covplots

package

v0.1.5 Latest Latest Go to latest Published: Mar 26, 2024 License: AGPL-3.0 Imports: 21 Imported by: 0

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Repository

github.com/jgbaldwinbrown/covplots

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Open Source Insights

Documentation ¶

Index ¶

func Abs(rs []io.Reader, args any) ([]io.Reader, error)
func Add(rs []io.Reader, args any) ([]io.Reader, error)
func AddFacet(rs []io.Reader, args any) ([]io.Reader, error)
func AddFacetToOneReader(r io.Reader, facetname string) io.Reader
func AllMultiplotParallel(cfgs []UltimateConfig, winsize, winstep, threads int, fullgenome bool, ...) error
func AlwaysParseFloat(str string) float64
func AppendLabels(entries []BedEntry, labels []string) error
func CheckPathExists(path string) bool
func ChrGrep(rs []io.Reader, apattern any) ([]io.Reader, error)
func ChrGrepSingle(r io.Reader, re *regexp.Regexp) io.Reader
func CloseAny[T any](ts ...T)
func ColGrep(rs []io.Reader, anyargs any) ([]io.Reader, error)
func ColGrepSingle(r io.Reader, col int, re *regexp.Regexp) io.Reader
func ColGrepSome(rs []io.Reader, anyargs any) ([]io.Reader, error)
func ColSed(rs []io.Reader, anyargs any) ([]io.Reader, error)
func ColSedSingle(r io.Reader, col int, re *regexp.Regexp, replace string) io.Reader
func ColSedSome(rs []io.Reader, anyargs any) ([]io.Reader, error)
func CollectEntries(posmap map[Pos][]float64, idx, nidx int, ebuffer *[]PosEntry, r io.Reader) error
func CollectEntriesDumb(posmap map[Span][]string, idx, nidx int, r io.Reader) error
func CollectEntry(text string, sl *[]PosEntry) error
func CollectVals(r io.Reader) (map[Pos]float64, error)
func Columns(rs []io.Reader, args any) ([]io.Reader, error)
func ColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)
func CombineSinglebpPlots(names []string, rs ...io.Reader) (*strings.Reader, error)
func CombineToOneLine(rs []io.Reader, args any) ([]io.Reader, error)
func CombineToOneLineDumb(rs []io.Reader, args any) ([]io.Reader, error)
func CombineToOneLineOld(rs []io.Reader, args any) ([]io.Reader, error)
func DumbSubtract(r1, r2 io.Reader) (*strings.Reader, error)
func DumbSubtractInternal(r1, r2 io.Reader) (map[Span]SubVal, error)
func DumbSubtractTwo(rs []io.Reader, args any) ([]io.Reader, error)
func E(e error) bool
func FilterMulti(chr string, start, end int, rs ...io.Reader) ([]io.Reader, error)
func FourColumns(rs []io.Reader, args any) ([]io.Reader, error)
func FourColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)
func FullFilterCov() error
func FullLabelOutliers() error
func GetBedEntryLabels(labeller func(BedEntry) string, entries ...BedEntry) []string
func GetBedVals(extract func(BedEntry) (float64, error), entries ...BedEntry) ([]float64, error)
func GetColFloat(col int) func(BedEntry) (float64, error)
func GetColSums(cols ...int) func(BedEntry) (float64, error)
func GetCols(r io.Reader, cols []int) io.Reader
func GetFunc(fstr string) func(rs []io.Reader, args any) ([]io.Reader, error)
func GetManualChrs(path string) (chrs []string, err error)
func GetMultipleCols(rs []io.Reader, cols []int) []io.Reader
func GetMultipleColsSome(rs []io.Reader, cols []int, rs_to_subset []int) []io.Reader
func GetPathSpanMap(path string) (map[Span]struct{}, error)
func GetPlotFunc(fstr string) ...
func Gunzip(rs []io.Reader, args any) ([]io.Reader, error)
func GunzipOne(r io.Reader) (io.Reader, error)
func GzPath(path string, threads int) error
func Handle(format string) func(...any) error
func HicNonovlColumns(rs []io.Reader, args any) ([]io.Reader, error)
func HicNonovlColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)
func HicNonovlPropColumns(rs []io.Reader, args any) ([]io.Reader, error)
func HicNonovlPropColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)
func HicNonovlPropFpkmColumns(rs []io.Reader, args any) ([]io.Reader, error)
func HicNonovlPropFpkmColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)
func HicOvlColumns(rs []io.Reader, args any) ([]io.Reader, error)
func HicOvlColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)
func HicOvlPropColumns(rs []io.Reader, args any) ([]io.Reader, error)
func HicOvlPropColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)
func HicOvlPropFpkmColumns(rs []io.Reader, args any) ([]io.Reader, error)
func HicOvlPropFpkmColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)
func HicPairColumns(rs []io.Reader, args any) ([]io.Reader, error)
func HicPairColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)
func HicPairFpkmColumns(rs []io.Reader, args any) ([]io.Reader, error)
func HicPairFpkmColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)
func HicPairPropColumns(rs []io.Reader, args any) ([]io.Reader, error)
func HicPairPropColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)
func HicPairPropFpkmColumns(rs []io.Reader, args any) ([]io.Reader, error)
func HicPairPropFpkmColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)
func HicSelfColumns(rs []io.Reader, args any) ([]io.Reader, error)
func HicSelfColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)
func HicSelfFpkmColumns(rs []io.Reader, args any) ([]io.Reader, error)
func HicSelfFpkmColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)
func InitEmptyStringSl(length int) []string
func InitNaNSl(length int) []float64
func LabelByDistOutliers(cols, distcols []int, outlierPerc, lowOutlierPerc float64, entries []BedEntry, ...) ([]string, error)
func Log10(rs []io.Reader, args any) ([]io.Reader, error)
func MultiplePerBp(rs []io.Reader) []io.Reader
func MultiplePerBpNormalize(rs []io.Reader, args any) ([]io.Reader, error)
func Multiplot(cfg UltimateConfig, chr string, start, end int) error
func MultiplotFullchr(cfg UltimateConfig) error
func MultiplotInputSet(cfg InputSet, chr string, start, end int, fullchr bool) (io.Reader, []io.Closer, error)
func MultiplotSelectWins(cfg UltimateConfig, wins []BedEntry) error
func MultiplotSlide(cfg UltimateConfig, winsize, winstep int) error
func MustGetColSums(cols ...int) func(BedEntry) (float64, error)
func MustStringSlice(arg any) []string
func Nop([]io.Reader, any) ([]io.Reader, error)
func Normalize(rs []io.Reader, args any) ([]io.Reader, error)
func NormalizeFloats(in []float64) []float64
func OneArgArith(r io.Reader, f func(float64) float64) io.Reader
func OneArgArithMulti(rs []io.Reader, f func(float64) float64) []io.Reader
func OneSlidingMean(r io.Reader, wargs SlidingMeanArgs) io.Reader
func OpenMaybeGz(path string) (io.ReadCloser, error)
func OpenPaths(paths ...string) ([]io.Reader, error)
func Panic([]io.Reader, any) ([]io.Reader, error)
func ParseSubArgs(args any) ([][]int, error)
func PerBp(r io.Reader) io.Reader
func PipeWrite(f func(io.Writer)) io.ReadCloser
func Plfmt(r io.Reader, outpre, chrbedpath string) error
func PlfmtPath(inpath, outpre string, margs MultiplotPlotFuncArgs) error
func PlfmtSmallRead(r io.Reader, manualChrs []string, useManualChrs bool) ([]PlfmtEntry, *Plformatter, error)
func PlfmtSmallWrite(outpre string, data []PlfmtEntry, f *Plformatter) error
func PlotBoxwhisker(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error
func PlotCovHist(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error
func PlotCovVsPair(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error
func PlotMulti(outpre string, ylim []float64) error
func PlotMultiAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error
func PlotMultiFacet(outpre string, ylim []float64) error
func PlotMultiFacetAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error
func PlotMultiFacetScales(outpre string, scalespath string) error
func PlotMultiFacetScalesAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error
func PlotMultiFacetScalesBoxed(outpre string, args PlotMultiFacetScalesBoxedArgs, margs MultiplotPlotFuncArgs) error
func PlotMultiFacetScalesBoxedAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error
func PlotMultiFacetnameScales(outpre string, scalespath string) error
func PlotMultiFacetnameScalesAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error
func PlotMultiFixedOrder(outpre string, ylim []float64) error
func PlotMultiFixedOrderAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error
func PlotMultiPretty(outpre string, ylim []float64, cfg PrettyCfg) error
func PlotMultiPrettyAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error
func PlotMultiPrettyBlue(outpre string, ylim []float64, cfg PrettyCfg) error
func PlotMultiPrettyBlueAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error
func PlotMultiPrettyColorseries(outpre string, ylim []float64, cfg PrettyCfg) error
func PlotMultiPrettyColorseriesAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error
func PlotMultiRescue(outpre string, scalespath string) error
func PlotMultiRescueAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error
func PlotMultiSawamura(outpre string, args PlotMultiSawamuraArgs, margs MultiplotPlotFuncArgs) error
func PlotMultiSawamuraAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error
func PlotMultiTissue(outpre string, scalespath string) error
func PlotMultiTissueAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error
func PlotPanic(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error
func PlotSelfVsPair(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error
func PlotSelfVsPairLim(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error
func PlotSelfVsPairPretty(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error
func PlotSelfVsPairPrettyFixed(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error
func PlotSingle(outpre string, subtract bool) error
func PlotWin(outpre string) error
func PosLess(p1, p2 Pos) bool
func ReChr(rs []io.Reader, abiolines any) ([]io.Reader, error)
func ReChrSingle(r io.Reader, biolines []string) io.Reader
func ReadCovFiltFlags() ([]int, float64)
