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This repository implements GA4GH schemas
/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.ga4gh.methods;
@SuppressWarnings("all")
@org.apache.avro.specific.AvroGenerated
public interface ReferenceMethods {
public static final org.apache.avro.Protocol PROTOCOL = org.apache.avro.Protocol.parse("{\"protocol\":\"ReferenceMethods\",\"namespace\":\"org.ga4gh.methods\",\"types\":[{\"type\":\"enum\",\"name\":\"Strand\",\"namespace\":\"org.ga4gh.models\",\"doc\":\"Indicates the DNA strand associate for some data item.\\n* `NEG_STRAND`: The negative (-) strand.\\n* `POS_STRAND`: The postive (+) strand.\",\"symbols\":[\"NEG_STRAND\",\"POS_STRAND\"]},{\"type\":\"record\",\"name\":\"Position\",\"namespace\":\"org.ga4gh.models\",\"doc\":\"A `Position` is an unoriented base in some `Reference`. A `Position` is\\nrepresented by a `Reference` name, and a base number on that `Reference`\\n(0-based).\",\"fields\":[{\"name\":\"referenceName\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The name of the `Reference` on which the `Position` is located.\"},{\"name\":\"position\",\"type\":\"long\",\"doc\":\"The 0-based offset from the start of the forward strand for that `Reference`.\\n Genomic positions are non-negative integers less than `Reference` length.\"},{\"name\":\"strand\",\"type\":\"Strand\",\"doc\":\"Strand the position is associated with.\"}]},{\"type\":\"record\",\"name\":\"ExternalIdentifier\",\"namespace\":\"org.ga4gh.models\",\"doc\":\"Identifier from a public database\",\"fields\":[{\"name\":\"database\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The source of the identifier.\\n (e.g. `Ensembl`)\"},{\"name\":\"identifier\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The ID defined by the external database.\\n (e.g. `ENST00000000000`)\"},{\"name\":\"version\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The version of the object or the database\\n (e.g. `78`)\"}]},{\"type\":\"enum\",\"name\":\"CigarOperation\",\"namespace\":\"org.ga4gh.models\",\"doc\":\"An enum for the different types of CIGAR alignment operations that exist.\\nUsed wherever CIGAR alignments are used. The different enumerated values\\nhave the following usage:\\n\\n* `ALIGNMENT_MATCH`: An alignment match indicates that a sequence can be\\n aligned to the reference without evidence of an INDEL. Unlike the\\n `SEQUENCE_MATCH` and `SEQUENCE_MISMATCH` operators, the `ALIGNMENT_MATCH`\\n operator does not indicate whether the reference and read sequences are an\\n exact match. This operator is equivalent to SAM's `M`.\\n* `INSERT`: The insert operator indicates that the read contains evidence of\\n bases being inserted into the reference. This operator is equivalent to\\n SAM's `I`.\\n* `DELETE`: The delete operator indicates that the read contains evidence of\\n bases being deleted from the reference. This operator is equivalent to\\n SAM's `D`.\\n* `SKIP`: The skip operator indicates that this read skips a long segment of\\n the reference, but the bases have not been deleted. This operator is\\n commonly used when working with RNA-seq data, where reads may skip long\\n segments of the reference between exons. This operator is equivalent to\\n SAM's 'N'.\\n* `CLIP_SOFT`: The soft clip operator indicates that bases at the start/end\\n of a read have not been considered during alignment. This may occur if the\\n majority of a read maps, except for low quality bases at the start/end of\\n a read. This operator is equivalent to SAM's 'S'. Bases that are soft clipped\\n will still be stored in the read.\\n* `CLIP_HARD`: The hard clip operator indicates that bases at the start/end of\\n a read have been omitted from this alignment. This may occur if this linear\\n alignment is part of a chimeric alignment, or if the read has been trimmed\\n (e.g., during error correction, or to trim poly-A tails for RNA-seq). This\\n operator is equivalent to SAM's 'H'.\\n* `PAD`: The pad operator indicates that there is padding in an alignment.\\n This operator is equivalent to SAM's 'P'.\\n* `SEQUENCE_MATCH`: This operator indicates that this portion of the aligned\\n sequence exactly matches the reference (e.g., all bases are equal to the\\n reference bases). This operator is equivalent to SAM's '='.\\n* `SEQUENCE_MISMATCH`: This operator indicates that this portion of the\\n aligned sequence is an alignment match to the reference, but a sequence\\n mismatch (e.g., the bases are not equal to the reference). This can\\n indicate a SNP or a read error. This operator is equivalent to SAM's 'X'.