broadinstitute / hellbender / 222

63%

master: 81%

push

travis-pro

Major changes to the command line parsing system
-using jopt-simple to do the actual parsing
-supports short (-h) and long (--help) styles
-supports boolean flags with or without an argument
-options are now case sensitive
-argument collections can be specified with @ArgumentCollection
-Option(fullname) is now respected if specified, if it isn't it defaults to use the field name
-several Option values are no longer used, overrideable
-NestedOptions removed -> replaced by ArgumentCollection
-Arguments must now be uniquely specified (no arguments targetting multiple fields any more)
-Collection defaults are now replaced rather than appended too

-opportunistically fixed a broken test in CreateSequenceDictionaryTest

227 of 227 new or added lines in 9 files covered. (100.0%)

7455 of 11741 relevant lines covered (63.5%)

0.63 hits per line