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gatk-3.8/java/src/org/broadinstitute/sting/gatk/refdata
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aaron 3aec76136f Removing the AllelicVariant interface, which is replaced by the Variation interface. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1770 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-10-06 17:44:24 +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 Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests. 2009-09-30 20:37:59 +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 Cut DeNovoSNPWalker over to the new Variation system, some renaming of methods on the Variation interface, and some corrections on the interface. 2009-09-25 04:35:52 +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 We need to return a null RODRecordList when the default value is null (as opposed to a list with a single null value), because that's what everyone is expecting. 2009-09-24 16:23:12 +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 A big fix for MergingSamRecordIterator, where we weren't correctly handling the comparisons of SAMRecords correctly (we weren't applying the new reference index first, so sometimes the MT contig would be ID 23, sometimes 24 in different records). 2009-10-02 19:35:35 +00:00
RodGeliText.java Removing the AllelicVariant interface, which is replaced by the Variation interface. 2009-10-06 17:44:24 +00:00
RodGenotypeChipAsGFF.java Removing the AllelicVariant interface, which is replaced by the Variation interface. 2009-10-06 17:44:24 +00:00
RodVCF.java Adjusted Genotype concordance to more accurately use the new Genotyping code, fixed the VCF rod, and temp. fix the build by reintroducing Shermans ReadCigarFormatter 2009-09-29 21:28:21 +00:00
SAMPileupRecord.java -add basic indel metrics to variant eval 2009-07-28 03:25:03 +00:00
SNPCallFromGenotypes.java Removing the AllelicVariant interface, which is replaced by the Variation interface. 2009-10-06 17:44:24 +00:00
SangerSNPROD.java Removing the AllelicVariant interface, which is replaced by the Variation interface. 2009-10-06 17:44:24 +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 Removing the AllelicVariant interface, which is replaced by the Variation interface. 2009-10-06 17:44:24 +00:00
SimpleIndelROD.java Removing the AllelicVariant interface, which is replaced by the Variation interface. 2009-10-06 17:44:24 +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 Removing the AllelicVariant interface, which is replaced by the Variation interface. 2009-10-06 17:44:24 +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