/** * 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()); }