Class
BamIOContext
The I/O context to use for BAM I/O.
Include Headers
bam_io.h
Parameters
The name store class. | |
The name store cache class. Default: NameStoreCache<TNameStore> |
Typedefs
The name store class. | |
The name store cache class. |
Member Functions
Constructor. |
Functions
Seek to orphans block in BAM BGZF stream using an index. | |
Seek in BAM BGZF stream using an index. | |
Return reference to name store from BamIOContext. | |
Return reference to name store cache from BamIOContext. | |
reads one record (e.g. a single DNA-sequence and its meta data) from a StreamConcept, by the means of RecordReader |
Examples
NameStoreCache<StringSet<CharString> > nameStoreCache(nameStore);
BamIOContext<StringSet<CharString> > bamIOContext(nameStore, nameStoreCache);
// ...
Using a BamIOContext with a FragmentStore.
typedef NameStoreCache<TNameStore> TNameStoreCache;
FragmentStore<> store;
// Optionally, do something with store.
typedef BamIOContext<TNameStore, TNameStoreCache> TBamIOContext;
TBamIOContext bamIOContext(store.contigNameStore, store.contigNameStoreCache);
// ...
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