Documentation ¶
Index ¶
- func AddKmers(kmap map[string]int64, k int, seq string)
- func AppendDequeBedFields[FT any](s []FT, d *Deque[BedEntry[FT]]) []FT
- func AppendQualScores(dest []float64, quals string) []float64
- func AppendQualsToAscii(w io.Writer, quals []int64) error
- func AppendSamples[T Formatter](out []string, s SampleSet[T]) ([]string, error)
- func AppendScoreQuals(w io.Writer, scores []float64) error
- func BasicStats(lens []FaLen, s *FaStats)
- func BedSortWin(r io.Reader, w io.Writer, f BedSortWinFlags) error
- func BuildQual(qual byte, length int) string
- func CheckAndPopMulti[T any](win ChrSpan, d *Deque[BedEntry[T]])
- func ChrSpanLess(x, y ChrSpan) bool
- func Chrlens(it iter.Iter[FaEntry]) *iter.Iterator[FaLen]
- func CollectChrSpanMap(cit iter.Iter[ChrSpan]) (map[string][]Span, error)
- func CountKmers(it iter.Iter[FaEntry], k int) (map[string]int64, error)
- func CreateMaybeGz(path string) (io.WriteCloser, error)
- func ExtractFasta(fit iter.Iter[FaEntry], cit iter.Iter[ChrSpan]) *iter.Iterator[FaEntry]
- func FaEntryWins(fe FaEntry, size int64, step int64) *iter.Iterator[BedEntry[string]]
- func FaQualMerge(fit iter.Puller[FaEntry], qit iter.Puller[[]int64]) iter.Iter[FqEntry]
- func FaToFq(fit iter.Iter[FaEntry], qual byte) *iter.Iterator[FqEntry]
- func FaWins(fa iter.Iter[FaEntry], size int64, step int64) *iter.Iterator[BedEntry[string]]
- func FlatToFloatBed(it iter.Iter[BedEntry[[]string]]) *iter.Iterator[BedEntry[float64]]
- func FormatSample[T Formatter, S ~[]T](format []string, sample S) (string, error)
- func FqChrlens(it iter.Iter[FqEntry]) *iter.Iterator[FaLen]
- func FullChrlens()
- func FullCountKmers()
- func FullFaStats()
- func FullFqChrlens()
- func FullFqStats()
- func FullKmerHist()
- func FullQualPerPos()
- func FullToFa()
- func FullyLeftOf(x, y ChrSpan) bool
- func GCFrac(seq string) float64
- func GCIter(views iter.Iter[BedEntry[string]]) *iter.Iterator[BedEntry[float64]]
- func GetAlleles(crossnames []string, dmap map[string]VcfEntry[struct{}]) (alleles []string, crossToIndex map[string]int)
- func GrowLen[T any](s []T, n int) []T
- func InfoToString[T any](is []InfoPair[T]) (string, error)
- func IsNaNOrInf(x float64) bool
- func KmerHist(it iter.Iter[Kmer]) ([]int64, error)
- func KmerIter(m map[string]int64) *iter.Iterator[Kmer]
- func Mean(fs ...float64) float64
- func MeanBedPerBp(bed []BedEntry[float64]) float64
- func MeanNoNaN(x []float64) float64
- func MeanQual(it iter.Iter[FqEntry]) (float64, error)
- func MeanReadQual(it iter.Iter[FqEntry]) (float64, error)
- func MeanWindowCounts(it iter.Iter[BedEntry[float64]], winsize, winstep int) *iter.Iterator[BedEntry[float64]]
- func Must(err error)
- func N50Stats(lens []FaLen, s *FaStats)
- func N90Stats(lens []FaLen, s *FaStats)
- func NStats(lens []FaLen, totalbp int64, nfrac float64, n, l, bpInN *int64)
- func NoNaNs(x []float64) []float64
- func NucdiffFullVcfMerge()
- func NucdiffReadGff(d *NucdiffData, crossname string, it iter.Iter[GffEntry[NucdiffAttr]]) error
- func NucdiffReadVcf(d *NucdiffVcfData, crossname string, it iter.Iter[VcfEntry[struct{}]]) error
- func NucdiffWriteVcf(d *NucdiffVcfData, w io.Writer) error
- func OpenMaybeGz(path string) (io.ReadCloser, error)
- func ParseBed[FT any](r io.Reader, fieldParse func([]string) (FT, error)) *iter.Iterator[BedEntry[FT]]
