Mark DePristo 5e593793af DiffEngine utility function simpleDiffFiles ... printSummaryReport now uses GATKReport for nice formating Moved print formatting arguments into inner class provided to printing functions themselves, not the class BAMDiffableReader only reads 1000 entries to avoid performance issue. Work around for BAM files with non-unique names Uncommented all of the incorrectly commented out CombineVariants integrationtests BaseTest now uses DiffEngine to provide inline differences to VCF and BAM files		2011-07-11 23:10:27 -04:00
..
R	Moving AnalyzeAnnotations into the archive because it has outlived its usefulness.	2011-07-02 10:39:53 -04:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	DiffEngine utility function simpleDiffFiles	2011-07-11 23:10:27 -04:00
packages	Removed TileCovariate as a dependency for AnalyzeCovariates.jar	2011-07-11 12:10:11 -04:00
perl	Moving these supported perl scripts to public	2011-07-01 17:26:25 -04:00
scala	Making the outputDir optional. Default = ./	2011-07-05 16:30:41 -04:00
testdata	First working version of the DiffNode readers for VCF and BAM files. Unit tests confirm the readers are approximately working. Skeleton of a working DiffObjects walker that will be able to provide detailed information about how exactly two files of the same type differ, so long as the files are supported by the DiffNode structure.	2011-07-04 16:11:42 -04:00