fastats

package

v0.1.25 Latest Latest Go to latest Published: Dec 5, 2025 License: AGPL-3.0 Imports: 22 Imported by: 3

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Repository

github.com/jgbaldwinbrown/fastats

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Documentation ¶

Index ¶

Variables
func AddKmers(kmap map[string]int64, k int, seq string)
func AppendDequeBedFields[FT any](s []FT, d *Deque[BedEntry[FT]]) []FT
func AppendLines(lines []string, s *bufio.Scanner, n int) ([]string, error)
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 AutoCorrelationWindows[B BedEnter[float64]](it iter.Seq[B], lags, winsize, winstep int) iter.Seq[BedEntry[float64]]
func BasicStats(lens []FaLen, s *FaStats)
func BasicStatsEfficient(lens []int64, counts map[int64]int64, s *FaStats)
func BedGraphSum[B BedEnter[float64]](it iter.Seq[B]) float64
func BedSortWin(r io.Reader, w io.Writer, f BedSortWinFlags) error
func BedWinImplicitChrs[B ChrSpanner](bed iter.Seq[B], winsize, winstep int64) map[ChrSpan][]B
func BedWinWithChrs[C, B ChrSpanner](chroms iter.Seq[C], bed iter.Seq[B], winsize, winstep int64) map[ChrSpan][]B
func BuildQual(qual byte, length int) string
func CheckAndPopMulti[B ChrSpanner](win ChrSpan, d *Deque[B])
func ChrSpanEq[C1, C2 ChrSpanner](c1 C1, c2 C2) bool
func ChrSpanLess[C ChrSpanner](x, y ChrSpanner) bool
func Chrlens[F FaEnter](it iter.Seq2[F, error]) iter.Seq2[FaLen, error]
func ColToFloat(col int) func([]string) (float64, error)
func Collect[T any](it iter.Seq[T]) []T
func CollectChrSpanMap[C ChrSpanner](cit iter.Seq2[C, error]) (map[string][]Span, error)
func CollectChrSpannerMap[C ChrSpanner](cit iter.Seq2[C, error]) (map[string][]C, error)
func CollectErr[T any](it iter.Seq2[T, error]) ([]T, error)
func CountKmers[F FaEnter](it iter.Seq2[F, error], k int) (map[string]int64, error)
func DivBed[B BedEnter[Tuple2[float64, float64]]](it iter.Seq[B]) iter.Seq[BedEntry[float64]]
func ExtractChrSpanFa[F FaEnter, C ChrSpanner](fit iter.Seq2[F, error], cit iter.Seq2[C, error]) iter.Seq2[ChrSpanFa[C, F], error]
func ExtractFasta[F FaEnter, C ChrSpanner](fit iter.Seq2[F, error], cit iter.Seq2[C, error]) iter.Seq2[FaEntry, error]
func FaEntryWins[F FaEnter](fe F, size int64, step int64) iter.Seq[BedEntry[string]]
func FaQualMerge[F FaEnter](fit iter.Seq2[F, error], qit iter.Seq2[[]int64, error]) iter.Seq2[FqEntry, error]
func FaToFq[FA FaEnter](fit iter.Seq2[FA, error], qual byte) iter.Seq2[FqEntry, error]
func FaWins[F FaEnter](fa iter.Seq2[F, error], size int64, step int64) iter.Seq2[BedEntry[string], error]
func FlatToFloatBed[B BedEnter[[]string]](it iter.Seq2[B, error]) iter.Seq2[BedEntry[float64], error]
func FormatSample[T Formatter, S ~[]T](format []string, sample S) (string, error)
func FqChrlens[F FqEnter](it iter.Seq2[F, error]) iter.Seq2[FaLen, error]
func FullAutoCorrelationWindows()
func FullBedZip()
func FullChrlens()
func FullCountKmers()
func FullDivCovs()
func FullFaStats()
func FullFqChrlens()
func FullFqStats()
func FullGCRegions()
func FullKmerHist()
func FullQualPerPos()
func FullRpkm()
func FullToFa()
func FullWinAvgSortedBed()
func FullWinSumSortedBed()
func FullyLeftOf(x, y ChrSpan) bool
func GCFrac(seq string) float64
func GCIter[B BedEnter[string]](views iter.Seq2[B, error]) iter.Seq2[BedEntry[float64], error]
func GcChrSpanFa[C ChrSpanner, F FaEnter](it iter.Seq2[ChrSpanFa[C, F], error]) iter.Seq2[ChrStat, error]
func GetAlleles[V VcfHeader](crossnames []string, dmap map[string]V) (alleles []string, crossToIndex map[string]int)
func GffPhaseStr[G GffHeader](g G) string
func GffScoreStr[G GffHeader](g G) string
func GrowLen[T any](s []T, n int) []T
func InfoToString[T any](is []InfoPair[T]) (string, error)
func IsNaNOrInf(x float64) bool
func IterateZipMap[T1, T2 any](m map[ChrSpan]OkTuple2[T1, T2]) iter.Seq[BedEntry[Tuple2[T1, T2]]]
func KmerHist(it iter.Seq[Kmer]) []int64
func KmerIter(m map[string]int64) iter.Seq[Kmer]
func LineCount(r io.Reader) (n int64, err error)
func LineCountPath(path string) (n int64, err error)
func Mean(fs ...float64) float64
func MeanBedPerBp[B BedEnter[float64]](bed []B) float64
func MeanNoNaN(x []float64) float64
func MeanQual[F FqEnter](it iter.Seq2[F, error]) (float64, error)
func MeanReadQual[F FqEnter](it iter.Seq2[F, error]) (float64, error)
func MeanWindowCounts[B BedEnter[float64]](it iter.Seq2[B, error], winsize, winstep int) iter.Seq2[BedEntry[float64], error]
func Must(err error)
func N50Stats(lens []FaLen, s *FaStats)
func N50StatsEfficient(lens []int64, count map[int64]int64, s *FaStats)
func N90Stats(lens []FaLen, s *FaStats)
func N90StatsEfficient(lens []int64, count map[int64]int64, s *FaStats)
func NStats(lens []FaLen, totalbp int64, nfrac float64, n, l, bpInN *int64)
