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533 Commits (1e8b3ca6ba71122cdcfaea3ea9db2b06c8c3dc18)

Author SHA1 Message Date
chartl 8738c544f1 Minor refactoring of CoverageStatistics to allow simultaneous output of per-sample and per-read group statistics. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2940 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 17:06:52 +00:00
hanna 7104a3a96c Fix for accumulator exception when running reduce by interval walkers without 
intervals.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2935 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 01:04:08 +00:00
aaron 366771d5a6 another test-with-multiple outputs fix 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2934 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 22:46:15 +00:00
chartl 706d49d84c Commit for Aaron 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2932 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 21:29:07 +00:00
aaron 54f04dc541 forgot to uncomment the auto-deletion of temp files... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2930 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 20:29:42 +00:00
aaron 80cc6bbeb4 add a way to test files generated by a walker that aren't command-line arguments; added some example code in CoverageStatisticsIntegrationTest for Chris. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2929 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 20:20:58 +00:00
ebanks 0dd65461a1 Various improvements to plink, variant context, and VCF code. 
We almost completely support indels. Not yet done with plink stuff.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2926 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 17:58:01 +00:00
aaron c8077b7a22 Waypoint check-in: a couple of changes to for Tribble, and adding some options to the integration test for passing in auxillary files that aren’t “%s” command line options. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2925 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 16:02:21 +00:00
aaron ca2cd9d4f5 a little clean-up: move setting the bases of generated reads into Artificial SAM Utils now that the clean read injector test is gone. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2919 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-03 16:31:45 +00:00
aaron 790d2a7776 adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2918 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-03 15:56:44 +00:00
ebanks 0e9a6826b0 Update to VCF code to get it up to spec. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2917 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-03 06:12:42 +00:00
ebanks 74a5223b11 oops - didn't mean to check this in 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2914 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-02 20:28:22 +00:00
ebanks 5f3c80d9aa 1. To make indel calls, we need to get rid of the SNP-centricity of our code. First step is to have the reference be a String, not a char in the Genotype. Note that this is just a temporary patch until the genotype code is ported over to use VariantContext. 
2. Significant refactoring of Plink code to work in the rods and use VariantContext.  More coming.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2913 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-02 20:26:40 +00:00
aaron d8fedd59be docs, cleanup, and some improvements to the iterators. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2901 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-26 22:36:04 +00:00
chartl 87f8fb7282 Quick commit in advance of Aaron's. Just a bunch of refactoring (private classes separated out, put in proper package). Also support added for coverage by read group rather than sample. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2897 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-26 16:39:47 +00:00
depristo 9a6b384adb Support for no qual fields in VCF; better support for Mendelian violation calculations 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2893 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-26 00:29:17 +00:00
aaron 246fa28386 RODs for reads phase 2: modified RODRecordList to implement List<ReferenceOrderedDatum> so I could stub it out for testing, added a FlashBackIterator which is needed to prevent the ResourcePool from opening infinity+1 iterators, and some other interfaces to make unit testing much smoother. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2892 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-25 22:48:55 +00:00
chartl 3d92e5a737 Initial commit of integration test(s) for CoverageStatistics, currently in progress [midway commit is for Matt] 
Modifications to CoverageStatistics - now includes and extends much of the behavior of DepthOfCoverage (per-base output, per-target output).

