9 Commits (787e5d85e99267fb1cf20ba635b0bbdd9506e360)

Author	SHA1	Message	Date
hanna	8e36a07bea	Convert GenomeLocParser into an instance variable. This change is required ... for anything that needs to be simultaneously aware of multiple references, eg Queue's interval sharding code, liftover support, distributed GATK etc. GenomeLocParser instances must now be used to create/parse GenomeLocs. GenomeLocParser instances are available in walkers by calling either -getToolkit().getGenomeLocParser() or -refContext.getGenomeLocParser() This is an intermediate change; GenomeLocParser will eventually be merged with the reference, but we're not clear exactly how to do that yet. This will become clearer when contig aliasing is implemented. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4642 348d0f76-0448-11de-a6fe-93d51630548a	2010-11-10 17:59:50 +00:00
hanna	8f9bf82aa7	Bamboo is correctly interpreting test fails. Reverting forced-fail test ... code. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4617 348d0f76-0448-11de-a6fe-93d51630548a	2010-11-02 19:32:34 +00:00
hanna	1df166b76e	Forcing a unit test fail to ensure that Bamboo is picking up on failed tests ... as well as successes. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4616 348d0f76-0448-11de-a6fe-93d51630548a	2010-11-02 19:03:12 +00:00
hanna	861ee3e37a	Changing testing framework from junit -> testng, for its enhanced configurability. ... Initial test to see how Bamboo will respond. More detailed email to follow. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4609 348d0f76-0448-11de-a6fe-93d51630548a	2010-11-01 21:31:44 +00:00
depristo	7880863eb7	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. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4267 348d0f76-0448-11de-a6fe-93d51630548a	2010-09-12 15:07:38 +00:00
depristo	7ad8fbdd5a	Moved GATKException to exceptions ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4266 348d0f76-0448-11de-a6fe-93d51630548a	2010-09-12 14:47:19 +00:00
depristo	40e6179911	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. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4258 348d0f76-0448-11de-a6fe-93d51630548a	2010-09-12 14:02:43 +00:00
hanna	8573b0bc6f	Refactoring intervals, separating the process of parsing interval lists, ... sorting and merging interval lists, and creating RODs from intervals. This gives Doug the ability to keep using our interval list parsing code when sorting intervals on our behalf. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3159 348d0f76-0448-11de-a6fe-93d51630548a	2010-04-13 15:50:38 +00:00
aaron	4014a8a674	A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests. ... Thanks! git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3135 348d0f76-0448-11de-a6fe-93d51630548a	2010-04-08 06:14:15 +00:00