Fix method doc signatures for multiline required parameters (#374)
* Fix method doc signatures for multiline required parameters.
Existing doc generator failed to recognize parameters as required when parameter descriptions
extended over more than one line. Besides presenting incorrect information, resulting
inconsistencies broke checks for automated sample generation.
* Regen docs
diff --git a/docs/dyn/genomics_v1.annotations.html b/docs/dyn/genomics_v1.annotations.html
index f67494e..8a88529 100644
--- a/docs/dyn/genomics_v1.annotations.html
+++ b/docs/dyn/genomics_v1.annotations.html
@@ -118,13 +118,6 @@
The object takes the form of:
{
- "requestId": "A String", # A unique request ID which enables the server to detect duplicated requests.
- # If provided, duplicated requests will result in the same response; if not
- # provided, duplicated requests may result in duplicated data. For a given
- # annotation set, callers should not reuse `request_id`s when writing
- # different batches of annotations - behavior in this case is undefined.
- # A common approach is to use a UUID. For batch jobs where worker crashes are
- # a possibility, consider using some unique variant of a worker or run ID.
"annotations": [ # The annotations to be created. At most 4096 can be specified in a single
# request.
{ # An annotation describes a region of reference genome. The value of an
@@ -142,53 +135,6 @@
"referenceId": "A String", # The ID of the Google Genomics reference associated with this range.
"end": "A String", # The end position of the range on the reference, 0-based exclusive.
"name": "A String", # The display name of this annotation.
- "type": "A String", # The data type for this annotation. Must match the containing annotation
- # set's type.
- "variant": { # A variant annotation, which describes the effect of a variant on the
- # genome, the coding sequence, and/or higher level consequences at the
- # organism level e.g. pathogenicity. This field is only set for annotations
- # of type `VARIANT`.
- "conditions": [ # The set of conditions associated with this variant.
- # A condition describes the way a variant influences human health.
- {
- "externalIds": [ # The set of external IDs for this condition.
- {
- "sourceName": "A String", # The name of the source of this data.
- "id": "A String", # The id used by the source of this data.
- },
- ],
- "conceptId": "A String", # The MedGen concept id associated with this gene.
- # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
- "omimId": "A String", # The OMIM id for this condition.
- # Search for these IDs at http://omim.org/
- "names": [ # A set of names for the condition.
- "A String",
- ],
- },
- ],
- "effect": "A String", # Effect of the variant on the coding sequence.
- "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These
- # should be provided when the variant is created.
- "A String",
- ],
- "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles
- # exist at this location, create a separate variant for each one, as they
- # may represent distinct conditions.
- "clinicalSignificance": "A String", # Describes the clinical significance of a variant.
- # It is adapted from the ClinVar controlled vocabulary for clinical
- # significance described at:
- # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
- "type": "A String", # Type has been adapted from ClinVar's list of variant types.
- "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should
- # be provided when the variant is created.
- },
- "start": "A String", # The start position of the range on the reference, 0-based inclusive.
- "annotationSetId": "A String", # The annotation set to which this annotation belongs.
- "referenceName": "A String", # The display name corresponding to the reference specified by
- # `referenceId`, for example `chr1`, `1`, or `chrX`.
- "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward
- # strand. Note that regardless of this field, the start/end position of the
- # range always refer to the forward strand.
"transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of
# the reference genome may be transcribed as RNA. An alternative splicing
# pattern would be represented as a separate transcript object. This field
@@ -252,9 +198,63 @@
],
"geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed.
},
+ "variant": { # A variant annotation, which describes the effect of a variant on the
+ # genome, the coding sequence, and/or higher level consequences at the
+ # organism level e.g. pathogenicity. This field is only set for annotations
+ # of type `VARIANT`.
+ "type": "A String", # Type has been adapted from ClinVar's list of variant types.
+ "effect": "A String", # Effect of the variant on the coding sequence.
+ "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These
+ # should be provided when the variant is created.
+ "A String",
+ ],
+ "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles
+ # exist at this location, create a separate variant for each one, as they
+ # may represent distinct conditions.
+ "clinicalSignificance": "A String", # Describes the clinical significance of a variant.
+ # It is adapted from the ClinVar controlled vocabulary for clinical
+ # significance described at:
+ # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
+ "conditions": [ # The set of conditions associated with this variant.
+ # A condition describes the way a variant influences human health.
+ {
+ "externalIds": [ # The set of external IDs for this condition.
+ {
+ "sourceName": "A String", # The name of the source of this data.