func NStatsEfficient(lens []int64, counts map[int64]int64, totalbp int64, nfrac float64, ...)
func NameSpan(chr string, start, end int64) string
func NoNaNs(x []float64) []float64
func NucdiffFullVcfMerge()
func NucdiffReadGff[G GffEnter[NucdiffAttr]](d *NucdiffData, crossname string, it iter.Seq2[G, error]) error
func NucdiffReadVcf[V VcfHeader](d *NucdiffVcfData[V], crossname string, it iter.Seq2[V, error]) error
func NucdiffWriteVcf[V VcfHeader](d *NucdiffVcfData[V], w io.Writer) error
func ParseBed[FT any](r io.Reader, fieldParse func([]string) (FT, error)) iter.Seq2[BedEntry[FT], error]
func ParseBedFlat(r io.Reader) iter.Seq2[BedEntry[[]string], error]
func ParseBedGraph(r io.Reader) iter.Seq2[BedEntry[float64], error]
func ParseByteArray(s string) ([]byte, error)
func ParseChrSpanner(path string) iter.Seq2[ChrSpanner, error]
func ParseFasta(r io.Reader) iter.Seq2[FaEntry, error]
func ParseFastq(r io.Reader) iter.Seq2[FqEntry, error]
func ParseFloatArray(fields []string) ([]float64, error)
func ParseGff[AT any](r io.Reader, attributeParse func(string) (AT, error)) iter.Seq2[GffEntry[AT], error]
func ParseGffFlat(r io.Reader) iter.Seq2[GffEntry[[]AttributePair], error]
func ParseInfo(info string) (keys, vals []string)
func ParseIntArray(fields []string) ([]int64, error)
func ParseNumArray(s string) (ntype byte, array any, err error)
func ParseSimpleVcf(r io.Reader) iter.Seq2[VcfEntry[struct{}], error]
func ParseVcf[T any](r io.Reader, f func(line []string) (T, error)) iter.Seq2[VcfEntry[T], error]
func ParseVcfCore[T any](cr *csv.Reader, f func(line []string) (T, error)) iter.Seq2[VcfEntry[T], error]
func ParseVcfFlat(r io.Reader) iter.Seq2[VcfEntry[[]string], error]
func ParseVcfMainFields[T any](v *VcfEntry[T], line []string) error
func ParseVcfPlusHeader[T any](r io.Reader, f func(line []string) (T, error)) ([]string, iter.Seq2[VcfEntry[T], error], error)
func PassLine(r io.ByteReader, w io.ByteWriter) error
func PrintFaLen(w io.Writer, l FaLen) error
func PrintNewick(w io.Writer, n *Newick) (nw int, err error)
func PrintNewickDetailed(w io.Writer, n *Newick) (nw int, err error)
func QualPerPos[F FqEnter](it iter.Seq2[F, error]) ([]float64, error)
func QualScore(qual byte) float64
func QualToAscii(qual int64) byte
func RevsortedLensEfficient(it iter.Seq2[FaLen, error]) (lens []int64, counts map[int64]int64, err error)
func Rpkm[B BedEnter[float64]](it iter.Seq[B], totalCov float64) iter.Seq[BedEntry[float64]]
func RpkmAndTotal[B BedEnter[float64]](it iter.Seq[B]) (rpkm iter.Seq[BedEntry[float64]], totalCov float64)
func RpkmOne[B BedEnter[float64]](b B, totalCov float64) float64
func RunBedSortWin()
func RunGC()
func ScanFour(dest []string, s *bufio.Scanner) ([]string, error)
func ScoreQual(score float64) byte
func ShouldFinishWin(win ChrSpan, next ChrSpan) bool
func ShouldUpdateWin(win, next ChrSpan) bool
func SliceIter2[S ~[]T, T any](s S) func(func(T, error) bool)
func SortBed[C ChrSpanner](bed []C)
func SortedBed[B ChrSpanner](it iter.Seq2[B, error]) ([]B, error)
func SplitChrs[C ChrSpanner](cit iter.Seq[C]) iter.Seq[iter.Seq[C]]
func SplitFq(pieces int, outdir string, paths ...string) error
func SplitOneFq(path, pathOutdir, base, outsuffix string, entriesPerPiece int64) (err error)
func SpreadBed[B BedEnter[T], T any](it iter.Seq[B]) func(func(BedEntry[T]) bool)
func SpreadBed2[B BedEnter[T], T any](it iter.Seq2[B, error]) func(func(BedEntry[T], error) bool)
func StartOneIndex[S Spanner](s S) int64
func StructuredVcfEntryToCsv[InfoT any, SampleT Formatter](buf []string, v VcfEntry[StructuredInfoSamples[InfoT, SampleT]]) ([]string, error)
func ToBedGraphEntry[B BedEnter[[]string]](col int) func(B) (BedEntry[float64], error)
func WinAvgSortedBed[B BedEnter[float64]](it iter.Seq2[B, error], winsize, winstep int) iter.Seq2[BedEntry[float64], error]
func WinSumSortedBed[B BedEnter[float64]](it iter.Seq2[B, error], winsize, winstep int, perBp bool) iter.Seq2[BedEntry[float64], error]
func WindowBed[B BedEnter[T], T any](it iter.Seq[B], winsize, winstep int) iter.Seq[BedEntry[[]T]]
func WindowBedWeak[B BedEnter[T], T any](it iter.Seq[B], winsize, winstep int) iter.Seq[BedEntry[[]T]]
func WindowSortedBed[B ChrSpanner](it iter.Seq2[B, error], winsize, winstep int) func(func(BedEntry[[]B], error) bool)
func Wins(start, end, size, step int64) iter.Seq[Span]
func WriteBedEnterFlat[B BedEnter[[]T], T any](w io.Writer, b B) error
func WriteBedEnterSingle[B BedEnter[T], T any](w io.Writer, b B) error
func WriteBedEntry[B BedEnter[T], T any](w io.Writer, b B, writeFields func(io.Writer, T) error) error
func WriteBedHeader[B ChrSpanner](w io.Writer, b B) error
func WriteFa[F FaEnter](w io.Writer, it iter.Seq2[F, error]) error
