/**
* 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;
}
// copied from LocusViewTemplate
protected GATKSAMRecord buildSAMRecord(
final String readName, final String contig, final int alignmentStart) {
GATKSAMRecord record = new GATKSAMRecord(header);
record.setReadName(readName);
record.setReferenceIndex(dictionary.getSequenceIndex(contig));
record.setAlignmentStart(alignmentStart);
record.setCigarString("1M");
record.setReadString("A");
record.setBaseQualityString("A");
record.setReadGroup(readGroup);
return record;
}
@Test(enabled = true)
public void testReadWithNsRefAfterDeletion() throws FileNotFoundException {
final IndexedFastaSequenceFile seq =
new CachingIndexedFastaSequenceFile(new File(b37KGReference));
final SAMFileHeader header =
ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
final int readLength = 76;
final GATKSAMRecord read =
ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 8975, readLength);
read.setReadBases(Utils.dupBytes((byte) 'A', readLength));
read.setBaseQualities(Utils.dupBytes((byte) 30, readLength));
read.setCigarString("3M414N1D73M");
final int result =
ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(
read, 9393, ReadUtils.ClippingTail.LEFT_TAIL);
Assert.assertEquals(result, 3);
}
@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[][] {});
}
