r963: expose mask_level
first HLA typing script
not used any more
better CLI; more comments
added the pipeline script
polished the run script
backup
proper homozygous typing; fixed a low-level bug
a bit code cleanup
type primary exons first and then the rest
control min-match-length

we still need this to kill false mapping/alignment
change the default max_len
more command line help
nothing, really
optionally output debegging info
map to individual HLA ALT for meaningful mapQ
to be moved to a separate project
move to a new project bwa-typeHLA

The two scripts cannot be used standalone anyway.
removed contig weight & code cleanup

Contig weight was calculated based on a false assumption. It is actually not useful.
mate chr is sometimes wrong