chmod +x scripts
change ~/uab_ngs to ./uab_ngs so can keep a git repository local to each analysis directory, instead of global
revert accidental file truncation in commit 8046f364243c5116aa65b524a9adf4c9a5c10349
get all references to is_indel changed to is_snp
remove spaces from patterns - when we added -Ew, must remove the space, or we get no output
printout the commands as they are executed
add line counts for more intermediate files