func RunAllMultiplot()
func RunAllSingle()
func RunAllSubtractSinglePlots()
func RunDumbSubset()
func RunSingle()
func ScanInts(dest *[]float64, src []string) error
func Shell(rs []io.Reader, args any) ([]io.Reader, error)
func ShellOne(r io.Reader, args []string) (io.Reader, error)
func ShellSome(rs []io.Reader, args any) ([]io.Reader, error)
func SinglePlot(r io.Reader, outpre, chr string, start, end int) error
func SinglePlotPath(path string, outpre, chr string, start, end int) error
func SinglePlotWins(inpath, chrlenpath, outpre string, winsize, winstep int) error
func SinglePlotWinsParallel(cfgs []Config, winsize, winstep, threads int) error
func SlidingMean(rs []io.Reader, args any) ([]io.Reader, error)
func SlidingMeansInternal(rs []io.Reader, wargs SlidingMeanArgs) []io.Reader
func SplitCommas(in string) []int
func SscanfMulti(line []string, fmts []string, ptrs ...any) (n int, err error)
func StripHeader(rs []io.Reader, args any) ([]io.Reader, error)
func StripHeaderSome(rs []io.Reader, args any) ([]io.Reader, error)
func StripOneHeader(r io.Reader) io.Reader
func StripParent(r io.Reader) (io.Reader, error)
func SubsetDumb(rs []io.Reader, args any) ([]io.Reader, error)
func SubsetDumbOne(r io.Reader, spanmap map[Span]struct{}) (io.Reader, error)
func SubsetDumbSome(rs []io.Reader, args any) ([]io.Reader, error)
func Subtract(r1, r2 io.Reader) (*strings.Reader, error)
func SubtractInternal(r1, r2 io.Reader) (map[Pos]SubVal, error)
func SubtractOld(r1, r2 io.Reader) (*strings.Reader, error)
func SubtractSinglePlot(r1, r2 io.Reader, outpre, chr string, start, end int) error
func SubtractSinglePlotPath(path1, path2 string, outpre, chr string, start, end int) error
func SubtractSinglePlotWins(inpath1, inpath2, chrlenpath, outpre string, winsize, winstep int) error
func SubtractSinglePlotWinsParallel(cfgs []Config, winsize, winstep, threads int) error
func SubtractTwo(rs []io.Reader, args any) ([]io.Reader, error)
func Tee(r io.Reader, npipes int) []io.ReadCloser
func TeeToPath(r io.Reader, path string) (io.Reader, *sync.WaitGroup, error)
func ToIntSlice(a any) []int
func ToIntSliceSlice(a any) [][]int
func ToPathAndInts(a any) (string, []int)
func ToStringSlice(arg any) ([]string, error)
func ToStrsAndInts(args any) ([]string, []int)
func TwoArgArith(r io.Reader, f func(float64, float64) float64) io.Reader
func TwoArgArithMulti(rs []io.Reader, f func(float64, float64) float64) []io.Reader
func Unchanged(rs []io.Reader, args any) ([]io.Reader, error)
func UnmarshalJsonOut(jsonOut any, dest any) error
func WindowCovColumns(rs []io.Reader, args any) ([]io.Reader, error)
func WindowCovColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)
func WriteBedEntries(w io.Writer, entries ...BedEntry) error
type AllSingleFlags
- func GetAllMultiplotFlags() AllSingleFlags
- func GetAllSingleFlags() AllSingleFlags
- func GetAllSubtractSingleFlags() AllSingleFlags
type BedEntry
- func FilterBedEntries(filt func(BedEntry) bool, entries ...BedEntry) []BedEntry
- func FilterByColsumStdevs(cols []int, stdevs float64, entries ...BedEntry) ([]BedEntry, error)
- func FilterByStdevs(col int, stdevs float64, entries ...BedEntry) ([]BedEntry, error)
- func ParseBedEntry(line []string) (BedEntry, error)
- func ReadBed(r io.Reader) ([]BedEntry, error)
- func ReadBedPath(path string) ([]BedEntry, error)
- func ReadPathBed(path string) ([]BedEntry, error)
type ChrLenSet
- func GetChrLens(chrlenpath string) ([]ChrLenSet, error)
- func ParseChrLenSet(line string) (ChrLenSet, error)
type ColGrepArgs
type ColGrepSomeArgs
type ColSedArgs
type ColSedSomeArgs
type Config
- func GetConfig(cfgpath string, subtract bool) ([]Config, error)
- func ReadConfig(r io.Reader, subtract bool) ([]Config, error)
type Entry
- func ParseEntry(line string) (Entry, error)
type Errors
- func (e Errors) Error() string
type Filterer
- func Filter(r io.Reader, chr string, start, end int) (*Filterer, error)
- func (f *Filterer) Read(out []byte) (n int, err error)
type Flags
- func GetFlags() Flags
type GzReader
- func (r *GzReader) Close() error
type InputSet
type LabellerArgs
- func ReadLabellerFlags() LabellerArgs
type MultiplotPlotFuncArgs
type PlfmtEntry
type Plformatter
- func PlfmtSmall(r io.Reader, outpre string, manualChrs []string, useManualChrs bool) (*Plformatter, error)
type PlotBoxwhiskerArgs
type PlotCovHistArgs
type PlotMultiFacetScalesBoxedArgs
type PlotMultiSawamuraArgs
type PlotSelfVsPairArgs
type Pos
- func SortAndUniqPoses[T any](maps ...map[Pos]T) []Pos
type PosEntry
- func ParsePosVal(line string, outbuf []PosEntry) ([]PosEntry, error)
type PrettyCfg
type Sentry
- func CollectEntryDumb(text string) (Sentry, error)
type SlidingMeanArgs
type Span
- func GetSpan(text string) (Span, error)
type SubVal
type UltimateConfig
- func GetUltimateConfig(path string) ([]UltimateConfig, error)
- func ReadUltimateConfig(r io.Reader) ([]UltimateConfig, error)

