[med-svn] [gatb-core] branch master created (now f3e3862)
Nadiya Sitdykova
rovenskasa-guest at moszumanska.debian.org
Tue Oct 10 23:27:05 UTC 2017
This is an automated email from the git hooks/post-receive script.
rovenskasa-guest pushed a change to branch master
in repository gatb-core.
at f3e3862 provisioning an ubuntu 16.04 LTS slave (for ci use with jenkins)
This branch includes the following new commits:
new ba9b4ba first version
new 24cad4c first version
new 117943d first version
new e6b30a9 first version
new 045a6e8 IteratorListener is now a smart pointer (ease its use)
new 9661223 Parameterization of the way kmers are computed
new f43bb7d Parameterization of the way kmers are computed
new c9d00b4 Parameterization of the way kmers are computed
new eed420b Parameterization of the way kmers are computed
new 58633c8 Parameterization of the way kmers are computed
new 08b8cfd 1) Parameterization of the way kmers are computed 2) move BankKmerIterator in its own file
new 0dda91d first version
new 9e8883f correct comments for doxygen
new b637028 correct comments for doxygen
new 948d45d cosmit
new 0e66fd1 first version
new 95bfbb2 Add missing include
new c7369b3 cosmit
new 3f9fd50 Add (commented) line for debug compilation with gprof
new cf74220 Use KMER_MINIMUM
new 47c72a9 Set output type to ASCII for BINARY to ASCII conversion
new d7ec0d3 Temporary comment
new 93673fd New structure for Model => to be improved
new b75f667 Add KmerMode dimension in the test
new 5248405 Improve test BUT comment some part (temporary) until Model support correctly revcomp for large integers
new 7c2f76b cosmit
new 231ec9d first version
new bb81e80 cosmit
new e01e4fa New organization for large integers calculus
new 9ddac62 First version
new f14b17d Inline all methods for performance
new 75453cf Setter for non reference (ie with copy of the provided data)
new 1094f71 Data is now a subclass of Vector<char>
new 7f5fba7 first version; comes mainly from plast code
new 78ac559 Add typedef for native 128 bits integer. WARNING ! should be improved for system not supporting such a native type
new 52d8c13 Add tests for Vector class
new 43ef095 1) API modification 2) add 'build' method
new 92d9e9a Remove namespaces in this specific case (defining only static data)
new f54358f Must add #include to force a correct name definitions
new 2c47087 First version
new e3ffe28 Massive changes. In particular, define a default KmerModel type (without template) using the default Integer type as kmer_type. 'kmer_type' is also typedefed as Integer
new 6a51ade Add BankVectorKmerIterator (iterates vector<kmer_type>)
new 1adb91a Add namespaces for consistency
new 95f7c2c add VectorIterator class
new e83e79f Mainly add 'setDataRef' method
new 565f35c Use Vector class (through Data) for the buffer read from the file => allow to reference sub buffers from it and ensure the buffer life cycle is coherent with the life cycle of the sub buffers
new 426bc91 Use Vector class (through Data) for the buffer read from the file => allow to reference sub buffers from it and ensure the buffer life cycle is coherent with the life cycle of the sub buffers
new 2228dc2 Use Vector class (through Data) for the buffer read from the file => allow to reference sub buffers from it and ensure the buffer life cycle is coherent with the life cycle of the sub buffers
new 57e8dcf Use Vector class (through Data) for the buffer read from the file => allow to reference sub buffers from it and ensure the buffer life cycle is coherent with the life cycle of the sub buffers
new 351c416 Correcting bad }
new 977c45a 'codeSeedRight' method
new 91d29c1 'codeSeedRight' method
new 9af5ac7 Update with new APIs
new 533292f Update with new APIs
new b46bb05 Update with new APIs
new 175d156 Update with new APIs
new 08ef013 cosmit
new 733b208 Add INTEGER_KIND
new 420956f Activate only first test
new c01f83d Add missing initialization
new 13e1203 Add file structure as comment
new 6b6124a Implementation of 'estimateNbSequences'. WARNING!!! unit tests have to be done for it
new 7faf21f API change for estimators management
new 5855de1 Abstract implementation of the IBank interface
new a4affb9 1) inherits from AbstractBank 2) estimators management
new cb5cbe8 1) inherits from AbstractBank 2) estimators management
new a88859d Possibility to update the message for an iterator listener
new 7d6de0c Introduce DSK binary
new 8dedfa5 Add a user paramater
new 14bd7e9 Optimization: introduce operators ^= and += (note that += is not tremendous since it is not so simple to optimize it)
new ab761ff Optimization: introduce operators ^= and += (note that += is not tremendous since it is not so simple to optimize it)
new a19ecc3 Introduction of DSK class
new f018828 Correct initialization
new 3799a8c Check kmer size wrt chosen large integers size
new cd194e7 cosmit
new af89cb4 remove bad spans values for default (64 bits) integers
new bed4486 Remove ttmath
new a013359 remove ttmath
new bba7ae0 Add new 'insert' method for inserting a vector of items. Trivial basic implem, but subclasses may have smarter implem
new 98a411b first version
new 124bc8a Use pointers for referencing the functors
new 18affc2 First version
new dff6d09 1) add KmerChecksum 2) add -fopenmp
new cc3076b First working revision
new ac1fa9f Read the file forward (and not backward)
new 49ec81d Correct missing include
new b6e84dc First version
new b1cc45a Deactivation (temporary)
new da941d2 Add openmp
new 7d73d8e first version
new a7d8ba9 Remove absolute path (need to add omptl sources)
new a35685e First version
new bc27356 Compute INTEGER_KIND and KMER_PRECISION according to the user provided k parameter
new 8169218 Remove typedef for integer on 128 bits
new 04fd164 Compile NativeInt128 class only if the INT128_FOUND compilation flag is defined
new f0208c7 Force setting of INT128_FOUND
new 8a738a1 Better implementation of the tests (use NativeIntXXX classes)
new e149d07 Set default KMER_PRECISION to 1
new 4931b9b cosmit
new 28c7a8c Add conditional compilation (with INT128_FOUND flag)
new eb63d00 Correct overflow on some systems (jenskin slave for instance)
new 6b2819b First version
new 4fdb32f Add KmerNeighborIterator class.
