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340 Commits (4d4db7fe6318b64697c07ff9aabafc2e16970d53)

Author SHA1 Message Date
ebanks 4c4d048f14 Moving VariantFiltration over to use VariantContext. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3048 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 18:35:23 +00:00
ebanks c88a2a3027 Fixing/cleaning up the vcf merge util 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3047 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 15:13:32 +00:00
ebanks 03480c955c And now the UnifiedGenotyper can officially annotate genotype (FORMAT) fields too. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3039 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 04:58:37 +00:00
ebanks 0311980668 The VariantAnnotator can now officially annotate genotype (FORMAT) fields. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3037 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 03:30:14 +00:00
ebanks 0247548400 Fixed one test and (temporarily) punted on another 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3030 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 06:22:48 +00:00
ebanks ee0e833616 Some significant changes to the annotator: 
1. Annotations can now be "decorated" with any arbitrary interface description - not just standard or experimental.
2. Users can now not only specify specific annotations to use, but also the interface names from #1.  Any number of them can be specified, e.g. -G Standard -G Experimental -A RankSumTest.
3. These same arguments can be used with the Unified Genotyper for when it calls into the Annotator.
4. There are now two types of annotations: those that are applied to the INFO field and those that are applied to specific genotypes (the FORMAT field) in the VCF (however, I haven't implemented any of these latter annotations just yet; coming soon).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3029 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 05:38:32 +00:00
hanna 2525ecaa43 Oops. Commented out some tests to improve performance and then checked in the commented out tests. Reverted. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3012 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 16:34:50 +00:00
hanna 6dd5f192e7 Performance improvements for RODs in conjunction with new sharding system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3010 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 14:54:12 +00:00
ebanks 411d25c8d1 -Integration tests for walkers that use original quals. 
-framework for pushing -OQ into GATK (not done)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3004 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-15 18:46:31 +00:00
aaron e365d308d4 add a new JEXLContext that lazy-evaluates JEXL expressions given the VariantContext. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3003 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-15 16:00:55 +00:00
aaron 88a48821ea removed the dependence on removeRegion() in GenomeLocSortedSet 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2993 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-12 22:35:49 +00:00
depristo b39b5edca8 Bug fix in variant eval 2. Preliminary (slow and buggy) support for -XL exclude lists. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2991 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-12 19:23:12 +00:00
aaron 661a043cef adding methods to get RODs by name or type in read traversals, performance improvements to RODs for Reads in general, and some more Tribble infrastructure. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2984 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 21:13:39 +00:00
hanna a7ba88e649 Rework the way the MicroScheduler handles locus shards to handle intervals that span shards 
with less memory consumption.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2981 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 18:40:31 +00:00
aaron dde9fd8a15 some rods-for-reads cleaning and performance improvements. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2979 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 22:54:58 +00:00
ebanks 40d305bc7e Added test of Nway cleaning for Matt; thanks to Aaron for the help. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2977 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 21:00:41 +00:00
ebanks 7ddd45d059 Hmm. I thought I removed this already. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2973 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 03:09:13 +00:00
ebanks 1a576525e9 misc improvements 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2972 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 03:00:28 +00:00
ebanks 6e855809e1 Renaming and moving relevant tools into a sequenom directory 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2971 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 02:31:10 +00:00
ebanks 5a20bf0e64 3 changes to UG which break integration tests: 
1. emit AA,AB,BB likelihoods in the FORMAT field for Mark
2. remove constraint that genotype alleles (in the GT field) need to be lexigraphically sorted.
3. Add bam file(s) used by genotyper to header for Kiran


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2963 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 17:16:47 +00:00
ebanks 9f3b99c11b Moving UnifiedGenotyper and VariantAnnotator over to VariantContext system. 
Removing obsolete genotyping classes.
First stage of removing dependence on old Genotype class.
More changes to come.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2960 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 03:41:07 +00:00
hanna a7fe07c404 A few stopgap fixes to get the GATK to the point where the old sharding 
infrastructure can be torn down:
1) New sharding system emulates old MonolithicSharding mechanism.
2) Better awareness of differences between fasta and BAM files when creating
   shards.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2948 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-07 21:01:25 +00:00
hanna dd6122f682 Fixed another bug in the original sharding system. Updated integration tests 
as appropriate.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2947 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-07 15:32:18 +00:00
hanna ee2ec7ced9 Fix off-by-one error in original implementation of read sharding. Tested by 
awking output of BamToFastq vs. samtools until the outputs matched exactly.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2945 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-06 18:52:53 +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
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 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
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
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
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
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
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
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