priorities

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

Start by reading the linked issues #73, #71, #61, #69, #72, #64, #67, #68, #70, #77, #78, #5, and #74 to understand their scope and current status. Done would require an agreed priority order and updated tracking of which items are already addressed; this issue names no files or tests to run.

Written by the indexing model from the issue text.