| BAMFormatter Class |
Writes a SequenceAlignmentMap to a particular location, usually a file.
The output is formatted according to the BAM file format.
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 BAMFormatter type exposes the following members.
Constructors| Name | Description | |
|---|---|---|
 | BAMFormatter | Initializes a new instance of the BAMFormatter class |
Properties| Name | Description | |
|---|---|---|
 | CreateIndexFile |
Gets or sets the value indicating that whether to create index file or not.
|
| CreateSortedBAMFile |
Gets or sets the value indicating that whether the output file to be sorted or not.
|
| Description |
Gets the description of the sequence alignment formatter being
implemented. This is intended to give the developer some
information of the formatter.
|
| Name |
Gets the name of the sequence alignment formatter being
implemented. This is intended to give the developer some
information of the formatter type.
|
| SortType |
Gets or sets type of sort needed.
|
| SupportedFileTypes |
Gets the file extensions that the formatter implementation
will support.
|
Methods| Name | Description | |
|---|---|---|
| CompressBAMFile |
Compress the specified stream (reader) and writes to the specified stream (writer).
|
| 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.) |
| Format(Stream, ISequenceAlignment) |
Writes specified alignment object to a stream.
The output is formatted according to the BAM specification.
Note that this method does not create index file.
|
| Format(Stream, IEnumerableISequenceAlignment) |
Write a collection of ISequenceAlignments to a file.
|
| Format(Stream, BAMIndexStorage, ISequenceAlignment) |
Writes specified alignment object to a stream.
The output is formatted according to the BAM specification.
|
| 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.) |
| ToString | Returns a string that represents the current object. (Inherited from Object.) |
| WriteAlignedSequence |
Writes SAMAlignedSequence to specified stream.
|
| WriteHeader |
Writes BAM header to the specified stream in BAM format.
|
See Also