hanna 7087c2f422 Very simple integration tests for basic VCF streaming functionality. ... Rather than try to fork the integration test process to get a pipe source and sink, creates a new named pipe by Runtime.exec()ing the 'mkfifo' shell command. We'll see whether this proves to be a reliable method for testing streaming. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5028 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-20 04:38:54 +00:00
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arguments	A significant refactoring of the ROD system, done largely to simplify the process of	2010-12-31 04:52:22 +00:00
contexts/variantcontext	Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test.	2010-12-08 17:22:29 +00:00
datasources	Fix concurrency issue that periodically kills VariantEvalIntegrationTest --	2011-01-14 18:52:21 +00:00
executive	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
filters	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
iterators	Implemented a new argument (-DQS --defaultQualityScore) that allows GATK to deal with BAM files missing quality scores. If a value is specified, all reads are filled with the default quality score. Appropriate exception is thrown if -DQS is not provided and BAM file doesn't have quality scores for every base.	2011-01-05 22:25:08 +00:00
refdata	Oops...forgot to commit the changes that allow primitive VCF streaming.	2011-01-12 21:54:51 +00:00
traversals	can explicitly set the now required ReferenceDataSource in unit tests	2011-01-12 18:25:12 +00:00
walkers	Very simple integration tests for basic VCF streaming functionality.	2011-01-20 04:38:54 +00:00
WalkerManagerUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00