Mark DePristo 1f45551a15 Bugfixes to G count types in VCF header ... -- Previously VCF header lines of count type G assumed that the sample would be diploid. -- Generalized the code to take a VariantContext and return the right result for G count types by calling into the correct numGenotypes in GenotypeLikelihoods class -- renamed calcNumGenotypes to numGenotypes, which uses a static cache in the class -- calcNumGenotypes is private, and is used to build the static cache or to compute on the fly for uncached No. allele / ploidy combinations -- VariantContext calls into getMaxPloidy in GenotypesContext, which caches the max ploidy among samples -- Added extensive unit tests that compare A and G type values in genotypes		2012-06-26 15:28:34 -04:00
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alignment	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
analyzecovariates	Bug fix in clipping function in ReadUtils for when the read ends at exactly the clipping boundary. Bug fixes in HaplotypeCaller GGA mode for when Smith-Waterman produces a different allele than what was given in the input alleles VCF. GGA mode now works with multiallelic records. Adding min pruning factor argument which is combined with the pruning factor that is determined dynamically by the coverage.	2012-06-04 10:55:36 -04:00
commandline	Feature request from Tim that could be useful to all: there's now an --interval_padding argument that specifies how many basepairs to add to each of the intervals provided with -L (on both ends). This is particularly useful when trying to run over the exome plus flanks and don't want to have to pre-compute the flanks (just use e.g. --interval_padding 50). Added integration test to cover this feature.	2012-06-18 21:36:27 -04:00
gatk	BCF2 cleanup	2012-06-26 15:28:33 -04:00
jna	Device files like /dev/null are now tracked as special by Queue and are not used to generate .out file paths, scattered into a temporary directory, gathered, deleted, etc.	2012-01-23 16:17:04 -05:00
queue	GATK now writes BCF output to any file with .bcf extension	2012-05-24 10:57:00 -04:00
utils	Bugfixes to G count types in VCF header	2012-06-26 15:28:34 -04:00