\",\"symbols\":[\"ALIGNMENT_MATCH\",\"INSERT\",\"DELETE\",\"SKIP\",\"CLIP_SOFT\",\"CLIP_HARD\",\"PAD\",\"SEQUENCE_MATCH\",\"SEQUENCE_MISMATCH\"]},{\"type\":\"record\",\"name\":\"CigarUnit\",\"namespace\":\"org.ga4gh.models\",\"doc\":\"A structure for an instance of a CIGAR operation.\\n`FIXME: This belongs under Reads (only readAlignment refers to this)`\",\"fields\":[{\"name\":\"operation\",\"type\":\"CigarOperation\",\"doc\":\"The operation type.\"},{\"name\":\"operationLength\",\"type\":\"long\",\"doc\":\"The number of bases that the operation runs for.\"},{\"name\":\"referenceSequence\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"`referenceSequence` is only used at mismatches (`SEQUENCE_MISMATCH`)\\n and deletions (`DELETE`). Filling this field replaces the MD tag.\\n If the relevant information is not available, leave this field as `null`.\",\"default\":null}]},{\"type\":\"error\",\"name\":\"GAException\",\"doc\":\"A general exception type.\",\"fields\":[{\"name\":\"message\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The error message\"},{\"name\":\"errorCode\",\"type\":\"int\",\"doc\":\"The numerical error code\",\"default\":-1}]},{\"type\":\"record\",\"name\":\"Reference\",\"namespace\":\"org.ga4gh.models\",\"doc\":\"A `Reference` is a canonical assembled contig, intended to act as a\\nreference coordinate space for other genomic annotations. A single\\n`Reference` might represent the human chromosome 1, for instance.\\n\\n`Reference`s are designed to be immutable.\",\"fields\":[{\"name\":\"id\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The reference ID. Unique within the repository.\"},{\"name\":\"length\",\"type\":\"long\",\"doc\":\"The length of this reference's sequence.\"},{\"name\":\"md5checksum\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The MD5 checksum uniquely representing this `Reference` as a lower-case\\n hexadecimal string, calculated as the MD5 of the upper-case sequence\\n excluding all whitespace characters (this is equivalent to SQ:M5 in SAM).\"},{\"name\":\"name\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The name of this reference. (e.g. '22').\"},{\"name\":\"sourceURI\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The URI from which the sequence was obtained. Specifies a FASTA format\\n file/string with one name, sequence pair. In most cases, clients should call\\n the `getReferenceBases()` method to obtain sequence bases for a `Reference`\\n instead of attempting to retrieve this URI.\",\"default\":null},{\"name\":\"sourceAccessions\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}},\"doc\":\"All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) which must include\\n a version number, e.g. `GCF_000001405.26`.\"},{\"name\":\"isDerived\",\"type\":\"boolean\",\"doc\":\"A sequence X is said to be derived from source sequence Y, if X and Y\\n are of the same length and the per-base sequence divergence at A/C/G/T bases\\n is sufficiently small. Two sequences derived from the same official\\n sequence share the same coordinates and annotations, and\\n can be replaced with the official sequence for certain use cases.\",\"default\":false},{\"name\":\"sourceDivergence\",\"type\":[\"null\",\"float\"],\"doc\":\"The `sourceDivergence` is the fraction of non-indel bases that do not match the\\n reference this record was derived from.\",\"default\":null},{\"name\":\"ncbiTaxonId\",\"type\":[\"null\",\"int\"],\"doc\":\"ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human).\",\"default\":null}]},{\"type\":\"record\",\"name\":\"ReferenceSet\",\"namespace\":\"org.ga4gh.models\",\"doc\":\"A `ReferenceSet` is a set of `Reference`s which typically comprise a\\nreference assembly, such as `GRCh38`. A `ReferenceSet` defines a common\\ncoordinate space for comparing reference-aligned experimental data.\",\"fields\":[{\"name\":\"id\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The reference set ID. Unique in the repository.\"},{\"name\":\"name\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The reference set name.\",\"default\":null},{\"name\":\"md5checksum\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc","\":\"Order-independent MD5 checksum which identifies this `ReferenceSet`.\\n\\n To compute this checksum, make a list of `Reference.md5checksum` for all\\n `Reference`s in this set. Then sort that list, and take the MD5 hash of\\n all the strings concatenated together. Express the hash as a lower-case\\n hexadecimal string.