/**
* 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;
}
