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gatk-3.8/java/test/org/broadinstitute/sting/gatk/walkers
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ebanks 3b5673d967 1. Removed -all; by default all modules are used; use -none for no modules. 
2. Don't make dbsnp track be a comp by default (to cut back on output). Please let me know if someone wants this back for some reason.
3. Cleaned up dbsnp module output to print the right numbers.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3220 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-04-21 02:46:42 +00:00
..
annotator Heads up everyone: 2010-04-09 05:37:25 +00:00
concordance Fixing/cleaning up the vcf merge util 2010-03-19 15:13:32 +00:00
fasta Moving over to VariantContext from Variation 2010-04-19 06:56:29 +00:00
filters Moving VariantFiltration over to use VariantContext. 2010-03-19 18:35:23 +00:00
genotyper Adding performance tests for the indel realigner; should take ~3 hours. 2010-04-11 04:45:22 +00:00
indels Fixing the performance tests: we need to catch the RuntimeException (not samtools' RuntimeIOExcpetion). Also, CountCovariates doesn't need the catch. 2010-04-19 14:28:12 +00:00
recalibration Fixing the performance tests: we need to catch the RuntimeException (not samtools' RuntimeIOExcpetion). Also, CountCovariates doesn't need the catch. 2010-04-19 14:28:12 +00:00
sequenom Redoing the conversion to VariantContext: instead of walkers passing in a ref allele, they pass in the ref context and the adaptors create the allele. This is the right way of doing it. 2010-04-19 05:47:17 +00:00
varianteval 1. Removed -all; by default all modules are used; use -none for no modules. 2010-04-21 02:46:42 +00:00
DepthOfCoverageIntegrationTest.java Execs() temporarily disabled after removal of bam file. New tests forthcoming. 2010-04-15 20:11:56 +00:00
PileupWalkerIntegrationTest.java Now that we changed how deletions are represented, got to update MD5... 2009-12-30 22:00:58 +00:00
PrintReadsWalkerUnitTest.java 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
VariantsToVCFIntegrationTest.java Redoing the conversion to VariantContext: instead of walkers passing in a ref allele, they pass in the ref context and the adaptors create the allele. This is the right way of doing it. 2010-04-19 05:47:17 +00:00