new e49a8fc First version
new 9b7ccbf Make sure the flush is valid, ie. we add something to flush to the referred bag
new 027821f In 'next' method, we have to copy the item => maybe to be improved in the future
new bd3f496 Add a new 'iterate' method: provide a functor representant that will be cloned N times for each thread
new 072ba03 Add 'hash' functions (used for bloom filters)
new 565ca9a First version
new d7d47fc First version
new 4694995 Take care of openmp
new ef539ed Take care of openmp
new 179d087 Pre-tests for deblooming => temporary version, clean up has to be made
new 77d875b Cpp config
new c8501da Modifying license headers
new aadec97 Adding kmer_direct iteration of kmers, printASCII
new eef30ca First prototype for Bloocoo
new ae9c3f0 Use smart pointer
new 0c95281 First version
new c4d879a Use smart pointer
new 4179eb3 Use smart pointer
new be4f751 First version
new d4ecf5e Add aggregated time for root property
new d422a38 Add LocalTimeInfo and TIME_INFO macro
new ff03aa2 Add operator[]
new c9f0d94 Add operator[]
new d7e7d6a Add debug and omp management
new 2ed35dc Use smart pointer
new 01116ae Many changes...
new 2f47251 Use smart pointer
new 025894c Use smart pointer
new 2b55b5f Use smart pointer
new 978b1ae Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new 52b6e33 bloocoo output filename, comments
new 5a9d9ec Add getHomeDirectory method
new 5264fc8 Add getSize method
new b35ab8c Change readFile proto and implementation
new 87f9570 change getProperties prototype
new c0e98d7 Better options management
new d936d51 a few API changes (using smart pointer)
new 4c12d2c Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new 01caa2e Major modifications for dsk and bloocoo
new 2dcb6bd many changes for dsk and bloocoo
new a2b389e Improve comment management for Sequence class
new 552169a Better structuration for Tool class
new 10d8ac9 Attempt to optimize when bloom size is a power of 2
new 072fe68 cosmit
new 7f3ce4f Several improvements (near to a correct version)
new 9271e0c Introduce IteratorFunctor
new ab98359 Introduce IteratorFunctor
new 412b973 New Sequence API
new e7addd7 Use empty main functions => temporary due to migration to gatb-tools
new 511748c Bug on Macos to be investigated
new 5cba311 New Sequence API
new 029f8bc cosmit
new 142edba Correct compilation issue on macos
new 8af1728 Better organization (including Tool class use)
new fcc5975 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new 7d20730 Make documentation optional => must be generated by "make doc"
new 8634aee Use OpenMP management by CMake
new 24ec19b Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new 602889e Add an optional target for launching unit tests
new fe2a9ee Better db path management
new 99ca98a Better db path management
new b4661e7 Better db path management
new 4914621 Correct compilation warnings (seen on CI slave)
new 307084f codeSeedRight mode
new f7051bf Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new 0e0b185 Correct bug in Model when kmer size is greater than read size
new fa0464c Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new d975806 Correct CMake file for OpenMP flags during link stage
new 11441ec remove bloocoo from gatb-core tools
new 8ffd653 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new e487539 Some targets are now optional; only library and unit tests are generated by default
new 7b1ac87 Add getBaseName method
new 28772d5 Change macro TIME_INFO implementation
new cc92821 Add some DEBUG traces
new 451d939 1) add getters 2) add ToolProxy for easing delegation
new cfa23bd now parse first arguments line for all tools in a composite tool
new b2aa8eb Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new 08ffcc2 add #include for basename
new 3e790a3 Add missing include for basename
new 7501f69 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new 6d364c3 1) better progress information for DSK 2) Histogram introduction
new 2207003 remove debug traces
new c889eb6 BloomCacheCoherent and bloom benchmark
new 75d434a bench bloom details
new 234c9b8 operator | for kmer_type
new 55b6cc7 First version
new 0d5956f Factorization and cleanup in CMake files
new 49162fe prefetch in bloom cachecoherent
new c63fea7 correc bug in interation of kmers fo KMER_DIRECT mode
new 1429175 minor
new 6bc02b0 take code from Minia original code
new 2bacab0 BloomBuilder is now a template class
new cb3fe86 add 'rename' method
new 94a704c Change inner template class name (due to collision with other code)
new 20091f9 Add default value (used by Hash16)
new d095240 Add full namespace for the TIME_INFO macro (otherwise, could lead to some compil issue if the namespace is not used)
new 4e7c901 srandomdev linux bench_bloom
new d892bd6 Merge branch 'master' of ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new 9077104 seq num in Sequence type
new 77617fd Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new f7bbae5 Use pointer for the iterator given to FilterIterator class (the idea is to use smartpointer facility)
new afdd642 Avoid multiple inheritance (to be improved...)
new f99fe3f First version
new 43d9e04 Introduce IBankFactory interface
new 3d1ce12 Add getIndex feature for the Sequence structure.
