FasterQDumpParams (BioFSharp)

FasterQDumpParams Type

Namespace: BioFSharp.BioContainers
Assembly: BioFSharp.BioContainers.dll
Parent Module: SRATools
Base Type: obj
All Interfaces: IEquatable<FasterQDumpParams> , IStructuralEquatable , IComparable<FasterQDumpParams> , IComparable , IStructuralComparable

DSL for command line arguments for the fasterq-dump tool contained in the SRA Toolkit

Union cases

Union case	Description
`AppendOutput` Full Usage: `AppendOutput`	append to output-file, instead of overwriting it
`BufferSize string` Full Usage: `BufferSize string` Parameters: Item : `string`	Item : `string`
`CartPath string` Full Usage: `CartPath string` Parameters: Item : `string`	Item : `string`
`CloudLocation string` Full Usage: `CloudLocation string` Parameters: Item : `string`	location in cloud Item : `string`
`CursorCacheSize string` Full Usage: `CursorCacheSize string` Parameters: Item : `string`	size of cursor-cache (dflt=10MB, takes number or number and unit) Item : `string`
`DisableMultiThreading` Full Usage: `DisableMultiThreading`	disable multithreading
`FilterBases string` Full Usage: `FilterBases string` Parameters: Item : `string`	filter output by matching against given bases Item : `string`
`Force` Full Usage: `Force`
`IncludeTechnical` Full Usage: `IncludeTechnical`	explicitly include technical reads
`LogLevel string` Full Usage: `LogLevel string` Parameters: Item : `string`	Item : `string`
`MinReadLength int` Full Usage: `MinReadLength int` Parameters: Item : `int`	filter by sequence-lenght Item : `int`
`NGCFilePath string` Full Usage: `NGCFilePath string` Parameters: Item : `string`	path to ngc file Item : `string`
`OptionFilePath string` Full Usage: `OptionFilePath string` Parameters: Item : `string`	Read more options and parameters from the file. Item : `string`
`OutDirectory string` Full Usage: `OutDirectory string` Parameters: Item : `string`	path for outputfile (overrides usage of current directory, but uses given accession) Item : `string`
`OutFile string` Full Usage: `OutFile string` Parameters: Item : `string`	full path of outputfile (overrides usage of current directory and given accession) Item : `string`
`PacBioTableName string` Full Usage: `PacBioTableName string` Parameters: Item : `string`	which seq-table to use in case of pacbio Item : `string`
`PermissionFilePath string` Full Usage: `PermissionFilePath string` Parameters: Item : `string`	path to permission file Item : `string`
`PrintDetails` Full Usage: `PrintDetails`	print details of all options selected
`PrintReadNumber` Full Usage: `PrintReadNumber`	include read-number in defline
`RowIdAsName` Full Usage: `RowIdAsName`	use rowid as name (avoids using the name column)
`ShowProgress` Full Usage: `ShowProgress`	show progress (not possible if stdout used)
`SkipTechnical` Full Usage: `SkipTechnical`	skip technical reads
`SortingMemoryLimit string` Full Usage: `SortingMemoryLimit string` Parameters: Item : `string`	memory limit for sorting (dflt=100MB, takes number or number and unit) Item : `string`
`Split SplitOptions` Full Usage: `Split SplitOptions` Parameters: Item : `SplitOptions`	Determine how to handle paired reads Item : `SplitOptions`
`StdOut` Full Usage: `StdOut`	print output to stdout
`Strict` Full Usage: `Strict`	terminate on invalid read
`TempDirectory string` Full Usage: `TempDirectory string` Parameters: Item : `string`	path to directory for temp. files (dflt=current dir.) Item : `string`
`Threads int` Full Usage: `Threads int` Parameters: Item : `int`	how many threads to use (dflt=6) Item : `int`
`Version` Full Usage: `Version`

Static members

Static member Description

Static member	Description
`FasterQDumpParams.makeCmd` Full Usage: `FasterQDumpParams.makeCmd` Returns: `FasterQDumpParams -> string list`	Returns: `FasterQDumpParams -> string list`
`FasterQDumpParams.makeCmdWith m` Full Usage: `FasterQDumpParams.makeCmdWith m` Parameters: m : `MountInfo` Returns: `FasterQDumpParams -> string list`	m : `MountInfo` Returns: `FasterQDumpParams -> string list`


                
                  
                    
                      FasterQDumpParams.makeCmd

Full Usage: FasterQDumpParams.makeCmd

Returns: FasterQDumpParams -> string list

Returns: FasterQDumpParams -> string list


                
                  
                    
                      FasterQDumpParams.makeCmdWith m

Full Usage: FasterQDumpParams.makeCmdWith m

Parameters:

m : MountInfo

Returns: FasterQDumpParams -> string list

m : MountInfo

Returns: FasterQDumpParams -> string list