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100 lines
3.9 KiB
Protocol Buffer
100 lines
3.9 KiB
Protocol Buffer
// Copyright 2016 Google Inc.
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//
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// Licensed under the Apache License, Version 2.0 (the "License");
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// you may not use this file except in compliance with the License.
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// You may obtain a copy of the License at
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//
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// http://www.apache.org/licenses/LICENSE-2.0
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//
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// Unless required by applicable law or agreed to in writing, software
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// distributed under the License is distributed on an "AS IS" BASIS,
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// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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// See the License for the specific language governing permissions and
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// limitations under the License.
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syntax = "proto3";
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package google.genomics.v1;
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import "google/api/annotations.proto";
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option cc_enable_arenas = true;
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option go_package = "google.golang.org/genproto/googleapis/genomics/v1;genomics";
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option java_multiple_files = true;
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option java_outer_classname = "CigarProto";
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option java_package = "com.google.genomics.v1";
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// A single CIGAR operation.
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message CigarUnit {
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// Describes the different types of CIGAR alignment operations that exist.
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// Used wherever CIGAR alignments are used.
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enum Operation {
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OPERATION_UNSPECIFIED = 0;
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// An alignment match indicates that a sequence can be aligned to the
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// reference without evidence of an INDEL. Unlike the
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// `SEQUENCE_MATCH` and `SEQUENCE_MISMATCH` operators,
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// the `ALIGNMENT_MATCH` operator does not indicate whether the
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// reference and read sequences are an exact match. This operator is
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// equivalent to SAM's `M`.
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ALIGNMENT_MATCH = 1;
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// The insert operator indicates that the read contains evidence of bases
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// being inserted into the reference. This operator is equivalent to SAM's
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// `I`.
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INSERT = 2;
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// The delete operator indicates that the read contains evidence of bases
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// being deleted from the reference. This operator is equivalent to SAM's
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// `D`.
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DELETE = 3;
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// The skip operator indicates that this read skips a long segment of the
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// reference, but the bases have not been deleted. This operator is commonly
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// used when working with RNA-seq data, where reads may skip long segments
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// of the reference between exons. This operator is equivalent to SAM's
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// `N`.
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SKIP = 4;
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// The soft clip operator indicates that bases at the start/end of a read
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// have not been considered during alignment. This may occur if the majority
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// of a read maps, except for low quality bases at the start/end of a read.
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// This operator is equivalent to SAM's `S`. Bases that are soft
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// clipped will still be stored in the read.
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CLIP_SOFT = 5;
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// The hard clip operator indicates that bases at the start/end of a read
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// have been omitted from this alignment. This may occur if this linear
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// alignment is part of a chimeric alignment, or if the read has been
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// trimmed (for example, during error correction or to trim poly-A tails for
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// RNA-seq). This operator is equivalent to SAM's `H`.
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CLIP_HARD = 6;
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// The pad operator indicates that there is padding in an alignment. This
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// operator is equivalent to SAM's `P`.
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PAD = 7;
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// This operator indicates that this portion of the aligned sequence exactly
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// matches the reference. This operator is equivalent to SAM's `=`.
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SEQUENCE_MATCH = 8;
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// This operator indicates that this portion of the aligned sequence is an
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// alignment match to the reference, but a sequence mismatch. This can
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// indicate a SNP or a read error. This operator is equivalent to SAM's
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// `X`.
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SEQUENCE_MISMATCH = 9;
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}
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Operation operation = 1;
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// The number of genomic bases that the operation runs for. Required.
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int64 operation_length = 2;
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// `referenceSequence` is only used at mismatches
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// (`SEQUENCE_MISMATCH`) and deletions (`DELETE`).
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// Filling this field replaces SAM's MD tag. If the relevant information is
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// not available, this field is unset.
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string reference_sequence = 3;
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}
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