SAMAlignedSequenceHeader Class |
Namespace: Bio.IO.SAM
The SAMAlignedSequenceHeader type exposes the following members.
Name | Description | |
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SAMAlignedSequenceHeader |
Creates new SAMAlignedSequenceHeader instance.
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Name | Description | |
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Bin |
Gets the Bin depending on the POS and CIGAR.
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CIGAR |
Extended CIGAR string.
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Flag |
SAM flags.
SAMFlags | |
ISize |
Inferred insert size.
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MapQ |
Mapping quality (phred-scaled posterior probability that the
mapping position of this read is incorrect).
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MPos |
One-based leftmost mate position of the clipped sequence.
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MRNM |
Mate reference sequence name.
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OptionalFields |
Optional fields.
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Pos |
One-based leftmost position/coordinate of the aligned sequence.
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QName |
Query pair name if paired; or Query name if unpaired.
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RefEndPos |
Gets one based alignment end position of reference sequence depending on CIGAR Value.
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RName |
Reference sequence name.
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Name | Description | |
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Equals | Determines whether the specified object is equal to the current object. (Inherited from Object.) | |
Finalize | Allows an object to try to free resources and perform other cleanup operations before it is reclaimed by garbage collection. (Inherited from Object.) | |
GetFlag(Int32) |
Gets the SAMFlag for the specified integer value.
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GetFlag(String) |
Gets the SAMFlag for the specified string value.
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GetHashCode | Serves as the default hash function. (Inherited from Object.) | |
GetType | Gets the Type of the current instance. (Inherited from Object.) | |
MemberwiseClone | Creates a shallow copy of the current Object. (Inherited from Object.) | |
RegionToBin |
Gets Bin for the specified region.
Note that this method returns zero for negative values.
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SetPreValidatedCIGAR |
Sets the value of an extended CIGAR string known to be valid
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SetPreValidatedMRNM |
Set the MRNM value without validating that it is a valid value
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SetPreValidatedRName |
Set the name of the reference without validating it by a regular expression, useful
when the same value is being repeatedly used.
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ToString | Returns a string that represents the current object. (Inherited from Object.) |
Name | Description | |
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RNameRegxExprPattern |
Regular expression pattern for RName.
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