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annotator
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Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test.
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2010-12-08 17:22:29 +00:00 |
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beagle
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Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test.
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2010-12-08 17:22:29 +00:00 |
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coverage
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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fasta
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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filters
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Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test.
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2010-12-08 17:22:29 +00:00 |
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genotyper
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No reason to convert the GLs to a String for formatting when they're just going to be converted to PLs later. That was 5% of the UG runtime...
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2010-12-29 22:06:19 +00:00 |
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indels
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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phasing
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Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test.
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2010-12-08 17:22:29 +00:00 |
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qc
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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recalibration
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Bug fix in CountCovariates, skip over indel records as well as SNPs in the dbsnp file. CountCovariates is now called CountCovariatesWalker. I've always hated that the name was swapped.
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2010-12-02 18:43:24 +00:00 |
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sequenom
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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varianteval
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Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test.
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2010-12-08 17:22:29 +00:00 |
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variantrecalibration
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Removed LibBat.SUB2_BSUB_BLOCK since the use of it exits the JVM.
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2010-12-14 19:57:20 +00:00 |
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variantutils
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Rename it so that nobody else falls into the trap laid out (the test is VariantToTable, the walker is Variant[s]ToTable)
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2010-12-15 11:43:00 +00:00 |
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ClipReadsWalkersIntegrationTest.java
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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PileupWalkerIntegrationTest.java
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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PrintReadsWalkerUnitTest.java
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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VariantsToVCFIntegrationTest.java
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Support for indels in hapmap. This was non-trivial because not only does hapmap not tell you whether the allele is an insertion or deletion, but it also has a completely different positioning strategy (rightmost base). I'll send out an email tomorrow when the new HapMap3.3 VCF is ready.
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2010-12-27 07:37:46 +00:00 |
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