\"},{\"name\":\"ncbiTaxonId\",\"type\":[\"null\",\"int\"],\"doc\":\"ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) indicating\\n the species which this assembly is intended to model. Note that contained\\n `Reference`s may specify a different `ncbiTaxonId`, as assemblies may\\n contain reference sequences which do not belong to the modeled species, e.g.\\n EBV in a human reference genome.\",\"default\":null},{\"name\":\"description\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Optional free text description of this reference set.\",\"default\":null},{\"name\":\"assemblyId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Public id of this reference set, such as `GRCh37`.\",\"default\":null},{\"name\":\"sourceURI\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Specifies a FASTA format file/string.\",\"default\":null},{\"name\":\"sourceAccessions\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}},\"doc\":\"All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally\\n with a version number, e.g. `NC_000001.11`.\"},{\"name\":\"isDerived\",\"type\":\"boolean\",\"doc\":\"A reference set may be derived from a source if it contains\\n additional sequences, or some of the sequences within it are derived\\n (see the definition of `isDerived` in `Reference`).\",\"default\":false}]},{\"type\":\"record\",\"name\":\"SearchReferenceSetsRequest\",\"doc\":\"This request maps to the body of `POST /referencesets/search`\\nas JSON.\",\"fields\":[{\"name\":\"md5checksum\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"If not null, return the reference sets for which the\\n `md5checksum` matches this string (case-sensitive, exact match).\\n See `ReferenceSet::md5checksum` for details.\",\"default\":null},{\"name\":\"accession\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"If not null, return the reference sets for which the `accession`\\n matches this string (case-sensitive, exact match).\",\"default\":null},{\"name\":\"assemblyId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"If not null, return the reference sets for which the `assemblyId`\\n matches this string (case-sensitive, exact match).\",\"default\":null},{\"name\":\"pageSize\",\"type\":[\"null\",\"int\"],\"doc\":\"Specifies the maximum number of results to return in a single page.\\n If unspecified, a system default will be used.\",\"default\":null},{\"name\":\"pageToken\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The continuation token, which is used to page through large result sets.\\n To get the next page of results, set this parameter to the value of\\n `nextPageToken` from the previous response.\",\"default\":null}]},{\"type\":\"record\",\"name\":\"SearchReferenceSetsResponse\",\"doc\":\"This is the response from `POST /referencesets/search`\\nexpressed as JSON.\",\"fields\":[{\"name\":\"referenceSets\",\"type\":{\"type\":\"array\",\"items\":\"org.ga4gh.models.ReferenceSet\"},\"doc\":\"The list of matching reference sets.\",\"default\":[]},{\"name\":\"nextPageToken\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The continuation token, which is used to page through large result sets.\\n Provide this value in a subsequent request to return the next page of\\n results. This field will be empty if there aren't any additional results.\",\"default\":null}]},{\"type\":\"record\",\"name\":\"SearchReferencesRequest\",\"doc\":\"This request maps to the body of `POST /references/search`\\nas JSON.\",\"fields\":[{\"name\":\"referenceSetId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The `ReferenceSet` to search.\"},{\"name\":\"md5checksum\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"If not null, return the references for which the\\n `md5checksum` matches this string (case-sensitive, exact match).\\n See `ReferenceSet::md5checksum` for details.\",\"default\":null},{\"name\":\"accession\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"If not null, return the references for which the `accession`\\n matches this string (case-sensitive, exact match).\",\"default\":null},{\"name\":\"pageSize\",\"type\":[\"null\",\"int\"],\"doc\":\"Specifies the maximum number of results to return in a single page.\\n If unspecified, a system default will be used.\",\"default\":null},{\"name\":\"pageToken\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The continuation token, which is used to page through large result sets.\\n To get the next page of results, set this parameter to the value of\\n `nextPageToken` from the previous response.