+        //runTest(test, "#comment\n" + test.fileContents, EnumSet.noneOf(PedReader.MissingPedFields.class));
+    }
+
+}

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

@@ -22,17 +22,17 @@ public class SampleUnitTest extends BaseTest {
     public void init() {
         db = new SampleDataSource();
 
-        fam1A = new Sample("1A", db, "fam1", "1B", "1C", Sample.Gender.UNKNOWN);
+        fam1A = new Sample("1A", db, "fam1", "1B", "1C", Gender.UNKNOWN);
-        fam1B = new Sample("1B", db, "fam1", null, null, Sample.Gender.MALE);
+        fam1B = new Sample("1B", db, "fam1", null, null, Gender.MALE);
-        fam1C = new Sample("1C", db, "fam1", null, null, Sample.Gender.FEMALE);
+        fam1C = new Sample("1C", db, "fam1", null, null, Gender.FEMALE);
 
         s1 = new Sample("s1", db);
         s2 = new Sample("s2", db);
 
-        trait1 = new Sample("t1", db, Sample.UNSET_QUANTITIATIVE_TRAIT_VALUE, Sample.Affection.AFFECTED);
+        trait1 = new Sample("t1", db, Affection.AFFECTED, Sample.UNSET_QT);
-        trait2 = new Sample("t2", db, Sample.UNSET_QUANTITIATIVE_TRAIT_VALUE, Sample.Affection.UNAFFECTED);
+        trait2 = new Sample("t2", db, Affection.UNAFFECTED, Sample.UNSET_QT);
-        trait3 = new Sample("t3", db, Sample.UNSET_QUANTITIATIVE_TRAIT_VALUE, Sample.Affection.UNKNOWN);
+        trait3 = new Sample("t3", db, Affection.UNKNOWN, Sample.UNSET_QT);
-        trait4 = new Sample("t4", db, 1.0, Sample.Affection.QUANTITATIVE);
+        trait4 = new Sample("t4", db, Affection.QUANTITATIVE, 1.0);
     }
 
     /**
@@ -47,8 +47,8 @@ public class SampleUnitTest extends BaseTest {
 
     @Test()
     public void testGenders() {
-        Assert.assertTrue(fam1A.getGender() == Sample.Gender.UNKNOWN);
+        Assert.assertTrue(fam1A.getGender() == Gender.UNKNOWN);
-        Assert.assertTrue(fam1B.getGender() == Sample.Gender.MALE);
+        Assert.assertTrue(fam1B.getGender() == Gender.MALE);
-        Assert.assertTrue(fam1C.getGender() == Sample.Gender.FEMALE);
+        Assert.assertTrue(fam1C.getGender() == Gender.FEMALE);
     }
 }