Versions in this module Expand all Collapse all v0 v0.1.5 Mar 26, 2024 Changes in this version + func PlotMultiSawamuraAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error v0.1.4 Mar 26, 2024 Changes in this version + func HicPairFpkmColumns(rs []io.Reader, args any) ([]io.Reader, error) + func HicPairFpkmColumnsSome(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 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 PlotMultiTissue(outpre string, scalespath string) error + func PlotMultiTissueAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error + func PlotSawamuraAny(outpre string, ylim []float64, args any, margs MultiplotPlotFuncArgs) error + type PlotMultiSawamuraArgs struct + Boxes string + Scales string v0.1.3 Jan 11, 2024 v0.1.2 Jan 10, 2024 Changes in this version + 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 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 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 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 struct + Config string + NoParent bool + SelectWins string + Threads int + WholeGenome bool + WinSize int + WinStep int + func GetAllMultiplotFlags() AllSingleFlags + func GetAllSingleFlags() AllSingleFlags + func GetAllSubtractSingleFlags() AllSingleFlags + type BedEntry struct + Chr string + End int64 + Fields []string + Start int64 + 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 struct + Chr string + Len int + func GetChrLens(chrlenpath string) ([]ChrLenSet, error) + func ParseChrLenSet(line string) (ChrLenSet, error) + type ColGrepArgs struct + Col int + Pattern string + type ColGrepSomeArgs struct + Col int + Files []int + Pattern string + type ColSedArgs struct + Col int + Pattern string + Replace string + type ColSedSomeArgs struct + Col int + Files []int + Pattern string + Replace string + type Config struct + Chrlenpath string + Inpath string + Inpath2 string + Outpre string + func GetConfig(cfgpath string, subtract bool) ([]Config, error) + func ReadConfig(r io.Reader, subtract bool) ([]Config, error) + type Entry struct + Val float64 + func ParseEntry(line string) (Entry, error) + type Errors []error + func (e Errors) Error() string + type Filterer struct + func Filter(r io.Reader, chr string, start, end int) (*Filterer, error) + func (f *Filterer) Read(out []byte) (n int, err error) + type Flags struct + Chr string + Chrbedpath string + End int + Outpre string + Start int + func GetFlags() Flags + type GzReader struct + func (r *GzReader) Close() error + type InputSet struct + Extra any + FunctionArgs []any + Functions []string + Name string + Paths []string + type LabellerArgs struct + DistCols []int + DistPath string + LowThreshPerc float64 + TestCols []int + TestPath string + ThreshPerc float64 + func ReadLabellerFlags() LabellerArgs + type MultiplotPlotFuncArgs struct + Cfg UltimateConfig + Chr string + End int + Fullchr bool + Plformatter *Plformatter + Start int + type PlfmtEntry struct + Chr string + ChrNum int + End int + EndOff int + Line []string + Start int + StartOff int + Text string + type Plformatter struct + Chrnums map[string]int + Chroffs map[string]int + Chrset map[string]struct{} + UseManualChrs bool + func PlfmtSmall(r io.Reader, outpre string, manualChrs []string, useManualChrs bool) (*Plformatter, error) + type PlotBoxwhiskerArgs struct + FillName string + Height float64 + ResScale float64 + TextSize float64 + Width float64 + Xlab string + Xmax float64 + Xmin float64 + Ylab string + type PlotCovHistArgs struct + Binwidth float64 + Height float64 + ResScale float64 + Width float64 + Xlab string + Xmax float64 + Xmin float64 + Ylab string + type PlotMultiFacetScalesBoxedArgs struct + Boxes string + Scales string + type PlotSelfVsPairArgs struct + Height float64 + ResScale float64 + TextSize float64 + Width float64 + Xlab string + Xmax float64 + Xmin float64 + Ylab string + type Pos struct + Bp int + Chr string + func SortAndUniqPoses[T any](maps ...map[Pos]T) []Pos + type PosEntry struct + Val float64 + func ParsePosVal(line string, outbuf []PosEntry) ([]PosEntry, error) + type PrettyCfg struct + Height float64 + Res float64 + TextSize float64 + Width float64 + Xlab string + Ylab string + type Sentry struct + Val string + func CollectEntryDumb(text string) (Sentry, error) + type SlidingMeanArgs struct + WinSize float64 + WinStep float64 + type Span struct + Chr string + End int + Start int + func GetSpan(text string) (Span, error) + type SubVal struct + Subtracted bool + Val float64 + type UltimateConfig struct + Chrlens string + Fullchr bool + InputSets []InputSet + ManualChrs []string + ManualChrsBedPath string + NoParent bool + Outpre string + Plotfunc string + PlotfuncArgs any + Ylim []float64 + func GetUltimateConfig(path string) ([]UltimateConfig, error) + func ReadUltimateConfig(r io.Reader) ([]UltimateConfig, error)