cleve

package module
v0.3.0 Latest Latest
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 Go to latest Published: Oct 1, 2024 License: GPL-3.0 Imports: 28 Imported by: 0

README

cleve — sequencing run database

Where does the name come from?

The name cleve is a tribute to what many consider to be the first female librarian in Sweden, Cecilia Cleve.

Documentation

Index

Constants

This section is empty.

Variables

View Source 
var LastRelease string = "v0.3.0" // x-release-please-version
View Source 
var ValidRunStates = map[string]RunState{
	"new":      New,
	"ready":    Ready,
	"pending":  Pending,
	"complete": Complete,
	"error":    Error,
	"moved":    Moved,
	"unknown":  Unknown,
}
View Source 
var Version string

Functions

func GetAPIDoc 

func GetAPIDoc() []byte

func GetAssetFS 

func GetAssetFS() (fs.FS, error)

func GetTemplateFS 

func GetTemplateFS() (fs.FS, error)

func GetVersion added in v0.2.0 

func GetVersion() string

func MostRecentSamplesheet 

func MostRecentSamplesheet(path string) (string, error)

Find the SampleSheet with the most recent modification time in a directory. The file name must be on the format `SampleSheet*.csv`.

Types

type APIKey 

type APIKey struct {
	Key     string
	User    string
	Created time.Time
}

func NewAPIKey 

func NewAPIKey(user string) *APIKey

type Analysis 

type Analysis struct {
	AnalysisId string           `bson:"analysis_id" json:"analysis_id"`
	Path       string           `bson:"path" json:"path"`
	State      RunState         `bson:"state" json:"state"`
	Summary    *AnalysisSummary `bson:"summary" json:"summary"`
}

func NewAnalysis 

func NewAnalysis(path string, state RunState, data []byte) (Analysis, error)

type AnalysisSummary 

type AnalysisSummary struct {
	RunID           string `bson:"run_id" json:"run_id"`
	Result          string `bson:"result" json:"result"`
	SoftwareVersion string `bson:"software_version" json:"software_version"`
	Workflows       []struct {
		WorkflowName      string `bson:"workflow_name" json:"workflow_name"`
		ReportAggregation string `bson:"report_aggregation" json:"report_aggregation"`
		Samples           []struct {
			SampleID          string `bson:"sample_id" json:"sample_id"`
			BclToFastq        string `bson:"bcl_to_fastq" json:"bcl_to_fastq"`
			OraCompression    string `bson:"ora_compression" json:"ora_compression"`
			SecondaryAnalysis string `bson:"secondary_analysis" json:"secondary_analysis"`
			ReportGeneration  string `bson:"report_generation" json:"report_generation"`
		} `bson:"samples" json:"samples"`
	} `bson:"workflows" json:"workflows"`
}

func ParseAnalysisSummary 

func ParseAnalysisSummary(data []byte) (AnalysisSummary, error)

type CustomTime 

type CustomTime time.Time

func (*CustomTime) Format 

func (c *CustomTime) Format(layout string) string

func (CustomTime) Local 

func (c CustomTime) Local() time.Time

func (CustomTime) MarshalBSONValue 

func (c CustomTime) MarshalBSONValue() (bsontype.Type, []byte, error)

func (CustomTime) MarshalJSON 

func (c CustomTime) MarshalJSON() ([]byte, error)

func (*CustomTime) String 

func (c *CustomTime) String() string

func (*CustomTime) UnmarshalBSONValue 

func (c *CustomTime) UnmarshalBSONValue(t bsontype.Type, b []byte) error

func (*CustomTime) UnmarshalXML 

func (c *CustomTime) UnmarshalXML(d *xml.Decoder, start xml.StartElement) error

type ImagingRecord 

type ImagingRecord struct {
	Lane  int `bson:"lane" json:"lane"`
	Tile  int `bson:"tile" json:"tile"`
	Cycle int `bson:"cycle" json:"cycle"`
	Read  int `bson:"read" json:"read"`

