Class BamIOContext

The I/O context to use for BAM I/O.

/*!
 * @class BamIOContext
 * 
 * @headerfile <seqan/bam_io.h>
 * 
 * @brief The I/O context to use for BAM I/O.
 * 
 * @signature template <typename TNameStore[, typename TNameStoreCache]> class
 *            BamIOContext;
 * 
 * @tparam TNameStore The name store class.
 * @tparam TNameStoreCache The name store cache class. Defaults to @link
 *                         NameStoreCache @endlink &lt;TNameStore&gtl;.
 * 
 * @section Examples
 * 
 * Creating a @link BamIOContext @endlink for a raw @link StringSet @endlink of
 * @link CharString @endlink.
 * 
 * @code{.cpp}
 * StringSet<CharString> nameStore;
 * NameStoreCache<StringSet<CharString> > nameStoreCache(nameStore);
 * BamIOContext<StringSet<CharString> > bamIOContext(nameStore, nameStoreCache);
 * // ...
 * @endcode
 * 
 * 
 * Using a @link BamIOContext @endlink with a @link FragmentStore @endlink.
 * 
 * @code{.cpp}
 * 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);
 * // ...
 * @endcode
 * 
 * 
 * @fn BamIOContext::BamIOContext
 * 
 * @headerfile <seqan/bam_io.h>
 * 
 * @brief Constructor.
 * 
 * @signature BamIOContext::BamIOContext();
 * 
 * Only the default constructor is provided.
 * 
 * @typedef BamIOContext::TNameStore
 * 
 * @brief The name store class.
 * 
 * @signature typedef (...) BamIOContext::TNameStore;
 * 
 * @typedef BamIOContext::TNameStoreCache
 * 
 * @brief The name store cache class.
 * 
 * @signature typedef (...) BamIOContext::TNameStoreCache;
 * 
 * @fn BamIOContext#nameStoreCache
 * 
 * @brief Return reference to name store cache from @link BamIOContext @endlink.
 * 
 * @signature TNameStoreRef nameStoreCache(context);
 * 
 * @param[in] context The @link BamIOContext @endlink to query.
 * 
 * @return TNameStoreRef A reference to the <tt>TNameStore</tt> of the context.
 * 
 * @fn BamIOContext#nameStore
 * 
 * @headerfile <seqan/bam_io.h>
 * 
 * @brief Return reference to name store from @link BamIOContext @endlink.
 * 
 * @signature TNameStoreCacheRef nameStore(context);
 * 
 * @param[in] context The @link BamIOContext @endlink to query.
 * 
 * @return TNameStoreCacheRef A reference to the <tt>TNameStoreCache</tt> of the
 *                            context.
 */