drivesim

package

v0.0.0-...-e0449dc Latest Latest Go to latest Published: Oct 10, 2025 License: AGPL-3.0 Imports: 16 Imported by: 0

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Valid go.mod file
Redistributable license
Tagged version
Stable version
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Repository

github.com/jgbaldwinbrown/drivesim

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Open Source Insights

Documentation ¶

Index ¶

Constants
func AddPosCols(inpath, outpath string) error
func BinomDistribSd(n, p float64) float64
func BinomDistribSdFromCoverage(cov float64) float64
func Bloodnorm(inpath, outpath string) error
func CmToBp(cmPerBp float64, cmPos float64) int64
func CombineCols(inpath, outpath string) error
func CombineColsPoswin(inpath, outpath string) error
func DistortDecay(strength, distPos, snpPos float64) float64
func Ftest(inpath, outpath string) error
func HighestDist(inpath, outpath, locpath string, win int64) error
func MultiFull(p GenomeParams, r *rand.Rand, wins []int64, outpre string, reps int64) error
func MultiFullDefault()
func NewGenome(p GenomeParams, rng *rand.Rand) iter.Seq2[int, *Chr]
func Normalizer(inpath, outpath string) error
func NormalizerVar(inpath, outpath string) error
func OneFull(p GenomeParams, r *rand.Rand, wins []int64, outpre string) error
func PlotSd(inpath, outpath, plotpath, locpath string, win int64) error
func Poswin(inpath, outpath string, win int64) error
func PrintChr(w io.Writer, name string, c *Chr) error
func PrintChrTestable(w io.Writer, name string, c *Chr) error
func PrintHeaderTestable(w io.Writer) error
func RunCmd(inpath, outpath, script string, args ...string) error
func RunDefault()
func RunOne(outFile, locFile string, p GenomeParams, r *rand.Rand) error
type Chr
- func NewChr(p ChrParams, rng *rand.Rand) *Chr
type ChrParams
type Flags
type GenomeParams
type Snp
- func MakeSnp(c *Chr, rng *rand.Rand) Snp

Constants ¶

View Source

const DefaultHumanChrlenBp = 1e8

View Source

const DefaultHumanCmPerBp = 1.0 / 1e6

Variables ¶

This section is empty.

Functions ¶

func AddPosCols ¶

func AddPosCols(inpath, outpath string) error

func BinomDistribSd ¶

func BinomDistribSd(n, p float64) float64

func BinomDistribSdFromCoverage ¶

func BinomDistribSdFromCoverage(cov float64) float64

func Bloodnorm ¶

func Bloodnorm(inpath, outpath string) error

func CmToBp ¶

func CmToBp(cmPerBp float64, cmPos float64) int64

func CombineCols ¶

func CombineCols(inpath, outpath string) error

func CombineColsPoswin ¶

func CombineColsPoswin(inpath, outpath string) error

func DistortDecay ¶

func DistortDecay(strength, distPos, snpPos float64) float64

func Ftest ¶

func Ftest(inpath, outpath string) error

func HighestDist ¶

func HighestDist(inpath, outpath, locpath string, win int64) error

func MultiFull ¶

func MultiFull(p GenomeParams, r *rand.Rand, wins []int64, outpre string, reps int64) error

func MultiFullDefault ¶

func MultiFullDefault()

func NewGenome ¶

func NewGenome(p GenomeParams, rng *rand.Rand) iter.Seq2[int, *Chr]

func Normalizer ¶

func Normalizer(inpath, outpath string) error

func NormalizerVar ¶

func NormalizerVar(inpath, outpath string) error

func OneFull ¶

func OneFull(p GenomeParams, r *rand.Rand, wins []int64, outpre string) error

func PlotSd ¶

func PlotSd(inpath, outpath, plotpath, locpath string, win int64) error

func Poswin ¶

func Poswin(inpath, outpath string, win int64) error

func PrintChr ¶

func PrintChr(w io.Writer, name string, c *Chr) error

func PrintChrTestable ¶

func PrintChrTestable(w io.Writer, name string, c *Chr) error

func PrintHeaderTestable ¶

func PrintHeaderTestable(w io.Writer) error

func RunCmd ¶

func RunCmd(inpath, outpath, script string, args ...string) error

func RunDefault ¶

func RunDefault()

func RunOne ¶

func RunOne(outFile, locFile string, p GenomeParams, r *rand.Rand) error

Types ¶

type Chr ¶

type Chr struct {
	Params         ChrParams
	Snps           []Snp
	DistorterCmPos float64
}

func NewChr ¶

func NewChr(p ChrParams, rng *rand.Rand) *Chr

type ChrParams ¶

type ChrParams struct {
	NumSnps            int64
	CmLen              float64
	HasDistorter       bool
	DistortionStrength float64
	CmPerBp            float64
	Coverage           float64
}

type Flags ¶

type Flags struct {
	Testable         bool
	DistorterPosFile string
}

type GenomeParams ¶

type GenomeParams struct {
	NDistortingChr int
	NCleanChr      int
	ChrParams      ChrParams
}

type Snp ¶

type Snp struct {
	CmPos          float64
	Counts         [2]float64
	DistortedHaplo int
}

func MakeSnp ¶

func MakeSnp(c *Chr, rng *rand.Rand) Snp

Source Files ¶

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