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Diffstat (limited to 'third_party/googleapis/google/genomics/v1/cigar.proto')
-rw-r--r-- | third_party/googleapis/google/genomics/v1/cigar.proto | 99 |
1 files changed, 99 insertions, 0 deletions
diff --git a/third_party/googleapis/google/genomics/v1/cigar.proto b/third_party/googleapis/google/genomics/v1/cigar.proto new file mode 100644 index 0000000000..e70e943877 --- /dev/null +++ b/third_party/googleapis/google/genomics/v1/cigar.proto @@ -0,0 +1,99 @@ +// Copyright 2016 Google Inc. +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +syntax = "proto3"; + +package google.genomics.v1; + +import "google/api/annotations.proto"; + +option cc_enable_arenas = true; +option go_package = "google.golang.org/genproto/googleapis/genomics/v1;genomics"; +option java_multiple_files = true; +option java_outer_classname = "CigarProto"; +option java_package = "com.google.genomics.v1"; + + +// A single CIGAR operation. +message CigarUnit { + // Describes the different types of CIGAR alignment operations that exist. + // Used wherever CIGAR alignments are used. + enum Operation { + OPERATION_UNSPECIFIED = 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`. + ALIGNMENT_MATCH = 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`. + INSERT = 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`. + DELETE = 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`. + SKIP = 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. + CLIP_SOFT = 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`. + CLIP_HARD = 6; + + // The pad operator indicates that there is padding in an alignment. This + // operator is equivalent to SAM's `P`. + PAD = 7; + + // This operator indicates that this portion of the aligned sequence exactly + // matches the reference. This operator is equivalent to SAM's `=`. + SEQUENCE_MATCH = 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`. + SEQUENCE_MISMATCH = 9; + } + + Operation operation = 1; + + // The number of genomic bases that the operation runs for. Required. + int64 operation_length = 2; + + // `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. + string reference_sequence = 3; +} |