add "deps" target
replace Region class with something useful
update ref-stats to use new RefStats object

this lets us use general strings instead of only search for a/t, c/g,
and cpg. this isn't exposed in the ui yet.
create new base class for commands

the idea is to reduce boilerplate related to option parsing and such.
migration will start soon.
add integration test for bed merge command
add integration test for snv-concordance-by-quality
add integration test for vcf-annotate
add integration test for vcf-filter
add integration test for vcf-site-filter
fix test names
add integration test for indel normalization
add integration test for vcf-report
add integration test for wig2bed
apply upstream patch for boost program options

its exceptions didn't correctly report option names containing dashes
add unit test for BedMergeCommand
add makeSimpleIntersector function for type inference

Using the class constructor directly requires specifying all the
template types.
always build boost

we're using a patched version now
refactor ui commands:

CommandBase is updated to help remove boilerplate from all the ui
commands.

All commands moved to lib/ui so they are easier to test.