Additional functionality (coverage without deletions, base counts, by read group instead of by sample) is upcoming.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2888 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-25 20:25:07 +00:00
hanna 553d39bb00 Clean up the code a bit following the introduction of reduceByInterval. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2887 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-25 01:20:22 +00:00
hanna 199b43fcf2 Reduce by interval alterations to interface with new sharding system. This checkin with be followed by a 
simplification of some of the locus traversal code.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2886 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-25 00:16:50 +00:00
aaron fef1154fc8 starting on RODs for Reads: made RODRecordList implement list<RODatum> (so we can sub in fake lists during testing), and removed unnecessary generic-ness. Removed BrokenRODSimulator, which isn't being used. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2884 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-24 22:11:53 +00:00
aaron 5546aa4416 adding code to deal with the off-spec situation where our minimum likelihood is above the GLF max of 255. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2871 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-22 22:27:39 +00:00
ebanks 8b555ff17c Killed the old cleaner code. Bye bye. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2868 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-22 20:49:58 +00:00
rpoplin 3e0e7aad2d Removing debug statement. oops. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2858 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-19 15:26:22 +00:00
rpoplin 7f19ff1fa1 Added a new option in the recalibrator to be used by people who have SOLiD data in which only a few of the reads have no-calls in the color space. These reads will be skipped over and left in the bam file untouched. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2857 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-19 15:25:23 +00:00
aaron b1a4e6d840 removing non-ascii characters from my Copyright and from VariantEval2Walker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2856 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-18 18:54:36 +00:00
aaron 33ae256186 a start to some of the infrastructure for Tribble, including dynamic detection of new RMD; not nearly wired in or complete yet. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2855 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-18 18:43:52 +00:00
ebanks 79ab7affda - Change sortOnDisk option to sortInMemory 
- Fix horrible cleaner bug
- Trivial optimizations to cleaner code - more significant ones coming soon.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2850 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-17 20:52:57 +00:00
aaron 653f70efa2 added methods to validate an interval before you try to make a GenomeLoc: boolean validGenomeLoc(). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2846 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-16 20:35:35 +00:00
depristo 8072e9aed5 should never commit without running intergration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2838 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 23:42:37 +00:00
depristo 5f74fffa02 Massive improvements to VE2 infrastructure. Now supports VCF writing of interesting sites; multiple comp and eval tracks. Eric will be taking it over and expanding functionality over the next few weeks until it's ready to replace VE1 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2832 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 15:26:52 +00:00
depristo 197dd540b5 added root GATKData variable 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2831 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 15:25:34 +00:00
depristo c66861746a improvements to ve2, including more meaningful mendelian violation counting. Support for VCF emitted interesting sites, annotated according to the evaluations themselves. Basic intergration test for VE2 started 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2819 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-10 16:12:29 +00:00
rpoplin 0b1e243a7b CountCovariates now sorts the list of standard covariate classes coming from PackageUtils.getClassesImplementingInterface(). As a result some of the integration tests now make use of -standard 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2817 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-10 15:52:20 +00:00
depristo 934d4b93a2 VariantContext to VCF converter. BeagleROD, and phasing of VCF calls. Integration tests galore :-) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2814 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-09 19:02:25 +00:00
depristo 94f892ad42 VCF->beagle and VCF phasing using beagle input. Appears to work fairly well. VariantContexts now support phased genotypes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2812 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-09 01:22:05 +00:00
kshakir fc810a1800 Updated VCF Reader to parse VCFs according to the VCFv3.3 spec. Column headers are tab separated since sample names might have spaces. 
Updated test files in /humgen/gsa-scr1/GATK_Data/Validation_Data/*.vcf to remove spaces except for when they are supposed to be in the sample name.
Added @Test before VCFReaderTest.testHeaderNoRecords()

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2809 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-08 22:55:59 +00:00
chartl 935e76daa1 Minor changes to oneoff walkers. PlinkRod altered but still commented. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2808 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-08 18:49:56 +00:00
ebanks ca1917507f Various improvements and fixes: 
In indel cleaner:

1. allow the user to specify that he wants to use Picard’s SAMFileWriter sorting on disk instead of having us sort in memory; this is useful if the input consists of long reads.

2. for N-way-out mode: output bams now use the original headers from the corresponding input bams - as opposed to the merged header.  This entailed some reworking of the datasources code.

3. intermediate check-in of code that allows user to input known indels to be used as alternate consenses.  Not done yet.

