/**
* Returns the reference index in the given header of the read's contig, or {@link
* SAMRecord#NO_ALIGNMENT_REFERENCE_INDEX} if the read is unmapped.
*
* @param read read whose reference index to look up
* @param header SAM header defining contig indices
* @return the reference index in the given header of the read's contig, or {@link
* SAMRecord#NO_ALIGNMENT_REFERENCE_INDEX} if the read is unmapped.
*/
public static int getReferenceIndex(final GATKRead read, final SAMFileHeader header) {
if (read.isUnmapped()) {
return SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX;
}
return header.getSequenceIndex(read.getContig());
}
