// Code generated by protoc-gen-go. DO NOT EDIT.
// source: google/genomics/v1/readalignment.proto

package genomics

import proto "github.com/golang/protobuf/proto"
import fmt "fmt"
import math "math"
import _ "google.golang.org/genproto/googleapis/api/annotations"
import google_protobuf3 "github.com/golang/protobuf/ptypes/struct"

// Reference imports to suppress errors if they are not otherwise used.
var _ = proto.Marshal
var _ = fmt.Errorf
var _ = math.Inf

// A linear alignment can be represented by one CIGAR string. Describes the
// mapped position and local alignment of the read to the reference.
type LinearAlignment struct {
	// The position of this alignment.
	Position *Position `protobuf:"bytes,1,opt,name=position" json:"position,omitempty"`
	// The mapping quality of this alignment. Represents how likely
	// the read maps to this position as opposed to other locations.
	//
	// Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to
	// the nearest integer.
	MappingQuality int32 `protobuf:"varint,2,opt,name=mapping_quality,json=mappingQuality" json:"mapping_quality,omitempty"`
	// Represents the local alignment of this sequence (alignment matches, indels,
	// etc) against the reference.
	Cigar []*CigarUnit `protobuf:"bytes,3,rep,name=cigar" json:"cigar,omitempty"`
}

func (m *LinearAlignment) Reset()                    { *m = LinearAlignment{} }
func (m *LinearAlignment) String() string            { return proto.CompactTextString(m) }
func (*LinearAlignment) ProtoMessage()               {}
func (*LinearAlignment) Descriptor() ([]byte, []int) { return fileDescriptor6, []int{0} }

func (m *LinearAlignment) GetPosition() *Position {
	if m != nil {
		return m.Position
	}
	return nil
}

func (m *LinearAlignment) GetMappingQuality() int32 {
	if m != nil {
		return m.MappingQuality
	}
	return 0
}

func (m *LinearAlignment) GetCigar() []*CigarUnit {
	if m != nil {
		return m.Cigar
	}
	return nil
}

