GATK tests use public/testdata not /humgen/ as much as possible

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

@@ -31,6 +31,7 @@ import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMSequenceDictionary;
 import org.apache.log4j.Logger;
 import org.broad.tribble.Feature;
+import org.broad.tribble.readers.PositionalBufferedStream;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
@@ -51,6 +52,8 @@ import org.broadinstitute.sting.gatk.samples.SampleDBBuilder;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.baq.BAQ;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.interval.IntervalSetRule;
@@ -58,6 +61,8 @@ import org.broadinstitute.sting.utils.interval.IntervalUtils;
 import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
 
 import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
 import java.util.*;
 
 /**
@@ -795,7 +800,17 @@ public class GenomeAnalysisEngine {
                                                                             SAMSequenceDictionary sequenceDictionary,
                                                                             GenomeLocParser genomeLocParser,
                                                                             ValidationExclusion.TYPE validationExclusionType) {
-        RMDTrackBuilder builder = new RMDTrackBuilder(sequenceDictionary,genomeLocParser,validationExclusionType);
+        VCFHeader header = null;
+        if ( getArguments().repairVCFHeader != null ) {
+            try {
+                final PositionalBufferedStream pbs = new PositionalBufferedStream(new FileInputStream(getArguments().repairVCFHeader));
+                header = (VCFHeader)new VCFCodec().readHeader(pbs).getHeaderValue();
+                pbs.close();
+            } catch ( IOException e ) {
+                throw new UserException.CouldNotReadInputFile(getArguments().repairVCFHeader, e);
+            }
+        }
+        RMDTrackBuilder builder = new RMDTrackBuilder(sequenceDictionary,genomeLocParser,header,validationExclusionType);
 
         List<ReferenceOrderedDataSource> dataSources = new ArrayList<ReferenceOrderedDataSource>();
         for (RMDTriplet fileDescriptor : referenceMetaDataFiles)

public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java

@@ -331,9 +331,18 @@ public class GATKArgumentCollection {
     //
     // --------------------------------------------------------------------------------------------------------------
 
-    @Argument(fullName="generateShadowBCF",doc="If provided, whenever we create a VCFWriter we will also write out a BCF file alongside it, for testing purposes",required=false)
+    @Argument(fullName="generateShadowBCF",shortName = "generateShadowBCF",doc="If provided, whenever we create a VCFWriter we will also write out a BCF file alongside it, for testing purposes",required=false)
     @Hidden
     public boolean generateShadowBCF = false;
     // TODO -- remove all code tagged with TODO -- remove me when argument generateShadowBCF is removed
+
+    /**
+     * The file pointed to by this argument must be a VCF file. The GATK will read in just the header of this file
+     * and then use the INFO, FORMAT, and FILTER field values from this file to repair the header file of any other
+     * VCF file that GATK reads in.  This allows us to have in effect a master set of header records and use these
+     * to fill in any missing ones in input VCF files.
+     */
+    @Argument(fullName="repairVCFHeader", shortName = "repairVCFHeader", doc="If provided, whenever we read a VCF file we will use the header in this file to repair the header of the input VCF files", required=false)
+    public File repairVCFHeader = null;
 }
 

public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java

@@ -252,7 +252,10 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
      * @return
      */
     public boolean alsoWriteBCFForTest() {
-        return ! isCompressed() && getFile() != null && engine.getArguments().generateShadowBCF;
+        return engine.getArguments().numberOfThreads == 1 && // only works single threaded
+                ! isCompressed() && // for non-compressed outputs
+                getFile() != null && // that are going to disk
+                engine.getArguments().generateShadowBCF; // and we actually want to do it
     }
 
     /**

public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java

@@ -33,6 +33,8 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.help.GATKDocUtils;
 
@@ -82,11 +84,17 @@ public class FeatureManager  {
 
     private final PluginManager<FeatureCodec> pluginManager;
     private final Collection<FeatureDescriptor> featureDescriptors = new TreeSet<FeatureDescriptor>();
+    private final VCFHeader headerForRepairs;
 
     /**
-     * Construct a FeatureManager
+     * Construct a FeatureManager without a master VCF header
      */
     public FeatureManager() {
+        this(null);
+    }
+
+    public FeatureManager(final VCFHeader headerForRepairs) {
+        this.headerForRepairs = headerForRepairs;
         pluginManager = new PluginManager<FeatureCodec>(FeatureCodec.class, "Codecs", "Codec");
 
         for (final String rawName: pluginManager.getPluginsByName().keySet()) {
@@ -244,6 +252,8 @@ public class FeatureManager  {
             ((NameAwareCodec)codex).setName(name);
         if ( codex instanceof ReferenceDependentFeatureCodec )
             ((ReferenceDependentFeatureCodec)codex).setGenomeLocParser(genomeLocParser);
+        if ( codex instanceof VCFCodec)
+            ((VCFCodec)codex).setHeaderForRepairs(headerForRepairs);
         return codex;
     }
 }

public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java

@@ -38,6 +38,7 @@ import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -65,22 +66,21 @@ public class RMDTrackBuilder { // extends PluginManager<FeatureCodec> {
      * our log, which we use to capture anything from this class
      */
     private final static Logger logger = Logger.getLogger(RMDTrackBuilder.class);
-    public final static boolean MEASURE_TRIBBLE_QUERY_PERFORMANCE = false;
 
     // private sequence dictionary we use to set our tracks with
-    private SAMSequenceDictionary dict = null;
+    private final SAMSequenceDictionary dict;
 
     /**
      * Private genome loc parser to use when building out new locs.
      */
-    private GenomeLocParser genomeLocParser;
+    private final GenomeLocParser genomeLocParser;
 
     /**
      * Validation exclusions, for validating the sequence dictionary.
      */
     private ValidationExclusion.TYPE validationExclusionType;
 
-    FeatureManager featureManager;
+    private final FeatureManager featureManager;
 
     /**
      * Construct an RMDTrackerBuilder, allowing the user to define tracks to build after-the-fact.  This is generally
@@ -88,21 +88,40 @@ public class RMDTrackBuilder { // extends PluginManager<FeatureCodec> {
      * please talk through your approach with the SE team.
      * @param dict Sequence dictionary to use.
      * @param genomeLocParser Location parser to use.
+     * @param headerForRepairs a VCF header that should be used to repair VCF headers.  Can be null
      * @param validationExclusionType Types of validations to exclude, for sequence dictionary verification.
      */
-    public RMDTrackBuilder(SAMSequenceDictionary dict,
+    public RMDTrackBuilder(final SAMSequenceDictionary dict,
-                           GenomeLocParser genomeLocParser,
+                           final GenomeLocParser genomeLocParser,
+                           final VCFHeader headerForRepairs,
                            ValidationExclusion.TYPE validationExclusionType) {
         this.dict = dict;
         this.validationExclusionType = validationExclusionType;
         this.genomeLocParser = genomeLocParser;
-        featureManager = new FeatureManager();
+        this.featureManager = new FeatureManager(headerForRepairs);
     }
 
+    /**
+     * Return the feature manager this RMDTrackBuilder is using the create tribble tracks
+     *
+     * @return
+     */
     public FeatureManager getFeatureManager() {
         return featureManager;
     }
 
+    /**
+     * Same as full constructor but makes one without a header for repairs
+     * @param dict
+     * @param genomeLocParser
+     * @param validationExclusionType
+     */
+    public RMDTrackBuilder(final SAMSequenceDictionary dict,
+                           final GenomeLocParser genomeLocParser,
+                           ValidationExclusion.TYPE validationExclusionType) {
+        this(dict, genomeLocParser, null, validationExclusionType);
+    }
+
     /**
      * create a RMDTrack of the specified type
      *

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java

@@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.samples.Sample;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
+import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts;
 import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel;
 import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
 import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
@@ -419,6 +420,8 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
             headerLines.add(new VCFFormatHeaderLine("AF_Orig", 1, VCFHeaderLineType.Float, "Original AF"));
             headerLines.add(new VCFFormatHeaderLine("AN_Orig", 1, VCFHeaderLineType.Integer, "Original AN"));
         }
+        headerLines.addAll(Arrays.asList(ChromosomeCounts.descriptions));
+        headerLines.add(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Depth of coverage"));
         vcfWriter.writeHeader(new VCFHeader(headerLines, samples));
 
         for (int i = 0; i < SELECT_EXPRESSIONS.size(); i++) {

public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Encoder.java

@@ -110,7 +110,7 @@ public class BCF2Encoder {
                 }
             }
         } catch ( ClassCastException e ) {
-            throw new ReviewedStingException("BUG: invalid type cast to " + type + " from " + value);
+            throw new ClassCastException("BUG: invalid type cast to " + type + " from " + value);
         }
     }
 

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java

@@ -10,10 +10,7 @@ import org.broad.tribble.util.BlockCompressedInputStream;
 import org.broad.tribble.util.ParsingUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.*;
-import org.broadinstitute.sting.utils.variantcontext.LazyGenotypesContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
 
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
@@ -53,11 +50,6 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
     // for performance we cache the hashmap of filter encodings for quick lookup
     protected HashMap<String,LinkedHashSet<String>> filterHash = new HashMap<String,LinkedHashSet<String>>();
 
-    // a mapping of the VCF fields to their type, filter fields, and format fields, for quick lookup to validate against
-    TreeMap<String, VCFHeaderLineType> infoFields = new TreeMap<String, VCFHeaderLineType>();
-    TreeMap<String, VCFHeaderLineType> formatFields = new TreeMap<String, VCFHeaderLineType>();
-    Set<String> filterFields = new HashSet<String>();
-
     // we store a name to give to each of the variant contexts we emit
     protected String name = "Unknown";
 
@@ -119,11 +111,12 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
     protected abstract Set<String> parseFilters(String filterString);
 
     /**
-     * create a VCF header
+     * create a VCF header from a set of header record lines
+     *
      * @param headerStrings a list of strings that represent all the ## and # entries
      * @return a VCFHeader object
      */
-    public static VCFHeader parseHeader(final List<String> headerStrings, final VCFHeaderVersion version) {
+    protected VCFHeader parseHeaderFromLines( final List<String> headerStrings, final VCFHeaderVersion version ) {
         Set<VCFHeaderLine> metaData = new TreeSet<VCFHeaderLine>();
         Set<String> sampleNames = new LinkedHashSet<String>();
         int contigCounter = 0;
@@ -186,12 +179,6 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
         return new VCFHeader(metaData, sampleNames);
     }
 
-    protected VCFHeader createAndSetVCFHeader(final List<String> headerStrings, final String line, final VCFHeaderVersion version) {
-        headerStrings.add(line);
-        header = parseHeader(headerStrings, version);
-        return header;
-    }
-
     /**
      * the fast decode function
      * @param line the line of text for the record

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java

@@ -58,7 +58,8 @@ public class VCF3Codec extends AbstractVCFCodec {
                     if (!foundHeaderVersion) {
                         throw new TribbleException.InvalidHeader("We never saw a header line specifying VCF version");
                     }
-                    return createAndSetVCFHeader(headerStrings, line, version);
+                    headerStrings.add(line);
+                    return super.parseHeaderFromLines(headerStrings, version);
                 }
                 else {
                     throw new TribbleException.InvalidHeader("We never saw the required CHROM header line (starting with one #) for the input VCF file");

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java

@@ -50,6 +50,13 @@ public class VCFCodec extends AbstractVCFCodec {
     public final static String VCF4_MAGIC_HEADER = "##fileformat=VCFv4";
     private VCFHeaderVersion version = null;
 
+    /**
+     * A VCF header the contains master info/filter/format records that we use to 'fill in'
+     * any missing records from our input VCF header.  This allows us to repair headers on
+     * the fly
+     */
+    private VCFHeader headerForRepairs = null;
+
     /**
      * @param reader the line reader to take header lines from
      * @return the number of header lines
@@ -80,7 +87,11 @@ public class VCFCodec extends AbstractVCFCodec {
                     if (!foundHeaderVersion) {
                         throw new TribbleException.InvalidHeader("We never saw a header line specifying VCF version");
                     }
-                    return createAndSetVCFHeader(headerStrings, line, version);
+                    headerStrings.add(line);
+                    this.header = super.parseHeaderFromLines(headerStrings, version);
+                    if ( headerForRepairs != null )
+                        this.header = repairHeader(this.header, headerForRepairs);
+                    return this.header;
                 }
                 else {
                     throw new TribbleException.InvalidHeader("We never saw the required CHROM header line (starting with one #) for the input VCF file");
@@ -93,6 +104,22 @@ public class VCFCodec extends AbstractVCFCodec {
         throw new TribbleException.InvalidHeader("We never saw the required CHROM header line (starting with one #) for the input VCF file");
     }
 
+    private final VCFHeader repairHeader(final VCFHeader readHeader, final VCFHeader masterHeader) {
+        final Set<VCFHeaderLine> lines = VCFUtils.smartMergeHeaders(Arrays.asList(readHeader, masterHeader), log);
+        return new VCFHeader(lines, readHeader.getGenotypeSamples());
+    }
+
+    /**
+     * Tells this VCFCodec to repair the incoming header files with the information in masterHeader
+     *
+     * @param headerForRepairs
+     */
+    public void setHeaderForRepairs(final VCFHeader headerForRepairs) {
+        log.info("Using master VCF header to repair missing files from incoming VCFs");
+        this.headerForRepairs = headerForRepairs;
+    }
+
+
 
     /**
      * parse the filter string, first checking to see if we already have parsed it in a previous attempt

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java

@@ -245,19 +245,19 @@ public class VCFHeader {
     }
 
     /**
-     * @param key    the header key name
+     * @param id the header key name
      * @return the meta data line, or null if there is none
      */
-    public VCFInfoHeaderLine getInfoHeaderLine(String key) {
+    public VCFInfoHeaderLine getInfoHeaderLine(String id) {
-        return mInfoMetaData.get(key);
+        return mInfoMetaData.get(id);
     }
 
     /**
-     * @param key    the header key name
+     * @param id    the header key name
      * @return the meta data line, or null if there is none
      */
-    public VCFFormatHeaderLine getFormatHeaderLine(String key) {
+    public VCFFormatHeaderLine getFormatHeaderLine(String id) {
-        return mFormatMetaData.get(key);
+        return mFormatMetaData.get(id);
     }
 
     /**

public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java

@@ -5,6 +5,7 @@ import org.broad.tribble.TribbleException;
 import org.broad.tribble.util.ParsingUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.util.*;
 
