prepfa

package

v0.1.1 Latest Latest Go to latest Published: Jul 3, 2024 License: AGPL-3.0 Imports: 20 Imported by: 0

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Valid go.mod file
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Stable version
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Repository

github.com/jgbaldwinbrown/pairviz

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Documentation ¶

Index ¶

func AddErr[T any](it iter.Seq[T]) iter.Seq2[T, error]
func AppendSplit(out []string, s string, sep string) []string
func AppendString(buf []byte, s string) []byte
func BedSet[T any](it iter.Seq2[fastats.BedEntry[T], error]) map[string]int
func CatPath(w io.Writer, path string) error
func CatPaths(out string, paths ...string) error
func ChrSpanEq(cs1, cs2 fastats.ChrSpan) bool
func ChrSpanLess(cs1, cs2 fastats.ChrSpan) bool
func Cleanup(f CleanupFlags) error
func CleanupCtx(ctx context.Context, arg Args, i int) error
func CollectBedWithHeader(path string) ([]fastats.BedEntry[[]string], error)
func CollectErr[T any](it iter.Seq2[T, error]) ([]T, error)
func CollectFa(path string) ([]fastats.FaEntry, error)
func CollectVCF(path string, cols ...int) (names []string, vcf []fastats.VcfEntry[[]string], err error)
func FaChrSpanSet(it iter.Seq2[fastats.FaEntry, error]) (map[string]int, error)
func FaFixedWins(fa []fastats.FaEntry, wins iter.Seq2[fastats.ChrSpan, error]) iter.Seq2[fastats.FaEntry, error]
func FaPosLess(f1, f2 fastats.FaEntry) bool
func FilterChrParent[T any](parent string, it iter.Seq2[fastats.BedEntry[T], error]) iter.Seq2[fastats.BedEntry[T], error]
func GetFaChrSpan(f fastats.FaEntry) (fastats.ChrSpan, error)
func Join(ctx context.Context, args Args) error
func KeepBedMatches[T any](css map[string]int, it iter.Seq2[fastats.BedEntry[T], error]) iter.Seq2[fastats.BedEntry[T], error]
func KeepFaMatches(css map[string]int, it iter.Seq2[fastats.FaEntry, error]) iter.Seq2[fastats.FaEntry, error]
func MakeWins(fa []fastats.FaEntry, coords []CoordsPair, size int, step int, width int) iter.Seq2[fastats.ChrSpan, error]
func PrepFa(f PrepFaFlags) error
func PrepareCtx(ctx context.Context, arg Args, i int) error
func ReadGenos(line []string) ([]string, error)
func ReadVCF(r io.Reader) (names []string, it iter.Seq2[fastats.VcfEntry[[]string], error], err error)
func ReadWinBed(r io.Reader) iter.Seq2[fastats.ChrSpan, error]
func RunCleanup()
func RunPrepAndClean()
func RunPrepFa()
func RunSeparate(ctx context.Context, arg Args, i int) error
func RunSeparates(ctx context.Context, args Args) error
func SliceIter[S ~[]T, T any](s S) iter.Seq[T]
func SortBed[T any](bed []fastats.BedEntry[T])
func SortFa(fa []fastats.FaEntry)
func StartSignalhandler(closef func()) (endf func())
func StripChrParent[T any](it iter.Seq2[fastats.BedEntry[T], error]) iter.Seq2[fastats.BedEntry[T], error]
func SubsetVCFCols(it iter.Seq2[fastats.VcfEntry[[]string], error], cols ...int) iter.Seq2[fastats.VcfEntry[[]string], error]
func TensorflowPredict(ctx context.Context, w io.Writer, f TensorflowFlags) error
func WriteBed(path string, bed iter.Seq2[fastats.BedEntry[[]string], error]) error
func WriteCoords(path string, it iter.Seq2[CoordsPair, error]) error
func WriteFasta(path string, it iter.Seq2[fastats.FaEntry, error]) error
type Args
- func GetArgs(r io.Reader) (Args, error)
- func (a Args) CrossCleanupFlags(i int) CleanupFlags
- func (a Args) CrossPrepFlags(i int) PrepFaFlags
- func (a Args) TensorflowArgs() TensorflowFlags
type CleanupFlags
- func GetCleanupFlags() (CleanupFlags, error)
type CoordsPair
- func BuildChr(entry fastats.FaEntry, vcf []fastats.VcfEntry[[]string]) (fa1, fa2 fastats.FaEntry, coord1, coord2 []CoordsPair)
- func BuildFas(fa []fastats.FaEntry, vcf []fastats.VcfEntry[[]string]) (fa1, fa2 []fastats.FaEntry, coords1, coords2 []CoordsPair)
type CrossArgs
type FullFlags
type PrepFaFlags
- func GetPrepFaFlags() (PrepFaFlags, error)
type StripNaNsOut
- func StripNaNs(col int, bed []fastats.BedEntry[[]string], fa1, fa2 []fastats.FaEntry) (StripNaNsOut, error)
type TensorflowFlags