func WriteFaEntries[F FaEnter](w io.Writer, fs ...F) error
func WriteFloatBed[B BedEnter[float64]](w io.Writer, it iter.Seq2[B, error]) (n int, err error)
func WriteFloatBedEntry[B BedEnter[float64]](w io.Writer, b B) (n int, err error)
func WriteGC[B BedEnter[float64]](w io.Writer, it iter.Seq2[B, error]) (n int, err error)
func WriteGffAttributePairs(w io.Writer, pairs []AttributePair) error
func WriteGffEntry[G GffEnter[T], T any](w io.Writer, g G, f func(io.Writer, T) error) error
func WriteGffFlat[G GffEnter[[]AttributePair]](w io.Writer, g G) error
func WriteGffHeader[G GffHeader](w io.Writer, g G) error
func WriteLines(w io.Writer, lines []string) error
func ZipMatchedSorted[B1 BedEnter[T1], B2 BedEnter[T2], T1, T2 any](it1 iter.Seq[B1], it2 iter.Seq[B2]) iter.Seq2[BedEntry[Tuple2[T1, T2]], error]
func ZipMatches[B1 BedEnter[T1], B2 BedEnter[T2], T1, T2 any](it1 iter.Seq[B1], it2 iter.Seq[B2]) map[ChrSpan]OkTuple2[T1, T2]
type AttributePair
- func ParseAttributePairs(field string) ([]AttributePair, error)
type AutoCorrelationFlags
type BedEnter
type BedEntry
- func BedZip[B1 BedEnter[[]string], B2 BedEnter[[]string]](it1 iter.Seq[B1], it2 iter.Seq[B2]) []BedEntry[[]string]
- func ParseBedEntry[FT any](line []string, fieldParse func([]string) (FT, error)) (BedEntry[FT], error)
- func ToBedEntry[B BedEnter[FieldsT], FieldsT any](b B) BedEntry[FieldsT]
- func (b BedEntry[T]) BedFields() T
type BedSortWinFlags
type CIGAREntry
- func ParseCIGAR(cigar string) ([]CIGAREntry, error)
type ChrSpan
- func GetSortedChrSpans[V VcfHeader](d *NucdiffVcfData[V]) []ChrSpan
- func ToChrSpan[C ChrSpanner](c C) ChrSpan
- func UpdateWin(win ChrSpan, chr string, winsize, winstep int) ChrSpan
- func (c ChrSpan) SpanChr() string
type ChrSpanFa
type ChrSpanner
type ChrStat
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 FaEnter
type FaEntry
- func ExtractOne(f FaEntry, s Span) (FaEntry, error)
- func ToFaEntry[F FaEnter](f F) FaEntry
- func (f FaEntry) FaHeader() string
- func (f FaEntry) FaSeq() string
type FaLen
- func Chrlen[F FaEnter](f F) FaLen
- func RevsortedLens(it iter.Seq2[FaLen, error]) ([]FaLen, error)
type FaStats
- func Stats(it iter.Seq2[FaLen, error]) (FaStats, error)
type Formatter
type FqEnter
type FqEntry
- func ToFqEntry[F FqEnter](f F) FqEntry
- func (f FqEntry) FqQual() string
type FullRpkmFlags
type GffEnter
type GffEntry
- func ParseGffEntry[AT any](line []string, attributeParse func(string) (AT, error)) (GffEntry[AT], error)
- func ToGffEntry[G GffEnter[AttT], AttT any](g G) GffEntry[AttT]
- func (g GffEntry[T]) GffAttributes() T
type GffHead
- func ToGffHead[G GffHeader](g G) GffHead
- func (g GffHead) GffHasPhase() bool
- func (g GffHead) GffHasScore() bool
- func (g GffHead) GffPhase() int
- func (g GffHead) GffScore() float64
- func (g GffHead) GffSource() string
- func (g GffHead) GffStrand() byte
- func (g GffHead) GffType() string
type GffHeader
type InfoPair
type Kmer
type Newick
- func ParseNewick(r io.Reader) (*Newick, error)
- func (n *Newick) String() string
type NucdiffAttr
- func ParseNucdiffAttr(in string) (NucdiffAttr, error)
type NucdiffData
- func NucdiffReadGffs(paths []string) (*NucdiffData, error)
type NucdiffGT
type NucdiffVcfData
- func NucdiffReadVcfs(refname string, crossnames []string, paths []string) (*NucdiffVcfData[VcfEntry[struct{}]], error)
type NucdiffVcfPair
- func ReadNucdiffVcfPairs(r io.Reader) ([]NucdiffVcfPair, error)
type OkTuple2
type SamAlignment
- func ParseSamAlignment(line []string) (SamAlignment, error)
type SamEntry
- func ParseSamEntry(s string) (SamEntry, error)
- func ParseSamHeading(s string) SamEntry
type SamOptional
- func ParseSamOptional(s string) (SamOptional, error)
- func ParseSamOptionals(s string) ([]SamOptional, error)
type SampleSet
type Span
- func ToSpan[S Spanner](s S) Span
- func (s Span) SpanEnd() int64
- func (s Span) SpanStart() int64
type Spanner
type StringFormatter
- func (f StringFormatter) Format(format string) string
type StructuredInfoSamples
type Tuple2
type VcfEnter
type VcfEntry
- func MergeNucdiffVcfEntries[V VcfHeader](d *NucdiffVcfData[V], 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)
- func ToVcfEntry[V VcfEnter[T], T any](v V) VcfEntry[T]
- func (v VcfEntry[T]) VcfInfoAndSamples() T
type VcfHead
- func ParseVcfHead(line []string) (VcfHead, error)
- func ToVcfHead[V VcfHeader](v V) VcfHead
- func (v VcfHead) VcfAlts() []string
- func (v VcfHead) VcfFilter() string
- func (v VcfHead) VcfID() string
- func (v VcfHead) VcfQual() float64
- func (v VcfHead) VcfRef() string
type VcfHeader
type VcfInfoSamples
- func ParseVcfInfoSamples(line []string) (VcfInfoSamples, error)
type WinAvgSortedBedFlags
type WinSumSortedBedFlags