@@ -1329,6 +1330,7 @@ public class VariantContext implements Feature { // to enable tribble integratio
     }
 
     private final Object decodeOne(final String field, final String string, final VCFCompoundHeaderLine format) {
+        try {
             if ( string.equals(VCFConstants.MISSING_VALUE_v4) )
                 return null;
             else {
@@ -1341,6 +1343,9 @@ public class VariantContext implements Feature { // to enable tribble integratio
                     default: throw new ReviewedStingException("Unexpected type for field" + field);
                 }
             }
+        } catch (NumberFormatException e) {
+            throw new UserException.MalformedVCF("Could not decode field " + field + " with value " + string + " of declared type " + format.getType());
+        }
     }
 
     private final void fullyDecodeGenotypes(final VariantContextBuilder builder, final VCFHeader header) {

public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java

@@ -49,7 +49,7 @@ public class VariantContextUtils {
 
     final public static JexlEngine engine = new JexlEngine();
     public static final int DEFAULT_PLOIDY = 2;
-    private final static boolean ASSUME_MISSING_FIELDS_ARE_STRINGS = true;
+    private final static boolean ASSUME_MISSING_FIELDS_ARE_STRINGS = false;
 
     static {
         engine.setSilent(false); // will throw errors now for selects that don't evaluate properly

public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java

@@ -260,6 +260,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
 
         startGenotypeField(field, numInFormatField, encoding.BCF2Type);
         for ( final Genotype g : vc.getGenotypes() ) {
+            try {
                 final Object fieldValue = g.getAttribute(field);
 
                 if ( numInFormatField == 1 ) {
@@ -273,6 +274,9 @@ class BCF2Writer extends IndexingVariantContextWriter {
                         encoder.encodeRawValue(i < nSampleValues ? asList.get(i) : null, encoding.BCF2Type);
                     }
                 }
+            } catch ( ClassCastException e ) {
+                throw new ReviewedStingException("Value stored in VariantContext incompatible with VCF header type for field " + field, e);
+            }
         }
     }
 

public/java/test/net/sf/picard/reference/FastaSequenceIndexBuilderUnitTest.java

@@ -55,7 +55,7 @@ public class FastaSequenceIndexBuilderUnitTest extends BaseTest {
     public void unixFileTest() {
         logger.warn("Executing unixFileTest");
 
-        fastaFile = new File(validationDataLocation + "exampleFASTA.fasta");
+        fastaFile = new File(testDir + "exampleFASTA.fasta");
         builder = new FastaSequenceIndexBuilder(fastaFile, false);
         FastaSequenceIndex index = builder.createIndex();
         controlIndex.add(new FastaSequenceIndexEntry("chr1", 6, 100000, 60, 61,0));
@@ -72,7 +72,7 @@ public class FastaSequenceIndexBuilderUnitTest extends BaseTest {
     public void windowsFileTest() {
         logger.warn("Executing windowsFileTest");
 
-        fastaFile = new File(validationDataLocation + "exampleFASTA-windows.fasta");
+        fastaFile = new File(testDir + "exampleFASTA-windows.fasta");
         builder = new FastaSequenceIndexBuilder(fastaFile, false);
         FastaSequenceIndex index = builder.createIndex();
         controlIndex.add(new FastaSequenceIndexEntry("chr2", 7, 29, 7, 9,0));
@@ -88,7 +88,7 @@ public class FastaSequenceIndexBuilderUnitTest extends BaseTest {
     public void combinedWindowsUnix() {
         logger.warn("Executing combinedWindowsUnix");
 
-        fastaFile = new File(validationDataLocation + "exampleFASTA-combined.fasta");
+        fastaFile = new File(testDir + "exampleFASTA-combined.fasta");
         builder = new FastaSequenceIndexBuilder(fastaFile, false);
         FastaSequenceIndex index = builder.createIndex();
         controlIndex.add(new FastaSequenceIndexEntry("chr1", 6, 100000, 60, 61,0));
@@ -105,7 +105,7 @@ public class FastaSequenceIndexBuilderUnitTest extends BaseTest {
     public void threeVariableLengthContigs() {
         logger.warn("Executing threeVariableLengthContigs");
 
-        fastaFile = new File(validationDataLocation + "exampleFASTA-3contigs.fasta");
+        fastaFile = new File(testDir + "exampleFASTA-3contigs.fasta");
         builder = new FastaSequenceIndexBuilder(fastaFile, false);
         FastaSequenceIndex index = builder.createIndex();
         controlIndex.add(new FastaSequenceIndexEntry("chr1", 6, 17, 5, 6,0));

public/java/test/org/broadinstitute/sting/WalkerTest.java

@@ -47,7 +47,7 @@ import java.io.IOException;
 import java.util.*;
 
 public class WalkerTest extends BaseTest {
-    private static final boolean GENERATE_SHADOW_BCF = true;
+    private static final boolean GENERATE_SHADOW_BCF = false;
     private static final boolean ENABLE_PHONE_HOME_FOR_TESTS = false;
     private static final boolean ENABLE_ON_THE_FLY_CHECK_FOR_VCF_INDEX = false;
 
@@ -145,6 +145,7 @@ public class WalkerTest extends BaseTest {
         Class expectedException = null;
         boolean includeImplicitArgs = true;
         boolean includeShadowBCF = true;
+        boolean repairHeader = false;
 
         // the default output path for the integration test
         private File outputFileLocation = null;
@@ -186,6 +187,8 @@ public class WalkerTest extends BaseTest {
                         String.format(" -et %s -K %s ", GATKRunReport.PhoneHomeOption.NO_ET, gatkKeyFile));
                 if ( includeShadowBCF && GENERATE_SHADOW_BCF )
                     args = args + " --generateShadowBCF ";
+                if ( repairHeader )
+                    args = args + " --repairVCFHeader public/data/vcfHeaderForRepairs.vcf ";
             }
 
             return args;
@@ -197,6 +200,7 @@ public class WalkerTest extends BaseTest {
          * which will ultimately blow up...
          */
         public void disableShadowBCF() { this.includeShadowBCF = false; }
+        public void repairHeaders() { this.repairHeader = true; }
         public void setOutputFileLocation(File outputFileLocation) {
             this.outputFileLocation = outputFileLocation;
         }        

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

@@ -94,13 +94,13 @@ public class GATKBAMIndexUnitTest extends BaseTest {
 
     @Test( expectedExceptions = UserException.MalformedFile.class )
     public void testDetectTruncatedBamIndexWordBoundary() {
-        GATKBAMIndex index = new GATKBAMIndex(new File(validationDataLocation + "truncated_at_word_boundary.bai"));
+        GATKBAMIndex index = new GATKBAMIndex(new File(testDir + "truncated_at_word_boundary.bai"));
         index.readReferenceSequence(0);
     }
 
     @Test( expectedExceptions = UserException.MalformedFile.class )
     public void testDetectTruncatedBamIndexNonWordBoundary() {
-        GATKBAMIndex index = new GATKBAMIndex(new File(validationDataLocation + "truncated_at_non_word_boundary.bai"));
+        GATKBAMIndex index = new GATKBAMIndex(new File(testDir + "truncated_at_non_word_boundary.bai"));
         index.readReferenceSequence(0);
     }
 

public/java/test/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java

@@ -188,7 +188,7 @@ public class ReadGroupBlackListFilterUnitTest extends BaseTest {
         }
 
         List<String> filterList = new ArrayList<String>();
-        filterList.add(validationDataLocation + "readgroupblacklisttest.txt");
+        filterList.add(testDir + "readgroupblacklisttest.txt");
 
         ReadGroupBlackListFilter filter = new ReadGroupBlackListFilter(filterList);
         int filtered = 0;
@@ -227,7 +227,7 @@ public class ReadGroupBlackListFilterUnitTest extends BaseTest {
         }
 
         List<String> filterList = new ArrayList<String>();
-        filterList.add(validationDataLocation + "readgroupblacklisttestlist.txt");
+        filterList.add(testDir + "readgroupblacklisttestlist.txt");
 
         ReadGroupBlackListFilter filter = new ReadGroupBlackListFilter(filterList);
         int filtered = 0;

public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java

@@ -52,8 +52,8 @@ import java.util.*;
  * UnitTests for RMD FeatureManager
  */
 public class FeatureManagerUnitTest extends BaseTest {
-    private static final File RANDOM_FILE = new File(validationDataLocation + "exampleGATKReport.eval");
+    private static final File RANDOM_FILE = new File(testDir + "exampleGATKReport.eval");
-    private static final File VCF3_FILE = new File(validationDataLocation + "vcfexample3.vcf");
+    private static final File VCF3_FILE = new File(testDir + "vcfexample3.vcf");
     private static final File VCF4_FILE = new File(testDir + "HiSeq.10000.vcf");
     private static final File VCF4_FILE_GZ = new File(testDir + "HiSeq.10000.vcf.gz");
     private static final File VCF4_FILE_BGZIP = new File(testDir + "HiSeq.10000.bgzip.vcf.gz");

public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilderUnitTest.java

@@ -79,7 +79,7 @@ public class RMDTrackBuilderUnitTest extends BaseTest {
     @Test
     // in this test, the index exists, but is out of date.
     public void testBuilderIndexUnwriteable() {
-        File vcfFile = new File(validationDataLocation + "/ROD_validation/read_only/relic.vcf");
+        File vcfFile = new File(testDir + "/ROD_validation/read_only/relic.vcf");
         try {
             builder.loadIndex(vcfFile, new VCF3Codec());
         } catch (IOException e) {
@@ -96,7 +96,7 @@ public class RMDTrackBuilderUnitTest extends BaseTest {
     // sure we don't do this
     @Test
     public void testDirIsLockedIndexFromDisk() {
-        File vcfFile = new File(validationDataLocation + "/ROD_validation/read_only/good_index.vcf");
+        File vcfFile = new File(testDir + "/ROD_validation/read_only/good_index.vcf");
         File vcfFileIndex = Tribble.indexFile(vcfFile);
         Index ind = null;
         try {
@@ -112,7 +112,7 @@ public class RMDTrackBuilderUnitTest extends BaseTest {
 
     @Test
     public void testBuilderIndexDirectoryUnwritable() {
-        File vcfFile = new File(validationDataLocation + "/ROD_validation/read_only/no_index.vcf");
+        File vcfFile = new File(testDir + "/ROD_validation/read_only/no_index.vcf");
         File vcfFileIndex = Tribble.indexFile(vcfFile);
 
         Index ind = null;
@@ -131,7 +131,7 @@ public class RMDTrackBuilderUnitTest extends BaseTest {
 
     @Test
     public void testGenerateIndexForUnindexedFile() {
-        File vcfFile = new File(validationDataLocation + "/ROD_validation/always_reindex.vcf");
+        File vcfFile = new File(testDir + "/ROD_validation/always_reindex.vcf");
         File vcfFileIndex = Tribble.indexFile(vcfFile);
 
         // if we can't write to the directory, don't fault the tester, just pass
@@ -157,7 +157,7 @@ public class RMDTrackBuilderUnitTest extends BaseTest {
     // test to make sure we get a full sequence dictionary from the VCF (when we set the dictionary in the builder)
     @Test
     public void testBuilderIndexSequenceDictionary() {
-        File vcfFile = createCorrectDateIndexFile(new File(validationDataLocation + "/ROD_validation/newerTribbleTrack.vcf"));
+        File vcfFile = createCorrectDateIndexFile(new File(testDir + "/ROD_validation/newerTribbleTrack.vcf"));
         Long indexTimeStamp = Tribble.indexFile(vcfFile).lastModified();
         try {
             Index idx = builder.loadIndex(vcfFile, new VCFCodec());

public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java

@@ -36,7 +36,7 @@ import java.io.PrintStream;
 public class GATKReportUnitTest extends BaseTest {
     @Test
     public void testParse() throws Exception {
-        String reportPath = validationDataLocation + "exampleGATKReportv2.tbl";
+        String reportPath = testDir + "exampleGATKReportv2.tbl";
         GATKReport report = new GATKReport(reportPath);
         Assert.assertEquals(report.getVersion(), GATKReportVersion.V1_1);
         Assert.assertEquals(report.getTables().size(), 5);

public/java/test/org/broadinstitute/sting/gatk/walkers/CNV/SymbolicAllelesIntegrationTest.java

@@ -10,7 +10,7 @@ public class SymbolicAllelesIntegrationTest extends WalkerTest {
     public static String baseTestString(String reference, String VCF) {
         return "-T CombineVariants" +
                 " -R " + reference +
-                " --variant:vcf " + validationDataLocation + VCF +
+                " --variant:vcf " + testDir + VCF +
                 " -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED" +
                 " -genotypeMergeOptions REQUIRE_UNIQUE" +
                 " -setKey null" +

public/java/test/org/broadinstitute/sting/gatk/walkers/ClipReadsWalkersIntegrationTest.java

@@ -36,7 +36,7 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-R " + hg18Reference +
                         " -T ClipReads " +
-                        "-I " + validationDataLocation + "clippingReadsTest.withRG.bam " +
+                        "-I " + testDir + "clippingReadsTest.withRG.bam " +
                         "-os %s " +
                         "-o %s " + args,
                 2, // just one output file
@@ -55,9 +55,9 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest {
     @Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "3061cf742f9e5526a61130128ae761a3"); }
 
     @Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "b89459f373e40f0b835c1faff2208839"); }
-    @Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + validationDataLocation + "seqsToClip.fasta", "d011a3152b31822475afbe0281491f8d", "24e19116ef16a37a6d095ed5c22c2466"); }
+    @Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + testDir + "seqsToClip.fasta", "d011a3152b31822475afbe0281491f8d", "24e19116ef16a37a6d095ed5c22c2466"); }
 
-    @Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + validationDataLocation + "seqsToClip.fasta -X CCCCC", "a23187bd9bfb06557f799706d98441de", "ad8d30300cb43d5e300fcc4d2450da8e"); }
+    @Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + testDir + "seqsToClip.fasta -X CCCCC", "a23187bd9bfb06557f799706d98441de", "ad8d30300cb43d5e300fcc4d2450da8e"); }
 
