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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).

This commit is contained in:
Eric Banks 2011-08-12 11:11:56 -04:00
parent f5b2cc4977
commit 27f0748b33
6 changed files with 40 additions and 40 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -6,7 +6,7 @@ import org.broad.tribble.gelitext.GeliTextFeature;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper; import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
import org.broadinstitute.sting.utils.classloader.PluginManager; 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.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.*; import org.broadinstitute.sting.utils.variantcontext.*;
@ -226,7 +226,7 @@ public class VariantContextAdaptors {
* @return HapMapFeature. * @return HapMapFeature.
*/ */
@Override @Override
public Class<? extends Feature> getAdaptableFeatureType() { return HapMapFeature.class; } public Class<? extends Feature> getAdaptableFeatureType() { return RawHapMapFeature.class; }
/** /**
* convert to a Variant Context, given: * convert to a Variant Context, given:
@ -240,7 +240,7 @@ public class VariantContextAdaptors {
if ( ref == null ) if ( ref == null )
throw new UnsupportedOperationException("Conversion from HapMap to VariantContext requires a reference context"); 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(); int index = hapmap.getStart() - ref.getWindow().getStart();
if ( index < 0 ) if ( index < 0 )
@ -255,7 +255,7 @@ public class VariantContextAdaptors {
// use the actual alleles, if available // use the actual alleles, if available
if ( alleleMap != null ) { if ( alleleMap != null ) {
alleles.addAll(alleleMap.values()); 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() ) if ( deletionAllele != null && deletionAllele.isReference() )
deletionLength = deletionAllele.length(); deletionLength = deletionAllele.length();
} else { } else {

16
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
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@ -40,7 +40,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils; 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.codecs.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Allele;
@ -124,19 +124,19 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
for ( Feature record : features ) { for ( Feature record : features ) {
if ( VariantContextAdaptors.canBeConvertedToVariantContext(record) ) { if ( VariantContextAdaptors.canBeConvertedToVariantContext(record) ) {
// we need to special case the HapMap format because indels aren't handled correctly // 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? // is it an indel?
HapMapFeature hapmap = (HapMapFeature)record; RawHapMapFeature hapmap = (RawHapMapFeature)record;
if ( hapmap.getAlleles()[0].equals(HapMapFeature.NULL_ALLELE_STRING) || hapmap.getAlleles()[1].equals(HapMapFeature.NULL_ALLELE_STRING) ) { 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) // get the dbsnp object corresponding to this record (needed to help us distinguish between insertions and deletions)
VariantContext dbsnpVC = getDbsnp(hapmap.getName()); VariantContext dbsnpVC = getDbsnp(hapmap.getName());
if ( dbsnpVC == null || dbsnpVC.isMixed() ) if ( dbsnpVC == null || dbsnpVC.isMixed() )
continue; continue;
Map<String, Allele> alleleMap = new HashMap<String, Allele>(2); Map<String, Allele> alleleMap = new HashMap<String, Allele>(2);
alleleMap.put(HapMapFeature.DELETION, Allele.create(Allele.NULL_ALLELE_STRING, dbsnpVC.isInsertion())); alleleMap.put(RawHapMapFeature.DELETION, Allele.create(Allele.NULL_ALLELE_STRING, dbsnpVC.isInsertion()));
alleleMap.put(HapMapFeature.INSERTION, Allele.create(((HapMapFeature)record).getAlleles()[1], !dbsnpVC.isInsertion())); alleleMap.put(RawHapMapFeature.INSERTION, Allele.create(((RawHapMapFeature)record).getAlleles()[1], !dbsnpVC.isInsertion()));
hapmap.setActualAlleles(alleleMap); hapmap.setActualAlleles(alleleMap);
// also, use the correct positioning for insertions // 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"); throw new IllegalStateException("No rod data is present, but we just created a VariantContext");
Feature f = features.get(0); Feature f = features.get(0);
if ( f instanceof HapMapFeature ) if ( f instanceof RawHapMapFeature )
samples.addAll(Arrays.asList(((HapMapFeature)f).getSampleIDs())); samples.addAll(Arrays.asList(((RawHapMapFeature)f).getSampleIDs()));
else else
samples.addAll(vc.getSampleNames()); samples.addAll(vc.getSampleNames());
} }

6
public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/HapMapCodec.java → public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java
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@ -40,7 +40,7 @@ import java.util.Arrays;
* in the file * in the file
* *
*/ */
public class HapMapCodec implements FeatureCodec { public class RawHapMapCodec implements FeatureCodec {
// the minimum number of features in the HapMap file line // the minimum number of features in the HapMap file line
private static final int minimumFeatureCount = 11; 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); 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 // create a new feature given the array
return new HapMapFeature(array[0], return new RawHapMapFeature(array[0],
array[1].split("/"), array[1].split("/"),
array[2], array[2],
Long.valueOf(array[3]), Long.valueOf(array[3]),
@ -83,7 +83,7 @@ public class HapMapCodec implements FeatureCodec {
} }
public Class getFeatureType() { public Class getFeatureType() {
return HapMapFeature.class; return RawHapMapFeature.class;
} }
public Object readHeader(LineReader reader) { public Object readHeader(LineReader reader) {

