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6515 Commits (d7b3f40259bbd6751afca82a7e38d2f68edd552c)

Author SHA1 Message Date
Eric Banks d7b3f40259 Merge remote-tracking branch 'unstable/master' 2011-07-22 14:45:24 -04:00
Mauricio Carneiro 4f78025b0b Merged bug fix from Stable into Unstable 2011-07-22 14:42:04 -04:00
Mauricio Carneiro 4080e2cd88 * Added the decoy reference to the bundle under the b37 resources. 
* 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
Matt Hanna f50145b872 Reinitialize random seed in the bwa bindings from the fixed seed stored in the 
BWA support files every time the support files are loaded.
 2011-07-22 13:41:53 -04:00
Guillermo del Angel 3d0853149b Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-22 08:13:58 -04:00
Guillermo del Angel 6afe63690d Two more true oneoffs (committed mostly for didactic purposes): codec that reads Mills/Devine indel table into a vcf and another (in progress) that will read indel chip genotype data and produce a vcf 2011-07-22 08:13:05 -04:00
Khalid Shakir 8b8f121cfb Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-21 23:01:11 -04:00
Khalid Shakir 59eb1f4663 Memory limits changed from Int to Double. 
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
Guillermo del Angel 87f991aee7 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-21 13:35:24 -04:00
Christopher Hartl 2f5d10d16b Fix bug wherein aligner could be closed prior to its being used to lowercase sequences. 2011-07-21 13:21:48 -04:00
Matt Hanna 7054c5342f When using the BWA bindings, you have to explicitly call close() to get the 
bindings to release memory.
It may or may not be possible to implicitly close triggered by the GC; I'll add a JIRA.
 2011-07-21 12:13:29 -04:00
Guillermo del Angel 84c66d4b92 Bug fixes 2011-07-21 11:52:51 -04:00
Guillermo del Angel c4684f4659 A true oneoff: walker that reads in vcf with multiallelic PL's in wrong ordering and flips them around to output in correct order 2011-07-21 11:20:46 -04:00
Christopher Hartl 15610ce0c3 Per Matt's request, disabling BWA-based integration tests so he can assess bamboo memory usage. 2011-07-21 11:04:22 -04:00
Guillermo del Angel 664246937c Try to resolve merge conflict 2011-07-21 10:19:26 -04:00
Guillermo del Angel 32730b1832 Fixed md5 due to new PL ordering 2011-07-20 22:17:15 -04:00
Matt Hanna 4b0b7f4b32 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-20 14:49:25 -04:00
Matt Hanna f14f20d718 Fix bug involving reuse of the sample variable. 
Cleaned up some otherwise unused comments and code.
 2011-07-20 14:48:33 -04:00
Guillermo del Angel 0a1d2df8cb Merged bug fix from Stable into Unstable 2011-07-20 13:19:35 -04:00
Guillermo del Angel f15023b7d2 Bad bug fix: output GLs in multiallelic records were in incorred order (misread spec) 2011-07-20 12:10:48 -04:00
Mauricio Carneiro c09f92ccee Fixing the illegal character accidently entered 2011-07-20 11:39:04 -04:00
Mauricio Carneiro 4e00666632 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-20 11:38:16 -04:00
Roger Zurawicki ea90af199c Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-20 11:17:36 -04:00
Roger Zurawicki d3a8363491 Changed MRAV to ADAV 
Updated ReducedBAMEvaluation to allow multiple parameters to be tested
Fixed previous error
 2011-07-20 10:49:50 -04:00
Guillermo del Angel b9c9e0e952 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-20 10:45:16 -04:00
Guillermo del Angel 7140280bf6 Further bug fixes/cleanups for PrintReadsWalker 2011-07-20 10:44:37 -04:00
Guillermo del Angel a2d90a3590 Bug fix: reverted logic so that default behavior skips over sample lookup 2011-07-20 10:23:10 -04:00
Guillermo del Angel e8409c80fa Further protection vs null pointers in PrintReadsWalker 2011-07-19 21:59:24 -04:00
Christopher Hartl 5d706c9e92 Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 
Removing PSP and CSM

