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."