Constants ¶

This section is empty.

Variables ¶

This section is empty.

Functions ¶

func Abs ¶

func Abs(rs []io.Reader, args any) ([]io.Reader, error)

func Add ¶

func Add(rs []io.Reader, args any) ([]io.Reader, error)

func AddFacet ¶

func AddFacet(rs []io.Reader, args any) ([]io.Reader, error)

func AddFacetToOneReader ¶

func AddFacetToOneReader(r io.Reader, facetname string) io.Reader

func AllMultiplotParallel ¶

func AllMultiplotParallel(cfgs []UltimateConfig, winsize, winstep, threads int, fullgenome bool, selectWins []BedEntry) error

func AlwaysParseFloat ¶

func AlwaysParseFloat(str string) float64

func AppendLabels ¶

func AppendLabels(entries []BedEntry, labels []string) error

func CheckPathExists ¶

func CheckPathExists(path string) bool

func ChrGrep ¶

func ChrGrep(rs []io.Reader, apattern any) ([]io.Reader, error)

func ChrGrepSingle ¶

func ChrGrepSingle(r io.Reader, re *regexp.Regexp) io.Reader

func CloseAny ¶

func CloseAny[T any](ts ...T)

func ColGrep ¶

func ColGrep(rs []io.Reader, anyargs any) ([]io.Reader, error)

func ColGrepSingle ¶

func ColGrepSingle(r io.Reader, col int, re *regexp.Regexp) io.Reader

func ColGrepSome ¶

func ColGrepSome(rs []io.Reader, anyargs any) ([]io.Reader, error)

func ColSed ¶

func ColSed(rs []io.Reader, anyargs any) ([]io.Reader, error)

func ColSedSingle ¶

func ColSedSingle(r io.Reader, col int, re *regexp.Regexp, replace string) io.Reader

func ColSedSome ¶

func ColSedSome(rs []io.Reader, anyargs any) ([]io.Reader, error)

func CollectEntries ¶

func CollectEntries(posmap map[Pos][]float64, idx, nidx int, ebuffer *[]PosEntry, r io.Reader) error

func CollectEntriesDumb ¶

func CollectEntriesDumb(posmap map[Span][]string, idx, nidx int, r io.Reader) error

func CollectEntry ¶

func CollectEntry(text string, sl *[]PosEntry) error

func CollectVals ¶

func CollectVals(r io.Reader) (map[Pos]float64, error)

func Columns ¶

func Columns(rs []io.Reader, args any) ([]io.Reader, error)

func ColumnsSome ¶

func ColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)

func CombineSinglebpPlots ¶

func CombineSinglebpPlots(names []string, rs ...io.Reader) (*strings.Reader, error)

func CombineToOneLine ¶

func CombineToOneLine(rs []io.Reader, args any) ([]io.Reader, error)

func CombineToOneLineDumb ¶

func CombineToOneLineDumb(rs []io.Reader, args any) ([]io.Reader, error)

func CombineToOneLineOld ¶

func CombineToOneLineOld(rs []io.Reader, args any) ([]io.Reader, error)

func DumbSubtract ¶

func DumbSubtract(r1, r2 io.Reader) (*strings.Reader, error)

func DumbSubtractInternal ¶

func DumbSubtractInternal(r1, r2 io.Reader) (map[Span]SubVal, error)

func DumbSubtractTwo ¶

func DumbSubtractTwo(rs []io.Reader, args any) ([]io.Reader, error)

func E ¶

func E(e error) bool

func FilterMulti ¶

func FilterMulti(chr string, start, end int, rs ...io.Reader) ([]io.Reader, error)

func FourColumns ¶

func FourColumns(rs []io.Reader, args any) ([]io.Reader, error)

func FourColumnsSome ¶

func FourColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)

func FullFilterCov ¶

func FullFilterCov() error

func FullLabelOutliers ¶

func FullLabelOutliers() error

func GetBedEntryLabels ¶

func GetBedEntryLabels(labeller func(BedEntry) string, entries ...BedEntry) []string

func GetBedVals ¶

func GetBedVals(extract func(BedEntry) (float64, error), entries ...BedEntry) ([]float64, error)

func GetColFloat ¶

func GetColFloat(col int) func(BedEntry) (float64, error)

func GetColSums ¶

func GetColSums(cols ...int) func(BedEntry) (float64, error)

func GetCols ¶

func GetCols(r io.Reader, cols []int) io.Reader

func GetFunc ¶

func GetFunc(fstr string) func(rs []io.Reader, args any) ([]io.Reader, error)

func GetManualChrs ¶

func GetManualChrs(path string) (chrs []string, err error)

func GetMultipleCols ¶

func GetMultipleCols(rs []io.Reader, cols []int) []io.Reader

func GetMultipleColsSome ¶

func GetMultipleColsSome(rs []io.Reader, cols []int, rs_to_subset []int) []io.Reader

func GetPathSpanMap ¶

func GetPathSpanMap(path string) (map[Span]struct{}, error)

func GetPlotFunc ¶

func GetPlotFunc(fstr string) func(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error

func Gunzip ¶

func Gunzip(rs []io.Reader, args any) ([]io.Reader, error)

func GunzipOne ¶

func GunzipOne(r io.Reader) (io.Reader, error)

func GzPath ¶

func GzPath(path string, threads int) error

func Handle ¶

func Handle(format string) func(...any) error

func HicNonovlColumns ¶

func HicNonovlColumns(rs []io.Reader, args any) ([]io.Reader, error)

func HicNonovlColumnsSome ¶

func HicNonovlColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)

func HicNonovlPropColumns ¶

func HicNonovlPropColumns(rs []io.Reader, args any) ([]io.Reader, error)

func HicNonovlPropColumnsSome ¶

func HicNonovlPropColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)

