DSTU2

This page is part of the FHIR Specification (v0.0.82: (v1.0.2: DSTU 1). 2). The current version which supercedes this version is 5.0.0 . For a full list of available versions, see the Directory of published versions

Extension Extension: CIGAR - Definition

URL for this extension: 


http://hl7.org/fhir/StructureDefinition/geneticsCIGAR

Status: draft. Extension maintained by: Health Level Seven, Intl - Clinical Genomics Seven International (Clinical Genomics)

A sequence of of base lengths and Extended CIGAR string for aligning the associated operation, used to indicate which bases align (either a match/mismatch) sequence with the reference, are deleted from the reference, and are insertions that are not in the reference. reference bases. See detailed documentation here .

Context of Use: Use on element: Observation

usage info: insert a list of places where this extension is used

Extension Content

Summary

Name Flags Card. Type Description & Constraints doco
.. extension 0..1 string URL = http://hl7.org/fhir/StructureDefinition/geneticsCIGAR
CIGAR: Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).
Use on element: Observation

doco Documentation for this format

Fulle Structure

identifies the meaning of the extension Fixed Value:
Name Flags Card. Type Description & Constraints doco
. . extension 0..1 Extension URL = http://hl7.org/fhir/StructureDefinition/geneticsCIGAR
CIGAR: A sequence of of base lengths and Extended CIGAR string for aligning the associated operation, used to indicate which bases align (either a match/mismatch) sequence with the reference, are deleted from the reference, and are insertions that are not in the reference. reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).
Use on element: Observation
. . . extension 0..* Extension 0 .. 0 Additional Content defined by implementations
. . . url 1..1 uri http://hl7.org/fhir/StructureDefinition/geneticsCIGAR "http://hl7.org/fhir/StructureDefinition/geneticsCIGAR"
. . . valueString 0..1 1..1 string Value of extension

doco Documentation for this format

XML Template 

<!-- CIGAR -->doco

< xmlns="http://hl7.org/fhir"

<extension xmlns="http://hl7.org/fhir"

     url="http://hl7.org/fhir/StructureDefinition/geneticsCIGAR" >
  <!-- from Element: extension -->
 <

 <valueString value="[string]"/><!-- 1..1 Value of extension -->

</extension>

JSON Template 

{ // CIGAR
  // from Element: extension
    "url" : "http://hl7.org/fhir/StructureDefinition/geneticsCIGAR", // R! 
    "

    "valueString" : "<string>" // R! Value of extension

  }

Summary

Name Flags Card. Type Description & Constraints doco
.. extension 0..1 string URL = http://hl7.org/fhir/StructureDefinition/geneticsCIGAR
CIGAR: Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).
Use on element: Observation

doco Documentation for this format

Full Structure

identifies the meaning of the extension Fixed Value:
Name Flags Card. Type Description & Constraints doco
. . extension 0..1 Extension URL = http://hl7.org/fhir/StructureDefinition/geneticsCIGAR
CIGAR: A sequence of of base lengths and Extended CIGAR string for aligning the associated operation, used to indicate which bases align (either a match/mismatch) sequence with the reference, are deleted from the reference, and are insertions that are not in the reference. reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).
Use on element: Observation
. . . extension 0..* Extension 0 .. 0 Additional Content defined by implementations
. . . url 1..1 uri http://hl7.org/fhir/StructureDefinition/geneticsCIGAR "http://hl7.org/fhir/StructureDefinition/geneticsCIGAR"
. . . valueString 0..1 1..1 string Value of extension

doco Documentation for this format

XML Template 

<!-- CIGAR -->doco

< xmlns="http://hl7.org/fhir"

<extension xmlns="http://hl7.org/fhir"

     url="http://hl7.org/fhir/StructureDefinition/geneticsCIGAR" >
  <!-- from Element: extension -->
 <

 <valueString value="[string]"/><!-- 1..1 Value of extension -->

</extension>

JSON Template

to do 
{ // CIGAR
  // from Element: extension
    "url" : "http://hl7.org/fhir/StructureDefinition/geneticsCIGAR", // R! 
    "valueString" : "<string>" // R! Value of extension
  }