| BAMParser Class |
A BAMParser reads from a source of binary data that is formatted according to the BAM
file specification, and converts the data to in-memory SequenceAlignmentMap object.
Documentation for the latest BAM file format can be found at
http://samtools.sourceforge.net/SAM1.pdf
Inheritance HierarchyNamespace: Bio.IO.BAM
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
SyntaxThe BAMParser type exposes the following members.
Constructors| Name | Description | |
|---|---|---|
 | BAMParser |
The default constructor which chooses the default encoding based on the alphabet.
|
Properties| Name | Description | |
|---|---|---|
 | Alphabet |
The alphabet to use for sequences in parsed SequenceAlignmentMap objects.
Always returns singleton instance of SAMDnaAlphabet.
|
| Description |
Gets the description of the sequence alignment parser being
implemented. This is intended to give the
developer some information of the parser.
|
| Name |
Gets the name of the sequence alignment parser being
implemented. This is intended to give the
developer some information of the parser type.
|
| RefSequences |
Reference sequences, used to resolve "=" symbol in the sequence data.
|
| SupportedFileTypes |
Gets the file extensions that the parser implementation
will support.
|
Methods| Name | Description | |
|---|---|---|
| Dispose |
Implements the IDisposable interface
|
 | Dispose(Boolean) |
Disposes this object.
|
| 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.) |
| GetAlignedSequence |
Returns an aligned sequence by parses the BAM file.
|
| GetHashCode | Serves as the default hash function. (Inherited from Object.) |
| GetHeader |
Gets the SAMAlignmentHeader from the specified stream.
Note that this method resets the specified stream to BOF before reading.
|
| GetIndexFromBAMStorage |
Returns BAMIndex by parsing specified BAM stream.
|
| GetType | Gets the Type of the current instance. (Inherited from Object.) |
| IsEOF |
Returns a boolean indicating whether the reader is reached end of file or not.
|
| MemberwiseClone | Creates a shallow copy of the current Object. (Inherited from Object.) |
| Parse |
Returns an iterator over a set of SAMAlignedSequences retrieved from a parsed BAM file.
|
| ParseOne |
Returns a SequenceAlignmentMap object by parsing a BAM file.
|
| ToString | Returns a string that represents the current object. (Inherited from Object.) |
See Also