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annotator
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Updated GenomicAnnotator integration tests to include the -NO_HEADER argument so that they tests op yelling about trtrivial differences
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2011-03-07 23:07:01 +00:00 |
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beagle
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There's no reason to special case no-calls if they already have PLs associated with them. Just use the PLs!
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2011-01-31 15:05:45 +00:00 |
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coverage
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-ct x no longer includes coverage in the previous bin
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2011-02-24 15:52:04 +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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Adding integration test for indels in VF
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2011-02-11 16:58:57 +00:00 |
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genotyper
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Added several integration tests for UG indel caller:
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2011-03-08 16:21:21 +00:00 |
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indels
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Adding performance test for case with very high coverage (> 600,000x) over an interval
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2011-02-28 19:48:56 +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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Updated integration test's MD5s reflect the fact that assay sequences were previously designed incorrectly for indels, the bug is now fixed.
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2011-01-28 23:00:22 +00:00 |
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varianteval
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Somehow missed this test when I was updating the md5s
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2011-03-07 23:53:42 +00:00 |
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variantrecalibration
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Minor bug fix in empiricalMu prior calculation in VQSR.
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2011-03-10 00:42:38 +00:00 |
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variantutils
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Switched the CVUnitTest broken info from an Integer to a String since as of r5383 Integers are no longer broken when converted to Floats.
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2011-03-07 16:33:14 +00:00 |
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BAQIntegrationTest.java
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Better query start / stop function that directly parses the cigar string, unlike the previous version. Now properly handles H (hard-clipped) reads. Added -baq OFF and -baq RECALCULATE integration tests on all three 1KG technologies. Please let me know if this new code somehow fails.
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2011-01-28 15:08:21 +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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