In UG: fix bug in beagle output for Jared.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2805 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-07 04:21:04 +00:00
depristo 3b1ab86d11 Added generic interfaces to RefMetaDataTracker to obtain VariantContext objects. More docs. Integration tests for VariantContexts using dbSNP and VCF. At this stage if you use dbSNP or VCF files only in your walkers, please move them over to the VariantContext, it's just nicer. If you've got RODs that implemented the old variation/genotype interfaces, and you want them to work in new walkers, please add an adaptor to VariantContextAdaptors in refdata package. It should be easy and will reduce burden in the long term when those interfaces are retired. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2803 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-06 16:26:06 +00:00
hanna c7e006a996 Bug fixes for interval batching in sharding system. Sharding system now batches intervals and passes 
basic tests for small and large intervals and intervals that cross bin boundaries.  Currently works
only with a single BAM file.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2800 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 21:47:54 +00:00
rpoplin be33d1852c Reverting 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2792 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 15:57:09 +00:00
rpoplin 0d8d6e0a14 Ti/Tv module in VariantEval shows known and novel ratios if possible 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2790 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 15:37:40 +00:00
depristo 1494dc875f fixing up tests. Moves are complete 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2789 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 14:24:00 +00:00
depristo c6d86da4b8 almost managed to move things around perfectly in move go 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2788 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 14:18:26 +00:00
depristo 1d86dd7fd1 Interface changes following Matt's advice. VariantContexts are now immutable, and there are special mutable versions, in case you need to change things. AttributedObject now a InferredGeneticContext and package protected. VariantContexts are now named, which makes them easier to use with the rod system 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2780 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-04 20:55:49 +00:00
aaron af7cd9cf58 some very old tests relied on cancer data that got moved. Reset one to use data in the validation directory, the other to the artificial sam utils (the best approach). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2767 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-02 23:13:10 +00:00
hanna 9dbdfff786 Moved VariantEval to core. Updated integration test md5s to reflect new Analysis class names. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2762 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-02 00:22:15 +00:00
depristo d9671dffba Documentation for VariantContext. Please read it and start using it. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2756 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-01 17:49:51 +00:00
ebanks e0808e6c37 Moved old EM model to archive 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2754 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-01 02:55:32 +00:00
ebanks f6da57dc79 1. For Matt: JIRA GSA-270. Other walkers needing to call into the Unified Genotyper now use static methods (e.g. runGenotyper()) instead of calling initialize and map. 
2. Set the default confidence cutoff to 50 (instead of 0).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2752 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-31 21:14:57 +00:00
depristo 62a80f2b6f fixed out of date tests. Also, tests uncovered a subtle bug in new implementation that was also fixed 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2741 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 20:03:48 +00:00
hanna e7f5c93fe5 Cleaning up the inheritance hierarchy from the previous commit. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2738 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 19:13:36 +00:00
depristo 1993472b38 Just like VariantFiltration but lets you match info fields out of the VCF instead of annotating them. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2736 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 15:38:03 +00:00
depristo 5aaf4e6434 VariantFiltration now accepts any number of --name --filter expressions, and annotates the VCF file with each name that matches. Very useful 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2732 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 12:13:08 +00:00
hanna 3d922a019f Basic support for very simple index-driven locus traversals. Interface has been changed to 
support batched intervals in a single shard, but intervals are not yet compressed into a single
shard.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2730 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 03:14:26 +00:00
depristo 956b570c8e V5 improvements to VariantContext. Now fully supports genotypes. Filtering enabled. Significant tests throughout system. Support for rebuilding variant contexts from subsets of genotypes. Some code cleanup around repository 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2721 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-28 18:37:17 +00:00
depristo f6bca7873c V3 of VariantContext. Support for Genotypes and NO_CALL alleles. QUAL fields fully implemented. Can parse VCF records and dbSNP. More complete validation. Detailed testing routines for VariantContext and Allele. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2718 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-28 04:10:16 +00:00
depristo 3399ad9691 Incremental update 2 -- refined allele and VariantContext classes; support for AttributedObject class; extensive testing for Allele class, and partial for VariantContext. Now possible to easily convert dbSNP to VariantContext. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2705 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-27 17:19:37 +00:00
ebanks 476d6f3076 RealignerTargetCreator is officially live 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2697 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-27 03:41:52 +00:00
ebanks 47440bc029 - Removed max_coverage argument from UG; Aaron will set it up so that we don't call when the GATK had to drop reads. 
- Reimplemented optimization in UG to not call when there are no non-ref bases.
- Compute reference confidence accurately in UG for ref calls.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2693 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-26 21:56:33 +00:00
rpoplin a1054efe8a Default platform and default read group are no longer set to values by default. The recalibrator throws an exception if needed values are empty in the bam file and the args weren't set by the user. This is done to make it more obvious to the user when the bam file is malformed. Similarly, the recalibrator now refuses to recalibrate any solid reads in which it can't find the color space information with an exception message explaining this. The recalibrator no longer maintains its own version number and instead uses the new global GATK version number. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2690 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-26 18:47:40 +00:00
depristo c231547204 Refactoring and migration of new allele/variantcontext/genotype code into oneoffprojects. NOT FOR USE. PlinkRod commented out due to dependence on this new, rapidly changing interface. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2687 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-26 13:53:29 +00:00
chartl d6b9b788a8 Renamed -- PlinkRodWithGenomeLoc --> PlinkRod 
Since binary files do not need encoded locus information in the SNP names there's no need to suggest that it is so in the name of the rod



