Is there an option in Hisat that is similar to `-g`/`--max-multihits` in Tophat? I can not find it in the parameter list on https://ccb.jhu.edu/software/hisat/manual.shtml#options. There is a Uniqueness class in here: https://github.com/infphilo/hisat/blob/master/unique.h, but when I grep for that class or the `bestIsUnique` function in the Hisat source folder I can't find it used anywhere.

Or would it work to use `samtools view -q 1`?

If anyone else is interested, I e-mailed the author and he said:

> One possible solution is to use the next best alignment score (ZS:i:, previously XS:i:). If the next alignment score is the same as the primary alignment score (AS:i:), that means there are at least two equivalent alignments found by HISAT. This additional SAM field (ZS:i:) is only available at HISAT github, which I'll include in the next release of HISAT.
<p>The most recent release of hisat (v0.1.6) uses NH tags in the BAM to specify the number of alignments for the read/pair (see release notes: <a href="https://ccb.jhu.edu/software/hisat/index.shtml">https://ccb.jhu.edu/software/hisat/index.shtml</a>). As far as I understand it, reads/pairs with NH:i:1 have a single best alignment and are therefore &quot;uniquely&quot; mapped.</p>
