genobase

package module

v0.8.3 Latest Latest Go to latest Published: Jan 10, 2024 License: MPL-2.0 Imports: 10 Imported by: 2

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A human genomics reference DB.

This section is empty.

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func NoSync(connStr string) string

NoSync disables flushing the database to disk after each write. This is unsafe, but significantly speeds up bulk imports.

func ReadOnly(connStr string) string

ReadOnly makes the database read-only (allowing for multiple concurrent readers).

type DB struct {
	// contains filtered or unexported fields
}

func Open(ctx context.Context, logger *slog.Logger, dbPath string, opts ...Option) (*DB, error)

Open opens a database connection and applies any necessary migrations.

func (db *DB) Close() error

func (db *DB) GetAlignment(ctx context.Context, chainID, refOffset int64) (*types.Alignment, error)

func (db *DB) GetAllele(ctx context.Context, id int64, reference, alternate string, ancestry types.AncestryGroup) (*types.Allele, error)

func (db *DB) GetAlleles(ctx context.Context, id int64) ([]types.Allele, error)

func (db *DB) GetChain(ctx context.Context, from types.Reference, chromosome types.Chromosome, position int64) (*types.Chain, error)

func (db *DB) GetVariant(ctx context.Context, id int64) (*types.Variant, error)

func (db *DB) GetVariants(ctx context.Context, chromosome types.Chromosome, position int64) ([]types.Variant, error)

func (db *DB) KnownAlleles(ctx context.Context) (map[int64]bool, error)

func (db *DB) StoreAlignments(ctx context.Context, chainID int64, alignments []types.Alignment) error

func (db *DB) StoreAlleles(ctx context.Context, alleles []types.Allele) error

func (db *DB) StoreChain(ctx context.Context, from types.Reference, chain *types.Chain) (int64, error)

func (db *DB) StoreVariants(ctx context.Context, variants []types.Variant) error

type Option func(string) string

Path	Synopsis
types