Renaming the HapMap codec and feature to RawHapMap so that we don't get esoteric errors when trying to bind a rod with the name 'hapmap' (since it was also a feature).

2011-08-12 11:11:56 -04:00 · 2011-08-12 11:11:56 -04:00 · 27f0748b33
parent f5b2cc4977
commit 27f0748b33
6 changed files with 40 additions and 40 deletions
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
@ -6,7 +6,7 @@ import org.broad.tribble.gelitext.GeliTextFeature;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
-import org.broadinstitute.sting.utils.codecs.hapmap.HapMapFeature;
+import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.variantcontext.*;
@ -226,7 +226,7 @@ public class VariantContextAdaptors {
         * @return HapMapFeature.
         */
        @Override
-        public Class<? extends Feature> getAdaptableFeatureType() { return HapMapFeature.class; }
+        public Class<? extends Feature> getAdaptableFeatureType() { return RawHapMapFeature.class; }

        /**
         * convert to a Variant Context, given:
@ -240,7 +240,7 @@ public class VariantContextAdaptors {
            if ( ref == null )
                throw new UnsupportedOperationException("Conversion from HapMap to VariantContext requires a reference context");

-            HapMapFeature hapmap = (HapMapFeature)input;
+            RawHapMapFeature hapmap = (RawHapMapFeature)input;

            int index = hapmap.getStart() - ref.getWindow().getStart();
            if ( index < 0 )
@ -255,7 +255,7 @@ public class VariantContextAdaptors {
            // use the actual alleles, if available
            if ( alleleMap != null ) {
                alleles.addAll(alleleMap.values());
-                Allele deletionAllele = alleleMap.get(HapMapFeature.INSERTION);  // yes, use insertion here (since we want the reference bases)
+                Allele deletionAllele = alleleMap.get(RawHapMapFeature.INSERTION);  // yes, use insertion here (since we want the reference bases)
                if ( deletionAllele != null && deletionAllele.isReference() )
                    deletionLength = deletionAllele.length();
            } else {
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
@ -40,7 +40,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.hapmap.HapMapFeature;
+import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
@ -124,19 +124,19 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
        for ( Feature record : features ) {
            if ( VariantContextAdaptors.canBeConvertedToVariantContext(record) ) {
                // we need to special case the HapMap format because indels aren't handled correctly
-                if ( record instanceof HapMapFeature) {
+                if ( record instanceof RawHapMapFeature) {

                    // is it an indel?
-                    HapMapFeature hapmap = (HapMapFeature)record;
-                    if ( hapmap.getAlleles()[0].equals(HapMapFeature.NULL_ALLELE_STRING) || hapmap.getAlleles()[1].equals(HapMapFeature.NULL_ALLELE_STRING) ) {
+                    RawHapMapFeature hapmap = (RawHapMapFeature)record;
+                    if ( hapmap.getAlleles()[0].equals(RawHapMapFeature.NULL_ALLELE_STRING) || hapmap.getAlleles()[1].equals(RawHapMapFeature.NULL_ALLELE_STRING) ) {
                        // get the dbsnp object corresponding to this record (needed to help us distinguish between insertions and deletions)
                        VariantContext dbsnpVC = getDbsnp(hapmap.getName());
                        if ( dbsnpVC == null || dbsnpVC.isMixed() )
                            continue;

                        Map<String, Allele> alleleMap = new HashMap<String, Allele>(2);
-                        alleleMap.put(HapMapFeature.DELETION, Allele.create(Allele.NULL_ALLELE_STRING, dbsnpVC.isInsertion()));
-                        alleleMap.put(HapMapFeature.INSERTION, Allele.create(((HapMapFeature)record).getAlleles()[1], !dbsnpVC.isInsertion()));
+                        alleleMap.put(RawHapMapFeature.DELETION, Allele.create(Allele.NULL_ALLELE_STRING, dbsnpVC.isInsertion()));
+                        alleleMap.put(RawHapMapFeature.INSERTION, Allele.create(((RawHapMapFeature)record).getAlleles()[1], !dbsnpVC.isInsertion()));
                        hapmap.setActualAlleles(alleleMap);

                        // also, use the correct positioning for insertions
@ -212,8 +212,8 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
                        throw new IllegalStateException("No rod data is present, but we just created a VariantContext");

                    Feature f = features.get(0);
-                    if ( f instanceof HapMapFeature )
-                        samples.addAll(Arrays.asList(((HapMapFeature)f).getSampleIDs()));
+                    if ( f instanceof RawHapMapFeature )
+                        samples.addAll(Arrays.asList(((RawHapMapFeature)f).getSampleIDs()));
                    else
                        samples.addAll(vc.getSampleNames());
                }
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java
@ -40,7 +40,7 @@ import java.util.Arrays;
 * in the file
 * 
 */
-public class HapMapCodec implements FeatureCodec {
+public class RawHapMapCodec implements FeatureCodec {
    // the minimum number of features in the HapMap file line
    private static final int minimumFeatureCount = 11;

