4d6cb33612
removing temporary bam index
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The clean bai file was left behind after the data processing pipeline was done
2011-08-08 10:49:28 -04:00
e5fde0d16b
Merge branch 'master' into rodRefactor
2011-08-08 10:08:43 -04:00
6693407bd8
Merged bug fix from Stable into Unstable
2011-08-07 17:39:03 -04:00
738e94efcb
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-08-07 17:36:45 -04:00
f534c2e7bb
Merged bug fix from Stable into Unstable
2011-08-06 10:43:52 -04:00
eaa2f16d83
When a job finishes successfully in the ShellJobRunner, mark it as DONE instead of FAILED.
2011-08-06 10:42:04 -04:00
58a60d4901
Merge branch 'master' into rodRefactor
2011-08-04 12:48:56 -04:00
21dc9a5543
Adding mills/devine indel dataset to the resource bundle
2011-08-04 12:31:28 -04:00
0739b7f75b
Merged bug fix from Stable into Unstable
2011-08-04 11:07:25 -04:00
aff681e407
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-08-04 11:05:25 -04:00
fa97bd8ac1
Merged bug fix from Stable into Unstable
2011-08-04 09:52:10 -04:00
23ec5b94cf
fixed a missing check for null
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There was a missed check for the case when you don't provide an indels vcf for the cleaner.
2011-08-04 09:50:02 -04:00
8981367307
Updating memory usage for picard programs
2011-08-03 15:48:28 -04:00
79e4a8f6d3
Merge
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Conflicts:
private/java/src/org/broadinstitute/sting/gatk/walkers/qc/TestVariantContextWalker.java
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
2011-08-03 15:09:47 -04:00
3e043a633c
Merged bug fix from Stable into Unstable
2011-08-03 02:23:16 -04:00
a587f38808
Fixed example unified genotyper pipeline to wrap filter expressions with quotes and use rod binding name "variant" instead of "vcf".
2011-08-03 02:21:01 -04:00
5dcac7b064
GATKReport v0.2:
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- Floating point column widths are measured correctly
- Using fixed width columns instead of white space separated which allows spaces embedded in cell values
- Legacy support for parsing white space separated v0.1 tables where the columns may not be fixed width
- Enforcing that table descriptions do not contain newlines so that tables can be parsed correctly
Replaced GATKReportTableParser with existing functionality in GATKReport
2011-08-03 00:24:47 -04:00
03741fb640
Merge branch 'master' into rodRefactor
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Conflicts:
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
2011-08-02 14:21:58 -04:00
4f8d830960
Updated to reflect new parse() function
2011-07-30 15:34:20 -04:00
2d94037ad0
Remove temporary index files (*.bai)
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some temporary index files were not being removed.
2011-07-30 02:05:22 -04:00
dcf21f379a
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-07-23 12:59:53 -04:00
f0a6dd27a1
Renaming the plot output directory names.
2011-07-23 12:59:37 -04:00
4f78025b0b
Merged bug fix from Stable into Unstable
2011-07-22 14:42:04 -04:00
4080e2cd88
* Added the decoy reference to the bundle under the b37 resources.
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* Updated the -svn argument to -ver since we don't use svn anymore (also updated the wiki).
2011-07-22 14:41:22 -04:00
59eb1f4663
Memory limits changed from Int to Double.
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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.
2011-07-21 22:57:18 -04:00
9ad5c7dfa4
Resolving simple conflicts in the data processing pipeline.
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Conflicts:
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
2011-07-19 08:05:11 -04:00
7688bda1a6
better progress report for the DPP
2011-07-18 23:39:47 -04:00
2b465ab43b
* added optional 'no validation' for the Data Processing pipeline.
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* some simplifications on the picard classes
2011-07-18 23:30:31 -04:00
4cf7a2af23
Removed broad specific default paths so people from outside the broad can use it.
2011-07-18 23:25:21 -04:00
449bf1b539
Testdata for diffObjects.
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PipelineTest updated to point to MD5DB.java
2011-07-18 10:47:03 -04:00
ecc8726f63
Merged bug fix from Stable into Unstable
2011-07-17 18:10:18 -04:00
1af76736b9
Guarantees that the list of files will always be in the same order.
2011-07-17 11:41:34 -04:00
5cb5a4ec75
Merged bug fix from Stable into Unstable
2011-07-16 00:23:59 -04:00
dd92a14b40
Made extra indel VCF optional but DBSNP mandatory.
