add support for peak regions for ASOC analysis

- ASOC analysis needs additional BED file for each sample that indicates peak regions found in each sample
- modify `prepare_counts-rna.r` and create a version (`prepare_counts-atac.r`?) that [finds overlaps with peak regions instead of genes ](https://github.com/aryarm/as_analysis/blob/994d3f21201ddea5313c429ea44d46c968f1d905/scripts/prepare_counts-rna.r#L63) and [reads in BED files instead of GTF file ](https://github.com/aryarm/as_analysis/blob/994d3f21201ddea5313c429ea44d46c968f1d905/scripts/prepare_counts-rna.r#L17)

Start with scripts/prepare_counts-rna.r, especially the input handling and overlap logic linked in the issue. Compare the RNA workflow with the proposed prepare_counts-atac.r design, then verify that each sample's BED file is read and overlaps are found against peak regions rather than genes. Done means the ATAC preparation path produces counts for the requested peak regions.

Written by the indexing model from the issue text.