Incorrect path to annotation files in diff_regions.sh

[ecroot]

Describe the bug
Running a diff for genebody or promoter regions silently quits.

I believe this is because the diff_regions script tries to access the relevant bed files at --BED ${SH_SCRIPT_DIR}/../Annotation/${assemblyid}_Refseq.${regions}.bed (line 435), which does not exist: the annotation .bed files are organised into assemblyid subdirectories, which is not accounted for in this part of the diff script. Additionally, the annotation directory uses a lowercase a

For gene regions diff, the path to the relevant bed files is given as --BED ${SH_SCRIPT_DIR}/../annotation/${assemblyid}/${assemblyid}_Refseq.promoter.bed, and this works.

I have edited the path in script to be --BED ${SH_SCRIPT_DIR}/../annotation/${assemblyid}/${assemblyid}_Refseq.${regions}.bed, and it now works.

To Reproduce
Try to run a diff command for genebody or promoter

Expected behavior
The command should find the relevant bed files in the correct location, and run successfully.