2011-07-16 00:23:35 -04:00
2fa5dbb0fe
Merged bug fix from Stable into Unstable
2011-07-16 00:15:19 -04:00
ed55182a4c
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)
2011-07-16 00:09:00 -04:00
43bd45fcad
Merged bug fix from Stable into Unstable
2011-07-15 19:40:02 -04:00
fd1df31ef0
changing the output directory names for Analyze Covariates
2011-07-15 19:39:42 -04:00
aa30f416a3
Resolving conflicts
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Conflicts:
private/scala/qscript/depristo/ExomePostQCEval.scala
private/scala/qscript/depristo/PostCallingQC.scala
private/scala/qscript/org/broadinstitute/sting/queue/qscripts/archive/ExomePostQCEval.scala
2011-07-15 16:21:42 -04:00
224d373997
No need to double overload the file constructor
2011-07-15 15:19:10 -04:00
7b7d40d5d9
A better name for the qscript utilities. Throw here every method you find yourself repeatedly implementing in your qscripts!
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Refactoring appropriately.
2011-07-15 14:34:50 -04:00
a670d6420a
Refactoring Qscript utils into queue general utils package.
2011-07-15 14:31:43 -04:00
f19862a643
Fixing conflicts.
2011-07-14 17:13:31 -04:00
43c6a8565b
looks better now.
2011-07-14 17:10:44 -04:00
09ffe277ae
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".
2011-07-14 17:09:35 -04:00
4f8230c750
Merged bug fix from Stable into Unstable
2011-07-14 16:44:57 -04:00
9f5180ab05
Recalibrates a list of bam files allowing multiple bams to be recalibrated out of a single 'mother' queue job.
2011-07-14 16:42:17 -04:00
df996a1a73
more progress report for the Data Processing Pipeline.
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Bam lists can now have empty lines, comments and whitespaces anywhere.
2011-07-13 14:53:58 -04:00
e2f2917bd2
Merged bug fix from Stable into Unstable
2011-07-13 13:00:55 -04:00
ff4e31c554
Changing the file names as per Kris request.
2011-07-13 12:59:18 -04:00
e93052a51e
When generating the QGraph, don't regenerate if there aren't scatter/gather jobs.
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Fixed a display issue with the number of milliseconds that Queue has tried to contact LSF.
2011-07-11 19:17:58 -04:00
5298e3a942
Making the outputDir optional. Default = ./
2011-07-05 16:30:41 -04:00
7d3dfdfdf2
Updating the MDCP to use the classpath for the GATK jar, removing -gatk parameter.
2011-07-05 16:30:10 -04:00
b6bc64a0c8
Cleanup of the utils.broad package.
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Using Picard IoUtils on sample names.
2011-07-01 20:47:03 -04:00
546e7777fa
Re-fixing paths in pipeline tests after example qscripts got moved.
2011-07-01 16:39:10 -04:00
b0fb63e20a
moving the example scala scripts to the qscripts package.
2011-07-01 16:14:59 -04:00
d19351f71a
Added capability of running multiple bam files in the same directory.
2011-07-01 16:02:28 -04:00
11d4af0e75
Path-related fixes to the private queue pipeline tests.
2011-07-01 13:41:34 -04:00
9644f104c4
Fixes to the queue pipeline tests to account for the new directory structure.
2011-07-01 13:13:24 -04:00
64048a67e8
cleaning up ghost scala scripts. Deleting clearly unused one and moving others to qscripts.archive
2011-06-30 15:20:43 -04:00
197b7141c1
Added an optional argument -bt <num_threads> for BWA to run multithreaded.
2011-06-30 14:41:57 -04:00
f4463d38ca
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.
2011-06-30 14:29:21 -04:00
efd99c3c11
new home for the core qscripts
2011-06-30 11:32:06 -04:00
1085df8b7b
Making the BQSR pipeline publicly available and supported.
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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.
2011-06-29 16:05:32 -04:00
3c9497788e
Reorganized the codebase beneath top-level public and private directories,
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removing the playground and oneoffprojects directories in the process. Updated
build.xml accordingly.
2011-06-28 06:55:19 -04:00
Mauricio Carneiro
Mark DePristo
Ryan Poplin
Khalid Shakir
David Roazen