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
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
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
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
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
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
e5fde0d16b
Merge branch 'master' into rodRefactor
2011-08-08 10:08:43 -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
4f8d830960
Updated to reflect new parse() function
2011-07-30 15:34:20 -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
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
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
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
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
Khalid Shakir
Mark DePristo
Eric Banks
David Roazen