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 |
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Mauricio Carneiro
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1085df8b7b
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Making the BQSR pipeline publicly available and supported.
this is for all the Pacbio validation that is going on right no in the cancer group. They are all using this script, and I'm happy to support it.
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2011-06-29 16:05:32 -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 |