AlignmentChimericOptions (BioFSharp) | BioFSharp

AlignmentChimericOptions Type

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

Union cases

Union case	Description
`ChimericAlignmentFilter ChimericAlignmentFilterOptions` Full Usage: `ChimericAlignmentFilter ChimericAlignmentFilterOptions` Parameters: Item : `ChimericAlignmentFilterOptions`	different filters for chimeric alignments Item : `ChimericAlignmentFilterOptions`
`ChimericAlignmentOutputType ChimericAlignmentOutputTypeOptions` Full Usage: `ChimericAlignmentOutputType ChimericAlignmentOutputTypeOptions` Parameters: Item : `ChimericAlignmentOutputTypeOptions`	type of chimeric output Item : `ChimericAlignmentOutputTypeOptions`
`JunctionOverhangMin int` Full Usage: `JunctionOverhangMin int` Parameters: Item : `int`	minimum overhang for a chimeric junction Item : `int`
`MainSegmentMultNmax int` Full Usage: `MainSegmentMultNmax int` Parameters: Item : `int`	maximum number of multi-alignments for the main chimeric segment. =1 will prohibit multimapping main segments. Item : `int`
`MultimapNmax int` Full Usage: `MultimapNmax int` Parameters: Item : `int`	maximum number of chimeric multi-alignments use the old scheme for chimeric detection which only considered unique alignments Item : `int`
`MultimapScoreRange int` Full Usage: `MultimapScoreRange int` Parameters: Item : `int`	the score range for multi-mapping chimeras below the best chimeric score. Only works with --chimMultimapNmax > 1 Item : `int`
`NonchimScoreDropMin int` Full Usage: `NonchimScoreDropMin int` Parameters: Item : `int`	to trigger chimeric detection, the drop in the best non-chimeric alignment score with respect to the read length has to be greater than this value Item : `int`
`OutJunctionFormat ChimericOutJunctionFormatOptions` Full Usage: `OutJunctionFormat ChimericOutJunctionFormatOptions` Parameters: Item : `ChimericOutJunctionFormatOptions`	formatting type for the Chimeric.out.junction file Item : `ChimericOutJunctionFormatOptions`
`ScoreDropMax int` Full Usage: `ScoreDropMax int` Parameters: Item : `int`	max drop (difference) of chimeric score (the sum of scores of all chimeric segments) from the read length Item : `int`
`ScoreJunctionNonGTAG int` Full Usage: `ScoreJunctionNonGTAG int` Parameters: Item : `int`	penalty for a non-GT/AG chimeric junction Item : `int`
`ScoreMin int` Full Usage: `ScoreMin int` Parameters: Item : `int`	minimum total (summed) score of the chimeric segments Item : `int`
`ScoreSeparation int` Full Usage: `ScoreSeparation int` Parameters: Item : `int`	minimum difference (separation) between the best chimeric score and the next one Item : `int`
`SegmentMin int` Full Usage: `SegmentMin int` Parameters: Item : `int`	minimum length of chimeric segment length, if ==0, no chimeric output Item : `int`
`SegmentReadGapMax int` Full Usage: `SegmentReadGapMax int` Parameters: Item : `int`	maximum gap in the read sequence between chimeric segments Item : `int`

Static members

Static member	Description
`AlignmentChimericOptions.makeCmd` Full Usage: `AlignmentChimericOptions.makeCmd` Returns: `AlignmentChimericOptions -> string list`	Returns: `AlignmentChimericOptions -> string list`