David Roazen 2eac97a76c Remove auto-creation of fai/dict files for fasta references ... -A UserException is now thrown if either the fai or dict file for the reference does not exist, with pointers to instructions for creating these files. -Gets rid of problematic file locking that was causing intermittent errors on our farm. -Integration tests to verify that correct exceptions are thrown in the case of a missing fai / dict file. GSA-866 #resolve		2013-04-02 18:34:08 -04:00
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commandline	Fixed the logic of the @Output annotation and its interaction with 'required'.	2013-03-14 11:58:51 -04:00
gatk	Remove auto-creation of fai/dict files for fasta references	2013-04-02 18:34:08 -04:00
jna	Fix more tests that fail when run in parallel on the farm	2013-03-12 16:53:30 -04:00
utils	Intervals: fix bug where we could fail to find the intersection of unsorted/missorted interval lists	2013-04-02 14:01:52 -04:00
BaseTest.java	Replace org.broadinstitute.variant with jar built from the Picard repo	2013-02-05 17:24:25 -05:00
ExampleToCopyUnitTest.java	Replace org.broadinstitute.variant with jar built from the Picard repo	2013-02-05 17:24:25 -05:00
MD5DB.java	Encrypt GATK AWS keys using the GATK private key, and decrypt as needed as a resource when uploading to AWS logs	2013-01-30 16:42:23 -05:00
MD5Mismatch.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
StingTextReporter.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
TestNGTestTransformer.java	Fix tests that were consistently or intermittently failing when run in parallel on the farm	2013-03-06 13:56:54 -05:00
WalkerTest.java	Replace org.broadinstitute.variant with jar built from the Picard repo	2013-02-05 17:24:25 -05:00