	PercentOccupied float64 `bson:"percent_occupied" json:"percent_occupied"`
	PercentPF       float64 `bson:"percent_pf" json:"percent_pf"`
}

type ImagingTable 

type ImagingTable struct {
	Records []ImagingRecord
}

func GenerateImagingTable 

func GenerateImagingTable(runId string, runDirectory string) (*ImagingTable, error)

func ParseImagingTable 

func ParseImagingTable(r *bufio.Reader) (*ImagingTable, error)

func (ImagingTable) LaneTileSummary 

func (t ImagingTable) LaneTileSummary() []TileSummary

type ImagingTableParser 

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

type InteropFile 

type InteropFile interface {
	GetVersion() uint8
	GetRecordSize() uint8
}

type InteropHeader 

type InteropHeader struct {
	Version    uint8
	RecordSize uint8
}

func (InteropHeader) GetRecordSize 

func (h InteropHeader) GetRecordSize() uint8

func (InteropHeader) GetVersion 

func (h InteropHeader) GetVersion() uint8

func (*InteropHeader) Parse 

func (h *InteropHeader) Parse(r io.Reader) error

type InteropQC 

type InteropQC struct {
	RunID          string          `bson:"run_id" json:"run_id"`
	InteropSummary *InteropSummary `bson:"summary" json:"summary"`
	TileSummary    []TileSummary   `bson:"imaging" json:"imaging"`
}

type InteropRecord 

type InteropRecord interface {
	Type() string
}

type InteropRecordHolder 

type InteropRecordHolder interface {
	Records() []InteropRecord
}

type InteropSummary 

type InteropSummary struct {
	Version       string                   `bson:"version" json:"version"`
	RunDirectory  string                   `bson:"run_directory" json:"run_directory"`
	RunSummary    map[string]RunSummary    `bson:"run_summmary" json:"run_summary"`
	ReadSummaries map[string][]ReadSummary `bson:"read_summary" json:"read_summary"`
}

func GenerateSummary 

func GenerateSummary(runDirectory string) (*InteropSummary, error)

func ParseInteropSummary 

func ParseInteropSummary(r *bufio.Reader) (*InteropSummary, error)

type JsonFloat 

type JsonFloat float64

func (JsonFloat) MarshalJSON 

func (x JsonFloat) MarshalJSON() ([]byte, error)

type MeanSd 

type MeanSd struct {
	Mean JsonFloat `bson:"mean" json:"mean"`
	SD   JsonFloat `bson:"sd" json:"sd"`
}

