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128 Commits (0a1d2df8cb5d7d21e61ed486fb15f8ca517f53c5)

Author SHA1 Message Date
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 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
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
Mark DePristo 51b0dd01c3 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-18 10:47:29 -04:00
Mark DePristo 6f26c07b85 Removed the SpecificDifference class. Now Difference classes always have the option to remember specific master and test values. This means that all summarized differences carry with them specific examples of their differences. Consequently, now even summarized differences give at least one example of the specific difference, even when the count of the difference is > 1. Unit tests updated. Added DiffObjects integrationtest. VCFDiffableReader now specifically reads the first line of the VCF file to capture the version number. 2011-07-18 10:42:35 -04:00
Kiran V Garimella b2b7d27fed Merge branch 'laptop' 2011-07-18 00:25:46 -04:00
Kiran V Garimella 497721a799 Added class documentation string. 2011-07-18 00:25:21 -04:00
Kiran V Garimella ac9c66138d Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-18 00:20:33 -04:00
Kiran V Garimella 8167aba601 Moved (poorly named) MergeAndMatchHaplotypes to public. Added integration test 2011-07-17 22:47:32 -04:00
Mark DePristo 9992c373be Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes. 2011-07-17 20:29:58 -04:00
Kiran V Garimella 4ea433f8e1 Moved PhaseByTransmission to public 2011-07-17 19:42:00 -04:00
Mark DePristo 4db2b13e9e Rev tribble. 
Just added more documentation for diffEngine and pointer to new wiki:

http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine
 2011-07-17 13:05:04 -04:00
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
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
Guillermo del Angel 9d59c2cb61 a) Made indel VQSR consensus script operational again, b) Made VariantsToTable more indel-friendly when printing out REF and ALT fields: strip out * from REF and print out alleles in the same way as the VCF so that offline processing is easier 2011-07-15 10:13:02 -04:00
Guillermo del Angel 10cf9245d7 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-14 19:18:05 -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 ed6beae1f3 Adding headers to diffable reading for VCFs 2011-07-14 13:55:35 -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
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
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
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 6007eea3ff Allowing VCF records without GTs in vf4.1 2011-07-13 09:56:08 -04:00
Guillermo del Angel 1e81d521c0 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-12 20:12:29 -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