394 lines
17 KiB
Go
394 lines
17 KiB
Go
// Code generated by protoc-gen-go. DO NOT EDIT.
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// source: google/genomics/v1/readalignment.proto
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package genomics
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import proto "github.com/golang/protobuf/proto"
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import fmt "fmt"
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import math "math"
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import _ "google.golang.org/genproto/googleapis/api/annotations"
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import google_protobuf3 "github.com/golang/protobuf/ptypes/struct"
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// Reference imports to suppress errors if they are not otherwise used.
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var _ = proto.Marshal
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var _ = fmt.Errorf
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var _ = math.Inf
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// A linear alignment can be represented by one CIGAR string. Describes the
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// mapped position and local alignment of the read to the reference.
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type LinearAlignment struct {
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// The position of this alignment.
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Position *Position `protobuf:"bytes,1,opt,name=position" json:"position,omitempty"`
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// The mapping quality of this alignment. Represents how likely
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// the read maps to this position as opposed to other locations.
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//
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// Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to
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// the nearest integer.
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MappingQuality int32 `protobuf:"varint,2,opt,name=mapping_quality,json=mappingQuality" json:"mapping_quality,omitempty"`
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// Represents the local alignment of this sequence (alignment matches, indels,
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// etc) against the reference.
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Cigar []*CigarUnit `protobuf:"bytes,3,rep,name=cigar" json:"cigar,omitempty"`
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}
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func (m *LinearAlignment) Reset() { *m = LinearAlignment{} }
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func (m *LinearAlignment) String() string { return proto.CompactTextString(m) }
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func (*LinearAlignment) ProtoMessage() {}
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func (*LinearAlignment) Descriptor() ([]byte, []int) { return fileDescriptor6, []int{0} }
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func (m *LinearAlignment) GetPosition() *Position {
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if m != nil {
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return m.Position
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}
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return nil
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}
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func (m *LinearAlignment) GetMappingQuality() int32 {
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if m != nil {
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return m.MappingQuality
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}
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return 0
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}
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func (m *LinearAlignment) GetCigar() []*CigarUnit {
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if m != nil {
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return m.Cigar
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}
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return nil
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}
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// A read alignment describes a linear alignment of a string of DNA to a
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// [reference sequence][google.genomics.v1.Reference], in addition to metadata
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// about the fragment (the molecule of DNA sequenced) and the read (the bases
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// which were read by the sequencer). A read is equivalent to a line in a SAM
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// file. A read belongs to exactly one read group and exactly one
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// [read group set][google.genomics.v1.ReadGroupSet].
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//
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// For more genomics resource definitions, see [Fundamentals of Google
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// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
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//
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// ### Reverse-stranded reads
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//
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// Mapped reads (reads having a non-null `alignment`) can be aligned to either
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// the forward or the reverse strand of their associated reference. Strandedness
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// of a mapped read is encoded by `alignment.position.reverseStrand`.
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//
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// If we consider the reference to be a forward-stranded coordinate space of
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// `[0, reference.length)` with `0` as the left-most position and
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// `reference.length` as the right-most position, reads are always aligned left
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// to right. That is, `alignment.position.position` always refers to the
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// left-most reference coordinate and `alignment.cigar` describes the alignment
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// of this read to the reference from left to right. All per-base fields such as
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// `alignedSequence` and `alignedQuality` share this same left-to-right
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// orientation; this is true of reads which are aligned to either strand. For
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// reverse-stranded reads, this means that `alignedSequence` is the reverse
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// complement of the bases that were originally reported by the sequencing
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// machine.
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//
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// ### Generating a reference-aligned sequence string
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//
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// When interacting with mapped reads, it's often useful to produce a string
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// representing the local alignment of the read to reference. The following
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// pseudocode demonstrates one way of doing this:
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//
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// out = ""
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// offset = 0
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// for c in read.alignment.cigar {
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// switch c.operation {
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// case "ALIGNMENT_MATCH", "SEQUENCE_MATCH", "SEQUENCE_MISMATCH":
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// out += read.alignedSequence[offset:offset+c.operationLength]
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// offset += c.operationLength
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// break
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// case "CLIP_SOFT", "INSERT":
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// offset += c.operationLength
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// break
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// case "PAD":
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// out += repeat("*", c.operationLength)
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// break
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// case "DELETE":
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// out += repeat("-", c.operationLength)
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// break
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// case "SKIP":
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// out += repeat(" ", c.operationLength)
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// break
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// case "CLIP_HARD":
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// break
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// }
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// }
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// return out
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//
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// ### Converting to SAM's CIGAR string
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//
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// The following pseudocode generates a SAM CIGAR string from the
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// `cigar` field. Note that this is a lossy conversion
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// (`cigar.referenceSequence` is lost).