new 78b9843 1) index field management for Sequence 2) implementation of IBankFactory
new 9722ec9 1) index field management for Sequence 2) implementation of IBankFactory
new 5c63fe9 Add a simple way to filter Sequence of a bank (class BankFiltered)
new d432a51 Add unit tests for BankRegistery class
new bab9bc3 Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new a3097f6 Set the same BINREADS_BUFFER value as minia
new d8889d6 Use reference instead of copy
new 46bb5fb Use BagCache (and not BagCacheSorted) when using OAHash class in DSK
new 2de750d cosmit
new dbdb962 1) change uint64_t into u_int64_t 2) introduce oahash for LargeInt
new f047e7d introduce oahash for NativeInt64 and NativeInt128
new 7c6d296 Use default attribute (and remove local one)
new 2eb0e29 Add a setRef method
new 769c454 Force updating when setting a new message
new a9c0027 Use serial dispatcher when nbcores==1
new 40e5777 First version
new 79a0971 Introduce a way to deal with BINARY data => remove the previously BINARY to INTEGER conversion. Note: could be improved (for perf)
new 3f4682b Introduce a way to deal with BINARY data
new 19da272 First version
new 6ea3357 Revert modif (due to bloocoo bad behavior)
new 7ef85b0 prefetch bug bloom cache coherent
new eeeaa69 skip NN in bankbinary conversion, bloombuilder uses BloomCacheCoherent
new 9db3ea7 bin2NT global
new a0b1666 Correct regression in unit tests due to split management in 'insert' method => introduction of a new parameter for configuration of BankBinary instances
new 482dc42 Correct regression in unit tests due to split management in 'insert' method => introduction of a new parameter for configuration of BankBinary instances
new 3484c67 Add an error status as result of 'build' method (we could retrieve no kmers at all if the provided sequence is too short)
new 19c67aa Correct printf format (warning during compilation on continous integration server)
new c9fd90f Correct constant (warning during compilation on continuous integration server)
new 6c862d1 cosmit
new 17b94b7 Add two examples for debruijn graph management
new e274274 First version
new 229f01c Add 'reverse' and 'toString' methods for a kmer
new 806ec05 Add virtual destructor (memory leak otherwise)
new 9ca7941 First version
new 445a706 Temporary (to be improved): BloomCacheCoherent::insert is concurrent access protected now
new 306d245 Add IterableFile class
new a2cb750 new 'add' method with variable arguments list
new 3146d87 Now distinction between MessageRepository and StringRepository => to be improved
new 9bb7ca7 LOCAL object macro improvement (use full namespace)
new 53ef32b Add toString method and operator[]
new 88f4768 First version (commented so far)
new da4cfab cosmit
new 2e3726a cosmit
new 02e5f84 cosmit
new a73efbd compilation issue
new 1fd70f8 oops, forgot to commit bloom cache coherent bug : insert parallel bug
new ee3f88d Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new ac0c99b bloom cc update
new 4b8806c assign operator for Vector class
new 9257e85 Factorization
new 1e6dd7a Add VectorIterator2 (ugly, to be improved...)
new dd11a9e Add 'setRef'
new 738b1f0 Add some strings
new 414e7cd first version
new c6682a4 first version
new 422fed0 Copy from gatb-tools -> when everything will be ok here, we will remove DSKAlgorithm class from gatb-tools
new 2dc6e61 Add tests for BankStrings class
new 71fadba first version
new 4ad7fee Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new afcf9e2 Double registration of suites => one in unamed registery, one in named registery
new 52df114 Improved test
new 7739ca0 Target 'test': must provide the name of the tests suite ('All Tests')
new 0e7615b Allow to dump the items
new 6e8db73 Add a getNbItems to the Iterable API
new 3021c75 Correct Iterator::reset management for the dispatcher
new 4d1a661 Add strings
new 446310b Possibility to choose which Bloom implementation should be used
new b202ae8 Improvements (including configuration in constructor)
new 53d79ce Copy from gatb-tools (should be removed in gatb-tools when all clean up will be done)
new 5634f5b Configuration for the Node::toString method
new d31c119 IMPORTANT: use u_int64_t (instead of u_int8_t) for nucleotides (otherwise, big shifts may fail)
new d18cf2d Add a new method for creating a graph
new 3541fe6 first version
new 0f0a671 Add tests for DeBruijn graph
new cb80ec9 cosmit
new d317781 bank printf
new bf761f9 Properly defined ISmartPointer interface (instead of direct SmartPointer implementation) => allows to inherit several times the ISmartPointer interface with only once implementation (SmartPointer)
new 4f3b873 Cleaner use of smart pointers
new 0d74e46 1) add getNearestBranchingRange method 2) force call to 'first' in 'nodes' method (allows to have something like graph.nodes().item())
new a9e80ba Add a method to build a graph from a bank and the kmer size (DSK and debloom are executed in this method)
new 2548133 Move code from hpp to cpp
new d4f72dd Restructure and add a test
new ffd432c Add TIME_START / TIME_STOP macros
new cd02bdd overload operator << for properties
new 3579273 Add statistics for DSK
new 17a5458 Add statistics for DSK
new f39fe69 first version
new 597dc9b Add missing inclure
new 7789892 Modify default value for nks (from 1 to 3)
new b21598f 1) cosmit 2) 'graph' management for Edge and Node 3) correct hash number management
new 277f687 cosmit
new 36ae4f4 Add example files
new a68d7e3 Change Edge constructor (default value allowed)
new 9f81275 1) use gatb_core.hpp 2) use another constructor for building the graph
new 6800fcc First version
new 78e8273 1) use gatb_core.hpp 2) use another constructor for building the graph
new 6e5b014 Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new e274335 Code factorization
new 27b97eb Possibility to add a default parent Property if non empty name is provided
new 695d59b Another way to call 'iterate' method
new 603d7ae 1) code factorization 2) cosmit
new 9c8b554 Cosmit
new d4ad533 cosmit
new b8f9bc5 First version
new 154e9ec Correct test order (avoid valgrind invalid reads)
new b791165 Code factorization
new b5afa62 Add virtual method 'execute'
new d37fd6a Cosmit
new e4086e1 Cosmit
new 4738379 cosmit
new 5bf5a7d Add time statistics for the bank conversion
new 5007498 Force flush in destructor for simpler code
new 87a46be Possibility to add a listener at SubjectIterator construction
new 1d0be7f Add a getNbItems method to the INodeIterator
new 808a589 Encapsulate nodes iterator for getting notifications
new 551b4dd first version
new 9dc18d0 first version
new eb559b4 first version
new e82ca8a Implementation of RangeIterator that supports parallel iteration
new 0643cc6 first version
new 21d4cb3 Implementation of STLIterator that supports parallel iteration
new aa90c60 Correct potential bug
new 40efa10 cosmit
new dbd728b Force file destruction before creation for writing
new 938912e virtual inheritance for IterableFile
new 8ea616d Major changes for using Product/Partition/Collection classes => first step before introducing HDF5. Note that these design changes should allow to easily configure what kind of persistency model we want (file, HDF5, ...)
