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gatk-3.8/java/test/org/broadinstitute/sting
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hanna 7fa6b2135b Added a back door so that integration tests can reset the sequence dictionary 
in the reference.  Reset routine is not accessible to any class outside
GenomeLocParser's package.

We'll have to do something more intelligent with this when the GATK goes
distributed.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4275 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-09-14 18:58:08 +00:00
..
alignment all fixed..thanks Matt! 2010-09-10 06:18:59 +00:00
commandline Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision. 2010-09-12 15:07:38 +00:00
gatk Improvements to the error display code to print out the SVN number in all messages. Fixes to CallableLoci and tests to check for that case 2010-09-13 18:36:45 +00:00
oneoffprojects/walkers Penultimate step in exception system overhaul. UserError is now UserException. This class should be used for all communication with the USER for problems with their inputs. Engine now validates sequence dictionaries for compatibility, detecting not only lack of overlap but now inconsistent headers (b36 ref with v37 BAM, for example) as well as ref / bam order inconsistency. New -U option to allow users to tolerate dangerous seq dict issues. WalkerTest system now supports testing for exceptions (see email and wiki for docs). Tests for vcf and bam vs. ref incompatibility. Waiting on Tribble seq dict improvements to detect b36 VCF with b37 ref (currently cannot tell this is wrong. 2010-09-12 14:02:43 +00:00
playground The battle is over. Picard is revved. 2010-09-03 05:28:01 +00:00
utils Added a back door so that integration tests can reset the sequence dictionary 2010-09-14 18:58:08 +00:00
BaseTest.java Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision. 2010-09-12 15:07:38 +00:00
WalkerTest.java Added a back door so that integration tests can reset the sequence dictionary 2010-09-14 18:58:08 +00:00