- func ParseBedFlat(r io.Reader) *iter.Iterator[BedEntry[[]string]]
- func ParseFasta(r io.Reader) *iter.Iterator[FaEntry]
- func ParseFastq(r io.Reader) *iter.Iterator[FqEntry]
- func ParseGff[AT any](r io.Reader, attributeParse func(string) (AT, error)) *iter.Iterator[GffEntry[AT]]
- func ParseGffFlat(r io.Reader) *iter.Iterator[GffEntry[[]AttributePair]]
- func ParseSimpleVcf(r io.Reader) *iter.Iterator[VcfEntry[struct{}]]
- func ParseVcf[T any](r io.Reader, f func(line []string) (T, error)) *iter.Iterator[VcfEntry[T]]
- func ParseVcfMainFields[T any](v *VcfEntry[T], line []string) error
- func PrintFaLen(w io.Writer, l FaLen) error
- func QualPerPos(it iter.Iter[FqEntry]) ([]float64, error)
- func QualScore(qual byte) float64
- func QualToAscii(qual int64) byte
- func RunBedSortWin()
- func RunGC()
- func Scan(line []string, ptrs ...any) (n int, err error)
- func ScanDot(line []string, ptrs ...any) (n int, err error)
- func ScanF(f func(string, any) (int, error), line []string, ptrs ...any) (n int, err error)
- func ScanFour(dest []string, s *bufio.Scanner) ([]string, error)
- func ScanOne(field string, ptr any) (n int, err error)
- func ScanOneDot(field string, ptr any) (n int, err error)
- func ScoreQual(score float64) byte
- func ShouldFinishWin(win ChrSpan, next ChrSpan) bool
- func ShouldUpdateWin(win, next ChrSpan) bool
- func SortBed[T any](bed []BedEntry[T])
- func SpreadBed[FT any](it iter.Iter[BedEntry[FT]]) *iter.Iterator[BedEntry[FT]]
- func StructuredVcfEntryToCsv[InfoT any, SampleT Formatter](buf []string, v VcfEntry[StructuredInfoSamples[InfoT, SampleT]]) ([]string, error)
- func ToFa(it iter.Iter[FqEntry]) *iter.Iterator[FaEntry]
- func WindowSortedBed[FT any](it iter.Iter[BedEntry[FT]], winsize, winstep int) *iter.Iterator[BedEntry[[]BedEntry[FT]]]
- func Wins(start, end, size, step int64) *iter.Iterator[Span]
- func WriteFa(w io.Writer, it iter.Iter[FaEntry]) error
- func WriteFaEntries(w io.Writer, fs ...FaEntry) error
- func WriteFloatBed(w io.Writer, it iter.Iter[BedEntry[float64]]) (n int, err error)
- func WriteFloatBedEntry(w io.Writer, b BedEntry[float64]) (n int, err error)
- func WriteGC(w io.Writer, it iter.Iter[BedEntry[float64]]) (n int, err error)
- type AttributePair
- type BedEntry
- type BedSortWinFlags
- type ChrSpan
- type Deque
- func (d *Deque[T]) AppendToSlice(s []T) []T
- func (d *Deque[T]) Get(i int) T
- func (d *Deque[T]) Grow()
- func (d *Deque[T]) Len() int
- func (d *Deque[T]) PopBack() (val T, ok bool)
- func (d *Deque[T]) PopFront() (val T, ok bool)
- func (d *Deque[T]) PushBack(vals ...T)
- func (d *Deque[T]) PushFront(val T)
- func (d *Deque[T]) Set(i int, val T) bool
- type FaEntry
- type FaLen
- type FaStats
- type Formatter
- type FqEntry
- type GffEntry
- type GzReader
- type GzWriter
- type InfoPair
- type Kmer
- type NucdiffAttr
- type NucdiffData
- type NucdiffGT
- type NucdiffVcfData
- type NucdiffVcfPair
- type Reader
- type SampleSet
- type Span
- type StringFormatter
- type StructuredInfoSamples
- type VcfEntry
- func MergeNucdiffVcfEntries(d *NucdiffVcfData, refname string, crossnames []string, ...) VcfEntry[StructuredInfoSamples[string, StringFormatter]]
- func ParseSimpleVcfEntry(line []string) (VcfEntry[struct{}], error)
- func ParseVcfEntry[T any](line []string, f func(line []string) (T, error)) (VcfEntry[T], error)
- type Writer
Constants ¶
This section is empty.