new 2a45cf3 first version
new fdadc3d Adaptation to the Product/Partition/Collection classes
new da71650 gcc 4.7 compil issue
new d019f4e first version
new cb857cf Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new 07c73e1 Better implementation of Product. Now, we can configure with a factory => preparation of HDF5 management
new ffbd8e6 Histogram management
new a3b0368 Delete the Bloom filter after the neighbors extension has been computed
new 391b7c5 cosmit
new c792016 cosmit
new 7e1ddb9 Remove flush during destructor
new 110d02a Add a 'const' to the input parameter
new 46a8415 Use Kmer structure instead of direct kmer code => allow to have kmer abundance in Node structure (for solid kmers)
new c631cac Use Kmer structure instead of direct kmer code => allow to have kmer abundance in Node structure (for solid kmers)
new 2b5e692 Use Kmer structure instead of direct kmer code => allow to have kmer abundance in Node structure (for solid kmers)
new 4a1e7fe cosmit
new 06920cc add a new 'insert' method that takes a raw buffer of items
new c3ee6a0 cosmit
new d4144f3 Use Kmer structure instead of direct kmer code => allow to have kmer abundance in Node structure (for solid kmers)
new b5513cf Add HDF5 package as a third party
new 1c03385 Create a specific file for library generation
new 247561f Better CMake management
new 8e67aa7 Better CMake management
new 55bf2e8 First version of graph builder binary
new 63a3a16 Better CMake management
new 55a1086 Add two includes
new c645d05 Add HDF5 management
new 147ecd9 Add getXML helper
new 5aa3460 First version
new 94e681f Add strings (in and out)
new b5b0ff1 Use raw vector instead of STL vector
new f9d0e63 Add HDF5 management
new ddd983e First version (needed for dumping Bloom filter in HDF5 format through Collection interface)
new 3429a47 Add utility (for Product/Group/Collection usage)
new 0a78b11 First version
new 1a59147 Add accessors to the raw bits field (used for file serialization)
new f1a6149 Add a "getItems" method; some implementors of Iterable could be able to provide in one raw vector all the items
new 869eb73 Add "property" methods
new 8265616 Add "property" methods. Add a "getItems" method; some implementors of Iterable could be able to provide in one raw vector all the items
new 1254901 API change
new 3b51de2 API changes
new 32a7580 Add "getId" method
new 633397c Add a new "load" method => NOTE: still clean up to do here
new e3268ce Add "build" method (preparation for improved design)
new 8a4a630 Add "build" method (preparation for improved design). Add a new constructor ("load" method)
new aea41f5 HDF5 introduction
new 140e8c5 HDF5 introduction
new dbd3805 cosmit
new b86939c Use "load" method
new 25587df Add -Wno-invalid-offsetof due to compilation warning on MacOs => BE CAREFUL, a small redesign should be done in order to get rid of this warning (due to HDF5 usage of offsetof macro)
new de58d60 Add "verbose" string
new 6139933 cosmit
new 24588bc First version (comes from plast code)
new f9a730f Modify constructor (provides nbcores parameter)
new 36dfa31 Parsing XML properties (from plast code)
new 92d60fe First version
new 66be043 Inherits from ArrayData
new a7083e5 First version (comes from plast code)
new e17da05 Add getRoot static method
new 4b91cb7 Several improvements
new 4553716 Add ArrayData type (used for factorization of math types)
new 5d4631a cosmit
new ef8b84a 1) some API changes 2) add "load" method
new 92eaaa6 1) cosmit 2) compute the total number of valid kmers
new cba2c81 cosmit
new 851f35e Several improvements
new 635e5da Deactivate (for the moment) HDF5 tools generation => on macos, crash of these tools
new e8df1e4 Add some options for the command line
new faaf218 Several improvements
new f5e9069 Build library as a sub project
new bab0493 Remove memory leak
new f24c190 Add a parameter to configure method
new df7fe09 cosmit
new b9dad99 cosmit
new 72cf8a2 Remove useless part
new 0d8afb6 Add a parameter for forcing product deletion if already existing
new 2ecd825 Modif on OptionParser
new fb96a11 Add a parameter for forcing product deletion if already existing
new 84f3513 Add OptionFailure management
new 8486318 Cosmit
new b26bf07 Add dbgcheck binary
new 57ab9ed Correct bad CMAKE value
new 9719c19 Rename DSKAlgorithm into SortingCountAlgorithm
new 79bb04d Add missing include
new 1a1de56 add statistics information
new 5919a2a Rename XXXCommandDispatcher to XXXDispatcher
new 6f9fa2e 1) rename XXXCommandDispatcher to XXXDispatcher 2) Return a status from 'iterate' methods
new cd217a3 first version
new 5e6e8f7 first version
new 798ec41 Rename XXXCommandDispatcher to XXXDispatcher
new 4bbf007 Add include
new fcec09c Add IteratorVariant
new c877617 Rename hash function (name collision)
new 49ae1f1 cosmit
new b04dda8 Rename hash function (name collision)
new 083a053 Improve class (copy constructor, assignment operator...)