+ "id": "A String", # The id used by the source of this data.
+ },
+ ],
+ "omimId": "A String", # The OMIM id for this condition.
+ # Search for these IDs at http://omim.org/
+ "conceptId": "A String", # The MedGen concept id associated with this gene.
+ # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
+ "names": [ # A set of names for the condition.
+ "A String",
+ ],
+ },
+ ],
+ "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should
+ # be provided when the variant is created.
+ },
+ "start": "A String", # The start position of the range on the reference, 0-based inclusive.
+ "annotationSetId": "A String", # The annotation set to which this annotation belongs.
+ "referenceName": "A String", # The display name corresponding to the reference specified by
+ # `referenceId`, for example `chr1`, `1`, or `chrX`.
+ "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward
+ # strand. Note that regardless of this field, the start/end position of the
+ # range always refer to the forward strand.
+ "type": "A String", # The data type for this annotation. Must match the containing annotation
+ # set's type.
"id": "A String", # The server-generated annotation ID, unique across all annotations.
},
],
+ "requestId": "A String", # A unique request ID which enables the server to detect duplicated requests.
+ # If provided, duplicated requests will result in the same response; if not
+ # provided, duplicated requests may result in duplicated data. For a given
+ # annotation set, callers should not reuse `request_id`s when writing
+ # different batches of annotations - behavior in this case is undefined.
+ # A common approach is to use a UUID. For batch jobs where worker crashes are
+ # a possibility, consider using some unique variant of a worker or run ID.
}
x__xgafv: string, V1 error format.
@@ -347,53 +347,6 @@
"referenceId": "A String", # The ID of the Google Genomics reference associated with this range.
"end": "A String", # The end position of the range on the reference, 0-based exclusive.
"name": "A String", # The display name of this annotation.
- "type": "A String", # The data type for this annotation. Must match the containing annotation
- # set's type.
- "variant": { # A variant annotation, which describes the effect of a variant on the
- # genome, the coding sequence, and/or higher level consequences at the
- # organism level e.g. pathogenicity. This field is only set for annotations
- # of type `VARIANT`.
- "conditions": [ # The set of conditions associated with this variant.
- # A condition describes the way a variant influences human health.
- {
- "externalIds": [ # The set of external IDs for this condition.
- {
- "sourceName": "A String", # The name of the source of this data.
- "id": "A String", # The id used by the source of this data.
- },
- ],
- "conceptId": "A String", # The MedGen concept id associated with this gene.
- # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
- "omimId": "A String", # The OMIM id for this condition.
- # Search for these IDs at http://omim.org/
- "names": [ # A set of names for the condition.
- "A String",
- ],
- },
- ],
- "effect": "A String", # Effect of the variant on the coding sequence.
- "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These
- # should be provided when the variant is created.
- "A String",
- ],
- "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles
- # exist at this location, create a separate variant for each one, as they
- # may represent distinct conditions.
- "clinicalSignificance": "A String", # Describes the clinical significance of a variant.
- # It is adapted from the ClinVar controlled vocabulary for clinical
- # significance described at:
- # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
- "type": "A String", # Type has been adapted from ClinVar's list of variant types.
- "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should
- # be provided when the variant is created.
- },
- "start": "A String", # The start position of the range on the reference, 0-based inclusive.
- "annotationSetId": "A String", # The annotation set to which this annotation belongs.
- "referenceName": "A String", # The display name corresponding to the reference specified by
- # `referenceId`, for example `chr1`, `1`, or `chrX`.
- "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward
- # strand. Note that regardless of this field, the start/end position of the
- # range always refer to the forward strand.
"transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of
# the reference genome may be transcribed as RNA. An alternative splicing
# pattern would be represented as a separate transcript object. This field
@@ -457,6 +410,53 @@
],
"geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed.
},
+ "variant": { # A variant annotation, which describes the effect of a variant on the
+ # genome, the coding sequence, and/or higher level consequences at the
+ # organism level e.g. pathogenicity. This field is only set for annotations
+ # of type `VARIANT`.
+ "type": "A String", # Type has been adapted from ClinVar's list of variant types.
+ "effect": "A String", # Effect of the variant on the coding sequence.
+ "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These
+ # should be provided when the variant is created.
+ "A String",
+ ],
+ "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles
+ # exist at this location, create a separate variant for each one, as they
+ # may represent distinct conditions.
+ "clinicalSignificance": "A String", # Describes the clinical significance of a variant.
