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gatk-3.8/java/test/org/broadinstitute/sting/gatk
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rpoplin 1931b2e1bd Three fixes for VariantFiltrationWalker: Trying to filter an empty VCF file will produce a well-formed VCF file with zero records instead of a blank file, needed for pipelines. The first record's genotype info fields are now in the same order as all the others. The VCF header lines are pulled from just the input variant rod instead of from all rods. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4341 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-09-24 13:52:56 +00:00
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arguments Removing the obsolete --hapmap and --hapmap_chip options 2010-08-31 16:57:05 +00:00
contexts/variantcontext Update integration tests to use the new ROD syntax. 2010-08-25 18:13:30 +00:00
datasources Sliced the GAE in half like a gordian knot to avoid the constant merge conflicts. 2010-09-23 23:28:55 +00:00
executive 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. 2010-04-08 06:14:15 +00:00
filters 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
iterators Eliminated -mrl option. 2010-08-26 21:38:03 +00:00
refdata one broken build short of the hat trick. Fixing the unix test which expects the sequence dictionary of the Tribble track to equal the reference; we actually return the sequence dictionary of the track iself, with each contig set to the length of the sequence dictionary contig entry. 2010-09-21 18:47:20 +00:00
traversals Command-line argument tagging is in, and the ROD system is hacked slightly to support the new syntax 2010-08-25 03:47:57 +00:00
walkers Three fixes for VariantFiltrationWalker: Trying to filter an empty VCF file will produce a well-formed VCF file with zero records instead of a blank file, needed for pipelines. The first record's genotype info fields are now in the same order as all the others. The VCF header lines are pulled from just the input variant rod instead of from all rods. 2010-09-24 13:52:56 +00:00