Java Code Examples for htsjdk.samtools.SAMRecord#clone()

The following examples show how to use htsjdk.samtools.SAMRecord#clone() . You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may check out the related API usage on the sidebar.
Example 1
Source File: IntervalTagComparatorTest.java    From Drop-seq with MIT License 5 votes vote down vote up 
private List<SAMRecord> createManyIntervalTaggedSAMRecords (final int desiredNumRecords) {
	List<SAMRecord> data = new ArrayList<>();

	SamReader inputSam = SamReaderFactory.makeDefault().open(this.dictFile);
	SAMRecord samRecordTemplate = new SAMRecord (inputSam.getFileHeader());

	SAMSequenceDictionary dict= inputSam.getFileHeader().getSequenceDictionary();
	List<SAMSequenceRecord> recs = dict.getSequences();
	int numRecs = recs.size();

	Random randomGenerator = new Random();
	for (int i=0; i<desiredNumRecords; i++) {
		SAMSequenceRecord r = recs.get(randomGenerator.nextInt(numRecs+1));
		String chr = r.getSequenceName();
		int seqLen = r.getSequenceLength();
		int s1 = randomGenerator.nextInt(seqLen);
		int s2 = randomGenerator.nextInt(seqLen);
		int s = Math.min(s1, s2);
		int e = Math.max(s1, s2);
		Interval interval = new Interval (chr, s1,s2);
		try {
			SAMRecord r1 = (SAMRecord) samRecordTemplate.clone();
			// I realize that using encoding the full interval can be a bit heavy handed.
			r1.setAttribute(this.intervalTag, interval.toString());
			data.add(r1);
		} catch (CloneNotSupportedException e1) {
			// this should never happen, sigh.
		}
	}
	return data;
}
Example 2
Source File: IndelShifter.java    From abra2 with MIT License 5 votes vote down vote up 
private SAMRecord cloneRead(SAMRecord read) {
	try {
		return (SAMRecord) read.clone();
	} catch (CloneNotSupportedException e) {
		// Infamous "this should never happen" comment here.
		e.printStackTrace();
		throw new RuntimeException(e);
	}
}
Example 3
Source File: SAMRecordUtils.java    From abra2 with MIT License 5 votes vote down vote up 
/**
 * Returns a clone of the input read
 */
public static SAMRecord cloneRead(SAMRecord read) {
	try {
		return (SAMRecord) read.clone();
	} catch (CloneNotSupportedException e) {
		// Infamous "this should never happen" comment here.
		e.printStackTrace();
		throw new RuntimeException(e);
	}
}
Example 4
Source File: AlignmentsTagsTest.java    From cramtools with Apache License 2.0 4 votes vote down vote up 
private void doTest(byte[] ref, int alignmentStart, byte[] readBases) throws IOException,
		CloneNotSupportedException {
	SAMSequenceRecord sequenceRecord = new SAMSequenceRecord("1", ref.length);
	SAMSequenceDictionary sequenceDictionary = new SAMSequenceDictionary();
	sequenceDictionary.addSequence(sequenceRecord);

	SAMFileHeader header = new SAMFileHeader();
	header.setSequenceDictionary(sequenceDictionary);
	SAMRecord samRecord = new SAMRecord(header);
	samRecord.setReadUnmappedFlag(false);
	samRecord.setAlignmentStart(alignmentStart);
	samRecord.setReferenceIndex(0);
	samRecord.setReadBases(readBases);
	samRecord.setCigarString(samRecord.getReadLength() + "M");

	ReferenceSource referenceSource = new ReferenceSource() {
		@Override
		public synchronized ReferenceRegion getRegion(SAMSequenceRecord record, int start_1based,
				int endInclusive_1based) throws IOException {
			int zbInclusiveStart = start_1based - 1;
			int zbExlcusiveEnd = endInclusive_1based;
			return new ReferenceRegion(Arrays.copyOfRange(ref, zbInclusiveStart, zbExlcusiveEnd),
					sequenceRecord.getSequenceIndex(), sequenceRecord.getSequenceName(), start_1based);
		}
	};

	AlignmentsTags.calculateMdAndNmTags(samRecord, referenceSource, sequenceDictionary, true, true);

	SAMRecord checkRecord = (SAMRecord) samRecord.clone();
	SequenceUtil.calculateMdAndNmTags(checkRecord, ref, true, true);
	// System.out.printf("TEST: ref %s, start %d, read bases %s\n", new
	// String(ref), alignmentStart, new String(
	// readBases));
	// System.out
	// .println(referenceSource.getRegion(sequenceRecord, alignmentStart,
	// alignmentStart + readBases.length));
	// System.out.printf("NM:  %s x %s\n", samRecord.getAttribute("NM"),
	// checkRecord.getAttribute("NM"));
	// System.out.printf("MD: %s x %s\n", samRecord.getAttribute("MD"),
	// checkRecord.getAttribute("MD"));

	Assert.assertEquals(checkRecord.getAttribute("NM"), samRecord.getAttribute("NM"));
	Assert.assertEquals(checkRecord.getAttribute("MD"), samRecord.getAttribute("MD"));
}