While going through the HISAT2 manual, one can see this:
Two alignments for the same individual read are "distinct" if they map the same read to different places. Specifically, we say that two alignments are distinct if there are no alignment positions where a particular read offset is aligned opposite a particular reference offset in both alignments with the same orientation. E.g. if the first alignment is in the forward orientation and aligns the read character at read offset 10 to the reference character at chromosome 3, offset 3,445,245, and the second alignment is also in the forward orientation and also aligns the read character at read offset 10 to the reference character at chromosome 3, offset 3,445,245, they are not distinct alignments.
Two alignments for the same pair are distinct if either the mate 1s in the two paired-end alignments are distinct or the mate 2s in the two alignments are distinct or both.
Default mode: search for one or more alignments, report each
and then there is -k parameter (analogous to bowtie2 -K parameter)
HISAT2 searches for up to N distinct, primary alignments for each read, where N equals the integer specified with the -k parameter. Primary alignments mean alignments whose alignment score is equal or higher than any other alignments. It is possible that multiple distinct alignments have the same score. That is, if -k 2 is specified, HISAT2 will search for at most 2 distinct alignments. The alignment score for a paired-end alignment equals the sum of the alignment scores of the individual mates. Each reported read or pair alignment beyond the first has the SAM 'secondary' bit (which equals 256) set in its FLAGS field. See the SAM specification for details.
This is a bit confusing, as the first quote means that HISAT2 finds all distinct valid alignment and reports them by default, and the second quote says that when -k option is used, it will only report a subset of alignments which it would have reported by default. Am I correct in this inference or does one needs to use -k option to enable "multi-mapping"?