@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[][] {});
}
