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bed2x

package module

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Versions in this module

v0

v0.0.6

Jul 6, 2020

v0.0.3

Jun 23, 2020

Changes in this version

+ func ChromSizes(genome string) error

+ func CigarToCoords(cigar sam.Cigar, offset int) ([]int, []int)

type Bed12

+ func SamRecordToBed12(s *sam.Record) *Bed12

+ type Bed3 interface

+ Chr func() string

+ End func() int

+ Start func() int

type Bed3i

+ func ParseRegion(s string) (Bed3i, bool)

+ type Bed4 struct

+ func (b Bed4) Chr() string

+ func (b Bed4) End() int

+ func (b Bed4) Id() string

+ func (b Bed4) Start() int

+ type BedI interface

+ Chr func() string

+ type BinIndex map[int][]NamedRangeI

+ type BinIndexMap struct

+ Data map[string]BinIndex

+ func NewBinIndexMap() *BinIndexMap

+ func (c *BinIndexMap) Insert(b NamedBedI) error

+ func (c *BinIndexMap) Load(b []NamedBedI) error

+ func (d *BinIndexMap) Delete(b NamedBedI) error

+ func (d *BinIndexMap) Query(b BedI) (<-chan NamedRangeI, error)

+ func (d *BinIndexMap) QueryRegion(chr string, start int, end int) (<-chan NamedRangeI, error)

+ type Db struct

+ func NewDb() Db

+ func (db Db) Get(id string) (Bed6i, error)

+ func (db Db) Load(fn string) error

+ func (db Db) Query(chr string, start int, end int) (<-chan Bed6i, error)

+ type NamedBedI interface

+ Id func() string

+ type NamedRangeI interface

+ Id func() string

+ type RangeI interface

+ End func() int

+ Start func() int

v0.0.1

Dec 12, 2017

Changes in this version

+ func IterBed12(fn string) (<-chan *Bed12, error)

+ func IterBed6(fn string) (<-chan *Bed6, error)

+ func IterBedLines(fn string) (<-chan string, error)

+ func RC(s string) string

+ type Bed12 struct

+ func ParseBed12(line string) (*Bed12, error)

+ func (b *Bed12) BlockCount() int

+ func (b *Bed12) BlockSizes() []int

+ func (b *Bed12) BlockStarts() []int

+ func (b *Bed12) CDS() (*Bed12, error)

+ func (b *Bed12) Chr() string

+ func (b *Bed12) End() int

+ func (b *Bed12) Exons() ([]*Bed6, error)

+ func (b *Bed12) Id() string

+ func (b *Bed12) Introns() ([]*Bed6, error)

+ func (b *Bed12) ItemRgb() string

+ func (b *Bed12) Score() float64

+ func (b *Bed12) Start() int

+ func (b *Bed12) Strand() string

+ func (b *Bed12) String() string

+ func (b *Bed12) ThickEnd() int

+ func (b *Bed12) ThickStart() int

+ func (b *Bed12) UTR3() (*Bed12, error)

+ func (b *Bed12) UTR5() (*Bed12, error)

+ type Bed3i interface

+ Chr func() string

+ End func() int

+ Start func() int

+ type Bed6 struct

+ func Downstream(b Bed6i, bp int) (*Bed6, error)

+ func ParseBed6(line string) (*Bed6, error)

+ func Promoter(b Bed6i, up int, down int) (*Bed6, error)

+ func Tss(b Bed6i) (*Bed6, error)

+ func Tts(b Bed6i) (*Bed6, error)

+ func Upstream(b Bed6i, bp int) (*Bed6, error)

+ func (b *Bed6) Chr() string

+ func (b *Bed6) End() int

+ func (b *Bed6) Exons() ([]*Bed6, error)

+ func (b *Bed6) Id() string

+ func (b *Bed6) Score() float64

+ func (b *Bed6) Start() int

+ func (b *Bed6) Strand() string

+ func (b *Bed6) String() string

+ type Bed6i interface

+ Id func() string

+ Score func() float64

+ Strand func() string