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gatk-3.8/java/test/org/broadinstitute/sting/gatk/walkers
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depristo 6a30617a60 Initial implementation of UserError exceptions and error message overhaul. UserErrors and their subclasses UserError.MalFormedBam for example should be used when the GATK detects errors on part of the user. The output for errors is now much clearer and hopefully will reduce GS posts. Please start using UserError and its subclasses in your code. I've replace some, but not all, of the StingExceptions in the GATK with UserError where appropriate. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4239 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-09-09 11:32:20 +00:00
..
annotator Moving supported tools to core 2010-08-26 13:56:19 +00:00
beagle Moving supported tools to core 2010-08-26 13:56:19 +00:00
coverage Updated tribble BED parsing code to use the official UCSC spec, and updated tests to match expected results. 2010-09-01 21:49:06 +00:00
fasta Update integration tests to use the new ROD syntax. 2010-08-25 18:13:30 +00:00
filters Update integration tests to use the new ROD syntax. 2010-08-25 18:13:30 +00:00
genotyper Remove the check in the Unified Genotyper for hitting the max reads at locus value. Instead, simply add a flag to the INFO field if any of the samples has been downsampled. 95% hooked up. 2010-08-26 05:50:47 +00:00
indels Addition for Tim: recalculate the NM and UQ tags after realignment. Also, don't fix the insert size calculation, since that's done by fix mate information. 2010-09-08 04:02:14 +00:00
qc Update integration tests to use the new ROD syntax. 2010-08-25 18:13:30 +00:00
recalibration Fix busted performance test (-outputBam has been deprecated in the BQ recalibrator in favor of -o) 2010-09-03 12:51:53 +00:00
sequenom Office-mate courtesy: fixing Andrey's busted integration test 2010-08-26 02:00:06 +00:00
varianteval 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
variantrecalibration Initial implementation of UserError exceptions and error message overhaul. UserErrors and their subclasses UserError.MalFormedBam for example should be used when the GATK detects errors on part of the user. The output for errors is now much clearer and hopefully will reduce GS posts. Please start using UserError and its subclasses in your code. I've replace some, but not all, of the StingExceptions in the GATK with UserError where appropriate. 2010-09-09 11:32:20 +00:00
variantutils Update integration tests to use the new ROD syntax. 2010-08-25 18:13:30 +00:00
ClipReadsWalkersIntegrationTest.java The battle is over. Picard is revved. 2010-09-03 05:28:01 +00:00
PileupWalkerIntegrationTest.java Removed hard-coded pointers to references 2010-08-04 17:59:37 +00:00
PrintReadsWalkerUnitTest.java Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting. 2010-08-22 14:27:05 +00:00
VariantsToVCFIntegrationTest.java Update integration tests to use the new ROD syntax. 2010-08-25 18:13:30 +00:00