Fix bug where input file is named alignment.bam
Fix bug where input file is named alignment.bam

LyonsLab/coge,asherkhb/coge,asherkhb/coge,asherkhb/coge,asherkhb/coge,LyonsLab/coge,asherkhb/coge,LyonsLab/coge,asherkhb/coge,LyonsLab/coge,asherkhb/coge,LyonsLab/coge,LyonsLab/coge,LyonsLab/coge,asherkhb/coge,LyonsLab/coge,asherkhb/coge,LyonsLab/coge