Examples of FeatureToGATKFeatureIterator

org.broadinstitute.gatk.engine.refdata.utils.FeatureToGATKFeatureIterator
@author aaron Class FeatureToGATKFeatureIterator a wrapper on Tribble feature iterators so that they produce GATKFeatures (which produce GenomeLocs)

Examples of org.broadinstitute.gatk.engine.refdata.utils.FeatureToGATKFeatureIterator

     * @return how to get an iterator of the underlying data.  This is all a track has to support,
     *         but other more advanced tracks support the query interface
     */
    public CloseableIterator<GATKFeature> getIterator() {
        try {
            return new FeatureToGATKFeatureIterator(genomeLocParser,reader.iterator(),this.getName());
        } catch (IOException e) {
            throw new UserException.CouldNotReadInputFile(getFile(), "Unable to read from file", e);
        }
    }

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Examples of org.broadinstitute.gatk.engine.refdata.utils.FeatureToGATKFeatureIterator

        }
    }


    public CloseableIterator<GATKFeature> query(GenomeLoc interval) throws IOException {
        CloseableTribbleIterator<Feature> iter = reader.query(interval.getContig(),interval.getStart(),interval.getStop());
        return new FeatureToGATKFeatureIterator(genomeLocParser, iter, this.getName());
    }

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