     @Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "57c05b6241db7110148a91fde2d431d0"); }
     @Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "2a1a3153e0942ab355fd8a6e082b30e0"); }
@@ -68,7 +68,7 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + hg18Reference +
                         " -T ClipReads" +
-                        " -I " + validationDataLocation + "originalQuals.chr1.1-1K.bam" +
+                        " -I " + testDir + "originalQuals.chr1.1-1K.bam" +
                         " -L chr1:1-1,000" +
                         " -OQ -QT 4 -CR WRITE_Q0S" +
                         " -o %s -os %s",

public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsIntegrationTest.java

@@ -47,7 +47,7 @@ public class PrintReadsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T PrintReads" +
                         " -R " + params.reference +
-                        " -I " + validationDataLocation + params.bam +
+                        " -I " + testDir + params.bam +
                         params.args +
                         " -o %s",
                 Arrays.asList(params.md5));

public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java

@@ -15,7 +15,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testHasAnnotsNotAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " --variant:VCF3 " + testDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("8a105fa5eebdfffe7326bc5b3d8ffd1c"));
         executeTest("test file has annotations, not asking for annotations, #1", spec);
     }
@@ -23,7 +23,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testHasAnnotsNotAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --variant:VCF3 " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
+                baseTestString() + " --variant:VCF3 " + testDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
                 Arrays.asList("964f1016ec9a3c55333f62dd834c14d6"));
         executeTest("test file has annotations, not asking for annotations, #2", spec);
     }
@@ -31,7 +31,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testHasAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -G Standard --variant:VCF3 " + testDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("3b7796fa7c7dc94878bedadf7938db4c"));
         executeTest("test file has annotations, asking for annotations, #1", spec);
     }
@@ -39,7 +39,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testHasAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
+                baseTestString() + " -G Standard --variant:VCF3 " + testDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
                 Arrays.asList("2977bb30c8b84a5f4094fe6090658561"));
         executeTest("test file has annotations, asking for annotations, #2", spec);
     }
@@ -47,7 +47,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testNoAnnotsNotAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --variant:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " --variant:VCF3 " + testDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("42ccee09fa9f8c58f4a0d4f1139c094f"));
         executeTest("test file doesn't have annotations, not asking for annotations, #1", spec);
     }
@@ -57,7 +57,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
         // the genotype annotations in this file are actually out of order.  If you don't parse the genotypes
         // they don't get reordered.  It's a good test of the genotype ordering system.
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
+                baseTestString() + " --variant:VCF3 " + testDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
                 Arrays.asList("f2ddfa8105c290b1f34b7a261a02a1ac"));
         executeTest("test file doesn't have annotations, not asking for annotations, #2", spec);
     }
@@ -65,7 +65,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testNoAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -G Standard --variant:VCF3 " + testDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("279cace364f747f9bae7fe391b5026f0"));
         executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
     }
@@ -73,7 +73,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testNoAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
+                baseTestString() + " -G Standard --variant:VCF3 " + testDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
                 Arrays.asList("0948cd1dba7d61f283cc4cf2a7757d92"));
         executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
     }
@@ -81,7 +81,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testExcludeAnnotations() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G Standard -XA FisherStrand -XA ReadPosRankSumTest --variant:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -G Standard -XA FisherStrand -XA ReadPosRankSumTest --variant:VCF3 " + testDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("e488abd05d6162758698a3a7579866a6"));
         executeTest("test exclude annotations", spec);
     }
@@ -89,7 +89,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testOverwritingHeader() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G Standard --variant " + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
+                baseTestString() + " -G Standard --variant " + testDir + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
                 Arrays.asList("062155edec46a8c52243475fbf3a2943"));
         executeTest("test overwriting header", spec);
     }
@@ -97,7 +97,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testNoReads() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G Standard --variant " + validationDataLocation + "vcfexample3empty.vcf -L " + validationDataLocation + "vcfexample3empty.vcf", 1,
+                baseTestString() + " -G Standard --variant " + testDir + "vcfexample3empty.vcf -L " + testDir + "vcfexample3empty.vcf", 1,
                 Arrays.asList("06635f2dd91b539bfbce9bf7914d8e43"));
         executeTest("not passing it any reads", spec);
     }
@@ -105,7 +105,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testDBTagWithDbsnp() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --dbsnp " + b36dbSNP129 + " -G Standard --variant " + validationDataLocation + "vcfexample3empty.vcf -L " + validationDataLocation + "vcfexample3empty.vcf", 1,
+                baseTestString() + " --dbsnp " + b36dbSNP129 + " -G Standard --variant " + testDir + "vcfexample3empty.vcf -L " + testDir + "vcfexample3empty.vcf", 1,
                 Arrays.asList("820eeba1f6e3a0758a69d937c524a38e"));
         executeTest("getting DB tag with dbSNP", spec);
     }
@@ -113,7 +113,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testMultipleIdsWithDbsnp() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --alwaysAppendDbsnpId --dbsnp " + b36dbSNP129 + " -G Standard --variant " + validationDataLocation + "vcfexample3withIDs.vcf -L " + validationDataLocation + "vcfexample3withIDs.vcf", 1,
+                baseTestString() + " --alwaysAppendDbsnpId --dbsnp " + b36dbSNP129 + " -G Standard --variant " + testDir + "vcfexample3withIDs.vcf -L " + testDir + "vcfexample3withIDs.vcf", 1,
                 Arrays.asList("cd7e3d43b8f5579c461b3e588a295fa8"));
         executeTest("adding multiple IDs with dbSNP", spec);
     }
@@ -121,7 +121,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testDBTagWithHapMap() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --comp:H3 " + validationDataLocation + "fakeHM3.vcf -G Standard --variant " + validationDataLocation + "vcfexample3empty.vcf -L " + validationDataLocation + "vcfexample3empty.vcf", 1,
+                baseTestString() + " --comp:H3 " + testDir + "fakeHM3.vcf -G Standard --variant " + testDir + "vcfexample3empty.vcf -L " + testDir + "vcfexample3empty.vcf", 1,
                 Arrays.asList("31cc2ce157dd20771418c08d6b3be1fa"));
         executeTest("getting DB tag with HM3", spec);
     }
@@ -129,7 +129,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testNoQuals() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --variant " + validationDataLocation + "noQual.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L " + validationDataLocation + "noQual.vcf -A QualByDepth", 1,
+                baseTestString() + " --variant " + testDir + "noQual.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L " + testDir + "noQual.vcf -A QualByDepth", 1,
                 Arrays.asList("e531c9f90c17f0f859cd1ac851a8edd8"));
         executeTest("test file doesn't have QUALs", spec);
     }
@@ -137,7 +137,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testUsingExpression() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --resource:foo " + validationDataLocation + "targetAnnotations.vcf -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -L " + validationDataLocation + "vcfexample3empty.vcf", 1,
+                baseTestString() + " --resource:foo " + testDir + "targetAnnotations.vcf -G Standard --variant:VCF3 " + testDir + "vcfexample3empty.vcf -E foo.AF -L " + testDir + "vcfexample3empty.vcf", 1,
                 Arrays.asList("074865f8f8c0ca7bfd58681f396c49e9"));
         executeTest("using expression", spec);
     }
@@ -145,7 +145,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testUsingExpressionWithID() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --resource:foo " + validationDataLocation + "targetAnnotations.vcf -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.ID -L " + validationDataLocation + "vcfexample3empty.vcf", 1,
+                baseTestString() + " --resource:foo " + testDir + "targetAnnotations.vcf -G Standard --variant:VCF3 " + testDir + "vcfexample3empty.vcf -E foo.ID -L " + testDir + "vcfexample3empty.vcf", 1,
                 Arrays.asList("97b26db8135d083566fb585a677fbe8a"));
         executeTest("using expression with ID", spec);
     }
@@ -189,8 +189,8 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testTDTAnnotation() {
         final String MD5 = "a78c1e950740d3c13c0258960c5fa8e1";
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-T VariantAnnotator -R " + b37KGReference + " -A TransmissionDisequilibriumTest --variant:vcf " + validationDataLocation + "ug.random50000.subset300bp.chr1.family.vcf" +
+                "-T VariantAnnotator -R " + b37KGReference + " -A TransmissionDisequilibriumTest --variant:vcf " + testDir + "ug.random50000.subset300bp.chr1.family.vcf" +
-                        " -L " + validationDataLocation + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + validationDataLocation + "ug.random50000.family.ped -o %s", 1,
+                        " -L " + testDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + testDir + "ug.random50000.family.ped -o %s", 1,
                 Arrays.asList(MD5));
         executeTest("Testing TDT annotation ", spec);
     }
@@ -200,8 +200,8 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testChromosomeCountsPed() {
         final String MD5 = "32df3ceb63c277df442ed55fb8684933";
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-T VariantAnnotator -R " + b37KGReference + " -A ChromosomeCounts --variant:vcf " + validationDataLocation + "ug.random50000.subset300bp.chr1.family.vcf" +
+                "-T VariantAnnotator -R " + b37KGReference + " -A ChromosomeCounts --variant:vcf " + testDir + "ug.random50000.subset300bp.chr1.family.vcf" +
-                        " -L " + validationDataLocation + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + validationDataLocation + "ug.random50000.family.ped -o %s", 1,
+                        " -L " + testDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + testDir + "ug.random50000.family.ped -o %s", 1,
                 Arrays.asList(MD5));
         executeTest("Testing ChromosomeCounts annotation with PED file", spec);
     }
@@ -210,8 +210,8 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testInbreedingCoeffPed() {
         final String MD5 = "7f1314fada5cb1f35ba1996f8a7a686b";
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-T VariantAnnotator -R " + b37KGReference + " -A InbreedingCoeff --variant:vcf " + validationDataLocation + "ug.random50000.subset300bp.chr1.family.vcf" +
+                "-T VariantAnnotator -R " + b37KGReference + " -A InbreedingCoeff --variant:vcf " + testDir + "ug.random50000.subset300bp.chr1.family.vcf" +
-                        " -L " + validationDataLocation + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + validationDataLocation + "ug.random50000.family.ped -o %s", 1,
+                        " -L " + testDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + testDir + "ug.random50000.family.ped -o %s", 1,
                 Arrays.asList(MD5));
         executeTest("Testing InbreedingCoeff annotation with PED file", spec);
     }

public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java

@@ -32,7 +32,7 @@ import java.util.Arrays;
  
 public class BeagleIntegrationTest extends WalkerTest {
 
-    private static final String beagleValidationDataLocation = validationDataLocation + "/Beagle/";
+    private static final String beagleValidationDataLocation = testDir + "/Beagle/";
     @Test
     public void testBeagleOutput() {
         WalkerTestSpec spec = new WalkerTestSpec(

public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java

@@ -15,7 +15,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     @Test
     public void testNoAction() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " --variant:VCF3 " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("8a105fa5eebdfffe7326bc5b3d8ffd1c"));
         executeTest("test no action", spec);
     }
@@ -23,7 +23,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     @Test
     public void testClusteredSnps() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -window 10 --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -window 10 --variant:VCF3 " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("27b13f179bb4920615dff3a32730d845"));
         executeTest("test clustered SNPs", spec);
     }
@@ -31,7 +31,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     @Test
     public void testMask1() {
         WalkerTestSpec spec1 = new WalkerTestSpec(
-                baseTestString() + " -maskName foo --mask:VCF3 " + validationDataLocation + "vcfexample2.vcf --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -maskName foo --mask:VCF3 " + testDir + "vcfexample2.vcf --variant:VCF3 " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("578f9e774784c25871678e6464fd212b"));
         executeTest("test mask all", spec1);
     }
@@ -39,7 +39,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     @Test
     public void testMask2() {
         WalkerTestSpec spec2 = new WalkerTestSpec(
-                baseTestString() + " -maskName foo --mask:VCF " + validationDataLocation + "vcfMask.vcf --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -maskName foo --mask:VCF " + testDir + "vcfMask.vcf --variant:VCF3 " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("bfa86a674aefca1b13d341cb14ab3c4f"));
         executeTest("test mask some", spec2);
     }
@@ -47,7 +47,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     @Test
     public void testMask3() {
         WalkerTestSpec spec3 = new WalkerTestSpec(
-                baseTestString() + " -maskName foo -maskExtend 10 --mask:VCF " + validationDataLocation + "vcfMask.vcf --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -maskName foo -maskExtend 10 --mask:VCF " + testDir + "vcfMask.vcf --variant:VCF3 " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("5939f80d14b32d88587373532d7b90e5"));
         executeTest("test mask extend", spec3);
     }
@@ -55,7 +55,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     @Test
     public void testFilter1() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo --variant:VCF3 " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("45219dbcfb6f81bba2ea0c35f5bfd368"));
         executeTest("test filter #1", spec);
     }
@@ -63,7 +63,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     @Test
     public void testFilter2() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar --variant:VCF3 " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("c95845e817da7352b9b72bc9794f18fb"));
         executeTest("test filter #2", spec);
     }
@@ -71,7 +71,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     @Test
     public void testFilterWithSeparateNames() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --filterName ABF -filter 'AlleleBalance < 0.7' --filterName FSF -filter 'FisherStrand == 1.4' --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " --filterName ABF -filter 'AlleleBalance < 0.7' --filterName FSF -filter 'FisherStrand == 1.4' --variant:VCF3 " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("b8cdd7f44ff1a395e0a9b06a87e1e530"));
         executeTest("test filter with separate names #2", spec);
     }
@@ -79,7 +79,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypeFilters1() {
         WalkerTestSpec spec1 = new WalkerTestSpec(
-                baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo --variant:VCF3 " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("96b61e4543a73fe725e433f007260039"));
         executeTest("test genotype filter #1", spec1);
     }
@@ -87,7 +87,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypeFilters2() {
         WalkerTestSpec spec2 = new WalkerTestSpec(
-                baseTestString() + " -G_filter 'AF == 0.04 && isHomVar == 1' -G_filterName foo --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -G_filter 'AF == 0.04 && isHomVar == 1' -G_filterName foo --variant:VCF3 " + testDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("6c8112ab17ce39c8022c891ae73bf38e"));
         executeTest("test genotype filter #2", spec2);
     }
@@ -95,7 +95,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     @Test
     public void testDeletions() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --filterExpression 'QUAL < 100' --filterName foo --variant:VCF " + validationDataLocation + "twoDeletions.vcf", 1,
+                baseTestString() + " --filterExpression 'QUAL < 100' --filterName foo --variant:VCF " + testDir + "twoDeletions.vcf", 1,
                 Arrays.asList("569546fd798afa0e65c5b61b440d07ac"));
         executeTest("test deletions", spec);
     }

