| // Code generated by protoc-gen-go. DO NOT EDIT. |
| // source: google/genomics/v1/cigar.proto |
| |
| package genomics // import "google.golang.org/genproto/googleapis/genomics/v1" |
| |
| import proto "github.com/golang/protobuf/proto" |
| import fmt "fmt" |
| import math "math" |
| import _ "google.golang.org/genproto/googleapis/api/annotations" |
| |
| // Reference imports to suppress errors if they are not otherwise used. |
| var _ = proto.Marshal |
| var _ = fmt.Errorf |
| var _ = math.Inf |
| |
| // This is a compile-time assertion to ensure that this generated file |
| // is compatible with the proto package it is being compiled against. |
| // A compilation error at this line likely means your copy of the |
| // proto package needs to be updated. |
| const _ = proto.ProtoPackageIsVersion2 // please upgrade the proto package |
| |
| // Describes the different types of CIGAR alignment operations that exist. |
| // Used wherever CIGAR alignments are used. |
| type CigarUnit_Operation int32 |
| |
| const ( |
| CigarUnit_OPERATION_UNSPECIFIED CigarUnit_Operation = 0 |
| // An alignment match indicates that a sequence can be aligned to the |
| // reference without evidence of an INDEL. Unlike the |
| // `SEQUENCE_MATCH` and `SEQUENCE_MISMATCH` operators, |
| // the `ALIGNMENT_MATCH` operator does not indicate whether the |
| // reference and read sequences are an exact match. This operator is |
| // equivalent to SAM's `M`. |
| CigarUnit_ALIGNMENT_MATCH CigarUnit_Operation = 1 |
| // The insert operator indicates that the read contains evidence of bases |
| // being inserted into the reference. This operator is equivalent to SAM's |
| // `I`. |
| CigarUnit_INSERT CigarUnit_Operation = 2 |
| // The delete operator indicates that the read contains evidence of bases |
| // being deleted from the reference. This operator is equivalent to SAM's |
| // `D`. |
| CigarUnit_DELETE CigarUnit_Operation = 3 |
| // The skip operator indicates that this read skips a long segment of the |
| // reference, but the bases have not been deleted. This operator is commonly |
| // used when working with RNA-seq data, where reads may skip long segments |
| // of the reference between exons. This operator is equivalent to SAM's |
| // `N`. |
| CigarUnit_SKIP CigarUnit_Operation = 4 |
| // The soft clip operator indicates that bases at the start/end of a read |
| // have not been considered during alignment. This may occur if the majority |
| // of a read maps, except for low quality bases at the start/end of a read. |
| // This operator is equivalent to SAM's `S`. Bases that are soft |
| // clipped will still be stored in the read. |
| CigarUnit_CLIP_SOFT CigarUnit_Operation = 5 |
| // The hard clip operator indicates that bases at the start/end of a read |
| // have been omitted from this alignment. This may occur if this linear |
| // alignment is part of a chimeric alignment, or if the read has been |
| // trimmed (for example, during error correction or to trim poly-A tails for |
| // RNA-seq). This operator is equivalent to SAM's `H`. |
| CigarUnit_CLIP_HARD CigarUnit_Operation = 6 |
| // The pad operator indicates that there is padding in an alignment. This |
| // operator is equivalent to SAM's `P`. |
| CigarUnit_PAD CigarUnit_Operation = 7 |
| // This operator indicates that this portion of the aligned sequence exactly |
| // matches the reference. This operator is equivalent to SAM's `=`. |
| CigarUnit_SEQUENCE_MATCH CigarUnit_Operation = 8 |
| // This operator indicates that this portion of the aligned sequence is an |
| // alignment match to the reference, but a sequence mismatch. This can |