// A read alignment describes a linear alignment of a string of DNA to a
// [reference sequence][google.genomics.v1.Reference], in addition to metadata
// about the fragment (the molecule of DNA sequenced) and the read (the bases
// which were read by the sequencer). A read is equivalent to a line in a SAM
// file. A read belongs to exactly one read group and exactly one
// [read group set][google.genomics.v1.ReadGroupSet].
//
// For more genomics resource definitions, see [Fundamentals of Google
// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
//
// ### Reverse-stranded reads
//
// Mapped reads (reads having a non-null `alignment`) can be aligned to either
// the forward or the reverse strand of their associated reference. Strandedness
// of a mapped read is encoded by `alignment.position.reverseStrand`.
//
// If we consider the reference to be a forward-stranded coordinate space of
// `[0, reference.length)` with `0` as the left-most position and
// `reference.length` as the right-most position, reads are always aligned left
// to right. That is, `alignment.position.position` always refers to the
// left-most reference coordinate and `alignment.cigar` describes the alignment
// of this read to the reference from left to right. All per-base fields such as
// `alignedSequence` and `alignedQuality` share this same left-to-right
// orientation; this is true of reads which are aligned to either strand. For
// reverse-stranded reads, this means that `alignedSequence` is the reverse
// complement of the bases that were originally reported by the sequencing
// machine.
//
// ### Generating a reference-aligned sequence string
//
// When interacting with mapped reads, it's often useful to produce a string
// representing the local alignment of the read to reference. The following
// pseudocode demonstrates one way of doing this:
//
//     out = ""
//     offset = 0
//     for c in read.alignment.cigar {
//       switch c.operation {
//       case "ALIGNMENT_MATCH", "SEQUENCE_MATCH", "SEQUENCE_MISMATCH":
//         out += read.alignedSequence[offset:offset+c.operationLength]
//         offset += c.operationLength
//         break
//       case "CLIP_SOFT", "INSERT":
//         offset += c.operationLength
//         break
//       case "PAD":
//         out += repeat("*", c.operationLength)
//         break
//       case "DELETE":
//         out += repeat("-", c.operationLength)
//         break
//       case "SKIP":
//         out += repeat(" ", c.operationLength)
//         break
//       case "CLIP_HARD":
//         break
//       }
//     }
//     return out
//
// ### Converting to SAM's CIGAR string
//
// The following pseudocode generates a SAM CIGAR string from the
// `cigar` field. Note that this is a lossy conversion
// (`cigar.referenceSequence` is lost).
//
//     cigarMap = {
//       "ALIGNMENT_MATCH": "M",
//       "INSERT": "I",
//       "DELETE": "D",
//       "SKIP": "N",
//       "CLIP_SOFT": "S",
//       "CLIP_HARD": "H",
//       "PAD": "P",
//       "SEQUENCE_MATCH": "=",
//       "SEQUENCE_MISMATCH": "X",
//     }
//     cigarStr = ""
//     for c in read.alignment.cigar {
//       cigarStr += c.operationLength + cigarMap[c.operation]
//     }
//     return cigarStr
type Read struct {
	// The server-generated read ID, unique across all reads. This is different
	// from the `fragmentName`.
	Id string `protobuf:"bytes,1,opt,name=id" json:"id,omitempty"`
	// The ID of the read group this read belongs to. A read belongs to exactly
	// one read group. This is a server-generated ID which is distinct from SAM's
	// RG tag (for that value, see
	// [ReadGroup.name][google.genomics.v1.ReadGroup.name]).
	ReadGroupId string `protobuf:"bytes,2,opt,name=read_group_id,json=readGroupId" json:"read_group_id,omitempty"`
	// The ID of the read group set this read belongs to. A read belongs to
	// exactly one read group set.
	ReadGroupSetId string `protobuf:"bytes,3,opt,name=read_group_set_id,json=readGroupSetId" json:"read_group_set_id,omitempty"`
	// The fragment name. Equivalent to QNAME (query template name) in SAM.
	FragmentName string `protobuf:"bytes,4,opt,name=fragment_name,json=fragmentName" json:"fragment_name,omitempty"`
	// The orientation and the distance between reads from the fragment are
	// consistent with the sequencing protocol (SAM flag 0x2).
	ProperPlacement bool `protobuf:"varint,5,opt,name=proper_placement,json=properPlacement" json:"proper_placement,omitempty"`
	// The fragment is a PCR or optical duplicate (SAM flag 0x400).
	DuplicateFragment bool `protobuf:"varint,6,opt,name=duplicate_fragment,json=duplicateFragment" json:"duplicate_fragment,omitempty"`
	// The observed length of the fragment, equivalent to TLEN in SAM.
	FragmentLength int32 `protobuf:"varint,7,opt,name=fragment_length,json=fragmentLength" json:"fragment_length,omitempty"`
	// The read number in sequencing. 0-based and less than numberReads. This
	// field replaces SAM flag 0x40 and 0x80.
	ReadNumber int32 `protobuf:"varint,8,opt,name=read_number,json=readNumber" json:"read_number,omitempty"`
	// The number of reads in the fragment (extension to SAM flag 0x1).
	NumberReads int32 `protobuf:"varint,9,opt,name=number_reads,json=numberReads" json:"number_reads,omitempty"`
	// Whether this read did not pass filters, such as platform or vendor quality
	// controls (SAM flag 0x200).
	FailedVendorQualityChecks bool `protobuf:"varint,10,opt,name=failed_vendor_quality_checks,json=failedVendorQualityChecks" json:"failed_vendor_quality_checks,omitempty"`
	// The linear alignment for this alignment record. This field is null for
	// unmapped reads.
	Alignment *LinearAlignment `protobuf:"bytes,11,opt,name=alignment" json:"alignment,omitempty"`
	// Whether this alignment is secondary. Equivalent to SAM flag 0x100.
	// A secondary alignment represents an alternative to the primary alignment
	// for this read. Aligners may return secondary alignments if a read can map
	// ambiguously to multiple coordinates in the genome. By convention, each read
	// has one and only one alignment where both `secondaryAlignment`
	// and `supplementaryAlignment` are false.
	SecondaryAlignment bool `protobuf:"varint,12,opt,name=secondary_alignment,json=secondaryAlignment" json:"secondary_alignment,omitempty"`
	// Whether this alignment is supplementary. Equivalent to SAM flag 0x800.
	// Supplementary alignments are used in the representation of a chimeric
	// alignment. In a chimeric alignment, a read is split into multiple
	// linear alignments that map to different reference contigs. The first
	// linear alignment in the read will be designated as the representative
	// alignment; the remaining linear alignments will be designated as
	// supplementary alignments. These alignments may have different mapping
	// quality scores. In each linear alignment in a chimeric alignment, the read
	// will be hard clipped. The `alignedSequence` and
	// `alignedQuality` fields in the alignment record will only
	// represent the bases for its respective linear alignment.
	SupplementaryAlignment bool `protobuf:"varint,13,opt,name=supplementary_alignment,json=supplementaryAlignment" json:"supplementary_alignment,omitempty"`
	// The bases of the read sequence contained in this alignment record,
	// **without CIGAR operations applied** (equivalent to SEQ in SAM).
	// `alignedSequence` and `alignedQuality` may be
	// shorter than the full read sequence and quality. This will occur if the
	// alignment is part of a chimeric alignment, or if the read was trimmed. When
	// this occurs, the CIGAR for this read will begin/end with a hard clip
	// operator that will indicate the length of the excised sequence.
	AlignedSequence string `protobuf:"bytes,14,opt,name=aligned_sequence,json=alignedSequence" json:"aligned_sequence,omitempty"`
	// The quality of the read sequence contained in this alignment record
	// (equivalent to QUAL in SAM).
	// `alignedSequence` and `alignedQuality` may be shorter than the full read
	// sequence and quality. This will occur if the alignment is part of a
	// chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR
	// for this read will begin/end with a hard clip operator that will indicate
	// the length of the excised sequence.
	AlignedQuality []int32 `protobuf:"varint,15,rep,packed,name=aligned_quality,json=alignedQuality" json:"aligned_quality,omitempty"`
	// The mapping of the primary alignment of the
	// `(readNumber+1)%numberReads` read in the fragment. It replaces
	// mate position and mate strand in SAM.
	NextMatePosition *Position `protobuf:"bytes,16,opt,name=next_mate_position,json=nextMatePosition" json:"next_mate_position,omitempty"`
	// A map of additional read alignment information. This must be of the form
	// map<string, string[]> (string key mapping to a list of string values).
	Info map[string]*google_protobuf3.ListValue `protobuf:"bytes,17,rep,name=info" json:"info,omitempty" protobuf_key:"bytes,1,opt,name=key" protobuf_val:"bytes,2,opt,name=value"`
}

