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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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disabling all BQSR unit tests
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2012-04-30 14:39:55 -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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GATKReport v1.0
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2012-03-12 23:09:19 -04:00 |
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diffengine
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Fixing MD5's (new GATKReport header was missing from old md5's)
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2012-03-19 15:28:45 -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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Don't allow N's in insertions when discovering indels. Maybe better solution will be to use them as wildcards and merge them with compatible regular insertion alleles but for now it's easier to ignore them. Minor refactoring of Allele.accepableAlleleBases to support this. Added unit test to test consensus allele counter in presence of N's
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2012-05-10 10:29:19 -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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AC strat now checks if evals will be merged before throwing an error on multiple eval files.
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2012-04-19 16:08:55 -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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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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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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