| // indicate a SNP or a read error. This operator is equivalent to SAM's |
| // `X`. |
| CigarUnit_SEQUENCE_MISMATCH CigarUnit_Operation = 9 |
| ) |
| |
| var CigarUnit_Operation_name = map[int32]string{ |
| 0: "OPERATION_UNSPECIFIED", |
| 1: "ALIGNMENT_MATCH", |
| 2: "INSERT", |
| 3: "DELETE", |
| 4: "SKIP", |
| 5: "CLIP_SOFT", |
| 6: "CLIP_HARD", |
| 7: "PAD", |
| 8: "SEQUENCE_MATCH", |
| 9: "SEQUENCE_MISMATCH", |
| } |
| var CigarUnit_Operation_value = map[string]int32{ |
| "OPERATION_UNSPECIFIED": 0, |
| "ALIGNMENT_MATCH": 1, |
| "INSERT": 2, |
| "DELETE": 3, |
| "SKIP": 4, |
| "CLIP_SOFT": 5, |
| "CLIP_HARD": 6, |
| "PAD": 7, |
| "SEQUENCE_MATCH": 8, |
| "SEQUENCE_MISMATCH": 9, |
| } |
| |
| func (x CigarUnit_Operation) String() string { |
| return proto.EnumName(CigarUnit_Operation_name, int32(x)) |
| } |
| func (CigarUnit_Operation) EnumDescriptor() ([]byte, []int) { |
| return fileDescriptor_cigar_ce8c8036b76f9461, []int{0, 0} |
| } |
| |
| // A single CIGAR operation. |
| type CigarUnit struct { |
| Operation CigarUnit_Operation `protobuf:"varint,1,opt,name=operation,proto3,enum=google.genomics.v1.CigarUnit_Operation" json:"operation,omitempty"` |
| // The number of genomic bases that the operation runs for. Required. |
| OperationLength int64 `protobuf:"varint,2,opt,name=operation_length,json=operationLength,proto3" json:"operation_length,omitempty"` |
| // `referenceSequence` is only used at mismatches |
| // (`SEQUENCE_MISMATCH`) and deletions (`DELETE`). |
| // Filling this field replaces SAM's MD tag. If the relevant information is |
| // not available, this field is unset. |
| ReferenceSequence string `protobuf:"bytes,3,opt,name=reference_sequence,json=referenceSequence,proto3" json:"reference_sequence,omitempty"` |
| XXX_NoUnkeyedLiteral struct{} `json:"-"` |
| XXX_unrecognized []byte `json:"-"` |
| XXX_sizecache int32 `json:"-"` |
| } |
| |
| func (m *CigarUnit) Reset() { *m = CigarUnit{} } |
| func (m *CigarUnit) String() string { return proto.CompactTextString(m) } |
| func (*CigarUnit) ProtoMessage() {} |
| func (*CigarUnit) Descriptor() ([]byte, []int) { |
| return fileDescriptor_cigar_ce8c8036b76f9461, []int{0} |
| } |
| func (m *CigarUnit) XXX_Unmarshal(b []byte) error { |
| return xxx_messageInfo_CigarUnit.Unmarshal(m, b) |
| } |
| func (m *CigarUnit) XXX_Marshal(b []byte, deterministic bool) ([]byte, error) { |
| return xxx_messageInfo_CigarUnit.Marshal(b, m, deterministic) |
| } |
| func (dst *CigarUnit) XXX_Merge(src proto.Message) { |
| xxx_messageInfo_CigarUnit.Merge(dst, src) |
| } |
| func (m *CigarUnit) XXX_Size() int { |
| return xxx_messageInfo_CigarUnit.Size(m) |
| } |
| func (m *CigarUnit) XXX_DiscardUnknown() { |
| xxx_messageInfo_CigarUnit.DiscardUnknown(m) |
| } |
| |
| var xxx_messageInfo_CigarUnit proto.InternalMessageInfo |
| |
| func (m *CigarUnit) GetOperation() CigarUnit_Operation { |
| if m != nil { |
| return m.Operation |
| } |
| return CigarUnit_OPERATION_UNSPECIFIED |
| } |
| |
| func (m *CigarUnit) GetOperationLength() int64 { |
| if m != nil { |
| return m.OperationLength |
| } |
| return 0 |
| } |
| |
| func (m *CigarUnit) GetReferenceSequence() string { |
| if m != nil { |
| return m.ReferenceSequence |
| } |
| return "" |
| } |
| |
| func init() { |
| proto.RegisterType((*CigarUnit)(nil), "google.genomics.v1.CigarUnit") |
| proto.RegisterEnum("google.genomics.v1.CigarUnit_Operation", CigarUnit_Operation_name, CigarUnit_Operation_value) |
| } |
| |
| func init() { |
| proto.RegisterFile("google/genomics/v1/cigar.proto", fileDescriptor_cigar_ce8c8036b76f9461) |
| } |
| |
| var fileDescriptor_cigar_ce8c8036b76f9461 = []byte{ |
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