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CNV
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Fixed bug that required symbolic alleles to be padded with reference base and added integration test to test parsing and output of symbolic alleles
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2011-08-12 12:23:44 -04:00 |
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annotator
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Renaming VariantAnnotator SnpEff keys
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2011-09-15 17:42:15 -04:00 |
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beagle
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Intermediate (but necessary) fix for Beagle walkers: if a marker is absent in the Beagle output files, but present in the input vcf, there's no reason why it should be omitted in the output vcf. Rather, the vc is written as is from the input vcf
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2011-09-13 16:57:37 -04:00 |
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coverage
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Moving more tools over to the new rod system
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2011-08-10 13:42:35 -04:00 |
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diffengine
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Spelling fix requires md5 updates
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2011-08-26 07:40:44 -04:00 |
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fasta
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More updates to be consistent with the new rod syntax.
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2011-08-09 10:11:37 -04:00 |
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filters
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Thanks to Mark for agreeing to transition from 'variants' back to 'variant'. I think I got them all but I've been jumping all around the code, so there might be a straggler or two.
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2011-08-09 12:04:55 -04:00 |
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genotyper
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Uncomment code to add deleted bases covering an indel to per-sample genotype reporting, update integration tests accordingly
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2011-09-10 19:41:01 -04:00 |
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indels
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Moving more tools over to the new rod system
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2011-08-10 13:42:35 -04:00 |
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phasing
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Update to new RodBinding system
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2011-08-11 17:54:16 -04:00 |
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qc
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Thanks to Mark for agreeing to transition from 'variants' back to 'variant'. I think I got them all but I've been jumping all around the code, so there might be a straggler or two.
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2011-08-09 12:04:55 -04:00 |
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recalibration
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Fixing syntax of BQSR and UG performance tests.
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2011-08-11 17:04:09 -04:00 |
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validation
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Continuing progress towards RodBinding 1.0
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2011-08-03 17:19:28 -04:00 |
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varianteval
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Renaming VariantAnnotator SnpEff keys
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2011-09-15 17:42:15 -04:00 |
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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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Forgot to git stash pop new MD5's for CombineVariants integration test
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2011-09-16 12:53:54 -04:00 |
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BAQIntegrationTest.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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ClipReadsWalkersIntegrationTest.java
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Swapped argument order but not MD5 order
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2011-08-19 16:55:56 -04:00 |
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PileupWalkerIntegrationTest.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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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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PrintReadsWalkerUnitTest.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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