public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java

@@ -37,7 +37,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testWithAllelesPassedIn1() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
-                baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
+                baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + testDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
                 Arrays.asList("ea5b5dcea3a6eef7ec60070b551c994e"));
         executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
     }
@@ -45,7 +45,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testWithAllelesPassedIn2() {
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
-                baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
+                baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + testDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
                 Arrays.asList("1899bdb956c62bbcbf160b18cd3aea60"));
         executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
     }
@@ -61,7 +61,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testMultipleSNPAlleles() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + validationDataLocation + "multiallelic.snps.bam -o %s -L " + validationDataLocation + "multiallelic.snps.intervals", 1,
+                "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + testDir + "multiallelic.snps.bam -o %s -L " + testDir + "multiallelic.snps.intervals", 1,
                 Arrays.asList("ec907c65da5ed9b6046404b0f81422d4"));
         executeTest("test Multiple SNP alleles", spec);
     }
@@ -69,7 +69,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testBadRead() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH -I " + validationDataLocation + "badRead.test.bam -o %s -L 1:22753424-22753464", 1,
+                "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH -I " + testDir + "badRead.test.bam -o %s -L 1:22753424-22753464", 1,
                 Arrays.asList("7678827a2ee21870a41c09d28d26b996"));
         executeTest("test bad read", spec);
     }
@@ -307,7 +307,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testWithIndelAllelesPassedIn1() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
+                baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + testDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
                 Arrays.asList("4a59fe207949b7d043481d7c1b786573"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in", spec);
@@ -317,7 +317,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testWithIndelAllelesPassedIn2() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
-                        + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
+                        + testDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
                 Arrays.asList("a8a9ccf30bddee94bb1d300600794ee7"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
@@ -341,7 +341,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testGGAwithNoEvidenceInReads() {
         final String vcf = "small.indel.test.vcf";
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + vcf + " -I " + validationDataLocation +
+                baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + testDir + vcf + " -I " + validationDataLocation +
                         "NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam -o %s -L " + validationDataLocation + vcf, 1,
                 Arrays.asList("7d069596597aee5e0d562964036141eb"));
         executeTest("test GENOTYPE_GIVEN_ALLELES with no evidence in reads", spec);

public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java

@@ -44,7 +44,7 @@ public class RealignerTargetCreatorIntegrationTest extends WalkerTest {
     @Test
     public void testKnownsOnly() {
         WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
-                "-T RealignerTargetCreator -R " + b36KGReference + " --known " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -L " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -o %s",
+                "-T RealignerTargetCreator -R " + b36KGReference + " --known " + testDir + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -L " + testDir + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -o %s",
                  1,
                  Arrays.asList("5206cee6c01b299417bf2feeb8b3dc96"));
         executeTest("test rods only", spec3);

public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java

@@ -6,7 +6,7 @@ import org.testng.annotations.Test;
 import java.util.Arrays;
 
 public class PhaseByTransmissionIntegrationTest extends WalkerTest {
-    private static String phaseByTransmissionTestDataRoot = validationDataLocation + "PhaseByTransmission/";
+    private static String phaseByTransmissionTestDataRoot = testDir + "PhaseByTransmission/";
     private static String goodFamilyFile =  phaseByTransmissionTestDataRoot + "PhaseByTransmission.IntegrationTest.goodFamilies.ped";
     private static String TNTest = phaseByTransmissionTestDataRoot + "PhaseByTransmission.IntegrationTest.TN.vcf";
     private static String TPTest = phaseByTransmissionTestDataRoot + "PhaseByTransmission.IntegrationTest.TP.vcf";

public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java

@@ -271,7 +271,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
 
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                     "-R " + b36KGReference +
-                            " -knownSites:anyNameABCD,VCF3 " + validationDataLocation + "vcfexample3.vcf" +
+                            " -knownSites:anyNameABCD,VCF3 " + testDir + "vcfexample3.vcf" +
                             " -T CountCovariates" +
                             " -I " + bam +
                             " -knownSites " + b36dbSNP129 +

public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java

@@ -17,8 +17,8 @@ public class ValidationAmpliconsIntegrationTest extends WalkerTest {
     @Test(enabled=true)
     public void testWikiExample() {
         String siteVCF = validationDataLocation + "sites_to_validate.vcf";
-        String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf";
+        String maskVCF = testDir + "amplicon_mask_sites.vcf";
-        String intervalTable = validationDataLocation + "amplicon_interval_table1.table";
+        String intervalTable = testDir + "amplicon_interval_table1.table";
         String testArgs = "-R " + b37KGReference + " -T ValidationAmplicons --ValidateAlleles:VCF "+siteVCF+" -o %s";
         testArgs += " --ProbeIntervals:table "+intervalTable+" -L:table "+intervalTable+" --MaskAlleles:VCF "+maskVCF;
         testArgs += " --virtualPrimerSize 30";
@@ -29,9 +29,9 @@ public class ValidationAmpliconsIntegrationTest extends WalkerTest {
 
     @Test(enabled=true)
     public void testWikiExampleNoBWA() {
-        String siteVCF = validationDataLocation + "sites_to_validate.vcf";
+        String siteVCF = testDir + "sites_to_validate.vcf";
-        String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf";
+        String maskVCF = testDir + "amplicon_mask_sites.vcf";
-        String intervalTable = validationDataLocation + "amplicon_interval_table1.table";
+        String intervalTable = testDir + "amplicon_interval_table1.table";
         String testArgs = "-R " + b37KGReference + " -T ValidationAmplicons --ValidateAlleles:VCF "+siteVCF+" -o %s";
         testArgs += " --ProbeIntervals:table "+intervalTable+" -L:table "+intervalTable+" --MaskAlleles:VCF "+maskVCF;
         testArgs += " --virtualPrimerSize 30 --doNotUseBWA";
@@ -42,9 +42,9 @@ public class ValidationAmpliconsIntegrationTest extends WalkerTest {
 
     @Test(enabled=true)
     public void testWikiExampleMonoFilter() {
-        String siteVCF = validationDataLocation + "sites_to_validate.vcf";
+        String siteVCF = testDir + "sites_to_validate.vcf";
-        String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf";
+        String maskVCF = testDir + "amplicon_mask_sites.vcf";
-        String intervalTable = validationDataLocation + "amplicon_interval_table1.table";
+        String intervalTable = testDir + "amplicon_interval_table1.table";
         String testArgs = "-R " + b37KGReference + " -T ValidationAmplicons --ValidateAlleles:VCF "+siteVCF+" -o %s";
         testArgs += " --ProbeIntervals:table "+intervalTable+" -L:table "+intervalTable+" --MaskAlleles:VCF "+maskVCF;
         testArgs += " --virtualPrimerSize 30 --filterMonomorphic";

public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java

@@ -349,7 +349,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
 
     @Test
     public void testCompOverlap() {
-        String extraArgs = "-T VariantEval -R " + b37KGReference + " -L " + validationDataLocation + "VariantEval/pacbio.hg19.intervals --comp:comphapmap " + comparisonDataLocation + "Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf --eval " + validationDataLocation + "VariantEval/pacbio.ts.recalibrated.vcf -noEV -EV CompOverlap -sn NA12878 -noST -ST Novelty -o %s";
+        String extraArgs = "-T VariantEval -R " + b37KGReference + " -L " + variantEvalTestDataRoot + "pacbio.hg19.intervals --comp:comphapmap " + comparisonDataLocation + "Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf --eval " + variantEvalTestDataRoot + "pacbio.ts.recalibrated.vcf -noEV -EV CompOverlap -sn NA12878 -noST -ST Novelty -o %s";
         WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("59ad39e03678011b5f62492fa83ede04"));
         executeTestParallel("testCompOverlap",spec);
     }
@@ -360,7 +360,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                            b37KGReference +
                            " -L 20" +
                            " --dbsnp " + b37dbSNP132 +
-                           " --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
+                           " --eval:evalBI " + variantEvalTestDataRoot + "ALL.20100201.chr20.bi.sites.vcf" +
                            " -noST -ST Novelty -o %s";
         WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("112bb3221688acad83f29542bfb33151"));
         executeTestParallel("testEvalTrackWithoutGenotypes",spec);
@@ -371,8 +371,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
         String extraArgs = "-T VariantEval -R " + b37KGReference +
                 " -L 20" +
                 " --dbsnp " + b37dbSNP132 +
-                " --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
+                " --eval:evalBI " + variantEvalTestDataRoot + "ALL.20100201.chr20.bi.sites.vcf" +
-                " --eval:evalBC " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
+                " --eval:evalBC " + variantEvalTestDataRoot + "ALL.20100201.chr20.bc.sites.vcf" +
                 " -noST -ST Novelty -o %s";
         WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("81dcdde458c1ebb9aa35289ea8f12bc8"));
         executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
@@ -384,8 +384,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
 
         String extraArgs =  "-T VariantEval" +
                            " -R " + b37KGReference +
-                           " --comp " + validationDataLocation + "/VariantEval/ALL.phase1.chr20.broad.snps.genotypes.subset.vcf" +
+                           " --comp " + variantEvalTestDataRoot + "ALL.phase1.chr20.broad.snps.genotypes.subset.vcf" +
-                           " --eval " + validationDataLocation + "/VariantEval/NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.subset.vcf" +
+                           " --eval " + variantEvalTestDataRoot + "NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.subset.vcf" +
                            " --dbsnp " + dbsnp +
                            " -L 20:10000000-10100000" +
                            " -noST -noEV -ST Novelty -EV CompOverlap" +

public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java

@@ -127,10 +127,10 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
                         " -L 20:1000100-1000500" +
                         " -mode BOTH" +
                         " --no_cmdline_in_header" +
-                        " -input " + validationDataLocation + "VQSR.mixedTest.input" +
+                        " -input " + testDir + "VQSR.mixedTest.input" +
                         " -o %s" +
-                        " -tranchesFile " + validationDataLocation + "VQSR.mixedTest.tranches" +
+                        " -tranchesFile " + testDir + "VQSR.mixedTest.tranches" +
-                        " -recalFile " + validationDataLocation + "VQSR.mixedTest.recal",
+                        " -recalFile " + testDir + "VQSR.mixedTest.recal",
                 Arrays.asList("9039576b63728df7ee2c881817c0e9eb"));
         executeTest("testApplyRecalibrationSnpAndIndelTogether", spec);
     }

public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java

@@ -38,7 +38,7 @@ public class LeftAlignVariantsIntegrationTest extends WalkerTest {
     @Test
     public void testLeftAlignment() {
          WalkerTestSpec spec = new WalkerTestSpec(
-                 "-T LeftAlignVariants -o %s -R " + b37KGReference + " --variant:vcf " + validationDataLocation + "forLeftAlignVariantsTest.vcf --no_cmdline_in_header",
+                 "-T LeftAlignVariants -o %s -R " + b37KGReference + " --variant:vcf " + testDir + "forLeftAlignVariantsTest.vcf --no_cmdline_in_header",
                  1,
                  Arrays.asList("8e0991576518823b339a4e2f83299d4f"));
          executeTest("test left alignment", spec);

public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java

@@ -56,7 +56,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
     @Test
     public void testhg18Tohg19Unsorted() {
          WalkerTestSpec spec = new WalkerTestSpec(
-                 "-T LiftoverVariants -o %s -R " + hg18Reference + " --variant:vcf " + validationDataLocation + "liftover_test.vcf -chain " + validationDataLocation + "hg18ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
+                 "-T LiftoverVariants -o %s -R " + hg18Reference + " --variant:vcf " + testDir + "liftover_test.vcf -chain " + validationDataLocation + "hg18ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
                  1,
                  Arrays.asList("ab2c6254225d7e2ecf52eee604d5673b"));
          executeTest("test hg18 to hg19, unsorted", spec);

public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java

@@ -20,7 +20,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
             1,
             Arrays.asList("d18516c1963802e92cb9e425c0b75fd6")
         );
-
+        spec.disableShadowBCF();
         executeTest("testComplexSelection--" + testfile, spec);
     }
 
@@ -34,13 +34,14 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
             1,
             Arrays.asList("730f021fd6ecf1d195dabbee2e233bfd")
         );
+        spec.disableShadowBCF();
 
         executeTest("testSampleExclusion--" + testfile, spec);
     }
 
     @Test
     public void testRepeatedLineSelection() {
-        String testfile = validationDataLocation + "test.dup.vcf";
+        String testfile = testDir + "test.dup.vcf";
 
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -sn A -sn B -sn C --variant " + testfile),
@@ -53,46 +54,49 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
 
     @Test
     public void testDiscordance() {
-        String testFile = validationDataLocation + "NA12878.hg19.example1.vcf";
+        String testFile = testDir + "NA12878.hg19.example1.vcf";
 
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 --variant " + b37hapmapGenotypes + " -disc " + testFile + " -o %s --no_cmdline_in_header",
                 1,
                 Arrays.asList("929bbb96381541c162dc7e5462e26ea2")
         );
+        spec.disableShadowBCF();
 
         executeTest("testDiscordance--" + testFile, spec);
     }
 
     @Test
     public void testDiscordanceNoSampleSpecified() {
-        String testFile = validationDataLocation + "NA12878.hg19.example1.vcf";
+        String testFile = testDir + "NA12878.hg19.example1.vcf";
 
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + hg19Reference + " -L 20:1012700-1020000 --variant " + b37hapmapGenotypes + " -disc " + testFile + " -o %s --no_cmdline_in_header",
                 1,
                 Arrays.asList("5d7d899c0c4954ec59104aebfe4addd5")
         );
+        spec.disableShadowBCF();
 
         executeTest("testDiscordanceNoSampleSpecified--" + testFile, spec);
     }
 
     @Test
     public void testConcordance() {
-        String testFile = validationDataLocation + "NA12878.hg19.example1.vcf";
+        String testFile = testDir + "NA12878.hg19.example1.vcf";
 
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 -conc " + b37hapmapGenotypes + " --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
                 Arrays.asList("d2ba3ea30a810f6f0fbfb1b643292b6a")
         );
+        spec.disableShadowBCF();
 
         executeTest("testConcordance--" + testFile, spec);
     }
 
     @Test
     public void testVariantTypeSelection() {
-        String testFile = validationDataLocation + "complexExample1.vcf";
+        String testFile = testDir + "complexExample1.vcf";
 
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -restrictAllelesTo MULTIALLELIC -selectType MIXED --variant " + testFile + " -o %s --no_cmdline_in_header",
@@ -105,7 +109,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
 
     @Test
     public void testUsingDbsnpName() {
-        String testFile = validationDataLocation + "combine.3.vcf";
+        String testFile = testDir + "combine.3.vcf";
 
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant:dbsnp " + testFile + " -o %s --no_cmdline_in_header",
@@ -118,7 +122,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
 
     @Test
     public void testRegenotype() {
-        String testFile = validationDataLocation + "combine.3.vcf";
+        String testFile = testDir + "combine.3.vcf";
 
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
@@ -131,7 +135,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
 
