asivache c252fec1bc synchronizing, no real changes ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@859 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-29 21:56:14 +00:00
..
AllelicVariant.java	First incarnation of the population-based SNP analysis tool. Also bug fixes throughout the GATK	2009-05-27 22:02:24 +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
Genotype.java	Genotype interface is extended: now it requires implementing object to be able to tell whether it isPointGenotype() or isIndelGenotype() (and the contract requires, e.g. alleles to be represented differently)	2009-05-22 17:14:46 +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	Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard...	2009-05-28 20:13:01 +00:00
PooledEMSNPROD.java	First incarnation of the population-based SNP analysis tool. Also bug fixes throughout the GATK	2009-05-27 22:02:24 +00:00
RefMetaDataTracker.java	First incarnation of the population-based SNP analysis tool. Also bug fixes throughout the GATK	2009-05-27 22:02:24 +00:00
ReferenceOrderedData.java	Oops. IteratorPool was occasionally creating too many RODIterators in cases where some reference-ordered data was missing. Fixed by better tracking position of RODIterator.	2009-05-29 21:00:31 +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
SAMPileupRecord.java	more efficient implementation of line parsing, runs at least 1.5 times faster	2009-05-29 21:09:06 +00:00
TabularROD.java	First incarnation of the population-based SNP analysis tool. Also bug fixes throughout the GATK	2009-05-27 22:02:24 +00:00
Transcript.java	'made public' implies the 'public' keyword, actually...	2009-05-27 17:57:01 +00:00
rodDbSNP.java	Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard...	2009-05-28 20:13:01 +00:00
rodGFF.java	Revised ROD system. Split the system in Basic type and interface. Enabled more control over rod accessing, including an initialize() function to fetch headers and other options from the file. Added general tabular rod, which has a named columns and supports a map<String,String> interface. Comes with shiny new Junit system for RODs. Also, added simple python script for accessing picard data.	2009-05-14 21:06:28 +00:00
rodRefSeq.java	synchronizing, no real changes	2009-05-29 21:56:14 +00:00
rodSAMPileup.java	more efficient implementation of line parsing, runs at least 1.5 times faster	2009-05-29 21:09:06 +00:00