/**
* Creates a new GATKSAMRecord with the source read's header, read group and mate information, but
* with the following fields set to user-supplied values: - Read Bases - Base Qualities - Base
* Insertion Qualities - Base Deletion Qualities
*
* <p>Cigar string is empty (not-null)
*
* <p>Use this method if you want to create a new GATKSAMRecord based on another GATKSAMRecord,
* but with modified bases and qualities
*
* @param read a read to copy the header from
* @param readBases an array containing the new bases you wish use in place of the originals
* @param baseQualities an array containing the new base qualities you wish use in place of the
* originals
* @param baseInsertionQualities an array containing the new base insertion qaulities
* @param baseDeletionQualities an array containing the new base deletion qualities
* @return a read with modified bases and qualities, safe for the GATK
*/
public static GATKSAMRecord createQualityModifiedRead(
final GATKSAMRecord read,
final byte[] readBases,
final byte[] baseQualities,
final byte[] baseInsertionQualities,
final byte[] baseDeletionQualities) {
if (baseQualities.length != readBases.length
|| baseInsertionQualities.length != readBases.length
|| baseDeletionQualities.length != readBases.length)
throw new IllegalArgumentException(
"Read bases and read quality arrays aren't the same size: Bases:"
+ readBases.length
+ " vs Base Q's:"
+ baseQualities.length
+ " vs Insert Q's:"
+ baseInsertionQualities.length
+ " vs Delete Q's:"
+ baseDeletionQualities.length);
final GATKSAMRecord processedRead = GATKSAMRecord.emptyRead(read);
processedRead.setReadBases(readBases);
processedRead.setBaseQualities(baseQualities, EventType.BASE_SUBSTITUTION);
processedRead.setBaseQualities(baseInsertionQualities, EventType.BASE_INSERTION);
processedRead.setBaseQualities(baseDeletionQualities, EventType.BASE_DELETION);
return processedRead;
}
/**
* 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;
}
@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);
}