type NextSeqParameters 

type NextSeqParameters struct {
	RunParametersVersion string `xml:"RunParametersVersion"`
	Setup                struct {
		SupportMultipleSurfacesInUI string `xml:"SupportMultipleSurfacesInUI"`
		ApplicationVersion          string `xml:"ApplicationVersion"`
		ApplicationName             string `xml:"ApplicationName"`
		NumTilesPerSwath            int    `xml:"NumTilesPerSwath"`
		NumSwaths                   int    `xml:"NumSwaths"`
		NumLanes                    int    `xml:"NumLanes"`
		Read1                       int    `xml:"Read1"`
		Read2                       int    `xml:"Read2"`
		Index1Read                  int    `xml:"Index1Read"`
		Index2Read                  int    `xml:"Index2Read"`
		SectionPerLane              int    `xml:"SectionPerLane"`
		LanePerSection              int    `xml:"LanePerSection"`
	} `xml:"Setup"`
	RunID                  string `xml:"RunID"`
	CopyServiceRunId       string `xml:"CopyServiceRunId"`
	InstrumentID           string `xml:"InstrumentID"`
	RunNumber              int    `xml:"RunNumber"`
	RTAVersion             string `xml:"RTAVersion"`
	SystemSuiteVersion     string `xml:"SystemSuiteVersion"`
	LocalRunManagerVersion string `xml:"LocalRunManagerVersion"`
	RecipeVersion          string `xml:"RecipeVersion"`
	FirmwareVersion        string `xml:"FirmwareVersion"`
	FlowCellRfidTag        struct {
		SerialNumber   string     `xml:"SerialNumber"`
		PartNumber     string     `xml:"PartNumber"`
		LotNumber      string     `xml:"LotNumber"`
		ExpirationDate CustomTime `xml:"ExpirationDate"`
	} `xml:"FlowCellRfidTag"`
	PR2BottleRfidTag struct {
		SerialNumber   string     `xml:"SerialNumber"`
		PartNumber     string     `xml:"PartNumber"`
		LotNumber      string     `xml:"LotNumber"`
		ExpirationDate CustomTime `xml:"ExpirationDate"`
	} `xml:"PR2BottleRfidTag"`
	ReagentKitRfidTag struct {
		SerialNumber   string     `xml:"SerialNumber"`
		PartNumber     string     `xml:"PartNumber"`
		LotNumber      string     `xml:"LotNumber"`
		ExpirationDate CustomTime `xml:"ExpirationDate"`
	} `xml:"ReagentKitRfidTag"`
	FlowCellSerial                        string `xml:"FlowCellSerial"`
	PR2BottleSerial                       string `xml:"PR2BottleSerial"`
	ReagentKitSerial                      string `xml:"ReagentKitSerial"`
	ReagentKitSerialWasEnteredInBaseSpace string `xml:"ReagentKitSerialWasEnteredInBaseSpace"`
	ExperimentName                        string `xml:"ExperimentName"`
	LibraryID                             string `xml:"LibraryID"`
	StateDescription                      string `xml:"StateDescription"`
	Chemistry                             string `xml:"Chemistry"`
	ChemistryVersion                      string `xml:"ChemistryVersion"`
	SelectedTiles                         struct {
		Tile []string `xml:"Tile,text"`
	} `xml:"SelectedTiles"`
	RunFolder                        string `xml:"RunFolder"`
	RTALogsFolder                    string `xml:"RTALogsFolder"`
	PreRunFolderRoot                 string `xml:"PreRunFolderRoot"`
	PreRunFolder                     string `xml:"PreRunFolder"`
	OutputFolder                     string `xml:"OutputFolder"`
	RecipeFolder                     string `xml:"RecipeFolder"`
	SimulationFolder                 string `xml:"SimulationFolder"`
	RunStartDate                     string `xml:"RunStartDate"`
	BaseSpaceUserName                string `xml:"BaseSpaceUserName"`
	LocalRunManagerUserName          string `xml:"LocalRunManagerUserName"`
	FocusMethod                      string `xml:"FocusMethod"`
	SurfaceToScan                    string `xml:"SurfaceToScan"`
	SaveFocusImages                  string `xml:"SaveFocusImages"`
	SaveScanImages                   string `xml:"SaveScanImages"`
	SelectiveSave                    string `xml:"SelectiveSave"`
	IsPairedEnd                      string `xml:"IsPairedEnd"`
	AnalysisWorkflowType             string `xml:"AnalysisWorkflowType"`
	CustomReadOnePrimer              string `xml:"CustomReadOnePrimer"`
	CustomReadTwoPrimer              string `xml:"CustomReadTwoPrimer"`
	CustomIndexOnePrimer             string `xml:"CustomIndexOnePrimer"`
	CustomIndexTwoPrimer             string `xml:"CustomIndexTwoPrimer"`
	UsesCustomReadOnePrimer          string `xml:"UsesCustomReadOnePrimer"`
	UsesCustomReadTwoPrimer          string `xml:"UsesCustomReadTwoPrimer"`
	UsesCustomIndexPrimer            string `xml:"UsesCustomIndexPrimer"`
	UsesCustomIndexTwoPrimer         string `xml:"UsesCustomIndexTwoPrimer"`
	BaseSpaceRunId                   string `xml:"BaseSpaceRunId"`
	LocalRunManagerRunId             string `xml:"LocalRunManagerRunId"`
	RunSetupType                     string `xml:"RunSetupType"`
	RunMode                          string `xml:"RunMode"`
	ComputerName                     string `xml:"ComputerName"`
	SequencingStarted                string `xml:"SequencingStarted"`
	PlannedRead1Cycles               string `xml:"PlannedRead1Cycles"`
	PlannedRead2Cycles               string `xml:"PlannedRead2Cycles"`
	PlannedIndex1ReadCycles          string `xml:"PlannedIndex1ReadCycles"`
	PlannedIndex2ReadCycles          string `xml:"PlannedIndex2ReadCycles"`
	IsRehyb                          string `xml:"IsRehyb"`
	PurgeConsumables                 string `xml:"PurgeConsumables"`
	MaxCyclesSupportedByReagentKit   string `xml:"MaxCyclesSupportedByReagentKit"`
	ExtraCyclesSupportedByReagentKit string `xml:"ExtraCyclesSupportedByReagentKit"`
	ModuleName                       string `xml:"ModuleName"`
	ModuleVersion                    string `xml:"ModuleVersion"`
	IncludedFile                     string `xml:"IncludedFile"`
}

