Keep a copy of the unscaffolded assembly
rename the contigs in an assembly
Merge pull request #190 from andrewjpage/set_contig_names_in_assemblies

Set contig names in assemblies
reset rna seq stage
remove second underscore from jids in rna seq
Merge pull request #191 from andrewjpage/add_rna_seq_expression_regex_to_vrtracking_tool

Add rna seq expression regex to vrtracking tool
delete original corrected bam file
Merge pull request #192 from andrewjpage/add_rna_seq_expression_regex_to_vrtracking_tool

delete original corrected bam file
Merge branch 'pipeline' of github.com:sanger-pathogens/vr-codebase into add_subsampling_to_pipeline

Conflicts:
	modules/VertRes/Pipelines/Assembly.pm
if you have a larger genome, use more RAM and the long queue
need a return value in bam parser otherwise c error on osx
Merge pull request #193 from andrewjpage/modify_bsub_opts_for_host

Modify bsub opts for host
basic structure of annotation pipeline
annotate assembly
full path to calc ref size
Merge pull request #194 from andrewjpage/ref_size

full path to calc ref size
Merge branch 'pipeline' of github.com:sanger-pathogens/vr-codebase into annotation_pipeline
Lookup genus of lane
vrlane instead of vlane
use sample accession rather than lane accession