When setting the HISAT2 alignment option -k to one (1), does that mean that it will only report the the Primary alignment with the best possible score or does it mean that it just reports one of the primary alignments that has any score. In the manual the following phrase is confusing. "HISAT2 does not "find" alignments in any specific order, so for reads that have more than N distinct, valid alignments, HISAT2 does not guarantee that the N alignments reported are the best possible in terms of alignment score.". Thanks Dave