r744: int overflow given MB query
Helpful scripts
r746: tuned heuristic for GRCh38

Reduced -c to 500 by default. As a compensation, we choose up to 1000 positions
if a seed has 500 or more occurrences. In addition, a read with big portion
from such seeds will have lower mapping quality.
r747: fixed a minor issue in the last (mis)commit
r748: reduced the default -m to 50
r749: max_hits tunable on CMD; default to 5
code backup
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.
Merge branch 'master' into mem