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140 Commits (a5bfcb1ed9f4ee0f5a94a744bd9e31bbd8d254a2)

Author SHA1 Message Date
Mark DePristo 92a1c0c278 Moved the varianteval/tags/DataPoint.java and varianteval/tags/Analysis.java to varianteval/utils. This allows rsync to see these files with the -C option, as tags is some kind of reserved CVS keyword. 2011-07-17 10:14:23 -04:00
Mark DePristo eacf205f40 Tests needed to be updated to reflect the code reorg of tribble. 2011-07-16 09:22:34 -04:00
Mauricio Carneiro 5cb5a4ec75 Merged bug fix from Stable into Unstable 2011-07-16 00:23:59 -04:00
Mauricio Carneiro dd92a14b40 Made extra indel VCF optional but DBSNP mandatory. 2011-07-16 00:23:35 -04:00
Mauricio Carneiro 2fa5dbb0fe Merged bug fix from Stable into Unstable 2011-07-16 00:15:19 -04:00
Mauricio Carneiro ed55182a4c Removing Broad specific paths from parameters and making them required. This should make it unambiguous for people inside and outside the Broad to use the DataProcessingPipeline (as per request in the GetSatisfaction) 2011-07-16 00:09:00 -04:00
Mauricio Carneiro 43bd45fcad Merged bug fix from Stable into Unstable 2011-07-15 19:40:02 -04:00
Mauricio Carneiro fd1df31ef0 changing the output directory names for Analyze Covariates 2011-07-15 19:39:42 -04:00
Menachem Fromer dc7d1d2f08 Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-15 17:49:13 -04:00
Menachem Fromer 72f4cf9c0e Walker to perform deterministic annotation of phasing by transmission (to be compatible with RBP's definition of consecutive pairwise phasing) 2011-07-15 17:44:31 -04:00
Mauricio Carneiro aa30f416a3 Resolving conflicts 
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
Mauricio Carneiro 224d373997 No need to double overload the file constructor 2011-07-15 15:19:10 -04:00
Mauricio Carneiro 7b7d40d5d9 A better name for the qscript utilities. Throw here every method you find yourself repeatedly implementing in your qscripts! 
Refactoring appropriately.
 2011-07-15 14:34:50 -04:00
Mauricio Carneiro a670d6420a Refactoring Qscript utils into queue general utils package. 2011-07-15 14:31:43 -04:00
Mauricio Carneiro f19862a643 Fixing conflicts. 2011-07-14 17:13:31 -04:00
Mauricio Carneiro 43c6a8565b looks better now. 2011-07-14 17:10:44 -04:00
Mauricio Carneiro 09ffe277ae Added a qscripts util package with some utility functions commonly shared across queue scripts. Refactored some of my public scripts to use it in an effort to make queue scripts more reusable and "supportable". 2011-07-14 17:09:35 -04:00
Mauricio Carneiro 4f8230c750 Merged bug fix from Stable into Unstable 2011-07-14 16:44:57 -04:00
Mauricio Carneiro 9f5180ab05 Recalibrates a list of bam files allowing multiple bams to be recalibrated out of a single 'mother' queue job. 2011-07-14 16:42:17 -04:00
Mark DePristo c0bbeb23ba Now providing more information when the index on the fly isn't equal to the one created by reading the file from disk. 2011-07-14 15:12:28 -04:00
Mark DePristo 5ffeddd3b1 better to use _ instead of ., as this is a special case later. 2011-07-14 14:45:16 -04:00
Eric Banks 9540df6998 Oops, forgot to update unit test 2011-07-14 14:00:19 -04:00
Eric Banks ed6beae1f3 Adding headers to diffable reading for VCFs 2011-07-14 13:55:35 -04:00
Eric Banks 57a90173f3 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-14 11:56:20 -04:00
Eric Banks 66c652d687 Added some extra error checks in the VCF codec. Now that we've moved this back into the GATK, changed some of the standard exceptions to be USerErrors (instead of TribbleExceptions). 2011-07-14 11:56:10 -04:00
Mauricio Carneiro a4ab19d040 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-13 15:14:06 -04:00
Eric Banks 0c54c796ed Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-13 14:57:33 -04:00
Eric Banks bb0e3a26fc Added integration test for VCF writing. Also, bug fix for writing the GT-free records. 2011-07-13 14:57:21 -04:00
Mauricio Carneiro df996a1a73 more progress report for the Data Processing Pipeline. 
