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arguments
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Okay, all public->protected dependencies are gone except for the BQSR arguments. I'll need to think through this but should be able to make that work too.
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2013-01-08 15:46:32 -05:00 |
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contexts
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Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package
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2012-12-19 10:25:22 -05:00 |
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datasources
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Archive the experimental Active Region Traversals
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2013-01-04 17:05:31 -05:00 |
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downsampling
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Fix bug in the PerSampleDownsamplingReadsIterator that could lead to excessive memory usage at traversal startup
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2012-12-19 02:05:36 -05:00 |
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examples
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Okay, all public->protected dependencies are gone except for the BQSR arguments. I'll need to think through this but should be able to make that work too.
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2013-01-08 15:46:32 -05:00 |
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executive
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Archive the experimental Active Region Traversals
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2013-01-04 17:05:31 -05:00 |
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filters
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Resolving merge conflicts from VCF move
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2013-01-06 14:32:31 -05:00 |
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io
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Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package
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2012-12-19 10:25:22 -05:00 |
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iterators
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Use the new downsampling implementation by default
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2012-12-10 09:44:50 -05:00 |
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phonehome
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Incorporating clover into build.xml
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2012-12-24 13:35:57 -05:00 |
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refdata
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Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package
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2012-12-19 10:25:22 -05:00 |
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report
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Added unit test for outputting sorted GATKReport Tables
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2013-01-03 16:53:59 -05:00 |
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resourcemanagement
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Fixed bug in ThreadAllocation getTotalNumberOfThreads
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2012-09-05 16:35:32 -04:00 |
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samples
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Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package
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2012-12-19 10:25:22 -05:00 |
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traversals
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Fixing bug in TraverseDuplicates.printProgress call: only passes in single location of genome loc
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2013-01-05 12:50:27 -05:00 |
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walkers
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Moved (nearly) all Walkers from public to protected and removed GATKLite utils
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2013-01-07 14:42:40 -05:00 |
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CommandLineExecutable.java
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Update URL for phone home / GATK key documentation output by the GATK upon error
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2012-08-08 09:29:54 -04:00 |
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CommandLineGATK.java
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Moving HelpConstants out of HelpUtils so that we stop getting these ProgramElementDoc errors when com.sun.javadoc cannot load on a user's system.
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2013-01-06 14:30:45 -05:00 |
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GenomeAnalysisEngine.java
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Moved (nearly) all Walkers from public to protected and removed GATKLite utils
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2013-01-07 14:42:40 -05:00 |
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ReadMetrics.java
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Mark I NanoScheduling TraverseLoci
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2012-09-05 15:45:23 -04:00 |
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ReadProperties.java
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Experimental, downsampler-friendly read shard balancer
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2012-09-21 22:17:58 -04:00 |
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WalkerManager.java
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Use the new downsampling implementation by default
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2012-12-10 09:44:50 -05:00 |
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package-info.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
f0bd1b5ae5