biopb

package
v0.0.0-...-9ba24aa Latest Latest
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 Go to latest Published: Mar 1, 2024 License: Apache-2.0 Imports: 7 Imported by: 0

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Index

Constants

View Source 
const (
	// InfinityPos is 1+ the largest possible alignment position.
	InfinityPos = math.MaxInt32

	// LimitValidRefID is a pseudo referenceID for a max possible valid
	// reference.  For example, passing RecRange{{0,0},{LimitValidRefID,
	// InfinityPos}} to ReadOpts.Range will read all mapped sequences.
	LimitValidRefID = math.MaxInt32 - 1

	// InfinityRefID is a pseudo referenceID for unmapped reads. For
	// example, passing RecRange{{UnmappedRefID,0},{UnmappedRefID,
	// InfinityPos}} to ReadOpts.Range will read all mapped sequences.
	InfinityRefID = int32(-1)
	// UnmappedRefID is a synonym of InfinityRefID.
	UnmappedRefID = InfinityRefID

	// InvalidRefID is used as a sentinel. We use -2 because -1 is is taken
	// by UnmappedRefID.
	InvalidRefID = int32(-2)
	// InvalidPos is a sentinel position value. We use -2 instead of -1
	// because -1 is sometimes used by the position of unmapped reads.
	InvalidPos = int32(-2)
)

Variables

View Source 
var (
	ErrInvalidLengthCoord = fmt.Errorf("proto: negative length found during unmarshaling")
	ErrIntOverflowCoord   = fmt.Errorf("proto: integer overflow")
)
View Source 
var (
	ErrInvalidLengthPam = fmt.Errorf("proto: negative length found during unmarshaling")
	ErrIntOverflowPam   = fmt.Errorf("proto: integer overflow")
)
View Source 
var (
	ErrInvalidLengthSort = fmt.Errorf("proto: negative length found during unmarshaling")
	ErrIntOverflowSort   = fmt.Errorf("proto: integer overflow")
)

Functions

This section is empty.

Types

type Coord 

type Coord struct {
	RefId int32 `protobuf:"varint,1,opt,name=ref_id,json=refId,proto3" json:"ref_id,omitempty"`
	Pos   int32 `protobuf:"varint,2,opt,name=pos,proto3" json:"pos,omitempty"`
	Seq   int32 `protobuf:"varint,3,opt,name=seq,proto3" json:"seq,omitempty"`
}

func (Coord) Compare 

func (r Coord) Compare(r1 Coord) int

Compare returns (negative int, 0, positive int) if (r<r1, r=r1, r>r1) respectively.

func (*Coord) Descriptor 

func (*Coord) Descriptor() ([]byte, []int)

func (Coord) EQ 

func (r Coord) EQ(r1 Coord) bool

EQ returns true iff r = r1.

func (Coord) GE 

func (r Coord) GE(r1 Coord) bool

GE returns true iff r >= r1

func (Coord) GT 

func (r Coord) GT(r1 Coord) bool

GT return true iff r > r1

func (*Coord) GetPos 

func (m *Coord) GetPos() int32

func (*Coord) GetRefId 

func (m *Coord) GetRefId() int32

func (*Coord) GetSeq 

func (m *Coord) GetSeq() int32

func (Coord) LE 

func (r Coord) LE(r1 Coord) bool

LE returns true iff r <= r1

func (Coord) LT 

func (r Coord) LT(r1 Coord) bool

LT returns true iff r < r1.

func (*Coord) Marshal 

func (m *Coord) Marshal() (dAtA []byte, err error)

func (*Coord) MarshalTo 

func (m *Coord) MarshalTo(dAtA []byte) (int, error)

func (*Coord) MarshalToSizedBuffer 

func (m *Coord) MarshalToSizedBuffer(dAtA []byte) (int, error)

func (Coord) Min 

func (r Coord) Min(r1 Coord) Coord

Min returns the smaller of r and r1.

