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Fixing up the RefSeqCodec so a bad entry in RefSeq (some transcripts are odd and have a negative length which may signify something special (?) ) doesn't cause failure, but issues a warning instead. Integration tests pass. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6021 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2011-06-21 14:07:58 +00:00
parent 7c322780d3
commit c5de06a641
1 changed files with 7 additions and 1 deletions
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6
java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqCodec.java
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@ -6,6 +6,7 @@ import org.broad.tribble.readers.LineReader;
import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec; import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import java.util.ArrayList; import java.util.ArrayList;
@ -35,7 +36,12 @@ public class RefSeqCodec implements ReferenceDependentFeatureCodec<RefSeqFeature
String fields[] = line.split("\t"); String fields[] = line.split("\t");
if (fields.length < 3) throw new TribbleException("RefSeq (decodeLoc) : Unable to parse line -> " + line + ", we expected at least 3 columns, we saw " + fields.length); if (fields.length < 3) throw new TribbleException("RefSeq (decodeLoc) : Unable to parse line -> " + line + ", we expected at least 3 columns, we saw " + fields.length);
String contig_name = fields[2]; String contig_name = fields[2];
try {
return new RefSeqFeature(genomeLocParser.createGenomeLoc(contig_name, Integer.parseInt(fields[4])+1, Integer.parseInt(fields[5]))); return new RefSeqFeature(genomeLocParser.createGenomeLoc(contig_name, Integer.parseInt(fields[4])+1, Integer.parseInt(fields[5])));
} catch ( UserException.MalformedGenomeLoc e ) {
Utils.warnUser("RefSeq file is potentially incorrect, as some transcripts or exons have a negative length ("+fields[2]+")");
return null;
}
} }
/** Fills this object from a text line in RefSeq (UCSC) text dump file */ /** Fills this object from a text line in RefSeq (UCSC) text dump file */