+ # It is adapted from the ClinVar controlled vocabulary for clinical
+ # significance described at:
+ # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
+ "conditions": [ # The set of conditions associated with this variant.
+ # A condition describes the way a variant influences human health.
+ {
+ "externalIds": [ # The set of external IDs for this condition.
+ {
+ "sourceName": "A String", # The name of the source of this data.
+ "id": "A String", # The id used by the source of this data.
+ },
+ ],
+ "omimId": "A String", # The OMIM id for this condition.
+ # Search for these IDs at http://omim.org/
+ "conceptId": "A String", # The MedGen concept id associated with this gene.
+ # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
+ "names": [ # A set of names for the condition.
+ "A String",
+ ],
+ },
+ ],
+ "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should
+ # be provided when the variant is created.
+ },
+ "start": "A String", # The start position of the range on the reference, 0-based inclusive.
+ "annotationSetId": "A String", # The annotation set to which this annotation belongs.
+ "referenceName": "A String", # The display name corresponding to the reference specified by
+ # `referenceId`, for example `chr1`, `1`, or `chrX`.
+ "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward
+ # strand. Note that regardless of this field, the start/end position of the
+ # range always refer to the forward strand.
+ "type": "A String", # The data type for this annotation. Must match the containing annotation
+ # set's type.
"id": "A String", # The server-generated annotation ID, unique across all annotations.
},
},
@@ -508,53 +508,6 @@
"referenceId": "A String", # The ID of the Google Genomics reference associated with this range.
"end": "A String", # The end position of the range on the reference, 0-based exclusive.
"name": "A String", # The display name of this annotation.
- "type": "A String", # The data type for this annotation. Must match the containing annotation
- # set's type.
- "variant": { # A variant annotation, which describes the effect of a variant on the
- # genome, the coding sequence, and/or higher level consequences at the
- # organism level e.g. pathogenicity. This field is only set for annotations
- # of type `VARIANT`.
- "conditions": [ # The set of conditions associated with this variant.
- # A condition describes the way a variant influences human health.
- {
- "externalIds": [ # The set of external IDs for this condition.
- {
- "sourceName": "A String", # The name of the source of this data.
- "id": "A String", # The id used by the source of this data.
- },
- ],
- "conceptId": "A String", # The MedGen concept id associated with this gene.
- # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
- "omimId": "A String", # The OMIM id for this condition.
- # Search for these IDs at http://omim.org/
- "names": [ # A set of names for the condition.
- "A String",
- ],
- },
- ],
- "effect": "A String", # Effect of the variant on the coding sequence.
- "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These
- # should be provided when the variant is created.
- "A String",
- ],
- "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles
- # exist at this location, create a separate variant for each one, as they
- # may represent distinct conditions.
- "clinicalSignificance": "A String", # Describes the clinical significance of a variant.
- # It is adapted from the ClinVar controlled vocabulary for clinical
- # significance described at:
- # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
- "type": "A String", # Type has been adapted from ClinVar's list of variant types.
- "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should
- # be provided when the variant is created.
- },
- "start": "A String", # The start position of the range on the reference, 0-based inclusive.
- "annotationSetId": "A String", # The annotation set to which this annotation belongs.
- "referenceName": "A String", # The display name corresponding to the reference specified by
- # `referenceId`, for example `chr1`, `1`, or `chrX`.
- "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward
- # strand. Note that regardless of this field, the start/end position of the
- # range always refer to the forward strand.
"transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of
# the reference genome may be transcribed as RNA. An alternative splicing
# pattern would be represented as a separate transcript object. This field
@@ -618,6 +571,53 @@
],
"geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed.
},
+ "variant": { # A variant annotation, which describes the effect of a variant on the
+ # genome, the coding sequence, and/or higher level consequences at the
+ # organism level e.g. pathogenicity. This field is only set for annotations
+ # of type `VARIANT`.
+ "type": "A String", # Type has been adapted from ClinVar's list of variant types.
+ "effect": "A String", # Effect of the variant on the coding sequence.
+ "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These
+ # should be provided when the variant is created.
+ "A String",
+ ],
+ "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles
+ # exist at this location, create a separate variant for each one, as they
+ # may represent distinct conditions.
+ "clinicalSignificance": "A String", # Describes the clinical significance of a variant.
+ # It is adapted from the ClinVar controlled vocabulary for clinical
+ # significance described at:
+ # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
+ "conditions": [ # The set of conditions associated with this variant.
+ # A condition describes the way a variant influences human health.
+ {
+ "externalIds": [ # The set of external IDs for this condition.