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//
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// cigarMap = {
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// "ALIGNMENT_MATCH": "M",
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// "INSERT": "I",
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// "DELETE": "D",
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// "SKIP": "N",
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// "CLIP_SOFT": "S",
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// "CLIP_HARD": "H",
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// "PAD": "P",
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// "SEQUENCE_MATCH": "=",
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// "SEQUENCE_MISMATCH": "X",
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// }
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// cigarStr = ""
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// for c in read.alignment.cigar {
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// cigarStr += c.operationLength + cigarMap[c.operation]
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// }
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// return cigarStr
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type Read struct {
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// The server-generated read ID, unique across all reads. This is different
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// from the `fragmentName`.
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Id string `protobuf:"bytes,1,opt,name=id" json:"id,omitempty"`
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// The ID of the read group this read belongs to. A read belongs to exactly
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// one read group. This is a server-generated ID which is distinct from SAM's
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// RG tag (for that value, see
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// [ReadGroup.name][google.genomics.v1.ReadGroup.name]).
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ReadGroupId string `protobuf:"bytes,2,opt,name=read_group_id,json=readGroupId" json:"read_group_id,omitempty"`
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// The ID of the read group set this read belongs to. A read belongs to
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// exactly one read group set.
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ReadGroupSetId string `protobuf:"bytes,3,opt,name=read_group_set_id,json=readGroupSetId" json:"read_group_set_id,omitempty"`
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// The fragment name. Equivalent to QNAME (query template name) in SAM.
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FragmentName string `protobuf:"bytes,4,opt,name=fragment_name,json=fragmentName" json:"fragment_name,omitempty"`
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// The orientation and the distance between reads from the fragment are
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// consistent with the sequencing protocol (SAM flag 0x2).
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ProperPlacement bool `protobuf:"varint,5,opt,name=proper_placement,json=properPlacement" json:"proper_placement,omitempty"`
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// The fragment is a PCR or optical duplicate (SAM flag 0x400).
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DuplicateFragment bool `protobuf:"varint,6,opt,name=duplicate_fragment,json=duplicateFragment" json:"duplicate_fragment,omitempty"`
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// The observed length of the fragment, equivalent to TLEN in SAM.
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FragmentLength int32 `protobuf:"varint,7,opt,name=fragment_length,json=fragmentLength" json:"fragment_length,omitempty"`
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// The read number in sequencing. 0-based and less than numberReads. This
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// field replaces SAM flag 0x40 and 0x80.
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ReadNumber int32 `protobuf:"varint,8,opt,name=read_number,json=readNumber" json:"read_number,omitempty"`
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// The number of reads in the fragment (extension to SAM flag 0x1).
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NumberReads int32 `protobuf:"varint,9,opt,name=number_reads,json=numberReads" json:"number_reads,omitempty"`
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// Whether this read did not pass filters, such as platform or vendor quality
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// controls (SAM flag 0x200).
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FailedVendorQualityChecks bool `protobuf:"varint,10,opt,name=failed_vendor_quality_checks,json=failedVendorQualityChecks" json:"failed_vendor_quality_checks,omitempty"`
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// The linear alignment for this alignment record. This field is null for
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// unmapped reads.
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Alignment *LinearAlignment `protobuf:"bytes,11,opt,name=alignment" json:"alignment,omitempty"`
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// Whether this alignment is secondary. Equivalent to SAM flag 0x100.
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// A secondary alignment represents an alternative to the primary alignment
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// for this read. Aligners may return secondary alignments if a read can map
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// ambiguously to multiple coordinates in the genome. By convention, each read
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// has one and only one alignment where both `secondaryAlignment`
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// and `supplementaryAlignment` are false.
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SecondaryAlignment bool `protobuf:"varint,12,opt,name=secondary_alignment,json=secondaryAlignment" json:"secondary_alignment,omitempty"`
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// Whether this alignment is supplementary. Equivalent to SAM flag 0x800.