Constants ¶

This section is empty.

Variables ¶

View Source

var ErrVcfFormat = errors.New("Vcf format error")

View Source

var ErrZipNoMatch = errors.New("Zip: bed entry spans do not match")

View Source

var ErrZipShort = errors.New("Zip: beds are not the same length")

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 AppendLines ¶ added in v0.1.13

func AppendLines(lines []string, s *bufio.Scanner, n int) ([]string, error)

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 AutoCorrelationWindows ¶ added in v0.1.13

func AutoCorrelationWindows[B BedEnter[float64]](it iter.Seq[B], lags, winsize, winstep int) iter.Seq[BedEntry[float64]]

Requires sorted bed entries

func BasicStats ¶

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

func BasicStatsEfficient ¶ added in v0.1.18

func BasicStatsEfficient(lens []int64, counts map[int64]int64, s *FaStats)

func BedGraphSum ¶ added in v0.1.13

func BedGraphSum[B BedEnter[float64]](it iter.Seq[B]) float64

func BedSortWin ¶ added in v0.1.3

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

func BedWinImplicitChrs ¶ added in v0.1.13

func BedWinImplicitChrs[B ChrSpanner](bed iter.Seq[B], winsize, winstep int64) map[ChrSpan][]B

func BedWinWithChrs ¶ added in v0.1.13

func BedWinWithChrs[C, B ChrSpanner](chroms iter.Seq[C], bed iter.Seq[B], winsize, winstep int64) map[ChrSpan][]B

func BuildQual ¶

func BuildQual(qual byte, length int) string

func CheckAndPopMulti ¶ added in v0.1.3

func CheckAndPopMulti[B ChrSpanner](win ChrSpan, d *Deque[B])

func ChrSpanEq ¶ added in v0.1.13

func ChrSpanEq[C1, C2 ChrSpanner](c1 C1, c2 C2) bool

func ChrSpanLess ¶

func ChrSpanLess[C ChrSpanner](x, y ChrSpanner) bool

func Chrlens ¶

func Chrlens[F FaEnter](it iter.Seq2[F, error]) iter.Seq2[FaLen, error]

func ColToFloat ¶ added in v0.1.13

func ColToFloat(col int) func([]string) (float64, error)

func Collect ¶ added in v0.1.7

func Collect[T any](it iter.Seq[T]) []T

func CollectChrSpanMap ¶

func CollectChrSpanMap[C ChrSpanner](cit iter.Seq2[C, error]) (map[string][]Span, error)

func CollectChrSpannerMap ¶ added in v0.1.13

func CollectChrSpannerMap[C ChrSpanner](cit iter.Seq2[C, error]) (map[string][]C, error)

func CollectErr ¶ added in v0.1.7

func CollectErr[T any](it iter.Seq2[T, error]) ([]T, error)

func CountKmers ¶

func CountKmers[F FaEnter](it iter.Seq2[F, error], k int) (map[string]int64, error)

func DivBed ¶ added in v0.1.13

func DivBed[B BedEnter[Tuple2[float64, float64]]](it iter.Seq[B]) iter.Seq[BedEntry[float64]]

func ExtractChrSpanFa ¶ added in v0.1.25

func ExtractChrSpanFa[F FaEnter, C ChrSpanner](fit iter.Seq2[F, error], cit iter.Seq2[C, error]) iter.Seq2[ChrSpanFa[C, F], error]

func ExtractFasta ¶

func ExtractFasta[F FaEnter, C ChrSpanner](fit iter.Seq2[F, error], cit iter.Seq2[C, error]) iter.Seq2[FaEntry, error]

func FaEntryWins ¶

func FaEntryWins[F FaEnter](fe F, size int64, step int64) iter.Seq[BedEntry[string]]

func FaQualMerge ¶

func FaQualMerge[F FaEnter](fit iter.Seq2[F, error], qit iter.Seq2[[]int64, error]) iter.Seq2[FqEntry, error]

func FaToFq ¶

func FaToFq[FA FaEnter](fit iter.Seq2[FA, error], qual byte) iter.Seq2[FqEntry, error]

func FaWins ¶

func FaWins[F FaEnter](fa iter.Seq2[F, error], size int64, step int64) iter.Seq2[BedEntry[string], error]

func FlatToFloatBed ¶ added in v0.1.3

func FlatToFloatBed[B BedEnter[[]string]](it iter.Seq2[B, error]) iter.Seq2[BedEntry[float64], error]

func FormatSample ¶

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

func FqChrlens ¶

func FqChrlens[F FqEnter](it iter.Seq2[F, error]) iter.Seq2[FaLen, error]

func FullAutoCorrelationWindows ¶ added in v0.1.13

func FullAutoCorrelationWindows()

func FullBedZip ¶ added in v0.1.13

func FullBedZip()

func FullChrlens ¶

func FullChrlens()

func FullCountKmers ¶

func FullCountKmers()

func FullDivCovs ¶ added in v0.1.13

func FullDivCovs()

func FullFaStats ¶

func FullFaStats()

func FullFqChrlens ¶

func FullFqChrlens()

func FullFqStats ¶

func FullFqStats()

func FullGCRegions ¶ added in v0.1.25

func FullGCRegions()

func FullKmerHist ¶

func FullKmerHist()

func FullQualPerPos ¶

func FullQualPerPos()

func FullRpkm ¶ added in v0.1.18

func FullRpkm()

func FullToFa ¶

func FullToFa()

func FullWinAvgSortedBed ¶ added in v0.1.13

func FullWinAvgSortedBed()

func FullWinSumSortedBed ¶ added in v0.1.18

func FullWinSumSortedBed()

