Eric Banks 8405156ae1 Refactored VariantsToTable so that 1) genotype-level fields can be specified (stabilized and supported code) and 2) the --moltenize argument could be supported to produce molten output of the data. Added tests that cover these capabilities.		2012-06-04 14:28:32 -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	Rev Tribble to r97, adding binary feature support	2012-05-03 07:31:48 -04:00
gatk	Refactored VariantsToTable so that 1) genotype-level fields can be specified (stabilized and supported code) and 2) the --moltenize argument could be supported to produce molten output of the data. Added tests that cover these capabilities.	2012-06-04 14:28:32 -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	Fixing the previous fix related to clipping. Adding extra reference padding in the HaplotypeCaller to get those larger alleles during GGA.	2012-06-04 12:49:36 -04:00