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gatk-3.8/java/src/org/broadinstitute/sting/gatk/refdata
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aaron d262cbd41c changes to add VCF to the rod system, fix VCF output in VariantsToVCF, and some other minor changes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1715 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-09-24 15:16:11 +00:00
..
AllelicVariant.java Changes: 2009-09-11 16:23:01 +00:00
BasicReferenceOrderedDatum.java Framework for ROD walkers -- totally experiment and not working right now 2009-09-12 19:13:15 +00:00
BrokenRODSimulator.java Little class that can be used to simulate the results returned by the old ROD system. This is needed to keep couple of tests from breaking. All the code that uses this class must be changed urgently to accomodate the data as returned by new ROD system, and the corresponding tests (MD5 sums) have to be modified as well since some data as seen through the new ROD system is indeed different. 2009-09-21 16:58:56 +00:00
CleanedOutSNPROD.java Allow this ROD to consist of just the positions 2009-09-01 12:43:18 +00:00
Genotype.java -add basic indel metrics to variant eval 2009-07-28 03:25:03 +00:00
GenotypeList.java a trivial wrapper interface for the objects capable of holding 'full' genotype, i.e. both point (as in ref/snp) and indel variants at the same reference position 2009-05-22 17:12:01 +00:00
HapMapAlleleFrequenciesROD.java Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future. 2009-06-22 14:39:41 +00:00
HapMapGenotypeROD.java Added ROD for parsing hapmap3 genotype files. 2009-07-05 16:28:24 +00:00
IntervalRod.java major restructuring of generalized variant analysis framework. Now trivally easy to add additional analyses. Easy partitioning of all analyses by features, such as singleton status. Now has transition/transversional bias, counting, dbSNP coverage, HWE violation, selecting of variants by presence/absense in dbs. Also restructured the ROD system to make it easier to add tracks. Also, added the interval track -- if you provide an interval list, then the system autoatmically makese this available to you as a bound rod -- you can always find out where you are in the interval at every site. Python scripts improved to handle more merging, etc, into population snps. 2009-06-05 23:34:37 +00:00
IntervalRodIterator.java Removed unused imports 2009-09-21 16:45:22 +00:00
PointIndelROD.java Add an indel rod which represents the initial point of the indel only 2009-09-02 19:32:29 +00:00
PooledEMSNPROD.java Changes: 2009-09-11 16:23:01 +00:00
RODRecordIterator.java Starting an update of ROD system. These basic classes will completely replace old ones, but with this update they are not linked to anything, so this checkpoint should be safe. 2009-09-18 15:58:37 +00:00
RODRecordList.java Starting an update of ROD system. These basic classes will completely replace old ones, but with this update they are not linked to anything, so this checkpoint should be safe. 2009-09-18 15:58:37 +00:00
RefMetaDataTracker.java Changing the carpet under your feet!! New incremental update to th eROD system has arrived. 2009-09-21 16:55:22 +00:00
ReferenceOrderedData.java changes to add VCF to the rod system, fix VCF output in VariantsToVCF, and some other minor changes 2009-09-24 15:16:11 +00:00
ReferenceOrderedDatum.java Better interface to the tabular ROD, now makes writing files easier. Also has corresponding test files 2009-05-14 23:20:11 +00:00
RodGLF.java adding an interface so that the current @Requires with ROD annotations work in walkers like VariantEval 2009-09-23 18:24:05 +00:00
RodGeliText.java adding an interface so that the current @Requires with ROD annotations work in walkers like VariantEval 2009-09-23 18:24:05 +00:00
RodGenotypeChipAsGFF.java adding an interface so that the current @Requires with ROD annotations work in walkers like VariantEval 2009-09-23 18:24:05 +00:00
RodVCF.java changes to add VCF to the rod system, fix VCF output in VariantsToVCF, and some other minor changes 2009-09-24 15:16:11 +00:00
SAMPileupRecord.java -add basic indel metrics to variant eval 2009-07-28 03:25:03 +00:00
SNPCallFromGenotypes.java Changes to switch Variant Eval over to the new Variation system. 2009-09-14 05:34:33 +00:00
SangerSNPROD.java Changes: 2009-09-11 16:23:01 +00:00
SeekableRODIterator.java Starting an update of ROD system. These basic classes will completely replace old ones, but with this update they are not linked to anything, so this checkpoint should be safe. 2009-09-18 15:58:37 +00:00
SequenomROD.java Added a sequenom rod to empower Carrie to convert 1KG validation SNPs to sequenom format 2009-09-23 20:22:09 +00:00
SimpleIndelROD.java adding an interface so that the current @Requires with ROD annotations work in walkers like VariantEval 2009-09-23 18:24:05 +00:00
TabularROD.java Allow RODs to specify that incomplete records are okay (i.e. that they allow optional fields) 2009-08-18 15:26:10 +00:00
Transcript.java Transcript is now simply an interface 2009-09-23 18:13:31 +00:00
VariationRod.java adding an interface so that the current @Requires with ROD annotations work in walkers like VariantEval 2009-09-23 18:24:05 +00:00
package.html More package-level documentation. 2009-06-17 16:28:45 +00:00
rodDbSNP.java adding an interface so that the current @Requires with ROD annotations work in walkers like VariantEval 2009-09-23 18:24:05 +00:00
rodGELI.java depricate this ROD yet again 2009-07-15 13:33:03 +00:00
rodRefSeq.java New, simpler rodRefSeq. Fully relies on the ROD system standard mechanisms. Multiple transcripts over a given location will be now returned by the ROD system itself as RodRecordList<rodRefSeq>; and yes, rodRefSeq does represent a single transcript record now and implements Transcript interface 2009-09-23 18:18:25 +00:00
rodSAMPileup.java Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future. 2009-06-22 14:39:41 +00:00