get_major_from_bam.py: Adding usage, rm magic numbers, commenting
pre-process-mt.sh: formatting, adding cli interface
test: Adding real test dataset
coverage-plot.R: Boris' script for plotting coverage across reference
test: added known good output dataset, verified current code produces it
pre-process-mt.sh: cleanup temp files, allow specifying output filename.
- verified output is identical, except one header line from picard.
test/run.sh: add automated functional test
pre-process-mt.sh, nm-ratio.select.py, rm_chim_in_pair.py: run from any pwd
test/run.sh, test/diff.sh: modularize BAM diff script