func HicNonovlPropFpkmColumns ¶

func HicNonovlPropFpkmColumns(rs []io.Reader, args any) ([]io.Reader, error)

func HicNonovlPropFpkmColumnsSome ¶

func HicNonovlPropFpkmColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)

func HicOvlColumns ¶

func HicOvlColumns(rs []io.Reader, args any) ([]io.Reader, error)

func HicOvlColumnsSome ¶

func HicOvlColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)

func HicOvlPropColumns ¶

func HicOvlPropColumns(rs []io.Reader, args any) ([]io.Reader, error)

func HicOvlPropColumnsSome ¶

func HicOvlPropColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)

func HicOvlPropFpkmColumns ¶

func HicOvlPropFpkmColumns(rs []io.Reader, args any) ([]io.Reader, error)

func HicOvlPropFpkmColumnsSome ¶

func HicOvlPropFpkmColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)

func HicPairColumns ¶

func HicPairColumns(rs []io.Reader, args any) ([]io.Reader, error)

func HicPairColumnsSome ¶

func HicPairColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)

func HicPairFpkmColumns ¶ added in v0.1.4

func HicPairFpkmColumns(rs []io.Reader, args any) ([]io.Reader, error)

func HicPairFpkmColumnsSome ¶ added in v0.1.4

func HicPairFpkmColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)

func HicPairPropColumns ¶

func HicPairPropColumns(rs []io.Reader, args any) ([]io.Reader, error)

func HicPairPropColumnsSome ¶

func HicPairPropColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)

func HicPairPropFpkmColumns ¶

func HicPairPropFpkmColumns(rs []io.Reader, args any) ([]io.Reader, error)

func HicPairPropFpkmColumnsSome ¶

func HicPairPropFpkmColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)

func HicSelfColumns ¶

func HicSelfColumns(rs []io.Reader, args any) ([]io.Reader, error)

func HicSelfColumnsSome ¶

func HicSelfColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)

func HicSelfFpkmColumns ¶ added in v0.1.4

func HicSelfFpkmColumns(rs []io.Reader, args any) ([]io.Reader, error)

func HicSelfFpkmColumnsSome ¶ added in v0.1.4

func HicSelfFpkmColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)

func InitEmptyStringSl ¶

func InitEmptyStringSl(length int) []string

func InitNaNSl ¶

func InitNaNSl(length int) []float64

func LabelByDistOutliers ¶

func LabelByDistOutliers(cols, distcols []int, outlierPerc, lowOutlierPerc float64, entries []BedEntry, dist []BedEntry) ([]string, error)

func Log10 ¶

func Log10(rs []io.Reader, args any) ([]io.Reader, error)

func MultiplePerBp ¶

func MultiplePerBp(rs []io.Reader) []io.Reader

func MultiplePerBpNormalize ¶

func MultiplePerBpNormalize(rs []io.Reader, args any) ([]io.Reader, error)

func Multiplot ¶

func Multiplot(cfg UltimateConfig, chr string, start, end int) error

func MultiplotFullchr ¶

func MultiplotFullchr(cfg UltimateConfig) error

func MultiplotInputSet ¶

func MultiplotInputSet(cfg InputSet, chr string, start, end int, fullchr bool) (io.Reader, []io.Closer, error)

func MultiplotSelectWins ¶

func MultiplotSelectWins(cfg UltimateConfig, wins []BedEntry) error

func MultiplotSlide ¶

func MultiplotSlide(cfg UltimateConfig, winsize, winstep int) error

func MustGetColSums ¶

func MustGetColSums(cols ...int) func(BedEntry) (float64, error)

func MustStringSlice ¶

func MustStringSlice(arg any) []string

func Nop ¶

func Nop([]io.Reader, any) ([]io.Reader, error)

func Normalize ¶

func Normalize(rs []io.Reader, args any) ([]io.Reader, error)

func NormalizeFloats ¶

func NormalizeFloats(in []float64) []float64

func OneArgArith ¶

func OneArgArith(r io.Reader, f func(float64) float64) io.Reader

func OneArgArithMulti ¶

func OneArgArithMulti(rs []io.Reader, f func(float64) float64) []io.Reader

func OneSlidingMean ¶

func OneSlidingMean(r io.Reader, wargs SlidingMeanArgs) io.Reader

func OpenMaybeGz ¶

func OpenMaybeGz(path string) (io.ReadCloser, error)

func OpenPaths ¶

func OpenPaths(paths ...string) ([]io.Reader, error)

func Panic ¶

func Panic([]io.Reader, any) ([]io.Reader, error)

func ParseSubArgs ¶

func ParseSubArgs(args any) ([][]int, error)

func PerBp ¶

func PerBp(r io.Reader) io.Reader

func PipeWrite ¶

func PipeWrite(f func(io.Writer)) io.ReadCloser

func Plfmt ¶

func Plfmt(r io.Reader, outpre, chrbedpath string) error

func PlfmtPath ¶

func PlfmtPath(inpath, outpre string, margs MultiplotPlotFuncArgs) error

func PlfmtSmallRead ¶

func PlfmtSmallRead(r io.Reader, manualChrs []string, useManualChrs bool) ([]PlfmtEntry, *Plformatter, error)

