code backup
genalt is working
more comments
r754: added command msg for -h
download link of data used by genalt
more debugging info at -v5
help on how to use bwa-helper.js
r758: fixed a typo

mostly negligible in practice
r759: bugfix - frac_rep not working

Also added commented code for a 3rd round seeding. Not used.
r760: removed commented code

It is slow and is not very effective. And I hate useless code.