     @Test
     public void testMultipleRecordsAtOnePosition() {
-        String testFile = validationDataLocation + "selectVariants.onePosition.vcf";
+        String testFile = testDir + "selectVariants.onePosition.vcf";
 
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -select 'KG_FREQ < 0.5' --variant " + testFile + " -o %s --no_cmdline_in_header",
@@ -144,7 +148,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
 
     @Test
     public void testNoGTs() {
-        String testFile = validationDataLocation + "vcf4.1.example.vcf";
+        String testFile = testDir + "vcf4.1.example.vcf";
 
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b37KGReference + " --variant " + testFile + " -o %s --no_cmdline_in_header",
@@ -166,6 +170,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
             1,
             Arrays.asList("d18516c1963802e92cb9e425c0b75fd6")
         );
+        spec.disableShadowBCF();
         executeTest("testParallelization (2 threads)--" + testfile, spec);
 
         spec = new WalkerTestSpec(
@@ -173,14 +178,15 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
             1,
             Arrays.asList("d18516c1963802e92cb9e425c0b75fd6")
         );
+        spec.disableShadowBCF();
 
         executeTest("testParallelization (4 threads)--" + testfile, spec);
     }
 
     @Test
     public void testSelectFromMultiAllelic() {
-        String testfile = validationDataLocation + "multi-allelic.bi-allelicInGIH.vcf";
+        String testfile = testDir + "multi-allelic.bi-allelicInGIH.vcf";
-        String samplesFile = validationDataLocation + "GIH.samples.list";
+        String samplesFile = testDir + "GIH.samples.list";
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header -sf " + samplesFile + " --excludeNonVariants --variant " + testfile,
                 1,

public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java

@@ -34,7 +34,7 @@ import java.util.Arrays;
 public class ValidateVariantsIntegrationTest extends WalkerTest {
 
     public static String baseTestString(String file, String type) {
-        return "-T ValidateVariants -R " + b36KGReference + " -L 1:10001292-10001303 --variant:vcf " + validationDataLocation + file + " --validationType " + type;
+        return "-T ValidateVariants -R " + b36KGReference + " -L 1:10001292-10001303 --variant:vcf " + testDir + file + " --validationType " + type;
     }
 
     @Test

public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java

@@ -33,7 +33,7 @@ import java.util.*;
 public class VariantsToTableIntegrationTest extends WalkerTest {
     private String variantsToTableCmd(String moreArgs) {
         return "-R " + hg18Reference +
-                " --variant:vcf " + validationDataLocation + "/soap_gatk_annotated.vcf" +
+                " --variant:vcf " + testDir + "/soap_gatk_annotated.vcf" +
                 " -T VariantsToTable" +
                 " -F CHROM -F POS -F ID -F REF -F ALT -F QUAL -F FILTER -F TRANSITION -F DP -F SB -F set -F RankSumP -F refseq.functionalClass*" +
                 " -L chr1 -o %s" + moreArgs;
@@ -41,7 +41,7 @@ public class VariantsToTableIntegrationTest extends WalkerTest {
 
     private String variantsToTableMultiAllelicCmd(String moreArgs) {
         return "-R " + b37KGReference +
-                " --variant " + validationDataLocation + "/multiallelic.vcf" +
+                " --variant " + testDir + "/multiallelic.vcf" +
                 " -T VariantsToTable" +
                 " -F CHROM -F POS -F ID -F REF -F ALT -F QUAL -F MULTI-ALLELIC -F AC -F AF" +
                 " -o %s" + moreArgs;

public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java

@@ -93,7 +93,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
-                        " --variant:VCF " + validationDataLocation + "complexExample.vcf4" +
+                        " --variant:VCF " + testDir + "complexExample.vcf4" +
                         " -T VariantsToVCF" +
                         " -o %s" +
                         " --no_cmdline_in_header",

public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java

@@ -13,7 +13,7 @@ public class VCFIntegrationTest extends WalkerTest {
     public void testReadingAndWritingWitHNoChanges() {
 
         String md5ofInputVCF = "a990ba187a69ca44cb9bc2bb44d00447";
-        String testVCF = validationDataLocation + "vcf4.1.example.vcf";
+        String testVCF = testDir + "vcf4.1.example.vcf";
 
         String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
 
@@ -41,7 +41,7 @@ public class VCFIntegrationTest extends WalkerTest {
 
     @Test
     public void testReadingAndWritingSamtools() {
-        String testVCF = validationDataLocation + "samtools.vcf";
+        String testVCF = testDir + "samtools.vcf";
 
         String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
 

public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java

@@ -264,7 +264,7 @@ public class IntervalIntegrationTest extends WalkerTest {
                         " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam" +
                         " -R " + b36KGReference +
                         " -o %s" +
-                        " -L " + validationDataLocation + "symbolic_alleles_1.vcf",
+                        " -L " + testDir + "symbolic_alleles_1.vcf",
                 1, // just one output file
                 Arrays.asList(md5));
         executeTest("testSymbolicAlleles", spec);

public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java

@@ -357,8 +357,8 @@ public class IntervalUtilsUnitTest extends BaseTest {
 
     @Test
     public void testIsIntervalFile() {
-        Assert.assertTrue(IntervalUtils.isIntervalFile(BaseTest.validationDataLocation + "empty_intervals.list"));
+        Assert.assertTrue(IntervalUtils.isIntervalFile(BaseTest.testDir + "empty_intervals.list"));
-        Assert.assertTrue(IntervalUtils.isIntervalFile(BaseTest.validationDataLocation + "empty_intervals.list", true));
+        Assert.assertTrue(IntervalUtils.isIntervalFile(BaseTest.testDir + "empty_intervals.list", true));
 
         List<String> extensions = Arrays.asList("bed", "interval_list", "intervals", "list", "picard");
         for (String extension: extensions) {
@@ -368,7 +368,7 @@ public class IntervalUtilsUnitTest extends BaseTest {
 
     @Test(expectedExceptions = UserException.CouldNotReadInputFile.class)
     public void testMissingIntervalFile() {
-        IntervalUtils.isIntervalFile(BaseTest.validationDataLocation + "no_such_intervals.list");
+        IntervalUtils.isIntervalFile(BaseTest.testDir + "no_such_intervals.list");
     }
 
     @Test
@@ -758,7 +758,7 @@ public class IntervalUtilsUnitTest extends BaseTest {
 
     @Test(dataProvider="unmergedIntervals")
     public void testUnmergedIntervals(String unmergedIntervals) {
-        List<GenomeLoc> locs = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Collections.singletonList(validationDataLocation + unmergedIntervals));
+        List<GenomeLoc> locs = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Collections.singletonList(testDir + unmergedIntervals));
         Assert.assertEquals(locs.size(), 2);
 
         List<GenomeLoc> merged = IntervalUtils.mergeIntervalLocations(locs, IntervalMergingRule.ALL);

public/testdata/FundamentalsTest.annotated.db.subset.final.HG00625.vcf

@@ -1,25 +0,0 @@
-##fileformat=VCFv4.0
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
-##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
-##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
-##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
-##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
-##SelectVariants="analysis_type=SelectVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-hpprojects/GATK/data/Validation_Data/VariantEval/FundamentalsTest.annotated.db.subset.final.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sample=[HG00625] select_expressions=[] excludeNonVariants=false excludeFiltered=false"
-##source=SelectVariants
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00625
-20	10003358	rs926982	A	C	92318.04	PASS	AC=2;AF=1.00;AN=2;DBSNP129;DBSNP132;DP=1	GT:DP:GQ:PL	1/1:1:3:27,3,0
-20	10003692	rs2064653	A	G	119873.04	PASS	AC=2;AF=1.00;AN=2;DBSNP129;DBSNP132;DP=3	GT:DP:GQ:PL	1/1:3:9:112,9,0
-20	10015679	rs113024248	C	.	2829.33	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;OMNI	GT:DP:PL	./.
-20	10015790	rs114356776	G	.	43.60	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.-300G>A;refseq.codingCoordStr_2=c.-236G>A;refseq.codingCoordStr_3=c.-300G>C;refseq.codingCoordStr_4=c.-236G>C;refseq.codingCoordStr_5=c.-300G>G;refseq.codingCoordStr_6=c.-236G>G;refseq.codingCoordStr_7=c.-300G>T;refseq.codingCoordStr_8=c.-236G>T;refseq.end_1=10015790;refseq.end_2=10015790;refseq.end_3=10015790;refseq.end_4=10015790;refseq.end_5=10015790;refseq.end_6=10015790;refseq.end_7=10015790;refseq.end_8=10015790;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=94;refseq.mrnaCoord_2=94;refseq.mrnaCoord_3=94;refseq.mrnaCoord_4=94;refseq.mrnaCoord_5=94;refseq.mrnaCoord_6=94;refseq.mrnaCoord_7=94;refseq.mrnaCoord_8=94;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.positionType_3=utr5;refseq.positionType_4=utr5;refseq.positionType_5=utr5;refseq.positionType_6=utr5;refseq.positionType_7=utr5;refseq.positionType_8=utr5;refseq.spliceDist_1=94;refseq.spliceDist_2=94;refseq.spliceDist_3=94;refseq.spliceDist_4=94;refseq.spliceDist_5=94;refseq.spliceDist_6=94;refseq.spliceDist_7=94;refseq.spliceDist_8=94;refseq.start_1=10015790;refseq.start_2=10015790;refseq.start_3=10015790;refseq.start_4=10015790;refseq.start_5=10015790;refseq.start_6=10015790;refseq.start_7=10015790;refseq.start_8=10015790;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:PL	./.
-20	10019093	rs575534	A	G	69795.04	PASS	AC=2;AF=1.00;AN=2;DBSNP129;DBSNP132;DP=5;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=20;refseq.chr_2=20;refseq.codingCoordStr_1=c.144A>G;refseq.codingCoordStr_2=c.144A>G;refseq.codonCoord_1=48;refseq.codonCoord_2=48;refseq.end_1=10019093;refseq.end_2=10019093;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=537;refseq.mrnaCoord_2=473;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G48G;refseq.proteinCoordStr_2=p.G48G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=188;refseq.spliceDist_2=188;refseq.start_1=10019093;refseq.start_2=10019093;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG	GT:DP:GQ:PL	1/1:5:15:172,15,0
-20	10019169	rs7260784	C	.	1193.61	PASS	AC=0;AF=0.00;AN=2;DBSNP129;DBSNP132;DP=4;HAPMAP;OMNI;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.220C>A;refseq.codingCoordStr_2=c.220C>A;refseq.codingCoordStr_3=c.220C>C;refseq.codingCoordStr_4=c.220C>C;refseq.codingCoordStr_5=c.220C>G;refseq.codingCoordStr_6=c.220C>G;refseq.codingCoordStr_7=c.220C>T;refseq.codingCoordStr_8=c.220C>T;refseq.codonCoord_1=74;refseq.codonCoord_2=74;refseq.codonCoord_3=74;refseq.codonCoord_4=74;refseq.codonCoord_5=74;refseq.codonCoord_6=74;refseq.codonCoord_7=74;refseq.codonCoord_8=74;refseq.end_1=10019169;refseq.end_2=10019169;refseq.end_3=10019169;refseq.end_4=10019169;refseq.end_5=10019169;refseq.end_6=10019169;refseq.end_7=10019169;refseq.end_8=10019169;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.haplotypeReference_7=C;refseq.haplotypeReference_8=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=613;refseq.mrnaCoord_2=549;refseq.mrnaCoord_3=613;refseq.mrnaCoord_4=549;refseq.mrnaCoord_5=613;refseq.mrnaCoord_6=549;refseq.mrnaCoord_7=613;refseq.mrnaCoord_8=549;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.P74T;refseq.proteinCoordStr_2=p.P74T;refseq.proteinCoordStr_3=p.P74P;refseq.proteinCoordStr_4=p.P74P;refseq.proteinCoordStr_5=p.P74A;refseq.proteinCoordStr_6=p.P74A;refseq.proteinCoordStr_7=p.P74S;refseq.proteinCoordStr_8=p.P74S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceAA_5=Pro;refseq.referenceAA_6=Pro;refseq.referenceAA_7=Pro;refseq.referenceAA_8=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.referenceCodon_3=CCT;refseq.referenceCodon_4=CCT;refseq.referenceCodon_5=CCT;refseq.referenceCodon_6=CCT;refseq.referenceCodon_7=CCT;refseq.referenceCodon_8=CCT;refseq.spliceDist_1=-127;refseq.spliceDist_2=-127;refseq.spliceDist_3=-127;refseq.spliceDist_4=-127;refseq.spliceDist_5=-127;refseq.spliceDist_6=-127;refseq.spliceDist_7=-127;refseq.spliceDist_8=-127;refseq.start_1=10019169;refseq.start_2=10019169;refseq.start_3=10019169;refseq.start_4=10019169;refseq.start_5=10019169;refseq.start_6=10019169;refseq.start_7=10019169;refseq.start_8=10019169;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Ala;refseq.variantAA_6=Ala;refseq.variantAA_7=Ser;refseq.variantAA_8=Ser;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;refseq.variantCodon_3=CCT;refseq.variantCodon_4=CCT;refseq.variantCodon_5=GCT;refseq.variantCodon_6=GCT;refseq.variantCodon_7=TCT;refseq.variantCodon_8=TCT	GT:DP:GQ:PL	0/0:4:12:0,12,144
-20	10032432	rs78089752	A	.	367.04	PASS	AC=0;AF=0.00;AN=2;DBSNP132;DP=5;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.1765A>A;refseq.codingCoordStr_2=c.1765A>A;refseq.codingCoordStr_3=c.1765A>C;refseq.codingCoordStr_4=c.1765A>C;refseq.codingCoordStr_5=c.1765A>G;refseq.codingCoordStr_6=c.1765A>G;refseq.codingCoordStr_7=c.1765A>T;refseq.codingCoordStr_8=c.1765A>T;refseq.codonCoord_1=589;refseq.codonCoord_2=589;refseq.codonCoord_3=589;refseq.codonCoord_4=589;refseq.codonCoord_5=589;refseq.codonCoord_6=589;refseq.codonCoord_7=589;refseq.codonCoord_8=589;refseq.end_1=10032432;refseq.end_2=10032432;refseq.end_3=10032432;refseq.end_4=10032432;refseq.end_5=10032432;refseq.end_6=10032432;refseq.end_7=10032432;refseq.end_8=10032432;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.haplotypeReference_6=A;refseq.haplotypeReference_7=A;refseq.haplotypeReference_8=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=2158;refseq.mrnaCoord_2=2094;refseq.mrnaCoord_3=2158;refseq.mrnaCoord_4=2094;refseq.mrnaCoord_5=2158;refseq.mrnaCoord_6=2094;refseq.mrnaCoord_7=2158;refseq.mrnaCoord_8=2094;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.I589I;refseq.proteinCoordStr_2=p.I589I;refseq.proteinCoordStr_3=p.I589L;refseq.proteinCoordStr_4=p.I589L;refseq.proteinCoordStr_5=p.I589V;refseq.proteinCoordStr_6=p.I589V;refseq.proteinCoordStr_7=p.I589F;refseq.proteinCoordStr_8=p.I589F;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceAA_5=Ile;refseq.referenceAA_6=Ile;refseq.referenceAA_7=Ile;refseq.referenceAA_8=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.referenceCodon_3=ATC;refseq.referenceCodon_4=ATC;refseq.referenceCodon_5=ATC;refseq.referenceCodon_6=ATC;refseq.referenceCodon_7=ATC;refseq.referenceCodon_8=ATC;refseq.spliceDist_1=-106;refseq.spliceDist_2=-106;refseq.spliceDist_3=-106;refseq.spliceDist_4=-106;refseq.spliceDist_5=-106;refseq.spliceDist_6=-106;refseq.spliceDist_7=-106;refseq.spliceDist_8=-106;refseq.start_1=10032432;refseq.start_2=10032432;refseq.start_3=10032432;refseq.start_4=10032432;refseq.start_5=10032432;refseq.start_6=10032432;refseq.start_7=10032432;refseq.start_8=10032432;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantAA_5=Val;refseq.variantAA_6=Val;refseq.variantAA_7=Phe;refseq.variantAA_8=Phe;refseq.variantCodon_1=ATC;refseq.variantCodon_2=ATC;refseq.variantCodon_3=CTC;refseq.variantCodon_4=CTC;refseq.variantCodon_5=GTC;refseq.variantCodon_6=GTC;refseq.variantCodon_7=TTC;refseq.variantCodon_8=TTC	GT:DP:GQ:PL	0/0:5:15:0,15,182
-20	10037119	.	G	.	469.85	PASS	AC=0;AF=0.00;AN=2;DBSNP129;DP=1;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.*811G>A;refseq.codingCoordStr_2=c.*811G>A;refseq.codingCoordStr_3=c.*811G>C;refseq.codingCoordStr_4=c.*811G>C;refseq.codingCoordStr_5=c.*811G>G;refseq.codingCoordStr_6=c.*811G>G;refseq.codingCoordStr_7=c.*811G>T;refseq.codingCoordStr_8=c.*811G>T;refseq.end_1=10037119;refseq.end_2=10037119;refseq.end_3=10037119;refseq.end_4=10037119;refseq.end_5=10037119;refseq.end_6=10037119;refseq.end_7=10037119;refseq.end_8=10037119;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=3535;refseq.mrnaCoord_2=3471;refseq.mrnaCoord_3=3535;refseq.mrnaCoord_4=3471;refseq.mrnaCoord_5=3535;refseq.mrnaCoord_6=3471;refseq.mrnaCoord_7=3535;refseq.mrnaCoord_8=3471;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.positionType_3=utr3;refseq.positionType_4=utr3;refseq.positionType_5=utr3;refseq.positionType_6=utr3;refseq.positionType_7=utr3;refseq.positionType_8=utr3;refseq.spliceDist_1=-289;refseq.spliceDist_2=-289;refseq.spliceDist_3=-289;refseq.spliceDist_4=-289;refseq.spliceDist_5=-289;refseq.spliceDist_6=-289;refseq.spliceDist_7=-289;refseq.spliceDist_8=-289;refseq.start_1=10037119;refseq.start_2=10037119;refseq.start_3=10037119;refseq.start_4=10037119;refseq.start_5=10037119;refseq.start_6=10037119;refseq.start_7=10037119;refseq.start_8=10037119;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:GQ:PL	0/0:1:3:0,3,37
-20	10047435	rs598275	G	A	82495.04	PASS	AC=2;AF=1.00;AN=2;DBSNP129;DBSNP132;DP=4;HAPMAP;OMNI	GT:DP:GQ:PL	1/1:4:12:139,12,0