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2671 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-23 18:19:28 +00:00
chartl ac983e7a0b Ran the rod on a binary plink file with indels and it just worked. Love it when that happens! Unit test to ensure this behaviour is maintained. 
****** PLINK ROD IS NOW READY TO GO ********




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2670 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-23 18:13:05 +00:00
chartl ae22d35212 PlinkRod now correctly parses binary files without indels; unit test added for this behavior. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2669 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-23 17:34:06 +00:00
chartl 94dc09c865 PlinkRod now successfully instantiates on the binary ped file trio (.bim, .bam, .fam) for non-indel files. 
Upcoming: Test that the instantiation is correct, do it for indel-containing files.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2668 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-23 16:13:24 +00:00
chartl 01db93299c PlinkRodWithGenomeLoc now properly handels indels. 
There is now a DELETION_REFERENCE allele type to allow for the storage of multi-base references rather than point-mutation references.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2667 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-23 07:34:52 +00:00
chartl 42fb85e7f3 PlinkRodWithGenomeLoc now properly parses text plink files. Unit test added to test this functionality. Indels and binary files to come. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2666 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-23 06:19:26 +00:00
aaron 2ea768d902 ant clean is your friend....fixed test code dependent on an interface change. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2660 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-22 20:07:46 +00:00
ebanks c1e09efb23 - Fixed output for beagle header 
- Better description for QualByDepth annotation



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2655 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-21 21:25:56 +00:00
chartl 5b2a1e483e Renamed SequenomToVCF as PlinkToVCF. Wiki will be changed accordingly. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2649 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-21 17:35:20 +00:00
ebanks 9c7b281b4f Set default value for max_coverage to be 100K (since 10K is too small). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2646 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-20 20:15:25 +00:00
aaron 8d1d37302c a quick change to GLF to keep as much precision in our likelihoods as long as possible, before we put it into byte space. Sanger was doing a diff at low coverage and noticed our calls didn't contain as much precision as theirs. Updated the MD5 for unified genotyper output. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2644 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-20 19:36:49 +00:00
aaron a1b4cc4baf changes to intelligently log overflowing locus pile-ups. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2640 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-20 08:09:48 +00:00
ebanks 4ac9eb7cb2 - Smarter strand bias calculation 
- Better debug/verbose printing



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2639 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-20 03:01:26 +00:00
depristo 9e0ae993c7 -B 1kg_ceu,VFC,CEU.vcf -B 1kg_yri,VCF,YRI.vcf system supported to allow 1KG % (like dbSNP%) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2632 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-19 21:33:13 +00:00
rpoplin c98df0a862 Updated solid_recal_modes to work with bfast aligned data. Added an integration test that uses the BFAST file provided by TGen. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2630 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-19 21:18:02 +00:00
ebanks 12453fa163 Misc cleanup of UG args 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2620 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-17 04:38:52 +00:00
depristo d8e74c5795 Update to MD5s for old tests and added extensive VCF testing 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2615 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-16 20:22:58 +00:00
ebanks b911b7df82 Fixing the AC annotation to be in line with the VCF spec 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2593 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 18:28:52 +00:00
rpoplin f2e539c52f As per discussions with Tim we are reverting the previous change regarding PairedReadOrderCovariate. The CycleCovariate now differentiates between first and second of pair by multiplying the cycle by -1. PairedReadOrderCovariate has been removed completely. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2592 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 18:18:59 +00:00
rpoplin df998041a8 Minor change to solid warning message. Added note for a future solid recalibration integration test when we get the required data file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2590 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 16:31:25 +00:00
hanna b19bb19f3d First successful test of new sharding system prototype. Can traverse over reads from a single 
BAM file.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2587 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 03:35:55 +00:00
aaron db9570ae29 Looks bigger than it is: 
* Moved GATKArgumentCollection into gatk.arguments folder to clean up the main folder, also added some associated argument classes (most of the changes).
* Added code the argument parsing system for default enums, we needed this so we could preserve the current unsafe flag, and at the same time allow finer grained control of unsafe operations.  You can now specify:

