pyxetabase 4.0.0.dev56__py3-none-any.whl

pyxetabase/rest_clients/variant_operation_client.py

@@ -0,0 +1,718 @@
+"""
+WARNING: AUTOGENERATED CODE
+
+    This code was generated by a tool.
+    
+    Manual changes to this file may cause unexpected behavior in your application.
+    Manual changes to this file will be overwritten if the code is regenerated.
+"""
+
+from pyxetabase.rest_clients._parent_rest_clients import _ParentRestClient
+
+
+class VariantOperation(_ParentRestClient):
+    """
+    This class contains methods for the 'Operations - Variant Storage' webservices
+    PATH: /{apiVersion}/operation
+    """
+
+    def __init__(self, configuration, token=None, login_handler=None, *args, **kwargs):
+        super(VariantOperation, self).__init__(configuration, token, login_handler, *args, **kwargs)
+
+    def configure_cellbase(self, data=None, **options):
+        """
+        Update Cellbase configuration.
+        PATH: /{apiVersion}/operation/cellbase/configure
+
+        :param str project: Project [organization@]project where project can
+            be either the ID or the alias.
+        :param bool annotation_update: Create and load variant annotations
+            into the database.
+        :param str annotation_save_id: Save a copy of the current variant
+            annotation at the database.
+        :param dict data: New cellbase configuration.
+        """
+
+        return self._post(category='operation', resource='configure', subcategory='cellbase', data=data, **options)
+
+    def aggregate_variant(self, data=None, **options):
+        """
+        Find variants where not all the samples are present, and fill the
+            empty values, excluding HOM-REF (0/0) values.
+        PATH: /{apiVersion}/operation/variant/aggregate
+
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param dict data: Variant aggregate params.
+        """
+
+        return self._post(category='operation', resource='aggregate', subcategory='variant', data=data, **options)
+
+    def delete_variant_annotation(self, **options):
+        """
+        Deletes a saved copy of variant annotation.
+        PATH: /{apiVersion}/operation/variant/annotation/delete
+
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        :param str project: Project [organization@]project where project can
+            be either the ID or the alias.
+        :param str annotation_id: Annotation identifier.
+        """
+
+        return self._delete(category='operation', resource='delete', subcategory='variant/annotation', **options)
+
+    def variant_annotation_extension_configure(self, data=None, **options):
+        """
+        Install a variant annotation extension and configure the project to
+            use it.
+        PATH: /{apiVersion}/operation/variant/annotation/extension/configure
+
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        :param str project: project.
+        :param dict data: Parameters to configure a variant annotation
+            extension.
+        """
+
+        return self._post(category='operation', resource='configure', subcategory='variant/annotation/extension', data=data, **options)
+
+    def index_variant_annotation(self, data=None, **options):
+        """
+        Create and load variant annotations into the database.
+        PATH: /{apiVersion}/operation/variant/annotation/index
+
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        :param str project: Project [organization@]project where project can
+            be either the ID or the alias.
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param dict data: Variant annotation index params.
+        """
+
+        return self._post(category='operation', resource='index', subcategory='variant/annotation', data=data, **options)
+
+    def save_variant_annotation(self, data=None, **options):
+        """
+        Save a copy of the current variant annotation at the database.
+        PATH: /{apiVersion}/operation/variant/annotation/save
+
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        :param str project: Project [organization@]project where project can
+            be either the ID or the alias.
+        :param dict data: Variant annotation save params.
+        """
+
+        return self._post(category='operation', resource='save', subcategory='variant/annotation', data=data, **options)
+
+    def configure_variant(self, data=None, **options):
+        """
+        Update Variant Storage Engine configuration. Can be updated at Project
+            or Study level.
+        PATH: /{apiVersion}/operation/variant/configure
+
+        :param str project: Project [organization@]project where project can
+            be either the ID or the alias.
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param dict data: Configuration params to update.
+        """
+
+        return self._post(category='operation', resource='configure', subcategory='variant', data=data, **options)
+
+    def delete_variant(self, data=None, **options):
+        """
+        Remove variant files from the variant storage.
+        PATH: /{apiVersion}/operation/variant/delete
+
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param dict data: Variant delete file params.
+        """
+
+        return self._post(category='operation', resource='delete', subcategory='variant', data=data, **options)
+
+    def aggregate_variant_family(self, data=None, **options):
+        """
+        Find variants where not all the samples are present, and fill the
+            empty values.
