| SAMParser Class |
A SAMParser reads from a source of text that is formatted according to the SAM
file specification (v1.4-r985), and converts the data to in-memory SequenceAlignmentMap object.
For advanced users, the ability to select an encoding for the internal memory representation is
provided. There is also a default encoding for each alphabet that may be encountered.
Documentation for the latest SAM file format can be found at
http://samtools.sourceforge.net/SAM1.pdf
Inheritance HierarchyNamespace: Bio.IO.SAM
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
SyntaxThe SAMParser type exposes the following members.
Constructors| Name | Description | |
|---|---|---|
 | SAMParser |
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 SAMDNAAlpabet.
|
| 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 | |
|---|---|---|
| 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.) |
| 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.) |
| Parse |
Parses a sequence alignment texts from a file.
|
| ParseOne |
Parses a sequence alignment texts from a stream.
|
| ParseOneWithSpecificFormat |
Parses alignments in SAM format from a reader into a SequenceAlignmentMap object.
|
 | ParseQualityNSequence(SAMAlignedSequence, IAlphabet, String, String) |
Parses sequence data and quality values and updates SAMAlignedSequence instance.
|
| ParseQualityNSequence(SAMAlignedSequence, IAlphabet, Byte, Byte, Boolean) |
Parses sequence data and quality values and updates SAMAlignedSequence instance.
|
| ParseSAMHeader(Stream) |
Parses SAM alignment header from specified stream.
|
| ParseSAMHeader(TextReader) |
Parses SAM alignment header from specified text reader.
|
| ParseSequence |
Parse a single sequence.
|
| ToString | Returns a string that represents the current object. (Inherited from Object.) |
Fields| Name | Description | |
|---|---|---|
 | AsteriskAsByte |
An asterisk encoded as a byte
|
| HeaderLinePattern |
Constant to hold SAM alignment header line pattern.
|
| OptionalFieldLinePattern |
Constant to hold SAM optional filed line pattern.
|
| QualityFormatType |
Holds the qualitative value type.
|
See Also