David Roazen 07b369ca7e Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package ... This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.		2012-12-19 10:25:22 -05:00
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Affection.java	Renaming quantitative trait to OtherPhenotype which is now a String not a double	2011-10-05 12:26:33 -07:00
Gender.java	Reorganization of Sample	2011-09-30 15:50:54 -04:00
PedReader.java	Renaming quantitative trait to OtherPhenotype which is now a String not a double	2011-10-05 12:26:33 -07:00
PedigreeValidationType.java	Final PED documentation	2011-10-05 15:17:41 -07:00
Sample.java	Added getParents() -> returns an arrayList containing the sample's parent(s) if available	2011-10-20 12:47:27 +02:00
SampleDB.java	Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package	2012-12-19 10:25:22 -05:00
SampleDBBuilder.java	Code improvements re: JIRA GSA-510. Trio class migrated into the Samples package - because the trio structure is so ubiquitously used, it makes sense, I think, to have a class which imposes the structure on the samples. Existing functions which slightly duplicated the getTrios() method look like they have bugs. These functions are now deprecated.	2012-08-25 08:48:27 -07:00
Trio.java	Code improvements re: JIRA GSA-510. Trio class migrated into the Samples package - because the trio structure is so ubiquitously used, it makes sense, I think, to have a class which imposes the structure on the samples. Existing functions which slightly duplicated the getTrios() method look like they have bugs. These functions are now deprecated.	2012-08-25 08:48:27 -07:00