cmd

const (
	// ProgramName is "elprep"
	ProgramName = "elprep"
	// ProgramVersion is the version of the elprep binary
	ProgramVersion = "3.06"
	// ProgramURL is the repository for the elprep source code
	ProgramURL = "http://github.com/exascience/elprep"
)

const DeprecatedFilterHelp = "Filter parameters: (deprecated, please use the filter command instead)\n" +
	"elprep sam-file sam-output-file\n" +
	"[--replace-reference-sequences sam-file]\n" +
	"[--filter-unmapped-reads [strict]]\n" +
	"[--replace-read-group read-group-string]\n" +
	"[--mark-duplicates [remove]]\n" +
	"[--sorting-order [keep | unknown | unsorted | queryname | coordinate]]\n" +
	"[--clean-sam]\n" +
	"[--nr-of-threads nr]\n" +
	"[--timed]\n" +
	"[--reference-t fai-file]\n" +
	"[--reference-T fasta-file]\n"

const FilterHelp = "Filter parameters:\n" +
	"elprep filter sam-file sam-output-file\n" +
	"[--replace-reference-sequences sam-file]\n" +
	"[--filter-unmapped-reads]\n" +
	"[--filter-unmapped-reads-strict]\n" +
	"[--filter-mapping-quality mapping-quality]\n" +
	"[--filter-non-exact-mapping-reads]\n" +
	"[--filter-non-exact-mapping-reads-strict]\n" +
	"[--filter-non-overlapping-reads bed-file]\n" +
	"[--replace-read-group read-group-string]\n" +
	"[--mark-duplicates]\n" +
	"[--remove-duplicates]\n" +
	"[--remove-optional-fields [all | list]]\n" +
	"[--keep-optional-fields [none | list]]\n" +
	"[--sorting-order [keep | unknown | unsorted | queryname | coordinate]]\n" +
	"[--clean-sam]\n" +
	"[--nr-of-threads nr]\n" +
	"[--timed]\n" +
	"[--reference-t fai-file]\n" +
	"[--reference-T fasta-file]\n"

const MergeHelp = "Merge parameters:\n" +
	"elprep merge /path/to/input sam-output-file\n" +
	"[--single-end]\n" +
	"[--nr-of-threads n]\n" +
	"[--reference-t fai-file]\n" +
	"[--reference-T fasta-file]\n"

const SplitHelp = "Split parameters:\n" +
	"elprep split (sam-file | /path/to/input/) /path/to/output/\n" +
	"[--output-prefix name]\n" +
	"[--output-type [sam | bam | cram]]\n" +
	"[--single-end]\n" +
	"[--nr-of-threads nr]\n" +
	"[--reference-t fai-file]\n" +
	"[--reference-T fasta-file]\n"