\",\"default\":null}]},{\"type\":\"record\",\"name\":\"SearchReferencesResponse\",\"doc\":\"This is the response from `POST /references/search` expressed as JSON.\",\"fields\":[{\"name\":\"references\",\"type\":{\"type\":\"array\",\"items\":\"org.ga4gh.models.Reference\"},\"doc\":\"The list of matching references.\",\"default\":[]},{\"name\":\"nextPageToken\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The continuation token, which is used to page through large result sets.\\n Provide this value in a subsequent request to return the next page of\\n results. This field will be empty if there aren't any additional results.\",\"default\":null}]},{\"type\":\"record\",\"name\":\"ListReferenceBasesRequest\",\"doc\":\"The query parameters for a request to `GET /references/{id}/bases`, for\\nexample:\\n\\n`GET /references/{id}/bases?start=100&end=200`\",\"fields\":[{\"name\":\"start\",\"type\":\"long\",\"doc\":\"The start position (0-based) of this query. Defaults to 0.\\n Genomic positions are non-negative integers less than reference length.\\n Requests spanning the join of circular genomes are represented as\\n two requests one on each side of the join (position 0).\",\"default\":0},{\"name\":\"end\",\"type\":[\"null\",\"long\"],\"doc\":\"The end position (0-based, exclusive) of this query. Defaults\\n to the length of this `Reference`.\",\"default\":null},{\"name\":\"pageToken\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The continuation token, which is used to page through large result sets.\\n To get the next page of results, set this parameter to the value of\\n `nextPageToken` from the previous response.\",\"default\":null}]},{\"type\":\"record\",\"name\":\"ListReferenceBasesResponse\",\"doc\":\"The response from `GET /references/{id}/bases` expressed as JSON.\",\"fields\":[{\"name\":\"offset\",\"type\":\"long\",\"doc\":\"The offset position (0-based) of the given sequence from the start of this\\n `Reference`. This value will differ for each page in a paginated request.\",\"default\":0},{\"name\":\"sequence\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"A substring of the bases that make up this reference. Bases are represented\\n as IUPAC-IUB codes; this string matches the regexp `[ACGTMRWSYKVHDBN]*`.\"},{\"name\":\"nextPageToken\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The continuation token, which is used to page through large result sets.\\n Provide this value in a subsequent request to return the next page of\\n results. This field will be empty if there aren't any additional results.\",\"default\":null}]}],\"messages\":{\"searchReferenceSets\":{\"doc\":\"Gets a list of `ReferenceSet` matching the search criteria.\\n\\n`POST /referencesets/search` must accept a JSON version of\\n`SearchReferenceSetsRequest` as the post body and will return a JSON\\nversion of `SearchReferenceSetsResponse`.\",\"request\":[{\"name\":\"request\",\"type\":\"SearchReferenceSetsRequest\"}],\"response\":\"SearchReferenceSetsResponse\",\"errors\":[\"GAException\"]},\"getReferenceSet\":{\"doc\":\"Gets a `ReferenceSet` by ID.\\n`GET /referencesets/{id}` will return a JSON version of `ReferenceSet`.\",\"request\":[{\"name\":\"id\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}],\"response\":\"org.ga4gh.models.ReferenceSet\",\"errors\":[\"GAException\"]},\"searchReferences\":{\"doc\":\"Gets a list of `Reference` matching the search criteria.\\n\\n`POST /references/sear","ch` must accept a JSON version of\\n`SearchReferencesRequest` as the post body and will return a JSON\\nversion of `SearchReferencesResponse`.\",\"request\":[{\"name\":\"request\",\"type\":\"SearchReferencesRequest\"}],\"response\":\"SearchReferencesResponse\",\"errors\":[\"GAException\"]},\"getReference\":{\"doc\":\"Gets a `Reference` by ID.\\n`GET /references/{id}` will return a JSON version of `Reference`.\",\"request\":[{\"name\":\"id\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}],\"response\":\"org.ga4gh.models.Reference\",\"errors\":[\"GAException\"]},\"getReferenceBases\":{\"doc\":\"Lists `Reference` bases by ID and optional range.\\n`GET /references/{id}/bases` will return a JSON version of\\n`ListReferenceBasesResponse`.\",\"request\":[{\"name\":\"id\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"}},{\"name\":\"request\",\"type\":\"ListReferenceBasesRequest\"}],\"response\":\"ListReferenceBasesResponse\",\"errors\":[\"GAException\"]}}}");
/** Gets a list of `ReferenceSet` matching the search criteria.
