gatk3的最后一个经典版本3.8

David Roazen f9c986be74 Remove com.sun.javadoc.* dependencies from the GATK proper, and isolate them for doclet use only ... Problem: Classes in com.sun.javadoc.* are non-standard. Since we can't depend on their availability for all users, the GATK proper should not have any runtime dependencies on this package. Solution: -Isolate com.sun.javadoc.* dependencies in a DocletUtils class for use only by doclets. The only users who need to run our doclets are those who compile from source, and they should be competent enough to figure out how to resolve a missing com.sun.* dependency. -HelpUtils now contains no com.sun.javadoc.* dependencies and can be safely used by walkers/other tools. -Added comments with instructions on when it is safe to use DocletUtils vs. HelpUtils [delivers #51450385] [delivers #50387199]		2013-06-13 15:52:41 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Merge pull request #273 from broadinstitute/rp_readIsPoorlyModelled	2013-06-13 08:40:24 -07:00
public	Remove com.sun.javadoc.* dependencies from the GATK proper, and isolate them for doclet use only	2013-06-13 15:52:41 -04:00
settings	Rev picard, sam-jdk, tribble, and variant to version 1.91.1453	2013-05-07 14:21:15 -04:00
.gitignore	Detect stuck lock-acquisition calls, and disable file locking for tests	2013-04-24 22:49:02 -04:00
build.xml	Restore scala compilation by default in build.xml	2013-05-31 11:28:29 -04:00
intellij_example.tar.bz2	Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!)	2012-09-27 11:04:56 -04:00
ivy.xml	Brought all of ReduceReads to fastutils	2013-02-23 22:53:23 -05:00