| SAMAlignedSequenceHeader Class |
Namespace: Bio.IO.SAM
The SAMAlignedSequenceHeader type exposes the following members.
| Name | Description | |
|---|---|---|
| SAMAlignedSequenceHeader |
Creates new SAMAlignedSequenceHeader instance.
|
| Name | Description | |
|---|---|---|
| Bin |
Gets the Bin depending on the POS and CIGAR.
| |
| CIGAR |
Extended CIGAR string.
| |
| Flag |
SAM flags.
SAMFlags | |
| ISize |
Inferred insert size.
| |
| MapQ |
Mapping quality (phred-scaled posterior probability that the
mapping position of this read is incorrect).
| |
| MPos |
One-based leftmost mate position of the clipped sequence.
| |
| MRNM |
Mate reference sequence name.
| |
| OptionalFields |
Optional fields.
| |
| Pos |
One-based leftmost position/coordinate of the aligned sequence.
| |
| QName |
Query pair name if paired; or Query name if unpaired.
| |
| RefEndPos |
Gets one based alignment end position of reference sequence depending on CIGAR Value.
| |
| RName |
Reference sequence name.
|
| Name | Description | |
|---|---|---|
| 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.
| |
| GetFlag(String) |
Gets the SAMFlag for the specified string value.
| |
| 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.
| |
| SetPreValidatedCIGAR |
Sets the value of an extended CIGAR string known to be valid
| |
| SetPreValidatedMRNM |
Set the MRNM value without validating that it is a valid value
| |
| SetPreValidatedRName |
Set the name of the reference without validating it by a regular expression, useful
when the same value is being repeatedly used.
| |
| ToString | Returns a string that represents the current object. (Inherited from Object.) |
| Name | Description | |
|---|---|---|
| RNameRegxExprPattern |
Regular expression pattern for RName.
|