move scripts to bin
add draft of Map::Redundant.pm to lib
add script for testing/developing Map::Redundant
rename subcluster-related methods
add functional build_clusters/calculate_coverage subs
fix hash dereferencing
quote meta characters for regex
fix unitilaized value warning for genes with no unique reads
pass arguments to best_hits() properly; increase default $max_best to 100
bypass instances where genes of interest are only suboptimal hits
add verbose option and autoflushing for STDERR & STDOUT
add output, input, and nytprof dirs to .gitignore
write coverage summary to file; combine adjacent loops
cleanup
Merge branch 'feature/make_modular' into develop