+ {
+ "sourceName": "A String", # The name of the source of this data.
+ "id": "A String", # The id used by the source of this data.
+ },
+ ],
+ "omimId": "A String", # The OMIM id for this condition.
+ # Search for these IDs at http://omim.org/
+ "conceptId": "A String", # The MedGen concept id associated with this gene.
+ # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
+ "names": [ # A set of names for the condition.
+ "A String",
+ ],
+ },
+ ],
+ "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should
+ # be provided when the variant is created.
+ },
+ "start": "A String", # The start position of the range on the reference, 0-based inclusive.
+ "annotationSetId": "A String", # The annotation set to which this annotation belongs.
+ "referenceName": "A String", # The display name corresponding to the reference specified by
+ # `referenceId`, for example `chr1`, `1`, or `chrX`.
+ "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward
+ # strand. Note that regardless of this field, the start/end position of the
+ # range always refer to the forward strand.
+ "type": "A String", # The data type for this annotation. Must match the containing annotation
+ # set's type.
"id": "A String", # The server-generated annotation ID, unique across all annotations.
}
@@ -644,53 +644,6 @@
"referenceId": "A String", # The ID of the Google Genomics reference associated with this range.
"end": "A String", # The end position of the range on the reference, 0-based exclusive.
"name": "A String", # The display name of this annotation.
- "type": "A String", # The data type for this annotation. Must match the containing annotation
- # set's type.
- "variant": { # A variant annotation, which describes the effect of a variant on the
- # genome, the coding sequence, and/or higher level consequences at the
- # organism level e.g. pathogenicity. This field is only set for annotations
- # of type `VARIANT`.
- "conditions": [ # The set of conditions associated with this variant.
- # A condition describes the way a variant influences human health.
- {
- "externalIds": [ # The set of external IDs for this condition.
- {
- "sourceName": "A String", # The name of the source of this data.
- "id": "A String", # The id used by the source of this data.
- },
- ],
- "conceptId": "A String", # The MedGen concept id associated with this gene.
- # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
- "omimId": "A String", # The OMIM id for this condition.
- # Search for these IDs at http://omim.org/
- "names": [ # A set of names for the condition.
- "A String",
- ],
- },
- ],
- "effect": "A String", # Effect of the variant on the coding sequence.
- "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These
- # should be provided when the variant is created.
- "A String",
- ],
- "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles
- # exist at this location, create a separate variant for each one, as they
- # may represent distinct conditions.
- "clinicalSignificance": "A String", # Describes the clinical significance of a variant.
- # It is adapted from the ClinVar controlled vocabulary for clinical
- # significance described at:
- # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
- "type": "A String", # Type has been adapted from ClinVar's list of variant types.
- "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should
- # be provided when the variant is created.
- },
- "start": "A String", # The start position of the range on the reference, 0-based inclusive.
- "annotationSetId": "A String", # The annotation set to which this annotation belongs.
- "referenceName": "A String", # The display name corresponding to the reference specified by
- # `referenceId`, for example `chr1`, `1`, or `chrX`.
- "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward
- # strand. Note that regardless of this field, the start/end position of the
- # range always refer to the forward strand.
"transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of
# the reference genome may be transcribed as RNA. An alternative splicing
# pattern would be represented as a separate transcript object. This field
@@ -754,6 +707,53 @@
],
"geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed.
},
+ "variant": { # A variant annotation, which describes the effect of a variant on the
+ # genome, the coding sequence, and/or higher level consequences at the
+ # organism level e.g. pathogenicity. This field is only set for annotations
+ # of type `VARIANT`.
+ "type": "A String", # Type has been adapted from ClinVar's list of variant types.
+ "effect": "A String", # Effect of the variant on the coding sequence.
+ "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These
+ # should be provided when the variant is created.
+ "A String",
+ ],
+ "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles
+ # exist at this location, create a separate variant for each one, as they
+ # may represent distinct conditions.
+ "clinicalSignificance": "A String", # Describes the clinical significance of a variant.
+ # It is adapted from the ClinVar controlled vocabulary for clinical
+ # significance described at:
+ # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
+ "conditions": [ # The set of conditions associated with this variant.
+ # A condition describes the way a variant influences human health.
+ {
+ "externalIds": [ # The set of external IDs for this condition.
+ {
+ "sourceName": "A String", # The name of the source of this data.
+ "id": "A String", # The id used by the source of this data.
+ },
+ ],
+ "omimId": "A String", # The OMIM id for this condition.