func ParseNextSeqRunParameters 

func ParseNextSeqRunParameters(d []byte) NextSeqParameters

func (NextSeqParameters) Flowcell 

func (p NextSeqParameters) Flowcell() string

func (NextSeqParameters) GetExperimentName 

func (p NextSeqParameters) GetExperimentName() string

func (NextSeqParameters) GetRunID 

func (p NextSeqParameters) GetRunID() string

func (NextSeqParameters) IsValid 

func (p NextSeqParameters) IsValid() bool

func (NextSeqParameters) Platform 

func (p NextSeqParameters) Platform() string

type NovaSeqParameters 

type NovaSeqParameters struct {
	Side                   string `xml:"Side"`
	Application            string `xml:"Application"`
	SystemSuiteVersion     string `xml:"SystemSuiteVersion"`
	OutputFolder           string `xml:"OutputFolder"`
	CloudUploadMode        string `xml:"CloudUploadMode"`
	RunSetupMode           string `xml:"RunSetupMode"`
	SecondaryAnalysisMode  string `xml:"SecondaryAnalysisMode"`
	InstrumentType         string `xml:"InstrumentType"`
	InstrumentSerialNumber string `xml:"InstrumentSerialNumber"`
	RunId                  string `xml:"RunId"`
	RunCounter             int    `xml:"RunCounter"`
	RecipeName             string `xml:"RecipeName"`
	RecipeVersion          string `xml:"RecipeVersion"`
	ExperimentName         string `xml:"ExperimentName"`
	FlowCellName           string `xml:"FlowCellName"`
	FlowCellType           string `xml:"FlowCellType"`
	ConsumableInfo         []struct {
		SerialNumber   string     `xml:"SerialNumber"`
		LotNumber      string     `xml:"LotNumber"`
		PartNumber     string     `xml:"PartNumber"`
		ExpirationDate CustomTime `xml:"ExpirationDate"`
		Type           string     `xml:"Type"`
		Mode           string     `xml:"Mode"`
		Version        string     `xml:"Version"`
		Name           string     `xml:"Name"`
	} `xml:"ConsumableInfo>ConsumableInfo"`
	PlannedReads struct {
		Read []struct {
			ReadName string `xml:"ReadName,attr"`
			Cycles   int    `xml:"Cycles,attr"`
		} `xml:"Read"`
	} `xml:"PlannedReads"`
	SecondaryAnalysisInfo struct {
		SecondaryAnalysisPlatformVersion string   `xml:"SecondaryAnalysisPlatformVersion"`
		SecondaryAnalysisWorkflow        []string `xml:"SecondaryAnalysisWorkflow>string"`
	} `xml:"SecondaryAnalysisInfo>SecondaryAnalysisInfo"`
	DisableBclCopy string `xml:"DisableBclCopy"`
}

func ParseNovaSeqRunParameters 

func ParseNovaSeqRunParameters(d []byte) NovaSeqParameters

func (NovaSeqParameters) Flowcell 

func (p NovaSeqParameters) Flowcell() string

func (NovaSeqParameters) GetExperimentName 

func (p NovaSeqParameters) GetExperimentName() string

func (NovaSeqParameters) GetRunID 

func (p NovaSeqParameters) GetRunID() string

func (NovaSeqParameters) IsValid 

func (p NovaSeqParameters) IsValid() bool

func (NovaSeqParameters) Platform 

func (p NovaSeqParameters) Platform() string

type PaginationFilter added in v0.3.0 

type PaginationFilter struct {
	Page     int `form:"page,default=1"`
	PageSize int `form:"page_size,default=10"`
}

Pagination filtering.

func (PaginationFilter) Validate added in v0.3.0 

func (f PaginationFilter) Validate() error

type PaginationMetadata 

type PaginationMetadata struct {
	TotalCount int `bson:"total_count" json:"total_count"`
	Count      int `bson:"count" json:"count"`
	Page       int `bson:"page" json:"page"`
	PageSize   int `bson:"page_size" json:"page_size"`
	TotalPages int `bson:"total_pages" json:"total_pages"`
}

type Pipeline added in v0.3.0 

type Pipeline struct {
	Name    string `bson:"name" json:"name"`
	Version string `bson:"version" json:"version"`
	URL     string `bson:"url" json:"url"`
}

