Mauricio Carneiro
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dcf21f379a
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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
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2011-07-23 12:59:53 -04:00 |
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Mauricio Carneiro
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f0a6dd27a1
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Renaming the plot output directory names.
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2011-07-23 12:59:37 -04:00 |
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Mauricio Carneiro
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4f78025b0b
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Merged bug fix from Stable into Unstable
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2011-07-22 14:42:04 -04:00 |
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Mauricio Carneiro
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4080e2cd88
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* Added the decoy reference to the bundle under the b37 resources.
* Updated the -svn argument to -ver since we don't use svn anymore (also updated the wiki).
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2011-07-22 14:41:22 -04:00 |
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Mauricio Carneiro
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9ad5c7dfa4
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Resolving simple conflicts in the data processing pipeline.
Conflicts:
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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2011-07-19 08:05:11 -04:00 |
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Mauricio Carneiro
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7688bda1a6
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better progress report for the DPP
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2011-07-18 23:39:47 -04:00 |
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Mauricio Carneiro
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2b465ab43b
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* added optional 'no validation' for the Data Processing pipeline.
* some simplifications on the picard classes
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2011-07-18 23:30:31 -04:00 |
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Mauricio Carneiro
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4cf7a2af23
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Removed broad specific default paths so people from outside the broad can use it.
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2011-07-18 23:25:21 -04:00 |
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Mauricio Carneiro
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5cb5a4ec75
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Merged bug fix from Stable into Unstable
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2011-07-16 00:23:59 -04:00 |
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Mauricio Carneiro
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dd92a14b40
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Made extra indel VCF optional but DBSNP mandatory.
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2011-07-16 00:23:35 -04:00 |
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Mauricio Carneiro
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2fa5dbb0fe
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Merged bug fix from Stable into Unstable
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2011-07-16 00:15:19 -04:00 |
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Mauricio Carneiro
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ed55182a4c
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Removing Broad specific paths from parameters and making them required. This should make it unambiguous for people inside and outside the Broad to use the DataProcessingPipeline (as per request in the GetSatisfaction)
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2011-07-16 00:09:00 -04:00 |
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Mauricio Carneiro
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43bd45fcad
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Merged bug fix from Stable into Unstable
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2011-07-15 19:40:02 -04:00 |
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Mauricio Carneiro
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fd1df31ef0
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changing the output directory names for Analyze Covariates
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2011-07-15 19:39:42 -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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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 |
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Mauricio Carneiro
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f19862a643
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Fixing conflicts.
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2011-07-14 17:13:31 -04:00 |
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Mauricio Carneiro
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43c6a8565b
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looks better now.
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2011-07-14 17:10:44 -04:00 |
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Mauricio Carneiro
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09ffe277ae
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Added a qscripts util package with some utility functions commonly shared across queue scripts. Refactored some of my public scripts to use it in an effort to make queue scripts more reusable and "supportable".
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2011-07-14 17:09:35 -04:00 |
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Mauricio Carneiro
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4f8230c750
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Merged bug fix from Stable into Unstable
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2011-07-14 16:44:57 -04:00 |
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Mauricio Carneiro
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9f5180ab05
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Recalibrates a list of bam files allowing multiple bams to be recalibrated out of a single 'mother' queue job.
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2011-07-14 16:42:17 -04:00 |
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Mauricio Carneiro
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df996a1a73
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more progress report for the Data Processing Pipeline.
Bam lists can now have empty lines, comments and whitespaces anywhere.
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2011-07-13 14:53:58 -04:00 |
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Mauricio Carneiro
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ff4e31c554
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Changing the file names as per Kris request.
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2011-07-13 12:59:18 -04:00 |
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Mauricio Carneiro
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5298e3a942
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Making the outputDir optional. Default = ./
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2011-07-05 16:30:41 -04:00 |
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Mauricio Carneiro
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7d3dfdfdf2
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Updating the MDCP to use the classpath for the GATK jar, removing -gatk parameter.
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2011-07-05 16:30:10 -04:00 |
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Mauricio Carneiro
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b0fb63e20a
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moving the example scala scripts to the qscripts package.
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2011-07-01 16:14:59 -04:00 |
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Mauricio Carneiro
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d19351f71a
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Added capability of running multiple bam files in the same directory.
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2011-07-01 16:02:28 -04:00 |
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Mauricio Carneiro
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197b7141c1
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Added an optional argument -bt <num_threads> for BWA to run multithreaded.
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2011-06-30 14:41:57 -04:00 |
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Mauricio Carneiro
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f4463d38ca
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BWA requires pair ended reads to be sorted by read names when operating over BAM files, but Picard sorts by coordinate, so in case we use BWA in pair ended reads, the pipeline now resorts the BAM in read name order, realigns it then sorts it in coordinate order.
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2011-06-30 14:29:21 -04:00 |
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Mauricio Carneiro
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efd99c3c11
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new home for the core qscripts
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2011-06-30 11:32:06 -04:00 |