api

package

v0.8.29 Latest Latest Go to latest Published: Oct 30, 2022 License: MIT Imports: 15 Imported by: 0

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Valid go.mod file
Redistributable license
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Stable version
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Repository

github.com/tikz/bcov

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Documentation ¶

Constants ¶

This section is empty.

Variables ¶

This section is empty.

Functions ¶

func BAMsEndpoint ¶

func BAMsEndpoint(c *gin.Context)

BAMsEndpoint returns all loaded BAM files for a given kit ID

func DepthCoveragesEndpoint ¶

func DepthCoveragesEndpoint(c *gin.Context)

DepthCoveragesEndpoint returns the depth coverage for a given kit and exon by database ID

func Endpoints ¶

func Endpoints() *gin.Engine

func GeneEndpoint ¶

func GeneEndpoint(c *gin.Context)

GeneEndpoint returns details about a given gene passed by database ID

func KitEndpoint ¶

func KitEndpoint(c *gin.Context)

KitEndpoint returns details about a given kit passed by database ID

func KitsEndpoint ¶

func KitsEndpoint(c *gin.Context)

KitsEndpoint returns all the kits in the database

func ReadsEndpoint ¶

func ReadsEndpoint(c *gin.Context)

ReadsEndpoint returns all reads for a given kit ID and exon ID

func RunServer ¶

func RunServer()

func SearchGenesEndpoint ¶

func SearchGenesEndpoint(c *gin.Context)

SearchGenesEndpoint returns a single gene that matches exactly or partially the HGNC name

func SearchKitsEndpoint ¶

func SearchKitsEndpoint(c *gin.Context)

SearchKitsEndpoint returns details about a given kit that matches exactly or partially the given name

func SearchVariantEndpoint ¶

func SearchVariantEndpoint(c *gin.Context)

SearchVariantEndpoint returns details about a given variant by exact database ID

func VariantsCSVEndpoint ¶

func VariantsCSVEndpoint(c *gin.Context)

VariantsCSVEndpoint returns a CSV file response for a given HGNC gene name

func VariantsEndpoint ¶

func VariantsEndpoint(c *gin.Context)

VariantsEndpoint returns a list of variants that fall inside given a kit and exon database ID

Types ¶

type DepthCoverage ¶

type DepthCoverage struct {
	Depth    uint64  `json:"depth"`
	Coverage float64 `json:"coverage"`
}

type DepthCoveragesResponse ¶

type DepthCoveragesResponse struct {
	KitName        string          `json:"kitName"`
	DepthCoverages []DepthCoverage `json:"depthCoverages"`
}

type ReadCount ¶

type ReadCount struct {
	Position uint64  `json:"position"`
	AvgCount float64 `json:"avgCount"`
}

type ReadCountsResponse ¶

type ReadCountsResponse struct {
	KitName    string      `json:"kitName"`
	ReadCounts []ReadCount `json:"readCounts"`
}

type Variant ¶

type Variant struct {
	ID            string `json:"id"`
	ClinSig       string `json:"clinSig"`
	ProteinChange string `json:"proteinChange"`
	Chromosome    string `json:"chromosome"`
	Start         uint64 `json:"start"`
	End           uint64 `json:"end"`
	Depth         uint64 `json:"depth"`
}

type VariantSearch ¶

type VariantSearch struct {
	ID         uint64  `json:"id"`
	Gene       db.Gene `json:"gene"`
	GeneName   string  `json:"geneName"`
	GeneID     uint64  `json:"geneId"`
	ExonNumber int     `json:"exonNumber"`
}

type VariantsResult ¶

type VariantsResult struct {
	TotalCount  int       `json:"totalCount"`
	Pages       int       `json:"pages"`
	CurrentPage int       `json:"currentPage"`
	Variants    []Variant `json:"variants"`
}

Source Files ¶

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