func (*Coord) ProtoMessage 

func (*Coord) ProtoMessage()

func (*Coord) Reset 

func (m *Coord) Reset()

func (*Coord) Size 

func (m *Coord) Size() (n int)

func (*Coord) String 

func (m *Coord) String() string

func (*Coord) Unmarshal 

func (m *Coord) Unmarshal(dAtA []byte) error

func (*Coord) XXX_DiscardUnknown 

func (m *Coord) XXX_DiscardUnknown()

func (*Coord) XXX_Marshal 

func (m *Coord) XXX_Marshal(b []byte, deterministic bool) ([]byte, error)

func (*Coord) XXX_Merge 

func (m *Coord) XXX_Merge(src proto.Message)

func (*Coord) XXX_Size 

func (m *Coord) XXX_Size() int

func (*Coord) XXX_Unmarshal 

func (m *Coord) XXX_Unmarshal(b []byte) error

type CoordRange 

type CoordRange struct {
	Start Coord `protobuf:"bytes,1,opt,name=start,proto3" json:"start"`
	Limit Coord `protobuf:"bytes,2,opt,name=limit,proto3" json:"limit"`
}

func (CoordRange) Contains 

func (r CoordRange) Contains(a Coord) bool

Contains checks if "a" is inside the "r"

func (CoordRange) ContainsRange 

func (r CoordRange) ContainsRange(a CoordRange) bool

ContainsRange returns true iff (a ∩ r) = a.

func (*CoordRange) Descriptor 

func (*CoordRange) Descriptor() ([]byte, []int)

func (CoordRange) EQ 

func (r CoordRange) EQ(r1 CoordRange) bool

EQ returns true iff. r=r1.

func (*CoordRange) GetLimit 

func (m *CoordRange) GetLimit() Coord

func (*CoordRange) GetStart 

func (m *CoordRange) GetStart() Coord

func (CoordRange) Intersects 

func (r CoordRange) Intersects(r1 CoordRange) bool

Intersects returns true iff (a ∩ r) != ∅

func (*CoordRange) Marshal 

func (m *CoordRange) Marshal() (dAtA []byte, err error)

func (*CoordRange) MarshalTo 

func (m *CoordRange) MarshalTo(dAtA []byte) (int, error)

func (*CoordRange) MarshalToSizedBuffer 

func (m *CoordRange) MarshalToSizedBuffer(dAtA []byte) (int, error)

func (*CoordRange) ProtoMessage 

func (*CoordRange) ProtoMessage()

func (*CoordRange) Reset 

func (m *CoordRange) Reset()

func (*CoordRange) Size 

func (m *CoordRange) Size() (n int)

func (*CoordRange) String 

func (m *CoordRange) String() string

func (*CoordRange) Unmarshal 

func (m *CoordRange) Unmarshal(dAtA []byte) error

func (*CoordRange) XXX_DiscardUnknown 

func (m *CoordRange) XXX_DiscardUnknown()

func (*CoordRange) XXX_Marshal 

func (m *CoordRange) XXX_Marshal(b []byte, deterministic bool) ([]byte, error)

func (*CoordRange) XXX_Merge 

func (m *CoordRange) XXX_Merge(src proto.Message)

func (*CoordRange) XXX_Size 

func (m *CoordRange) XXX_Size() int

func (*CoordRange) XXX_Unmarshal 

func (m *CoordRange) XXX_Unmarshal(b []byte) error

type PAMBlockHeader 

type PAMBlockHeader struct {
	Offset     uint32 `protobuf:"varint,2,opt,name=offset,proto3" json:"offset,omitempty"`
	BlobOffset uint32 `protobuf:"varint,3,opt,name=blob_offset,json=blobOffset,proto3" json:"blob_offset,omitempty"`
}

func (*PAMBlockHeader) Descriptor 

func (*PAMBlockHeader) Descriptor() ([]byte, []int)

