648b959361
Minor change to log an info message when a signal such as Ctrl-C is caught.
2011-09-27 00:50:19 -04:00
d3cc25454c
Updating the MDCP
2011-09-22 11:27:40 -04:00
623c49765d
NO BAQ ON EXOMES!
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says the boss.
2011-09-22 11:13:40 -04:00
5d0f284305
Fixing exome specific arguments to the VQSR in the methods development calling pipeline
2011-09-21 20:26:28 -04:00
758ecf2d43
Bringing latest updates of ReduceReads to the master repository
2011-09-20 16:35:09 -04:00
08ffb18b96
Renaming datasets in the MDCP
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Making dataset names and files generated by the MDCP more uniform.
2011-09-20 11:02:51 -04:00
ba150570f3
Updating to use new rod system syntax plus name change for CountRODs
2011-09-19 13:30:32 -04:00
095f75ff7d
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-19 12:24:12 -04:00
85626e7a5d
We no longer want people to use the August 2010 Dindel calls for indel realignment but instead Guillermo's new whole genome bi-allelic indel calls; updating the bundle accordingly. Also, there was some confusion by the 1000G data processing folks as to exactly what these indel files are, so I've renamed them so that it's clear. Wiki updated too.
2011-09-19 12:24:05 -04:00
6ea57bf036
Merge branch 'master' into sgintervals
2011-09-19 09:50:19 -04:00
33967a4e0c
Fixed issue reported by chartl where cloned functions lost tags on @Inputs.
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Updated ExampleUnifiedGenotyper.scala with new syntax.
2011-09-16 12:46:07 -04:00
981b78ea50
Changing the VQSR command line syntax back to the parsed tags approach. This cleans up the code and makes sure we won't be parsing the same rod file multiple times. I've tried to update the appropriate qscripts.
2011-09-12 12:17:43 -04:00
7f9000382e
Making indel calls default in the MDCP
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You can turn off indel calling by using -noIndels.
2011-09-09 14:09:26 -04:00
06cb20f2a5
Intermediate commit cleaning up scatter intervals
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-- Adding unit tests to ensure uniformity of intervals
2011-09-09 12:56:45 -04:00
510d5e7730
Merged bug fix from Stable into Unstable
2011-09-09 01:34:55 -04:00
367bbee25a
Fixed typo when printing the contents or last N lines of a file. Thanks to larryns.
2011-09-09 01:33:25 -04:00
ee9d599558
Just cleaning up
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clean up old commented code from tha data processing pipeline.
2011-09-07 13:32:40 -04:00
28d782b4c7
Allowing multiple dnsnp and indel files in the DPP
2011-09-02 13:38:47 -04:00
ad4ea0b80b
Merged bug fix from Stable into Unstable
2011-09-01 18:14:45 -04:00
e253f6f05d
Fixing typo in DPP
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platform and library were exchanged when rebuilding the read group information
2011-09-01 18:13:52 -04:00
d2a33beff7
Added WGS/WEX b37-decoy CEU trio datasets
2011-09-01 13:14:40 -04:00
61633c95a8
Default jobreport is now jobPrefix, so you see logs like Q-2508.jobreport.txt
2011-08-28 19:19:45 -04:00
b38de1fa35
Now captures the exechost in the job report
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-- Works for in process, shell, and LSF runners
-- Cleanup of debugging output
2011-08-28 12:05:56 -04:00
e37a638e09
Fix for disallowed characters in GATKReportTable
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-- Illegal characters are automatically replaced with _
2011-08-26 13:24:06 -04:00
0cb1605df0
Clean documentation for JobRunInfo
2011-08-26 09:22:58 -04:00
415d5d5301
LSF long times are in seconds, convert to milliseconds to meet standard
2011-08-26 09:18:28 -04:00
eef1ac415a
Merge branch 'master' into rodTesting
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Conflicts:
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
2011-08-26 00:35:41 -04:00
e03dfdb0ab
Automatic iteration field addition works properly.
2011-08-25 16:59:02 -04:00
e01273ca7c
Queue now writes out queueJobReport.pdf
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-- General purpose RScript executor in java (please use when invoking RScripts)
-- Removed groupName. This is now analysisName
-- Explicitly added capability to enable/disable individual QFunction
2011-08-25 16:57:11 -04:00
0f4be2c4a4
Argument to disable queueJobReport entirely
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-- Minor improvements to RodPerformanceGoals
2011-08-25 13:32:03 -04:00
d65faf509c
Default output name for Queue JobReport is queue_jobreport.gatkreport.txt
2011-08-25 13:15:20 -04:00
a7d6946b22
Refactored QJobReport and QFunction, which is now automatically tracked
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-- All QFunctions, including sg ones, are tracked
-- Removed memory information
2011-08-25 13:13:55 -04:00
16caca0822
BLASR BAMs and new BWA parameters
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*Added the functions to turn a BLASR generated BAM file into a usable BAM file.
*Modified the bwa parameters according to test results from NA12878 pb2k dataset.
2011-08-24 17:04:07 -04:00
e3f5d7067a
Added ReorderSam queue binding
2011-08-24 17:03:11 -04:00
08fb21f127
Removing hostname
2011-08-24 16:45:50 -04:00
dc8398e165
fixing bai output for indel cleaning.
