r807: allow to change block size in bwt_gen

For a very large reference genome, the default is too small.
r808: a minor bug with the new index -b
r809: new strategy for the -a mode
r810: add err_puts()

puts() adds '\n', but fputs() does not.
r815: optionally output ref fasta header

Also fixed a bug in reading .ann files
r816: read .alt file (not tested)
code backup
code backup
r819: bugfix - added too many sub-SMEMs
Merge branch 'hotfix-utgaln' into dev

Conflicts:
	main.c
r821: more relax on containing seeds
Merge branch 'dev' into alt
r823: towards ALT support
r824: ALT mapping seems working
r826: improved alt mapping for PE
r827: an alt hit as good as a pri hit as supp
r828: changed the default scoring for pacbio
r829: killed a harmless gcc warning
r830: optionally fixed chunk size
Removed instruction on ALT alignment

Favoring the new method