new 04446bd Definition of "generic" integer class with the boost::variant class
new fbb0b13 add toString method
new dff2283 Add cast operator
new ab5dd90 Rename hash function (name collision)
new 413c00e 1) Rename hash function (name collision) 2) add specialization for prec=1 and prec=2
new d903014 Add getters
new e8a84e4 Add ThreadContainer class
new 9569ee1 Rename Dispatcher classes
new 9cceb22 Make method static
new 575514b cosmit
new bff4835 1) Improve Kmer class (to be used with boost::variant) 2) move some enums from graph to here
new 2e36421 cosmit
new 64d322a Clean up with integer types
new 55d273a Improve class (to be used with boost::variant)
new 03a2631 Make method static
new 4cc21b0 Brand new design of graph that doesn't rely on templates. Instead, we use a "generic" Integer class (as a boost::variant)
new 3a1f4d9 cosmit
new f2d70a6 Tests update according to the new graph design
new bf60013 Tools update according to the new graph design
new 87caf5c add -std=c++0x
new 1d70dcc Correct crash due to lack of use/forget management for the 'nodes' object
new a28839f Remove compilation errors on macos
new d4c17bc Add boost dependency (boost::variant)
new 49ad4fb cosmit
new d9c163f Add missing include
new c627efb Correct bad "contains" test
new ce93a1c 1) add isBranching method 2) correct but in getPredecessors
new 6e3b404 correct bug in getEdges_visitor
new 98c7149 move from package "dp" to "system" => now can be used with some system low level objects (like IThread for instance)
new 8553618 1) define IThreadGroup 2) use ISmartPointer
new 574eaf7 1) use ISmartPointer 2) add IThread::getId implementations
new 7dc03e2 1) ThreadGroup implementation 2) ThreadObject implementation
new dfa6ecb move from package "dp" to "system"
new 4ff2074 1) rename Dispatcher (instead of ParallelDispatcher) 2) remove useless IteratorFunctor
new cd89a55 move SmartPointer from package "dp" to "system"
new 537c28e New implementation that relies on ThreadGroup
new f650df4 move SmartPointer from package "dp" to "system"
new e5a6cea Better implementation of ProgressSynchro (better value semantics)
new 5604f1a move SmartPointer from package "dp" to "system"
new 729b06b Use synchronizer as a smart pointer
new 4a7dcfd cosmit
new 6e6fbdb move SmartPointer from package "dp" to "system"
new 46e2fd1 1) remove IteratorFunctor 2) mv ParallelDispatcher to Dispatcher
new 454f4c0 1) move SmartPointer from package "dp" to "system" 2) add iterateNeighbors method
new 93ab898 remove functor classes "BuildKmerExtension" and "EndDebloomPartition" => use lambda expressions for simpler code
new 25ae8d5 Use ISynchronizer as a smart pointer
new c5f2a11 First version
new 65395cb Major revision (1) don't use IGraph anymore 2) add branching nodes management)
new 6e5725f move SmartPointer from package "dp" to "system"
new 76af516 Remove include
new 3bf8fb0 Major revision (including branching nodes management)
new f5eddbe Correct compilation issues due to modifications
new 557439e Correct compilation issues due to modifications
new bd9ed4d Correct compilation issue on Macos
new 2a0fd36 Correct compilation issue on Macos
new aae424b add getThreadSelf method
new 18555d9 cosmit
new 615982e first version
new a107a95 Branching kmers sorting
new 1dae114 Add #include
new 95c861f comment some parts (temporary ?)
new bc33b67 Improvements for Nucleotide management (add 'ascii' and 'reverse')
new 3105473 Improvements set during Minia gatb integration
new f8a0d7a Modif coming from gatb-tools (during Minia integration)
new 41728e8 Correction of toString method
new 25feea3 cosmit
new 59337e8 New stuff for Sequence and Model
new 470cefa Modify a test for Model::getKmer
new af962d4 Correct compilation issue on macos
new 9eedfbe Few improvement about Node
new a6bc96a Add toString method
new db5d0a8 Modify return type of method 'getKmer'
new 3e1a7ca 1) add possibility to create an empty Graph (with a given kmer size) 2) add 'reverse' and 'getNode' methods
new 26a5e64 Tests update due to API changes
new b7ae155 Changes due to minia tool
new 5945539 1) cosmit 2) add in Graph class for getting neighbors for a kmer value (and not a node)
new 39829b6 Update due to minia development
new da3c61c Go back to Graph::Vector instead of std::vector for performances consideration
new 16ee2e3 Cleanup and documentation
new bfb06a8 add 'Graph::getNode'
new a980cc4 Add a shortcut method
new 8f70040 Renaming getNode to buildNode
new 0a322bb First version
new e30fc31 1) add 'rank' method 2) move 'getNbItems' to 'size'
new 7585096 API changes
new c8a5c7a API changes
new f8893a9 New tests and documentation
new 9abfb41 Correct API change
new d759ba3 Improve code documentation (correct a few errors detected by doxygen)
new 970cd84 CMake management for install target
new 1e9511f cosmit
new 569e17a first version
new 3cad49b 1) modify hdf5 build/install 2) modify code for hdf5 includes
new 8e3b8f3 first version
new f66ef87 simplification
new 10fdaf0 Simplification (and avoids unwanted systematic re-compilation for the gatb core library)
new 4014f45 Add simple path iteration
new 2a84ee9 Add simple path iteration (doc and test)