func PlfmtSmallWrite ¶

func PlfmtSmallWrite(outpre string, data []PlfmtEntry, f *Plformatter) error

func PlotBoxwhisker ¶

func PlotBoxwhisker(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error

func PlotCovHist ¶

func PlotCovHist(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error

func PlotCovVsPair ¶

func PlotCovVsPair(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error

func PlotMulti ¶

func PlotMulti(outpre string, ylim []float64) error

func PlotMultiAny ¶

func PlotMultiAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error

func PlotMultiFacet ¶

func PlotMultiFacet(outpre string, ylim []float64) error

func PlotMultiFacetAny ¶

func PlotMultiFacetAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error

func PlotMultiFacetScales ¶

func PlotMultiFacetScales(outpre string, scalespath string) error

func PlotMultiFacetScalesAny ¶

func PlotMultiFacetScalesAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error

func PlotMultiFacetScalesBoxed ¶

func PlotMultiFacetScalesBoxed(outpre string, args PlotMultiFacetScalesBoxedArgs, margs MultiplotPlotFuncArgs) error

func PlotMultiFacetScalesBoxedAny ¶

func PlotMultiFacetScalesBoxedAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error

func PlotMultiFacetnameScales ¶

func PlotMultiFacetnameScales(outpre string, scalespath string) error

func PlotMultiFacetnameScalesAny ¶

func PlotMultiFacetnameScalesAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error

func PlotMultiFixedOrder ¶

func PlotMultiFixedOrder(outpre string, ylim []float64) error

func PlotMultiFixedOrderAny ¶

func PlotMultiFixedOrderAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error

func PlotMultiPretty ¶

func PlotMultiPretty(outpre string, ylim []float64, cfg PrettyCfg) error

func PlotMultiPrettyAny ¶

func PlotMultiPrettyAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error

func PlotMultiPrettyBlue ¶

func PlotMultiPrettyBlue(outpre string, ylim []float64, cfg PrettyCfg) error

func PlotMultiPrettyBlueAny ¶

func PlotMultiPrettyBlueAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error

func PlotMultiPrettyColorseries ¶

func PlotMultiPrettyColorseries(outpre string, ylim []float64, cfg PrettyCfg) error

func PlotMultiPrettyColorseriesAny ¶

func PlotMultiPrettyColorseriesAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error

func PlotMultiRescue ¶ added in v0.1.4

func PlotMultiRescue(outpre string, scalespath string) error

func PlotMultiRescueAny ¶ added in v0.1.4

func PlotMultiRescueAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error

func PlotMultiSawamura ¶ added in v0.1.4

func PlotMultiSawamura(outpre string, args PlotMultiSawamuraArgs, margs MultiplotPlotFuncArgs) error

func PlotMultiSawamuraAny ¶ added in v0.1.5

func PlotMultiSawamuraAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error

func PlotMultiTissue ¶ added in v0.1.4

func PlotMultiTissue(outpre string, scalespath string) error

func PlotMultiTissueAny ¶ added in v0.1.4

func PlotMultiTissueAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error

func PlotPanic ¶

func PlotPanic(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error

func PlotSelfVsPair ¶

func PlotSelfVsPair(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error

func PlotSelfVsPairLim ¶

func PlotSelfVsPairLim(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error

func PlotSelfVsPairPretty ¶

func PlotSelfVsPairPretty(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error

func PlotSelfVsPairPrettyFixed ¶

func PlotSelfVsPairPrettyFixed(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error

func PlotSingle ¶

func PlotSingle(outpre string, subtract bool) error

func PlotWin ¶

func PlotWin(outpre string) error

func PosLess ¶

func PosLess(p1, p2 Pos) bool

func ReChr ¶

func ReChr(rs []io.Reader, abiolines any) ([]io.Reader, error)

func ReChrSingle ¶

func ReChrSingle(r io.Reader, biolines []string) io.Reader

func ReadCovFiltFlags ¶

func ReadCovFiltFlags() ([]int, float64)

func RunAllMultiplot ¶

func RunAllMultiplot()

func RunAllSingle ¶

func RunAllSingle()

func RunAllSubtractSinglePlots ¶

func RunAllSubtractSinglePlots()

func RunDumbSubset ¶

func RunDumbSubset()

func RunSingle ¶

func RunSingle()

func ScanInts ¶

func ScanInts(dest *[]float64, src []string) error

func Shell ¶

func Shell(rs []io.Reader, args any) ([]io.Reader, error)

func ShellOne ¶

func ShellOne(r io.Reader, args []string) (io.Reader, error)

func ShellSome ¶

func ShellSome(rs []io.Reader, args any) ([]io.Reader, error)

func SinglePlot ¶

func SinglePlot(r io.Reader, outpre, chr string, start, end int) error

func SinglePlotPath ¶

func SinglePlotPath(path string, outpre, chr string, start, end int) error

func SinglePlotWins ¶

func SinglePlotWins(inpath, chrlenpath, outpre string, winsize, winstep int) error

func SinglePlotWinsParallel ¶

func SinglePlotWinsParallel(cfgs []Config, winsize, winstep, threads int) error

func SlidingMean ¶

func SlidingMean(rs []io.Reader, args any) ([]io.Reader, error)

func SlidingMeansInternal ¶

func SlidingMeansInternal(rs []io.Reader, wargs SlidingMeanArgs) []io.Reader

func SplitCommas ¶

func SplitCommas(in string) []int

func SscanfMulti ¶

func SscanfMulti(line []string, fmts []string, ptrs ...any) (n int, err error)

func StripHeader ¶

func StripHeader(rs []io.Reader, args any) ([]io.Reader, error)

func StripHeaderSome ¶

func StripHeaderSome(rs []io.Reader, args any) ([]io.Reader, error)

