Handling of multi-mappers

[funnell]

Hello, thank you for developing this tool!

I was wondering how x-mapper treats reads that align equally well to more than one location in the reference. Does it output just one alignment or is there a way to output all equally optimal alignments per read?

[mathjeff]

Thanks!

If there is a read that aligns equally well to more than one location in the reference, Mapper aims to report each one.

See for example this unit test

If you'd also like to output some alignments that are worse than the best alignment, you can set --max-penalty-span

Let us know whether it works for you. Thanks!