Versions in this module Expand all Collapse all v1 v1.0.1 Jan 31, 2017 v1.0.0 Jan 10, 2017 Changes in this version + const FlagDecimal + const FlagHex + const FlagString + func IsValidRecord(r *Record) bool + type ASCII byte + type Aux []byte + func NewAux(t Tag, value interface{}) (Aux, error) + func ParseAux(text []byte) (Aux, error) + func (a Aux) Kind() byte + func (a Aux) String() string + func (a Aux) Tag() Tag + func (a Aux) Type() byte + func (a Aux) Value() interface{} + type AuxFields []Aux + func (a AuxFields) Get(tag Tag) Aux + type Cigar []CigarOp + func ParseCigar(b []byte) (Cigar, error) + func (c Cigar) IsValid(length int) bool + func (c Cigar) Lengths() (ref, read int) + func (c Cigar) String() string + type CigarOp uint32 + func NewCigarOp(t CigarOpType, n int) CigarOp + func (co CigarOp) Len() int + func (co CigarOp) String() string + func (co CigarOp) Type() CigarOpType + type CigarOpType byte + const CigarBack + const CigarDeletion + const CigarEqual + const CigarHardClipped + const CigarInsertion + const CigarMatch + const CigarMismatch + const CigarPadded + const CigarSkipped + const CigarSoftClipped + func (ct CigarOpType) Consumes() Consume + func (ct CigarOpType) String() string + type Consume struct + Query int + Reference int + type Doublet byte + type Flags uint16 + const Duplicate + const MateReverse + const MateUnmapped + const Paired + const ProperPair + const QCFail + const Read1 + const Read2 + const Reverse + const Secondary + const Supplementary + const Unmapped + func (f Flags) String() string + type GroupOrder int + const GroupNone + const GroupQuery + const GroupReference + const GroupUnspecified + func (g GroupOrder) String() string + type Header struct + Comments []string + GroupOrder GroupOrder + SortOrder SortOrder + Version string + func NewHeader(text []byte, r []*Reference) (*Header, error) + func (bh *Header) AddProgram(p *Program) error + func (bh *Header) AddReadGroup(rg *ReadGroup) error + func (bh *Header) AddReference(r *Reference) error + func (bh *Header) Clone() *Header + func (bh *Header) DecodeBinary(r io.Reader) error + func (bh *Header) EncodeBinary(w io.Writer) error + func (bh *Header) Get(t Tag) string + func (bh *Header) MarshalBinary() ([]byte, error) + func (bh *Header) MarshalText() ([]byte, error) + func (bh *Header) Progs() []*Program + func (bh *Header) RGs() []*ReadGroup + func (bh *Header) Refs() []*Reference + func (bh *Header) Set(t Tag, value string) error + func (bh *Header) UnmarshalBinary(b []byte) error + func (bh *Header) UnmarshalText(text []byte) error + func (bh *Header) Validate(r *Record) error + type Hex []byte + type Iterator struct + func NewIterator(r RecordReader) *Iterator + func (i *Iterator) Error() error + func (i *Iterator) Next() bool + func (i *Iterator) Record() *Record + type Program struct + func NewProgram(uid, name, command, prev, v string) *Program + func (p *Program) Clone() *Program + func (p *Program) Command() string + func (p *Program) Get(t Tag) string + func (p *Program) ID() int + func (p *Program) Name() string + func (p *Program) Previous() string + func (p *Program) Set(t Tag, value string) error + func (p *Program) String() string + func (p *Program) UID() string + func (p *Program) Version() string + type ReadGroup struct + func NewReadGroup(name, center, desc, lib, prog, plat, unit, sample, flow, key string, ...) (*ReadGroup, error) + func (r *ReadGroup) Clone() *ReadGroup + func (r *ReadGroup) Get(t Tag) string + func (r *ReadGroup) ID() int + func (r *ReadGroup) Library() string + func (r *ReadGroup) Name() string + func (r *ReadGroup) PlatformUnit() string + func (r *ReadGroup) Set(t Tag, value string) error + func (r *ReadGroup) String() string + func (r *ReadGroup) Time() time.Time + type Reader struct + func NewReader(r io.Reader) (*Reader, error) + func (r *Reader) Header() *Header + func (r *Reader) Read() (*Record, error) + type Record struct + AuxFields AuxFields + Cigar Cigar + Flags Flags + MapQ byte + MatePos int + MateRef *Reference + Name string + Pos int + Qual []byte + Ref *Reference + Seq Seq + TempLen int + func NewRecord(name string, ref, mRef *Reference, p, mPos, tLen int, mapQ byte, co []CigarOp, ...) (*Record, error) + func (r *Record) Bin() int + func (r *Record) End() int + func (r *Record) Len() int + func (r *Record) MarshalSAM(flags int) ([]byte, error) + func (r *Record) MarshalText() ([]byte, error) + func (r *Record) RefID() int + func (r *Record) Start() int + func (r *Record) Strand() int8 + func (r *Record) String() string + func (r *Record) Tag(tag []byte) (v Aux, ok bool) + func (r *Record) UnmarshalSAM(h *Header, b []byte) error + func (r *Record) UnmarshalText(b []byte) error + type RecordReader interface + Read func() (*Record, error) + type Reference struct + func NewReference(name, assemID, species string, length int, md5 []byte, uri *url.URL) (*Reference, error) + func (r *Reference) AssemblyID() string + func (r *Reference) Clone() *Reference + func (r *Reference) Get(t Tag) string + func (r *Reference) ID() int + func (r *Reference) Len() int + func (r *Reference) MD5() []byte + func (r *Reference) Name() string + func (r *Reference) Set(t Tag, value string) error + func (r *Reference) SetLen(l int) error + func (r *Reference) Species() string + func (r *Reference) String() string + func (r *Reference) URI() string + type Seq struct + Length int + Seq []Doublet + func NewSeq(s []byte) Seq + func (ns Seq) Expand() []byte + type SortOrder int + const Coordinate + const QueryName + const UnknownOrder + const Unsorted + func (so SortOrder) String() string + type Tag [2]byte + func NewTag(tag string) Tag + func (t Tag) String() string + type Text []byte + type Writer struct + func NewWriter(w io.Writer, h *Header, flags int) (*Writer, error) + func (w *Writer) Write(r *Record) error