gatb.core-API-0.0.0
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Split a given bank in pieces. More...
#include <BankSplitter.hpp>
Public Member Functions | |
BankSplitter (IBank *reference, size_t readMeanSize, size_t overlap, u_int8_t coverage) | |
~BankSplitter () | |
std::string | getId () |
tools::dp::Iterator< Sequence > * | iterator () |
int64_t | getNbItems () |
void | insert (const Sequence &item) |
void | flush () |
u_int64_t | getSize () |
void | estimate (u_int64_t &number, u_int64_t &totalSize, u_int64_t &maxSize) |
Public Member Functions inherited from AbstractBank | |
AbstractBank () | |
std::string | getIdNb (int i) |
int64_t | estimateNbItemsBanki (int i) |
const std::vector< IBank * > | getBanks () const |
int64_t | estimateNbItems () |
u_int64_t | estimateSequencesSize () |
u_int64_t | getEstimateThreshold () |
void | setEstimateThreshold (u_int64_t nbSeq) |
void | remove () |
void | finalize () |
size_t | getCompositionNb () |
Public Member Functions inherited from Iterable< Sequence > | |
void | iterate (Functor f) |
virtual Sequence * | getItems (Sequence *&buffer) |
virtual size_t | getItems (Sequence *&buffer, size_t start, size_t nb) |
Public Member Functions inherited from ISmartPointer | |
virtual | ~ISmartPointer () |
Public Member Functions inherited from Bag< Sequence > | |
virtual void | insert (const Sequence &item)=0 |
virtual void | insert (const std::vector< Sequence > &items, size_t length=0) |
virtual void | insert (const Sequence *items, size_t length) |
Public Member Functions inherited from SmartPointer | |
void | use () |
void | forget () |
Static Public Member Functions | |
static const char * | name () |
static size_t | getMaxNbFiles () |
Additional Inherited Members | |
Protected Member Functions inherited from SmartPointer | |
SmartPointer () | |
virtual | ~SmartPointer () |
Split a given bank in pieces.
This class allows to iterate the sequences of a given bank by splitting them.
BankSplitter | ( | IBank * | reference, |
size_t | readMeanSize, | ||
size_t | overlap, | ||
u_int8_t | coverage | ||
) |
Constructor.
[in] | reference | : reference bank that provides the sequences to be split |
[in] | readMeanSize | : size of a read |
[in] | overlap | : nucleotides number that overlap between two consecutive reads |
[in] | coverage | : number of occurrences for the reads |
~BankSplitter | ( | ) |
Destructor.
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virtual |
Give an estimation of sequences information in the bank.
[out] | number | : sequences number |
[out] | totalSize | : sequences size (in bytes) |
[out] | maxSize | : max size size (in bytes) |
Implements IBank.
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inlinevirtual |
Flush the current content. May be useful for implementation that uses a cache.
Implements Bag< Sequence >.
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inlinevirtual |
Implements IBank.
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inlinestatic |
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inlinevirtual |
Return the number of items. If a specific implementation doesn't know the value, it should return -1 by convention.
Implements Iterable< Sequence >.
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inlinevirtual |
Return the size of the bank (comments + data)
The returned value may be an approximation in some case. For instance, if we use a zipped bank, an implementation may be not able to give accurate answer to the size of the original file.
Implements IBank.
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inlinevirtual |
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inlinevirtual |
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inlinestatic |
Returns the name of the bank format.