sam

Documentation

Overview

Package sam decodes and encodes SAM files.

This package uses the format described in: https://en.wikipedia.org/wiki/SAM_(file_format)

Index

• Constants
• type Reader
  • func NewReader(r io.Reader) *Reader
  • func (r *Reader) NextHeader() (string, error)
  • func (r *Reader) Read() (*SAM, error)
• type SAM
  • func (s *SAM) MarshalText() ([]byte, error)

Constants

const (
	FlagMultiple           = 1 << iota // Template having multiple segments in sequencing
	FlagEach                           // Each segment properly aligned according to the aligner
	FlagUnmapped                       // Segment unmapped
	FlagUnmapped2                      // Next segment in the template unmapped
	FlagReverseComplement              // SEQ being reverse complemented
	FlagReverseComplement2             // SEQ of the next segment in the template being reverse complemented
	FlagFirst                          // The first segment in the template
	FlagLast                           // The last segment in the template
	FlagSecondary                      // Secondary alignment
	FlagNotPassing                     // Not passing filters, such as platform/vendor quality controls
	FlagDuplicate                      // PCR or optical duplicate
	FlagSupplementary                  // Supplementary alignment
)

Bit values of the flag field.

Types

type Reader

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

A Reader reads and parses SAM lines.

func NewReader

func NewReader(r io.Reader) *Reader

NewReader returns a new SAM reader that reads from r.

func (*Reader) NextHeader

func (r *Reader) NextHeader() (string, error)

NextHeader returns the next header line as a raw string, including the '@'. Returns EOF when out of header lines, then Next can be called for the data lines.

func (*Reader) Read

func (r *Reader) Read() (*SAM, error)

Read returns the next SAM line, skipping any unread header lines.

type SAM

type SAM struct {
	Qname string                 // Query name
	Flag  int                    // Bitwise flag
	Rname string                 // Reference sequence name
	Pos   int                    // Mapping position (1-based)
	Mapq  int                    // Mapping quality
	Cigar string                 // CIGAR string
	Rnext string                 // Ref. name of the mate/next read
	Pnext int                    // Position of the mate/next read
	Tlen  int                    // Observed template length
	Seq   string                 // Sequence
	Qual  string                 // Phred qualities (ASCII)
	Tags  map[string]interface{} // Typed optional tags.
}

SAM is a single line (alignment) in a SAM file.

func (*SAM) MarshalText

func (s *SAM) MarshalText() ([]byte, error)

MarshalText returns the textual representation of s in SAM format. Includes a trailing new line.