Conflicts:

	public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java
	public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
 2011-07-19 20:25:33 -04:00
Guillermo del Angel fb2d475c22 Bug fix to prevent null pointer 2011-07-19 20:13:56 -04:00
Christopher Hartl 92c7cfa1c8 BWA bindings and tests moved to public (was required for ValidationAmplicons) 
Integration tests for ValidationAmplicons. New argument to disable BWA, lowercase letters only for repetitiveness instead.
 2011-07-19 20:11:31 -04:00
David Roazen baae381acb Revert "Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable" 
This reverts commit 039a6bb01f345322ce2be50ae3634308bb24e77e, reversing
changes made to b9c9973d1c638dfc9f8c19b5eb845e99844f9d29.
 2011-07-19 18:38:53 -04:00
David Roazen eb63b48414 Revert "Resolving conflict" 
This reverts commit 87f0d4a8b0627b3be86acdfef5a9f2fc6ea923ee.
 2011-07-19 18:36:53 -04:00
Roger Zurawicki a3cecf0668 Resolving conflict 2011-07-19 17:20:27 -04:00
Roger Zurawicki 3d72b98a35 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 
Conflicts:
	private/java/test/org/broadinstitute/sting/gatk/walkers/reducereads/ReduceReadsIntegrationTest.java
 2011-07-19 17:16:20 -04:00
Roger Zurawicki d92d00a85d Changed MRAV to ADAV to reflect real implementation (Max reads to Average Depth at Variant Sites). 
Optimized Mapping Quality calculation.
 Correctly filtered reads below minimum Mapping Quality threshold
 2011-07-19 16:59:06 -04:00
Mauricio Carneiro 8a7e698883 better debug output for plotting. 2011-07-19 15:28:54 -04:00
Christopher Hartl 07e716d23a PickSequenomProbes2 expanded functionality: lowercasing based on sequence uniqueness, preserving reference base prior to indel (not a part of the VC as I thought it was), masking deletion bases with 'N's, flanking insertion with 'N's, output is a fasta formatted file. Renamed to ValidationAmplicons since this is really not for picking sequenom probes, but for generating amplicon sequence from which other applications (like sequenom) can choose PCR primers. Moved from private to public. 2011-07-19 15:21:47 -04:00
Guillermo del Angel 6181d1e4cb Fixed integration test for VariantsToTable: now the * in REF column is not output 2011-07-19 14:42:11 -04:00
Guillermo del Angel e6d306458c Merge bug fixes 2011-07-19 14:36:20 -04:00
Guillermo del Angel 989dd17f95 a) Add ability in PrintReads to specify a sample file to easily subset samples, useful for IGV visualization, b) VariantsToTable is more R-friendly with Indels when printing ref/alt columns, c) Changes to SelectVariants ability to speficy a mask to randomly sample from a given AF distribution 2011-07-19 14:29:07 -04:00
Matt Hanna 005adf377f Derive MEDIAN_INSERT_SIZE plot from base plot with additional faceting. 2011-07-19 10:48:45 -04:00
Matt Hanna 9a1394d7e7 Clean up MEDIAN_INSERT_SIZE plot for consistency with other plots. 2011-07-19 10:34:50 -04:00
Matt Hanna 5d3112c665 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-19 09:32:01 -04:00
Matt Hanna 0cec2c6759 When sorting samples by date, only use filtered samples to avoid discontinuities 
in the plot.  Add brief documentation for running the R script.
 2011-07-19 09:28:51 -04:00
Mauricio Carneiro 9ad5c7dfa4 Resolving simple conflicts in the data processing pipeline. 
Conflicts:
	public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
 2011-07-19 08:05:11 -04:00
Mauricio Carneiro 7688bda1a6 better progress report for the DPP 2011-07-18 23:39:47 -04:00
Mauricio Carneiro 2b465ab43b * added optional 'no validation' for the Data Processing pipeline. 
* some simplifications on the picard classes
 2011-07-18 23:30:31 -04:00
Mauricio Carneiro 4cf7a2af23 Removed broad specific default paths so people from outside the broad can use it. 2011-07-18 23:25:21 -04:00
Khalid Shakir 9b446020f9 Using picard implementations for accessing aggregation directories. 
Added more utilities to PicardPrivate.
Revved picard.
 2011-07-18 21:49:03 -04:00