AlignmentGeneralOptions (BioFSharp) | BioFSharp

AlignmentGeneralOptions Type

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

Union cases

Union case	Description
`EndsProtrusion AlignmentEndsProtrusionOptions` Full Usage: `EndsProtrusion AlignmentEndsProtrusionOptions` Parameters: Item : `AlignmentEndsProtrusionOptions`	maximum and type of allowed allow protrusion of alignment ends, i.e. start (end) of the +strand mate downstream of the start (end) of the -strand mate Item : `AlignmentEndsProtrusionOptions`
`EndsType AlignmentEndsTypeOptions` Full Usage: `EndsType AlignmentEndsTypeOptions` Parameters: Item : `AlignmentEndsTypeOptions`	type of read ends alignment Item : `AlignmentEndsTypeOptions`
`InsertionFlush AlignmentInsertionFlushOptions` Full Usage: `InsertionFlush AlignmentInsertionFlushOptions` Parameters: Item : `AlignmentInsertionFlushOptions`	string: how to flush ambiguous insertion positions Item : `AlignmentInsertionFlushOptions`
`IntronMax int` Full Usage: `IntronMax int` Parameters: Item : `int`	maximum intron size, if 0, max intron size will be determined by (2^winBinNbits)*winAnchorDistNbins Item : `int`
`IntronMin int` Full Usage: `IntronMin int` Parameters: Item : `int`	minimum intron size: genomic gap is considered intron if its length>=alignIntronMin, otherwise it is considered Deletion Item : `int`
`MatesGapMax int` Full Usage: `MatesGapMax int` Parameters: Item : `int`	maximum gap between two mates, if 0, max intron gap will be determined by (2^winBinNbits)*winAnchorDistNbins Item : `int`
`PairedEndReadOptions AligmentPairedEndReadOptions list` Full Usage: `PairedEndReadOptions AligmentPairedEndReadOptions list` Parameters: Item : `AligmentPairedEndReadOptions list`	options how to handle paired end reads Item : `AligmentPairedEndReadOptions list`
`SJDBoverhangMin int` Full Usage: `SJDBoverhangMin int` Parameters: Item : `int`	minimum overhang (i.e. block size) for annotated (sjdb) spliced alignments Item : `int`
`SJoverhangMin int` Full Usage: `SJoverhangMin int` Parameters: Item : `int`	minimum overhang (i.e. block size) for spliced alignments Item : `int`
`SJstitchMismatchNmax int * int * int * int` Full Usage: `SJstitchMismatchNmax int * int * int * int` Parameters: Item : `int * int * int * int`	maximum number of mismatches for stitching of the splice junctions (-1: no limit). (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif. Item : `int * int * int * int`
`SoftClipAtReferenceEnds bool` Full Usage: `SoftClipAtReferenceEnds bool` Parameters: Item : `bool`	allow the soft-clipping of the alignments past the end of the chromosomes: allow, or prohibit(useful for compatibility with Cufflinks) Item : `bool`
`SplicedMateMapLmin int` Full Usage: `SplicedMateMapLmin int` Parameters: Item : `int`	minimum mapped length for a read mate that is spliced Item : `int`
`SplicedMateMapLminOverLmate float` Full Usage: `SplicedMateMapLminOverLmate float` Parameters: Item : `float`	alignSplicedMateMapLmin normalized to mate length Item : `float`
`TranscriptsPerReadNmax int` Full Usage: `TranscriptsPerReadNmax int` Parameters: Item : `int`	max number of different alignments per read to consider Item : `int`
`TranscriptsPerWindowNmax int` Full Usage: `TranscriptsPerWindowNmax int` Parameters: Item : `int`	max number of transcripts per window Item : `int`
`WindowsPerReadNmax int` Full Usage: `WindowsPerReadNmax int` Parameters: Item : `int`	max number of windows per read Item : `int`

Static members

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