asivache d5bb4d9ba9 Auxiliary class that can read one line from samtools pileup file. Used by rodSAMPileup to read pairs of lines as needed. NOTE: this class implements Genotype and (a trivial) GenotypeList, but it is NOT a rod! ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@798 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-22 17:20:01 +00:00
..
AllelicVariant.java	Added isReference() to AllelicVariant and updated rodDbSNP accordingly	2009-04-07 14:49:20 +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	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
RefMetaDataTracker.java	New ROD accessing system, including a generalized interface for binding ROD on the command line that doesn't require you to chance GenomeAnalysisTK.java	2009-04-09 22:04:59 +00:00
ReferenceOrderedData.java	Better integration of reference-ordered data into the data sharding system.	2009-05-21 20:09:32 +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	Auxiliary class that can read one line from samtools pileup file. Used by rodSAMPileup to read pairs of lines as needed. NOTE: this class implements Genotype and (a trivial) GenotypeList, but it is NOT a rod!	2009-05-22 17:20:01 +00:00
TabularROD.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
rodDbSNP.java	Intermediate checking for evaluation -- now supports transition / transversion evaluation	2009-05-22 17:05:06 +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
rodSAMPileup.java	ALERT, ALERT! rodSAMPileup is now a GenotypeList, not a Genotype! Now it can intelligently read full samtools pileup files (containing, in general, both point and indel genotypes at the same position). No need to split/synchronize pileups from different individuals anymore, hooray!	2009-05-22 17:17:59 +00:00