-- use the general function type.convert from read.table to automagically convert the string data to booleans, factors, and numeric types as appropriate. Vastly better than the previous behavior which only worked for numerics, in some cases.
-- Includes paired end status (T/F)
-- Includes count of reads used in calculation
-- Includes simple read type (2x76 for example)
-- Better handling of insert size, read length when there's no data, or the data isn't paired end by emitting NA not 0
-- ReadGroupProperties: Emits a GATKReport containing read group, sample, library, platform, center, median insert size and median read length for each read group in every BAM file.
-- Median tool that collects up to a given maximum number of elements and returns the median of the elements.
-- Unit and integration tests for everything.
-- Making name of TestProvider protected so subclasses and override name more easily
* All contexts with 'N' bases are now collapsed as uninformative
* Context size is now represented internally as a BitSet but output as a dna string
* Temporarily disabled sorted outputs because of null objects
* Turns DNA sequences (for context covariates) into bit sets for maximum compression
* Allows variable context size representation guaranteeing uniqueness.
* Works with long precision, so it is limited to a context size of 31 bases (can be extended with BigNumber precision if necessary).
* Unit Tests added
-- Now include combinatorial testing for all input parameters: base quality, indel quality, continuation penalty, base identity, and indel length
-- Disabled default the results coming back are not correct
-- Currently disabled as the likelihood function doesn't pass basic unit tests
-- Also make low-level function in LikelihoodCalculationEngine protected
-- As these represent the bulk of the StingExceptions coming from BAMSchedule and are caused by simple problems like the user providing bad input tmp directories, etc.
-- DoC now by default ignores bases with reference Ns, so these are not included in the coverage calculations at any stage.
-- Added option --includeRefNSites that will include them in the calculation
-- Added integration tests that ensures the per base tables (and so all subsequent calculations) work with and without reference N bases included
-- Reorganized command line options, tagging advanced options with @Advanced
Mark DePristo
Ryan Poplin
Mauricio Carneiro
Eric Banks
Menachem Fromer
Khalid Shakir
Guillermo del Angel