/**
* Shallow copy of everything, except for the attribute list and the temporary attributes. A new
* list of the attributes is created for both, but the attributes themselves are copied by
* reference. This should be safe because callers should never modify a mutable value returned by
* any of the get() methods anyway.
*
* @return a shallow copy of the GATKSAMRecord
*/
@Override
public Object clone() {
try {
final GATKSAMRecord clone = (GATKSAMRecord) super.clone();
if (temporaryAttributes != null) {
clone.temporaryAttributes = new HashMap<>();
for (Object attribute : temporaryAttributes.keySet())
clone.setTemporaryAttribute(attribute, temporaryAttributes.get(attribute));
}
return clone;
} catch (final CloneNotSupportedException e) {
throw new RuntimeException(e);
}
}
/**
* 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;
}