cmd

Documentation

Overview

Package cmd provides implementations for the elprep command line.

Index

• Constants
• Variables
• func BedToElsites() error
• func DeprecatedFilter() error
• func FastaToElfasta() error
• func Filter() error
• func Merge() error
• func Sfm() error
• func Split() error
• func VcfToElsites() error

Constants

const (
	// ProgramName is "elprep"
	ProgramName = "elprep"
	// ProgramVersion is the version of the elprep binary
	ProgramVersion = "4.1.1"
	// 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"

BedToElsitesHelp is the help string for this command.

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" +
	"[--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" +
	"[--single-end] (sfm only)\n" +
	"[--contig-group-size nr] (sfm only)\n"

CombinedSfmFilterHelp is a help string that combines the help strings for the filter and sfm commands.

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"

DeprecatedFilterHelp is the help string for this command.

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

FastaToElfastaHelp is the help string for this command.

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

FilterExtendedHelp is the extended help string for this command.

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" +
	"[--known-sites list]\n" +
	"[--nr-of-threads nr]\n" +
	"[--timed]\n" +
	"[--log-path path]\n"

FilterHelp is the help string for this command.

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

HelpMessage is printed to show the --help and --help-extended flags

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"

MergeHelp is the help string for this command.

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" +
	"[--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" +
	"[--single-end]\n" +
	"[--contig-group-size nr]\n"

SfmHelp is the help string for this command.

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"

SplitHelp is the help string for this command.

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

VcfToElsitesHelp is the help string for this command.

Variables

var ProgramMessage string

ProgramMessage is the first line printed when the elprep binary is called.

Functions

func BedToElsites

func BedToElsites() error

BedToElsites implements the elprep bed-to-elsites command.

func DeprecatedFilter

func DeprecatedFilter() error

DeprecatedFilter parses the command line for elprep filter in the style of previous elprep versions (1.x and 2.x), for backwards compatibility. This command is deprecated and will be removed at a later stage.

func FastaToElfasta

func FastaToElfasta() error

FastaToElfasta implements the elprep fasta-to-elfasta command.

func Filter

func Filter() error

Filter implements the elprep filter command.

func Merge

func Merge() error

Merge implements the elprep merge command.

func Sfm

func Sfm() error

Sfm implements the elprep sfm command.

func Split

func Split() error

Split implements the elprep split command.

func VcfToElsites

func VcfToElsites() error

VcfToElsites implements the elprep vcf-to-elsites command.