bgen

type Allele string

type BGEN struct {
	FilePath         string                  // TODO: Make private, expose fully resolved path by method?
	File             genomisc.ReaderAtCloser // TODO: Make private, expose by method (if at all)?
	NVariants        uint32                  // TODO: Make private, expose by method?
	NSamples         uint32                  // TODO: Make private, expose by method?
	FlagCompression  Compression
	FlagLayout       Layout
	FlagHasSampleIDs bool
	SamplesStart     uint32 // TODO: Make private, expose by method (if at all)?
	VariantsStart    uint32 // TODO: Make private, expose by method (if at all)?
}

type BGIIndex struct {
	DB       *sqlx.DB
	Metadata *BGIMetadata
}

type BGIMetadata struct {
	Filename           string
	FileSize           uint   `db:"file_size"`
	LastWriteTime      Time   `db:"last_write_time"`
	FirstThousandBytes []byte `db:"first_1000_bytes"`
	IndexCreationTime  Time   `db:"index_creation_time"`
}

type Compression uint32

type Layout uint32

type Sample struct {
	SampleID string
}

type SampleProbability struct {
	Missing       bool
	Ploidy        uint8 // Limited to 0-63
	Probabilities []float64
}

type Time time.Time

type Variant struct {
	// Set up front
	ID         string
	RSID       string
	Chromosome string
	Position   uint32
	NSamples   uint32 // Populated only in Layout1
	NAlleles   uint16
	Alleles    []Allele

	// Conditional based on Layout
	MinimumPloidy       uint8
	MaximumPloidy       uint8
	Phased              bool
	NProbabilityBits    uint8
	SampleProbabilities []SampleProbability
}

type VariantIndex struct {
	Chromosome        string
	Position          uint32
	RSID              string `db:"rsid"`
	NAlleles          uint16 `db:"number_of_alleles"`
	Allele1           Allele
	Allele2           Allele
	FileStartPosition uint `db:"file_start_position"`
	SizeInBytes       uint `db:"size_in_bytes"`
}

type VariantReader struct {
	VariantsSeen uint32
	// contains filtered or unexported fields
}