fastats

package
v0.1.6 Latest Latest
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 Go to latest Published: Apr 23, 2024 License: AGPL-3.0 Imports: 17 Imported by: 0

Documentation

Index

Constants

This section is empty.

Variables

This section is empty.

Functions

func AddKmers 

func AddKmers(kmap map[string]int64, k int, seq string)

func AppendDequeBedFields added in v0.1.3 

func AppendDequeBedFields[FT any](s []FT, d *Deque[BedEntry[FT]]) []FT

func AppendQualScores 

func AppendQualScores(dest []float64, quals string) []float64

func AppendQualsToAscii 

func AppendQualsToAscii(w io.Writer, quals []int64) error

func AppendSamples 

func AppendSamples[T Formatter](out []string, s SampleSet[T]) ([]string, error)

func AppendScoreQuals 

func AppendScoreQuals(w io.Writer, scores []float64) error

func BasicStats 

func BasicStats(lens []FaLen, s *FaStats)

func BedSortWin added in v0.1.3 

func BedSortWin(r io.Reader, w io.Writer, f BedSortWinFlags) error

func BuildQual 

func BuildQual(qual byte, length int) string

func CheckAndPopMulti added in v0.1.3 

func CheckAndPopMulti[T any](win ChrSpan, d *Deque[BedEntry[T]])

func ChrSpanLess 

func ChrSpanLess(x, y ChrSpan) bool

func Chrlens 

func Chrlens(it iter.Iter[FaEntry]) *iter.Iterator[FaLen]

func CollectChrSpanMap 

func CollectChrSpanMap(cit iter.Iter[ChrSpan]) (map[string][]Span, error)

func CountKmers 

func CountKmers(it iter.Iter[FaEntry], k int) (map[string]int64, error)

func CreateMaybeGz 

func CreateMaybeGz(path string) (io.WriteCloser, error)

func ExtractFasta 

func ExtractFasta(fit iter.Iter[FaEntry], cit iter.Iter[ChrSpan]) *iter.Iterator[FaEntry]

func FaEntryWins 

func FaEntryWins(fe FaEntry, size int64, step int64) *iter.Iterator[BedEntry[string]]

func FaQualMerge 

func FaQualMerge(fit iter.Puller[FaEntry], qit iter.Puller[[]int64]) iter.Iter[FqEntry]

func FaToFq 

func FaToFq(fit iter.Iter[FaEntry], qual byte) *iter.Iterator[FqEntry]

func FaWins 

func FaWins(fa iter.Iter[FaEntry], size int64, step int64) *iter.Iterator[BedEntry[string]]

func FlatToFloatBed added in v0.1.3 

func FlatToFloatBed(it iter.Iter[BedEntry[[]string]]) *iter.Iterator[BedEntry[float64]]

func FormatSample 

func FormatSample[T Formatter, S ~[]T](format []string, sample S) (string, error)

func FqChrlens 

func FqChrlens(it iter.Iter[FqEntry]) *iter.Iterator[FaLen]

func FullChrlens 

func FullChrlens()

func FullCountKmers 

func FullCountKmers()

func FullFaStats 

func FullFaStats()

func FullFqChrlens 

func FullFqChrlens()

func FullFqStats 

func FullFqStats()

func FullKmerHist 

func FullKmerHist()

func FullQualPerPos 

func FullQualPerPos()

func FullToFa 

func FullToFa()

func FullyLeftOf added in v0.1.3 

func FullyLeftOf(x, y ChrSpan) bool

func GCFrac 

func GCFrac(seq string) float64

func GCIter 

func GCIter(views iter.Iter[BedEntry[string]]) *iter.Iterator[BedEntry[float64]]

func GetAlleles 

func GetAlleles(crossnames []string, dmap map[string]VcfEntry[struct{}]) (alleles []string, crossToIndex map[string]int)

func GrowLen 

func GrowLen[T any](s []T, n int) []T

func InfoToString 

func InfoToString[T any](is []InfoPair[T]) (string, error)

func IsNaNOrInf added in v0.1.3 

func IsNaNOrInf(x float64) bool

func KmerHist 

func KmerHist(it iter.Iter[Kmer]) ([]int64, error)