public/testdata/FundamentalsTest.annotated.db.subset.final.NA12045.vcf

@@ -1,23 +0,0 @@
-##fileformat=VCFv4.1
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
-##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
-##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
-##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
-##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12045
-20	10003358	rs926982	A	C	92318.04	PASS	DBSNP129;DBSNP132;DP=5	GT:DP:GQ:PL	0/1:5:51:51,0,95
-20	10003692	rs2064653	A	G	119873.04	PASS	DBSNP129;DBSNP132;DP=4	GT:DP:GQ:PL	0/1:4:20:20,0,85
-20	10015679	rs113024248	C	.	2829.33	PASS	DBSNP132;DP=0;OMNI	GT:DP:PL	./.
-20	10015790	rs114356776	G	.	43.60	PASS	DBSNP132;DP=0	GT:DP:PL	./.
-20	10019093	rs575534	A	G	69795.04	PASS	DBSNP129;DBSNP132;DP=6;OMNI	GT:DP:GQ:PL	0/0:6:18:0,18,211
-20	10019169	rs7260784	C	.	1193.61	PASS	DBSNP129;DBSNP132;DP=6;HAPMAP;OMNI	GT:DP:GQ:PL	0/0:6:18:0,18,211
-20	10032432	rs78089752	A	.	367.04	PASS	DBSNP132;DP=8;OMNI	GT:DP:GQ:PL	0/0:8:24:0,24,293
-20	10037119	.	G	.	469.85	PASS	DBSNP129;DP=2	GT:DP:GQ:PL	0/0:2:6:0,6,65
-20	10047435	rs598275	G	A	82495.04	PASS	DBSNP129;DBSNP132;DP=2;HAPMAP;OMNI	GT:DP:GQ:PL	1/1:2:6:69,6,0

public/testdata/FundamentalsTest.annotated.db.subset.final.split_1_of_2.vcf

@@ -1,19 +0,0 @@
-##fileformat=VCFv4.0
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
-##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
-##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
-##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
-##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
-20	10003358	rs926982	A	C	92318.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=7	GT:DP:GQ:PL	1/1:1:3:34,3,0	0/1:5:51:51,0,95	1/1:1:3:27,3,0
-20	10003692	rs2064653	A	G	119873.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=9	GT:DP:GQ:PL	1/1:2:6:66,6,0	0/1:4:20:20,0,85	1/1:3:9:112,9,0
-20	10015679	rs113024248	C	.	2829.33	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;OMNI	GT:DP:PL	./.	./.	./.
-20	10015790	rs114356776	G	.	43.60	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.-300G>A;refseq.codingCoordStr_2=c.-236G>A;refseq.codingCoordStr_3=c.-300G>C;refseq.codingCoordStr_4=c.-236G>C;refseq.codingCoordStr_5=c.-300G>G;refseq.codingCoordStr_6=c.-236G>G;refseq.codingCoordStr_7=c.-300G>T;refseq.codingCoordStr_8=c.-236G>T;refseq.end_1=10015790;refseq.end_2=10015790;refseq.end_3=10015790;refseq.end_4=10015790;refseq.end_5=10015790;refseq.end_6=10015790;refseq.end_7=10015790;refseq.end_8=10015790;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=94;refseq.mrnaCoord_2=94;refseq.mrnaCoord_3=94;refseq.mrnaCoord_4=94;refseq.mrnaCoord_5=94;refseq.mrnaCoord_6=94;refseq.mrnaCoord_7=94;refseq.mrnaCoord_8=94;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.positionType_3=utr5;refseq.positionType_4=utr5;refseq.positionType_5=utr5;refseq.positionType_6=utr5;refseq.positionType_7=utr5;refseq.positionType_8=utr5;refseq.spliceDist_1=94;refseq.spliceDist_2=94;refseq.spliceDist_3=94;refseq.spliceDist_4=94;refseq.spliceDist_5=94;refseq.spliceDist_6=94;refseq.spliceDist_7=94;refseq.spliceDist_8=94;refseq.start_1=10015790;refseq.start_2=10015790;refseq.start_3=10015790;refseq.start_4=10015790;refseq.start_5=10015790;refseq.start_6=10015790;refseq.start_7=10015790;refseq.start_8=10015790;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:PL	./.	./.	./.
-20	10019093	rs575534	A	G	69795.04	PASS	AC=3;AF=0.50;AN=6;DBSNP129;DBSNP132;DP=14;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=20;refseq.chr_2=20;refseq.codingCoordStr_1=c.144A>G;refseq.codingCoordStr_2=c.144A>G;refseq.codonCoord_1=48;refseq.codonCoord_2=48;refseq.end_1=10019093;refseq.end_2=10019093;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=537;refseq.mrnaCoord_2=473;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G48G;refseq.proteinCoordStr_2=p.G48G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=188;refseq.spliceDist_2=188;refseq.start_1=10019093;refseq.start_2=10019093;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG	GT:DP:GQ:PL	0/1:3:24:24,0,60	0/0:6:18:0,18,211	1/1:5:15:172,15,0

public/testdata/FundamentalsTest.annotated.db.subset.final.split_2_of_2.vcf

@@ -1,18 +0,0 @@
-##fileformat=VCFv4.0
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
-##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
-##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
-##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
-##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
-20	10019169	rs7260784	C	.	1193.61	PASS	AC=0;AF=0.00;AN=6;DBSNP129;DBSNP132;DP=14;HAPMAP;OMNI;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.220C>A;refseq.codingCoordStr_2=c.220C>A;refseq.codingCoordStr_3=c.220C>C;refseq.codingCoordStr_4=c.220C>C;refseq.codingCoordStr_5=c.220C>G;refseq.codingCoordStr_6=c.220C>G;refseq.codingCoordStr_7=c.220C>T;refseq.codingCoordStr_8=c.220C>T;refseq.codonCoord_1=74;refseq.codonCoord_2=74;refseq.codonCoord_3=74;refseq.codonCoord_4=74;refseq.codonCoord_5=74;refseq.codonCoord_6=74;refseq.codonCoord_7=74;refseq.codonCoord_8=74;refseq.end_1=10019169;refseq.end_2=10019169;refseq.end_3=10019169;refseq.end_4=10019169;refseq.end_5=10019169;refseq.end_6=10019169;refseq.end_7=10019169;refseq.end_8=10019169;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.haplotypeReference_7=C;refseq.haplotypeReference_8=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=613;refseq.mrnaCoord_2=549;refseq.mrnaCoord_3=613;refseq.mrnaCoord_4=549;refseq.mrnaCoord_5=613;refseq.mrnaCoord_6=549;refseq.mrnaCoord_7=613;refseq.mrnaCoord_8=549;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.P74T;refseq.proteinCoordStr_2=p.P74T;refseq.proteinCoordStr_3=p.P74P;refseq.proteinCoordStr_4=p.P74P;refseq.proteinCoordStr_5=p.P74A;refseq.proteinCoordStr_6=p.P74A;refseq.proteinCoordStr_7=p.P74S;refseq.proteinCoordStr_8=p.P74S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceAA_5=Pro;refseq.referenceAA_6=Pro;refseq.referenceAA_7=Pro;refseq.referenceAA_8=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.referenceCodon_3=CCT;refseq.referenceCodon_4=CCT;refseq.referenceCodon_5=CCT;refseq.referenceCodon_6=CCT;refseq.referenceCodon_7=CCT;refseq.referenceCodon_8=CCT;refseq.spliceDist_1=-127;refseq.spliceDist_2=-127;refseq.spliceDist_3=-127;refseq.spliceDist_4=-127;refseq.spliceDist_5=-127;refseq.spliceDist_6=-127;refseq.spliceDist_7=-127;refseq.spliceDist_8=-127;refseq.start_1=10019169;refseq.start_2=10019169;refseq.start_3=10019169;refseq.start_4=10019169;refseq.start_5=10019169;refseq.start_6=10019169;refseq.start_7=10019169;refseq.start_8=10019169;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Ala;refseq.variantAA_6=Ala;refseq.variantAA_7=Ser;refseq.variantAA_8=Ser;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;refseq.variantCodon_3=CCT;refseq.variantCodon_4=CCT;refseq.variantCodon_5=GCT;refseq.variantCodon_6=GCT;refseq.variantCodon_7=TCT;refseq.variantCodon_8=TCT	GT:DP:GQ:PL	0/0:4:12:0,12,138	0/0:6:18:0,18,211	0/0:4:12:0,12,144
-20	10032432	rs78089752	A	.	367.04	PASS	AC=0;AF=0.00;AN=6;DBSNP132;DP=18;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.1765A>A;refseq.codingCoordStr_2=c.1765A>A;refseq.codingCoordStr_3=c.1765A>C;refseq.codingCoordStr_4=c.1765A>C;refseq.codingCoordStr_5=c.1765A>G;refseq.codingCoordStr_6=c.1765A>G;refseq.codingCoordStr_7=c.1765A>T;refseq.codingCoordStr_8=c.1765A>T;refseq.codonCoord_1=589;refseq.codonCoord_2=589;refseq.codonCoord_3=589;refseq.codonCoord_4=589;refseq.codonCoord_5=589;refseq.codonCoord_6=589;refseq.codonCoord_7=589;refseq.codonCoord_8=589;refseq.end_1=10032432;refseq.end_2=10032432;refseq.end_3=10032432;refseq.end_4=10032432;refseq.end_5=10032432;refseq.end_6=10032432;refseq.end_7=10032432;refseq.end_8=10032432;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.haplotypeReference_6=A;refseq.haplotypeReference_7=A;refseq.haplotypeReference_8=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=2158;refseq.mrnaCoord_2=2094;refseq.mrnaCoord_3=2158;refseq.mrnaCoord_4=2094;refseq.mrnaCoord_5=2158;refseq.mrnaCoord_6=2094;refseq.mrnaCoord_7=2158;refseq.mrnaCoord_8=2094;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.I589I;refseq.proteinCoordStr_2=p.I589I;refseq.proteinCoordStr_3=p.I589L;refseq.proteinCoordStr_4=p.I589L;refseq.proteinCoordStr_5=p.I589V;refseq.proteinCoordStr_6=p.I589V;refseq.proteinCoordStr_7=p.I589F;refseq.proteinCoordStr_8=p.I589F;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceAA_5=Ile;refseq.referenceAA_6=Ile;refseq.referenceAA_7=Ile;refseq.referenceAA_8=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.referenceCodon_3=ATC;refseq.referenceCodon_4=ATC;refseq.referenceCodon_5=ATC;refseq.referenceCodon_6=ATC;refseq.referenceCodon_7=ATC;refseq.referenceCodon_8=ATC;refseq.spliceDist_1=-106;refseq.spliceDist_2=-106;refseq.spliceDist_3=-106;refseq.spliceDist_4=-106;refseq.spliceDist_5=-106;refseq.spliceDist_6=-106;refseq.spliceDist_7=-106;refseq.spliceDist_8=-106;refseq.start_1=10032432;refseq.start_2=10032432;refseq.start_3=10032432;refseq.start_4=10032432;refseq.start_5=10032432;refseq.start_6=10032432;refseq.start_7=10032432;refseq.start_8=10032432;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantAA_5=Val;refseq.variantAA_6=Val;refseq.variantAA_7=Phe;refseq.variantAA_8=Phe;refseq.variantCodon_1=ATC;refseq.variantCodon_2=ATC;refseq.variantCodon_3=CTC;refseq.variantCodon_4=CTC;refseq.variantCodon_5=GTC;refseq.variantCodon_6=GTC;refseq.variantCodon_7=TTC;refseq.variantCodon_8=TTC	GT:DP:GQ:PL	0/0:5:15:0,15,175	0/0:8:24:0,24,293	0/0:5:15:0,15,182
-20	10037119	.	G	.	469.85	PASS	AC=0;AF=0.00;AN=4;DBSNP129;DP=3;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.*811G>A;refseq.codingCoordStr_2=c.*811G>A;refseq.codingCoordStr_3=c.*811G>C;refseq.codingCoordStr_4=c.*811G>C;refseq.codingCoordStr_5=c.*811G>G;refseq.codingCoordStr_6=c.*811G>G;refseq.codingCoordStr_7=c.*811G>T;refseq.codingCoordStr_8=c.*811G>T;refseq.end_1=10037119;refseq.end_2=10037119;refseq.end_3=10037119;refseq.end_4=10037119;refseq.end_5=10037119;refseq.end_6=10037119;refseq.end_7=10037119;refseq.end_8=10037119;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=3535;refseq.mrnaCoord_2=3471;refseq.mrnaCoord_3=3535;refseq.mrnaCoord_4=3471;refseq.mrnaCoord_5=3535;refseq.mrnaCoord_6=3471;refseq.mrnaCoord_7=3535;refseq.mrnaCoord_8=3471;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.positionType_3=utr3;refseq.positionType_4=utr3;refseq.positionType_5=utr3;refseq.positionType_6=utr3;refseq.positionType_7=utr3;refseq.positionType_8=utr3;refseq.spliceDist_1=-289;refseq.spliceDist_2=-289;refseq.spliceDist_3=-289;refseq.spliceDist_4=-289;refseq.spliceDist_5=-289;refseq.spliceDist_6=-289;refseq.spliceDist_7=-289;refseq.spliceDist_8=-289;refseq.start_1=10037119;refseq.start_2=10037119;refseq.start_3=10037119;refseq.start_4=10037119;refseq.start_5=10037119;refseq.start_6=10037119;refseq.start_7=10037119;refseq.start_8=10037119;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:GQ:PL	./.	0/0:2:6:0,6,65	0/0:1:3:0,3,37
-20	10047435	rs598275	G	A	82495.04	PASS	AC=6;AF=1.00;AN=6;DBSNP129;DBSNP132;DP=8;HAPMAP;OMNI	GT:DP:GQ:PL	1/1:2:6:69,6,0	1/1:2:6:69,6,0	1/1:4:12:139,12,0

