complete replacement of hard-coded "/gsc/scripts/lib/java" with $ENV{GENOME_SW_LEGACY_JAVA}
update the log4perl observer to dump a call stack if it gets inappropriate parameters
ClinSeq - update snv summary and convergence
updated ur submodule to a10c039
Merge branch 'master' of ssh://git/srv/git/genome
updated test cases to produce more helpful debug output