func KmerIter 

func KmerIter(m map[string]int64) *iter.Iterator[Kmer]

func Mean 

func Mean(fs ...float64) float64

func MeanBedPerBp added in v0.1.3 

func MeanBedPerBp(bed []BedEntry[float64]) float64

func MeanNoNaN added in v0.1.3 

func MeanNoNaN(x []float64) float64

func MeanQual 

func MeanQual(it iter.Iter[FqEntry]) (float64, error)

func MeanReadQual 

func MeanReadQual(it iter.Iter[FqEntry]) (float64, error)

func MeanWindowCounts added in v0.1.3 

func MeanWindowCounts(it iter.Iter[BedEntry[float64]], winsize, winstep int) *iter.Iterator[BedEntry[float64]]

func Must 

func Must(err error)

func N50Stats 

func N50Stats(lens []FaLen, s *FaStats)

func N90Stats 

func N90Stats(lens []FaLen, s *FaStats)

func NStats 

func NStats(lens []FaLen, totalbp int64, nfrac float64, n, l, bpInN *int64)

func NoNaNs added in v0.1.3 

func NoNaNs(x []float64) []float64

func NucdiffFullVcfMerge 

func NucdiffFullVcfMerge()

func NucdiffReadGff 

func NucdiffReadGff(d *NucdiffData, crossname string, it iter.Iter[GffEntry[NucdiffAttr]]) error

func NucdiffReadVcf 

func NucdiffReadVcf(d *NucdiffVcfData, crossname string, it iter.Iter[VcfEntry[struct{}]]) error

func NucdiffWriteVcf 

func NucdiffWriteVcf(d *NucdiffVcfData, w io.Writer) error

func OpenMaybeGz 

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

func ParseBed 

func ParseBed[FT any](r io.Reader, fieldParse func([]string) (FT, error)) *iter.Iterator[BedEntry[FT]]

func ParseBedFlat 

func ParseBedFlat(r io.Reader) *iter.Iterator[BedEntry[[]string]]

func ParseFasta 

func ParseFasta(r io.Reader) *iter.Iterator[FaEntry]

func ParseFastq 

func ParseFastq(r io.Reader) *iter.Iterator[FqEntry]

func ParseGff 

func ParseGff[AT any](r io.Reader, attributeParse func(string) (AT, error)) *iter.Iterator[GffEntry[AT]]

func ParseGffFlat 

func ParseGffFlat(r io.Reader) *iter.Iterator[GffEntry[[]AttributePair]]

func ParseSimpleVcf 

func ParseSimpleVcf(r io.Reader) *iter.Iterator[VcfEntry[struct{}]]

func ParseVcf 

func ParseVcf[T any](r io.Reader, f func(line []string) (T, error)) *iter.Iterator[VcfEntry[T]]

func ParseVcfMainFields added in v0.1.2 

func ParseVcfMainFields[T any](v *VcfEntry[T], line []string) error

func PrintFaLen 

func PrintFaLen(w io.Writer, l FaLen) error

func QualPerPos 

func QualPerPos(it iter.Iter[FqEntry]) ([]float64, error)

func QualScore 

func QualScore(qual byte) float64

func QualToAscii 

func QualToAscii(qual int64) byte

func RunBedSortWin added in v0.1.3 

func RunBedSortWin()

func RunGC 

func RunGC()

func Scan 

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

func ScanDot 

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

func ScanF 

func ScanF(f func(string, any) (int, error), line []string, ptrs ...any) (n int, err error)

func ScanFour 

func ScanFour(dest []string, s *bufio.Scanner) ([]string, error)

func ScanOne 

func ScanOne(field string, ptr any) (n int, err error)

func ScanOneDot 

func ScanOneDot(field string, ptr any) (n int, err error)

func ScoreQual 

func ScoreQual(score float64) byte

func ShouldFinishWin added in v0.1.3 

func ShouldFinishWin(win ChrSpan, next ChrSpan) bool

func ShouldUpdateWin added in v0.1.3 

func ShouldUpdateWin(win, next ChrSpan) bool

func SortBed added in v0.1.3 

func SortBed[T any](bed []BedEntry[T])

