Fix karyotype with underscores

This release contains a fix from @Adoni5, removing a filter that kept contigs with an underscore out of the karyotype (#20 and #21). Unplaced contigs (using an ensembl genome) will also be part of the karyotype, as there is no good way to filter those out. Possibly users could, in the future, optionally specify a file with chromosomes they want to see in the karyotype, but that is not yet supported or planned.

Additionally, there is a fix to no longer subtract the softclipped sequences from the read length when running in --ubam mode.