/usr/share/gocode/src/google.golang.org/genproto/googleapis/genomics/v1/cigar.pb.go is in golang-google-genproto-dev 0.0~git20171123.7f0da29-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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// source: google/genomics/v1/cigar.proto
package genomics
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
// 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 fileDescriptor1, []int{0, 0} }
// A single CIGAR operation.
type CigarUnit struct {
Operation CigarUnit_Operation `protobuf:"varint,1,opt,name=operation,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" 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" json:"reference_sequence,omitempty"`
}
func (m *CigarUnit) Reset() { *m = CigarUnit{} }
func (m *CigarUnit) String() string { return proto.CompactTextString(m) }
func (*CigarUnit) ProtoMessage() {}
func (*CigarUnit) Descriptor() ([]byte, []int) { return fileDescriptor1, []int{0} }
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", fileDescriptor1) }
var fileDescriptor1 = []byte{
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