func (*PAMBlockHeader) GetBlobOffset 

func (m *PAMBlockHeader) GetBlobOffset() uint32

func (*PAMBlockHeader) GetOffset 

func (m *PAMBlockHeader) GetOffset() uint32

func (*PAMBlockHeader) Marshal 

func (m *PAMBlockHeader) Marshal() (dAtA []byte, err error)

func (*PAMBlockHeader) MarshalTo 

func (m *PAMBlockHeader) MarshalTo(dAtA []byte) (int, error)

func (*PAMBlockHeader) MarshalToSizedBuffer 

func (m *PAMBlockHeader) MarshalToSizedBuffer(dAtA []byte) (int, error)

func (*PAMBlockHeader) ProtoMessage 

func (*PAMBlockHeader) ProtoMessage()

func (*PAMBlockHeader) Reset 

func (m *PAMBlockHeader) Reset()

func (*PAMBlockHeader) Size 

func (m *PAMBlockHeader) Size() (n int)

func (*PAMBlockHeader) String 

func (m *PAMBlockHeader) String() string

func (*PAMBlockHeader) Unmarshal 

func (m *PAMBlockHeader) Unmarshal(dAtA []byte) error

func (*PAMBlockHeader) XXX_DiscardUnknown 

func (m *PAMBlockHeader) XXX_DiscardUnknown()

func (*PAMBlockHeader) XXX_Marshal 

func (m *PAMBlockHeader) XXX_Marshal(b []byte, deterministic bool) ([]byte, error)

func (*PAMBlockHeader) XXX_Merge 

func (m *PAMBlockHeader) XXX_Merge(src proto.Message)

func (*PAMBlockHeader) XXX_Size 

func (m *PAMBlockHeader) XXX_Size() int

func (*PAMBlockHeader) XXX_Unmarshal 

func (m *PAMBlockHeader) XXX_Unmarshal(b []byte) error

type PAMBlockIndexEntry 

type PAMBlockIndexEntry struct {
	FileOffset uint64 `protobuf:"varint,1,opt,name=file_offset,json=fileOffset,proto3" json:"file_offset,omitempty"`
	NumRecords uint32 `protobuf:"varint,3,opt,name=num_records,json=numRecords,proto3" json:"num_records,omitempty"`
	StartAddr  Coord  `protobuf:"bytes,4,opt,name=start_addr,json=startAddr,proto3" json:"start_addr"`
	EndAddr    Coord  `protobuf:"bytes,5,opt,name=end_addr,json=endAddr,proto3" json:"end_addr"`
}

func (*PAMBlockIndexEntry) Descriptor 

func (*PAMBlockIndexEntry) Descriptor() ([]byte, []int)

func (*PAMBlockIndexEntry) GetEndAddr 

func (m *PAMBlockIndexEntry) GetEndAddr() Coord

func (*PAMBlockIndexEntry) GetFileOffset 

func (m *PAMBlockIndexEntry) GetFileOffset() uint64

func (*PAMBlockIndexEntry) GetNumRecords 

func (m *PAMBlockIndexEntry) GetNumRecords() uint32

func (*PAMBlockIndexEntry) GetStartAddr 

func (m *PAMBlockIndexEntry) GetStartAddr() Coord

func (*PAMBlockIndexEntry) Marshal 

func (m *PAMBlockIndexEntry) Marshal() (dAtA []byte, err error)

func (*PAMBlockIndexEntry) MarshalTo 

func (m *PAMBlockIndexEntry) MarshalTo(dAtA []byte) (int, error)

func (*PAMBlockIndexEntry) MarshalToSizedBuffer 

func (m *PAMBlockIndexEntry) MarshalToSizedBuffer(dAtA []byte) (int, error)

func (*PAMBlockIndexEntry) ProtoMessage 

func (*PAMBlockIndexEntry) ProtoMessage()

func (*PAMBlockIndexEntry) Reset 

func (m *PAMBlockIndexEntry) Reset()

func (*PAMBlockIndexEntry) Size 

func (m *PAMBlockIndexEntry) Size() (n int)

