got unit testing working in idea
clean up warnings
clean up warnings
add IDEA project files since it was a pain getting scala and java tests running
add insertions
parse insertions from gff
get tests passing, fix off-by-one errors
script that assigns zygosity to variants
update tests for script
add variant type to output bed file
fix some problems with cloudbreak full script and documentation
filter on internal insert
comments
handle variant type properly in output file
add an error check if the variants file has more than one chromosome listed in it
get bed spans to cover the entire outer fragment length
output span of inner insert size
initial script to convert CB bed spans to modil format
commands to explicitly extract deletion and insertion calls
support for insertions