This is a small tool that helps quantifying linked mutations from sequencing data. It takes a bed-like file as input, where one can specify positions of interest, together with wildtype and (several) mutant alleles. The tool then iterates through a bam file to count for each read the number of matches to the wildtype or mutant base, thus resulting in a match score. This is written out into a csv file.
The format to specify positions of interest is derived from the bed format, except that there can be multiple columns for different mismatch patterns.
The software is a single binary that can be either downloaded from the Releases page, or alternatively (if it doesn't run on your system) you can compile it yourself.
This software is written in Rust and can thus be compiled with cargo. Follow the
install instructions specific to your OS, then clone this github, cd into it and
run cargo build --release. The compiled binary will then be at target/release/bampile.