Fix proposal for 313
Make sure no clobbering between out files occur in case of al, un, al-conc or un-conc.
Fixed 313 and also added a regression.

I changed the behavior for --un-conc, al-conc, --un and --al since some users
provide only a path with no base name and they mistakenly believe bowtie2
outputs no seqs for those options.
Updated the regressions.
fixed spurious assert