Bam lists can now have empty lines, comments and whitespaces anywhere.
 2011-07-13 14:53:58 -04:00
Eric Banks 6a431da554 Don't output source and ref header lines anymore. Short-term motivation for this is that I'd like this tool when run on a VCF to emit the exact same VCF. Long-term motivation is that these tags should be output by the VCF writer itself for all tools. 2011-07-13 14:40:01 -04:00
Mauricio Carneiro e2f2917bd2 Merged bug fix from Stable into Unstable 2011-07-13 13:00:55 -04:00
Mauricio Carneiro ff4e31c554 Changing the file names as per Kris request. 2011-07-13 12:59:18 -04:00
Menachem Fromer 74aa49e423 Merged bug fix from Stable into Unstable 2011-07-13 12:12:42 -04:00
Menachem Fromer fa3ff53508 Filters should only be applied to the new VC if the old VC had filters applied 2011-07-13 11:58:16 -04:00
Eric Banks 969227c657 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-13 10:01:28 -04:00
Eric Banks 797c50e689 Fixing integration tests I broke yesterday; removing batch merging test since we don't support that anymore. 2011-07-13 10:01:23 -04:00
Eric Banks 6007eea3ff Allowing VCF records without GTs in vf4.1 2011-07-13 09:56:08 -04:00
Ryan Poplin 837fb8f689 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-12 15:39:26 -04:00
Ryan Poplin 5077c94d85 Adding MappingQualityUnavailableReadFilter to the SNP and indel CountCovariates 2011-07-12 15:39:07 -04:00
Mark DePristo 01fd6a6949 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-12 15:20:44 -04:00
Mark DePristo ccedd6ff4c Difference is now the general form -- used to be SummarizedDifference. The old Difference class is now a subclass of Difference that includes pointers to specific the master and test DiffElements. 
Added a size() function that calculates the number of elements tree from a DiffElement.
 2011-07-12 15:20:28 -04:00
Eric Banks a2597e7f00 This commit incorporates several different changes that each pretty much break all the VCF-based integration tests, so I bunched them all together. We now officially emit VCF4.1 files (woo hoo), which means that the VCF headers are now all different (header version is 4.1 plus counts for some of the annotations are 'A' or 'G'). Also, I've added a Read Filter for reads with MQ=255 ('unavailable' in the SAM spec) and have applied this to the UG and the RMS MQ annotation. 2011-07-12 14:11:53 -04:00
Ryan Poplin 329c3d8050 Merged bug fix from Stable into Unstable 2011-07-12 13:55:51 -04:00
Ryan Poplin 73735863b0 Fix for the case of requesting genotype for a sample that doesn't exist in a VariantContext 2011-07-12 13:55:21 -04:00
Guillermo del Angel c4c145afb9 Merged bug fix from Stable into Unstable 2011-07-12 13:44:48 -04:00
Guillermo del Angel cfe43e3971 Bug fix for Genotype given alleles: if we are in INDEL mode ignore SNPs and MNPs instead of emitting an empty site with alleles but no annotations 2011-07-12 13:43:46 -04:00
Mark DePristo 05212aea62 reader now takes an argument for the maximum number of elements to read from the file. 2011-07-12 08:53:19 -04:00
Mark DePristo 8056a3fe89 getElement() now uses O(1) get from hash instead of linear O(n) search. Enables us to read large files easily. 2011-07-12 08:52:31 -04:00
Mark DePristo f313e14e4e Now deletes the dump directory on ant clean 
Moving diffengine tests from private to public
 2011-07-12 08:50:58 -04:00
Eric Banks d7d15019dd Adding support for other simple header line types (e.g. ALT) and cleaning up the interface a bit. 2011-07-12 01:16:21 -04:00