vcf-subset: more types recognised with -t option; ref must be given explicitly.
adding new vrpipe siteconfig dir to rsync list
New stats: number of QC failed reads, non-primary alignments, number of filtered vs raw sequences
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop
escape out backslash
Merge pull request #166 from andrewjpage/escape_out_backslash

escape out backslash
Merge branch 'develop' of http://github.com/VertebrateResequencing/vr-codebase into pipeline
allow for no coverage
use latest plot-bamcheck in qc pipeline
extend range to 100 to accomidate empty
don't modify original lane limits
Merge pull request #167 from andrewjpage/empty_values_from_bamcheck_qc_pipeline

Empty values from bamcheck qc pipeline
bamcheck summary mappings for parser
Merge pull request #168 from andrewjpage/empty_values_from_bamcheck_qc_pipeline

bamcheck summary mappings for parser
Merge remote branch 'sangerpathogens/pipeline' into pipeline