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+// Copyright 2018 Google LLC.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions
+// are met:
+//
+// 1. Redistributions of source code must retain the above copyright notice,
+//    this list of conditions and the following disclaimer.
+//
+// 2. Redistributions in binary form must reproduce the above copyright
+//    notice, this list of conditions and the following disclaimer in the
+//    documentation and/or other materials provided with the distribution.
+//
+// 3. Neither the name of the copyright holder nor the names of its
+//    contributors may be used to endorse or promote products derived from this
+//    software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+// LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+// CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+// SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+// INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+// CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+// ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+// POSSIBILITY OF SUCH DAMAGE.
+syntax = "proto3";
+
+import "third_party/nucleus/protos/range.proto";
+
+package nucleus.genomics.v1;
+
+// This file contains information about a reference genome assembly. It
+// currently only defines a message to represent a single contig, but can be
+// extended to capture information about an entire assembly as well (e.g.
+// all contigs present on an assembly, the species, build, etc.).
+
+// This record type records information about a contig. This is used both in
+// VCF header parsing and by GenomeReference objects for querying references.
+// Due to its generality, this message is also used by the FastaReader to
+// provide detailed information on the description line of a FASTA record even
+// in cases where the record does not correspond to a reference genome contig.
+message ContigInfo {
+  // Required. The name of the contig. Canonically this is the first
+  // non-whitespace-containing string after the > marker in a FASTA file.
+  // For example, the line:
+  //      >chr1 more info here
+  // has a name of "chr1" and a description of "more info here"
+  string name = 1;
+
+  // Ideally this record is filled in as described above, but not all FASTA
+  // readers capture the description information after the name. Since a
+  // description is not required by the FASTA spec, we cannot distinguish cases
+  // where a description was not present and where a parser ignored it.
+  string description = 2;
+
+  // The length of this contig in basepairs.
+  int64 n_bases = 3;
+
+  // Additional information used when reading and writing VCF headers. An
+  // example map of key-value extra fields would transform an input line
+  // containing 'assembly=B36,taxonomy=x,species="Homo sapiens"' to a map with
+  // "assembly" -> "B36", "taxonomy" -> "x", "species" -> "Homo sapiens". We
+  // never use this information internally, other than reading it in so we can
+  // write the contig out again.
+  map<string, string> extra = 5;
+
+  // The position of this contig in the src_fasta file. The first contig would
+  // have position 0.
+  // TODO: rename to something more generic.
+  int32 pos_in_fasta = 4;
+}
+
+// A full, or partial, sequence of bases from a contig in a reference genome.
+message ReferenceSequence {
+  // The location on the genome this sequence of bases comes from.
+  Range region = 1;
+
+  // The bases of this part of the reference genome.
+  string bases = 2;
+}