Constants ¶

This section is empty.

Variables ¶

This section is empty.

Functions ¶

func AddErr ¶

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

func AppendSplit ¶

func AppendSplit(out []string, s string, sep string) []string

func AppendString ¶

func AppendString(buf []byte, s string) []byte

func BedSet ¶

func BedSet[T any](it iter.Seq2[fastats.BedEntry[T], error]) map[string]int

func CatPath ¶

func CatPath(w io.Writer, path string) error

func CatPaths ¶

func CatPaths(out string, paths ...string) error

func ChrSpanEq ¶

func ChrSpanEq(cs1, cs2 fastats.ChrSpan) bool

func ChrSpanLess ¶

func ChrSpanLess(cs1, cs2 fastats.ChrSpan) bool

func Cleanup ¶

func Cleanup(f CleanupFlags) error

func CleanupCtx ¶

func CleanupCtx(ctx context.Context, arg Args, i int) error

func CollectBedWithHeader ¶

func CollectBedWithHeader(path string) ([]fastats.BedEntry[[]string], error)

func CollectErr ¶

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

func CollectFa ¶

func CollectFa(path string) ([]fastats.FaEntry, error)

func CollectVCF ¶

func CollectVCF(path string, cols ...int) (names []string, vcf []fastats.VcfEntry[[]string], err error)

func FaChrSpanSet ¶

func FaChrSpanSet(it iter.Seq2[fastats.FaEntry, error]) (map[string]int, error)

func FaFixedWins ¶

func FaFixedWins(fa []fastats.FaEntry, wins iter.Seq2[fastats.ChrSpan, error]) iter.Seq2[fastats.FaEntry, error]

func FaPosLess ¶

func FaPosLess(f1, f2 fastats.FaEntry) bool

func FilterChrParent ¶

func FilterChrParent[T any](parent string, it iter.Seq2[fastats.BedEntry[T], error]) iter.Seq2[fastats.BedEntry[T], error]

func GetFaChrSpan ¶

func GetFaChrSpan(f fastats.FaEntry) (fastats.ChrSpan, error)

func Join ¶

func Join(ctx context.Context, args Args) error

func KeepBedMatches ¶

func KeepBedMatches[T any](css map[string]int, it iter.Seq2[fastats.BedEntry[T], error]) iter.Seq2[fastats.BedEntry[T], error]

func KeepFaMatches ¶

func KeepFaMatches(css map[string]int, it iter.Seq2[fastats.FaEntry, error]) iter.Seq2[fastats.FaEntry, error]

func MakeWins ¶

func MakeWins(fa []fastats.FaEntry, coords []CoordsPair, size int, step int, width int) iter.Seq2[fastats.ChrSpan, error]

func PrepFa ¶

func PrepFa(f PrepFaFlags) error

func PrepareCtx ¶

func PrepareCtx(ctx context.Context, arg Args, i int) error

func ReadGenos ¶

func ReadGenos(line []string) ([]string, error)

func ReadVCF ¶

func ReadVCF(r io.Reader) (names []string, it iter.Seq2[fastats.VcfEntry[[]string], error], err error)

func ReadWinBed ¶

func ReadWinBed(r io.Reader) iter.Seq2[fastats.ChrSpan, error]

func RunCleanup ¶

func RunCleanup()

