@Test
public void realignAtContigBorderTest() {
final int contigEnd = header.getSequence(0).getSequenceLength();
final GATKSAMRecord read =
ArtificialSAMUtils.createArtificialRead(header, "goodRead", 0, contigEnd - 1, 2);
read.setCigarString("2M");
Assert.assertEquals(IndelRealigner.realignmentProducesBadAlignment(read, contigEnd), false);
read.setCigarString("1M1D1M");
Assert.assertEquals(IndelRealigner.realignmentProducesBadAlignment(read, contigEnd), true);
}
/**
* Creates an empty GATKSAMRecord with the read's header, read group and mate information, but
* empty (not-null) fields: - Cigar String - Read Bases - Base Qualities
*
* <p>Use this method if you want to create a new empty GATKSAMRecord based on another
* GATKSAMRecord
*
* @param read a read to copy the header from
* @return a read with no bases but safe for the GATK
*/
public static GATKSAMRecord emptyRead(GATKSAMRecord read) {
final GATKSAMRecord emptyRead = new GATKSAMRecord(read.getHeader());
emptyRead.setReferenceIndex(read.getReferenceIndex());
emptyRead.setAlignmentStart(0);
emptyRead.setMappingQuality(0);
// setting read indexing bin last
emptyRead.setFlags(read.getFlags());
emptyRead.setMateReferenceIndex(read.getMateReferenceIndex());
emptyRead.setMateAlignmentStart(read.getMateAlignmentStart());
emptyRead.setInferredInsertSize(read.getInferredInsertSize());
emptyRead.setCigarString("");
emptyRead.setReadBases(new byte[0]);
emptyRead.setBaseQualities(new byte[0]);
SAMReadGroupRecord samRG = read.getReadGroup();
emptyRead.clearAttributes();
if (samRG != null) {
GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(samRG);
emptyRead.setReadGroup(rg);
}
GATKBin.setReadIndexingBin(emptyRead, 0);
return emptyRead;
}
private List<PileupElement> makeReads(final int n, final int mapq, final String op) {
final int readLength = 3;
final List<PileupElement> elts = new LinkedList<PileupElement>();
for (int i = 0; i < n; i++) {
GATKSAMRecord read =
ArtificialSAMUtils.createArtificialRead(header, "read", 0, 1, readLength);
read.setReadBases(Utils.dupBytes((byte) 'A', readLength));
read.setBaseQualities(Utils.dupBytes((byte) 30, readLength));
read.setCigarString("1M1" + op + "1M");
read.setMappingQuality(mapq);
final int baseOffset = op.equals("M") ? 1 : 0;
final CigarElement cigarElement = read.getCigar().getCigarElement(1);
elts.add(new PileupElement(read, baseOffset, cigarElement, 1, 0));
}
return elts;
}
@Test
public void testRBPMappingQuals() {
// create a read with high MQ
final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read", 0, 1, 10);
read.setReadBases(Utils.dupBytes((byte) 'A', 10));
read.setBaseQualities(Utils.dupBytes((byte) 30, 10));
read.setCigarString("10M");
read.setMappingQuality(200); // set a MQ higher than max signed byte
// now create the RBP
final List<PileupElement> elts = new LinkedList<>();
elts.add(new PileupElement(read, 0, read.getCigar().getCigarElement(0), 0, 0));
final Map<String, ReadBackedPileupImpl> pileupsBySample = new HashMap<>();
pileupsBySample.put("foo", new ReadBackedPileupImpl(loc, elts));
final ReadBackedPileup pileup = new ReadBackedPileupImpl(loc, pileupsBySample);
Assert.assertEquals(pileup.getMappingQuals()[0], 200);
}