Class
BamIOContextThe I/O context to use for BAM I/O.
The I/O context to use for BAM I/O.
Defined in | <seqan/bam_io.h> |
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Signature |
template <typename TNameStore[, typename TNameStoreCache]>
class BamIOContext;
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Template Parameters
TNameStore |
The type used to represent the names. |
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TNameStoreCache |
The type used to cache the names. Defaults to NameStoreCache <TNameStore>l;. |
Member Function Overview
Interface Function Overview
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TLengthStoreRef contigLengths(context);
Return reference to contig lengths from BamIOContext. -
TNameStoreRef contigNames(context);
Return reference to contig names from BamIOContext. -
TNameStoreCacheRef contigNamesCache(context);
Return reference to contig names cache from BamIOContext.
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. |
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Returns
TLengthStoreRef |
A reference to the TLengthStore of the context. |
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Data Races
Thread safety unknown!
TNameStoreRef contigNames(context);
Return reference to contig names from BamIOContext.
Parameters
context
|
The BamIOContext to query. |
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Returns
TNameStoreRef |
A reference to the TNameStore of the context. |
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Data Races
Thread safety unknown!
TNameStoreCacheRef contigNamesCache(context);
Return reference to contig names cache from BamIOContext.
Parameters
context
|
The BamIOContext to query. |
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Returns
TNameStoreCacheRef |
A reference to the TNameStoreCache of the context. |
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Data Races
Thread safety unknown!