Package org.broadinstitute.gatk.engine.refdata

Examples of org.broadinstitute.gatk.engine.refdata.RODRecordListImpl

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    public RODRecordList getOverlapping(final GenomeLoc loc) {
        if ( lastQuery != null && loc.getStart() < lastQuery.getStart() )
            throw new IllegalArgumentException(String.format("BUG: query interval (%s) starts before the previous interval %s", loc, lastQuery));

        readOverlappingFutureFeatures(loc);
        return new RODRecordListImpl(name, subsetToOverlapping(loc, currentFeatures), loc);
    }
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            GenomeLoc loc = first.getLocation();
            for ( final GATKFeature feature : myFeatures )
                loc = loc.merge(feature.getLocation());

            return new RODRecordListImpl(name, myFeatures, loc); // is this safe?
        }
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Related Classes of org.broadinstitute.gatk.engine.refdata.RODRecordListImpl

  • org.broadinstitute.gatk.engine.datasources.providers.IntervalOverlappingRODsFromStream
  • org.broadinstitute.gatk.engine.datasources.providers.IntervalReferenceOrderedViewUnitTest$TribbleIteratorFromCollection
  • org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException
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