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// Supplementary alignments are used in the representation of a chimeric
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// alignment. In a chimeric alignment, a read is split into multiple
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// linear alignments that map to different reference contigs. The first
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// linear alignment in the read will be designated as the representative
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// alignment; the remaining linear alignments will be designated as
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// supplementary alignments. These alignments may have different mapping
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// quality scores. In each linear alignment in a chimeric alignment, the read
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// will be hard clipped. The `alignedSequence` and
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// `alignedQuality` fields in the alignment record will only
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// represent the bases for its respective linear alignment.
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SupplementaryAlignment bool `protobuf:"varint,13,opt,name=supplementary_alignment,json=supplementaryAlignment" json:"supplementary_alignment,omitempty"`
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// The bases of the read sequence contained in this alignment record,
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// **without CIGAR operations applied** (equivalent to SEQ in SAM).
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// `alignedSequence` and `alignedQuality` may be
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// shorter than the full read sequence and quality. This will occur if the
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// alignment is part of a chimeric alignment, or if the read was trimmed. When
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// this occurs, the CIGAR for this read will begin/end with a hard clip
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// operator that will indicate the length of the excised sequence.
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AlignedSequence string `protobuf:"bytes,14,opt,name=aligned_sequence,json=alignedSequence" json:"aligned_sequence,omitempty"`
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// The quality of the read sequence contained in this alignment record
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// (equivalent to QUAL in SAM).
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// `alignedSequence` and `alignedQuality` may be shorter than the full read
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// sequence and quality. This will occur if the alignment is part of a
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// chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR
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// for this read will begin/end with a hard clip operator that will indicate
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// the length of the excised sequence.
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AlignedQuality []int32 `protobuf:"varint,15,rep,packed,name=aligned_quality,json=alignedQuality" json:"aligned_quality,omitempty"`
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// The mapping of the primary alignment of the
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// `(readNumber+1)%numberReads` read in the fragment. It replaces
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// mate position and mate strand in SAM.
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NextMatePosition *Position `protobuf:"bytes,16,opt,name=next_mate_position,json=nextMatePosition" json:"next_mate_position,omitempty"`
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// A map of additional read alignment information. This must be of the form
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// map<string, string[]> (string key mapping to a list of string values).
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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"`
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}
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func (m *Read) Reset() { *m = Read{} }
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func (m *Read) String() string { return proto.CompactTextString(m) }
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func (*Read) ProtoMessage() {}
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func (*Read) Descriptor() ([]byte, []int) { return fileDescriptor6, []int{1} }
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func (m *Read) GetId() string {
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if m != nil {
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return m.Id
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}
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return ""
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}
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func (m *Read) GetReadGroupId() string {
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if m != nil {
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return m.ReadGroupId
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}
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return ""
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}
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func (m *Read) GetReadGroupSetId() string {
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if m != nil {
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return m.ReadGroupSetId
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}
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return ""
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}
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func (m *Read) GetFragmentName() string {
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if m != nil {
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return m.FragmentName
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}
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return ""
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}
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func (m *Read) GetProperPlacement() bool {
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if m != nil {
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return m.ProperPlacement
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}
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return false
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}
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func (m *Read) GetDuplicateFragment() bool {
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if m != nil {
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return m.DuplicateFragment
