pipeline

type AlignCmd struct {
	Fasta           bool
	BloomFilter     bool
	MinKmerCoverage float64
	BAMout          string
	NoExactAlign    bool // turn off the exact alignment and BAM output - only used by WASP currently
}

type DataStreamer struct {
	// contains filtered or unexported fields
}

type EMpathFinder struct {
	// contains filtered or unexported fields
}

type FastqChecker struct {
	// contains filtered or unexported fields
}

type FastqHandler struct {
	// contains filtered or unexported fields
}

type GFAreader struct {
	// contains filtered or unexported fields
}

type GraphPruner struct {
	// contains filtered or unexported fields
}

type GraphSketcher struct {
	// contains filtered or unexported fields
}

type HaploCmd struct {
	Cutoff        float64
	MinIterations int
	MaxIterations int
	TotalKmers    int
	HaploDir      string
}

type HaplotypeParser struct {
	// contains filtered or unexported fields
}

type Info struct {
	Version              string
	NumProc              int
	Profiling            bool
	KmerSize             int
	SketchSize           int
	WindowSize           int
	NumPart              int
	MaxK                 int
	MaxSketchSpan        int
	ContainmentThreshold float64
	IndexDir             string
	Store                graph.Store

	// the following fields are not written to disk
	Sketch    AlignCmd
	Haplotype HaploCmd
	// contains filtered or unexported fields
}

type MSAconverter struct {
	// contains filtered or unexported fields
}

type Pipeline struct {
	// contains filtered or unexported fields
}

type ReadMapper struct {
	// contains filtered or unexported fields
}

type SketchIndexer struct {
	// contains filtered or unexported fields
}

type WASMstreamer struct {
	// contains filtered or unexported fields
}