diff --git a/src/main/java/htsjdk/samtools/util/SequenceUtil.java b/src/main/java/htsjdk/samtools/util/SequenceUtil.java index 73b46b1bf8..3108cee0d6 100644 --- a/src/main/java/htsjdk/samtools/util/SequenceUtil.java +++ b/src/main/java/htsjdk/samtools/util/SequenceUtil.java @@ -890,10 +890,11 @@ public static byte[] calculateMD5(final byte[] data, final int offset, final int /** * Calculate MD and NM similarly to Samtools, except that N->N is a match. * - * @param record - * @param ref - * @param calcMD - * @return + * @param record Input record for which to calculate NM and MD. + * The appropriate tags will be added/updated in the record + * @param ref The reference bases for the sequence to which the record is mapped + * @param calcMD A flag indicating whether to update the MD tag in the record + * @param calcNM A flag indicating whether to update the NM tag in the record */ public static void calculateMdAndNmTags(final SAMRecord record, final byte[] ref, final boolean calcMD, final boolean calcNM) {