parsers

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

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 (*Bam) Related

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 (*Interval) Related

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 (*Variant) Related

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