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gatk-3.8/java/test/org/broadinstitute/sting/gatk/walkers
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hanna 3dc78855fd Command-line argument tagging is in, and the ROD system is hacked slightly to support the new syntax 
(-B:name,type file) as well as the old syntax.  Also, a bonus feature: BAMs can now be tagged at the
command-line, which should allow us to get rid of some of the hackier calls in GenomeAnalysisEngine.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4105 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-08-25 03:47:57 +00:00
..
annotator Alleles are now returned in a consistent order, so we can deal with tri-allelic sites 2010-08-10 15:21:10 +00:00
coverage Removed hard-coded pointers to references 2010-08-04 17:59:37 +00:00
fasta Removed hard-coded pointers to references 2010-08-04 17:59:37 +00:00
filters Adding command-line header to VA and VF 2010-08-08 05:21:15 +00:00
genotyper Forgot to update UG performance test to reflect the new -o argument. 2010-08-23 00:57:16 +00:00
indels Deprecated 'O' in favor of 'o' in the cleaner 2010-08-23 18:09:24 +00:00
qc Fixed epic generic paths fail. 2010-05-13 15:59:57 +00:00
recalibration Removed hard-coded pointers to references 2010-08-04 17:59:37 +00:00
sequenom Removed hard-coded pointers to references 2010-08-04 17:59:37 +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 Some clean up for the variant recalibrator. Now uses @Input and @Output so that it can join the Queue party. Users now specify a -o, -clusterFile, -tranchesFile, and -reportDatFile. Example on the wiki. ApplyVariantCuts now has an integration test. Base quality recalibrator now requires a dbsnp rod or vcf file. Now that the base quality recalibrator is using @Output the PrintStream shouldn't be closed in OnTraversalDone. 2010-08-24 20:14:58 +00:00
variantutils Simple change to allow a list of samples or regular expressions to be provided in a text file (one line per sample). 2010-08-21 00:01:48 +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 Removed hard-coded pointers to references 2010-08-04 17:59:37 +00:00