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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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GenotypesContext no longer have immutability in constructor
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2011-11-21 14:34:31 -05:00 |
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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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Removing the legacy -L "interval1;interval2" syntax
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2011-11-21 13:18:53 -05:00 |
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diffengine
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DiffObjects no longer prints out the file name in the status so MD5 are stable
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2011-10-10 15:10:57 -04:00 |
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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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UG now encoding NO_CALLs as ./. not ./.:.:4:0,0,0
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2011-11-22 08:22:32 -05:00 |
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indels
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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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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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Update MD5s for SOLiD recalibration
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2011-10-13 18:01:51 -04:00 |
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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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Added MendelianViolationEvaluator integration test
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2011-11-30 10:09:20 +01:00 |
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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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Fix for changed MD5 in streaming VCF test
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2011-11-23 19:01:33 -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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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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GATKSAMRecord refactor
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2011-11-03 15:43:26 -04:00 |
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