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SAMAlignmentHeader Class
Class to hold SAM Headers.
Inheritance Hierarchy
SystemObject
  Bio.IO.SAMSAMAlignmentHeader

Namespace: Bio.IO.SAM
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
Syntax
public class SAMAlignmentHeader

The SAMAlignmentHeader type exposes the following members.

Constructors
  NameDescription
Public methodSAMAlignmentHeader
Creates SAMAlignmentHeader instance.
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Properties
  NameDescription
Public propertyComments
List of comment headers.
Public propertyRecordFields
List of record fields. It holds all available record fields except comments.
Public propertyReferenceSequences
Holds the list of reference sequences name and length. SAMParser update this property from SQ header if present, else this will be updated from the each alignment information in this case length of reference sequence will be unknown thus set to zero. BAMParser update this property from reference information block and not from the SQ header. BAMFormatter uses this information to write reference information block. SAMFormatter does not requires this information, thus ignores this info.
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Methods
  NameDescription
Public methodEquals
Determines whether the specified object is equal to the current object.
(Inherited from Object.)
Protected methodFinalize
Allows an object to try to free resources and perform other cleanup operations before it is reclaimed by garbage collection.
(Inherited from Object.)
Public methodGetHashCode
Serves as the default hash function.
(Inherited from Object.)
Public methodGetReferenceSequenceRanges
Returns list of SequenceRanges objects which represents ReferenceSequenceInfo present in this header.
Public methodGetReferenceSequencesInfoFromSQHeader
Returns list of reference sequences name and length present in SQ header.
Public methodGetType
Gets the Type of the current instance.
(Inherited from Object.)
Public methodIsValid
VAlidates mandatory tags.
Protected methodMemberwiseClone
Creates a shallow copy of the current Object.
(Inherited from Object.)
Public methodToString
Returns a string that represents the current object.
(Inherited from Object.)
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Fields
  NameDescription
Public fieldStatic memberMandatoryTagsForFieldTypes
Holds the mapping of record field types to its mandatory tags. This will be used in the IsValid() method to validate the specified SAMAlignmentHeader.
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See Also