depristo 3949b4ac72 commented out version of next() and hasNext() that appear to be correct but are causing testing problems ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1596 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-12 19:09:21 +00:00
..
AllelicVariant.java	Changes:	2009-09-11 16:23:01 +00:00
BasicReferenceOrderedDatum.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
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	First pass at passing lists of files / lists of interval arguments work. Note that the interval	2009-06-25 20:44:23 +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
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	Changes:	2009-09-11 16:23:01 +00:00
RodGeliText.java	Fixed bad compareTo operator	2009-09-12 19:07:10 +00:00
RodGenotypeChipAsGFF.java	Changes:	2009-09-11 16:23:01 +00:00
SAMPileupRecord.java	-add basic indel metrics to variant eval	2009-07-28 03:25:03 +00:00
SNPCallFromGenotypes.java	Refactoring of the traversal engine base class, I removed a lot of old code.	2009-07-09 21:57:00 +00:00
SangerSNPROD.java	Changes:	2009-09-11 16:23:01 +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	Changes:	2009-09-11 16:23:01 +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