Eric Banks 9aecd50473 Adding ability to exclude annotations from the VA and UG lists. As described in the docs, this argument trumps all others (including -all) so that we can get around the SnpEff issue brought up by Menachem. Added integration test for it.		2011-10-12 15:44:54 -04:00
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net/sf	Removed annoying FastaSequenceIndexBuilderProgressListener infrastructure that was just a boolean switch on whether to print progress or not.	2011-07-27 22:06:23 -04:00
org/broadinstitute/sting	Adding ability to exclude annotations from the VA and UG lists. As described in the docs, this argument trumps all others (including -all) so that we can get around the SnpEff issue brought up by Menachem. Added integration test for it.	2011-10-12 15:44:54 -04:00