/**
* 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 GATKSAMRecord makeRead(final int fragmentSize, final int mateStart) {
final byte[] bases = {'A', 'C', 'G', 'T', 'A', 'C', 'G', 'T'};
final byte[] quals = {30, 30, 30, 30, 30, 30, 30, 30};
final String cigar = "8M";
GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(bases, quals, cigar);
read.setProperPairFlag(true);
read.setReadPairedFlag(true);
read.setMateAlignmentStart(mateStart);
read.setInferredInsertSize(fragmentSize);
return read;
}
@Test(dataProvider = "AdaptorGetter")
public void testGetAdaptorBoundary(final GetAdaptorFunc get) {
final int fragmentSize = 10;
final int mateStart = 1000;
final int BEFORE = mateStart - 2;
final int AFTER = mateStart + 2;
int myStart, boundary;
GATKSAMRecord read;
// Test case 1: positive strand, first read
read = makeRead(fragmentSize, mateStart);
myStart = BEFORE;
read.setAlignmentStart(myStart);
read.setReadNegativeStrandFlag(false);
read.setMateNegativeStrandFlag(true);
boundary = get.getAdaptor(read);
Assert.assertEquals(boundary, myStart + fragmentSize + 1);
// Test case 2: positive strand, second read
read = makeRead(fragmentSize, mateStart);
myStart = AFTER;
read.setAlignmentStart(myStart);
read.setReadNegativeStrandFlag(false);
read.setMateNegativeStrandFlag(true);
boundary = get.getAdaptor(read);
Assert.assertEquals(boundary, myStart + fragmentSize + 1);
// Test case 3: negative strand, second read
read = makeRead(fragmentSize, mateStart);
myStart = AFTER;
read.setAlignmentStart(myStart);
read.setReadNegativeStrandFlag(true);
read.setMateNegativeStrandFlag(false);
boundary = get.getAdaptor(read);
Assert.assertEquals(boundary, mateStart - 1);
// Test case 4: negative strand, first read
read = makeRead(fragmentSize, mateStart);
myStart = BEFORE;
read.setAlignmentStart(myStart);
read.setReadNegativeStrandFlag(true);
read.setMateNegativeStrandFlag(false);
boundary = get.getAdaptor(read);
Assert.assertEquals(boundary, mateStart - 1);
// Test case 5: mate is mapped to another chromosome (test both strands)
read = makeRead(fragmentSize, mateStart);
read.setInferredInsertSize(0);
read.setReadNegativeStrandFlag(true);
read.setMateNegativeStrandFlag(false);
boundary = get.getAdaptor(read);
Assert.assertEquals(boundary, ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY);
read.setReadNegativeStrandFlag(false);
read.setMateNegativeStrandFlag(true);
boundary = get.getAdaptor(read);
Assert.assertEquals(boundary, ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY);
read.setInferredInsertSize(10);
// Test case 6: read is unmapped
read = makeRead(fragmentSize, mateStart);
read.setReadUnmappedFlag(true);
boundary = get.getAdaptor(read);
Assert.assertEquals(boundary, ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY);
read.setReadUnmappedFlag(false);
// Test case 7: reads don't overlap and look like this:
// <--------|
// |------>
// first read:
read = makeRead(fragmentSize, mateStart);
myStart = 980;
read.setAlignmentStart(myStart);
read.setInferredInsertSize(20);
read.setReadNegativeStrandFlag(true);
boundary = get.getAdaptor(read);
Assert.assertEquals(boundary, ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY);
// second read:
read = makeRead(fragmentSize, mateStart);
myStart = 1000;
read.setAlignmentStart(myStart);
read.setInferredInsertSize(20);
read.setMateAlignmentStart(980);
read.setReadNegativeStrandFlag(false);
boundary = get.getAdaptor(read);
Assert.assertEquals(boundary, ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY);
// Test case 8: read doesn't have proper pair flag set
