Replaced reference size check.
Merge pull request #170 from CraigPorter/genome_coverage_test

Replaced reference size check.
evaluate a config file as a hash ref
save params outside eval
Merge pull request #171 from andrewjpage/evalutate_configs_as_ref

Evalutate configs as ref
add bowtie2
tests for bowtie2
Merge pull request #172 from andrewjpage/bowtie2_mapper

Bowtie2 mapper
bowtie_2_specify_output_param
Merge pull request #173 from andrewjpage/bowtie_2_specify_output_param

bowtie_2_specify_output_param
Merge branch 'pipeline' of github.com:sanger-pathogens/vr-codebase into add_sga_step_to_pipeline