func RunPrepAndClean ¶

func RunPrepAndClean()

func RunPrepFa ¶

func RunPrepFa()

func RunSeparate ¶

func RunSeparate(ctx context.Context, arg Args, i int) error

func RunSeparates ¶

func RunSeparates(ctx context.Context, args Args) error

func SliceIter ¶

func SliceIter[S ~[]T, T any](s S) iter.Seq[T]

func SortBed ¶

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

func SortFa ¶

func SortFa(fa []fastats.FaEntry)

func StartSignalhandler ¶

func StartSignalhandler(closef func()) (endf func())

func StripChrParent ¶

func StripChrParent[T any](it iter.Seq2[fastats.BedEntry[T], error]) iter.Seq2[fastats.BedEntry[T], error]

func SubsetVCFCols ¶

func SubsetVCFCols(it iter.Seq2[fastats.VcfEntry[[]string], error], cols ...int) iter.Seq2[fastats.VcfEntry[[]string], error]

func TensorflowPredict ¶

func TensorflowPredict(ctx context.Context, w io.Writer, f TensorflowFlags) error

func WriteBed ¶

func WriteBed(path string, bed iter.Seq2[fastats.BedEntry[[]string], error]) error

func WriteCoords ¶

func WriteCoords(path string, it iter.Seq2[CoordsPair, error]) error

func WriteFasta ¶

func WriteFasta(path string, it iter.Seq2[fastats.FaEntry, error]) error

Types ¶

type Args ¶

type Args struct {
	Crosses []CrossArgs
	Size    int
	Step    int
	Width   int
	Outpre  string
	Threads int
	Paircol int
	Prepare bool
	Cleanup bool
	Combine bool
	Predict bool
}

func GetArgs ¶

func GetArgs(r io.Reader) (Args, error)

func (Args) CrossCleanupFlags ¶

func (a Args) CrossCleanupFlags(i int) CleanupFlags

func (Args) CrossPrepFlags ¶

func (a Args) CrossPrepFlags(i int) PrepFaFlags

func (Args) TensorflowArgs ¶

func (a Args) TensorflowArgs() TensorflowFlags

type CleanupFlags ¶

type CleanupFlags struct {
	Fa1     string
	Fa2     string
	Bed     string
	Outpre  string
	Parent  string
	Paircol int
}

func GetCleanupFlags ¶

func GetCleanupFlags() (CleanupFlags, error)

type CoordsPair ¶

type CoordsPair struct {
	Original fastats.ChrSpan
	New      fastats.ChrSpan
}

func BuildChr ¶

func BuildChr(entry fastats.FaEntry, vcf []fastats.VcfEntry[[]string]) (fa1, fa2 fastats.FaEntry, coord1, coord2 []CoordsPair)

func BuildFas ¶

func BuildFas(fa []fastats.FaEntry, vcf []fastats.VcfEntry[[]string]) (fa1, fa2 []fastats.FaEntry, coords1, coords2 []CoordsPair)

type CrossArgs ¶

type CrossArgs struct {
	Fa     string
	Vcf    string
	Bed    string
	C0     int
	C1     int
	Parent string
}

type FullFlags ¶

type FullFlags struct {
	NoPrepare   bool
	NoCleanup   bool
	NoPredict   bool
	NoCombine   bool
	PredictOnly bool
}

type PrepFaFlags ¶

type PrepFaFlags struct {
	Fa     string
	Vcf    string
	C0     int
	C1     int
	Size   int
	Step   int
	Width  int
	Outpre string
}

func GetPrepFaFlags ¶

func GetPrepFaFlags() (PrepFaFlags, error)

type StripNaNsOut ¶

type StripNaNsOut struct {
	Bed []fastats.BedEntry[[]string]
	Fa1 []fastats.FaEntry
	Fa2 []fastats.FaEntry
}

func StripNaNs ¶

func StripNaNs(col int, bed []fastats.BedEntry[[]string], fa1, fa2 []fastats.FaEntry) (StripNaNsOut, error)

type TensorflowFlags ¶

type TensorflowFlags struct {
	Fa1     string
	Fa2     string
	Bed     string
	Paircol int
	Width   int
}

Source Files ¶

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