gatb.core-API-1.3.0
File List
Here is a list of all documented files with brief descriptions:
[detail level 123456]
  src
  gatb
  bank
  api
 IAlphabet.hppInterface definition for genomic alphabets
 IBank.hppInterface definition for genomic databases management
 Sequence.hppDefinition of what a genomic sequence is
  impl
 AbstractBank.hppAbstract implementation of the IBank interface
 Alphabet.hppImplementation for genomic alphabets
 Bank.hppUser front end for opening genomic banks in a generic way
 BankAlbum.hppBank format that holds other banks URI
 BankBinary.hppBinary bank format
 BankComposite.hppComposite bank, ie. a bank made of other banks
 BankConverterAlgorithm.hppBank conversion from one IBank to another IBank
 BankFasta.hppFASTA bank format
 BankHelpers.hppHelpers for managing IBank objects
 BankRandom.hppRandom bank format
 Banks.hppInclude all IBank implementations
 BankSplitter.hppInterface definition for genomic databases management
 BankStrings.hppHard coded genomic bank (mainly for tests)
  debruijn
  api
 IContainerNode.hppContainer interface
  impl
 BranchingAlgorithm.hppAlgorithm that computes the branching nodes of a De Bruijn graph
 ContainerNode.hppContainer implementation
 Graph.hppGraph class
  kmer
  api
 IModel.hppInterface definition for the kmer model
  impl
 BankKmerIterator.hppKmer iterator on sequences of a bank
 BankKmers.hppKmer iterator on sequences of a bank
 BloomAlgorithm.hppBloom algorithm, ie. compute a Bloom filter from a set of reads
 BloomBuilder.hppBuild bloom filter from an iterator of kmers
 DebloomAlgorithm.hppDebloom algorithm, ie. compute false positive sets for a Bloom filter
 DebloomAlgorithmFactory.hppFactory for Debloom algorithms
 DebloomMinimizerAlgorithm.hppDebloom algorithm, ie. compute false positive sets for a Bloom filter
 LinearCounter.hppLinear counter for kmers using a bloom
 Model.hppKmer management
 RepartitionAlgorithm.hppRepartition algorithm, ie. compute statistics on kmers
 Sequence2SuperKmer.hpp
 SortingCountAlgorithm.hppCounting kmers from a set of sequences
  system
  api
 Exception.hppOperating System common abstraction
 IFileSystem.hppOperating System abstraction for file system management
 IMemory.hppImplementation of an abstraction for dynamic memory allocation
 ISmartPointer.hppSmart Pointer Design Pattern interface
 ISystemInfo.hppInterface providing information about the operating system
 IThread.hppInterface for threads
 ITime.hppInterface for time retrieval
 types.hppTypes definition for GATB
  impl
 FileSystemCommon.hppImplementations common to various OS
 FileSystemLinux.hppImplementation for Linux
 FileSystemMacos.hppImplementation for MacOs
 MemoryCommon.hppImplementations common to various OS
 System.hppEntry point class for accessing operating system operations
 SystemInfoCommon.hppImplementations common to various OS
 ThreadLinux.hppThread management for Linux
 ThreadMacos.hppThread management for Macos
 TimeCommon.hppImplementations common to various OS
  tools
  collections
  api
  impl
  designpattern
  api
  impl
  math
 FastMinimizer.hppFast computation of lexicographical minimizers wtih no-AA-inside constraint
 Integer.hppEntry point class for large integer usage
 LargeInt.hppClass that manages large integers
 NativeInt128.hppInteger class relying on native 128 bits integer type
 NativeInt16.hppInteger class relying on native u_int16_t type
 NativeInt32.hppInteger class relying on native u_int32_t type
 NativeInt64.hppInteger class relying on native u_int64_t type
 NativeInt8.hppInteger class relying on native u_int8_t type
  misc
  api
  impl
  storage
  api
  impl
 gatb_core.hppGlobal header file