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

TNameStore | The name store class.
TNameStoreCache | The name store cache class.

Member Functions

BamIOContext | Constructor.

Functions

jumpToOrphans | Seek to orphans block in BAM BGZF stream using an index.
jumpToRegion | Seek in BAM BGZF stream using an index.
nameStore | Return reference to name store from BamIOContext.
nameStoreCache | Return reference to name store cache from BamIOContext.
readRecord | reads 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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