sam

package

v0.3.5 Latest Latest Go to latest Published: Nov 19, 2019 License: BSD-3-Clause Imports: 9 Imported by: 0

Details

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Repository

github.com/guigolab/bamstats

Links

Open Source Insights

Documentation ¶

Index ¶

Variables
func NewBamReader(bamFile string, cfg *config.Config) (*bam.Reader, error)
type Iterator
- func NewIterator(br *bam.Reader, data *RefChunk, reads int) (*Iterator, error)
- func (i *Iterator) Next() bool
- func (i *Iterator) Record() *Record
type Reader
- func NewReader(bamFile string, cfg *config.Config) (*Reader, error)
type Record
- func NewRecord(r *sam.Record) *Record
type RefChunk
- func NewRefChunk(ref *sam.Reference, chunk []bgzf.Chunk) *RefChunk

Constants ¶

This section is empty.

Variables ¶

View Source

var (
	NewTag = sam.NewTag
	NewAux = sam.NewAux
)

Export original sam.Record functions

Functions ¶

func NewBamReader ¶

func NewBamReader(bamFile string, cfg *config.Config) (*bam.Reader, error)

Types ¶

type Iterator ¶

type Iterator struct {
	*bam.Iterator
	MaxReads, Reads int
	// contains filtered or unexported fields
}

func NewIterator ¶

func NewIterator(br *bam.Reader, data *RefChunk, reads int) (*Iterator, error)

func (*Iterator) Next ¶

func (i *Iterator) Next() bool

func (*Iterator) Record ¶

func (i *Iterator) Record() *Record

type Reader ¶

type Reader struct {
	*bam.Reader
	FileName string
	Workers  int
	Index    *bam.Index
	Refs     []*sam.Reference
	Channels []interface{}
	// contains filtered or unexported fields
}

func NewReader ¶

func NewReader(bamFile string, cfg *config.Config) (*Reader, error)

func (*Reader) Clone ¶

func (r *Reader) Clone() *Reader

func (*Reader) Read ¶

func (r *Reader) Read()

func (*Reader) Unmapped ¶

func (r *Reader) Unmapped() uint64

type Record ¶

type Record struct {
	*sam.Record
}

func NewRecord ¶

func NewRecord(r *sam.Record) *Record

func (*Record) GetBlocks ¶

func (r *Record) GetBlocks() []*annotation.Location

func (*Record) HasMateUnmapped ¶

func (r *Record) HasMateUnmapped() bool

func (*Record) IsDuplicate ¶

func (r *Record) IsDuplicate() bool

func (*Record) IsFirstOfValidPair ¶

func (r *Record) IsFirstOfValidPair() bool

func (*Record) IsPaired ¶

func (r *Record) IsPaired() bool

func (*Record) IsPrimary ¶

func (r *Record) IsPrimary() bool

func (*Record) IsProperlyPaired ¶

func (r *Record) IsProperlyPaired() bool

func (*Record) IsQCFail ¶ added in v0.3.4

func (r *Record) IsQCFail() bool

func (*Record) IsRead1 ¶

func (r *Record) IsRead1() bool

func (*Record) IsRead2 ¶

func (r *Record) IsRead2() bool

func (*Record) IsSplit ¶

func (r *Record) IsSplit() bool

func (*Record) IsUniq ¶

func (r *Record) IsUniq() bool

func (*Record) IsUnmapped ¶

func (r *Record) IsUnmapped() bool

type RefChunk ¶

type RefChunk struct {
	Ref    *sam.Reference
	Chunks []bgzf.Chunk
}

func NewRefChunk ¶

func NewRefChunk(ref *sam.Reference, chunk []bgzf.Chunk) *RefChunk

Source Files ¶

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