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Fix RawHapMapCodec so that it can build indexes. Minor fixes to VCF codec.

This commit is contained in:
Eric Banks 2012-10-21 01:29:59 -04:00
parent 841a906f21
commit d44d5b8275
2 changed files with 10 additions and 3 deletions
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9
public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java
View File

@ -25,8 +25,11 @@
package org.broadinstitute.sting.utils.codecs.hapmap; package org.broadinstitute.sting.utils.codecs.hapmap;
import org.broad.tribble.AsciiFeatureCodec; import org.broad.tribble.AsciiFeatureCodec;
import org.broad.tribble.FeatureCodecHeader;
import org.broad.tribble.annotation.Strand; import org.broad.tribble.annotation.Strand;
import org.broad.tribble.readers.AsciiLineReader;
import org.broad.tribble.readers.LineReader; import org.broad.tribble.readers.LineReader;
import org.broad.tribble.readers.PositionalBufferedStream;
import java.io.IOException; import java.io.IOException;
import java.util.Arrays; import java.util.Arrays;
@ -116,4 +119,10 @@ public class RawHapMapCodec extends AsciiFeatureCodec<RawHapMapFeature> {
} }
return headerLine; return headerLine;
} }
@Override
public FeatureCodecHeader readHeader(final PositionalBufferedStream stream) throws IOException {
final AsciiLineReader br = new AsciiLineReader(stream);
return new FeatureCodecHeader(readHeader(br), br.getPosition());
}
} }

4
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
View File

@ -2,8 +2,6 @@ package org.broadinstitute.sting.utils.codecs.vcf;
import org.broad.tribble.TribbleException; import org.broad.tribble.TribbleException;
import org.broad.tribble.readers.LineReader; import org.broad.tribble.readers.LineReader;
import org.broad.tribble.util.ParsingUtils;
import org.broadinstitute.sting.utils.variantcontext.*;
import java.io.IOException; import java.io.IOException;
import java.util.*; import java.util.*;
@ -119,7 +117,7 @@ public class VCFCodec extends AbstractVCFCodec {
// empty set for passes filters // empty set for passes filters
List<String> fFields = new LinkedList<String>(); List<String> fFields = new LinkedList<String>();
// otherwise we have to parse and cache the value // otherwise we have to parse and cache the value
if ( filterString.indexOf(VCFConstants.FILTER_CODE_SEPARATOR) == -1 ) if ( !filterString.contains(VCFConstants.FILTER_CODE_SEPARATOR) )
fFields.add(filterString); fFields.add(filterString);
else else
fFields.addAll(Arrays.asList(filterString.split(VCFConstants.FILTER_CODE_SEPARATOR))); fFields.addAll(Arrays.asList(filterString.split(VCFConstants.FILTER_CODE_SEPARATOR)));