:py:mod:`spark_auto_mapper_fhir.backbone_elements.molecular_sequence_variant`
=============================================================================

.. py:module:: spark_auto_mapper_fhir.backbone_elements.molecular_sequence_variant


Module Contents
---------------

Classes
~~~~~~~

.. autoapisummary::

   spark_auto_mapper_fhir.backbone_elements.molecular_sequence_variant.MolecularSequenceVariant




.. py:class:: MolecularSequenceVariant(*, id_ = None, extension = None, modifierExtension = None, start = None, end = None, observedAllele = None, referenceAllele = None, cigar = None, variantPointer = None)

   Bases: :py:obj:`spark_auto_mapper_fhir.base_types.fhir_backbone_element_base.FhirBackboneElementBase`

   MolecularSequence.Variant
       Raw data describing a biological sequence.

       Raw data describing a biological sequence.

       :param id_: None
       :param extension: May be used to represent additional information that is not part of the basic
   definition of the element. To make the use of extensions safe and manageable,
   there is a strict set of governance  applied to the definition and use of
   extensions. Though any implementer can define an extension, there is a set of
   requirements that SHALL be met as part of the definition of the extension.
       :param modifierExtension: May be used to represent additional information that is not part of the basic
   definition of the element and that modifies the understanding of the element
   in which it is contained and/or the understanding of the containing element's
   descendants. Usually modifier elements provide negation or qualification. To
   make the use of extensions safe and manageable, there is a strict set of
   governance applied to the definition and use of extensions. Though any
   implementer can define an extension, there is a set of requirements that SHALL
   be met as part of the definition of the extension. Applications processing a
   resource are required to check for modifier extensions.

   Modifier extensions SHALL NOT change the meaning of any elements on Resource
   or DomainResource (including cannot change the meaning of modifierExtension
   itself).
       :param start: Start position of the variant on the  reference sequence. If the coordinate
   system is either 0-based or 1-based, then start position is inclusive.
       :param end: End position of the variant on the reference sequence. If the coordinate
   system is 0-based then end is exclusive and does not include the last
   position. If the coordinate system is 1-base, then end is inclusive and
   includes the last position.
       :param observedAllele: An allele is one of a set of coexisting sequence variants of a gene ([SO:00010
   23](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)).
   Nucleotide(s)/amino acids from start position of sequence to stop position of
   sequence on the positive (+) strand of the observed  sequence. When the
   sequence  type is DNA, it should be the sequence on the positive (+) strand.
   This will lay in the range between variant.start and variant.end.
       :param referenceAllele: An allele is one of a set of coexisting sequence variants of a gene ([SO:00010
   23](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)).
   Nucleotide(s)/amino acids from start position of sequence to stop position of
   sequence on the positive (+) strand of the reference sequence. When the
   sequence  type is DNA, it should be the sequence on the positive (+) strand.
   This will lay in the range between variant.start and variant.end.
       :param cigar: Extended CIGAR string for aligning the sequence with reference bases. See
   detailed documentation [here](http://support.illumina.com/help/SequencingAnaly
   sisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_Ext
   endedCIGARFormat.htm).
       :param variantPointer: A pointer to an Observation containing variant information.