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Fix for dynamic type determination for bgzip files 

-- GZipInputStream handles bgzip files under linux, but not mac
-- Added BlockCompressedInputStream test as well, which works properly on bgzip files
This commit is contained in:
Mark DePristo 2011-09-21 15:39:19 -04:00
parent 9f6f0c443c
commit 6bcfce225f
2 changed files with 7 additions and 1 deletions
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6
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
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@ -6,6 +6,7 @@ import org.broad.tribble.FeatureCodec;
import org.broad.tribble.NameAwareCodec;
import org.broad.tribble.TribbleException;
import org.broad.tribble.readers.LineReader;
import org.broad.tribble.util.BlockCompressedInputStream;
import org.broad.tribble.util.ParsingUtils;
import org.broadinstitute.sting.gatk.refdata.SelfScopingFeatureCodec;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@ -590,7 +591,8 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
public final static boolean canDecodeFile(final File potentialInput, final String MAGIC_HEADER_LINE) {
try {
return isVCFStream(new FileInputStream(potentialInput), MAGIC_HEADER_LINE) ||
isVCFStream(new GZIPInputStream(new FileInputStream(potentialInput)), MAGIC_HEADER_LINE);
isVCFStream(new GZIPInputStream(new FileInputStream(potentialInput)), MAGIC_HEADER_LINE) ||
isVCFStream(new BlockCompressedInputStream(new FileInputStream(potentialInput)), MAGIC_HEADER_LINE);
} catch ( FileNotFoundException e ) {
return false;
} catch ( IOException e ) {
@ -608,6 +610,8 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
// return firstLine.startsWith(MAGIC_HEADER_LINE);
} catch ( IOException e ) {
return false;
} catch ( RuntimeException e ) {
return false;
} finally {
try { stream.close(); } catch ( IOException e ) {}
}

2
public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java
View File

@ -56,6 +56,7 @@ public class FeatureManagerUnitTest extends BaseTest {
private static final File VCF3_FILE = new File(validationDataLocation + "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");
private FeatureManager manager;
private GenomeLocParser genomeLocParser;
@ -109,6 +110,7 @@ public class FeatureManagerUnitTest extends BaseTest {
new FMTest(VariantContext.class, VCF3Codec.class, "VCF3", VCF3_FILE);
new FMTest(VariantContext.class, VCFCodec.class, "VCF", VCF4_FILE);
new FMTest(VariantContext.class, VCFCodec.class, "VCF", VCF4_FILE_GZ);
new FMTest(VariantContext.class, VCFCodec.class, "VCF", VCF4_FILE_BGZIP);
new FMTest(TableFeature.class, BedTableCodec.class, "bedtable", null);
return FMTest.getTests(FMTest.class);
}