zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Remove reference dependence in BCF2Codec 

-- Adding BCF2Codec to VCF.jar and associated unit tests

Signed-off-by: Mark DePristo <depristo@broadinstitute.org>
This commit is contained in:
Mark DePristo 2012-07-24 17:22:40 -04:00
parent 19a257a5c1
commit fcefa61bce
3 changed files with 9 additions and 22 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
build.xml
View File

@ -646,7 +646,7 @@
<jar jarfile="${dist.dir}/vcf.jar">
<fileset dir="${java.classes}">
<include name="org/broadinstitute/sting/utils/codecs/vcf/**/*.class"/>
<!-- <include name="org/broadinstitute/sting/utils/codecs/bcf2/**/*.class"/> -->
<include name="org/broadinstitute/sting/utils/codecs/bcf2/**/*.class"/>
<include name="org/broadinstitute/sting/utils/variantcontext/**/*.class"/>
<include name="org/broadinstitute/sting/utils/exceptions/**"/>
<include name="org/broadinstitute/sting/utils/help/DocumentedGATKFeature.class"/>

25
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
View File

@ -26,15 +26,12 @@ package org.broadinstitute.sting.utils.codecs.bcf2;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import net.sf.samtools.SAMSequenceRecord;
import org.apache.log4j.Logger;
import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec;
import org.broad.tribble.FeatureCodecHeader;
import org.broad.tribble.readers.AsciiLineReader;
import org.broad.tribble.readers.PositionalBufferedStream;
import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -44,12 +41,15 @@ import java.io.ByteArrayInputStream;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.*;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* Decode BCF2 files
*/
public final class BCF2Codec implements FeatureCodec<VariantContext>, ReferenceDependentFeatureCodec {
public final class BCF2Codec implements FeatureCodec<VariantContext> {
final protected static Logger logger = Logger.getLogger(BCF2Codec.class);
private final static boolean FORBID_SYMBOLICS = false;
@ -162,7 +162,7 @@ public final class BCF2Codec implements FeatureCodec<VariantContext>, ReferenceD
contigNames.add(contig.getID());
}
} else {
logger.info("Didn't find any contig lines in BCF2 file, falling back (dangerously) to GATK reference dictionary");
throw new UserException.MalformedBCF2("Didn't find any contig lines in BCF2 file header");
}
// create the string dictionary
@ -201,19 +201,6 @@ public final class BCF2Codec implements FeatureCodec<VariantContext>, ReferenceD
}
}
// --------------------------------------------------------------------------------
//
// Reference dependence
//
// --------------------------------------------------------------------------------
@Override
public void setGenomeLocParser(final GenomeLocParser genomeLocParser) {
// initialize contigNames to standard ones in reference
for ( final SAMSequenceRecord contig : genomeLocParser.getContigs().getSequences() )
contigNames.add(contig.getSequenceName());
}
// --------------------------------------------------------------------------------
//
// implicit block

4
public/java/test/org/broadinstitute/sting/utils/variantcontext/VCFJarClassLoadingUnitTest.java
View File

@ -50,12 +50,12 @@ public class VCFJarClassLoadingUnitTest {
ClassLoader classLoader = new URLClassLoader(jarURLs, null);
classLoader.loadClass("org.broadinstitute.sting.utils.variantcontext.VariantContext");
// TODO -- uncomment when we include BCF2 codec
// classLoader.loadClass("org.broadinstitute.sting.utils.codecs.bcf2.BCF2Codec");
classLoader.loadClass("org.broadinstitute.sting.utils.codecs.bcf2.BCF2Codec");
classLoader.loadClass("org.broadinstitute.sting.utils.codecs.vcf.VCFCodec");
classLoader.loadClass("org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec");
classLoader.loadClass("org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter");
classLoader.loadClass("org.broadinstitute.sting.utils.variantcontext.writer.VCFWriter");
classLoader.loadClass("org.broadinstitute.sting.utils.variantcontext.writer.BCF2Writer");
}
/**