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treat

package module

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Versions in this module

v0

v0.0.4

Aug 21, 2019

v0.0.3

Jan 26, 2017

Changes in this version

type AlignmentKey

+ KnockDown string

+ Replicate int

+ Tetracycline bool

type Template

+ func (tmpl *Template) SetOffset(offset int)

v0.0.2

Jan 6, 2016

Changes in this version

type Fragment

+ func (f *Fragment) DecodeMsgpack(dec *msgpack.Decoder) error

+ func (f *Fragment) EncodeMsgpack(enc *msgpack.Encoder) error

+ func (f *Fragment) Len() int

type Template

+ EditOffset uint32

+ func (tmpl *Template) IndexLabel(i int) int

v0.0.1

Nov 4, 2015

Changes in this version

+ var BASE_COMP = map[byte]byte

+ type Alignment struct

+ AltEditing uint8

+ EditStop uint32

+ HasMutation uint8

+ Id uint64

+ Indel uint8

+ JuncEnd uint32

+ JuncLen uint32

+ JuncSeq string

+ JuncStart uint32

+ Key *AlignmentKey

+ Mismatches uint8

+ Norm float64

+ ReadCount uint32

+ func NewAlignment(frag *Fragment, template *Template, excludeSnps bool) *Alignment

+ func (a *Alignment) MarshalBinary() ([]byte, error)

+ func (a *Alignment) SimpleAlign(f1, f2 *Fragment) (string, string)

+ func (a *Alignment) UnmarshalBinary(buf []byte) error

+ func (a *Alignment) WriteTo(w io.Writer, frag *Fragment, template *Template, tw int) error

+ type AlignmentKey struct

+ Gene string

+ Sample string

+ func (k *AlignmentKey) MarshalBinary() ([]byte, error)

+ func (k *AlignmentKey) UnmarshalBinary(data []byte) error

+ type AltRegion struct

+ End int

+ Start int

+ type BaseCountType uint32

+ type Fragment struct

+ Bases string

+ EditBase rune

+ EditSite []BaseCountType

+ Name string

+ Norm float64

+ ReadCount uint32

+ func NewFragment(name, seq string, orientation OrientationType, reads uint32, norm float64, ...) *Fragment

+ func (f *Fragment) MarshalBytes() ([]byte, error)

+ func (f *Fragment) String() string

+ func (f *Fragment) StripPrimer(primer5, primer3 int) (string, error)

+ func (f *Fragment) ToFasta() string

+ func (f *Fragment) UnmarshalBytes(data []byte) error

+ type OrientationType int8

+ const FORWARD

+ const REVERSE

+ type Template struct

+ AltRegion []*AltRegion

+ BaseIndex []uint32

+ Bases string

+ EditBase rune

+ EditSite [][]BaseCountType

+ EditStop uint32

+ Primer3 int

+ Primer5 int

+ func NewTemplate(full, pre *Fragment, alt []*Fragment, altRegion []*AltRegion) (*Template, error)

+ func NewTemplateFromFasta(path string, orientation OrientationType, base rune) (*Template, error)

+ func (tmpl *Template) Len() int

+ func (tmpl *Template) MarshalBytes() ([]byte, error)

+ func (tmpl *Template) Max(i int) BaseCountType

+ func (tmpl *Template) SetPrimer3(primer string) error

+ func (tmpl *Template) SetPrimer5(primer string) error

+ func (tmpl *Template) Size() int

+ func (tmpl *Template) String() string

+ func (tmpl *Template) UnmarshalBytes(data []byte) error