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gatk-3.8/java/src/org/broadinstitute/sting/gatk/refdata
History
asivache 4c67a49ccb Removed unused imports 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1666 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-09-21 16:45:22 +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
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
RODIterator.java commented out version of next() and hasNext() that appear to be correct but are causing testing problems 2009-09-12 19:09:21 +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 getBoundRods() convenience method 2009-09-12 19:07:57 +00:00
ReferenceOrderedData.java General WalkerTest framework. Includes some minor changes to GATK core to enable creation of true command-line like GATK modules in the code. Extensive first-pass tests for SSG 2009-09-04 19:13:37 +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 the VCF ROD. Also changed the VCF objects to much more user friendly. 2009-09-18 20:19:34 +00:00
RodGeliText.java little fixes; also fixed a tyPo 2009-09-18 22:38:51 +00:00
RodGenotypeChipAsGFF.java little fixes; also fixed a tyPo 2009-09-18 22:38:51 +00:00
RodVCF.java little fixes; also fixed a tyPo 2009-09-18 22:38:51 +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
SimpleIndelROD.java Changes: 2009-09-11 16:23:01 +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 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
package.html More package-level documentation. 2009-06-17 16:28:45 +00:00
rodDbSNP.java little fixes; also fixed a tyPo 2009-09-18 22:38:51 +00:00
rodGELI.java depricate this ROD yet again 2009-07-15 13:33:03 +00:00
rodRefSeq.java synchronyzing; debug statements commented out, so nothing changed really 2009-07-10 16:38:33 +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