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

Defined in <seqan/bam_io.h>
Signature template <typename TNameStore[, typename TNameStoreCache]> class BamIOContext;

Template Parameters

TNameStore The type used to represent the names.
TNameStoreCache The type used to cache the names. Defaults to NameStoreCache <TNameStore>l;.

Member Function Overview

Interface Function Overview

Detailed Description

BamIOContext objects store the names of (and provide a cache for) reference contig names.

Examples

Creating a BamIOContext for a raw StringSet of CharString.

StringSet<CharString> contigNames;
NameStoreCache<StringSet<CharString> > contigNamesCache(contigNames);
BamIOContext<StringSet<CharString> > bamIOContext(contigNames, contigNamesCache);
// ...

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);
// ...

Member Functions Detail

BamIOContext::BamIOContext(); BamIOContext::BamIOContext(contigNameStore, contigNamesStoreCache);

Constructor.

Default constructor or construction with references to sequence and sample names.

Data Races

Thread safety unknown!

Interface Functions Detail

TLengthStoreRef contigLengths(context);

Return reference to contig lengths from BamIOContext.

Parameters

context The BamIOContext to query.

Returns

TLengthStoreRef A reference to the TLengthStore of the context.

Data Races

Thread safety unknown!

TNameStoreRef contigNames(context);

Return reference to contig names from BamIOContext.

Parameters

context The BamIOContext to query.

Returns

TNameStoreRef A reference to the TNameStore of the context.

Data Races

Thread safety unknown!

TNameStoreCacheRef contigNamesCache(context);

Return reference to contig names cache from BamIOContext.

Parameters

context The BamIOContext to query.

Returns

TNameStoreCacheRef A reference to the TNameStoreCache of the context.

Data Races

Thread safety unknown!