func (*PAMBlockIndexEntry) String 

func (m *PAMBlockIndexEntry) String() string

func (*PAMBlockIndexEntry) Unmarshal 

func (m *PAMBlockIndexEntry) Unmarshal(dAtA []byte) error

func (*PAMBlockIndexEntry) XXX_DiscardUnknown 

func (m *PAMBlockIndexEntry) XXX_DiscardUnknown()

func (*PAMBlockIndexEntry) XXX_Marshal 

func (m *PAMBlockIndexEntry) XXX_Marshal(b []byte, deterministic bool) ([]byte, error)

func (*PAMBlockIndexEntry) XXX_Merge 

func (m *PAMBlockIndexEntry) XXX_Merge(src proto.Message)

func (*PAMBlockIndexEntry) XXX_Size 

func (m *PAMBlockIndexEntry) XXX_Size() int

func (*PAMBlockIndexEntry) XXX_Unmarshal 

func (m *PAMBlockIndexEntry) XXX_Unmarshal(b []byte) error

type PAMFieldIndex 

type PAMFieldIndex struct {
	Magic   uint64               `protobuf:"fixed64,1,opt,name=magic,proto3" json:"magic,omitempty"`
	Version string               `protobuf:"bytes,3,opt,name=version,proto3" json:"version,omitempty"`
	Field   int32                `protobuf:"varint,4,opt,name=field,proto3" json:"field,omitempty"`
	Blocks  []PAMBlockIndexEntry `protobuf:"bytes,16,rep,name=blocks,proto3" json:"blocks"`
}

func (*PAMFieldIndex) Descriptor 

func (*PAMFieldIndex) Descriptor() ([]byte, []int)

func (*PAMFieldIndex) GetBlocks 

func (m *PAMFieldIndex) GetBlocks() []PAMBlockIndexEntry

func (*PAMFieldIndex) GetField 

func (m *PAMFieldIndex) GetField() int32

func (*PAMFieldIndex) GetMagic 

func (m *PAMFieldIndex) GetMagic() uint64

func (*PAMFieldIndex) GetVersion 

func (m *PAMFieldIndex) GetVersion() string

func (*PAMFieldIndex) Marshal 

func (m *PAMFieldIndex) Marshal() (dAtA []byte, err error)

func (*PAMFieldIndex) MarshalTo 

func (m *PAMFieldIndex) MarshalTo(dAtA []byte) (int, error)

func (*PAMFieldIndex) MarshalToSizedBuffer 

func (m *PAMFieldIndex) MarshalToSizedBuffer(dAtA []byte) (int, error)

func (*PAMFieldIndex) ProtoMessage 

func (*PAMFieldIndex) ProtoMessage()

func (*PAMFieldIndex) Reset 

func (m *PAMFieldIndex) Reset()

func (*PAMFieldIndex) Size 

func (m *PAMFieldIndex) Size() (n int)

func (*PAMFieldIndex) String 

func (m *PAMFieldIndex) String() string

func (*PAMFieldIndex) Unmarshal 

func (m *PAMFieldIndex) Unmarshal(dAtA []byte) error

func (*PAMFieldIndex) XXX_DiscardUnknown 

func (m *PAMFieldIndex) XXX_DiscardUnknown()

func (*PAMFieldIndex) XXX_Marshal 

func (m *PAMFieldIndex) XXX_Marshal(b []byte, deterministic bool) ([]byte, error)

func (*PAMFieldIndex) XXX_Merge 

func (m *PAMFieldIndex) XXX_Merge(src proto.Message)

func (*PAMFieldIndex) XXX_Size 

func (m *PAMFieldIndex) XXX_Size() int

func (*PAMFieldIndex) XXX_Unmarshal 

func (m *PAMFieldIndex) XXX_Unmarshal(b []byte) error

type PAMShardIndex 

type PAMShardIndex struct {
	Magic            uint64     `protobuf:"fixed64,1,opt,name=magic,proto3" json:"magic,omitempty"`
	Version          string     `protobuf:"bytes,3,opt,name=version,proto3" json:"version,omitempty"`
	Range            CoordRange `protobuf:"bytes,4,opt,name=range,proto3" json:"range"`
	EncodedBamHeader []byte     `protobuf:"bytes,15,opt,name=encoded_bam_header,json=encodedBamHeader,proto3" json:"encoded_bam_header,omitempty"`
}

