hanna 5e8c08ee63 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... ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@849 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-28 20:13:01 +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	First incarnation of the population-based SNP analysis tool. Also bug fixes throughout the GATK	2009-05-27 22:02:24 +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	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
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	package name corrected	2009-05-27 18:20:43 +00:00
rodSAMPileup.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