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 |
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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Khalid Shakir
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b6bc64a0c8
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Cleanup of the utils.broad package.
Using Picard IoUtils on sample names.
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2011-07-01 20:47:03 -04:00 |
David Roazen
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546e7777fa
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Re-fixing paths in pipeline tests after example qscripts got moved.
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2011-07-01 16:39:10 -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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David Roazen
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11d4af0e75
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Path-related fixes to the private queue pipeline tests.
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2011-07-01 13:41:34 -04:00 |
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David Roazen
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9644f104c4
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Fixes to the queue pipeline tests to account for the new directory structure.
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2011-07-01 13:13:24 -04:00 |
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Mauricio Carneiro
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64048a67e8
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cleaning up ghost scala scripts. Deleting clearly unused one and moving others to qscripts.archive
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2011-06-30 15:20:43 -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 |
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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 |