vincenthahaut/FLASH-Seq — reverse-engineered prompt

I want this turned into a usable R based analysis toolkit for FLASH Seq data instead of a loose pile of scripts. The goal is that someone can go from raw sequencing files to the main analysis steps with clear instructions and as little manual guesswork as possible. Please wire together the existing pieces for pre processing, UMI detection in read 2, mapping and counting related steps, variant calling, and the BAM filtering step for suspected strand invasion events. Keep the older draft and experimental stuff separate so it is obvious what is stable and what is not.

Please add a simple top level workflow, sensible defaults, and a short example showing what input files are expected and what outputs each step creates. I would also like the repo cleaned up so the important scripts are easy to find, with a README that explains the pipeline in plain English and how to run it end to end. If anything is unclear, look up the current docs online and make reasonable choices.