Pipeline represents an analysis pipeline.

type Platform 

type Platform struct {
	Name         string `bson:"name" json:"name" binding:"required"`
	SerialTag    string `bson:"serial_tag" json:"serial_tag" binding:"required"`
	SerialPrefix string `bson:"serial_prefix" json:"serial_prefix" binding:"required"`
	ReadyMarker  string `bson:"ready_marker" json:"ready_marker"`
}

func NewPlatform 

func NewPlatform(name, serialTag, serialPrefix, readyMarker string) *Platform

type QcFilter 

type QcFilter struct {
	RunID     string
	Platform  string
	StartDate time.Time
	EndDate   time.Time
	PaginationFilter
}

QC filtering.

func (QcFilter) UrlParams 

func (f QcFilter) UrlParams() string

type QcResult 

type QcResult struct {
	PaginationMetadata `bson:"metadata" json:"metadata"`
	Qc                 []QcResultItem `bson:"qc" json:"qc"`
}

type QcResultItem 

type QcResultItem struct {
	InteropQC `bson:",inline" json:",inline"`
	Run       Run `bson:"run" json:"run"`
}

type Range 

type Range struct {
	Start int `bson:"start" json:"start"`
	End   int `bson:"end" json:"end"`
}

type ReadConfig 

type ReadConfig struct {
	ReadLengths map[int]int
}

func (ReadConfig) CycleToRead 

func (r ReadConfig) CycleToRead(cycle int) int

type ReadSummary 

type ReadSummary struct {
	Lane             int       `bson:"lane" json:"lane"`
	Tiles            int       `bson:"tiles" json:"tiles"`
	Density          MeanSd    `bson:"density" json:"density"`
	ClusterPF        MeanSd    `bson:"cluster_pf" json:"cluster_pf"`
	PhasingRate      JsonFloat `bson:"phasing_rate" json:"phasing_rate"`
	PrephasingRate   JsonFloat `bson:"prephasing_rate" json:"prephasing_rate"`
	PhasingSlope     JsonFloat `bson:"phasing_slope" json:"phasing_slope"`
	PhasingOffset    JsonFloat `bson:"phasing_offset" json:"phasing_offset"`
	PrephasingSlope  JsonFloat `bson:"prephasing_slope" json:"prephasing_slope"`
	PrephasingOffset JsonFloat `bson:"prephasing_offset" json:"prephasing_offset"`
	Reads            int       `bson:"reads" json:"reads"`
	ReadsPF          int       `bson:"reads_pf" json:"reads_pf"`
	PercentQ30       JsonFloat `bson:"percent_q30" json:"percent_q30"`
	Yield            int       `bson:"yield" json:"yield"`
	CyclesError      Range     `bson:"cycles_error" json:"cycles_error"`
	PercentAligned   MeanSd    `bson:"percent_aligned" json:"percent_aligned"`
	Error            MeanSd    `bson:"error" json:"error"`
	Error35          MeanSd    `bson:"error35" json:"error35"`
	Error75          MeanSd    `bson:"error75" json:"error75"`
	Error100         MeanSd    `bson:"error100" json:"error100"`
	PercentOccupied  MeanSd    `bson:"percent_occupied" json:"percent_occupied"`
	IntensityC1      MeanSd    `bson:"intensity_c1" json:"intensity_c1"`
}

func ParseReadSummary 

func ParseReadSummary(r *bufio.Reader) (string, []ReadSummary, error)

type Run 

type Run struct {
	ID               primitive.ObjectID `bson:"_id" json:"id"`
	RunID            string             `bson:"run_id" json:"run_id"`
	ExperimentName   string             `bson:"experiment_name" json:"experiment_name"`
	Path             string             `bson:"path" json:"path"`
	Platform         string             `bson:"platform" json:"platform"`
	Created          time.Time          `bson:"created" json:"created"`
	StateHistory     []TimedRunState    `bson:"state_history" json:"state_history"`
	SampleSheet      *SampleSheetInfo   `bson:"samplesheet,omitempty" json:"samplesheet"`
	SampleSheetFiles []SampleSheetInfo  `bson:"samplesheets,omitempty" json:"samplesheets"`
	RunParameters    RunParameters      `bson:"run_parameters,omitempty" json:"run_parameters,omitempty"`
	RunInfo          RunInfo            `bson:"run_info,omitempty" json:"run_info,omitempty"`
	Analysis         []*Analysis        `bson:"analysis,omitempty" json:"analysis,omitempty"`
	AnalysisCount    int32              `bson:"analysis_count" json:"analysis_count"`
}

