Set chromap to not shift reads by default #381
Description
Description of feature
The parameters used by chromap are the ones suggested for ATAC-seq in their documentation, see here. This includes the --Tn5-shift; thus, the shift is applied by default, unlike the rest of the aligners. As the --shift_reads parameter has been implemented now, it would make sense to not shift reads by default and only use the --Tn5-shift chromap parameter when the --shift_reads is set.