Java Code Examples for htsjdk.samtools.util.Interval#getContig()

/** Emits a file with per base coverage if an output file has been set. */
private void emitPerBaseCoverageIfRequested() {
    if (this.perBaseOutput == null) return;

    final PrintWriter out = new PrintWriter(IOUtil.openFileForBufferedWriting(this.perBaseOutput));
    out.println("chrom\tpos\ttarget\tcoverage");
    for (final Map.Entry<Interval,Coverage> entry : this.highQualityCoverageByTarget.entrySet()) {
        final Interval interval = entry.getKey();
        final String chrom = interval.getContig();
        final int firstBase = interval.getStart();

        final int[] cov = entry.getValue().getDepths();
        for (int i = 0; i < cov.length; ++i) {
            out.print(chrom);
            out.print('\t');
            out.print(firstBase + i);
            out.print('\t');
            out.print(interval.getName());
            out.print('\t');
            out.print(cov[i]);
            out.println();
        }
    }

    out.close();
}
 

@Override
List<Bait> design(final BaitDesigner designer, final Interval target, final ReferenceSequence reference) {
    final List<Bait> baits = new LinkedList<Bait>();
    final int baitSize = designer.BAIT_SIZE;
    final int baitOffset = designer.BAIT_OFFSET;
    final int lastPossibleBaitStart = Math.min(target.getEnd(), reference.length() - baitSize);
    final int baitCount = 1 + (int) Math.floor((lastPossibleBaitStart - target.getStart()) / (double) baitOffset);

    int i = 0;
    for (int start = target.getStart(); start < lastPossibleBaitStart; start += baitOffset) {
        final Bait bait = new Bait(target.getContig(),
                start,
                CoordMath.getEnd(start, baitSize),
                target.isNegativeStrand(),
                designer.makeBaitName(target.getName(), ++i, baitCount));
        bait.addBases(reference, designer.DESIGN_ON_TARGET_STRAND);
        baits.add(bait);
    }
    return baits;
}
 

/**
 * Converts an interval in SimpleInterval format into an htsjdk QueryInterval.
 *
 * In doing so, a header lookup is performed to convert from contig name to index
 *
 * @param interval interval to convert
 * @param sequenceDictionary sequence dictionary used to perform the conversion
 * @return an equivalent interval in QueryInterval format
 */
private static QueryInterval convertSimpleIntervalToQueryInterval( final Interval interval,	final SAMSequenceDictionary sequenceDictionary ) {
	if (interval == null) {
		throw new IllegalArgumentException("interval may not be null");
	}
	if (sequenceDictionary == null) {
		throw new IllegalArgumentException("sequence dictionary may not be null");
	}

	final int contigIndex = sequenceDictionary.getSequenceIndex(interval.getContig());
	if ( contigIndex == -1 ) {
		throw new IllegalArgumentException("Contig " + interval.getContig() + " not present in reads sequence " +
				"dictionary");
	}

	return new QueryInterval(contigIndex, interval.getStart(), interval.getEnd());
}
 

private Map<String, List<Interval>> getIntervalsForContig (final IntervalList iList) {
	Map<String,List<Interval>> result = new HashMap<>();
	for (Interval i: iList.getIntervals()) {
		String contig = i.getContig();
		List<Interval> r= result.get(contig);
		if (r==null) {
			r = new ArrayList<>();
			result.put(contig, r);
		}
		r.add(i);
	}
	return result;
}
 

@Override
public List<Interval> takeSome(final Interval interval, final long idealSplitWeight, final long currentSize, final double projectSizeOfRemaining) {
    final long amount = idealSplitWeight - currentSize;

    if (amount >= interval.length()) {
        return CollectionUtil.makeList(interval, null);
    }

    if (amount == 0) {
        return CollectionUtil.makeList(null, interval);
    }

    final Interval left = new Interval(
            interval.getContig(),
            interval.getStart(),
            interval.getStart() + (int) amount - 1,
            interval.isNegativeStrand(),
            interval.getName()
    );
    final Interval right = new Interval(
            interval.getContig(),
            interval.getStart() + (int) amount,
            interval.getEnd(),
            interval.isNegativeStrand(),
            interval.getName()
    );
    return CollectionUtil.makeList(left, right);
}
 

@Test(enabled=true)
public void testGeneSNPSplitting () {
	List<String> cellBarcodeList = ParseBarcodeFile.readCellBarcodeFile(cellBCFile);
	IntervalList loci = IntervalList.fromFile(snpIntervals);
	// make a new SNP that is 10 bases before the first SNP.  Reads in the test data will hit both.
	Interval i1 = loci.getIntervals().iterator().next();
	Interval i2 = new Interval (i1.getContig(), i1.getStart()-10, i1.getStart()-10, true, "testSNP1");
	loci.add(i2);



	//A read that hits only the default SNP: start read at 76227020
	SAMRecord r1 = getReadByName("NS500217:67:H14GMBGXX:1:11308:22039:11268", smallBAMFile);
	Collection<SAMRecord> tempList = processOneRead(r1, loci, cellBarcodeList);
	Assert.assertTrue(tempList.size()==1);
	Assert.assertEquals(1, getNumGenes(tempList));
	Assert.assertEquals(1, getNumSNPs(tempList));

	//A read that hits both the default SNP and the new SNP: start read at 76227000
	r1 = getReadByName("NS500217:67:H14GMBGXX:1:13202:10555:15929", smallBAMFile);
	tempList = processOneRead(r1, loci, cellBarcodeList);
	Assert.assertTrue(tempList.size()==2);
	Assert.assertEquals(1, getNumGenes(tempList));
	Assert.assertEquals(2, getNumSNPs(tempList));


	//  A read that hits only the default SNP: start read at 76227020, has 2 genes.
	r1 = getReadByName("NS500217:67:H14GMBGXX:1:21206:20467:19854", smallBAMFile);
	tempList = processOneRead(r1, loci, cellBarcodeList);
	Assert.assertTrue(tempList.size()==2);
	Assert.assertEquals(2, getNumGenes(tempList));
	Assert.assertEquals(1, getNumSNPs(tempList));


	//A read that hits both the default SNP and the new SNP: start read at 76227000, has 2 genes.
	r1 = getReadByName("NS500217:67:H14GMBGXX:1:22302:3826:3320", smallBAMFile);
	tempList = processOneRead(r1, loci, cellBarcodeList);
	Assert.assertTrue(tempList.size()==4);
	Assert.assertEquals(2, getNumGenes(tempList));
	Assert.assertEquals(2, getNumSNPs(tempList));


}
 

/**
 * Converts an Interval object into a string representation that can be parsed by fromString.
 * Not using the Interval.toString method, because it has tabs, which might really screw up something else...
 * Instead, use ENCODE_DELIMITER as a delimiter for all fields except the range fields start-end.
 * @param i The interval to parse
 * @return A string representation of the interval.
 */
public static String toString (final Interval i) {
	// chr1:1-10	+	foo
	String result = i.getContig() + ENCODE_DELIMITER + i.getStart() + "-" + i.getEnd() + ENCODE_DELIMITER + (i.isNegativeStrand() ? '-' : '+') + ENCODE_DELIMITER + ((null == i.getName()) ? '.' : i.getName());
	return result;
}