greater than/equal for LOD thresholds
updated svtyper
serious bug in annotate_rd was outputting each variant twice
default speedseq to search its own directory for proper binaries
update config
updated config
removed bwa from python install script
dont' attempt to annotate GL contigs with VEP in svs
merged
added lumpy back
fixed bug that occurs when not using full pathname for speedseq.config
Merge branch 'tgi'
added parameter to specify amount of sort memory  for sambamba
default to installing VEP cache in speedseq/annotations
vep installed into annotations directory by default, updated speedseq.config to reflect changes
fixed aln -M flag
fixed default pairend distro
update svtyper
force python2.7 use
python