new 7704592 first version of the configuration file
new 0d01b5c include configuration file (generated by cmake)
new a3af66b configuration file generation
new 7fe503d configuration file management
new 04fcda2 Correct compilation instructions
new 88e5e02 Correcting install targets (and cosmit)
new cf39315 cosmit
new bf8f7cc Re introduce hdf5_postbuild dependency here (should be improved)
new 76792cb Define default 0 value for INT128_FOUND
new e6229f5 Correct INT128_FOUND usage
new 2d3c3b8 first version
new 2824baf add reference to download page
new fccbb41 cosmit
new 0daa3c4 cosmit
new 8d9b110 first version
new 738bb44 Better structuration for De Bruijn snippets
new aa6df82 Implementation of Graph::neighbors<BranchingNode>
new 8e4aedc Tests for Graph::neighbors<BranchingNode>
new bd86702 Implementation of Graph::neighbors<BranchingNode>
new 05ac8ec first version
new 38f663b add Graph::neighbors<BranchingEdge>
new eee16c7 add "go back to top"
new b2a7506 cosmit
new c47cdb6 cosmit
new d994974 cosmit
new 0265589 nucleotide of the BranchingEdge is the nucleotide of the first transition between the source branching node and its first neighbor on the simple path that leads to the target branching node
new df4d532 Add a test for Graph::sucessors<BranchingEdge>
new dca54ac first version
new 1fe7bd8 cosmit
new 5ff3a4c Add a snippet (debruijn18)
new bbd20ee Add 'size' method for ProgressIterator class
new 13859f1 cosmit
new 2107be5 cosmit
new 42a5001 Generate a search box for HTML documentation
new 4f079e5 First version
new d372f57 cosmit (including Graph::getName)
new c6a9bbe Set SEARCHENGINE to NO (because gatb-core web site not supporting it)
new 5d10191 Add minimal doc for example debruijn19
new 8906048 Remove OS snippets for the moment
new 0a5b791 1) add a set<T> Graph::neighbors (first, last) that computes all neighbors for all items iterated through the [first,last] two iterators 2) improve command line options parser
new ef20f74 Add "-out-dir" option
new 0d26333 Allow to provide the h5 filename to the product constructor (instead of the file name without the h5 extension)
new 06b9f5b Use Graph options parser
new 38a063e first version
new b1be5d6 Use a set-based approach for computing BFS
new 27486f3 cosmit
new 3fb868e cosmit
new b771c1d cosmit
new 11e9e72 cosmit
new d59c2a2 Provide a (non optimal) multithreads implemention for getting neighbors for branching nodes
new 88b46a4 cosmit
new 29be138 Renaming Bank into BankFasta
new 579d151 first version
new 3a41ce0 add Sequence::setComment method
new 448de67 renaming OptionsParser::add in OptionsParser::push_back
new 7647cce cosmit
new b11edca add includes
new 7811995 Improvements for OptionsParser class
new 4cc5e79 improvements due to changes in OptionsParser class
new 9368951 first version
new 670281d improvements due to changes in OptionsParser class
new a02b7f1 add bankgen program
new 5dee7b6 Add an entry for compiling all examples
new 2eade75 cleanup
new 41e471d Add tests for BankSplitter and BankRandom
new 9222b25 Add tests for BankSplitter
new 0ee8506 correction due to API change
new 35d4f98 Improvements
new b4e1aab robustification
new a82616a Add affectation operator for Data
new 08c833c Update one test on random banks
new ae1af77 Change name (from 'test' to 'aProduct') to avoid possible name collision
new 6853756 add a setName method
new e72ce69 Use options parser from Graph class
new a4926a5 Change default coverage value (from 1 to 3)
new ec640cc Change default values
new 462c805 readXML method at interface level
new 1cff6fc save/load information of the graph as an attribute in the hdf5 file
new d362f0c first version
new 55ddab8 Add dgbinfo executable
new 3ff3485 first version
new d09a2a8 Cosmit for doxygen
new 34ef8ca cosmit
new 6752212 Major update for kmer management
new a415c57 Define default value for 'span' template parameter
new 27222ec Define default value for 'span' template parameter
new 1d0d1f4 Remove OpenMP management (not used anymore)
new 7ee446d remove OMP management
new 435a254 first version
new de9f827 1) bank management (renaming Bank.[hc]pp to BankFasta.[hc]pp) 2) Move IteratorWrappers.hpp contents to IteratorHelpers.hpp 3) Rename CartesianIterator to ProductIterator
new 9a8e4b9 First version (mainly files move from collections package)
new f5985b4 updates due to 'storage' package creation
new 4d7c143 #includes update
new 86d2c80 Modification for managing *.tpp files (template files)
new c6b9a7f "Product" management is now longer managed with templates.
new 411a50c moved from TestCollection
new de62d76 "Product" management is now longer managed with templates.
new 1d7caeb remove ModelAbstract.hpp
new 77a4599 Add missing "using namespace" for new "storage" package
new 1c2be56 Comments
new e98f0bd cosmit
new 3f96122 Verbosity has now one param (set to 1 by default => bargraphs enabled)
new a7f37f5 Since verbosity is set to 1 by default, use "-verbose 0" for unit tests
new f4023dd Improvement with data variant management
new ae2eccc Renaming product into storage
new 8f1f8ec Don't display variables not useful anymore. Note that we keep the variables computation (should be reused in the future ?)
