OutputFormattingOptions (BioFSharp)

OutputFormattingOptions Type

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

Union cases

Union case	Description
`AttributeIHSTart int` Full Usage: `AttributeIHSTart int` Parameters: Item : `int`	start value for the IH attribute. 0 may be required by some downstream software, such as Cufflinks or StringTie. Item : `int`
`Attributes AttributeOptions list` Full Usage: `Attributes AttributeOptions list` Parameters: Item : `AttributeOptions list`	desired SAM attributes, in the order desired for the output SAM Item : `AttributeOptions list`
`CommentLineFile string` Full Usage: `CommentLineFile string` Parameters: Item : `string`	path to the file with @CO (comment) lines of the SAM header Item : `string`
`Filter OutputFilterOptions` Full Usage: `Filter OutputFilterOptions` Parameters: Item : `OutputFilterOptions`	filter the output into main SAM/BAM files Item : `OutputFilterOptions`
`FlagAND int` Full Usage: `FlagAND int` Parameters: Item : `int`	0 to 65535: sam FLAG will be bitwise AND'd with this value, i.e. FLAG=FLAG & outSAMflagOR. This is applied after all flags have been set by STAR, but before outSAMflagOR. Can be used to unset specific bits that are not set otherwise. Item : `int`
`FlagOR int` Full Usage: `FlagOR int` Parameters: Item : `int`	0 to 65535: sam FLAG will be bitwise OR'd with this value, i.e. FLAG=FLAG \| outSAMflagOR. This is applied after all flags have been set by STAR, and after outSAMflagAND. Can be used to set specific bits that are not set otherwise. Item : `int`
`HeaderLine string` Full Usage: `HeaderLine string` Parameters: Item : `string`	@HD (header) line of the SAM header Item : `string`
`MAPQUinque int` Full Usage: `MAPQUinque int` Parameters: Item : `int`	0 to 255: the MAPQ value for unique mappers Item : `int`
`MaxMultipleAlignments int` Full Usage: `MaxMultipleAlignments int` Parameters: Item : `int`	max number of multiple alignments for a read that will be output to the SAM/BAM files. Item : `int`
`OutputMode OutputModeOptions` Full Usage: `OutputMode OutputModeOptions` Parameters: Item : `OutputModeOptions`	mode of SAM output Item : `OutputModeOptions`
`PGLine string` Full Usage: `PGLine string` Parameters: Item : `string`	extra @PG (software) line of the SAM header (in addition to STAR) Item : `string`
`PrimaryFlag PrimaryFlagOptions` Full Usage: `PrimaryFlag PrimaryFlagOptions` Parameters: Item : `PrimaryFlagOptions`	which alignments are considered primary - all others will be marked with 0x100 bit in the FLAG Item : `PrimaryFlagOptions`
`ReadGroupLine string` Full Usage: `ReadGroupLine string` Parameters: Item : `string`	SAM/BAM read group line. The first word contains the read group identifier and must start with "ID:", e.g. --outSAMattrRGline ID:xxx CN:yy "DS:z z z".xxx will be added as RG tag to each output alignment. Any spaces in the tag values have to be double quoted. Comma separated RG lines correspons to different (comma separated) input files in --readFilesIn. Commas have to be surrounded by spaces, e.g. --outSAMattrRGline ID:xxx , ID:zzz "DS:z z" , ID:yyy DS:yyyy Item : `string`
`ReadID ReadIDOptions` Full Usage: `ReadID ReadIDOptions` Parameters: Item : `ReadIDOptions`	read ID record type Item : `ReadIDOptions`
`Sorting OutputSortingOptions` Full Usage: `Sorting OutputSortingOptions` Parameters: Item : `OutputSortingOptions`	type of sorting for the SAM output Item : `OutputSortingOptions`
`StrandField StrandFieldOptions` Full Usage: `StrandField StrandFieldOptions` Parameters: Item : `StrandFieldOptions`	Cufflinks-like strand field flag Item : `StrandFieldOptions`
`TLenCalculation int` Full Usage: `TLenCalculation int` Parameters: Item : `int`	calculation method for the TLEN field in the SAM/BAM files. 1 ... leftmost base of the (+)strand mate to rightmost base of the (-)mate. (+)sign for the (+)strand mate 2 ... leftmost base of any mate to rightmost base of any mate. (+)sign for the mate with the leftmost base. This is different from 1 for overlapping mates with protruding ends Item : `int`
`UnmappedReads UnmappedReadOptions` Full Usage: `UnmappedReads UnmappedReadOptions` Parameters: Item : `UnmappedReadOptions`	output of unmapped reads in the SAM format Item : `UnmappedReadOptions`

Static members

Static member Description

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


                
                  
                    
                      OutputFormattingOptions.makeCmd

Full Usage: OutputFormattingOptions.makeCmd

Returns: OutputFormattingOptions -> string list

Returns: OutputFormattingOptions -> string list


                
                  
                    
                      OutputFormattingOptions.makeCmdWith m

Full Usage: OutputFormattingOptions.makeCmdWith m

Parameters:

m : MountInfo

Returns: OutputFormattingOptions -> string list

m : MountInfo

Returns: OutputFormattingOptions -> string list