"-U" (for all unsafe operations), "-U ALLOW_UNINDEXED_BAM" (only allow unindexed BAMs), "-U NO_READ_ORDER_VERIFICATION", etc.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2586 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 00:14:35 +00:00
asivache cff8b705c0 Oh, and the test would not work anymore... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2585 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-14 17:47:09 +00:00
rpoplin 9bf0d7250a Fixing the testOtherOutput UG integration test so it will run. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2580 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-14 13:40:14 +00:00
chartl 424d1b57f7 Sequenom to VCF now allows user to specify filters for QC, and they will appear in the filter field of the output VCF 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2577 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-13 23:22:37 +00:00
rpoplin f96b2b211e My last checkin updating R code broke an unrelated UnifiedGenotyper integration test. Eric says that I should take out the verbose test. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2576 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-13 22:28:10 +00:00
rpoplin 49c44e7b36 PairedReadOrderCovariate is now a standard covariate and because of this CycleCovariate no longer multiplies by negative one for second of pair reads. Added PairedReadOrderCovariate to some of the integration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2574 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-13 20:09:10 +00:00
ebanks 8ca5bba738 We emit genotype data in the VCF record if the format string instructs us to (regardless of whether or not genotypes are provided - this was the wrong test). 
SequenomToVCF now correctly has no-calls when probes fail.
Re-enabled SequenomToVCF integration test.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2572 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-13 15:40:27 +00:00
chartl 6d1107a4ed Update to SequenomToVCF 
Output changing slightly so integration test disabled temporarily



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2571 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-13 15:32:05 +00:00
ebanks f99586f91b Added integration test for beagle and verbose output in UG. 
Minor cleanup of VCFRecord code.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2570 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-13 03:55:24 +00:00
rpoplin 189829841b The recalibrator now uses all input RODs when looking for known polymorphic sites not just the one named dbsnp. Added an integration test which uses both dbsnp and an input vcf file and skips over the union of the two. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2564 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-12 18:50:39 +00:00
aaron 16777e3875 more fixes for the empty interval list problem; you can now run LocusWindow traversals with an empty interval list, but the GATK will give you a warning (unless you're running in unsafe mode). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2563 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-12 18:47:43 +00:00
ebanks 03b7d5f5c7 1. Fixed small but embarrassing bug in weighted Allele Balance annotation calculation. 
2. Made RankSumTest abstract; added 2 subclasses: BaseQualityRST and MappingQualityRST (the latter based on a suggestion from Mark Daly).  Untested so they're still experimental.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2561 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-12 18:33:53 +00:00
ebanks 040fdfee61 Cleaned up the interface to VCFRecord. It's now possible (and easy) to create records and then write them with a VCFWriter. 
I've updated HapMap2VCF to use the new interface; Chris agreed to take care of Sequenom2VCF.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2558 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-11 21:42:12 +00:00
ebanks 42aff1d2c3 Annotator in general should be able to annotate monomorphic or tri-allelic sites. 
It's up to the individual annotations to decide whether they want to annotate or not.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2556 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-11 19:52:18 +00:00
chartl dfa3c3b875 Added: 
SequenomToVCF - Takes a sequenom ped file and converts it to a VCF file with the proper metrics for QC. It's currently a rough draft,
but is working as expected on a test ped file, which is included as an integration test.

Modified:

VCFGenotypeCall -- added a cloneCall() method that returns a clone of the call

Hapmap2VCF -- removed a VCFGenotypeCall object that gets instantiated and modified but never used
(caused me all kinds of confusion when I was basing SequenomToVCF off of it)



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2554 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-11 17:17:21 +00:00
rpoplin 62dd2fa5be Fixing another bug in solid recal regarding negative strand reads. The isInconsistentColorSpace method incorrectly used the inconsistent tag added by parseColorSpace, the inconsistent tag is in the direction of the read like the color space tag, and not in the direction of the reference like everything else. This affects the recalibrated quality scores but the improvment in SNP calling performance is minor when using the default UG settings (min base quality 10). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2553 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-11 14:28:52 +00:00