func SpreadBed 

func SpreadBed[FT any](it iter.Iter[BedEntry[FT]]) *iter.Iterator[BedEntry[FT]]

func StructuredVcfEntryToCsv 

func StructuredVcfEntryToCsv[InfoT any, SampleT Formatter](buf []string, v VcfEntry[StructuredInfoSamples[InfoT, SampleT]]) ([]string, error)

func ToFa 

func ToFa(it iter.Iter[FqEntry]) *iter.Iterator[FaEntry]

func WindowSortedBed added in v0.1.3 

func WindowSortedBed[FT any](it iter.Iter[BedEntry[FT]], winsize, winstep int) *iter.Iterator[BedEntry[[]BedEntry[FT]]]

func Wins 

func Wins(start, end, size, step int64) *iter.Iterator[Span]

func WriteFa added in v0.1.5 

func WriteFa(w io.Writer, it iter.Iter[FaEntry]) error

func WriteFaEntries added in v0.1.5 

func WriteFaEntries(w io.Writer, fs ...FaEntry) error

func WriteFloatBed added in v0.1.3 

func WriteFloatBed(w io.Writer, it iter.Iter[BedEntry[float64]]) (n int, err error)

func WriteFloatBedEntry added in v0.1.3 

func WriteFloatBedEntry(w io.Writer, b BedEntry[float64]) (n int, err error)

func WriteGC 

func WriteGC(w io.Writer, it iter.Iter[BedEntry[float64]]) (n int, err error)

Types

type AttributePair 

type AttributePair struct {
	Tag   string
	Value string
}

func ParseAttributePairs 

func ParseAttributePairs(field string) ([]AttributePair, error)

type BedEntry 

type BedEntry[FieldsT any] struct {
	ChrSpan
	Fields FieldsT
}

func ParseBedEntry 

func ParseBedEntry[FT any](line []string, fieldParse func([]string) (FT, error)) (BedEntry[FT], error)

func SortedBed added in v0.1.3 

func SortedBed[T any](it iter.Iter[BedEntry[T]]) ([]BedEntry[T], error)

type BedSortWinFlags added in v0.1.3 

type BedSortWinFlags struct {
	Sorted  bool
	Winsize int
	Winstep int
}

type ChrSpan 

type ChrSpan struct {
	Chr string
	Span
}

func GetSortedChrSpans 

func GetSortedChrSpans(d *NucdiffVcfData) []ChrSpan

func UpdateWin added in v0.1.3 

func UpdateWin(win ChrSpan, chr string, winsize, winstep int) ChrSpan

type Deque added in v0.1.3 

type Deque[T any] struct {
	// contains filtered or unexported fields
}

func (*Deque[T]) AppendToSlice added in v0.1.3 

func (d *Deque[T]) AppendToSlice(s []T) []T

func (*Deque[T]) Get added in v0.1.3 

func (d *Deque[T]) Get(i int) T

func (*Deque[T]) Grow added in v0.1.3 

func (d *Deque[T]) Grow()

func (*Deque[T]) Len added in v0.1.3 

func (d *Deque[T]) Len() int

func (*Deque[T]) PopBack added in v0.1.3 

func (d *Deque[T]) PopBack() (val T, ok bool)

func (*Deque[T]) PopFront added in v0.1.3 

func (d *Deque[T]) PopFront() (val T, ok bool)

func (*Deque[T]) PushBack added in v0.1.3 

func (d *Deque[T]) PushBack(vals ...T)

func (*Deque[T]) PushFront added in v0.1.3 

func (d *Deque[T]) PushFront(val T)

func (*Deque[T]) Set added in v0.1.3 

func (d *Deque[T]) Set(i int, val T) bool

type FaEntry 

type FaEntry struct {
	Header string
	Seq    string
}

func ExtractOne 

func ExtractOne(f FaEntry, s Span) (FaEntry, error)

type FaLen 

type FaLen struct {
	Name string
	Len  int64
}

func Chrlen 

func Chrlen(f FaEntry) FaLen

func RevsortedLens 

func RevsortedLens(it iter.Iter[FaLen]) ([]FaLen, error)

type FaStats 

type FaStats struct {
	Bp      int64
	MeanLen float64
	NumSeqs int64
	N50     int64
	L50     int64
	BpInN50 int64
	N90     int64
	L90     int64
	BpInN90 int64
}

