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6535 Commits (738e94efcbccce9e85a2e459585f8f2995a96df5)

Author SHA1 Message Date
Ryan Poplin 738e94efcb Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable 2011-08-07 17:36:45 -04:00
Khalid Shakir eaa2f16d83 When a job finishes successfully in the ShellJobRunner, mark it as DONE instead of FAILED. 2011-08-06 10:42:04 -04:00
Ryan Poplin 98a96f07c1 Updated standard deviation parameter in VQSR to our current recommended value 2011-08-04 14:06:26 -04:00
Ryan Poplin 21dc9a5543 Adding mills/devine indel dataset to the resource bundle 2011-08-04 12:31:28 -04:00
Mauricio Carneiro aff681e407 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable 2011-08-04 11:05:25 -04:00
Mauricio Carneiro 23ec5b94cf fixed a missing check for null 
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
Mauricio Carneiro 8981367307 Updating memory usage for picard programs 2011-08-03 15:48:28 -04:00
Khalid Shakir 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
Mauricio Carneiro 2d94037ad0 Remove temporary index files (*.bai) 
some temporary index files were not being removed.
 2011-07-30 02:05:22 -04:00
Ryan Poplin c0d4110ffd Correcting redundant warning text. 2011-07-29 10:01:11 -04:00
Eric Banks 1afc49a297 There are some really 'interesting' (but apparently valid) records in the Mus musculus dbSNP file. Generalized the handling of complex cases in the dbSNP adaptor to handle it all. I just grabbed the actual Mus musculus dbSNP file as a test, ran it whole genome, and confirmed that we finally produce a valid VCF on it. Should be the last commit needed on this adaptor. 2011-07-28 13:55:58 -04:00
Eric Banks 6230315ff2 Along with my half-written commit message from earlier, I also forgot to commit the integration test updates. This is what happens when you try to do things 30 seconds before you leave for the day. To finish up from before: complex events weren't being padded with the reference base as per the VCF spec. They are now. 2011-07-27 22:51:21 -04:00
Eric Banks 64aad67b5f Fixing dbSNP adaptor for complex indels (wasn) 2011-07-27 16:13:45 -04:00
Kiran V Garimella 6ebd83478b Fixed build.xml to reflect path changes for gsalib 2011-07-27 12:37:00 -04:00
Kiran V Garimella ca35defdcd Moved gsalib sources from private/ to public/ 2011-07-27 12:29:43 -04:00
Matt Hanna 6f43284053 Switch to including our entire exception tree rather than just UserException. 2011-07-25 15:19:41 -04:00
Matt Hanna a00e302321 Fix formatting issue. 2011-07-25 14:31:40 -04:00
Khalid Shakir 1f8fc4a041 Added edu.mit.broad.picard to Queue packaged jar. 
Added hack to workaround EDU.oswego namespace and staging on mac case-insensitive filesystems.
 2011-07-23 14:40:29 -04:00
Mauricio Carneiro dcf21f379a Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable 2011-07-23 12:59:53 -04:00
Mauricio Carneiro f0a6dd27a1 Renaming the plot output directory names. 2011-07-23 12:59:37 -04:00
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