operations

package
v0.2.3 Latest Latest
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 Go to latest Published: Mar 15, 2025 License: MPL-2.0 Imports: 13 Imported by: 0

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Index

Constants

View Source 
const (
	TrimAlignNW = iota
	TrimBKTrim
	TrimBKTrimPaired
	TrimSearch
	TrimMatch
	TrimQuality
)

Variables

This section is empty.

Functions

func GetBarcodes 

func GetBarcodes(name []byte) [][]byte

Types

type Clip 

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

func NewClip 

func NewClip(data []byte) (*Clip, error)

func (*Clip) GetDpx 

func (op *Clip) GetDpx(idx int) ([][]byte, int)

func (*Clip) IsThreadSafe 

func (op *Clip) IsThreadSafe() bool

func (*Clip) Label added in v0.2.0 

func (op *Clip) Label() string

func (*Clip) Name 

func (op *Clip) Name() string

func (*Clip) Transform 

func (op *Clip) Transform(p *fastq.ExtPair, r int, ot *OpStat, verboseLevel int) int

type Demultiplex 

type Demultiplex struct {
	Barcodes   [][]byte
	BarcodesID []int
	// contains filtered or unexported fields
}

func NewDemultiplex 

func NewDemultiplex(data []byte) (*Demultiplex, error)

func (*Demultiplex) GetDpx 

func (op *Demultiplex) GetDpx(idx int) ([][]byte, int)

func (*Demultiplex) IsThreadSafe 

func (op *Demultiplex) IsThreadSafe() bool

func (*Demultiplex) Label added in v0.2.0 

func (op *Demultiplex) Label() string

func (*Demultiplex) Name 

func (op *Demultiplex) Name() string

func (*Demultiplex) Transform 

func (op *Demultiplex) Transform(p *fastq.ExtPair, r int, ot *OpStat, verboseLevel int) int

type Length 

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

func NewLength 

func NewLength(data []byte) (*Length, error)

func (*Length) GetDpx 

func (op *Length) GetDpx(idx int) ([][]byte, int)

func (*Length) IsThreadSafe 

func (op *Length) IsThreadSafe() bool

func (*Length) Label added in v0.2.0 

func (op *Length) Label() string

func (*Length) Name 

func (op *Length) Name() string

func (*Length) Transform 

func (op *Length) Transform(p *fastq.ExtPair, r int, ot *OpStat, verboseLevel int) int

type OpStat 

type OpStat struct {
	OpsR1, OpsR2        map[string]map[string]uint64
	KeptPair, TotalPair uint64

	ReportPath, Label string
	// contains filtered or unexported fields
}

func NewOpStat 

func NewOpStat(statsInPath string, statsOutPath string, reportPath string, label string, maxReadLength int, maxQual int, asciiMin int, paired bool, opsR1 []Operation, opsR2 []Operation) *OpStat

func (*OpStat) CountIn 

func (ot *OpStat) CountIn(p *fastq.ExtPair)

func (*OpStat) CountOut 

func (ot *OpStat) CountOut(p *fastq.ExtPair)

func (*OpStat) Update 

func (ot *OpStat) Update(otn *OpStat)

func (*OpStat) Write 

func (ot *OpStat) Write() error

type Operation 

type Operation interface {
	Name() string
	Label() string
	IsThreadSafe() bool
	GetDpx(int) ([][]byte, int)
	Transform(*fastq.ExtPair, int, *OpStat, int) int
}

func ReadOps 

func ReadOps(data []byte, param param.Parameters) ([]Operation, error)

type Quality added in v0.2.0 

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

func NewQuality added in v0.2.0 

func NewQuality(data []byte, param param.Parameters) (*Quality, error)

func (*Quality) GetDpx added in v0.2.0 

func (op *Quality) GetDpx(idx int) ([][]byte, int)

func (*Quality) IsThreadSafe added in v0.2.0 

func (op *Quality) IsThreadSafe() bool

func (*Quality) Label added in v0.2.0 

func (op *Quality) Label() string

func (*Quality) Name added in v0.2.0 

func (op *Quality) Name() string

func (*Quality) Transform added in v0.2.0 

func (op *Quality) Transform(p *fastq.ExtPair, r int, ot *OpStat, verboseLevel int) int

type Random 

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

func NewRandom 

func NewRandom(data []byte) (*Random, error)

func (*Random) GetDpx 

func (op *Random) GetDpx(idx int) ([][]byte, int)

func (*Random) IsThreadSafe 

func (op *Random) IsThreadSafe() bool

func (*Random) Label added in v0.2.0 

func (op *Random) Label() string

func (*Random) Name 

func (op *Random) Name() string

func (*Random) Transform 

func (op *Random) Transform(p *fastq.ExtPair, r int, ot *OpStat, verboseLevel int) int

type Rename 

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

func NewRename 

func NewRename(data []byte) (*Rename, error)

func (*Rename) GetDpx 

func (op *Rename) GetDpx(idx int) ([][]byte, int)

func (*Rename) IsThreadSafe 

func (op *Rename) IsThreadSafe() bool

func (*Rename) Label added in v0.2.0 

func (op *Rename) Label() string

func (*Rename) Name 

func (op *Rename) Name() string

func (*Rename) Transform 

func (op *Rename) Transform(p *fastq.ExtPair, r int, ot *OpStat, verboseLevel int) int

type Trim 

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

func NewTrim 

func NewTrim(data []byte, param param.Parameters) (*Trim, error)

func (*Trim) GetDpx 

func (op *Trim) GetDpx(idx int) ([][]byte, int)

func (*Trim) IsThreadSafe 

func (op *Trim) IsThreadSafe() bool

func (*Trim) Label added in v0.2.0 

func (op *Trim) Label() string

func (*Trim) Name 

func (op *Trim) Name() string

func (*Trim) Transform 

func (op *Trim) Transform(p *fastq.ExtPair, r int, ot *OpStat, verboseLevel int) int

Source Files

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