Package htsjdk.tribble

Examples of htsjdk.tribble.TribbleException

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            if ( contextMatchesLoc(vc, loc) ) {
                final Allele myRef = vc.getReference();
                if ( ref == null || ref.length() < myRef.length() )
                    ref = myRef;
                else if ( ref.length() == myRef.length() && ! ref.equals(myRef) )
                    throw new TribbleException(String.format("The provided variant file(s) have inconsistent references for the same position(s) at %s:%d, %s vs. %s", vc.getChr(), vc.getStart(), ref, myRef));
            }
        }

        return ref;
    }
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    @Override
    public Feature decodeLoc(final LineIterator lineIterator) {
        final String line = lineIterator.next();
        if (line.startsWith("#")) return null;
        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);
        String contig_name = fields[2];
        try {
            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]+")");
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    public RefSeqFeature decode(String line) {
        if (line.startsWith("#")) return null;
        String fields[] = line.split("\t");

        // we reference postion 15 in the split array below, make sure we have at least that many columns
        if (fields.length < 16) throw new TribbleException("RefSeq (decode) : Unable to parse line -> " + line + ", we expected at least 16 columns, we saw " + fields.length);
        String contig_name = fields[2];
        RefSeqFeature feature = new RefSeqFeature(genomeLocParser.createGenomeLoc(contig_name, Integer.parseInt(fields[4])+1, Integer.parseInt(fields[5])));

        feature.setTranscript_id(fields[1]);
        if ( fields[3].length()==1 && fields[3].charAt(0)=='+') feature.setStrand(1);
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Related Classes of htsjdk.tribble.TribbleException

  • org.broadinstitute.gatk.utils.codecs.refseq.RefSeqCodec
  • org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils
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