+ # Search for these IDs at http://omim.org/
+ "conceptId": "A String", # The MedGen concept id associated with this gene.
+ # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
+ "names": [ # A set of names for the condition.
+ "A String",
+ ],
+ },
+ ],
+ "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should
+ # be provided when the variant is created.
+ },
+ "start": "A String", # The start position of the range on the reference, 0-based inclusive.
+ "annotationSetId": "A String", # The annotation set to which this annotation belongs.
+ "referenceName": "A String", # The display name corresponding to the reference specified by
+ # `referenceId`, for example `chr1`, `1`, or `chrX`.
+ "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward
+ # strand. Note that regardless of this field, the start/end position of the
+ # range always refer to the forward strand.
+ "type": "A String", # The data type for this annotation. Must match the containing annotation
+ # set's type.
"id": "A String", # The server-generated annotation ID, unique across all annotations.
}</pre>
</div>
@@ -815,53 +815,6 @@
"referenceId": "A String", # The ID of the Google Genomics reference associated with this range.
"end": "A String", # The end position of the range on the reference, 0-based exclusive.
"name": "A String", # The display name of this annotation.
- "type": "A String", # The data type for this annotation. Must match the containing annotation
- # set's type.
- "variant": { # A variant annotation, which describes the effect of a variant on the
- # genome, the coding sequence, and/or higher level consequences at the
- # organism level e.g. pathogenicity. This field is only set for annotations
- # of type `VARIANT`.
- "conditions": [ # The set of conditions associated with this variant.
- # A condition describes the way a variant influences human health.
- {
- "externalIds": [ # The set of external IDs for this condition.
- {
- "sourceName": "A String", # The name of the source of this data.
- "id": "A String", # The id used by the source of this data.
- },
- ],
- "conceptId": "A String", # The MedGen concept id associated with this gene.
- # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
- "omimId": "A String", # The OMIM id for this condition.
- # Search for these IDs at http://omim.org/
- "names": [ # A set of names for the condition.
- "A String",
- ],
- },
- ],
- "effect": "A String", # Effect of the variant on the coding sequence.
- "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These
- # should be provided when the variant is created.
- "A String",
- ],
- "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles
- # exist at this location, create a separate variant for each one, as they
- # may represent distinct conditions.
- "clinicalSignificance": "A String", # Describes the clinical significance of a variant.
- # It is adapted from the ClinVar controlled vocabulary for clinical
- # significance described at:
- # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
- "type": "A String", # Type has been adapted from ClinVar's list of variant types.
- "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should
- # be provided when the variant is created.
- },
- "start": "A String", # The start position of the range on the reference, 0-based inclusive.
- "annotationSetId": "A String", # The annotation set to which this annotation belongs.
- "referenceName": "A String", # The display name corresponding to the reference specified by
- # `referenceId`, for example `chr1`, `1`, or `chrX`.
- "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward
- # strand. Note that regardless of this field, the start/end position of the
- # range always refer to the forward strand.
"transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of
# the reference genome may be transcribed as RNA. An alternative splicing
# pattern would be represented as a separate transcript object. This field
@@ -925,6 +878,53 @@
],
"geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed.
},
+ "variant": { # A variant annotation, which describes the effect of a variant on the
+ # genome, the coding sequence, and/or higher level consequences at the
+ # organism level e.g. pathogenicity. This field is only set for annotations
+ # of type `VARIANT`.
+ "type": "A String", # Type has been adapted from ClinVar's list of variant types.
+ "effect": "A String", # Effect of the variant on the coding sequence.
+ "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These
+ # should be provided when the variant is created.
+ "A String",
+ ],
+ "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles
+ # exist at this location, create a separate variant for each one, as they
+ # may represent distinct conditions.
+ "clinicalSignificance": "A String", # Describes the clinical significance of a variant.
+ # It is adapted from the ClinVar controlled vocabulary for clinical
+ # significance described at:
+ # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
+ "conditions": [ # The set of conditions associated with this variant.
+ # A condition describes the way a variant influences human health.
+ {
+ "externalIds": [ # The set of external IDs for this condition.
+ {
+ "sourceName": "A String", # The name of the source of this data.
+ "id": "A String", # The id used by the source of this data.
+ },
+ ],
+ "omimId": "A String", # The OMIM id for this condition.
+ # Search for these IDs at http://omim.org/
+ "conceptId": "A String", # The MedGen concept id associated with this gene.
+ # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
+ "names": [ # A set of names for the condition.
+ "A String",
+ ],
+ },
+ ],
+ "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should
+ # be provided when the variant is created.