func (*Run) UnmarshalBSON 

func (r *Run) UnmarshalBSON(data []byte) error

type RunCompletionStatus 

type RunCompletionStatus struct {
	Status  string
	Message string
}

func ParseRunCompletionStatus 

func ParseRunCompletionStatus(data []byte) (RunCompletionStatus, error)

func ReadRunCompletionStatus 

func ReadRunCompletionStatus(filename string) (RunCompletionStatus, error)

type RunFilter 

type RunFilter struct {
	RunID            string    `form:"run_id"`
	RunIdQuery       string    `form:"run_id_query"`
	Brief            bool      `form:"brief"`
	Platform         string    `form:"platform"`
	State            string    `form:"state"`
	From             time.Time `form:"from"`
	To               time.Time `form:"to"`
	PaginationFilter `form:",inline"`
}

Run filtering.

func (RunFilter) UrlParams 

func (f RunFilter) UrlParams() string

Convert a run filter to URL query parameters.

type RunInfo 

type RunInfo struct {
	Version int `xml:"Version,attr" bson:"version" json:"version"`
	Run     struct {
		RunID      string     `xml:"Id,attr" bson:"run_id" json:"run_id"`
		Number     int        `xml:"Number,attr" bson:"number" json:"number"`
		Flowcell   string     `xml:"Flowcell" bson:"flowcell" json:"flowcell"`
		Instrument string     `xml:"Instrument" bson:"instrument" json:"instrument"`
		Date       CustomTime `xml:"Date" bson:"date" json:"date"`
		Reads      struct {
			Read []struct {
				Number              int    `xml:"Number,attr" bson:"number" json:"number"`
				NumCycles           int    `xml:"NumCycles,attr" bson:"num_cycles" json:"num_cycles"`
				IsIndexedRead       string `xml:"IsIndexedRead,attr" bson:"is_indexed_read" json:"is_indexed_read"`
				IsReverseComplement string `xml:"IsReverseComplement,attr" bson:"is_reverse_complement" json:"is_reverse_complement"`
			} `xml:"Read" bson:"read" json:"read"`
		} `xml:"Reads" bson:"reads" json:"reads"`
		FlowcellLayout struct {
			LaneCount      int `xml:"LaneCount,attr" bson:"lane_count" json:"lane_count"`
			SurfaceCount   int `xml:"SurfaceCount,attr" bson:"surface_count" json:"surface_count"`
			SwathCount     int `xml:"SwathCount,attr" bson:"swath_count" json:"swath_count"`
			TileCount      int `xml:"TileCount,attr" bson:"tile_count" json:"tile_count"`
			SectionPerLane int `xml:"SectionPerLane,attr,omitempty" bson:"section_per_lane,omitempty" json:"section_per_lane,omitempty"`
			LanePerSection int `xml:"LanePerSection,attr,omitempty" bson:"lane_per_section,omitempty" json:"lane_per_section,omitempty"`
			TileSet        struct {
				TileNamingConvention string   `xml:"TileNamingConvention,attr" bson:"tile_naming_convention" json:"tile_naming_convention"`
				Tiles                []string `xml:"Tiles>Tile" bson:"tiles" json:"tiles"`
			} `xml:"TileSet" bson:"tileset" json:"tileset"`
		} `xml:"FlowcellLayout" bson:"flowcell_layout" json:"flowcell_layout"`
		ImageDimensions struct {
			Width  int `xml:"Width,attr" bson:"width" json:"width"`
			Height int `xml:"Height,attr" bson:"height" json:"height"`
		} `xml:"ImageDimensions" bson:"image_dimensions" json:"image_dimensions"`
		ImageChannels []string `xml:"ImageChannels>Name" bson:"image_channels" json:"image_channels"`
	} `xml:"Run" bson:"run" json:"run"`
}