new f373887 use "gatb-core-flags" variable for binaries that use the gatb core lib
new 8ff0f08 cosmit
new 4bdf3ff Avoid 'span' as variable name since it may be already the name of a template parameter
new f6f0df0 boost include
new 4bfe045 Add a few information strings generated during cmake phase
new 256d745 1) improve -std=xxx management 2) add variables used in code (like build date)
new ebeacf1 Add a string to the strings repository
new cac3033 Force a version for cmake
new 70bfceb output fastq
new 2761eab Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new 74d4676 cosmit (had warnings on macos with clang)
new dbbf9e0 Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new d8ec9f6 avoid warning on macos with clang
new a5236ac avoid warning on macos with clang
new b845812 Remove string(timestamp) management and required 2.8.11 cmake version, because some servers (like igrida) have old cmake versions
new 246ffdd First version
new a5ac5b2 Version management
new a335260 current date retrieval (rely on perl rather than string(timestamp))
new 91a6242 first version
new ba7195b Modify headers of *.hpp and *.cpp => Affero GPL
new e15b7f3 rename System::info::getOsName into System::info::getBuildSystem
new 5f641a7 Add compiler information (used for the library generation)
new 3e05227 first version
new 96a6a1c Library generation info
new ebfdb16 Simplification (use directly static method instead of singleton)
new c12b1ce Add dbginfo to the tools installation target
new 45263fd Use conditional copy of HDF5 headers file => avoid many unwanted recompilations
new 8f69a68 setQuality method in Sequence
new 7905d02 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new bbc8952 first version
new 4d407f4 Add BankComposite
new 5703c17 Management of FASTA URI lists
new 405966f 1) correct missing info retrieval 2) use BankRegistrery for creating the bank from an uri (no more FASTA hard coded)
new 13ae032 Implementation of CompositeIterator
new f7c5cb3 Add missing include
new 54ad67a first version
new 46ab68f Add a test for BankComposite
new ad6f704 improve test
new 7f1daf6 Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new 7aa6e93 (re)set the hdf5_postbuild dependency. Note that we don't face any more the unwanted recompilations issue (due to use of copy_if... in HDF5 part)
new da33c8b first version (mainly from examples debruijn18 and debruijn19)
new 67b5cd1 add dbgtopology
new e3efe17 cosmit
new e1788ed cosmit
new abc1307 first version
new e982bad Add include
new 452a51a Correct bug (sequence is wrong if the same iterator is iterated more than once)
new 34f10fd Improvements for BankAlbum design
new ccf37c1 Add 'getRealPath' method
new db05c3f first version
new 41e7dd2 add 'getDirectory'
new 20187d7 Correct memory leak
new e4ea97b Use album directory when uri in the album are pure filenames (ie without directory)
new 16e5f7f new test (split a bank into several parts)
new ddbec6f new tests for BankAlbum
new 23a8caf Improve file management
new 0e4de51 cosmit
new 6297b0e Add direct iteration through a functor from an Iterable instance => useful with lambda expressions
new e966981 Add BloomGroup class
new cba5140 Add 'iterate' for Model
new a16a545 Improvements while development of bpart
new 8bbf6a6 First version
new a35e672 Add Sequence::toString
new c6887a8 Correct unit test failure (due to "album.txt" git file unwanted modification)
new 9aab3d0 Improvement for ThreadObject class
new 49325c8 Add BloomGroupCacheCoherent (not fully tested)
new e5f2297 Add some operations
new 933f713 Add BankKmers include. Note it is not added in the Banks.hpp file since it is a IBank implementation specific for Kmers (and we don't want to create a dependency from bank to kmer packages)
new e56cc12 1) Redesign of the Model files content => add a Model.tpp 2) add "iterate" method for all possible kmer iteration
new ceb8bd4 first version
new afa6813 add test for BankKmers
new f24cc43 output gz bank
new 0bdfad5 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new 18663fe Add 'double' management
new d785dfd Several improvements (BankComposite and BankAlbum mainly)
new 7f058cb Modif for BloomGroup (temporary version, to be improved)
new c7e2231 cosmit
new 1841c71 first version
new fd1dbc5 Redesign of the example
new e97801a Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new 7bd4412 kmer getVal
new 516c9f6 first version
new 2346d75 Correct bad test
new ff78b1f WARNING ! Remove test in native HDF5 cmake file => necessary to allow conditional install of the hdf5 library (could be seen as a bug in this cmake file)
new 692819a Introduce GATB_CORE_INSTALL_EXCLUDE variable in order to install gatb tools without getting all the gatb core stuff
new ff14515 Allow maximal memory configuration for BloomGroup (to be improved)
new 8013c63 Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new d6148f2 First version
new 564ecb7 Add a gatb-core-cmake variable for sub-projects
new 5834af9 first version
new 2dc4ac5 cosmit
new 4b6e4bf Delivery target
new cf30a22 Use USER variable (works both on unix and macos)
new e0addae first version
new 6b6bb0b cosmit
new ea0d300 Use Delivery.cmake file
new 585eb78 cosmit
new d5ad7fa first version
new 314a9d1 improvements (based now on an external script)
new e883b9d add GetCurrentDateShort
new 458d564 Set no operating system for sources archive
new 87c998b Add missing include
new ec149f0 New implementation that doesn't rely on functional (ie c++11)
new b0a5bdd Avoid to use c++ features not supported by old compilers (structures definition inside methods, 'auto' type)
new c4380de Add a compilation flag WITH_LAMBDA_EXPRESSIONS
new baf2bb9 Avoid use of lambda expressions
new a49da44 Avoid to use c++ features not supported by old compilers (structures definition inside methods, 'auto' type, lambda expressions...)
new 26ce6f3 Management of WITH_LAMBDA_EXPRESSIONS flag
new a9b697d Remove useless 'typename' (compilation error on genocluster)
new 05b4dae Simplify template type (don't compile on macos otherwise)
new 84441d8 Conditional compilation of examples using lambda expressions in case the compiler doesn't support it.