func FullyLeftOf ¶ added in v0.1.3

func FullyLeftOf(x, y ChrSpan) bool

func GCFrac ¶

func GCFrac(seq string) float64

func GCIter ¶

func GCIter[B BedEnter[string]](views iter.Seq2[B, error]) iter.Seq2[BedEntry[float64], error]

func GcChrSpanFa ¶ added in v0.1.25

func GcChrSpanFa[C ChrSpanner, F FaEnter](it iter.Seq2[ChrSpanFa[C, F], error]) iter.Seq2[ChrStat, error]

func GetAlleles ¶

func GetAlleles[V VcfHeader](crossnames []string, dmap map[string]V) (alleles []string, crossToIndex map[string]int)

func GffPhaseStr ¶ added in v0.1.23

func GffPhaseStr[G GffHeader](g G) string

func GffScoreStr ¶ added in v0.1.23

func GffScoreStr[G GffHeader](g G) string

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 IterateZipMap ¶ added in v0.1.13

func IterateZipMap[T1, T2 any](m map[ChrSpan]OkTuple2[T1, T2]) iter.Seq[BedEntry[Tuple2[T1, T2]]]

func KmerHist ¶

func KmerHist(it iter.Seq[Kmer]) []int64

func KmerIter ¶

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

func LineCount ¶ added in v0.1.13

func LineCount(r io.Reader) (n int64, err error)

func LineCountPath ¶ added in v0.1.13

func LineCountPath(path string) (n int64, err error)

func Mean ¶

func Mean(fs ...float64) float64

func MeanBedPerBp ¶ added in v0.1.3

func MeanBedPerBp[B BedEnter[float64]](bed []B) float64

func MeanNoNaN ¶ added in v0.1.3

func MeanNoNaN(x []float64) float64

func MeanQual ¶

func MeanQual[F FqEnter](it iter.Seq2[F, error]) (float64, error)

func MeanReadQual ¶

func MeanReadQual[F FqEnter](it iter.Seq2[F, error]) (float64, error)

func MeanWindowCounts ¶ added in v0.1.3

func MeanWindowCounts[B BedEnter[float64]](it iter.Seq2[B, error], winsize, winstep int) iter.Seq2[BedEntry[float64], error]

func Must ¶

func Must(err error)

func N50Stats ¶

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

func N50StatsEfficient ¶ added in v0.1.18

func N50StatsEfficient(lens []int64, count map[int64]int64, s *FaStats)

func N90Stats ¶

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

func N90StatsEfficient ¶ added in v0.1.18

func N90StatsEfficient(lens []int64, count map[int64]int64, s *FaStats)

func NStats ¶

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

func NStatsEfficient ¶ added in v0.1.18

func NStatsEfficient(lens []int64, counts map[int64]int64, totalbp int64, nfrac float64, n, l, bpInN *int64)

func NameSpan ¶ added in v0.1.25

func NameSpan(chr string, start, end int64) string

func NoNaNs ¶ added in v0.1.3

func NoNaNs(x []float64) []float64

func NucdiffFullVcfMerge ¶

func NucdiffFullVcfMerge()

func NucdiffReadGff ¶

func NucdiffReadGff[G GffEnter[NucdiffAttr]](d *NucdiffData, crossname string, it iter.Seq2[G, error]) error

func NucdiffReadVcf ¶

func NucdiffReadVcf[V VcfHeader](d *NucdiffVcfData[V], crossname string, it iter.Seq2[V, error]) error

func NucdiffWriteVcf ¶

func NucdiffWriteVcf[V VcfHeader](d *NucdiffVcfData[V], w io.Writer) error

func ParseBed ¶

func ParseBed[FT any](r io.Reader, fieldParse func([]string) (FT, error)) iter.Seq2[BedEntry[FT], error]

func ParseBedFlat ¶

func ParseBedFlat(r io.Reader) iter.Seq2[BedEntry[[]string], error]

func ParseBedGraph ¶ added in v0.1.13

func ParseBedGraph(r io.Reader) iter.Seq2[BedEntry[float64], error]

func ParseByteArray ¶ added in v0.1.18

func ParseByteArray(s string) ([]byte, error)

func ParseChrSpanner ¶ added in v0.1.25

func ParseChrSpanner(path string) iter.Seq2[ChrSpanner, error]

func ParseFasta ¶

func ParseFasta(r io.Reader) iter.Seq2[FaEntry, error]

func ParseFastq ¶

func ParseFastq(r io.Reader) iter.Seq2[FqEntry, error]

func ParseFloatArray ¶ added in v0.1.18

func ParseFloatArray(fields []string) ([]float64, error)

func ParseGff ¶

func ParseGff[AT any](r io.Reader, attributeParse func(string) (AT, error)) iter.Seq2[GffEntry[AT], error]

func ParseGffFlat ¶

func ParseGffFlat(r io.Reader) iter.Seq2[GffEntry[[]AttributePair], error]

func ParseInfo ¶ added in v0.1.19

func ParseInfo(info string) (keys, vals []string)

func ParseIntArray ¶ added in v0.1.18

func ParseIntArray(fields []string) ([]int64, error)

func ParseNumArray ¶ added in v0.1.18

func ParseNumArray(s string) (ntype byte, array any, err error)

func ParseSimpleVcf ¶

func ParseSimpleVcf(r io.Reader) iter.Seq2[VcfEntry[struct{}], error]

func ParseVcf ¶

func ParseVcf[T any](r io.Reader, f func(line []string) (T, error)) iter.Seq2[VcfEntry[T], error]

func ParseVcfCore ¶ added in v0.1.20

func ParseVcfCore[T any](cr *csv.Reader, f func(line []string) (T, error)) iter.Seq2[VcfEntry[T], error]

func ParseVcfFlat ¶ added in v0.1.18

func ParseVcfFlat(r io.Reader) iter.Seq2[VcfEntry[[]string], error]

func ParseVcfMainFields ¶ added in v0.1.2

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

func ParseVcfPlusHeader ¶ added in v0.1.20

func ParseVcfPlusHeader[T any](r io.Reader, f func(line []string) (T, error)) ([]string, iter.Seq2[VcfEntry[T], error], error)

