Documentation
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Index ¶
- func Load(bamPath string, kit string)
- type Coverage
- type Depth
- type Exon
- func (r *Exon) AddDepth(pos Position, depth Depth)
- func (r *Exon) AddDepthFromTo(fromPos Position, toPos Position, depth Depth)
- func (r *Exon) ComputeDepthCoverage(depth Depth) Coverage
- func (r *Exon) ComputeDepthCoverageRange(fromDepth Depth, toDepth Depth)
- func (r *Exon) StoreDepthCoverages(bamFileID uint)
- func (r *Exon) StoreReadCounts(bamFileID uint)
- type Position
Constants ¶
This section is empty.
Variables ¶
This section is empty.
Functions ¶
Types ¶
type Exon ¶
type Exon struct {
Chromosome string
Start uint64
End uint64
PositionDepth map[Position]Depth
DepthCoverages map[Depth]Coverage
ID uint
GeneID uint
ExonNumber uint
}
func ExonDepth ¶
ExonDepth calculates the read depth given BAM file and chromosomic coordinates, returning an Exon instance.
func NewExonsFromDB ¶
func NewExonsFromDB() []Exon
NewExonsFromDB returns a slice of all the exons that are already loaded in the database.
func (*Exon) AddDepth ¶
AddDepth increases the depth counter for a given position If the position falls outside the exon it isn't counted.
func (*Exon) AddDepthFromTo ¶
AddDepthFromTo increases the depth counter for a given position range. Positions that fall outside the exon aren't counted.
func (*Exon) ComputeDepthCoverage ¶
ComputeDepthCoverage computes the coverage at the given depth.
func (*Exon) ComputeDepthCoverageRange ¶
ComputeDepthCoverageRange computes the coverage at the given depths range. Stores the result in Exon.DepthCoverages.
func (*Exon) StoreDepthCoverages ¶
StoreDepthCoverages computes and stores the depth coverages in the DB, under the given BAM file ID.
func (*Exon) StoreReadCounts ¶
StoreReadCounts stores the read counts in the DB, under the given BAM file ID.
Source Files