func (*PAMShardIndex) Descriptor 

func (*PAMShardIndex) Descriptor() ([]byte, []int)

func (*PAMShardIndex) GetEncodedBamHeader 

func (m *PAMShardIndex) GetEncodedBamHeader() []byte

func (*PAMShardIndex) GetMagic 

func (m *PAMShardIndex) GetMagic() uint64

func (*PAMShardIndex) GetRange 

func (m *PAMShardIndex) GetRange() CoordRange

func (*PAMShardIndex) GetVersion 

func (m *PAMShardIndex) GetVersion() string

func (*PAMShardIndex) Marshal 

func (m *PAMShardIndex) Marshal() (dAtA []byte, err error)

func (*PAMShardIndex) MarshalTo 

func (m *PAMShardIndex) MarshalTo(dAtA []byte) (int, error)

func (*PAMShardIndex) MarshalToSizedBuffer 

func (m *PAMShardIndex) MarshalToSizedBuffer(dAtA []byte) (int, error)

func (*PAMShardIndex) ProtoMessage 

func (*PAMShardIndex) ProtoMessage()

func (*PAMShardIndex) Reset 

func (m *PAMShardIndex) Reset()

func (*PAMShardIndex) Size 

func (m *PAMShardIndex) Size() (n int)

func (*PAMShardIndex) String 

func (m *PAMShardIndex) String() string

func (*PAMShardIndex) Unmarshal 

func (m *PAMShardIndex) Unmarshal(dAtA []byte) error

func (*PAMShardIndex) XXX_DiscardUnknown 

func (m *PAMShardIndex) XXX_DiscardUnknown()

func (*PAMShardIndex) XXX_Marshal 

func (m *PAMShardIndex) XXX_Marshal(b []byte, deterministic bool) ([]byte, error)

func (*PAMShardIndex) XXX_Merge 

func (m *PAMShardIndex) XXX_Merge(src proto.Message)

func (*PAMShardIndex) XXX_Size 

func (m *PAMShardIndex) XXX_Size() int

func (*PAMShardIndex) XXX_Unmarshal 

func (m *PAMShardIndex) XXX_Unmarshal(b []byte) error

type SortShardBlockIndex 

type SortShardBlockIndex struct {
	StartKey   uint64 `protobuf:"varint,1,opt,name=start_key,json=startKey,proto3" json:"start_key,omitempty"`
	FileOffset uint64 `protobuf:"varint,2,opt,name=file_offset,json=fileOffset,proto3" json:"file_offset,omitempty"`
	NumRecords uint32 `protobuf:"varint,3,opt,name=num_records,json=numRecords,proto3" json:"num_records,omitempty"`
}

func (*SortShardBlockIndex) Descriptor 

func (*SortShardBlockIndex) Descriptor() ([]byte, []int)

func (*SortShardBlockIndex) GetFileOffset 

func (m *SortShardBlockIndex) GetFileOffset() uint64

func (*SortShardBlockIndex) GetNumRecords 

func (m *SortShardBlockIndex) GetNumRecords() uint32

func (*SortShardBlockIndex) GetStartKey 

func (m *SortShardBlockIndex) GetStartKey() uint64

func (*SortShardBlockIndex) Marshal 

func (m *SortShardBlockIndex) Marshal() (dAtA []byte, err error)

func (*SortShardBlockIndex) MarshalTo 

func (m *SortShardBlockIndex) MarshalTo(dAtA []byte) (int, error)

func (*SortShardBlockIndex) MarshalToSizedBuffer 

func (m *SortShardBlockIndex) MarshalToSizedBuffer(dAtA []byte) (int, error)