+ },
+ "start": "A String", # The start position of the range on the reference, 0-based inclusive.
+ "annotationSetId": "A String", # The annotation set to which this annotation belongs.
+ "referenceName": "A String", # The display name corresponding to the reference specified by
+ # `referenceId`, for example `chr1`, `1`, or `chrX`.
+ "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward
+ # strand. Note that regardless of this field, the start/end position of the
+ # range always refer to the forward strand.
+ "type": "A String", # The data type for this annotation. Must match the containing annotation
+ # set's type.
"id": "A String", # The server-generated annotation ID, unique across all annotations.
}</pre>
</div>
@@ -996,53 +996,6 @@
"referenceId": "A String", # The ID of the Google Genomics reference associated with this range.
"end": "A String", # The end position of the range on the reference, 0-based exclusive.
"name": "A String", # The display name of this annotation.
- "type": "A String", # The data type for this annotation. Must match the containing annotation
- # set's type.
- "variant": { # A variant annotation, which describes the effect of a variant on the
- # genome, the coding sequence, and/or higher level consequences at the
- # organism level e.g. pathogenicity. This field is only set for annotations
- # of type `VARIANT`.
- "conditions": [ # The set of conditions associated with this variant.
- # A condition describes the way a variant influences human health.
- {
- "externalIds": [ # The set of external IDs for this condition.
- {
- "sourceName": "A String", # The name of the source of this data.
- "id": "A String", # The id used by the source of this data.
- },
- ],
- "conceptId": "A String", # The MedGen concept id associated with this gene.
- # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
- "omimId": "A String", # The OMIM id for this condition.
- # Search for these IDs at http://omim.org/
- "names": [ # A set of names for the condition.
- "A String",
- ],
- },
- ],
- "effect": "A String", # Effect of the variant on the coding sequence.
- "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These
- # should be provided when the variant is created.
- "A String",
- ],
- "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles
- # exist at this location, create a separate variant for each one, as they
- # may represent distinct conditions.
- "clinicalSignificance": "A String", # Describes the clinical significance of a variant.
- # It is adapted from the ClinVar controlled vocabulary for clinical
- # significance described at:
- # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
- "type": "A String", # Type has been adapted from ClinVar's list of variant types.
- "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should
- # be provided when the variant is created.
- },
- "start": "A String", # The start position of the range on the reference, 0-based inclusive.
- "annotationSetId": "A String", # The annotation set to which this annotation belongs.
- "referenceName": "A String", # The display name corresponding to the reference specified by
- # `referenceId`, for example `chr1`, `1`, or `chrX`.
- "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward
- # strand. Note that regardless of this field, the start/end position of the
- # range always refer to the forward strand.
"transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of
# the reference genome may be transcribed as RNA. An alternative splicing
# pattern would be represented as a separate transcript object. This field
@@ -1106,6 +1059,53 @@
],
"geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed.
},
+ "variant": { # A variant annotation, which describes the effect of a variant on the
+ # genome, the coding sequence, and/or higher level consequences at the
+ # organism level e.g. pathogenicity. This field is only set for annotations
+ # of type `VARIANT`.
+ "type": "A String", # Type has been adapted from ClinVar's list of variant types.
+ "effect": "A String", # Effect of the variant on the coding sequence.
+ "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These
+ # should be provided when the variant is created.
+ "A String",
+ ],
+ "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles
+ # exist at this location, create a separate variant for each one, as they
+ # may represent distinct conditions.
+ "clinicalSignificance": "A String", # Describes the clinical significance of a variant.
+ # It is adapted from the ClinVar controlled vocabulary for clinical
+ # significance described at:
+ # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
+ "conditions": [ # The set of conditions associated with this variant.
+ # A condition describes the way a variant influences human health.
+ {
+ "externalIds": [ # The set of external IDs for this condition.
+ {
+ "sourceName": "A String", # The name of the source of this data.
+ "id": "A String", # The id used by the source of this data.
+ },
+ ],
+ "omimId": "A String", # The OMIM id for this condition.
+ # Search for these IDs at http://omim.org/
+ "conceptId": "A String", # The MedGen concept id associated with this gene.
+ # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
+ "names": [ # A set of names for the condition.
+ "A String",
+ ],
+ },
+ ],
+ "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should
+ # be provided when the variant is created.
+ },
+ "start": "A String", # The start position of the range on the reference, 0-based inclusive.
+ "annotationSetId": "A String", # The annotation set to which this annotation belongs.