func StripOneHeader ¶

func StripOneHeader(r io.Reader) io.Reader

func StripParent ¶

func StripParent(r io.Reader) (io.Reader, error)

func SubsetDumb ¶

func SubsetDumb(rs []io.Reader, args any) ([]io.Reader, error)

func SubsetDumbOne ¶

func SubsetDumbOne(r io.Reader, spanmap map[Span]struct{}) (io.Reader, error)

func SubsetDumbSome ¶

func SubsetDumbSome(rs []io.Reader, args any) ([]io.Reader, error)

func Subtract ¶

func Subtract(r1, r2 io.Reader) (*strings.Reader, error)

func SubtractInternal ¶

func SubtractInternal(r1, r2 io.Reader) (map[Pos]SubVal, error)

func SubtractOld ¶

func SubtractOld(r1, r2 io.Reader) (*strings.Reader, error)

func SubtractSinglePlot ¶

func SubtractSinglePlot(r1, r2 io.Reader, outpre, chr string, start, end int) error

func SubtractSinglePlotPath ¶

func SubtractSinglePlotPath(path1, path2 string, outpre, chr string, start, end int) error

func SubtractSinglePlotWins ¶

func SubtractSinglePlotWins(inpath1, inpath2, chrlenpath, outpre string, winsize, winstep int) error

func SubtractSinglePlotWinsParallel ¶

func SubtractSinglePlotWinsParallel(cfgs []Config, winsize, winstep, threads int) error

func SubtractTwo ¶

func SubtractTwo(rs []io.Reader, args any) ([]io.Reader, error)

func Tee ¶

func Tee(r io.Reader, npipes int) []io.ReadCloser

func TeeToPath ¶

func TeeToPath(r io.Reader, path string) (io.Reader, *sync.WaitGroup, error)

func ToIntSlice ¶

func ToIntSlice(a any) []int

func ToIntSliceSlice ¶

func ToIntSliceSlice(a any) [][]int

func ToPathAndInts ¶

func ToPathAndInts(a any) (string, []int)

func ToStringSlice ¶

func ToStringSlice(arg any) ([]string, error)

func ToStrsAndInts ¶

func ToStrsAndInts(args any) ([]string, []int)

func TwoArgArith ¶

func TwoArgArith(r io.Reader, f func(float64, float64) float64) io.Reader

func TwoArgArithMulti ¶

func TwoArgArithMulti(rs []io.Reader, f func(float64, float64) float64) []io.Reader

func Unchanged ¶

func Unchanged(rs []io.Reader, args any) ([]io.Reader, error)

func UnmarshalJsonOut ¶

func UnmarshalJsonOut(jsonOut any, dest any) error

func WindowCovColumns ¶

func WindowCovColumns(rs []io.Reader, args any) ([]io.Reader, error)

func WindowCovColumnsSome ¶

func WindowCovColumnsSome(rs []io.Reader, args any) ([]io.Reader, error)

func WriteBedEntries ¶

func WriteBedEntries(w io.Writer, entries ...BedEntry) error

Types ¶

type AllSingleFlags ¶

type AllSingleFlags struct {
	Config      string
	WinSize     int
	WinStep     int
	Threads     int
	WholeGenome bool
	SelectWins  string
	NoParent    bool
}

func GetAllMultiplotFlags ¶

func GetAllMultiplotFlags() AllSingleFlags

func GetAllSingleFlags ¶

func GetAllSingleFlags() AllSingleFlags

func GetAllSubtractSingleFlags ¶

func GetAllSubtractSingleFlags() AllSingleFlags

type BedEntry ¶

type BedEntry struct {
	Chr    string
	Start  int64
	End    int64
	Fields []string
}

func FilterBedEntries ¶

func FilterBedEntries(filt func(BedEntry) bool, entries ...BedEntry) []BedEntry

func FilterByColsumStdevs ¶

func FilterByColsumStdevs(cols []int, stdevs float64, entries ...BedEntry) ([]BedEntry, error)

func FilterByStdevs ¶

func FilterByStdevs(col int, stdevs float64, entries ...BedEntry) ([]BedEntry, error)

func ParseBedEntry ¶

func ParseBedEntry(line []string) (BedEntry, error)

func ReadBed ¶

func ReadBed(r io.Reader) ([]BedEntry, error)

func ReadBedPath ¶

func ReadBedPath(path string) ([]BedEntry, error)

func ReadPathBed ¶

func ReadPathBed(path string) ([]BedEntry, error)

type ChrLenSet ¶

type ChrLenSet struct {
	Chr string
	Len int
}

func GetChrLens ¶

func GetChrLens(chrlenpath string) ([]ChrLenSet, error)

func ParseChrLenSet ¶

func ParseChrLenSet(line string) (ChrLenSet, error)

type ColGrepArgs ¶

type ColGrepArgs struct {
	Col     int
	Pattern string
}

type ColGrepSomeArgs ¶

type ColGrepSomeArgs struct {
	Files   []int
	Col     int
	Pattern string
}

type ColSedArgs ¶

type ColSedArgs struct {
	Col     int
	Pattern string
	Replace string
}

type ColSedSomeArgs ¶

type ColSedSomeArgs struct {
	Files   []int
	Col     int
	Pattern string
	Replace string
}

type Config ¶

type Config struct {
	Inpath     string
	Chrlenpath string
	Outpre     string
	Inpath2    string
}

