Examples of RODRecordList

org.broadinstitute.gatk.engine.refdata.utils.RODRecordList
@author aaron
Class RODRecordList
make the RODRecord list an interface, so we can stub in other implementations during testing.

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

        return ! queue.isEmpty();
    }


    public RODRecordList next() {
        Element e = queue.poll();
        RODRecordList value = e.next(); // next() will also update next location cached by the Element


        if ( e.nextLoc != null ) // we have more data in the track
            queue.add(e); // add the element back to queue (note: its next location, on which priority is based, was updated


        //System.out.printf("Element is %s%n", e.value);

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


            return nextLoc.compareTo(other.nextLoc);
        }


        public RODRecordList next() {
            RODRecordList value = it.next();
            update();
            return value;
        }

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

                                                  List<T> values,
                                                  final GenomeLoc curLocation,
                                                  final boolean requireStartHere,
                                                  final boolean takeFirstOnly ) {
        for ( String name : names ) {
            RODRecordList rodList = getTrackDataByName(name); // require that the name is an exact match
            values = addValues(name, type, values, rodList, curLocation, requireStartHere, takeFirstOnly );
            if ( takeFirstOnly && ! values.isEmpty() )
                break;
        }

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

     * @param name                track name
     * @return track data for the given rod
     */
    private RODRecordList getTrackDataByName(final String name) {
        final String luName = canonicalName(name);
        RODRecordList l = bindings.get(luName);
        return l == null ? EMPTY_ROD_RECORD_LIST : l;
    }

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

     * @return Next covered locus context in the shard.
     * @throw NoSuchElementException if no such element exists.
     */
    public AlignmentContext next() {
        if ( DEBUG ) System.out.printf("In RodLocusView.next()...%n");
        RODRecordList datum = rodQueue.next();
        if ( DEBUG ) System.out.printf("In RodLocusView.next(); datum = %s...%n", datum.getLocation());


        if ( DEBUG ) System.out.printf("In RodLocusView.next(): creating tracker...%n");


        allTracksHere = getSpanningTracks(datum);
        GenomeLoc rodSite = datum.getLocation();
        GenomeLoc site = genomeLocParser.createGenomeLoc( rodSite.getContig(), rodSite.getStart(), rodSite.getStart());


        if ( DEBUG ) System.out.printf("rodLocusView.next() is at %s%n", site);


        // calculate the number of skipped bases, and update lastLoc so we can do that again in the next()

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

    //blatantly stolen from Andrew Kernytsky
    private String getGeneName(GenomeLoc target, LocationAwareSeekableRODIterator refseqIterator) {
        logger.debug("Examining "+target.toString());
        if (refseqIterator == null) { return "UNKNOWN"; }


        RODRecordList annotationList = refseqIterator.seekForward(target);
        logger.debug("Annotation list is " + (annotationList == null ? "null" : annotationList.getName()));
        if (annotationList == null) { return "UNKNOWN"; }


        for(GATKFeature rec : annotationList) {
            if ( ((RefSeqFeature)rec.getUnderlyingObject()).overlapsExonP(target) ) {
                logger.debug("We do overlap "+ rec.getUnderlyingObject().toString());

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

        }
    }


    private void testRODStream(final ReadMetaDataTrackerRODStreamTest test, final IntervalOverlappingRODsFromStream stream, final List<GenomeLoc> intervals) {
        for ( final GenomeLoc interval : intervals ) {
            final RODRecordList query = stream.getOverlapping(interval);
            final HashSet<Feature> queryFeatures = new HashSet<Feature>();
            for ( final GATKFeature f : query ) queryFeatures.add((Feature)f.getUnderlyingObject());
            final Set<Feature> overlaps = test.getExpectedOverlaps(interval);


            Assert.assertEquals(queryFeatures.size(), overlaps.size(), "IntervalOverlappingRODsFromStream didn't return the expected set of overlapping features." +

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