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CNV
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Updating md5 because the file changed
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2011-09-23 07:33:20 -04:00 |
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annotator
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Updating integration tests now that standard annotations support multiple alleles
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2012-02-27 11:32:26 -05:00 |
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beagle
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Minor tweaks to T2D-related qscripts. Replacing old md5s from the BeagleIntegrationTest. All differences boiled down either to the accounting of genotypes changed (./. --> 0/0 is no longer a "changed" genotype, and original genotypes that were ./. are represented as OG=. rather than OG=./. .)
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2012-01-23 08:25:34 -05:00 |
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bqsr
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Unit tests for the context covariate
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2012-03-01 17:56:45 -05:00 |
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coverage
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DoC now properly handles reference N bases + misc. additional cleanups
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2012-02-25 11:32:50 -05:00 |
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diagnostics
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Workaround for bug in Picard in ReadGroupProperties
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2012-03-02 18:53:45 -05:00 |
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diffengine
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Right aligning GATKReport numeric columns and updated MD5s in tests.
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2011-12-05 23:22:15 -05:00 |
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fasta
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Removing the legacy -L "interval1;interval2" syntax
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2011-11-21 13:18:53 -05:00 |
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filters
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Again, fixing the add call when we really mean replace
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2011-11-21 19:15:56 -05:00 |
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genotyper
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Updating integration tests now that standard annotations support multiple alleles
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2012-02-27 11:32:26 -05:00 |
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indels
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Rename *PerformanceTest test classes to *LargeScaleTest
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2011-12-22 10:38:49 -05:00 |
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phasing
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Merge with master
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2011-11-19 09:56:06 -05:00 |
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qc
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First version of VariantContextBuilder
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2011-11-18 11:06:15 -05:00 |
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recalibration
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Patching special case in the adaptor clipping
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2012-01-11 17:47:44 -05:00 |
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validation
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Removing all instances of -BTI (in tests and in GATKdocs) and replacing them with the appropriate alternative.
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2011-10-27 23:55:11 -04:00 |
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varianteval
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Bug fix for VariantSummary
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2012-01-05 21:51:06 -05:00 |
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variantrecalibration
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Changing the VQSR command line syntax back to the parsed tags approach. This cleans up the code and makes sure we won't be parsing the same rod file multiple times. I've tried to update the appropriate qscripts.
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2011-09-12 12:17:43 -04:00 |
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variantutils
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Another test where we no longer print out 'NaN' for the AF.
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2012-02-27 15:19:08 -05:00 |
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BAQIntegrationTest.java
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merge master
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2011-10-25 16:08:39 -04:00 |
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ClipReadsWalkersIntegrationTest.java
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Updating MD5s for updated BAM with read groups
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2011-10-06 12:15:48 -07:00 |
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PileupWalkerIntegrationTest.java
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Updated integration tests for the new adaptor clipping fix.
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2011-12-30 18:47:14 -05:00 |
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PrintReadsIntegrationTest.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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PrintReadsUnitTest.java
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Better location for the downsampling of reads in PrintReads
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2012-01-14 14:06:09 -05:00 |
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