func GetConfig ¶

func GetConfig(cfgpath string, subtract bool) ([]Config, error)

func ReadConfig ¶

func ReadConfig(r io.Reader, subtract bool) ([]Config, error)

type Entry ¶

type Entry struct {
	Span
	Val float64
}

func ParseEntry ¶

func ParseEntry(line string) (Entry, error)

type Errors ¶

type Errors []error

func (Errors) Error ¶

func (e Errors) Error() string

type Filterer ¶

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

func Filter ¶

func Filter(r io.Reader, chr string, start, end int) (*Filterer, error)

func (*Filterer) Read ¶

func (f *Filterer) Read(out []byte) (n int, err error)

type Flags ¶

type Flags struct {
	Outpre     string
	Chrbedpath string
	Chr        string
	Start      int
	End        int
}

func GetFlags ¶

func GetFlags() Flags

type GzReader ¶

type GzReader struct {
	*gzip.Reader
	// contains filtered or unexported fields
}

func (*GzReader) Close ¶

func (r *GzReader) Close() error

type InputSet ¶

type InputSet struct {
	Paths        []string `json:"paths"`
	Name         string   `json:"name"`
	Functions    []string `json:"functions"`
	FunctionArgs []any    `json: "functionargs"`
	Extra        any      `json: "extra"`
}

type LabellerArgs ¶

type LabellerArgs struct {
	TestCols      []int
	TestPath      string
	ThreshPerc    float64
	LowThreshPerc float64
	DistCols      []int
	DistPath      string
}

func ReadLabellerFlags ¶

func ReadLabellerFlags() LabellerArgs

type MultiplotPlotFuncArgs ¶

type MultiplotPlotFuncArgs struct {
	Plformatter *Plformatter
	Cfg         UltimateConfig
	Chr         string
	Start       int
	End         int
	Fullchr     bool
}

type PlfmtEntry ¶

type PlfmtEntry struct {
	Chr      string
	Start    int
	End      int
	Text     string
	Line     []string
	ChrNum   int
	StartOff int
	EndOff   int
}

type Plformatter ¶

type Plformatter struct {
	UseManualChrs bool
	Chrset        map[string]struct{}
	Chroffs       map[string]int
	Chrnums       map[string]int
}

func PlfmtSmall ¶

func PlfmtSmall(r io.Reader, outpre string, manualChrs []string, useManualChrs bool) (*Plformatter, error)

type PlotBoxwhiskerArgs ¶

type PlotBoxwhiskerArgs struct {
	Xmin     float64
	Xmax     float64
	Ylab     string
	Xlab     string
	Width    float64
	Height   float64
	ResScale float64
	TextSize float64
	FillName string
}

type PlotCovHistArgs ¶

type PlotCovHistArgs struct {
	Xmin     float64
	Xmax     float64
	Ylab     string
	Xlab     string
	Binwidth float64
	Width    float64
	Height   float64
	ResScale float64
}

type PlotMultiFacetScalesBoxedArgs ¶

type PlotMultiFacetScalesBoxedArgs struct {
	Scales string
	Boxes  string
}

type PlotMultiSawamuraArgs ¶ added in v0.1.4

type PlotMultiSawamuraArgs struct {
	Scales string
	Boxes  string
}

type PlotSelfVsPairArgs ¶

type PlotSelfVsPairArgs struct {
	Xmin     float64
	Xmax     float64
	Ylab     string
	Xlab     string
	Width    float64
	Height   float64
	ResScale float64
	TextSize float64
}

type Pos ¶

type Pos struct {
	Chr string
	Bp  int
}

func SortAndUniqPoses ¶

func SortAndUniqPoses[T any](maps ...map[Pos]T) []Pos

type PosEntry ¶

type PosEntry struct {
	Pos
	Val float64
}

func ParsePosVal ¶

func ParsePosVal(line string, outbuf []PosEntry) ([]PosEntry, error)

type PrettyCfg ¶

type PrettyCfg struct {
	Xlab     string
	Ylab     string
	Width    float64
	Height   float64
	Res      float64
	TextSize float64
}

type Sentry ¶

type Sentry struct {
	Span
	Val string
}

func CollectEntryDumb ¶

func CollectEntryDumb(text string) (Sentry, error)

type SlidingMeanArgs ¶

type SlidingMeanArgs struct {
	WinSize float64
	WinStep float64
}

type Span ¶

type Span struct {
	Chr   string
	Start int
	End   int
}

func GetSpan ¶

func GetSpan(text string) (Span, error)

type SubVal ¶

type SubVal struct {
	Val        float64
	Subtracted bool
}

type UltimateConfig ¶

type UltimateConfig struct {
	InputSets         []InputSet `json:"inputsets"`
	Chrlens           string     `json:"chrlens"`
	Outpre            string     `json:"outpre"`
	Ylim              []float64  `json:"ylim"`
	Plotfunc          string     `json: "plotfunc"`
	PlotfuncArgs      any        `json: "plotfuncargs"`
	Fullchr           bool       `json: "fullchr"`
	NoParent          bool       `json: "noparent"`
	ManualChrs        []string   `json: "manualchrs"`
	ManualChrsBedPath string     `json: "manualchrsbedpath"]`
}

func GetUltimateConfig ¶

func GetUltimateConfig(path string) ([]UltimateConfig, error)

func ReadUltimateConfig ¶

func ReadUltimateConfig(r io.Reader) ([]UltimateConfig, error)

Source Files ¶

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