db

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v0.8.29 Latest Latest Go to latest Published: Oct 30, 2022 License: MIT Imports: 12 Imported by: 0

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Valid go.mod file
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Repository

github.com/tikz/bcov

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Documentation ¶

Index ¶

Variables
func ConnectDB()
func ConnectPostgres()
func ConnectSQLite()
func StoreExons(geneID uint, exons []ensembl.Exon)
func StoreFile(file string, hash string, kitID uint, size int64) (bamFileID uint, created bool)
func StoreGene(hgncAccession string, geneAccession string, name string, description string, ...) (geneID uint, created bool)
func StoreKit(name string) (kitID uint, created bool)
func StoreSynonyms(geneID uint, synonyms []ensembl.Synonym) (created bool)
func StoreVariant(allele clinvar.Allele, exonId uint) (variantID uint)
type BAMFile
type Coverage
type Depth
type DepthCoverage
type Exon
- func GetExons() []Exon
type ExonDepthCoverage
type ExonReadCount
type Gene
type GeneSynonym
type Kit
type ReadCount
type Variant

Constants ¶

This section is empty.

Variables ¶

View Source

var DB *gorm.DB

Functions ¶

func ConnectDB ¶

func ConnectDB()

ConnectDB handles the connection and migrations depending on the configured database engine.

func ConnectPostgres ¶

func ConnectPostgres()

TODO: DELETE THIS feature<<<<<, change to MySQL for compatibility with already written manual queries

func ConnectSQLite ¶

func ConnectSQLite()

ConnectSQLite manages the creation and connection to a local SQLite file. Includes extra PRAGMA statements and settings for improved write performance.

func StoreExons ¶

func StoreExons(geneID uint, exons []ensembl.Exon)

StoreExons stores in the database a record for a gene exon

func StoreFile ¶

func StoreFile(file string, hash string, kitID uint, size int64) (bamFileID uint, created bool)

StoreFile stores in the database an associated record to an original BAM file source

func StoreGene ¶

func StoreGene(hgncAccession string, geneAccession string, name string, description string, transcriptAccession string) (geneID uint, created bool)

StoreGene stores in the database a record for a gene

func StoreKit ¶

func StoreKit(name string) (kitID uint, created bool)

StoreKit stores in the database a commercial exon capture kit name and associated details

func StoreSynonyms ¶

func StoreSynonyms(geneID uint, synonyms []ensembl.Synonym) (created bool)

StoreSynonyms stores in the database a record for a gene synonym mapping

func StoreVariant ¶

func StoreVariant(allele clinvar.Allele, exonId uint) (variantID uint)

StoreExons stores in the database a single variant (rs) from ClinVar

Types ¶

type BAMFile ¶

type BAMFile struct {
	ID                 uint                `gorm:"primarykey"`
	SHA256Sum          string              `gorm:"uniqueIndex"`
	Size               uint64              `json:"size"`
	Name               string              `json:"name"`
	KitID              uint                `json:"-"`
	ExonDepthCoverages []ExonDepthCoverage `gorm:"constraint:OnDelete:CASCADE;" json:"-"`
}

type Coverage ¶

type Coverage float64

type Depth ¶

type Depth uint8

type DepthCoverage ¶

type DepthCoverage struct {
	ID                  uint  `gorm:"primarykey" json:"-"`
	ExonDepthCoverageID uint  `gorm:"index" json:"-"`
	Depth               uint8 `json:"depth"`
	Coverage            uint8 `json:"coverage"`
}

type Exon ¶

type Exon struct {
	ID                 uint                `gorm:"primarykey" json:"id"`
	GeneID             uint                `json:"-"`
	Strand             int                 `json:"strand"`
	Chromosome         string              `gorm:"index" json:"chromosome"`
	Start              uint64              `gorm:"index" json:"start"`
	End                uint64              `json:"end"`
	ExonNumber         uint                `json:"exonNumber"`
	ExonDepthCoverages []ExonDepthCoverage `json:"-"`
	Variants           []Variant           `json:"-"`
}

func GetExons ¶

func GetExons() []Exon

GetExons returns a slice of all exons in the database

type ExonDepthCoverage ¶

type ExonDepthCoverage struct {
	ID             uint            `gorm:"primarykey" json:"-"`
	ExonID         uint            `gorm:"index" json:"-"`
	BAMFileID      uint            `gorm:"index" json:"-"`
	BAMFile        BAMFile         `json:"bamFile"`
	DepthCoverages []DepthCoverage `gorm:"constraint:OnDelete:CASCADE;" json:"depthCoverages"`
}

type ExonReadCount ¶

type ExonReadCount struct {
	ID         uint        `gorm:"primarykey" json:"-"`
	ExonID     uint        `gorm:"index" json:"-"`
	BAMFileID  uint        `gorm:"index" json:"-"`
	BAMFile    BAMFile     `json:"bamFile"`
	ReadCounts []ReadCount `gorm:"constraint:OnDelete:CASCADE;" json:"readCounts"`
}

type Gene ¶

type Gene struct {
	ID                  uint          `gorm:"primarykey" json:"id"`
	HGNCAccession       string        `gorm:"unique" json:"hgncAccession"`
	GeneAccession       string        `gorm:"uniqueIndex" json:"geneAccession"`
	Name                string        `gorm:"uniqueIndex" json:"name"`
	Description         string        `json:"description"`
	TranscriptAccession string        `json:"transcriptAccession"`
	Exons               []Exon        `json:"exons"`
	GeneSynonyms        []GeneSynonym `json:"synonyms"`
}

type GeneSynonym ¶

type GeneSynonym struct {
	ID      uint   `gorm:"primarykey" json:"id"`
	GeneID  uint   `json:"-"`
	Synonym string `json:"synonym"`
}

type Kit ¶

type Kit struct {
	ID       uint      `gorm:"primarykey" json:"id"`
	Name     string    `json:"name"`
	BAMFiles []BAMFile `json:"-"`
}

type ReadCount ¶

type ReadCount struct {
	ID              uint   `gorm:"primarykey" json:"-"`
	ExonReadCountID uint   `gorm:"index" json:"-"`
	Position        uint64 `json:"depth"`
	Count           uint64 `json:"coverage"`
}

type Variant ¶

type Variant struct {
	ID            uint   `gorm:"primarykey" json:"-"`
	VariantID     string `gorm:"uniqueIndex" json:"variantId"`
	Name          string `json:"-"`
	ClinSig       string `json:"clinSig"`
	ClinSigSimple int    `json:"-"`
	ProteinChange string `json:"-"`
	ReviewStatus  string `json:"-"`
	Phenotypes    string `json:"-"`
	Chromosome    string `gorm:"index" json:"chromosome"`
	Start         uint64 `gorm:"index" json:"start"`
	End           uint64 `gorm:"index" json:"end"`
	ExonID        uint   `gorm:"index" json:"exonId"`
}

Source Files ¶

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