cmd

const (
	// ProgramName is "elprep"
	ProgramName = "elprep"
	// ProgramVersion is the version of the elprep binary
	ProgramVersion = "4.1.6"
	// ProgramURL is the repository for the elprep source code
	ProgramURL = "http://github.com/exascience/elprep"
)

const BedToElsitesHelp = "\nbed-to-elsites parameters:\n" +
	"elprep bed-to-elsites bed-file elsites-file\n" +
	"[--log-path path]\n"

const CombinedSfmFilterHelp = "filter/sfm parameters:\n" +
	"elprep [filter | sfm] 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" +
	"[--mark-optical-duplicates file]\n" +
	"[--optical-duplicates-pixel-distance nr]\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" +
	"[--bqsr recal-file]\n" +
	"[--bqsr-reference elfasta]\n" +
	"[--quantize-levels nr]\n" +
	"[--sqq list]\n" +
	"[--max-cycle nr]\n" +
	"[--known-sites list]\n" +
	"[--nr-of-threads nr]\n" +
	"[--timed]\n" +
	"[--log-path path]\n" +
	"[--intermediate-files-output-prefix name] (sfm only)\n" +
	"[--intermediate-files-output-type [sam | bam]] (sfm only)\n" +
	"[--tmp-path path]\n" +
	"[--single-end] (sfm only)\n" +
	"[--contig-group-size nr] (sfm only)\n"

const DeprecatedFilterHelp = "\nFilter 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"

const FastaToElfastaHelp = "fasta-to-elfasta parameters:\n" +
	"elprep fasta-to-elfasta fasta-file elfasta-file\n" +
	"[--log-path path]\n"

const FilterExtendedHelp = FilterHelp +
	"[--mark-optical-duplicates-intermediate file]\n" +
	"[--bqsr-tables-only table-file]\n" +
	"[--bqsr-apply path]\n" +
	"[--recal-file file]\n"

const FilterHelp = "\nfilter 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" +
	"[--mark-optical-duplicates file]\n" +
	"[--optical-duplicates-pixel-distance nr]\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" +
	"[--bqsr recal-file]\n" +
	"[--bqsr-reference elfasta]\n" +
	"[--quantize-levels nr]\n" +
	"[--sqq list]\n" +
	"[--max-cycle nr]\n" +
	"[--known-sites list]\n" +
	"[--nr-of-threads nr]\n" +
	"[--timed]\n" +
	"[--log-path path]\n"

const HelpMessage = "Print command details:\n" +
	"[--help]\n" +
	"[--help-extended]\n"

const MergeHelp = "\nmerge parameters:\n" +
	"elprep merge /path/to/input sam-output-file\n" +
	"[--single-end]\n" +
	"[--nr-of-threads n]\n" +
	"[--timed]\n" +
	"[--log-path path]\n"

const MergeOpticalDuplicatesMetricsHelp = "\nmerge-optical-duplicates-metrics parameters:\n" +
	"elprep merge-optical-duplicates-metrics sam-input-file sam-output-file metrics-file /path/to/intermediate/metrics\n" +
	"[--remove-duplicates]\n" +
	"[--nr-of-threads nr]\n" +
	"[--timed]\n" +
	"[--log-path path]\n"

const SfmHelp = "\nsfm parameters:\n" +
	"elprep sfm 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" +
	"[--mark-optical-duplicates file]\n" +
	"[--optical-duplicates-pixel-distance nr]\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" +
	"[--bqsr]\n" +
	"[--bqsr-reference elfasta]\n" +
	"[--quantize-levels nr]\n" +
	"[--sqq list]\n" +
	"[--max-cycle nr]\n" +
	"[--known-sites list]\n" +
	"[--nr-of-threads nr]\n" +
	"[--timed]\n" +
	"[--log-path path]\n" +
	"[--intermediate-files-output-prefix name]\n" +
	"[--intermediate-files-output-type [sam | bam]]\n" +
	"[--tmp-path path]\n" +
	"[--single-end]\n" +
	"[--contig-group-size nr]\n"

const SplitHelp = "\nsplit parameters:\n" +
	"elprep split (sam-file | /path/to/input/) /path/to/output/\n" +
	"[--output-prefix name]\n" +
	"[--output-type [sam | bam]]\n" +
	"[--single-end]\n" +
	"[--nr-of-threads nr]\n" +
	"[--timed]\n" +
	"[--log-path path]\n" +
	"[--contig-group-size nr]\n"

const VcfToElsitesHelp = "vcf-to-elsites parameters:\n" +
	"elprep vcf-to-elsites vcf-file elsites-file\n" +
	"[--log-path path]\n"