read = makeRead(fragmentSize, mateStart);
read.setReadPairedFlag(true);
read.setProperPairFlag(false);
Assert.assertEquals(get.getAdaptor(read), ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY);
// Test case 9: read and mate have same negative flag setting
for (final boolean negFlag : Arrays.asList(true, false)) {
read = makeRead(fragmentSize, mateStart);
read.setAlignmentStart(BEFORE);
read.setReadPairedFlag(true);
read.setProperPairFlag(true);
read.setReadNegativeStrandFlag(negFlag);
read.setMateNegativeStrandFlag(!negFlag);
Assert.assertTrue(
get.getAdaptor(read) != ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY,
"Get adaptor should have succeeded");
read = makeRead(fragmentSize, mateStart);
read.setAlignmentStart(BEFORE);
read.setReadPairedFlag(true);
read.setProperPairFlag(true);
read.setReadNegativeStrandFlag(negFlag);
read.setMateNegativeStrandFlag(negFlag);
Assert.assertEquals(
get.getAdaptor(read),
ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY,
"Get adaptor should have failed for reads with bad alignment orientation");
}
}
@DataProvider(name = "HasWellDefinedFragmentSizeData")
public Object[][] makeHasWellDefinedFragmentSizeData() throws Exception {
final List<Object[]> tests = new LinkedList<Object[]>();
// setup a basic read that will work
final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader();
final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 10, 10);
read.setReadPairedFlag(true);
read.setProperPairFlag(true);
read.setReadUnmappedFlag(false);
read.setMateUnmappedFlag(false);
read.setAlignmentStart(100);
read.setCigarString("50M");
read.setMateAlignmentStart(130);
read.setInferredInsertSize(80);
read.setFirstOfPairFlag(true);
read.setReadNegativeStrandFlag(false);
read.setMateNegativeStrandFlag(true);
tests.add(new Object[] {"basic case", read.clone(), true});
{
final GATKSAMRecord bad1 = (GATKSAMRecord) read.clone();
bad1.setReadPairedFlag(false);
tests.add(new Object[] {"not paired", bad1, false});
}
{
final GATKSAMRecord bad = (GATKSAMRecord) read.clone();
bad.setProperPairFlag(false);
// we currently don't require the proper pair flag to be set
tests.add(new Object[] {"not proper pair", bad, true});
// tests.add( new Object[]{ "not proper pair", bad, false });
}
{
final GATKSAMRecord bad = (GATKSAMRecord) read.clone();
bad.setReadUnmappedFlag(true);
tests.add(new Object[] {"read is unmapped", bad, false});
}
{
final GATKSAMRecord bad = (GATKSAMRecord) read.clone();
bad.setMateUnmappedFlag(true);
tests.add(new Object[] {"mate is unmapped", bad, false});
}
{
final GATKSAMRecord bad = (GATKSAMRecord) read.clone();
bad.setMateNegativeStrandFlag(false);
tests.add(new Object[] {"read and mate both on positive strand", bad, false});
}
{
final GATKSAMRecord bad = (GATKSAMRecord) read.clone();
bad.setReadNegativeStrandFlag(true);
tests.add(new Object[] {"read and mate both on negative strand", bad, false});
}
{
final GATKSAMRecord bad = (GATKSAMRecord) read.clone();
bad.setInferredInsertSize(0);
tests.add(new Object[] {"insert size is 0", bad, false});
}
{
final GATKSAMRecord bad = (GATKSAMRecord) read.clone();
bad.setAlignmentStart(1000);
tests.add(new Object[] {"positve read starts after mate end", bad, false});
}
{
final GATKSAMRecord bad = (GATKSAMRecord) read.clone();
bad.setReadNegativeStrandFlag(true);
bad.setMateNegativeStrandFlag(false);
bad.setMateAlignmentStart(1000);
tests.add(new Object[] {"negative strand read ends before mate starts", bad, false});
}
return tests.toArray(new Object[][] {});
}