Class
BamIOContext
The I/O context to use for BAM I/O.
BamIOContext<TNameStore[, TNameStoreCache]>
Include Headers
bam_io.h
Parameters
TNameStore
The name store class.
TNameStoreCache
The name store cache class.
Default: NameStoreCache<TNameStore>
Typedefs
TNameStoreThe name store class.
TNameStoreCacheThe name store cache class.
Member Functions
BamIOContextConstructor.
Functions
jumpToOrphansSeek to orphans block in BAM BGZF stream using an index.
jumpToRegionSeek in BAM BGZF stream using an index.
nameStoreReturn reference to name store from BamIOContext.
nameStoreCacheReturn reference to name store cache from BamIOContext.
readRecordreads one record (e.g. a single DNA-sequence and its meta data) from a StreamConcept, by the means of RecordReader
Examples
Creating a BamIOContext for a raw StringSet of CharString.
StringSet<CharString> nameStore;
NameStoreCache<StringSet<CharString> > nameStoreCache(nameStore);
BamIOContext<StringSet<CharString> > bamIOContext(nameStore, nameStoreCache);
// ...
Using a BamIOContext with a FragmentStore.
typedef FragmentStore<>::TContigNameStore         TNameStore;
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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