HISAT2 - are all multi mapped reads reported by default?
You said:


  ...the first quote means that HISAT2 finds all distinct valid alignment and reports them by default.


Not exactly. The first section you quoted doesn't say it will find and report all distinct alignments, but rather that it would find and report one or more distinct alignments. It's a subtle difference, but an important one.

That section describes how distinct mappings are defined, not how many are reported. The second section you quoted, as well as the documentation for the -k parameter, are all consistent with this interpretation.


-k &lt;int&gt;        It searches for at most &lt;int&gt; distinct, primary alignments for
                each read. Primary alignments mean alignments whose alignment
                score is equal or higher than any other alignments. The search
                terminates when it can't find more distinct valid alignments, or
                when it finds &lt;int&gt;, whichever happens first. 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. For reads that have more
                than &lt;int&gt; distinct, valid alignments, hisat2 does not guarantee
                that the &lt;int&gt; alignments reported are the best possible in
                terms of alignment score. Default: 5 (HFM) or 10 (HGFM)

                Note: HISAT2 is not designed with large values for -k in mind,
                and when aligning reads to long, repetitive genomes large -k can
                be very, very slow.



By default, 5 or 10 distinct mappings are reported (depending on the mode), but you can control this with the -k parameter.