func PassLine ¶ added in v0.1.13

func PassLine(r io.ByteReader, w io.ByteWriter) error

func PrintFaLen ¶

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

func PrintNewick ¶ added in v0.1.18

func PrintNewick(w io.Writer, n *Newick) (nw int, err error)

func PrintNewickDetailed ¶ added in v0.1.18

func PrintNewickDetailed(w io.Writer, n *Newick) (nw int, err error)

func QualPerPos ¶

func QualPerPos[F FqEnter](it iter.Seq2[F, error]) ([]float64, error)

func QualScore ¶

func QualScore(qual byte) float64

func QualToAscii ¶

func QualToAscii(qual int64) byte

func RevsortedLensEfficient ¶ added in v0.1.18

func RevsortedLensEfficient(it iter.Seq2[FaLen, error]) (lens []int64, counts map[int64]int64, err error)

func Rpkm ¶ added in v0.1.13

func Rpkm[B BedEnter[float64]](it iter.Seq[B], totalCov float64) iter.Seq[BedEntry[float64]]

func RpkmAndTotal ¶ added in v0.1.13

func RpkmAndTotal[B BedEnter[float64]](it iter.Seq[B]) (rpkm iter.Seq[BedEntry[float64]], totalCov float64)

"it" must be reuseable

func RpkmOne ¶ added in v0.1.13

func RpkmOne[B BedEnter[float64]](b B, totalCov float64) float64

func RunBedSortWin ¶ added in v0.1.3

func RunBedSortWin()

func RunGC ¶

func RunGC()

func ScanFour ¶

func ScanFour(dest []string, s *bufio.Scanner) ([]string, 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 SliceIter2 ¶ added in v0.1.7

func SliceIter2[S ~[]T, T any](s S) func(func(T, error) bool)

func SortBed ¶ added in v0.1.3

func SortBed[C ChrSpanner](bed []C)

func SortedBed ¶ added in v0.1.3

func SortedBed[B ChrSpanner](it iter.Seq2[B, error]) ([]B, error)

func SplitChrs ¶ added in v0.1.13

func SplitChrs[C ChrSpanner](cit iter.Seq[C]) iter.Seq[iter.Seq[C]]

Requires sorted bed entries

func SplitFq ¶ added in v0.1.13

func SplitFq(pieces int, outdir string, paths ...string) error

func SplitOneFq ¶ added in v0.1.13

func SplitOneFq(path, pathOutdir, base, outsuffix string, entriesPerPiece int64) (err error)

func SpreadBed ¶

func SpreadBed[B BedEnter[T], T any](it iter.Seq[B]) func(func(BedEntry[T]) bool)

func SpreadBed2 ¶ added in v0.1.12

func SpreadBed2[B BedEnter[T], T any](it iter.Seq2[B, error]) func(func(BedEntry[T], error) bool)

func StartOneIndex ¶ added in v0.1.10

func StartOneIndex[S Spanner](s S) int64

func StructuredVcfEntryToCsv ¶

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

func ToBedGraphEntry ¶ added in v0.1.13

func ToBedGraphEntry[B BedEnter[[]string]](col int) func(B) (BedEntry[float64], error)

func WinAvgSortedBed ¶ added in v0.1.13

func WinAvgSortedBed[B BedEnter[float64]](it iter.Seq2[B, error], winsize, winstep int) iter.Seq2[BedEntry[float64], error]

func WinSumSortedBed ¶ added in v0.1.18

func WinSumSortedBed[B BedEnter[float64]](it iter.Seq2[B, error], winsize, winstep int, perBp bool) iter.Seq2[BedEntry[float64], error]

func WindowBed ¶ added in v0.1.13

func WindowBed[B BedEnter[T], T any](it iter.Seq[B], winsize, winstep int) iter.Seq[BedEntry[[]T]]

Requires sorted bed entries

func WindowBedWeak ¶ added in v0.1.13

func WindowBedWeak[B BedEnter[T], T any](it iter.Seq[B], winsize, winstep int) iter.Seq[BedEntry[[]T]]

Requires sorted bed entries

func WindowSortedBed ¶ added in v0.1.3

func WindowSortedBed[B ChrSpanner](it iter.Seq2[B, error], winsize, winstep int) func(func(BedEntry[[]B], error) bool)

func Wins ¶

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

func WriteBedEnterFlat ¶ added in v0.1.23

func WriteBedEnterFlat[B BedEnter[[]T], T any](w io.Writer, b B) error

func WriteBedEnterSingle ¶ added in v0.1.23

func WriteBedEnterSingle[B BedEnter[T], T any](w io.Writer, b B) error

func WriteBedEntry ¶ added in v0.1.23

func WriteBedEntry[B BedEnter[T], T any](w io.Writer, b B, writeFields func(io.Writer, T) error) error

func WriteBedHeader ¶ added in v0.1.23

func WriteBedHeader[B ChrSpanner](w io.Writer, b B) error

func WriteFa ¶ added in v0.1.5

func WriteFa[F FaEnter](w io.Writer, it iter.Seq2[F, error]) error

func WriteFaEntries ¶ added in v0.1.5

func WriteFaEntries[F FaEnter](w io.Writer, fs ...F) error

func WriteFloatBed ¶ added in v0.1.3

func WriteFloatBed[B BedEnter[float64]](w io.Writer, it iter.Seq2[B, error]) (n int, err error)

func WriteFloatBedEntry ¶ added in v0.1.3

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

func WriteGC ¶

func WriteGC[B BedEnter[float64]](w io.Writer, it iter.Seq2[B, error]) (n int, err error)

func WriteGffAttributePairs ¶ added in v0.1.23

func WriteGffAttributePairs(w io.Writer, pairs []AttributePair) error

func WriteGffEntry ¶ added in v0.1.23

func WriteGffEntry[G GffEnter[T], T any](w io.Writer, g G, f func(io.Writer, T) error) error

func WriteGffFlat ¶ added in v0.1.23

func WriteGffFlat[G GffEnter[[]AttributePair]](w io.Writer, g G) error

func WriteGffHeader ¶ added in v0.1.23

func WriteGffHeader[G GffHeader](w io.Writer, g G) error

func WriteLines ¶ added in v0.1.13

func WriteLines(w io.Writer, lines []string) error

func ZipMatchedSorted ¶ added in v0.1.13

func ZipMatchedSorted[B1 BedEnter[T1], B2 BedEnter[T2], T1, T2 any](it1 iter.Seq[B1], it2 iter.Seq[B2]) iter.Seq2[BedEntry[Tuple2[T1, T2]], error]

func ZipMatches ¶ added in v0.1.13

func ZipMatches[B1 BedEnter[T1], B2 BedEnter[T2], T1, T2 any](it1 iter.Seq[B1], it2 iter.Seq[B2]) map[ChrSpan]OkTuple2[T1, T2]