func (*SortShardBlockIndex) ProtoMessage 

func (*SortShardBlockIndex) ProtoMessage()

func (*SortShardBlockIndex) Reset 

func (m *SortShardBlockIndex) Reset()

func (*SortShardBlockIndex) Size 

func (m *SortShardBlockIndex) Size() (n int)

func (*SortShardBlockIndex) String 

func (m *SortShardBlockIndex) String() string

func (*SortShardBlockIndex) Unmarshal 

func (m *SortShardBlockIndex) Unmarshal(dAtA []byte) error

func (*SortShardBlockIndex) XXX_DiscardUnknown 

func (m *SortShardBlockIndex) XXX_DiscardUnknown()

func (*SortShardBlockIndex) XXX_Marshal 

func (m *SortShardBlockIndex) XXX_Marshal(b []byte, deterministic bool) ([]byte, error)

func (*SortShardBlockIndex) XXX_Merge 

func (m *SortShardBlockIndex) XXX_Merge(src proto.Message)

func (*SortShardBlockIndex) XXX_Size 

func (m *SortShardBlockIndex) XXX_Size() int

func (*SortShardBlockIndex) XXX_Unmarshal 

func (m *SortShardBlockIndex) XXX_Unmarshal(b []byte) error

type SortShardIndex 

type SortShardIndex struct {
	NumRecords       int64                 `protobuf:"varint,1,opt,name=num_records,json=numRecords,proto3" json:"num_records,omitempty"`
	Snappy           bool                  `protobuf:"varint,2,opt,name=snappy,proto3" json:"snappy,omitempty"`
	EncodedBamHeader []byte                `protobuf:"bytes,15,opt,name=encoded_bam_header,json=encodedBamHeader,proto3" json:"encoded_bam_header,omitempty"`
	Blocks           []SortShardBlockIndex `protobuf:"bytes,16,rep,name=blocks,proto3" json:"blocks"`
}

func (*SortShardIndex) Descriptor 

func (*SortShardIndex) Descriptor() ([]byte, []int)

func (*SortShardIndex) GetBlocks 

func (m *SortShardIndex) GetBlocks() []SortShardBlockIndex

func (*SortShardIndex) GetEncodedBamHeader 

func (m *SortShardIndex) GetEncodedBamHeader() []byte

func (*SortShardIndex) GetNumRecords 

func (m *SortShardIndex) GetNumRecords() int64

func (*SortShardIndex) GetSnappy 

func (m *SortShardIndex) GetSnappy() bool

func (*SortShardIndex) Marshal 

func (m *SortShardIndex) Marshal() (dAtA []byte, err error)

func (*SortShardIndex) MarshalTo 

func (m *SortShardIndex) MarshalTo(dAtA []byte) (int, error)

func (*SortShardIndex) MarshalToSizedBuffer 

func (m *SortShardIndex) MarshalToSizedBuffer(dAtA []byte) (int, error)

func (*SortShardIndex) ProtoMessage 

func (*SortShardIndex) ProtoMessage()

func (*SortShardIndex) Reset 

func (m *SortShardIndex) Reset()

func (*SortShardIndex) Size 

func (m *SortShardIndex) Size() (n int)

func (*SortShardIndex) String 

func (m *SortShardIndex) String() string

func (*SortShardIndex) Unmarshal 

func (m *SortShardIndex) Unmarshal(dAtA []byte) error

func (*SortShardIndex) XXX_DiscardUnknown 

func (m *SortShardIndex) XXX_DiscardUnknown()

func (*SortShardIndex) XXX_Marshal 

func (m *SortShardIndex) XXX_Marshal(b []byte, deterministic bool) ([]byte, error)

func (*SortShardIndex) XXX_Merge 

func (m *SortShardIndex) XXX_Merge(src proto.Message)

func (*SortShardIndex) XXX_Size 

func (m *SortShardIndex) XXX_Size() int

func (*SortShardIndex) XXX_Unmarshal 

func (m *SortShardIndex) XXX_Unmarshal(b []byte) error

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