bcbio.run.clhelp — bcbio.run 0.0.6

Helper functionality for writing command lines that deal with biological file formats.

check-missing clj

(check-missing options required)

Report messages on required missing command line arguments

error-msg clj

(error-msg errors)

exit clj

(exit status msg)

vcf-bam-args clj

(vcf-bam-args xs)

Retrieve VCF, BAM and CRAM files from supplied command line arguments. Returns a map of file types with available and missing.