bthomas 9d6a341d15 Fixing the error messages thrown with bad interval arguments. I simplified the exception handling and made the messages more verbose. ... Note: the -L argument takes both interval strings and filenames. If you specify an interval string that is also a file, an error will be thrown to move the file: ie. if you have a file "chr1" in the parent directory, GATK will ask you to move/delete it. But, this only happens with interval string arguments, NOT with intervals that are contained in files, which is a majority of the use case. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3602 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-21 21:49:41 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	Fixing the error messages thrown with bad interval arguments. I simplified the exception handling and made the messages more verbose.	2010-06-21 21:49:41 +00:00
test/org/broadinstitute/sting	Updating the way reference data is processed, so GATK creates the .fasta.fai and .dict files automatically. If either (or both) don't exist, GATK will create them in the same folder as the fasta file. If it can't write the file, GATK will fail with a message to create them manually.	2010-06-21 21:42:42 +00:00