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Fixed long-standing bug in beagle codec that was passing on the header record for decoding

This commit is contained in:
Mark DePristo 2012-05-28 20:17:26 -04:00
parent dcad4b865c
commit 1818c29371
1 changed files with 4 additions and 3 deletions
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7
public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java
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@ -34,8 +34,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import java.io.IOException; import java.io.IOException;
import java.util.ArrayList; import java.util.*;
import java.util.HashMap;
import java.util.regex.Pattern; import java.util.regex.Pattern;
/** /**
@ -70,6 +69,7 @@ public class BeagleCodec extends AsciiFeatureCodec<BeagleFeature> implements Ref
private int markerPosition; private int markerPosition;
private ArrayList<String> sampleNames; private ArrayList<String> sampleNames;
private int expectedTokensPerLine; private int expectedTokensPerLine;
private final static Set<String> HEADER_IDs = new HashSet<String>(Arrays.asList("marker", "I"));
private static final String delimiterRegex = "\\s+"; private static final String delimiterRegex = "\\s+";
@ -180,7 +180,8 @@ public class BeagleCodec extends AsciiFeatureCodec<BeagleFeature> implements Ref
if (tokens.length != expectedTokensPerLine) if (tokens.length != expectedTokensPerLine)
throw new CodecLineParsingException("Incorrect number of fields in Beagle input on line "+line); throw new CodecLineParsingException("Incorrect number of fields in Beagle input on line "+line);
if ( HEADER_IDs.contains(tokens[0]) )
return null;
BeagleFeature bglFeature = new BeagleFeature(); BeagleFeature bglFeature = new BeagleFeature();