+        PATH: /{apiVersion}/operation/variant/family/aggregate
+
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param dict data: Variant aggregate family params.
+        """
+
+        return self._post(category='operation', resource='aggregate', subcategory='variant/family', data=data, **options)
+
+    def index_variant_family(self, data=None, **options):
+        """
+        DEPRECATED: integrated in index (DEPRECATED Build the family index).
+        PATH: /{apiVersion}/operation/variant/family/index
+
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param dict data: Variant family index params.
+        """
+
+        return self._post(category='operation', resource='index', subcategory='variant/family', data=data, **options)
+
+    def index_variant(self, data=None, **options):
+        """
+        Index variant files into the variant storage.
+        PATH: /{apiVersion}/operation/variant/index
+
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param dict data: Variant index params.
+        """
+
+        return self._post(category='operation', resource='index', subcategory='variant', data=data, **options)
+
+    def launcher_variant_index(self, data=None, **options):
+        """
+        Detect non-indexed VCF files in the study, and submit a job for
+            indexing them.
+        PATH: /{apiVersion}/operation/variant/index/launcher
+
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param dict data: .
+        """
+
+        return self._post(category='operation', resource='launcher', subcategory='variant/index', data=data, **options)
+
+    def run_variant_julie(self, data=None, **options):
+        """
+        Transform VariantStats into PopulationFrequency values and updates the
+            VariantAnnotation.
+        PATH: /{apiVersion}/operation/variant/julie/run
+
+        :param dict data: Julie tool params. Specify list of cohorts from
+            multiple studies with {study}:{cohort}. (REQUIRED)
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        :param str project: project.
+        """
+
+        return self._post(category='operation', resource='run', subcategory='variant/julie', data=data, **options)
+
+    def repair_variant_metadata(self, data=None, **options):
+        """
+        Execute some repairs on Variant Storage Metadata. Advanced users only.
+        PATH: /{apiVersion}/operation/variant/metadata/repair
+
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        :param dict data: Variant storage metadata repair params.
+        """
+
+        return self._post(category='operation', resource='repair', subcategory='variant/metadata', data=data, **options)
+
+    def synchronize_variant_metadata(self, data=None, **options):
+        """
+        Synchronize catalog with variant storage metadata.
+        PATH: /{apiVersion}/operation/variant/metadata/synchronize
+
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param dict data: Variant storage metadata synchronize params.
+        """
+
+        return self._post(category='operation', resource='synchronize', subcategory='variant/metadata', data=data, **options)
+
+    def prune_variant(self, data=None, **options):
+        """
+        Prune orphan variants from studies in a project.
+        PATH: /{apiVersion}/operation/variant/prune
+
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        :param dict data: Variant prune params. Use dry-run to just generate a
+            report with the orphan variants.
+        """
+
+        return self._post(category='operation', resource='prune', subcategory='variant', data=data, **options)
+
+    def delete_variant_sample(self, data=None, **options):
+        """
+        Remove variant samples from the variant storage.
+        PATH: /{apiVersion}/operation/variant/sample/delete
+
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param dict data: Variant delete sample params.
+        """
+
+        return self._post(category='operation', resource='delete', subcategory='variant/sample', data=data, **options)
+
+    def index_variant_sample(self, data=None, **options):
+        """
+        DEPRECATED You should use the new sample index method instead.
+        PATH: /{apiVersion}/operation/variant/sample/index
+
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param dict data: Variant sample index params.
+        """
+
+        return self._post(category='operation', resource='index', subcategory='variant/sample', data=data, **options)
+
+    def variant_sample_index_configure(self, data=None, **options):
+        """
+        DEPRECATED You should use the new sample index configure method.
+        PATH: /{apiVersion}/operation/variant/sample/index/configure
+
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param bool skip_rebuild: Skip sample index re-build.
+        :param dict data: New SampleIndexConfiguration.
+        """
+
+        return self._post(category='operation', resource='configure', subcategory='variant/sample/index', data=data, **options)
+
+    def delete_variant_score(self, **options):
+        """
+        Remove a variant score in the database.
+        PATH: /{apiVersion}/operation/variant/score/delete
+
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param str name: Unique name of the score within the study.
+        :param bool resume: Resume a previously failed remove.
+        :param bool force: Force remove of partially indexed scores.
+        """
+
+        return self._delete(category='operation', resource='delete', subcategory='variant/score', **options)
+
+    def index_variant_score(self, data=None, **options):
+        """
+        Index a variant score in the database.