@ -67,7 +67,7 @@ public class HapMapCodec implements FeatureCodec {
            throw new IllegalArgumentException("Unable to parse line " + line + ", the length of split features is less than the minimum of " + minimumFeatureCount);

        // create a new feature given the array
-        return new HapMapFeature(array[0],
+        return new RawHapMapFeature(array[0],
                array[1].split("/"),
                array[2],
                Long.valueOf(array[3]),
@ -83,7 +83,7 @@ public class HapMapCodec implements FeatureCodec {
    }

    public Class getFeatureType() {
-        return HapMapFeature.class;
+        return RawHapMapFeature.class;
    }

    public Object readHeader(LineReader reader) {
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapFeature.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapFeature.java
@ -35,7 +35,7 @@ import java.util.Map;
 * a feature returned by the HapMap Codec - it represents contig, position, name,
 * alleles, other hapmap information, and genotypes for specified samples
 */
-public class HapMapFeature implements Feature {
+public class RawHapMapFeature implements Feature {

    public static final String NULL_ALLELE_STRING = "-";
    public static final String INSERTION = "I";
@ -72,19 +72,19 @@ public class HapMapFeature implements Feature {
     * @param qccode ??
     * @param genotypes a list of strings, representing the genotypes for the list of samples
     */
-    public HapMapFeature(String name,
-                         String[] alleles,
-                         String contig,
-                         Long position,
-                         Strand strand,
-                         String assembly,
-                         String center,
-                         String protLSID,
-                         String assayLSID,
-                         String panelLSID,
-                         String qccode,
-                         String[] genotypes,
-                         String headerLine) {
+    public RawHapMapFeature(String name,
+                            String[] alleles,
+                            String contig,
+                            Long position,
+                            Strand strand,
+                            String assembly,
+                            String center,
+                            String protLSID,
+                            String assayLSID,
+                            String panelLSID,
+                            String qccode,
+                            String[] genotypes,
+                            String headerLine) {
        this.name = name;
        this.alleles = alleles;
        this.contig = contig;
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
@ -76,7 +76,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {

        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                "-R " + b36KGReference +
-                        " --variant:HapMap " + validationDataLocation + "rawHapMap.yri.chr1.txt" +
+                        " --variant:RawHapMap " + validationDataLocation + "rawHapMap.yri.chr1.txt" +
                        " -T VariantsToVCF" +
                        " -L 1:1-1,000,000" +
                        " -o %s" +
--- a/public/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java
@ -49,12 +49,12 @@ public class HapMapUnitTest {
     */
    @Test
    public void testReadHeader() {
-        HapMapCodec codec = new HapMapCodec();
+        RawHapMapCodec codec = new RawHapMapCodec();
        AsciiLineReader reader = getReader();
        try {
            String header = reader.readLine();
            reader.close();
-            Assert.assertTrue(header.equals((String)codec.readHeader(getReader())));
+            Assert.assertTrue(header.equals(codec.readHeader(getReader())));
        } catch (IOException e) {
            Assert.fail("Unable to read from file " + hapMapFile);
        }
@ -63,8 +63,8 @@ public class HapMapUnitTest {

    @Test
    public void testKnownRecordConversion() {
-        HapMapCodec codec = new HapMapCodec();
-        HapMapFeature feature = (HapMapFeature)codec.decode(knownLine);
+        RawHapMapCodec codec = new RawHapMapCodec();
+        RawHapMapFeature feature = (RawHapMapFeature)codec.decode(knownLine);


        // check that the alleles are right
@ -110,16 +110,16 @@ public class HapMapUnitTest {
    @Test
    public void testReadCorrectNumberOfRecords() {
        // setup the record for reading our 500 line file (499 records, 1 header line)
-        HapMapCodec codec = new HapMapCodec();
+        RawHapMapCodec codec = new RawHapMapCodec();
        AsciiLineReader reader = getReader();

-        String line = null;
+        String line;
        int count = 0;
        try {
            codec.readHeader(reader);
            line = reader.readLine();
            while (line != null) {
-                HapMapFeature feature = (HapMapFeature) codec.decode(line);
+                codec.decode(line);
                line = reader.readLine();
                ++count;
            }
@ -133,14 +133,14 @@ public class HapMapUnitTest {
    @Test
    public void testGetSampleNames() {
        // setup the record for reading our 500 line file (499 records, 1 header line)
-        HapMapCodec codec = new HapMapCodec();
+        RawHapMapCodec codec = new RawHapMapCodec();
        AsciiLineReader reader = getReader();

-        String line = null;
+        String line;
        try {
            codec.readHeader(reader);
            line = reader.readLine();
-            HapMapFeature feature = (HapMapFeature) codec.decode(line);
+            RawHapMapFeature feature = (RawHapMapFeature) codec.decode(line);
            Assert.assertEquals(feature.getSampleIDs().length,87);

        } catch (IOException e) {