Java CloseableTribbleIterator.hasNext方法代码示例

import htsjdk.tribble.CloseableTribbleIterator; //导入方法依赖的package包/类
public static  <F extends Feature, S> int checkFileSorted(File ofile, final FeatureCodec<F, S> codec)
        throws IOException {
    int numlines = 0;

    AbstractFeatureReader<F, S> reader =
            AbstractFeatureReader.getFeatureReader(ofile.getAbsolutePath(), codec, false);
    CloseableTribbleIterator<F> iterator = reader.iterator();

    final Map<String, Feature> visitedChromos = new HashMap<>(40);
    Feature lastFeature = null;
    while (iterator.hasNext()) {
        Feature currentFeature = iterator.next();
        numlines++;

        checkSorted(ofile, lastFeature, currentFeature, visitedChromos);

        lastFeature = currentFeature;
    }

    return numlines;
}
 

import htsjdk.tribble.CloseableTribbleIterator; //导入方法依赖的package包/类
@Override
public Iterator<Feature> query(String chr, int start, int end) throws IOException {

    // Tribble iterators must be closed, so we need to copy the features and insure closure before exiting.
    CloseableTribbleIterator<Feature> iter = null;
    try {
        iter = wrappedReader.query(chr, start, end);
        List<Feature> featureList = new ArrayList<Feature>();
        while (iter.hasNext()) {
            Feature f = iter.next();
            if (f.getStart() > end) {
                break;
            } else if (f.getEnd() < start) {
                continue;
            } else {
                featureList.add(f);
            }
        }
        return featureList.iterator();
    } finally {
        if(iter != null) iter.close();
    }
}
 

import htsjdk.tribble.CloseableTribbleIterator; //导入方法依赖的package包/类
@Override
protected Iterator<Feature> queryRaw(String chr, int start, int end) throws IOException {

    // Tribble iterators must be closed, so we need to copy the features and insure closure before exiting.
    CloseableTribbleIterator<Feature> iter = null;
    try {
        iter = tribbleFeatureReader.query(chr, start, end);
        List<Feature> featureList = new ArrayList<Feature>();
        while (iter.hasNext()) {
            Feature f = iter.next();
            if (f.getStart() > end) {
                break;
            } else if (f.getEnd() < start) {
                continue;
            } else {
                featureList.add(f);
            }
        }
        return featureList.iterator();
    } finally {
        if (iter != null) iter.close();
    }
}
 

import htsjdk.tribble.CloseableTribbleIterator; //导入方法依赖的package包/类
public LongISLNDReadAlignmentMap(final Collection<String> readAlignmentMapFiles) throws IOException {
    for (final String readAlignmentMapFileName : readAlignmentMapFiles) {
        log.info("Reading in read map from " + readAlignmentMapFileName);
        final AbstractFeatureReader<BEDFeature, LineIterator> featureReader = AbstractFeatureReader.getFeatureReader(readAlignmentMapFileName, new BEDCodec(), false);
        try {
            final CloseableTribbleIterator<BEDFeature> featureIterator = featureReader.iterator();
            while (featureIterator.hasNext()) {
                final BEDFeature feature = featureIterator.next();
                readAlignmentMap.put(feature.getName(), new LongISLNDReadMapRecord(feature).toReadMapRecord());
            }
        } finally {
            featureReader.close();
        }
    }
}
 

import htsjdk.tribble.CloseableTribbleIterator; //导入方法依赖的package包/类
@Override
protected int doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsReadable(SEQUENCE_DICTIONARY);
    IOUtil.assertFileIsWritable(OUTPUT);
    try {
        // create a new header that we will assign the dictionary provided by the SAMSequenceDictionaryExtractor to.
        final SAMFileHeader header = new SAMFileHeader();
        final SAMSequenceDictionary samSequenceDictionary = SAMSequenceDictionaryExtractor.extractDictionary(SEQUENCE_DICTIONARY.toPath());
        header.setSequenceDictionary(samSequenceDictionary);
        // set the sort order to be sorted by coordinate, which is actually done below
        // by getting the .uniqued() intervals list before we write out the file
        header.setSortOrder(SAMFileHeader.SortOrder.coordinate);
        final IntervalList intervalList = new IntervalList(header);

        /**
         * NB: BED is zero-based, but a BEDCodec by default (since it is returns tribble Features) has an offset of one,
         * so it returns 1-based starts.  Ugh.  Set to zero.
         */
        final FeatureReader<BEDFeature> bedReader = AbstractFeatureReader.getFeatureReader(INPUT.getAbsolutePath(), new BEDCodec(BEDCodec.StartOffset.ZERO), false);
        final CloseableTribbleIterator<BEDFeature> iterator = bedReader.iterator();
        final ProgressLogger progressLogger = new ProgressLogger(LOG, (int) 1e6);

        while (iterator.hasNext()) {
            final BEDFeature bedFeature = iterator.next();
            final String sequenceName = bedFeature.getContig();
            /**
             * NB: BED is zero-based, so we need to add one here to make it one-based.  Please observe we set the start
             * offset to zero when creating the BEDCodec.
             */
            final int start = bedFeature.getStart() + 1;
            /**
             * NB: BED is 0-based OPEN (which, for the end is equivalent to 1-based closed).
             */
            final int end = bedFeature.getEnd();
            // NB: do not use an empty name within an interval
            String name = bedFeature.getName();
            if (name.isEmpty()) name = null;

            final SAMSequenceRecord sequenceRecord = header.getSequenceDictionary().getSequence(sequenceName);

            // Do some validation
            if (null == sequenceRecord) {
                throw new PicardException(String.format("Sequence '%s' was not found in the sequence dictionary", sequenceName));
            } else if (start < 1) {
                throw new PicardException(String.format("Start on sequence '%s' was less than one: %d", sequenceName, start));
            } else if (sequenceRecord.getSequenceLength() < start) {
                throw new PicardException(String.format("Start on sequence '%s' was past the end: %d < %d", sequenceName, sequenceRecord.getSequenceLength(), start));
            } else if (end < 1) {
                throw new PicardException(String.format("End on sequence '%s' was less than one: %d", sequenceName, end));
            } else if (sequenceRecord.getSequenceLength() < end) {
                throw new PicardException(String.format("End on sequence '%s' was past the end: %d < %d", sequenceName, sequenceRecord.getSequenceLength(), end));
            } else if (end < start - 1) {
                throw new PicardException(String.format("On sequence '%s', end < start-1: %d <= %d", sequenceName, end, start));
            }

            final boolean isNegativeStrand = bedFeature.getStrand() == Strand.NEGATIVE;
            final Interval interval = new Interval(sequenceName, start, end, isNegativeStrand, name);
            intervalList.add(interval);

            progressLogger.record(sequenceName, start);
        }
        CloserUtil.close(bedReader);

        // Sort and write the output
        IntervalList out = intervalList;
        if (SORT) out = out.sorted();
        if (UNIQUE) out = out.uniqued();
        out.write(OUTPUT);

    } catch (final IOException e) {
        throw new RuntimeException(e);
    }

    return 0;
}