func (m *Read) Reset()                    { *m = Read{} }
func (m *Read) String() string            { return proto.CompactTextString(m) }
func (*Read) ProtoMessage()               {}
func (*Read) Descriptor() ([]byte, []int) { return fileDescriptor6, []int{1} }

func (m *Read) GetId() string {
	if m != nil {
		return m.Id
	}
	return ""
}

func (m *Read) GetReadGroupId() string {
	if m != nil {
		return m.ReadGroupId
	}
	return ""
}

func (m *Read) GetReadGroupSetId() string {
	if m != nil {
		return m.ReadGroupSetId
	}
	return ""
}

func (m *Read) GetFragmentName() string {
	if m != nil {
		return m.FragmentName
	}
	return ""
}

func (m *Read) GetProperPlacement() bool {
	if m != nil {
		return m.ProperPlacement
	}
	return false
}

func (m *Read) GetDuplicateFragment() bool {
	if m != nil {
		return m.DuplicateFragment
	}
	return false
}

func (m *Read) GetFragmentLength() int32 {
	if m != nil {
		return m.FragmentLength
	}
	return 0
}

func (m *Read) GetReadNumber() int32 {
	if m != nil {
		return m.ReadNumber
	}
	return 0
}

func (m *Read) GetNumberReads() int32 {
	if m != nil {
		return m.NumberReads
	}
	return 0
}

func (m *Read) GetFailedVendorQualityChecks() bool {
	if m != nil {
		return m.FailedVendorQualityChecks
	}
	return false
}

func (m *Read) GetAlignment() *LinearAlignment {
	if m != nil {
		return m.Alignment
	}
	return nil
}

func (m *Read) GetSecondaryAlignment() bool {
	if m != nil {
		return m.SecondaryAlignment
	}
	return false
}

func (m *Read) GetSupplementaryAlignment() bool {
	if m != nil {
		return m.SupplementaryAlignment
	}
	return false
}

func (m *Read) GetAlignedSequence() string {
	if m != nil {
		return m.AlignedSequence
	}
	return ""
}

func (m *Read) GetAlignedQuality() []int32 {
	if m != nil {
		return m.AlignedQuality
	}
	return nil
}

func (m *Read) GetNextMatePosition() *Position {
	if m != nil {
		return m.NextMatePosition
	}
	return nil
}

func (m *Read) GetInfo() map[string]*google_protobuf3.ListValue {
	if m != nil {
		return m.Info
	}
	return nil
}

func init() {
	proto.RegisterType((*LinearAlignment)(nil), "google.genomics.v1.LinearAlignment")
	proto.RegisterType((*Read)(nil), "google.genomics.v1.Read")
}

func init() { proto.RegisterFile("google/genomics/v1/readalignment.proto", fileDescriptor6) }

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