gatk3的最后一个经典版本3.8

Christopher Hartl 79ef3325bd Fix a NullPointerException that could occur in DoC if the user requested an interval summary but never provided a -L argument. This situation is now checked for and a UserError thrown instead. Also (after a great struggle) pushing some old VR3 code into the central repository which had been improperly pushed (e.g. with rsync rather than git push) into my repository on the server, and never migrated to unstable. In addition, minor convenience function added to the GATKReport that allows an entire row to be added, and a walker that parses out annotations from a tool called VariantEffectPredictor and summarizes annotations across transcripts, and consensus annotations.		2012-06-19 07:50:13 -04:00
licensing	Remove old licensing	2012-04-25 12:23:08 -04:00
protected/java/src/org/broadinstitute/sting	build system overhaul	2012-05-17 15:16:29 -04:00
public	Fix a NullPointerException that could occur in DoC if the user requested an interval summary but never provided a -L argument. This situation is now checked for and a UserError thrown instead. Also (after a great struggle) pushing some old VR3 code into the central repository which had been improperly pushed (e.g. with rsync rather than git push) into my repository on the server, and never migrated to unstable. In addition, minor convenience function added to the GATKReport that allows an entire row to be added, and a walker that parses out annotations from a tool called VariantEffectPredictor and summarizes annotations across transcripts, and consensus annotations.	2012-06-19 07:50:13 -04:00
settings	Testing of BCF codec	2012-05-24 10:57:01 -04:00
.gitignore	Minor additions to the shared .gitignore file, now that Mark has checked one in.	2011-10-26 12:24:28 -04:00
build.xml	ant fasttest: for when you just can't wait	2012-06-01 15:17:18 -04:00
ivy.xml	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -04:00