svync_api

Documentation

Index

• func Execute(Cctx *cli.Context, config *Config)
• func ResolveValue(input string, variant *Variant, format *VariantFormat, Cctx *cli.Context) string
• type Config
  • func ReadConfig(Cctx *cli.Context) *Config
• type ConfigInput
• type Header
• type HeaderLineIdDescription
• type HeaderLineIdLength
• type HeaderLineIdNumberTypeDescription
• type MapConfigInput
• type Variant
  • func (v *Variant) String(config *Config) string
• type VariantFormat

Functions

func Execute

func Execute(Cctx *cli.Context, config *Config)

Read the VCF file and return it as a VCF struct

func ResolveValue

func ResolveValue(input string, variant *Variant, format *VariantFormat, Cctx *cli.Context) string

Resolve a value

Types

type Config

type Config struct {
	Id     string
	Alt    map[string]string
	Info   MapConfigInput
	Format MapConfigInput
}

func ReadConfig

func ReadConfig(Cctx *cli.Context) *Config

Read the configuration file, cast it to its struct and validate

type ConfigInput

type ConfigInput struct {
	Value       string
	Description string
	Number      string
	Type        string
	Alts        map[string]string
}

type Header

type Header struct {
	Info    map[string]HeaderLineIdNumberTypeDescription
	Format  map[string]HeaderLineIdNumberTypeDescription
	Alt     map[string]HeaderLineIdDescription
	Filter  map[string]HeaderLineIdDescription
	Contig  []HeaderLineIdLength
	Other   []string
	Samples []string
}

type HeaderLineIdDescription

type HeaderLineIdDescription struct {
	Id          string
	Description string
}

type HeaderLineIdLength

type HeaderLineIdLength struct {
	Id     string
	Length int64
}

type HeaderLineIdNumberTypeDescription

type HeaderLineIdNumberTypeDescription struct {
	Id          string
	Number      string
	Type        string
	Description string
}

type MapConfigInput

type MapConfigInput map[string]ConfigInput

type Variant

type Variant struct {
	Chromosome string
	Pos        int64
	Id         string
	Ref        string
	Alt        string
	Qual       string
	Filter     string
	Header     *Header
	Info       map[string][]string
	Format     map[string]VariantFormat
	Parsed     bool
}

func (*Variant) String

func (v *Variant) String(config *Config) string

Convert a variant to a string

type VariantFormat

type VariantFormat struct {
	Sample  string
	Content map[string][]string
}