depristo 29857f5ba6 Fix for instability in output of fasta alternative reference maker when snpmask and snp files are provided and have overlapping records. The order of the records changed due to optimization of the refmetadatatracker, and uncovered this non-determinanism. Now preferrentially masks out includes sites from snps before considering masking out sites in snpmask ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5669 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-20 21:54:09 +00:00
..
config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	Fix for instability in output of fasta alternative reference maker when snpmask and snp files are provided and have overlapping records. The order of the records changed due to optimization of the refmetadatatracker, and uncovered this non-determinanism. Now preferrentially masks out includes sites from snps before considering masking out sites in snpmask	2011-04-20 21:54:09 +00:00
test	Added a utility method to retrieve the contig lengths for WG chunking.	2011-04-20 19:22:21 +00:00