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227 Commits (eaa2f16d837aeec9ad6d4e35d6ff9607972f7c89)

Author SHA1 Message Date
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
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 ca35defdcd Moved gsalib sources from private/ to public/ 2011-07-27 12:29:43 -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
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
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
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
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 32730b1832 Fixed md5 due to new PL ordering 2011-07-20 22:17:15 -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
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
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
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
Mark DePristo 8f0badc52b Updating md5s, as the diffobjects walker now emits the summary in reverse order. 2011-07-18 15:44:21 -04:00
Mark DePristo c05451047c Support for multiple records at the same site. The first record gets chr:start, and subsequent records get chr:start_2, chr:start_3, etc. 2011-07-18 15:43:52 -04:00
Mark DePristo 782a05e9b5 Support for sorting the diff output in reverse order. 2011-07-18 15:43:01 -04:00
Mark DePristo 45702d3084 Now supports a mode where the primary key isn't sorted. In this case the records are displayed in the order in which they are added to to the table. 2011-07-18 15:40:15 -04:00
Eric Banks 83ba2c066a Making it deterministic 2011-07-18 13:59:02 -04:00
Eric Banks 92fa410450 Check that it's a valid bam file before parsing or bad things can happen 2011-07-18 13:43:34 -04:00
Eric Banks 80b5c5261a CombineVariants no longer combines records of different types. So now when combining SNP and indel callsets, overlapping calls get their own records. Useful for Khalid in the pipeline. For those interested, it turns out the previous behavior was doing the wrong thing occasionally (and this was even captured in the integration tests). 2011-07-18 13:42:45 -04:00
Eric Banks bc8b5da698 Added docs while I was reading through the code to understand it 2011-07-18 12:25:54 -04:00