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230 Commits (504b3ef5ef32eb2c7ed10b9d8e355c59fa6b0017)

Author SHA1 Message Date
Kiran V Garimella 0b43ee117c Added the required=false tag to the -noST and -noEV arguments so the auto-help output doesn't look weird (i.e. listing arguments as required when their value has already been specified by default). 2011-07-25 11:35:34 -04:00
Kiran V Garimella 0b36b6540f Merge branch 'laptop' 2011-07-23 01:44:54 -04:00
Kiran V Garimella e23cb27451 Modified MD5 to account for the triple hets that shouldn't be phased 2011-07-23 01:44:44 -04:00
Kiran V Garimella 1dba8b768c Merge branch 'laptop' 2011-07-23 01:39:15 -04:00
Kiran V Garimella 57e3d136eb Don't try to phase triple-hets either. 2011-07-23 01:38:58 -04:00
Kiran V Garimella f366124778 Merge branch 'laptop' 2011-07-23 01:25:36 -04:00
Kiran V Garimella 45f2ca8d99 Changed MD5 to reflect latest changes to PhaseByTransmission. 2011-07-23 01:21:07 -04:00
Kiran V Garimella 5af9d50183 Merge branch 'laptop' 2011-07-23 01:12:06 -04:00
Kiran V Garimella 5521919cc9 Fixed bug where variants to phase were not being selected properly. 2011-07-23 01:11:28 -04:00
Kiran V Garimella 7da99388ac Merge branch 'laptop' 2011-07-23 01:01:11 -04:00
Kiran V Garimella 58eed20b83 Copy all entries from the attributes map, rather than attempting to modify an unmodifiable map. 2011-07-23 01:00:46 -04:00
Kiran V Garimella b5deff48e6 Merge branch 'laptop' 2011-07-23 00:56:50 -04:00
Kiran V Garimella 5638017137 Removed the nofilters argument specification in the integrationtest 2011-07-23 00:56:23 -04:00
Kiran V Garimella ffa361f57f Merge branch 'laptop' 2011-07-23 00:50:38 -04:00
Kiran V Garimella 9417ba8c2c Modified to accept multi-sample VCFs, removed the application of filters, and changed transmission probability field to be a genotype field rather than an INFO field. 2011-07-23 00:48:26 -04:00
Kiran V Garimella 051c1dc639 Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-22 15:59:00 -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
Kiran V Garimella b8a0fd2a8d Multiply fractionRandom by 100.0 so that the line that indicates the percentage of variants that will be output says (for instance) 90%, not 0.9% 2011-07-22 11:54:59 -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