r878: XA is given to the best alignment

Non-ALT hits may get ALT hits in the XA tag. This will simplify haplotype
assignment.
code backup
r880: bug in writing .ann file
code backup
code backup
code backup
code backup
code backup
ALT genotyping semi-working, but ...

... the result is not good.
changed weighting
requiring full overlap
bug in the last commit
r890: bns_intv2rid() may wrongly return -1
use weight1 by default
improved CLI
wrong flag in the SAM output
r895: increase the default max_XA_hits_alt to 200

Because there are >100 HLA haplotypes
r896: more flexible ALT reading
updated README, a bit
r898: read the index into a single memory block

Prepare for shared memory. Not used now.