+ "referenceName": "A String", # The display name corresponding to the reference specified by
+ # `referenceId`, for example `chr1`, `1`, or `chrX`.
+ "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward
+ # strand. Note that regardless of this field, the start/end position of the
+ # range always refer to the forward strand.
+ "type": "A String", # The data type for this annotation. Must match the containing annotation
+ # set's type.
"id": "A String", # The server-generated annotation ID, unique across all annotations.
},
],
@@ -1151,53 +1151,6 @@
"referenceId": "A String", # The ID of the Google Genomics reference associated with this range.
"end": "A String", # The end position of the range on the reference, 0-based exclusive.
"name": "A String", # The display name of this annotation.
- "type": "A String", # The data type for this annotation. Must match the containing annotation
- # set's type.
- "variant": { # A variant annotation, which describes the effect of a variant on the
- # genome, the coding sequence, and/or higher level consequences at the
- # organism level e.g. pathogenicity. This field is only set for annotations
- # of type `VARIANT`.
- "conditions": [ # The set of conditions associated with this variant.
- # A condition describes the way a variant influences human health.
- {
- "externalIds": [ # The set of external IDs for this condition.
- {
- "sourceName": "A String", # The name of the source of this data.
- "id": "A String", # The id used by the source of this data.
- },
- ],
- "conceptId": "A String", # The MedGen concept id associated with this gene.
- # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
- "omimId": "A String", # The OMIM id for this condition.
- # Search for these IDs at http://omim.org/
- "names": [ # A set of names for the condition.
- "A String",
- ],
- },
- ],
- "effect": "A String", # Effect of the variant on the coding sequence.
- "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These
- # should be provided when the variant is created.
- "A String",
- ],
- "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles
- # exist at this location, create a separate variant for each one, as they
- # may represent distinct conditions.
- "clinicalSignificance": "A String", # Describes the clinical significance of a variant.
- # It is adapted from the ClinVar controlled vocabulary for clinical
- # significance described at:
- # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
- "type": "A String", # Type has been adapted from ClinVar's list of variant types.
- "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should
- # be provided when the variant is created.
- },
- "start": "A String", # The start position of the range on the reference, 0-based inclusive.
- "annotationSetId": "A String", # The annotation set to which this annotation belongs.
- "referenceName": "A String", # The display name corresponding to the reference specified by
- # `referenceId`, for example `chr1`, `1`, or `chrX`.
- "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward
- # strand. Note that regardless of this field, the start/end position of the
- # range always refer to the forward strand.
"transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of
# the reference genome may be transcribed as RNA. An alternative splicing
# pattern would be represented as a separate transcript object. This field
@@ -1261,6 +1214,53 @@
],
"geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed.
},
+ "variant": { # A variant annotation, which describes the effect of a variant on the
+ # genome, the coding sequence, and/or higher level consequences at the
+ # organism level e.g. pathogenicity. This field is only set for annotations
+ # of type `VARIANT`.
+ "type": "A String", # Type has been adapted from ClinVar's list of variant types.
+ "effect": "A String", # Effect of the variant on the coding sequence.
+ "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These
+ # should be provided when the variant is created.
+ "A String",
+ ],
+ "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles
+ # exist at this location, create a separate variant for each one, as they
+ # may represent distinct conditions.
+ "clinicalSignificance": "A String", # Describes the clinical significance of a variant.
+ # It is adapted from the ClinVar controlled vocabulary for clinical
+ # significance described at:
+ # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
+ "conditions": [ # The set of conditions associated with this variant.
+ # A condition describes the way a variant influences human health.
+ {
+ "externalIds": [ # The set of external IDs for this condition.
+ {
+ "sourceName": "A String", # The name of the source of this data.
+ "id": "A String", # The id used by the source of this data.
+ },
+ ],
+ "omimId": "A String", # The OMIM id for this condition.
+ # Search for these IDs at http://omim.org/
+ "conceptId": "A String", # The MedGen concept id associated with this gene.
+ # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
+ "names": [ # A set of names for the condition.
+ "A String",
+ ],
+ },
+ ],
+ "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should
+ # be provided when the variant is created.
+ },
+ "start": "A String", # The start position of the range on the reference, 0-based inclusive.
+ "annotationSetId": "A String", # The annotation set to which this annotation belongs.
+ "referenceName": "A String", # The display name corresponding to the reference specified by
+ # `referenceId`, for example `chr1`, `1`, or `chrX`.
+ "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward
+ # strand. Note that regardless of this field, the start/end position of the
+ # range always refer to the forward strand.