Variables ¶
This section is empty.
Functions ¶
func AppendDequeBedFields ¶ added in v0.1.3
func AppendQualScores ¶
func AppendSamples ¶
func BasicStats ¶
func BedSortWin ¶ added in v0.1.3
func CheckAndPopMulti ¶ added in v0.1.3
func ChrSpanLess ¶
func CreateMaybeGz ¶
func CreateMaybeGz(path string) (io.WriteCloser, error)
func ExtractFasta ¶
func FaEntryWins ¶
func FaQualMerge ¶
func FlatToFloatBed ¶ added in v0.1.3
func FormatSample ¶
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 FullyLeftOf ¶ added in v0.1.3
func GetAlleles ¶
func IsNaNOrInf ¶ added in v0.1.3
func MeanBedPerBp ¶ added in v0.1.3
func MeanWindowCounts ¶ added in v0.1.3
func NucdiffFullVcfMerge ¶
func NucdiffFullVcfMerge()
func NucdiffReadGff ¶
func NucdiffReadGff(d *NucdiffData, crossname string, it iter.Iter[GffEntry[NucdiffAttr]]) error
func NucdiffReadVcf ¶
func NucdiffWriteVcf ¶
func NucdiffWriteVcf(d *NucdiffVcfData, w io.Writer) error
func OpenMaybeGz ¶
func OpenMaybeGz(path string) (io.ReadCloser, error)
func ParseGffFlat ¶
func ParseVcfMainFields ¶ added in v0.1.2
func QualToAscii ¶
func RunBedSortWin ¶ added in v0.1.3
func RunBedSortWin()
func ShouldFinishWin ¶ added in v0.1.3
func ShouldUpdateWin ¶ added in v0.1.3
func StructuredVcfEntryToCsv ¶
func WindowSortedBed ¶ added in v0.1.3
func WriteFloatBed ¶ added in v0.1.3
func WriteFloatBedEntry ¶ added in v0.1.3
Types ¶
type AttributePair ¶
func ParseAttributePairs ¶
func ParseAttributePairs(field string) ([]AttributePair, error)
type BedEntry ¶
func ParseBedEntry ¶
type BedSortWinFlags ¶ added in v0.1.3
type ChrSpan ¶
func GetSortedChrSpans ¶
func GetSortedChrSpans(d *NucdiffVcfData) []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
type FaStats ¶
type GffEntry ¶
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 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 ¶
func ReadNucdiffVcfPairs ¶
func ReadNucdiffVcfPairs(r io.Reader) ([]NucdiffVcfPair, error)
type StringFormatter ¶
type StringFormatter string
func (StringFormatter) Format ¶
func (f StringFormatter) Format(format string) string
type StructuredInfoSamples ¶
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 ¶
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