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arguments
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Final PED documentation
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2011-10-05 15:17:41 -07:00 |
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contexts
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Renamed ReadBackedPileup getXSampleName() functions to getXSample
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2011-09-30 10:02:57 -04:00 |
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datasources
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GATK read group requirement iron hand
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2011-10-06 08:40:35 -07:00 |
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examples
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@Hidden for DocumentationTest and GATKDocsExample
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2011-09-23 09:03:37 -04:00 |
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executive
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Removed Nx counting of reads in metrics with -nt > 1
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2011-10-06 18:29:26 -07:00 |
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filters
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Adding documentation before the release for GATK wiki page
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2011-09-15 13:56:23 -04:00 |
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io
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Fixed long-standing bug in tribble index creation
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2011-09-20 10:53:18 -04:00 |
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iterators
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GATK read group requirement iron hand
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2011-10-06 08:40:35 -07:00 |
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phonehome
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Explicit info message about uploading S3 log
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2011-09-12 22:16:52 -04:00 |
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refdata
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Removing this command-line tool. Purposely not doing this in stable so that users who may still use it have time to find other options. But the docs are no longer on the wiki.
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2011-09-28 13:18:32 -04:00 |
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report
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Failed to commit changes to the GATKReport required for more easy access when using the files as data sources (read: histograms) for walkers
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2011-09-21 18:15:23 -04:00 |
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samples
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Added getParents() -> returns an arrayList containing the sample's parent(s) if available
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2011-10-20 12:47:27 +02:00 |
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traversals
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Counts of records failing filters are displayed sorted
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2011-10-06 18:42:26 -07:00 |
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walkers
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- Genotype assignment in case of equally likeli combination is now random
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2011-10-26 19:57:09 +02:00 |
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CommandLineExecutable.java
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Removed -B support. Now explodes with error if -B provided.
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2011-08-16 16:13:47 -04:00 |
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CommandLineGATK.java
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Only concrete classes are now documented
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2011-08-18 14:04:47 -04:00 |
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DownsampleType.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 |
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DownsamplingMethod.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 |
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GenomeAnalysisEngine.java
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Filter application order is now deterministic, in the order defined by the walker
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2011-10-06 18:51:40 -07:00 |
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ReadMetrics.java
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Counts of records failing filters are displayed sorted
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2011-10-06 18:42:26 -07:00 |
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ReadProperties.java
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Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.
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2011-07-17 20:29:58 -04:00 |
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WalkerManager.java
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Removed support for RMD in @Requires and @Allows
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2011-08-03 15:36:55 -04:00 |
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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 |
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