func ParseRunInfo 

func ParseRunInfo(data []byte) (RunInfo, error)

type RunParameters 

type RunParameters interface {
	IsValid() bool
	GetExperimentName() string
	GetRunID() string
	Platform() string
	Flowcell() string
}

func ParseRunParameters 

func ParseRunParameters(paramsData []byte) (RunParameters, error)

type RunResult 

type RunResult struct {
	PaginationMetadata `bson:"metadata" json:"metadata"`
	Runs               []*Run `bson:"runs" json:"runs"`
}

type RunState 

type RunState int
const (
	New RunState = iota
	Ready
	Pending
	Complete
	Error
	Moved
	Unknown
)

func (RunState) MarshalBSONValue 

func (r RunState) MarshalBSONValue() (bsontype.Type, []byte, error)

func (RunState) MarshalJSON 

func (r RunState) MarshalJSON() ([]byte, error)

func (*RunState) Set 

func (s *RunState) Set(v string) error

func (RunState) String 

func (s RunState) String() string

func (*RunState) Type 

func (s *RunState) Type() string

func (*RunState) UnmarshalBSONValue 

func (r *RunState) UnmarshalBSONValue(t bsontype.Type, data []byte) error

func (*RunState) UnmarshalJSON 

func (r *RunState) UnmarshalJSON(data []byte) error

type RunSummary 

type RunSummary struct {
	Level           string    `bson:"level" json:"level"`
	Yield           int       `bson:"yield" json:"yield"`
	ProjectedYield  int       `bson:"projected_yield" json:"projected_yield"`
	PercentAligned  JsonFloat `bson:"percent_aligned" json:"percent_aligned"`
	ErrorRate       JsonFloat `bson:"error_rate" json:"error_rate"`
	IntensityC1     JsonFloat `bson:"intensity_c1" json:"intensity_c1"`
	PercentQ30      JsonFloat `bson:"percent_q30" json:"percent_q30"`
	PercentOccupied JsonFloat `bson:"percent_occupied" json:"percent_occupied"`
}

type RunningSummary 

type RunningSummary[T uint32 | uint64 | float32 | float64] struct {
	Sum T

	Mean float64
	// contains filtered or unexported fields
}

func NewRunningSummary 

func NewRunningSummary[T uint32 | uint64 | float32 | float64](weighted bool) *RunningSummary[T]

func (*RunningSummary[T]) Push 

func (v *RunningSummary[T]) Push(x T, weight ...T) error

func (RunningSummary[T]) SD 

func (v RunningSummary[T]) SD() float64

func (RunningSummary[T]) Var 

func (v RunningSummary[T]) Var() float64

type Sample added in v0.3.0 

type Sample struct {
	// Sample name. If missing it should be set to the sample ID.
	Name string `bson:"name" json:"name"`
	// Sample ID as listed in the samplesheet.
	Id string `bson:"id" json:"id"`
	// Paths to fastq files related to the sample.
	Fastq []string `bson:"fastq" json:"fastq"`
	// Analyses associated with the sample.
	Analyses []*SampleAnalysis `bson:"analyses" json:"analyses"`
}

Sample represents a sequenced sample with associated analyses.

type SampleAnalysis added in v0.3.0 

type SampleAnalysis struct {
	Pipeline `bson:"pipeline" json:"pipeline"`
	Results  []SampleAnalysisResult `bson:"path" json:"path"`
}

SampleAnalysis represents a collection of analysis results from an analysis pipeline.

type SampleAnalysisResult added in v0.3.0 

type SampleAnalysisResult struct {
	Type        string   `bson:"type" json:"type"`
	Description string   `bson:"description" json:"description"`
	Path        []string `bson:"path" json:"path"`
}

SampleAnalysisResult is a specific result from an analysis pipeline.

type SampleFilter added in v0.3.0 

type SampleFilter struct {
	Name             string `form:"sample_name"`
	Id               string `form:"sample_id"`
	RunId            string `form:"run_id"`
	Analysis         string `form:"analysis"`
	PaginationFilter `form:",inline"`
}

Sample filtering.

func (SampleFilter) UrlParams added in v0.3.0 

func (f SampleFilter) UrlParams() string

Convert a sample filter to URL query parameters.