Types ¶

type AttributePair ¶

type AttributePair struct {
	Tag   string
	Value string
}

func ParseAttributePairs ¶

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

type AutoCorrelationFlags ¶ added in v0.1.13

type AutoCorrelationFlags struct {
	Lag     int
	Winsize int
	Winstep int
	Col     int
}

type BedEnter ¶ added in v0.1.7

type BedEnter[FieldsT any] interface {
	ChrSpanner
	BedFields() FieldsT
}

type BedEntry ¶

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

func BedZip ¶ added in v0.1.13

func BedZip[B1 BedEnter[[]string], B2 BedEnter[[]string]](it1 iter.Seq[B1], it2 iter.Seq[B2]) []BedEntry[[]string]

func ParseBedEntry ¶

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

func ToBedEntry ¶ added in v0.1.8

func ToBedEntry[B BedEnter[FieldsT], FieldsT any](b B) BedEntry[FieldsT]

func (BedEntry[T]) BedFields ¶ added in v0.1.7

func (b BedEntry[T]) BedFields() T

type BedSortWinFlags ¶ added in v0.1.3

type BedSortWinFlags struct {
	Sorted  bool
	Winsize int
	Winstep int
}

type CIGAREntry ¶ added in v0.1.18

type CIGAREntry struct {
	Letter byte
	Count  int64
}

func ParseCIGAR ¶ added in v0.1.18

func ParseCIGAR(cigar string) ([]CIGAREntry, error)

type ChrSpan ¶

type ChrSpan struct {
	Chr string
	Span
}

func GetSortedChrSpans ¶

func GetSortedChrSpans[V VcfHeader](d *NucdiffVcfData[V]) []ChrSpan

func ToChrSpan ¶ added in v0.1.8

func ToChrSpan[C ChrSpanner](c C) ChrSpan

func UpdateWin ¶ added in v0.1.3

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

func (ChrSpan) SpanChr ¶ added in v0.1.7

func (c ChrSpan) SpanChr() string

type ChrSpanFa ¶ added in v0.1.25

type ChrSpanFa[C ChrSpanner, F FaEnter] struct {
	ChrSpanner C
	FaEnter    F
}

type ChrSpanner ¶ added in v0.1.7

type ChrSpanner interface {
	Spanner
	SpanChr() string
}

type ChrStat ¶ added in v0.1.25

type ChrStat struct {
	Chr  string
	Stat float64
}

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 FaEnter ¶ added in v0.1.7

type FaEnter interface {
	FaHeader() string
	FaSeq() string
}

type FaEntry ¶

type FaEntry struct {
	Header string
	Seq    string
}

func ExtractOne ¶

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

func ToFaEntry ¶ added in v0.1.8

func ToFaEntry[F FaEnter](f F) FaEntry

func (FaEntry) FaHeader ¶ added in v0.1.7

func (f FaEntry) FaHeader() string

func (FaEntry) FaSeq ¶ added in v0.1.7

func (f FaEntry) FaSeq() string

type FaLen ¶

type FaLen struct {
	Name string
	Len  int64
}

func Chrlen ¶

func Chrlen[F FaEnter](f F) FaLen

func RevsortedLens ¶

func RevsortedLens(it iter.Seq2[FaLen, error]) ([]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.Seq2[FaLen, error]) (FaStats, error)

type Formatter ¶

type Formatter interface {
	Format(format string) string
}

type FqEnter ¶ added in v0.1.7

type FqEnter interface {
	FaEnter
	FqQual() string
}

type FqEntry ¶

type FqEntry struct {
	FaEntry
	Qual string
}

func ToFqEntry ¶ added in v0.1.8

func ToFqEntry[F FqEnter](f F) FqEntry

func (FqEntry) FqQual ¶ added in v0.1.7

func (f FqEntry) FqQual() string

type FullRpkmFlags ¶ added in v0.1.23

type FullRpkmFlags struct {
	BedPath       string
	TotalCoverage float64
}

type GffEnter ¶ added in v0.1.7

type GffEnter[AttT any] interface {
	GffHeader
	GffAttributes() AttT
}

type GffEntry ¶

type GffEntry[AttT any] struct {
	GffHead
	Attributes AttT
}

func ParseGffEntry ¶

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

func ToGffEntry ¶ added in v0.1.8

func ToGffEntry[G GffEnter[AttT], AttT any](g G) GffEntry[AttT]

func (GffEntry[T]) GffAttributes ¶ added in v0.1.7

func (g GffEntry[T]) GffAttributes() T

type GffHead ¶ added in v0.1.7

type GffHead struct {
	ChrSpan
	Source   string
	Type     string
	Score    float64
	HasScore bool
	Strand   byte
	Phase    int
	HasPhase bool
}

func ToGffHead ¶ added in v0.1.8

func ToGffHead[G GffHeader](g G) GffHead

func (GffHead) GffHasPhase ¶ added in v0.1.7

func (g GffHead) GffHasPhase() bool

func (GffHead) GffHasScore ¶ added in v0.1.7

func (g GffHead) GffHasScore() bool

func (GffHead) GffPhase ¶ added in v0.1.7

func (g GffHead) GffPhase() int

func (GffHead) GffScore ¶ added in v0.1.7

func (g GffHead) GffScore() float64

func (GffHead) GffSource ¶ added in v0.1.7

func (g GffHead) GffSource() string

func (GffHead) GffStrand ¶ added in v0.1.7

func (g GffHead) GffStrand() byte

func (GffHead) GffType ¶ added in v0.1.7

func (g GffHead) GffType() string

type GffHeader ¶ added in v0.1.7

type GffHeader interface {
	ChrSpanner
	GffSource() string
	GffType() string
	GffScore() float64
	GffHasScore() bool
	GffStrand() byte
	GffPhase() int
	GffHasPhase() bool
}

