| BAMReferenceIndexes Class |
Class to hold BAM file index information related to a reference sequence.
Holds bin and linear index information for a reference sequence.
Inheritance HierarchyNamespace: Bio.IO.BAM
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
SyntaxThe BAMReferenceIndexes type exposes the following members.
Constructors| Name | Description | |
|---|---|---|
 | BAMReferenceIndexes |
Create a new instance of the class that will be populated with data to make an instance.
|
| BAMReferenceIndexes(Int32) |
Creates new instance of BAMReferenceIndexes class. That will be populated with data to make an
index
|
Properties| Name | Description | |
|---|---|---|
 | Bins |
Gets list of Bin index information.
|
| FirstOffSetSeen |
The location of the first offset in this file for a read from this index
|
| HasMetaData |
Does this read have meta data associated with it? (number of mapped/unmapped reads?)
Note that the meta-data is not standardized yet across implementations
|
| LastOffSetSeen |
The location of the last offset in this file for a read from this index.
|
| LinearIndex |
Gets list of Linear file offsets.
An array holding the linear offsets to be output
|
| MappedReadsCount |
Count of the number of mapped reads, may be inferred from index file.
|
| UnMappedReadsCount |
Count of the number of unmapped reads (Typically
those where a read does not align to a reference but its
mate does, though this is not guaranteed).
|
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.) |
| ToString | Returns a string that represents the current object. (Inherited from Object.) |
See Also