+        PATH: /{apiVersion}/operation/variant/score/index
+
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param dict data: Variant score index params. scoreName: Unique name
+            of the score within the study. cohort1: Cohort used to compute the
+            score. Use the cohort 'ALL' if all samples from the study where
+            used to compute the score. cohort2: Second cohort used to compute
+            the score, typically to compare against the first cohort. If only
+            one cohort was used to compute the score, leave empty.
+            inputColumns: Indicate which columns to load from the input file.
+            Provide the column position (starting in 0) for the column with the
+            score with 'SCORE=n'. Optionally, the PValue column with
+            'PVALUE=n'. The, to indicate the variant associated with the score,
+            provide either the columns ['CHROM', 'POS', 'REF', 'ALT'], or the
+            column 'VAR' containing a variant representation with format
+            'chr:start:ref:alt'. e.g.
+            'CHROM=0,POS=1,REF=3,ALT=4,SCORE=5,PVALUE=6' or
+            'VAR=0,SCORE=1,PVALUE=2'. resume: Resume a previously failed
+            indexation.
+        """
+
+        return self._post(category='operation', resource='index', subcategory='variant/score', data=data, **options)
+
+    def variant_secondary_annotation_index(self, data=None, **options):
+        """
+        Creates a secondary index using a search engine. If samples are
+            provided, sample data will be added to the secondary index. (New!).
+        PATH: /{apiVersion}/operation/variant/secondary/annotation/index
+
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        :param str project: Project [organization@]project where project can
+            be either the ID or the alias.
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param dict data: Variant secondary annotation index params.
+        """
+
+        return self._post(category='operation', resource='index', subcategory='variant/secondary/annotation', data=data, **options)
+
+    def variant_secondary_sample_index(self, data=None, **options):
+        """
+        Build and annotate the sample index. (New!) .
+        PATH: /{apiVersion}/operation/variant/secondary/sample/index
+
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param dict data: Variant sample index params.
+        """
+
+        return self._post(category='operation', resource='index', subcategory='variant/secondary/sample', data=data, **options)
+
+    def configure_variant_secondary_sample_index(self, data=None, **options):
+        """
+        Update SampleIndex configuration (New!).
+        PATH: /{apiVersion}/operation/variant/secondary/sample/index/configure
+
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param bool skip_rebuild: Skip sample index re-build.
+        :param dict data: New SampleIndexConfiguration.
+        """
+
+        return self._post(category='operation', resource='configure', subcategory='variant/secondary/sample/index', data=data, **options)
+
+    def secondary_index_variant(self, data=None, **options):
+        """
+        DEPRECATED you should use the new annotation index method instead.
+        PATH: /{apiVersion}/operation/variant/secondaryIndex
+
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        :param str project: Project [organization@]project where project can
+            be either the ID or the alias.
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param dict data: Variant secondary annotation index params.
+        """
+
+        return self._post(category='operation', resource='secondaryIndex', subcategory='variant', data=data, **options)
+
+    def setup_variant(self, data=None, **options):
+        """
+        Execute Variant Setup to allow using the variant engine. This setup is
+            necessary before starting any variant operation.
+        PATH: /{apiVersion}/operation/variant/setup
+
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param dict data: Variant setup params.
+        """
+
+        return self._post(category='operation', resource='setup', subcategory='variant', data=data, **options)
+
+    def delete_variant_stats(self, data=None, **options):
+        """
+        Deletes the VariantStats of a cohort/s from the database.
+        PATH: /{apiVersion}/operation/variant/stats/delete
+
+        :param dict data: Variant stats delete params. (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        """
+
+        return self._post(category='operation', resource='delete', subcategory='variant/stats', data=data, **options)
+
+    def index_variant_stats(self, data=None, **options):
+        """
+        Compute variant stats for any cohort and any set of variants and index
+            the result in the variant storage database.
+        PATH: /{apiVersion}/operation/variant/stats/index
+
+        :param dict data: Variant stats params. (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        """
+
+        return self._post(category='operation', resource='index', subcategory='variant/stats', data=data, **options)
+
+    def delete_variant_study(self, data=None, **options):
+        """
+        Remove whole study from the variant storage.
+        PATH: /{apiVersion}/operation/variant/study/delete
+
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param dict data: Variant delete study params.
+        """
+
+        return self._post(category='operation', resource='delete', subcategory='variant/study', data=data, **options)
+