2011-08-24 15:58:34 -04:00
06e30a81d1
Fixes throughout for getting job information
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-- no more hostname -- it's just not going to be important
2011-08-24 15:30:09 -04:00
4918519a58
No more NPE in getRuntime() when you cntr-c out of Queue
2011-08-24 14:14:01 -04:00
16d8360592
QJobReport is now the official capability name
2011-08-24 13:59:14 -04:00
d047c19ad1
Writes output to file
2011-08-24 13:52:05 -04:00
3ae68e2397
JobLogging trait now writes out GATKReport log of jobs
2011-08-24 13:36:39 -04:00
cd12f7f286
Fixed list dependency
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Instead of creating a bam list file, I dynamically create a scala list and pass as parameters. This way the intermediate bam files don't get deleted before they should.
2011-08-24 11:12:46 -04:00
219252a566
Adapting to the new RodBinding framework
2011-08-24 11:12:46 -04:00
b8bc03bb42
JobRunInfo improvements
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-- dry-run now adds some info, for testing
-- InProcessRunner adds some, but not all, of the information we want
2011-08-23 17:11:22 -04:00
31ec6e316c
First implementation of JobRunInfo
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-- onExecutionDone(Map(QFunction, JobRunInfo)) is the new signature, so that you can walk over your jobs and inspect their success/failure and runtime characteristics
2011-08-23 16:51:54 -04:00
a9ba945595
onExecutionDone(jobs, successFlag) added to QScript.
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-- This function is called when the Qscript ends, so scripts can overload this function if they want to run some code after all of the jobs have completed
2011-08-23 10:09:51 -04:00
136f0eb685
Creating sample-bam list instead of joining
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This should save us at least one day in the trio decoy processing.
2011-08-22 18:03:39 -04:00
04d8bcaf19
Fixed bai removal on picard tools
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BAM index files were not being deleted because picard replaces the name of the file with bai instead of appending to it.
2011-08-22 18:03:39 -04:00
8aed151a71
Created RevertSam queue class
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Class for the picard tool RevertSam with all the options for queue scripts.
2011-08-22 18:03:39 -04:00
caebc88e9a
Consensus mode and new RodBinding framework.
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The DPP was not using the parameter correctly. It didn't matter for the default option (which is the only one we have been testing) but it would not work for knowns only or smith waterman. It is fixed now.
It now complies with the new rod binding framework.
2011-08-22 18:03:39 -04:00
c4c90c8826
Updates to JobRunners from the Queue developer community and from running the WholeGenomePipeline:
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- Ability to pass a different resident memory reservation and limits. Useful for large pileups of low pass genome data that sometimes need high -Xmx6g but usually don't exceed 2-3g in actual heap size.
- Fixed jobPriority to work for all job runners. Now must be a integer between 0 and 100- even for GridEngine- and will be mapped to the correct values.
- Passing parallel environment and job resource requests to LSF and GridEngine. Useful for passing tokens like iodine_io=1 and -pe pe_slots 8
- Refactored GridEngine JobRunner to also provide basic support for other job dispatchers with DRMAA implementations such as Torque/PBS. Should work for basic running but advanced users must pass their own jobNativeArgs from the command line or in customized QScripts until someone maps properties like jobQueue, jobPriority, residentRequest, etc. into a Torque/PBS/etc. dispatcher.
2011-08-22 15:13:27 -04:00
f93a554b01
updating exome specific parameters in MDCP
2011-08-21 10:25:36 -04:00
b008676878
fixing the previous fix
2011-08-20 21:21:55 -04:00
539e157ecd
Fixing misc parameters in MDCP. The pipeline now does VariantEval of output by default. Fix for NaN vqslod values in VQSR
2011-08-20 11:28:48 -04:00
ddb5045e14
Updating the methods development calling pipeline for the new rod binding syntax and the new best practices.
2011-08-19 19:29:51 -04:00
46051c36c6
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-10 16:57:34 -04:00
b0ff5b1ff7
a better name for the pacbio processing pipeline
2011-08-10 16:16:53 -04:00
9e53fd6880
Fixed VCFGatherFunction to not provide incorrect rod_priority_list
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-- simply don't provide one, since you are just 'cating' the files together and genotypes never overlap
2011-08-10 07:28:35 -04:00
481630da00
BWA parameters added
2011-08-09 17:05:24 -04:00
22d2563823
added BWA SW alignment
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The pipeline now accepts fasta/fastq files and aligns them using BWA SW, adds default basequalities, creates read groups and performs BQSR.
2011-08-09 17:05:24 -04:00
bd1cf4c7bc
Pacbio Pipeline
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Added the base quality "filling" step to allow the pipeline to handle raw pacbio BAM files. This is the first step towards a generic pacbio data processing pipeline.
2011-08-09 17:05:24 -04:00
5a3c99b7b9
Fixing 'variants' change in qscript
2011-08-09 12:30:46 -04:00
cb28875c2a
Updated rod binding syntax usage on CombineVariants from .rodBind to .variants.
2011-08-09 00:46:39 -04:00
f8a56bc64b
Merge branch 'master' into rodRefactor
2011-08-08 16:58:18 -04:00
383bb6f0e0
Merge branch 'master' into rodRefactor
2011-08-08 15:25:55 -04:00
99e3a72343
Merged bug fix from Stable into Unstable
2011-08-08 12:36:17 -04:00
8072bd9831
Updating resource bundle generation qscript for changeover to git
2011-08-08 12:35:39 -04:00
0db46d0648
Merged bug fix from Stable into Unstable
2011-08-08 10:50:09 -04:00
2fd101135c
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-08-08 10:49:43 -04:00
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
Khalid Shakir
Mauricio Carneiro
Ryan Poplin
Eric Banks
Mark DePristo