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SAMAlignedSequenceHeader Class
SAMAlignedSequenceHeader holds aligned sequence headers of the sam file format.
Inheritance Hierarchy
SystemObject
  Bio.IO.SAMSAMAlignedSequenceHeader

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

The SAMAlignedSequenceHeader type exposes the following members.

Constructors
  NameDescription
Public methodSAMAlignedSequenceHeader
Creates new SAMAlignedSequenceHeader instance.
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Properties
  NameDescription
Public propertyBin
Gets the Bin depending on the POS and CIGAR.
Public propertyCIGAR
Extended CIGAR string.
Public propertyFlag
SAM flags. SAMFlags
Public propertyISize
Inferred insert size.
Public propertyMapQ
Mapping quality (phred-scaled posterior probability that the mapping position of this read is incorrect).
Public propertyMPos
One-based leftmost mate position of the clipped sequence.
Public propertyMRNM
Mate reference sequence name.
Public propertyOptionalFields
Optional fields.
Public propertyPos
One-based leftmost position/coordinate of the aligned sequence.
Public propertyQName
Query pair name if paired; or Query name if unpaired.
Public propertyRefEndPos
Gets one based alignment end position of reference sequence depending on CIGAR Value.
Public propertyRName
Reference sequence name.
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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 methodStatic memberGetFlag(Int32)
Gets the SAMFlag for the specified integer value.
Public methodStatic memberGetFlag(String)
Gets the SAMFlag for the specified string value.
Public methodGetHashCode
Serves as the default hash function.
(Inherited from Object.)
Public methodGetType
Gets the Type of the current instance.
(Inherited from Object.)
Protected methodMemberwiseClone
Creates a shallow copy of the current Object.
(Inherited from Object.)
Public methodStatic memberRegionToBin
Gets Bin for the specified region. Note that this method returns zero for negative values.
Public methodSetPreValidatedCIGAR
Sets the value of an extended CIGAR string known to be valid
Public methodSetPreValidatedMRNM
Set the MRNM value without validating that it is a valid value
Public methodSetPreValidatedRName
Set the name of the reference without validating it by a regular expression, useful when the same value is being repeatedly used.
Public methodToString
Returns a string that represents the current object.
(Inherited from Object.)
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Fields
  NameDescription
Public fieldStatic memberRNameRegxExprPattern
Regular expression pattern for RName.
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See Also