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gatk-3.8/java/test/org/broadinstitute/sting
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aaron 32f324a009 incremental changes to the VCF4 codec, including allele clipping down to the minimum reference allele; adding unit testing for certain aspects of the parsing. Not ready for prime-time yet. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3604 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-06-22 06:31:05 +00:00
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alignment Forgot to uncomment the AlignerIntegrationTest before committing. And yes, matt, commenting it out is, in fact, easier than just setting my classpath. 2010-04-01 17:17:16 +00:00
commandline The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had 2010-04-20 15:26:32 +00:00
gatk incremental changes to the VCF4 codec, including allele clipping down to the minimum reference allele; adding unit testing for certain aspects of the parsing. Not ready for prime-time yet. 2010-06-22 06:31:05 +00:00
playground Initial HLA Caller integration tests. Kind of painful, but will improve with code refactoring. 2010-06-18 20:35:27 +00:00
utils Updating the way reference data is processed, so GATK creates the .fasta.fai and .dict files automatically. If either (or both) don't exist, GATK will create them in the same folder as the fasta file. If it can't write the file, GATK will fail with a message to create them manually. 2010-06-21 21:42:42 +00:00
BaseTest.java incremental changes to the VCF4 codec, including allele clipping down to the minimum reference allele; adding unit testing for certain aspects of the parsing. Not ready for prime-time yet. 2010-06-22 06:31:05 +00:00
WalkerTest.java GATK now does automatic adaptor filtering in locus iterators (but not expt. downsampling iterator). General support for LocusIteratorFilters just like read filters but only applying at particular bases. Updated tools with new MD5 sums due to adaptor bases in their integrationtest data. Not that as a side effect here reads close to each other with odd orientations are also filtered out. Updated minor argument to VariantRecalibrator to change the qStep value on the command line 2010-06-02 22:26:32 +00:00