`POST /referencesets/search` must accept a JSON version of
`SearchReferenceSetsRequest` as the post body and will return a JSON
version of `SearchReferenceSetsResponse`. */
org.ga4gh.methods.SearchReferenceSetsResponse searchReferenceSets(org.ga4gh.methods.SearchReferenceSetsRequest request) throws org.apache.avro.AvroRemoteException, org.ga4gh.methods.GAException;
/** Gets a `ReferenceSet` by ID.
`GET /referencesets/{id}` will return a JSON version of `ReferenceSet`. */
org.ga4gh.models.ReferenceSet getReferenceSet(java.lang.String id) throws org.apache.avro.AvroRemoteException, org.ga4gh.methods.GAException;
/** Gets a list of `Reference` matching the search criteria.
`POST /references/search` must accept a JSON version of
`SearchReferencesRequest` as the post body and will return a JSON
version of `SearchReferencesResponse`. */
org.ga4gh.methods.SearchReferencesResponse searchReferences(org.ga4gh.methods.SearchReferencesRequest request) throws org.apache.avro.AvroRemoteException, org.ga4gh.methods.GAException;
/** Gets a `Reference` by ID.
`GET /references/{id}` will return a JSON version of `Reference`. */
org.ga4gh.models.Reference getReference(java.lang.String id) throws org.apache.avro.AvroRemoteException, org.ga4gh.methods.GAException;
/** Lists `Reference` bases by ID and optional range.
`GET /references/{id}/bases` will return a JSON version of
`ListReferenceBasesResponse`. */
org.ga4gh.methods.ListReferenceBasesResponse getReferenceBases(java.lang.String id, org.ga4gh.methods.ListReferenceBasesRequest request) throws org.apache.avro.AvroRemoteException, org.ga4gh.methods.GAException;
@SuppressWarnings("all")
public interface Callback extends ReferenceMethods {
public static final org.apache.avro.Protocol PROTOCOL = org.ga4gh.methods.ReferenceMethods.PROTOCOL;
/** Gets a list of `ReferenceSet` matching the search criteria.
`POST /referencesets/search` must accept a JSON version of
`SearchReferenceSetsRequest` as the post body and will return a JSON
version of `SearchReferenceSetsResponse`. */
void searchReferenceSets(org.ga4gh.methods.SearchReferenceSetsRequest request, org.apache.avro.ipc.Callback callback) throws java.io.IOException;
/** Gets a `ReferenceSet` by ID.
`GET /referencesets/{id}` will return a JSON version of `ReferenceSet`. */
void getReferenceSet(java.lang.String id, org.apache.avro.ipc.Callback callback) throws java.io.IOException;
/** Gets a list of `Reference` matching the search criteria.
`POST /references/search` must accept a JSON version of
`SearchReferencesRequest` as the post body and will return a JSON
version of `SearchReferencesResponse`. */
void searchReferences(org.ga4gh.methods.SearchReferencesRequest request, org.apache.avro.ipc.Callback callback) throws java.io.IOException;
/** Gets a `Reference` by ID.
`GET /references/{id}` will return a JSON version of `Reference`. */
void getReference(java.lang.String id, org.apache.avro.ipc.Callback callback) throws java.io.IOException;
/** Lists `Reference` bases by ID and optional range.
`GET /references/{id}/bases` will return a JSON version of
`ListReferenceBasesResponse`. */
void getReferenceBases(java.lang.String id, org.ga4gh.methods.ListReferenceBasesRequest request, org.apache.avro.ipc.Callback callback) throws java.io.IOException;
}
}