type InfoPair ¶

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

type Kmer ¶

type Kmer struct {
	Seq   string
	Count int64
}

type Newick ¶ added in v0.1.18

type Newick struct {
	Name     string
	Length   float64
	Children []*Newick
}

func ParseNewick ¶ added in v0.1.18

func ParseNewick(r io.Reader) (*Newick, error)

func (*Newick) String ¶ added in v0.1.18

func (n *Newick) String() string

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[V VcfHeader] struct {
	RefName    string
	CrossNames []string
	M          map[ChrSpan]map[string]V
}

func NucdiffReadVcfs ¶

func NucdiffReadVcfs(refname string, crossnames []string, paths []string) (*NucdiffVcfData[VcfEntry[struct{}]], error)

type NucdiffVcfPair ¶

type NucdiffVcfPair struct {
	Name string
	Path string
}

func ReadNucdiffVcfPairs ¶

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

type OkTuple2 ¶ added in v0.1.13

type OkTuple2[T, U any] struct {
	Tuple2[T, U]
	Ok bool
}

type SamAlignment ¶ added in v0.1.18

type SamAlignment struct {
	Qname string
	Flag  uint16
	Rname string
	Pos   int64
	Mapq  int64
	CIGAR string
	Rnext string
	Pnext int64
	Tlen  int64
	Seq   string
	Qual  string
}

func ParseSamAlignment ¶ added in v0.1.18

func ParseSamAlignment(line []string) (SamAlignment, error)

type SamEntry ¶ added in v0.1.18

type SamEntry struct {
	IsHeader bool
	Header   string
	SamAlignment
	Optional []SamOptional
}

func ParseSamEntry ¶ added in v0.1.18

func ParseSamEntry(s string) (SamEntry, error)

func ParseSamHeading ¶ added in v0.1.18

func ParseSamHeading(s string) SamEntry

type SamOptional ¶ added in v0.1.18

type SamOptional struct {
	Tag          [2]byte
	Type         byte
	Char         byte
	Int          int64
	Float        float64
	String       string
	ByteArray    []byte
	NumArrayType byte
	IntArray     []int64
	FloatArray   []float64
}

func ParseSamOptional ¶ added in v0.1.18

func ParseSamOptional(s string) (SamOptional, error)

func ParseSamOptionals ¶ added in v0.1.18

func ParseSamOptionals(s string) ([]SamOptional, error)

type SampleSet ¶

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

type Span ¶

type Span struct {
	Start int64
	End   int64
}

func ToSpan ¶ added in v0.1.8

func ToSpan[S Spanner](s S) Span

func (Span) SpanEnd ¶ added in v0.1.7

func (s Span) SpanEnd() int64

func (Span) SpanStart ¶ added in v0.1.7

func (s Span) SpanStart() int64

type Spanner ¶ added in v0.1.7

type Spanner interface {
	SpanStart() int64
	SpanEnd() 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 Tuple2 ¶ added in v0.1.13

type Tuple2[T, U any] struct {
	V1 T
	V2 U
}

type VcfEnter ¶ added in v0.1.7

type VcfEnter[T any] interface {
	VcfHeader
	VcfInfoAndSamples() T
}

type VcfEntry ¶

type VcfEntry[T any] struct {
	VcfHead
	InfoAndSamples T
}

func MergeNucdiffVcfEntries ¶

func MergeNucdiffVcfEntries[V VcfHeader](d *NucdiffVcfData[V], 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)

func ToVcfEntry ¶ added in v0.1.8

func ToVcfEntry[V VcfEnter[T], T any](v V) VcfEntry[T]

func (VcfEntry[T]) VcfInfoAndSamples ¶ added in v0.1.7

func (v VcfEntry[T]) VcfInfoAndSamples() T

type VcfHead ¶ added in v0.1.7

type VcfHead struct {
	ChrSpan
	ID     string
	Ref    string
	Alts   []string
	Qual   float64
	Filter string
}

func ParseVcfHead ¶ added in v0.1.10

func ParseVcfHead(line []string) (VcfHead, error)

func ToVcfHead ¶ added in v0.1.8

func ToVcfHead[V VcfHeader](v V) VcfHead

func (VcfHead) VcfAlts ¶ added in v0.1.7

func (v VcfHead) VcfAlts() []string

func (VcfHead) VcfFilter ¶ added in v0.1.7

func (v VcfHead) VcfFilter() string

func (VcfHead) VcfID ¶ added in v0.1.7

func (v VcfHead) VcfID() string

func (VcfHead) VcfQual ¶ added in v0.1.7

func (v VcfHead) VcfQual() float64

func (VcfHead) VcfRef ¶ added in v0.1.7

func (v VcfHead) VcfRef() string

type VcfHeader ¶ added in v0.1.7

type VcfHeader interface {
	ChrSpanner
	VcfID() string
	VcfRef() string
	VcfAlts() []string
	VcfQual() float64
	VcfFilter() string
}

type VcfInfoSamples ¶ added in v0.1.23

type VcfInfoSamples struct {
	InfoKeys []string
	InfoVals []string
	Format   []string
	Samples  [][]string
}

func ParseVcfInfoSamples ¶ added in v0.1.23

func ParseVcfInfoSamples(line []string) (VcfInfoSamples, error)

type WinAvgSortedBedFlags ¶ added in v0.1.13

type WinAvgSortedBedFlags struct {
	WinSize int
	WinStep int
}

type WinSumSortedBedFlags ¶ added in v0.1.18

type WinSumSortedBedFlags struct {
	WinSize int
	WinStep int
	PerBp   bool
}

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