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}
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return false
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}
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func (m *Read) GetFragmentLength() int32 {
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if m != nil {
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return m.FragmentLength
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}
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return 0
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}
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func (m *Read) GetReadNumber() int32 {
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if m != nil {
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return m.ReadNumber
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}
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return 0
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}
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func (m *Read) GetNumberReads() int32 {
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if m != nil {
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return m.NumberReads
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}
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return 0
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}
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func (m *Read) GetFailedVendorQualityChecks() bool {
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if m != nil {
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return m.FailedVendorQualityChecks
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}
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return false
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}
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func (m *Read) GetAlignment() *LinearAlignment {
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if m != nil {
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return m.Alignment
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}
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return nil
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}
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func (m *Read) GetSecondaryAlignment() bool {
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if m != nil {
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return m.SecondaryAlignment
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}
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return false
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}
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func (m *Read) GetSupplementaryAlignment() bool {
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if m != nil {
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return m.SupplementaryAlignment
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}
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return false
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}
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func (m *Read) GetAlignedSequence() string {
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if m != nil {
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return m.AlignedSequence
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}
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return ""
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}
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func (m *Read) GetAlignedQuality() []int32 {
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if m != nil {
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return m.AlignedQuality
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}
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return nil
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}
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func (m *Read) GetNextMatePosition() *Position {
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if m != nil {
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return m.NextMatePosition
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}
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return nil
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}
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func (m *Read) GetInfo() map[string]*google_protobuf3.ListValue {
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if m != nil {
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return m.Info
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}
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return nil
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}
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func init() {
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proto.RegisterType((*LinearAlignment)(nil), "google.genomics.v1.LinearAlignment")
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proto.RegisterType((*Read)(nil), "google.genomics.v1.Read")
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}
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func init() { proto.RegisterFile("google/genomics/v1/readalignment.proto", fileDescriptor6) }
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var fileDescriptor6 = []byte{
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// 683 bytes of a gzipped FileDescriptorProto
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|
|
0x77, 0xf4, 0xb6, 0xec, 0x2e, 0x9b, 0xe6, 0x2f, 0x4b, 0xe6, 0x2d, 0xbc, 0x88, 0x0b, 0x7f, 0xe7,
|
|
0x18, 0x08, 0x1e, 0xd2, 0x6c, 0xee, 0x2f, 0x82, 0xad, 0xeb, 0xd4, 0xa4, 0x36, 0x2d, 0x16, 0xf4,
|
|
0x15, 0xfc, 0x93, 0x17, 0x69, 0x1a, 0xeb, 0xf6, 0x3e, 0x76, 0xda, 0xd0, 0x4e, 0x5b, 0x8f, 0xcc,
|
|
0x0b, 0xc7, 0x3d, 0xe8, 0x6b, 0x14, 0x43, 0x3f, 0xc7, 0xfb, 0x02, 0x79, 0x80, 0x76, 0x57, 0x0f,
|
|
0xb7, 0x57, 0xe9, 0x57, 0x95, 0xac, 0xa6, 0x60, 0x50, 0xb3, 0xca, 0xbd, 0x61, 0x53, 0x4d, 0xa1,
|
|
0x92, 0xcd, 0x2a, 0x7f, 0x00, 0xc2, 0xf1, 0xab, 0xf4, 0x13, 0x35, 0xdd, 0xfa, 0x6e, 0xfa, 0x7f,
|
|
0x70, 0x37, 0x7d, 0xe5, 0xf7, 0x91, 0x4a, 0x34, 0x0a, 0x79, 0x09, 0x2b, 0x8c, 0x4f, 0x85, 0xbd,
|
|
0xa9, 0xaf, 0x62, 0xb4, 0xcc, 0x5b, 0x8d, 0xcd, 0x39, 0xe7, 0x53, 0xf1, 0x96, 0xcb, 0x6c, 0xee,
|
|
0x69, 0x7e, 0x70, 0x05, 0xed, 0x5a, 0x22, 0x7d, 0x68, 0xde, 0xe1, 0xbc, 0x3a, 0x0f, 0xf5, 0x93,
|
|
0xbc, 0x80, 0xd6, 0x8c, 0xc6, 0x05, 0xea, 0xbb, 0xe8, 0x1c, 0x0c, 0x4c, 0x5c, 0xf3, 0x24, 0x38,
|
|
0x17, 0x2c, 0x97, 0xd7, 0x8a, 0xf0, 0x4a, 0xf0, 0xb8, 0x71, 0x64, 0x9d, 0x26, 0xb0, 0x15, 0x88,
|
|
0x64, 0x49, 0x0d, 0xa7, 0x44, 0x15, 0x51, 0x77, 0x75, 0xa2, 0xa2, 0x4c, 0xac, 0x2f, 0xc7, 0x86,
|
|
0x14, 0x31, 0xe5, 0x91, 0x23, 0xb2, 0x48, 0x3d, 0x4b, 0x3a, 0x87, 0x5b, 0x9a, 0x68, 0xca, 0xf2,
|
|
0x87, 0x4f, 0xd5, 0x6b, 0xf3, 0xfb, 0x87, 0x65, 0xdd, 0xac, 0x6a, 0xf2, 0xf0, 0x67, 0x00, 0x00,
|
|
0x00, 0xff, 0xff, 0xd0, 0xe1, 0xf6, 0x57, 0x4d, 0x05, 0x00, 0x00,
|
|
}
|