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SnpEffCodec now implements SelfScopingFeatureCodec so that we no longer have to specify the codec name on the command line for SnpEff files.

This commit is contained in:
David Roazen 2011-08-10 12:56:31 -04:00
parent 577f861f69
commit 0497170bc9
2 changed files with 20 additions and 3 deletions
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19
public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffCodec.java
View File

@ -27,11 +27,16 @@ package org.broadinstitute.sting.utils.codecs.snpEff;
import org.broad.tribble.Feature; import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec; import org.broad.tribble.FeatureCodec;
import org.broad.tribble.TribbleException; import org.broad.tribble.TribbleException;
import org.broad.tribble.readers.AsciiLineReader;
import org.broad.tribble.readers.LineReader; import org.broad.tribble.readers.LineReader;
import org.broadinstitute.sting.gatk.refdata.SelfScopingFeatureCodec;
import static org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants.EffectType; import static org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants.EffectType;
import static org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants.ChangeType; import static org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants.ChangeType;
import static org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants.Zygosity; import static org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants.Zygosity;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException; import java.io.IOException;
/** /**
@ -68,7 +73,7 @@ import java.io.IOException;
* *
* @author David Roazen * @author David Roazen
*/ */
public class SnpEffCodec implements FeatureCodec { public class SnpEffCodec implements FeatureCodec, SelfScopingFeatureCodec {
public static final int EXPECTED_NUMBER_OF_FIELDS = 23; public static final int EXPECTED_NUMBER_OF_FIELDS = 23;
public static final String FIELD_DELIMITER_PATTERN = "\\t"; public static final String FIELD_DELIMITER_PATTERN = "\\t";
@ -255,4 +260,16 @@ public class SnpEffCodec implements FeatureCodec {
} }
} }
} }
public boolean canDecode ( final File potentialInput ) {
try {
LineReader reader = new AsciiLineReader(new FileInputStream(potentialInput));
readHeader(reader);
}
catch ( Exception e ) {
return false;
}
return true;
}
} }

4
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -129,8 +129,8 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test @Test
public void testSnpEffAnnotations() { public void testSnpEffAnnotations() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantAnnotator -R " + b37KGReference + " -NO_HEADER -o %s -A SnpEff --variant:VCF " + "-T VariantAnnotator -R " + b37KGReference + " -NO_HEADER -o %s -A SnpEff --variant " +
validationDataLocation + "1000G.exomes.vcf --snpEffFile:SnpEff " + validationDataLocation + validationDataLocation + "1000G.exomes.vcf --snpEffFile " + validationDataLocation +
"snpEff_1.9.6_1000G.exomes.vcf_hg37.61.out -L 1:26,000,000-26,500,000", "snpEff_1.9.6_1000G.exomes.vcf_hg37.61.out -L 1:26,000,000-26,500,000",
1, 1,
Arrays.asList("c08648a078368c80530bff004b3157f1") Arrays.asList("c08648a078368c80530bff004b3157f1")