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

.. py:module:: spark_auto_mapper_fhir.backbone_elements.molecular_sequence_quality


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

Classes
~~~~~~~

.. autoapisummary::

   spark_auto_mapper_fhir.backbone_elements.molecular_sequence_quality.MolecularSequenceQuality




.. py:class:: MolecularSequenceQuality(*, id_ = None, extension = None, modifierExtension = None, type_, standardSequence = None, start = None, end = None, score = None, method = None, truthTP = None, queryTP = None, truthFN = None, queryFP = None, gtFP = None, precision = None, recall = None, fScore = None, roc = None)

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

   MolecularSequence.Quality
       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 type_: INDEL / SNP / Undefined variant.
       :param standardSequence: Gold standard sequence used for comparing against.
       :param start: Start position of the sequence. If the coordinate system is either 0-based or
   1-based, then start position is inclusive.
       :param end: End position of the 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 score: The score of an experimentally derived feature such as a p-value ([SO:0001685]
   (http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).
       :param method: Which method is used to get sequence quality.
       :param truthTP: True positives, from the perspective of the truth data, i.e. the number of
   sites in the Truth Call Set for which there are paths through the Query Call
   Set that are consistent with all of the alleles at this site, and for which
   there is an accurate genotype call for the event.
       :param queryTP: True positives, from the perspective of the query data, i.e. the number of
   sites in the Query Call Set for which there are paths through the Truth Call
   Set that are consistent with all of the alleles at this site, and for which
   there is an accurate genotype call for the event.
       :param truthFN: False negatives, i.e. the number of sites in the Truth Call Set for which
   there is no path through the Query Call Set that is consistent with all of the
   alleles at this site, or sites for which there is an inaccurate genotype call
   for the event. Sites with correct variant but incorrect genotype are counted
   here.
       :param queryFP: False positives, i.e. the number of sites in the Query Call Set for which
   there is no path through the Truth Call Set that is consistent with this site.
   Sites with correct variant but incorrect genotype are counted here.
       :param gtFP: The number of false positives where the non-REF alleles in the Truth and Query
   Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or
   similar).
       :param precision: QUERY.TP / (QUERY.TP + QUERY.FP).
       :param recall: TRUTH.TP / (TRUTH.TP + TRUTH.FN).
       :param fScore: Harmonic mean of Recall and Precision, computed as: 2 * precision * recall /
   (precision + recall).
       :param roc: Receiver Operator Characteristic (ROC) Curve  to give sensitivity/specificity
   tradeoff.