Mark DePristo
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9e53fd6880
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Fixed VCFGatherFunction to not provide incorrect rod_priority_list
-- simply don't provide one, since you are just 'cating' the files together and genotypes never overlap
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2011-08-10 07:28:35 -04:00 |
Mauricio Carneiro
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22d2563823
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added BWA SW alignment
The pipeline now accepts fasta/fastq files and aligns them using BWA SW, adds default basequalities, creates read groups and performs BQSR.
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2011-08-09 17:05:24 -04:00 |
Eric Banks
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5a3c99b7b9
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Fixing 'variants' change in qscript
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2011-08-09 12:30:46 -04:00 |
Khalid Shakir
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cb28875c2a
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Updated rod binding syntax usage on CombineVariants from .rodBind to .variants.
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2011-08-09 00:46:39 -04:00 |
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Mark DePristo
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e5fde0d16b
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Merge branch 'master' into rodRefactor
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2011-08-08 10:08:43 -04:00 |
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Khalid Shakir
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eaa2f16d83
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When a job finishes successfully in the ShellJobRunner, mark it as DONE instead of FAILED.
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2011-08-06 10:42:04 -04:00 |
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Mark DePristo
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4f8d830960
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Updated to reflect new parse() function
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2011-07-30 15:34:20 -04:00 |
|
Khalid Shakir
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59eb1f4663
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Memory limits changed from Int to Double.
Updated LSF calls to read memory units from config along with tweaks to select hosts.
Moved some common code from GridEngine and LSF to super classes.
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2011-07-21 22:57:18 -04:00 |
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Mauricio Carneiro
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ecc8726f63
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Merged bug fix from Stable into Unstable
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2011-07-17 18:10:18 -04:00 |
|
Mauricio Carneiro
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1af76736b9
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Guarantees that the list of files will always be in the same order.
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2011-07-17 11:41:34 -04:00 |
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Mauricio Carneiro
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aa30f416a3
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Resolving conflicts
Conflicts:
private/scala/qscript/depristo/ExomePostQCEval.scala
private/scala/qscript/depristo/PostCallingQC.scala
private/scala/qscript/org/broadinstitute/sting/queue/qscripts/archive/ExomePostQCEval.scala
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2011-07-15 16:21:42 -04:00 |
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Mauricio Carneiro
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224d373997
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No need to double overload the file constructor
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2011-07-15 15:19:10 -04:00 |
|
Mauricio Carneiro
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7b7d40d5d9
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A better name for the qscript utilities. Throw here every method you find yourself repeatedly implementing in your qscripts!
Refactoring appropriately.
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2011-07-15 14:34:50 -04:00 |
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Mauricio Carneiro
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a670d6420a
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Refactoring Qscript utils into queue general utils package.
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2011-07-15 14:31:43 -04:00 |
|
Khalid Shakir
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e93052a51e
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When generating the QGraph, don't regenerate if there aren't scatter/gather jobs.
Fixed a display issue with the number of milliseconds that Queue has tried to contact LSF.
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2011-07-11 19:17:58 -04:00 |
David Roazen
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3c9497788e
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Reorganized the codebase beneath top-level public and private directories,
removing the playground and oneoffprojects directories in the process. Updated
build.xml accordingly.
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2011-06-28 06:55:19 -04:00 |