SamRecordIntervalIteratorFactory.java

/*
 * The MIT License
 *
 * Copyright (c) 2010 The Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
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 * The above copyright notice and this permission notice shall be included in
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 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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package htsjdk.samtools.util;

import htsjdk.samtools.QueryInterval;
import htsjdk.samtools.SAMFileReader;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.filter.IntervalFilter;
import htsjdk.samtools.filter.SamRecordFilter;

import java.util.Iterator;
import java.util.List;
import java.util.NoSuchElementException;

/**
 * Create an iterator over a SAMFileReader that only returns reads that overlap one of the intervals
 * in an interval list.
 *
 * @author alecw@broadinstitute.org
 */
public class SamRecordIntervalIteratorFactory {

    /**
     * @param samReader
     * @param uniqueIntervals list of intervals of interest, with overlaps merged, in coordinate order
     * @param useIndex if false, do not use a BAM index even if it is present.
     * @return an iterator that will be filtered so that only SAMRecords overlapping the intervals
     * in uniqueIntervals will be returned.  If a BAM index is available, it will be used to improve performance.
     * Note however that if there are many intervals that cover a great deal of the genome, using the BAM
     * index may actually make performance worse.
     */
    public CloseableIterator<SAMRecord> makeSamRecordIntervalIterator(final SAMFileReader samReader,
                                                               final List<Interval> uniqueIntervals,
                                                               final boolean useIndex) {
        if (!samReader.hasIndex() || !useIndex) {
            final int stopAfterSequence;
            final int stopAfterPosition;
            if (uniqueIntervals.isEmpty()) {
                stopAfterSequence = -1;
                stopAfterPosition = -1;
            } else {
                final Interval lastInterval = uniqueIntervals.get(uniqueIntervals.size() - 1);
                stopAfterSequence = samReader.getFileHeader().getSequenceIndex(lastInterval.getSequence());
                stopAfterPosition = lastInterval.getEnd();
            }
            final IntervalFilter intervalFilter = new IntervalFilter(uniqueIntervals, samReader.getFileHeader());
            return new StopAfterFilteringIterator(samReader.iterator(), intervalFilter, stopAfterSequence, stopAfterPosition);
        } else {
            final QueryInterval[] queryIntervals = new QueryInterval[uniqueIntervals.size()];
            for (int i = 0; i < queryIntervals.length; ++i) {
                final Interval inputInterval = uniqueIntervals.get(i);
                queryIntervals[i] = samReader.makeQueryInterval(inputInterval.getSequence(),
                        inputInterval.getStart(), inputInterval.getEnd());
            }
            return samReader.queryOverlapping(queryIntervals);
        }
    }

    /**
     * Halt iteration after a read is encountered that starts after the given sequence and position.
     * Note that most of this code is copied from FilteringIterator.  It would be nice just to override getNextRecord,
     * but that method is called FilteringIterator ctor, so the stopAfter members can't be initialized before
     * it is called.
     * FilteringIterator ctor could take a boolean "advance" that would tell it whether or not to call getNextRecord
     * in the ctor, so that it could be delayed in the subclass.  If this pattern happens again, we should do that. 
     */
    private class StopAfterFilteringIterator implements CloseableIterator<SAMRecord> {
        private final int stopAfterSequence;
        private final int stopAfterPosition;
        private final Iterator<SAMRecord> iterator;
        private final SamRecordFilter filter;
        private SAMRecord next = null;

        private StopAfterFilteringIterator(Iterator<SAMRecord> iterator, SamRecordFilter filter,
                                           int stopAfterSequence, int stopAfterPosition) {
            this.stopAfterSequence = stopAfterSequence;
            this.stopAfterPosition = stopAfterPosition;
            this.iterator = iterator;
            this.filter = filter;
            next = getNextRecord();
        }


        /**
         * Returns true if the iteration has more elements.
         *
         * @return  true if the iteration has more elements.  Otherwise returns false.
         */
        public boolean hasNext() {
            return next != null;
        }

        /**
         * Returns the next element in the iteration.
         *
         * @return  the next element in the iteration
         * @throws java.util.NoSuchElementException
         */
        public SAMRecord next() {
            if (next == null) {
                throw new NoSuchElementException("Iterator has no more elements.");
            }
            final SAMRecord result = next;
            next = getNextRecord();
            return result;
        }

        /**
         * Required method for Iterator API.
         *
         * @throws UnsupportedOperationException
         */
        public void remove() {
            throw new UnsupportedOperationException("Remove() not supported by FilteringIterator");
        }

        public void close() {
            CloserUtil.close(iterator);
        }

        protected SAMRecord getNextRecord() {
            while (iterator.hasNext()) {
                SAMRecord record = iterator.next();
                if (record.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) return null;
                else if (record.getReferenceIndex() > stopAfterSequence) return null;
                else if (record.getReferenceIndex() == stopAfterSequence && record.getAlignmentStart() > stopAfterPosition) {
                    return null;
                }
                if (!filter.filterOut(record)) {
                    return record;
                }
            }
            return null;
        }
    }
}