GenomeIndexingOptions (BioFSharp) | BioFSharp

GenomeIndexingOptions Type

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

Genome Indexing Parameters - only used with --runMode genomeGenerate

Union cases

Union case	Description
`ChrBinNbits int` Full Usage: `ChrBinNbits int` Parameters: Item : `int`	=log2(chrBin), where chrBin is the size of the bins for genome storage: each chromosome will occupy an integer number of bins. For a genome with large number of contigs, it is recommended to scale this parameter as min(18, log2[max(GenomeLength/NumberOfReferences,ReadLength)]). Item : `int`
`SAindexNbases int` Full Usage: `SAindexNbases int` Parameters: Item : `int`	length (bases) of the SA pre-indexing string. Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter --genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1). Item : `int`
`SAsparseD int` Full Usage: `SAsparseD int` Parameters: Item : `int`	suffux array sparsity, i.e. distance between indices: use bigger numbers to decrease needed RAM at the cost of mapping speed reduction Item : `int`
`SuffixLengthMax int` Full Usage: `SuffixLengthMax int` Parameters: Item : `int`	maximum length of the suffixes, has to be longer than read length. -1 = infinite. Item : `int`

Static members

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