+ "type": "A String", # The data type for this annotation. Must match the containing annotation
+ # set's type.
"id": "A String", # The server-generated annotation ID, unique across all annotations.
}
@@ -1293,53 +1293,6 @@
"referenceId": "A String", # The ID of the Google Genomics reference associated with this range.
"end": "A String", # The end position of the range on the reference, 0-based exclusive.
"name": "A String", # The display name of this annotation.
- "type": "A String", # The data type for this annotation. Must match the containing annotation
- # set's type.
- "variant": { # A variant annotation, which describes the effect of a variant on the
- # genome, the coding sequence, and/or higher level consequences at the
- # organism level e.g. pathogenicity. This field is only set for annotations
- # of type `VARIANT`.
- "conditions": [ # The set of conditions associated with this variant.
- # A condition describes the way a variant influences human health.
- {
- "externalIds": [ # The set of external IDs for this condition.
- {
- "sourceName": "A String", # The name of the source of this data.
- "id": "A String", # The id used by the source of this data.
- },
- ],
- "conceptId": "A String", # The MedGen concept id associated with this gene.
- # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
- "omimId": "A String", # The OMIM id for this condition.
- # Search for these IDs at http://omim.org/
- "names": [ # A set of names for the condition.
- "A String",
- ],
- },
- ],
- "effect": "A String", # Effect of the variant on the coding sequence.
- "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These
- # should be provided when the variant is created.
- "A String",
- ],
- "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles
- # exist at this location, create a separate variant for each one, as they
- # may represent distinct conditions.
- "clinicalSignificance": "A String", # Describes the clinical significance of a variant.
- # It is adapted from the ClinVar controlled vocabulary for clinical
- # significance described at:
- # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
- "type": "A String", # Type has been adapted from ClinVar's list of variant types.
- "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should
- # be provided when the variant is created.
- },
- "start": "A String", # The start position of the range on the reference, 0-based inclusive.
- "annotationSetId": "A String", # The annotation set to which this annotation belongs.
- "referenceName": "A String", # The display name corresponding to the reference specified by
- # `referenceId`, for example `chr1`, `1`, or `chrX`.
- "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward
- # strand. Note that regardless of this field, the start/end position of the
- # range always refer to the forward strand.
"transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of
# the reference genome may be transcribed as RNA. An alternative splicing
# pattern would be represented as a separate transcript object. This field
@@ -1403,6 +1356,53 @@
],
"geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed.
},
+ "variant": { # A variant annotation, which describes the effect of a variant on the
+ # genome, the coding sequence, and/or higher level consequences at the
+ # organism level e.g. pathogenicity. This field is only set for annotations
+ # of type `VARIANT`.
+ "type": "A String", # Type has been adapted from ClinVar's list of variant types.
+ "effect": "A String", # Effect of the variant on the coding sequence.
+ "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These
+ # should be provided when the variant is created.
+ "A String",
+ ],
+ "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles
+ # exist at this location, create a separate variant for each one, as they
+ # may represent distinct conditions.
+ "clinicalSignificance": "A String", # Describes the clinical significance of a variant.
+ # It is adapted from the ClinVar controlled vocabulary for clinical
+ # significance described at:
+ # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
+ "conditions": [ # The set of conditions associated with this variant.
+ # A condition describes the way a variant influences human health.
+ {
+ "externalIds": [ # The set of external IDs for this condition.
+ {
+ "sourceName": "A String", # The name of the source of this data.
+ "id": "A String", # The id used by the source of this data.
+ },
+ ],
+ "omimId": "A String", # The OMIM id for this condition.
+ # Search for these IDs at http://omim.org/
+ "conceptId": "A String", # The MedGen concept id associated with this gene.
+ # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
+ "names": [ # A set of names for the condition.
+ "A String",
+ ],
+ },
+ ],
+ "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should
+ # be provided when the variant is created.
+ },
+ "start": "A String", # The start position of the range on the reference, 0-based inclusive.
+ "annotationSetId": "A String", # The annotation set to which this annotation belongs.
+ "referenceName": "A String", # The display name corresponding to the reference specified by
+ # `referenceId`, for example `chr1`, `1`, or `chrX`.
+ "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward
+ # strand. Note that regardless of this field, the start/end position of the
+ # range always refer to the forward strand.
+ "type": "A String", # The data type for this annotation. Must match the containing annotation
+ # set's type.
"id": "A String", # The server-generated annotation ID, unique across all annotations.
}</pre>
</div>