type SampleResult added in v0.3.0 

type SampleResult struct {
	PaginationMetadata `bson:"metadata" json:"metadata"`
	Samples            []Sample `bson:"samples" json:"samples"`
}

type SampleSheet 

type SampleSheet struct {
	RunID    *string           `bson:"run_id" json:"run_id"`
	UUID     *uuid.UUID        `bson:"uuid" json:"uuid"`
	Files    []SampleSheetInfo `bson:"files" json:"files"`
	Sections []Section         `bson:"sections" json:"sections"`
}

func ParseSampleSheet 

func ParseSampleSheet(r *bufio.Reader) (SampleSheet, error)

func ReadSampleSheet 

func ReadSampleSheet(filename string) (SampleSheet, error)

func (SampleSheet) IsValid 

func (s SampleSheet) IsValid() bool

func (SampleSheet) LastModified added in v0.3.0 

func (s SampleSheet) LastModified() (time.Time, error)

func (SampleSheet) Merge added in v0.3.0 

func (s SampleSheet) Merge(other *SampleSheet) (*SampleSheet, error)

Merge two sample sheets. Merging is only allowed if the UUIDs of the sample sheets are the same, and the run IDs are the same. An exception to this is if the run ID of the current sample sheet is nil. If the run ID in the current sample sheet is non-nil and different from the other sample sheet, or if the UUIDs are different, an error is returned.

func (SampleSheet) Section 

func (s SampleSheet) Section(name string) *Section

func (SampleSheet) Version 

func (s SampleSheet) Version() int

type SampleSheetInfo 

type SampleSheetInfo struct {
	Path             string    `bson:"path" json:"path"`
	ModificationTime time.Time `bson:"modification_time" json:"modification_time"`
}

type Section 

type Section struct {
	Name string      `bson:"name" json:"name"`
	Type SectionType `bson:"type" json:"type"`
	Rows [][]string  `bson:"rows" json:"rows"`
}

func (Section) Get 

func (s Section) Get(name string, index ...int) (string, error)

func (Section) GetColumn 

func (s Section) GetColumn(name string) ([]string, error)

func (Section) GetFloat 

func (s Section) GetFloat(name string, index ...int) (float64, error)

func (Section) GetInt 

func (s Section) GetInt(name string, index ...int) (int, error)

type SectionType 

type SectionType int
const (
	UnknownSection SectionType = iota
	SettingsSection
	DataSection
)

func (SectionType) MarshalBSONValue 

func (s SectionType) MarshalBSONValue() (bsontype.Type, []byte, error)

func (SectionType) MarshalJSON 

func (s SectionType) MarshalJSON() ([]byte, error)

func (SectionType) String 

func (s SectionType) String() string

func (*SectionType) UnmarshalBSONValue 

func (s *SectionType) UnmarshalBSONValue(t bsontype.Type, b []byte) error

type StatsMap1 

type StatsMap1 = map[int]*RunningSummary[float64]

type StatsMap2 

type StatsMap2 = map[int]map[int]*RunningSummary[float64]

type StatsMap3 

type StatsMap3 = map[int]map[int]map[int]*RunningSummary[float64]

type Tile 

type Tile interface {
	Parse(io.Reader) error
}

type Tile16 

type Tile16 uint16

func (*Tile16) Parse 

func (t *Tile16) Parse(r io.Reader) error

type Tile32 

type Tile32 uint32

func (*Tile32) Parse 

func (t *Tile32) Parse(r io.Reader) error

type TileSummary 

type TileSummary struct {
	Lane            int     `bson:"lane" json:"lane"`
	Tile            int     `bson:"tile" json:"tile"`
	PercentOccupied float64 `bson:"percent_occupied" json:"percent_occupied"`
	PercentPF       float64 `bson:"percent_pf" json:"percent_pf"`
}

type TimedRunState 

type TimedRunState struct {
	State RunState  `bson:"state" json:"state"`
	Time  time.Time `bson:"time" json:"time"`
}

type UpdateResult 

type UpdateResult = mongo.UpdateResult

Source Files

View all Source files

Directories

Path Synopsis
cmd
cleve
cleve/db
cleve/key
cleve/platform
cleve/run
cleve/samplesheet

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