cmd

Documentation

Overview

Package cmd provides implementations for the elprep command line.

Index

• Constants
• Variables
• func DeprecatedFilter() error
• func Filter() error
• func Merge() error
• func Split() error

Constants

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"

DeprecatedFilterHelp is the help string for this command.

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"

FilterHelp is the help string for this command.

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"

MergeHelp is the help string for this command.

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"

SplitHelp 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 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 Filter

func Filter() error

Filter implements the elprep filter command.

func Merge

func Merge() error

Merge implements the elprep merge command.

func Split

func Split() error

Split implements the elprep split command.