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CNV
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Nope, loads of integration tests had to be changed.
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2012-05-07 14:30:42 -04:00 |
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annotator
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Nope, loads of integration tests had to be changed.
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2012-05-07 14:30:42 -04:00 |
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beagle
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Minor tweaks to T2D-related qscripts. Replacing old md5s from the BeagleIntegrationTest. All differences boiled down either to the accounting of genotypes changed (./. --> 0/0 is no longer a "changed" genotype, and original genotypes that were ./. are represented as OG=. rather than OG=./. .)
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2012-01-23 08:25:34 -05:00 |
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bqsr
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Removed old GATKReport code and moved the new stuff in its place.
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2012-05-18 01:44:31 -04:00 |
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coverage
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DoC now properly handles reference N bases + misc. additional cleanups
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2012-02-25 11:32:50 -05:00 |
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diagnostics
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Extensive refactoring of the GATKReports. This was a beast.
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2012-05-18 01:11:26 -04:00 |
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diffengine
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Has anyone else ever noticed that the DiffEngine outputs were always doubled for some reason? That no longer happens with the new reports.
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2012-05-18 02:32:20 -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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a) Fully functional and working multiallelic exact model for pools. Needs cleanup/more testing. b) Better unit test for pool genotype likelihoods - it now optionally generates actual noisy pileups that can be used for assessing GL accuracy, c) Totally experimental, hidden option in VariantsToTable to output genotype fields. Specifying -GF will output columns of form Sample.FieldName - needs also more testing
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2012-05-14 10:55:35 -04:00 |
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indels
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Revving Picard to pick up new SamFileHeaderMerger.
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2012-05-02 16:47:28 -04:00 |
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phasing
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- Added option to output the father's allele first in phased child haplotypes - BUG corrected causing wrong phasing of child/father pairs
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2012-05-03 10:36:49 -04:00 |
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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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Patching special case in the adaptor clipping
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2012-01-11 17:47:44 -05:00 |
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validation
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Nope, loads of integration tests had to be changed.
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2012-05-07 14:30:42 -04:00 |
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varianteval
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Extensive refactoring of the GATKReports. This was a beast.
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2012-05-18 01:11:26 -04:00 |
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variantrecalibration
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Nope, loads of integration tests had to be changed.
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2012-05-07 14:30:42 -04:00 |
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variantutils
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Forgot that the VCFStreamingOntegrationTest uses VE
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2012-05-18 02:51:53 -04:00 |
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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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FlagStatIntegrationTest.java
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Adding integration test for Flag Stat
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2012-04-10 22:40:38 -04:00 |
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PileupWalkerIntegrationTest.java
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Had some free time, so I unplugged extended events from the walkers. Now they exist only in LocusIteratorByState, but ReadProperties.generateExtendedEvents() always returns false so that block is never actually executed anymore. I don't want to touch LIBS because I think David is in there right now.
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2012-04-02 14:27:36 -04:00 |
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PrintReadsIntegrationTest.java
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Bug fix for: https://getsatisfaction.com/gsa/topics/problem_with_indelrealigner_and_l_unmapped
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2012-04-27 09:58:38 -04:00 |
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PrintReadsUnitTest.java
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Better location for the downsampling of reads in PrintReads
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2012-01-14 14:06:09 -05:00 |
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