public/testdata/FundamentalsTest.annotated.db.subset.final.vcf

@@ -1,23 +0,0 @@
-##fileformat=VCFv4.0
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
-##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
-##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
-##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
-##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
-20	10003358	rs926982	A	C	92318.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=7	GT:DP:GQ:PL	1/1:1:3:34,3,0	0/1:5:51:51,0,95	1/1:1:3:27,3,0
-20	10003692	rs2064653	A	G	119873.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=9	GT:DP:GQ:PL	1/1:2:6:66,6,0	0/1:4:20:20,0,85	1/1:3:9:112,9,0
-20	10015679	rs113024248	C	.	2829.33	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;OMNI	GT:DP:PL	./.	./.	./.
-20	10015790	rs114356776	G	.	43.60	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.-300G>A;refseq.codingCoordStr_2=c.-236G>A;refseq.codingCoordStr_3=c.-300G>C;refseq.codingCoordStr_4=c.-236G>C;refseq.codingCoordStr_5=c.-300G>G;refseq.codingCoordStr_6=c.-236G>G;refseq.codingCoordStr_7=c.-300G>T;refseq.codingCoordStr_8=c.-236G>T;refseq.end_1=10015790;refseq.end_2=10015790;refseq.end_3=10015790;refseq.end_4=10015790;refseq.end_5=10015790;refseq.end_6=10015790;refseq.end_7=10015790;refseq.end_8=10015790;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=94;refseq.mrnaCoord_2=94;refseq.mrnaCoord_3=94;refseq.mrnaCoord_4=94;refseq.mrnaCoord_5=94;refseq.mrnaCoord_6=94;refseq.mrnaCoord_7=94;refseq.mrnaCoord_8=94;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.positionType_3=utr5;refseq.positionType_4=utr5;refseq.positionType_5=utr5;refseq.positionType_6=utr5;refseq.positionType_7=utr5;refseq.positionType_8=utr5;refseq.spliceDist_1=94;refseq.spliceDist_2=94;refseq.spliceDist_3=94;refseq.spliceDist_4=94;refseq.spliceDist_5=94;refseq.spliceDist_6=94;refseq.spliceDist_7=94;refseq.spliceDist_8=94;refseq.start_1=10015790;refseq.start_2=10015790;refseq.start_3=10015790;refseq.start_4=10015790;refseq.start_5=10015790;refseq.start_6=10015790;refseq.start_7=10015790;refseq.start_8=10015790;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:PL	./.	./.	./.
-20	10019093	rs575534	A	G	69795.04	PASS	AC=3;AF=0.50;AN=6;DBSNP129;DBSNP132;DP=14;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=20;refseq.chr_2=20;refseq.codingCoordStr_1=c.144A>G;refseq.codingCoordStr_2=c.144A>G;refseq.codonCoord_1=48;refseq.codonCoord_2=48;refseq.end_1=10019093;refseq.end_2=10019093;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=537;refseq.mrnaCoord_2=473;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G48G;refseq.proteinCoordStr_2=p.G48G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=188;refseq.spliceDist_2=188;refseq.start_1=10019093;refseq.start_2=10019093;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG	GT:DP:GQ:PL	0/1:3:24:24,0,60	0/0:6:18:0,18,211	1/1:5:15:172,15,0
-20	10019169	rs7260784	C	.	1193.61	PASS	AC=0;AF=0.00;AN=6;DBSNP129;DBSNP132;DP=14;HAPMAP;OMNI;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.220C>A;refseq.codingCoordStr_2=c.220C>A;refseq.codingCoordStr_3=c.220C>C;refseq.codingCoordStr_4=c.220C>C;refseq.codingCoordStr_5=c.220C>G;refseq.codingCoordStr_6=c.220C>G;refseq.codingCoordStr_7=c.220C>T;refseq.codingCoordStr_8=c.220C>T;refseq.codonCoord_1=74;refseq.codonCoord_2=74;refseq.codonCoord_3=74;refseq.codonCoord_4=74;refseq.codonCoord_5=74;refseq.codonCoord_6=74;refseq.codonCoord_7=74;refseq.codonCoord_8=74;refseq.end_1=10019169;refseq.end_2=10019169;refseq.end_3=10019169;refseq.end_4=10019169;refseq.end_5=10019169;refseq.end_6=10019169;refseq.end_7=10019169;refseq.end_8=10019169;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.haplotypeReference_7=C;refseq.haplotypeReference_8=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=613;refseq.mrnaCoord_2=549;refseq.mrnaCoord_3=613;refseq.mrnaCoord_4=549;refseq.mrnaCoord_5=613;refseq.mrnaCoord_6=549;refseq.mrnaCoord_7=613;refseq.mrnaCoord_8=549;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.P74T;refseq.proteinCoordStr_2=p.P74T;refseq.proteinCoordStr_3=p.P74P;refseq.proteinCoordStr_4=p.P74P;refseq.proteinCoordStr_5=p.P74A;refseq.proteinCoordStr_6=p.P74A;refseq.proteinCoordStr_7=p.P74S;refseq.proteinCoordStr_8=p.P74S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceAA_5=Pro;refseq.referenceAA_6=Pro;refseq.referenceAA_7=Pro;refseq.referenceAA_8=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.referenceCodon_3=CCT;refseq.referenceCodon_4=CCT;refseq.referenceCodon_5=CCT;refseq.referenceCodon_6=CCT;refseq.referenceCodon_7=CCT;refseq.referenceCodon_8=CCT;refseq.spliceDist_1=-127;refseq.spliceDist_2=-127;refseq.spliceDist_3=-127;refseq.spliceDist_4=-127;refseq.spliceDist_5=-127;refseq.spliceDist_6=-127;refseq.spliceDist_7=-127;refseq.spliceDist_8=-127;refseq.start_1=10019169;refseq.start_2=10019169;refseq.start_3=10019169;refseq.start_4=10019169;refseq.start_5=10019169;refseq.start_6=10019169;refseq.start_7=10019169;refseq.start_8=10019169;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Ala;refseq.variantAA_6=Ala;refseq.variantAA_7=Ser;refseq.variantAA_8=Ser;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;refseq.variantCodon_3=CCT;refseq.variantCodon_4=CCT;refseq.variantCodon_5=GCT;refseq.variantCodon_6=GCT;refseq.variantCodon_7=TCT;refseq.variantCodon_8=TCT	GT:DP:GQ:PL	0/0:4:12:0,12,138	0/0:6:18:0,18,211	0/0:4:12:0,12,144
-20	10032432	rs78089752	A	.	367.04	PASS	AC=0;AF=0.00;AN=6;DBSNP132;DP=18;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.1765A>A;refseq.codingCoordStr_2=c.1765A>A;refseq.codingCoordStr_3=c.1765A>C;refseq.codingCoordStr_4=c.1765A>C;refseq.codingCoordStr_5=c.1765A>G;refseq.codingCoordStr_6=c.1765A>G;refseq.codingCoordStr_7=c.1765A>T;refseq.codingCoordStr_8=c.1765A>T;refseq.codonCoord_1=589;refseq.codonCoord_2=589;refseq.codonCoord_3=589;refseq.codonCoord_4=589;refseq.codonCoord_5=589;refseq.codonCoord_6=589;refseq.codonCoord_7=589;refseq.codonCoord_8=589;refseq.end_1=10032432;refseq.end_2=10032432;refseq.end_3=10032432;refseq.end_4=10032432;refseq.end_5=10032432;refseq.end_6=10032432;refseq.end_7=10032432;refseq.end_8=10032432;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.haplotypeReference_6=A;refseq.haplotypeReference_7=A;refseq.haplotypeReference_8=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=2158;refseq.mrnaCoord_2=2094;refseq.mrnaCoord_3=2158;refseq.mrnaCoord_4=2094;refseq.mrnaCoord_5=2158;refseq.mrnaCoord_6=2094;refseq.mrnaCoord_7=2158;refseq.mrnaCoord_8=2094;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.I589I;refseq.proteinCoordStr_2=p.I589I;refseq.proteinCoordStr_3=p.I589L;refseq.proteinCoordStr_4=p.I589L;refseq.proteinCoordStr_5=p.I589V;refseq.proteinCoordStr_6=p.I589V;refseq.proteinCoordStr_7=p.I589F;refseq.proteinCoordStr_8=p.I589F;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceAA_5=Ile;refseq.referenceAA_6=Ile;refseq.referenceAA_7=Ile;refseq.referenceAA_8=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.referenceCodon_3=ATC;refseq.referenceCodon_4=ATC;refseq.referenceCodon_5=ATC;refseq.referenceCodon_6=ATC;refseq.referenceCodon_7=ATC;refseq.referenceCodon_8=ATC;refseq.spliceDist_1=-106;refseq.spliceDist_2=-106;refseq.spliceDist_3=-106;refseq.spliceDist_4=-106;refseq.spliceDist_5=-106;refseq.spliceDist_6=-106;refseq.spliceDist_7=-106;refseq.spliceDist_8=-106;refseq.start_1=10032432;refseq.start_2=10032432;refseq.start_3=10032432;refseq.start_4=10032432;refseq.start_5=10032432;refseq.start_6=10032432;refseq.start_7=10032432;refseq.start_8=10032432;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantAA_5=Val;refseq.variantAA_6=Val;refseq.variantAA_7=Phe;refseq.variantAA_8=Phe;refseq.variantCodon_1=ATC;refseq.variantCodon_2=ATC;refseq.variantCodon_3=CTC;refseq.variantCodon_4=CTC;refseq.variantCodon_5=GTC;refseq.variantCodon_6=GTC;refseq.variantCodon_7=TTC;refseq.variantCodon_8=TTC	GT:DP:GQ:PL	0/0:5:15:0,15,175	0/0:8:24:0,24,293	0/0:5:15:0,15,182
-20	10037119	.	G	.	469.85	PASS	AC=0;AF=0.00;AN=4;DBSNP129;DP=3;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.*811G>A;refseq.codingCoordStr_2=c.*811G>A;refseq.codingCoordStr_3=c.*811G>C;refseq.codingCoordStr_4=c.*811G>C;refseq.codingCoordStr_5=c.*811G>G;refseq.codingCoordStr_6=c.*811G>G;refseq.codingCoordStr_7=c.*811G>T;refseq.codingCoordStr_8=c.*811G>T;refseq.end_1=10037119;refseq.end_2=10037119;refseq.end_3=10037119;refseq.end_4=10037119;refseq.end_5=10037119;refseq.end_6=10037119;refseq.end_7=10037119;refseq.end_8=10037119;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=3535;refseq.mrnaCoord_2=3471;refseq.mrnaCoord_3=3535;refseq.mrnaCoord_4=3471;refseq.mrnaCoord_5=3535;refseq.mrnaCoord_6=3471;refseq.mrnaCoord_7=3535;refseq.mrnaCoord_8=3471;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.positionType_3=utr3;refseq.positionType_4=utr3;refseq.positionType_5=utr3;refseq.positionType_6=utr3;refseq.positionType_7=utr3;refseq.positionType_8=utr3;refseq.spliceDist_1=-289;refseq.spliceDist_2=-289;refseq.spliceDist_3=-289;refseq.spliceDist_4=-289;refseq.spliceDist_5=-289;refseq.spliceDist_6=-289;refseq.spliceDist_7=-289;refseq.spliceDist_8=-289;refseq.start_1=10037119;refseq.start_2=10037119;refseq.start_3=10037119;refseq.start_4=10037119;refseq.start_5=10037119;refseq.start_6=10037119;refseq.start_7=10037119;refseq.start_8=10037119;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:GQ:PL	./.	0/0:2:6:0,6,65	0/0:1:3:0,3,37
-20	10047435	rs598275	G	A	82495.04	PASS	AC=6;AF=1.00;AN=6;DBSNP129;DBSNP132;DP=8;HAPMAP;OMNI	GT:DP:GQ:PL	1/1:2:6:69,6,0	1/1:2:6:69,6,0	1/1:4:12:139,12,0

