priorities

[aryarm]

We should probably do these issues in this order. But since @zrcjessica needed quick changes to the pipeline, I tried to address a few of the issues whilst disregarding the order of this list.

• [ ] Test dataset #73
• [ ] BAM file input #71 (@aryarm has mostly done this)
• [ ] ATAC-seq support #61, #69 (@aryarm has mostly done this)
• [ ] Specifying samples #72
• [ ] Small changes
  • [ ] gzipping fastas and GTFs #64 (@aryarm is doing this)
  • [ ] remove quoting in CSVs #67 (@zrcjessica already has uncommited changes)
  • [ ] add error messages for empty dataframes #68
  • [ ] changing name of ref allele proportion #70
  • [ ] allow changing read depth cutoff #77
• [ ] better documentation #78
• [ ] making this into a command-line tool and/or adding config option validation #5, #74