func Stats 

func Stats(it iter.Iter[FaLen]) (FaStats, error)

type Formatter 

type Formatter interface {
	Format(format string) string
}

type FqEntry 

type FqEntry struct {
	FaEntry
	Qual string
}

type GffEntry 

type GffEntry[AttT any] struct {
	ChrSpan
	Source     string
	Type       string
	Score      float64
	HasScore   bool
	Strand     byte
	Phase      int
	HasPhase   bool
	Attributes AttT
}

func ParseGffEntry 

func ParseGffEntry[AT any](line []string, attributeParse func(string) (AT, error)) (GffEntry[AT], error)

type GzReader 

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

func OpenGz 

func OpenGz(path string) (*GzReader, error)

func (*GzReader) Close 

func (r *GzReader) Close() error

type GzWriter 

type GzWriter struct {
	*gzip.Writer
	// contains filtered or unexported fields
}

func CreateGz 

func CreateGz(path string) (*GzWriter, error)

func (*GzWriter) Close 

func (r *GzWriter) Close() error

type InfoPair 

type InfoPair[T any] struct {
	Key string
	Val T
}

type Kmer 

type Kmer struct {
	Seq   string
	Count int64
}

type NucdiffAttr 

type NucdiffAttr struct {
	ID         string
	Name       string
	Len        int
	QueryDir   int
	QuerySeq   string
	QueryStart int
	QueryEnd   int
	QueryBases string
	RefBases   string
	Color      string
}

func ParseNucdiffAttr 

func ParseNucdiffAttr(in string) (NucdiffAttr, error)

type NucdiffData 

type NucdiffData struct {
	CrossNames []string
	M          map[ChrSpan]map[string]NucdiffAttr
}

func NucdiffReadGffs 

func NucdiffReadGffs(paths []string) (*NucdiffData, error)

type NucdiffGT 

type NucdiffGT struct {
	Ref    int
	Alt    int
	Phased bool
}

type NucdiffVcfData 

type NucdiffVcfData struct {
	RefName    string
	CrossNames []string
	M          map[ChrSpan]map[string]VcfEntry[struct{}]
}

func NucdiffReadVcfs 

func NucdiffReadVcfs(refname string, crossnames []string, paths []string) (*NucdiffVcfData, error)

type NucdiffVcfPair 

type NucdiffVcfPair struct {
	Name string
	Path string
}

func ReadNucdiffVcfPairs 

func ReadNucdiffVcfPairs(r io.Reader) ([]NucdiffVcfPair, error)

type Reader 

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

func Open 

func Open(path string) (*Reader, error)

func (*Reader) Close 

func (r *Reader) Close() error

type SampleSet 

type SampleSet[T Formatter] struct {
	Format  []string
	Samples [][]T
}

type Span 

type Span struct {
	Start int64
	End   int64
}

type StringFormatter 

type StringFormatter string

func (StringFormatter) Format 

func (f StringFormatter) Format(format string) string

type StructuredInfoSamples 

type StructuredInfoSamples[InfoT any, SampleT Formatter] struct {
	Info    []InfoPair[InfoT]
	Samples SampleSet[SampleT]
}

type VcfEntry 

type VcfEntry[T any] struct {
	ChrSpan
	ID             string
	Ref            string
	Alts           []string
	Qual           int
	Filter         string
	InfoAndSamples T
}

func MergeNucdiffVcfEntries 

func MergeNucdiffVcfEntries(d *NucdiffVcfData, refname string, crossnames []string, crossidxs map[string]int, chrspan ChrSpan) VcfEntry[StructuredInfoSamples[string, StringFormatter]]

func ParseSimpleVcfEntry 

func ParseSimpleVcfEntry(line []string) (VcfEntry[struct{}], error)

func ParseVcfEntry 

func ParseVcfEntry[T any](line []string, f func(line []string) (T, error)) (VcfEntry[T], error)

type Writer 

type Writer struct {
	*bufio.Writer
	// contains filtered or unexported fields
}

func Create 

func Create(path string) (*Writer, error)

func (*Writer) Close 

func (w *Writer) Close() error

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