public/testdata/FundamentalsTest.annotated.db.subset.snps_and_indels.vcf

@@ -1,26 +0,0 @@
-##fileformat=VCFv4.0
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
-##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
-##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
-##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
-##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
-20	4680094	rs112637437	CCATGGTGGTGGCTGGGGACAGCCT	C	3590.76	PASS	NONCPG;AC=12;AF=0.0625;AN=192;DB;DP=1386;Dels=0.04;HRun=1;HaplotypeScore=3.9792;MQ=57.75;MQ0=6;QD=21.89;SB=-1275.83;sumGLbyD=21.89	GT:DP:GQ:PL	0/0:28:51.14:0,51,1539	0/1:8:99:287,0,160	0/1:10:99:549,0,338
-20	10003358	rs926982	A	C	92318.04	PASS	NONCPG;AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=7	GT:DP:GQ:PL	1/1:1:3:34,3,0	0/1:5:51:51,0,95	1/1:1:3:27,3,0
-20	10003692	rs2064653	A	G	119873.04	PASS	NONCPG;AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=9	GT:DP:GQ:PL	1/1:2:6:66,6,0	0/1:4:20:20,0,85	1/1:3:9:112,9,0
-20	10015679	rs113024248	C	.	2829.33	PASS	CPG;AC=0;AF=0.00;AN=0;DBSNP132;DP=0;OMNI	GT:DP:PL	./.	./.	./.
-20	10015790	rs114356776	G	.	43.60	FAIL	CPG;AC=0;AF=0.00;AN=0;DBSNP132;DP=0;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.-300G>A;refseq.codingCoordStr_2=c.-236G>A;refseq.codingCoordStr_3=c.-300G>C;refseq.codingCoordStr_4=c.-236G>C;refseq.codingCoordStr_5=c.-300G>G;refseq.codingCoordStr_6=c.-236G>G;refseq.codingCoordStr_7=c.-300G>T;refseq.codingCoordStr_8=c.-236G>T;refseq.end_1=10015790;refseq.end_2=10015790;refseq.end_3=10015790;refseq.end_4=10015790;refseq.end_5=10015790;refseq.end_6=10015790;refseq.end_7=10015790;refseq.end_8=10015790;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=94;refseq.mrnaCoord_2=94;refseq.mrnaCoord_3=94;refseq.mrnaCoord_4=94;refseq.mrnaCoord_5=94;refseq.mrnaCoord_6=94;refseq.mrnaCoord_7=94;refseq.mrnaCoord_8=94;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.positionType_3=utr5;refseq.positionType_4=utr5;refseq.positionType_5=utr5;refseq.positionType_6=utr5;refseq.positionType_7=utr5;refseq.positionType_8=utr5;refseq.spliceDist_1=94;refseq.spliceDist_2=94;refseq.spliceDist_3=94;refseq.spliceDist_4=94;refseq.spliceDist_5=94;refseq.spliceDist_6=94;refseq.spliceDist_7=94;refseq.spliceDist_8=94;refseq.start_1=10015790;refseq.start_2=10015790;refseq.start_3=10015790;refseq.start_4=10015790;refseq.start_5=10015790;refseq.start_6=10015790;refseq.start_7=10015790;refseq.start_8=10015790;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:PL	./.	./.	./.
-20	10019093	rs575534	A	G	69795.04	PASS	NONCPG;AC=3;AF=0.50;AN=6;DBSNP129;DBSNP132;DP=14;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=20;refseq.chr_2=20;refseq.codingCoordStr_1=c.144A>G;refseq.codingCoordStr_2=c.144A>G;refseq.codonCoord_1=48;refseq.codonCoord_2=48;refseq.end_1=10019093;refseq.end_2=10019093;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=537;refseq.mrnaCoord_2=473;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G48G;refseq.proteinCoordStr_2=p.G48G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=188;refseq.spliceDist_2=188;refseq.start_1=10019093;refseq.start_2=10019093;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG	GT:DP:GQ:PL	0/1:3:24:24,0,60	0/0:6:18:0,18,211	1/1:5:15:172,15,0
-20	10019169	rs7260784	C	.	1193.61	PASS	NONCPG;AC=0;AF=0.00;AN=6;DBSNP129;DBSNP132;DP=14;HAPMAP;OMNI;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.220C>A;refseq.codingCoordStr_2=c.220C>A;refseq.codingCoordStr_3=c.220C>C;refseq.codingCoordStr_4=c.220C>C;refseq.codingCoordStr_5=c.220C>G;refseq.codingCoordStr_6=c.220C>G;refseq.codingCoordStr_7=c.220C>T;refseq.codingCoordStr_8=c.220C>T;refseq.codonCoord_1=74;refseq.codonCoord_2=74;refseq.codonCoord_3=74;refseq.codonCoord_4=74;refseq.codonCoord_5=74;refseq.codonCoord_6=74;refseq.codonCoord_7=74;refseq.codonCoord_8=74;refseq.end_1=10019169;refseq.end_2=10019169;refseq.end_3=10019169;refseq.end_4=10019169;refseq.end_5=10019169;refseq.end_6=10019169;refseq.end_7=10019169;refseq.end_8=10019169;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.haplotypeReference_7=C;refseq.haplotypeReference_8=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=613;refseq.mrnaCoord_2=549;refseq.mrnaCoord_3=613;refseq.mrnaCoord_4=549;refseq.mrnaCoord_5=613;refseq.mrnaCoord_6=549;refseq.mrnaCoord_7=613;refseq.mrnaCoord_8=549;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.P74T;refseq.proteinCoordStr_2=p.P74T;refseq.proteinCoordStr_3=p.P74P;refseq.proteinCoordStr_4=p.P74P;refseq.proteinCoordStr_5=p.P74A;refseq.proteinCoordStr_6=p.P74A;refseq.proteinCoordStr_7=p.P74S;refseq.proteinCoordStr_8=p.P74S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceAA_5=Pro;refseq.referenceAA_6=Pro;refseq.referenceAA_7=Pro;refseq.referenceAA_8=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.referenceCodon_3=CCT;refseq.referenceCodon_4=CCT;refseq.referenceCodon_5=CCT;refseq.referenceCodon_6=CCT;refseq.referenceCodon_7=CCT;refseq.referenceCodon_8=CCT;refseq.spliceDist_1=-127;refseq.spliceDist_2=-127;refseq.spliceDist_3=-127;refseq.spliceDist_4=-127;refseq.spliceDist_5=-127;refseq.spliceDist_6=-127;refseq.spliceDist_7=-127;refseq.spliceDist_8=-127;refseq.start_1=10019169;refseq.start_2=10019169;refseq.start_3=10019169;refseq.start_4=10019169;refseq.start_5=10019169;refseq.start_6=10019169;refseq.start_7=10019169;refseq.start_8=10019169;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Ala;refseq.variantAA_6=Ala;refseq.variantAA_7=Ser;refseq.variantAA_8=Ser;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;refseq.variantCodon_3=CCT;refseq.variantCodon_4=CCT;refseq.variantCodon_5=GCT;refseq.variantCodon_6=GCT;refseq.variantCodon_7=TCT;refseq.variantCodon_8=TCT	GT:DP:GQ:PL	0/0:4:12:0,12,138	0/0:6:18:0,18,211	0/0:4:12:0,12,144
-20	10032432	rs78089752	A	.	367.04	PASS	NONCPG;AC=0;AF=0.00;AN=6;DBSNP132;DP=18;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.1765A>A;refseq.codingCoordStr_2=c.1765A>A;refseq.codingCoordStr_3=c.1765A>C;refseq.codingCoordStr_4=c.1765A>C;refseq.codingCoordStr_5=c.1765A>G;refseq.codingCoordStr_6=c.1765A>G;refseq.codingCoordStr_7=c.1765A>T;refseq.codingCoordStr_8=c.1765A>T;refseq.codonCoord_1=589;refseq.codonCoord_2=589;refseq.codonCoord_3=589;refseq.codonCoord_4=589;refseq.codonCoord_5=589;refseq.codonCoord_6=589;refseq.codonCoord_7=589;refseq.codonCoord_8=589;refseq.end_1=10032432;refseq.end_2=10032432;refseq.end_3=10032432;refseq.end_4=10032432;refseq.end_5=10032432;refseq.end_6=10032432;refseq.end_7=10032432;refseq.end_8=10032432;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.haplotypeReference_6=A;refseq.haplotypeReference_7=A;refseq.haplotypeReference_8=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=2158;refseq.mrnaCoord_2=2094;refseq.mrnaCoord_3=2158;refseq.mrnaCoord_4=2094;refseq.mrnaCoord_5=2158;refseq.mrnaCoord_6=2094;refseq.mrnaCoord_7=2158;refseq.mrnaCoord_8=2094;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.I589I;refseq.proteinCoordStr_2=p.I589I;refseq.proteinCoordStr_3=p.I589L;refseq.proteinCoordStr_4=p.I589L;refseq.proteinCoordStr_5=p.I589V;refseq.proteinCoordStr_6=p.I589V;refseq.proteinCoordStr_7=p.I589F;refseq.proteinCoordStr_8=p.I589F;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceAA_5=Ile;refseq.referenceAA_6=Ile;refseq.referenceAA_7=Ile;refseq.referenceAA_8=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.referenceCodon_3=ATC;refseq.referenceCodon_4=ATC;refseq.referenceCodon_5=ATC;refseq.referenceCodon_6=ATC;refseq.referenceCodon_7=ATC;refseq.referenceCodon_8=ATC;refseq.spliceDist_1=-106;refseq.spliceDist_2=-106;refseq.spliceDist_3=-106;refseq.spliceDist_4=-106;refseq.spliceDist_5=-106;refseq.spliceDist_6=-106;refseq.spliceDist_7=-106;refseq.spliceDist_8=-106;refseq.start_1=10032432;refseq.start_2=10032432;refseq.start_3=10032432;refseq.start_4=10032432;refseq.start_5=10032432;refseq.start_6=10032432;refseq.start_7=10032432;refseq.start_8=10032432;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantAA_5=Val;refseq.variantAA_6=Val;refseq.variantAA_7=Phe;refseq.variantAA_8=Phe;refseq.variantCodon_1=ATC;refseq.variantCodon_2=ATC;refseq.variantCodon_3=CTC;refseq.variantCodon_4=CTC;refseq.variantCodon_5=GTC;refseq.variantCodon_6=GTC;refseq.variantCodon_7=TTC;refseq.variantCodon_8=TTC	GT:DP:GQ:PL	0/0:5:15:0,15,175	0/0:8:24:0,24,293	0/0:5:15:0,15,182
-20	10037119	.	G	.	469.85	PASS	NONCPG;AC=0;AF=0.00;AN=4;DBSNP129;DP=3;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.*811G>A;refseq.codingCoordStr_2=c.*811G>A;refseq.codingCoordStr_3=c.*811G>C;refseq.codingCoordStr_4=c.*811G>C;refseq.codingCoordStr_5=c.*811G>G;refseq.codingCoordStr_6=c.*811G>G;refseq.codingCoordStr_7=c.*811G>T;refseq.codingCoordStr_8=c.*811G>T;refseq.end_1=10037119;refseq.end_2=10037119;refseq.end_3=10037119;refseq.end_4=10037119;refseq.end_5=10037119;refseq.end_6=10037119;refseq.end_7=10037119;refseq.end_8=10037119;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=3535;refseq.mrnaCoord_2=3471;refseq.mrnaCoord_3=3535;refseq.mrnaCoord_4=3471;refseq.mrnaCoord_5=3535;refseq.mrnaCoord_6=3471;refseq.mrnaCoord_7=3535;refseq.mrnaCoord_8=3471;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.positionType_3=utr3;refseq.positionType_4=utr3;refseq.positionType_5=utr3;refseq.positionType_6=utr3;refseq.positionType_7=utr3;refseq.positionType_8=utr3;refseq.spliceDist_1=-289;refseq.spliceDist_2=-289;refseq.spliceDist_3=-289;refseq.spliceDist_4=-289;refseq.spliceDist_5=-289;refseq.spliceDist_6=-289;refseq.spliceDist_7=-289;refseq.spliceDist_8=-289;refseq.start_1=10037119;refseq.start_2=10037119;refseq.start_3=10037119;refseq.start_4=10037119;refseq.start_5=10037119;refseq.start_6=10037119;refseq.start_7=10037119;refseq.start_8=10037119;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:GQ:PL	./.	0/0:2:6:0,6,65	0/0:1:3:0,3,37
-20	10047435	rs598275	G	A	82495.04	FAIL	CPG;AC=6;AF=1.00;AN=6;DBSNP129;DBSNP132;DP=8;HAPMAP;OMNI	GT:DP:GQ:PL	1/1:2:6:69,6,0	1/1:2:6:69,6,0	1/1:4:12:139,12,0
-20	31384616	.	A	AG	12610.94	PASS	NONCPG;AC=96;AF=0.5000;AN=192;DP=5288;Dels=0.00;HRun=2;HaplotypeScore=9.2447;MQ=61.14;MQ0=0;QD=2.38;SB=-2.03;sumGLbyD=2.39	GT:DP:GQ:PL	0/1:50:99:161,0,486	0/1:55:99:123,0,615	0/1:51:87.95:88,0,647
-20	62172300	.	CGG	C	440.96	FAIL	CPG;AC=25;AF=0.1316;AN=190;DP=2673;Dels=0.01;HRun=1;HaplotypeScore=12.2310;MQ=58.24;MQ0=0;QD=0.63;SB=-58.90;sumGLbyD=1.00	GT:DP:GQ:PL	0/0:29:45.69:0,46,1437	0/0:16:16.13:0,16,799	0/1:31:32.81:33,0,1141