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annotator
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Rank sum test annotations are the Z-scores from the test instead of the p-value.
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2011-04-28 14:35:00 +00:00 |
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beagle
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Continuing the epic fail, some of our existing integration tests were wrong because of the lazy loading failure.
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2011-04-29 17:54:41 +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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Continuing the epic fail, some of our existing integration tests were wrong because of the lazy loading failure.
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2011-04-29 17:54:41 +00:00 |
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genotyper
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Rank sum test annotations are the Z-scores from the test instead of the p-value.
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2011-04-28 14:35:00 +00:00 |
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indels
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As I threatened yesterday, I've moved the various and disparate randomization code out of the walkers. Now they all (except VQSRv1, whose days are numbered anyways) use a static generator available in the engine itself. Please use this from now on. The seed is reset before every individual integration test is run. I think there may still be an issue with the IndelRealigner but I need to confirm with the commit to see what testNG does. Integration tests are already broken anyways, so no big deal.
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2011-04-07 17:03:48 +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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As I threatened yesterday, I've moved the various and disparate randomization code out of the walkers. Now they all (except VQSRv1, whose days are numbered anyways) use a static generator available in the engine itself. Please use this from now on. The seed is reset before every individual integration test is run. I think there may still be an issue with the IndelRealigner but I need to confirm with the commit to see what testNG does. Integration tests are already broken anyways, so no big deal.
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2011-04-07 17:03:48 +00:00 |
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sequenom
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continuing from last night, the integration tests weren't covering the right behavior either
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2011-04-28 13:30:57 +00:00 |
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varianteval
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My fixes to Tribble yesterday revealed that some of the test VCFs for integration tests were actually malformed. Also, Guillermo updated the b37 dbSNP VCF and that broke some tests. Should be good for now.
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2011-04-17 03:39:11 +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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Epic failure on the lazy loading of genotypes: if the input VCF had its samples unsorted and we used a walker that didn't require genotypes, then we would sort the samples but not load genotypes (and therefore the genotypes wouldn't match the samples anymore). Added simple integration test to cover this case.
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2011-04-29 16:03:45 +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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Updated to now longer include 2nd-best base output
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2011-04-03 20:13:10 +00:00 |
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PrintReadsIntegrationTest.java
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--simplifyBAM is now in the SAMFileWriterArgumentTypeDescriptor, as suggested by map. PrintReads has an integrationtest now that writes out a 1 MB bit of HiSeq normally, with compress 0, and with simplifyBAM on.
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2011-03-26 14:57:18 +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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