diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java b/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java index a50679052..66d52d1b5 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java @@ -31,6 +31,7 @@ import java.io.IOException; import java.util.ArrayList; import org.apache.log4j.Logger; +import org.broad.tribble.Feature; import org.broad.tribble.FeatureCodec; import org.broad.tribble.exception.CodecLineParsingException; import org.broad.tribble.util.AsciiLineReader; @@ -74,7 +75,11 @@ public class AnnotatorInputTableCodec implements FeatureCodec { private static final String delimiterRegex = "\\s+"; + public Feature decodeLoc(String line) { + return decode(line); + } + public static String[] readHeader(final File source) throws IOException { FileInputStream is = new FileInputStream(source); try { diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java b/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java index f239f9dcc..28ddb28e0 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java @@ -76,6 +76,10 @@ public class SAMPileupCodec implements FeatureCodec { return null; // we don't have a header } + public Feature decodeLoc(String line) { + return decode(line); + } + public SAMPileupFeature decode(String line) { // 0 1 2 3 4 5 6 7 //* chrX 466 T Y 170 170 88 32 ... (piles of read bases and quals follow) diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java b/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java index 893f8a85e..242afb81e 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java @@ -24,6 +24,7 @@ package org.broadinstitute.sting.gatk.refdata.features.samread; +import org.broad.tribble.Feature; import org.broad.tribble.FeatureCodec; import org.broad.tribble.exception.CodecLineParsingException; import org.broad.tribble.util.ParsingUtils; @@ -66,6 +67,10 @@ public class SAMReadCodec implements FeatureCodec { return null; // we haven't stored the header } + public Feature decodeLoc(String line) { + return decode(line); + } + /** * Decode a single line in a SAM text file. * @param line line to decode. diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java b/java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java index 3a150e4cf..432243459 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java @@ -135,6 +135,10 @@ public class VCF4Codec implements FeatureCodec { // a key optimization -- we need a per thread string parts array, so we don't allocate a big array over and over private String[] parts = null; + public Feature decodeLoc(String line) { + return decode(line); + } + public Feature decode(String line) { if ( parts == null ) parts = REQUIRE_HEADER ? new String[header.getColumnCount()] : new String[10000]; // todo -- remove require header diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index 992b36ad6..4194fd03e 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -122,7 +122,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testDBTag() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -D " + GATKDataLocation + "dbsnp_129_b36.rod -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1, - Arrays.asList("05a9dcb87efc65e5c726c201460192d9")); + Arrays.asList("c3e0361af8e98bda1bc3a27260cb2c4a")); executeTest("getting DB tag", spec); } -} \ No newline at end of file +} diff --git a/settings/repository/org.broad/tribble-104.jar b/settings/repository/org.broad/tribble-105.jar similarity index 82% rename from settings/repository/org.broad/tribble-104.jar rename to settings/repository/org.broad/tribble-105.jar index 77a600608..3a994562c 100644 Binary files a/settings/repository/org.broad/tribble-104.jar and b/settings/repository/org.broad/tribble-105.jar differ diff --git a/settings/repository/org.broad/tribble-104.xml b/settings/repository/org.broad/tribble-105.xml similarity index 64% rename from settings/repository/org.broad/tribble-104.xml rename to settings/repository/org.broad/tribble-105.xml index b42a646ec..1254a7d61 100644 --- a/settings/repository/org.broad/tribble-104.xml +++ b/settings/repository/org.broad/tribble-105.xml @@ -1,3 +1,3 @@ - +