28
public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/HapMapFeature.java → public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapFeature.java
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@ -35,7 +35,7 @@ import java.util.Map;
* a feature returned by the HapMap Codec - it represents contig, position, name, * a feature returned by the HapMap Codec - it represents contig, position, name,
* alleles, other hapmap information, and genotypes for specified samples * 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 NULL_ALLELE_STRING = "-";
public static final String INSERTION = "I"; public static final String INSERTION = "I";
@ -72,19 +72,19 @@ public class HapMapFeature implements Feature {
* @param qccode ?? * @param qccode ??
* @param genotypes a list of strings, representing the genotypes for the list of samples * @param genotypes a list of strings, representing the genotypes for the list of samples
*/ */
public HapMapFeature(String name, public RawHapMapFeature(String name,
String[] alleles, String[] alleles,
String contig, String contig,
Long position, Long position,
Strand strand, Strand strand,
String assembly, String assembly,
String center, String center,
String protLSID, String protLSID,
String assayLSID, String assayLSID,
String panelLSID, String panelLSID,
String qccode, String qccode,
String[] genotypes, String[] genotypes,
String headerLine) { String headerLine) {
this.name = name; this.name = name;
this.alleles = alleles; this.alleles = alleles;
this.contig = contig; this.contig = contig;

2
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
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@ -76,7 +76,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference + "-R " + b36KGReference +
" --variant:HapMap " + validationDataLocation + "rawHapMap.yri.chr1.txt" + " --variant:RawHapMap " + validationDataLocation + "rawHapMap.yri.chr1.txt" +
" -T VariantsToVCF" + " -T VariantsToVCF" +
" -L 1:1-1,000,000" + " -L 1:1-1,000,000" +
" -o %s" + " -o %s" +

20
public/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java
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@ -49,12 +49,12 @@ public class HapMapUnitTest {
*/ */
@Test @Test
public void testReadHeader() { public void testReadHeader() {
HapMapCodec codec = new HapMapCodec(); RawHapMapCodec codec = new RawHapMapCodec();
AsciiLineReader reader = getReader(); AsciiLineReader reader = getReader();
try { try {
String header = reader.readLine(); String header = reader.readLine();
reader.close(); reader.close();
Assert.assertTrue(header.equals((String)codec.readHeader(getReader()))); Assert.assertTrue(header.equals(codec.readHeader(getReader())));
} catch (IOException e) { } catch (IOException e) {
Assert.fail("Unable to read from file " + hapMapFile); Assert.fail("Unable to read from file " + hapMapFile);
} }
@ -63,8 +63,8 @@ public class HapMapUnitTest {
@Test @Test
public void testKnownRecordConversion() { public void testKnownRecordConversion() {
HapMapCodec codec = new HapMapCodec(); RawHapMapCodec codec = new RawHapMapCodec();
HapMapFeature feature = (HapMapFeature)codec.decode(knownLine); RawHapMapFeature feature = (RawHapMapFeature)codec.decode(knownLine);
// check that the alleles are right // check that the alleles are right
@ -110,16 +110,16 @@ public class HapMapUnitTest {
@Test @Test
public void testReadCorrectNumberOfRecords() { public void testReadCorrectNumberOfRecords() {
// setup the record for reading our 500 line file (499 records, 1 header line) // 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(); AsciiLineReader reader = getReader();
String line = null; String line;
int count = 0; int count = 0;
try { try {
codec.readHeader(reader); codec.readHeader(reader);
line = reader.readLine(); line = reader.readLine();
while (line != null) { while (line != null) {
HapMapFeature feature = (HapMapFeature) codec.decode(line); codec.decode(line);
line = reader.readLine(); line = reader.readLine();
++count; ++count;
} }
@ -133,14 +133,14 @@ public class HapMapUnitTest {
@Test @Test
public void testGetSampleNames() { public void testGetSampleNames() {
// setup the record for reading our 500 line file (499 records, 1 header line) // 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(); AsciiLineReader reader = getReader();
String line = null; String line;
try { try {
codec.readHeader(reader); codec.readHeader(reader);
line = reader.readLine(); line = reader.readLine();
HapMapFeature feature = (HapMapFeature) codec.decode(line); RawHapMapFeature feature = (RawHapMapFeature) codec.decode(line);
Assert.assertEquals(feature.getSampleIDs().length,87); Assert.assertEquals(feature.getSampleIDs().length,87);
} catch (IOException e) { } catch (IOException e) {