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R
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R issue in Queue fixed.
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2013-01-28 14:42:20 -05:00 |
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activeregion
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Use base List and Map types in the HaplotypeCaller when possible.
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2013-01-30 17:09:27 -05:00 |
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analysis
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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baq
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Fixing BQSR/BAQ bug:
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2013-01-31 11:03:17 -05:00 |
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classloader
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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clipping
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Use base List and Map types in the HaplotypeCaller when possible.
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2013-01-30 17:09:27 -05:00 |
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codecs
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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collections
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-Added Per-Sample Contamination Removal to UnifiedGenotyper: Added an @Advanced option to the StandardCallerArgumentCollection, a file which should
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2013-02-04 18:24:36 -05:00 |
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crypt
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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duplicates
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Move BaseUtils back to the GATK by request, along with associated utility methods
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2013-01-30 13:09:44 -05:00 |
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exceptions
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Refactored GATKDocs categories some more ( GSATDG-62 )
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2013-02-13 16:49:18 -05:00 |
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fasta
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Move BaseUtils back to the GATK by request, along with associated utility methods
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2013-01-30 13:09:44 -05:00 |
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file
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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fragments
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Move some VCF/VariantContext methods back to the GATK based on feedback
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2013-01-29 16:56:55 -05:00 |
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genotyper
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Fixed non-determinism in HaplotypeCaller and some UG calls -
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2013-02-12 15:43:29 -05:00 |
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help
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Refactored GATKDocs categories some more ( GSATDG-62 )
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2013-02-13 16:49:18 -05:00 |
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instrumentation
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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interval
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Move some VCF/VariantContext methods back to the GATK based on feedback
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2013-01-29 16:56:55 -05:00 |
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io
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Encrypt GATK AWS keys using the GATK private key, and decrypt as needed as a resource when uploading to AWS logs
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2013-01-30 16:42:23 -05:00 |
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locusiterator
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LIBS optimization for adapter clipping
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2013-01-25 16:05:17 -05:00 |
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nanoScheduler
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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pairhmm
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Final version of PairHMMs with correct edge conditions
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2013-02-09 19:19:22 -05:00 |
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pileup
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Move BaseUtils back to the GATK by request, along with associated utility methods
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2013-01-30 13:09:44 -05:00 |
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pileup2
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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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progressmeter
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Resolves Genome Sequence Analysis GSA-750 Don't print an endless series of starting messages from the ProgressMeter
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2013-02-04 15:47:30 -05:00 |
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recalibration
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The Bayesian calculation of Qemp in the BQSR is now hierarchical. This fixes issues in which the covariate bins were very sparse and the prior estimate being used was the original quality score. This resulted in large correction factors for each covariate which breaks the equation. There is also now a new option, qlobalQScorePrior, which can be used to ignore the given (very high) quality scores and instead use this value as the prior.
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2013-01-28 15:56:33 -05:00 |
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runtime
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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sam
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PrintReads writes a header when used with -BQSR
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2013-02-14 22:19:14 -05:00 |
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text
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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threading
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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variant
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Replace org.broadinstitute.variant with jar built from the Picard repo
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2013-02-05 17:24:25 -05:00 |
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wiggle
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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AutoFormattingTime.java
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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BaseUtils.java
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- Added more comprehensive tests for consensus creation to RR. Still need to add tests for I/D ops.
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2013-02-01 15:37:19 -05:00 |
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BitSetUtils.java
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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ContigComparator.java
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Generalize and fixup ContigComparator
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2013-02-09 09:52:13 -05:00 |
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GenomeLoc.java
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Added distance across contigs calculation to GenomeLocs
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2013-02-07 16:31:41 -05:00 |
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GenomeLocParser.java
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Refactoring and unit testing GenomeLocParser
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2013-01-30 09:47:47 -05:00 |
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GenomeLocSortedSet.java
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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Haplotype.java
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Use base List and Map types in the HaplotypeCaller when possible.
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2013-01-30 17:09:27 -05:00 |
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HasGenomeLocation.java
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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HeapSizeMonitor.java
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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IndelUtils.java
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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LRUCache.java
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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MRUCachingSAMSequenceDictionary.java
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Refactoring and unit testing GenomeLocParser
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2013-01-30 09:47:47 -05:00 |
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MannWhitneyU.java
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Move some VCF/VariantContext methods back to the GATK based on feedback
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2013-01-29 16:56:55 -05:00 |
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MathUtils.java
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Making band pass filter size, sigma, active region max size and extension all accessible from the command line
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2013-01-24 13:47:59 -05:00 |
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Median.java
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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MendelianViolation.java
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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MultiThreadedErrorTracker.java
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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NGSPlatform.java
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Expand NGSPlatform to meet SAM 1.4 spec, with full unit tests
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2013-02-09 11:16:21 -05:00 |
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PathUtils.java
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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QualityUtils.java
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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SWPairwiseAlignment.java
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Updating licenses manually
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2013-01-29 17:27:53 -05:00 |
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SampleUtils.java
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Move some VCF/VariantContext methods back to the GATK based on feedback
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2013-01-29 16:56:55 -05:00 |
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SequenceDictionaryUtils.java
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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SimpleTimer.java
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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UnvalidatingGenomeLoc.java
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Refactoring the SimpleGenomeLoc into the now public utility UnvalidatingGenomeLoc and the RR-specific FinishedGenomeLoc.
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2013-01-30 10:45:29 -05:00 |
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Utils.java
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Final version of PairHMMs with correct edge conditions
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2013-02-09 19:19:22 -05:00 |
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package-info.java
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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