parsers

package

v0.0.0-...-5c4d9d6 Latest Latest Go to latest Published: Nov 4, 2021 License: MIT Imports: 13 Imported by: 1

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Repository

github.com/jakehagen/irelate

Links

Open Source Insights

Documentation ¶

Index ¶

func BamToRelatable(f io.Reader) (interfaces.RelatableChannel, error)
func IntervalFromBedLine(line []byte) (interfaces.Relatable, error)
func StreamVCF(vcf *vcfgo.Reader) interfaces.RelatableChannel
func VCFIterator(buf io.Reader) (interfaces.RelatableIterator, *vcfgo.Reader, error)
func Vopen(rdr io.Reader, hdr *vcfgo.Header) (*vcfgo.Reader, error)
type Bam
- func (a *Bam) AddRelated(b interfaces.Relatable)
- func (a *Bam) Chrom() string
- func (a *Bam) End() uint32
- func (a *Bam) MapQ() int
- func (a *Bam) Related() []interfaces.Relatable
- func (a *Bam) SetSource(src uint32)
- func (a *Bam) Source() uint32
- func (a *Bam) Start() uint32
type BamIterator
- func NewBamIterator(f string) (*BamIterator, error)
- func (b *BamIterator) Close() error
- func (b *BamIterator) Next() (interfaces.Relatable, error)
type BamQueryable
- func NewBamQueryable(path string, workers ...int) (*BamQueryable, error)
- func (b *BamQueryable) Close() error
- func (b *BamQueryable) Query(region interfaces.IPosition) (interfaces.RelatableIterator, error)
type Interval
- func NewInterval(chrom string, start uint32, end uint32, fields [][]byte, source uint32, ...) *Interval
- func (i *Interval) AddRelated(b interfaces.Relatable)
- func (i *Interval) Chrom() string
- func (i *Interval) End() uint32
- func (i *Interval) Related() []interfaces.Relatable
- func (i *Interval) SetSource(src uint32)
- func (i *Interval) Source() uint32
- func (i *Interval) Start() uint32
- func (i *Interval) String() string
type RefAltInterval
- func (i *RefAltInterval) Alt() []string
- func (i *RefAltInterval) End() uint32
- func (i *RefAltInterval) Ref() string
- func (i *RefAltInterval) SetRefAlt(ra []int)
type Variant
- func NewVariant(v interfaces.IVariant, source uint32, related []interfaces.Relatable) *Variant
- func (v *Variant) AddRelated(r interfaces.Relatable)
- func (v *Variant) Related() []interfaces.Relatable
- func (v *Variant) SetSource(src uint32)
- func (v *Variant) Source() uint32
- func (v *Variant) String() string

Constants ¶

This section is empty.

Variables ¶

This section is empty.

Functions ¶

func BamToRelatable ¶

func BamToRelatable(f io.Reader) (interfaces.RelatableChannel, error)

func IntervalFromBedLine ¶

func IntervalFromBedLine(line []byte) (interfaces.Relatable, error)

func StreamVCF ¶

func StreamVCF(vcf *vcfgo.Reader) interfaces.RelatableChannel

func VCFIterator ¶

func VCFIterator(buf io.Reader) (interfaces.RelatableIterator, *vcfgo.Reader, error)

func Vopen ¶

func Vopen(rdr io.Reader, hdr *vcfgo.Header) (*vcfgo.Reader, error)

Types ¶

type Bam ¶

type Bam struct {
	*sam.Record

	Chromosome string
	// contains filtered or unexported fields
}

func (*Bam) AddRelated ¶

func (a *Bam) AddRelated(b interfaces.Relatable)

func (*Bam) Chrom ¶

func (a *Bam) Chrom() string

func (*Bam) End ¶

func (a *Bam) End() uint32

func (*Bam) MapQ ¶

func (a *Bam) MapQ() int

func (a *Bam) Related() []interfaces.Relatable

func (*Bam) SetSource ¶

func (a *Bam) SetSource(src uint32)

func (*Bam) Source ¶

func (a *Bam) Source() uint32

func (*Bam) Start ¶

func (a *Bam) Start() uint32

cast to 32 bits.

type BamIterator ¶

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

func NewBamIterator ¶

func NewBamIterator(f string) (*BamIterator, error)

func (*BamIterator) Close ¶

func (b *BamIterator) Close() error

func (*BamIterator) Next ¶

func (b *BamIterator) Next() (interfaces.Relatable, error)

type BamQueryable ¶

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

func NewBamQueryable ¶

func NewBamQueryable(path string, workers ...int) (*BamQueryable, error)

func (*BamQueryable) Close ¶

func (b *BamQueryable) Close() error

func (*BamQueryable) Query ¶

func (b *BamQueryable) Query(region interfaces.IPosition) (interfaces.RelatableIterator, error)

type Interval ¶

type Interval struct {
	Fields [][]byte
	// contains filtered or unexported fields
}

Interval satisfies the Relatable interface.

func NewInterval ¶

func NewInterval(chrom string, start uint32, end uint32, fields [][]byte, source uint32, related []interfaces.Relatable) *Interval

func (*Interval) AddRelated ¶

func (i *Interval) AddRelated(b interfaces.Relatable)

func (*Interval) Chrom ¶

func (i *Interval) Chrom() string

func (*Interval) End ¶

func (i *Interval) End() uint32

func (i *Interval) Related() []interfaces.Relatable

func (*Interval) SetSource ¶

func (i *Interval) SetSource(src uint32)

func (*Interval) Source ¶

func (i *Interval) Source() uint32

func (*Interval) Start ¶

func (i *Interval) Start() uint32

func (*Interval) String ¶

func (i *Interval) String() string

type RefAltInterval ¶

type RefAltInterval struct {
	Interval

	HasEnd bool
	// contains filtered or unexported fields
}

func (*RefAltInterval) Alt ¶

func (i *RefAltInterval) Alt() []string

func (*RefAltInterval) End ¶

func (i *RefAltInterval) End() uint32

func (*RefAltInterval) Ref ¶

func (i *RefAltInterval) Ref() string

func (*RefAltInterval) SetRefAlt ¶

func (i *RefAltInterval) SetRefAlt(ra []int)

type Variant ¶

type Variant struct {
	interfaces.IVariant
	// contains filtered or unexported fields
}

func NewVariant ¶

func NewVariant(v interfaces.IVariant, source uint32, related []interfaces.Relatable) *Variant

func (*Variant) AddRelated ¶

func (v *Variant) AddRelated(r interfaces.Relatable)

func (v *Variant) Related() []interfaces.Relatable

func (*Variant) SetSource ¶

func (v *Variant) SetSource(src uint32)

func (*Variant) Source ¶

func (v *Variant) Source() uint32

func (*Variant) String ¶

func (v *Variant) String() string

Source Files ¶

View all Source files

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