new 983d5d6 cosmit
new 38381e2 cosmit
new a0391c8 Increase buffer size (crash otherwise on the CI server)
new cf98b98 hybrid_mode for DSK-GATB
new c071b6d Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new cc0f1c0 Add getMemoryPhysicalFree and getMemoryProject
new f0a406e Management of default value for STR_MAX_MEMORY parameter
new ea5e61f Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new 04d50a5 remove dbgtopology for installation
new 2276608 Add HDF5 tools generation
new d077af2 add getMemoryPhysicalTotal and getMemoryPhysicalUsed for MacOs
new cb1e458 Use static library for cppunit
new f5ba951 use static library for cppunit
new 827fc66 cosmit
new bf59ee4 Add implemention for BagHDF5::insert (const Item& item) (not optimized)
new 85fd32d rename createStorage in create
new e459cbb cosmit
new b877444 first version
new 200ab55 cosmit
new e3ad3ac storage4.cpp uses lambda expressions
new f5cf58f Add storage snippets
new 83d3010 Correct bad copy constructor (had always abundance=0 for branching nodes)
new f438daa Use NO_DEFAULT_PATH
new e86f4a5 remove GraphHelpers.*pp
new 4361de2 Remove GraphHelpers
new 666d947 Replace mode "a+" to "r+" (otherwise issue on macos)
new 57e0466 switch from MemorySizeStore (issue with clang on NativeInt128) to MemoryCommon
new 6958774 use -Wno-ambiguous-member-template (irrelevant clang error, not with gcc)
new ad361c0 force usage of c++0x
new 8913333 Go back to implementation with lambda expressions
new 1da601e cosmit
new e450c43 New OptionsParser::add method
new 97584b2 cosmit
new f3fab0c License information
new 937e541 Check directories existence (test doc examples) before doing an 'add_subdirectory'
new de27ef7 first version
new 096c1e6 some updates
new 928778c cosmit
new 0faddea cosmit
new 1a1fb77 File access settings
new fd06afb Delivery management
new 5f6bb7f add strings for bloom type and cfp type
new c342050 first version
new c6a0090 Add IMemoryComponent interface
new 29ba4d3 Add a constructor with a Storage object => get directly the collection from the Storage object
new e498263 Add a IContainerNode interface for a combo Bloom/CFP.
new b688b4f first version
new 5fffd13 first version
new b1a0aea Add a constructor with a Storage object => get directly the collection from the Storage object
new 543ee04 'iterate' method may use/forget pointers
new 4e47ed0 1) add a few getters 2) improvements for BloomFactory
new 5d18130 note
new 263163f Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new 686b055 Update bloom and debloom strings
new 24fdecd Add missing #include
new ab266cf Add pre-computed rvalues for cascading Bloom filters
new 8aab76d cosmit
new 0ae69f5 Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new 3e1d0eb configure DebloomAlgorithm with bloom/debloom types
new d152c0b Introduce cascading Bloom filters
new b91b663 cosmit
new 44a6150 add 'getGroup' method
new 2aea869 add 'readXML' method with an XML string as input
new f8454d0 first version
new d7d23f5 Add storage5 example
new a1d7544 cosmit
new c816290 download page at gatb.inria.fr
new ae58a86 first version
new 963ad3a initial guess moved to storage6
new c54a4c6 cosmit
new d9eff2c first version
new 90d14d4 reorder snippets
new 1f1ac33 cosmit
new dfefc0c Modify groupSize management
new f48ddcc multithread snippets
new 498a5cc first version
new a2cfc67 multithread snippets
new 44fe9aa cosmit
new e1a5fe6 Possibility to dump data on a single line
new 49236fd first version
new cc28e9c distribution of kmers
new f0de8ce use estimateNbItems instead of estimateNbSequences
new 766910d Use ProgressGraphIterator instead of ProgressIterator
new 9c96e85 first version
new e8251ea Use ProgressGraphIterator instead of ProgressIterator
new d64d874 1) Use ProgressGraphIterator instead of ProgressIterator 2) use estimateNbItems instead of estimateNbSequences
new ddb7465 Add estimateNbItems method
new 9da28d5 1) allow insert of one item 2) add estimateNbItems
new 4aecdc6 Add estimateNbItems method
new c91bf9d cosmit
new 5e3bc8c ProgressGraphIterator changes
new da26acc add 'polynom' and 'toInt' methods
new 5887ef7 add IterableHelpers include
new bec2f3a move metadata copy from graph to algos (SortingCount and Debloom)
new 844c674 Modifs made during gatb-tools development
new 36d7454 Improve verbose management
new 045f868 Skip h5ls build (keep only h5dump)
new 88c9724 Keep only dbgh5 and dbginfo
new 3e4d699 switch ProgressTimer and Progress
new e7fd055 count branching nodes per read
new 2ee8e8e Shortcut 'createBank'
new 1c13270 Remove cFP temporary file
new f7b7bc9 Move HDF5 stuff to Abundance structure
new 2820df2 first version
new 4ce173a Abundance type management
new 49b86a4 Add shortcut method
new 949c7d2 Abundance type management
new 3788434 Improvements...
new 388929f Add GATB_CORE_EXCLUDE_XXX flags (to be used by gatb-tools)
new ecdd321 Add ICollection::addProperty (...)
new 693134c Snippet showing add/get Property for Collection
new e1f47e2 Range is now an Iterable
new c1ce0ba first version
new f3aa8a3 Add tools snippets
new 389a56f LibraryInfo management
new 87003d4 cosmit
new 5ee9941 first version
new f0a1942 New architecture for new project management
new 5077bb2 first version
new 73fa0ac Modifs copied from gatb-tools
new 2bbb0a1 cosmit
new a4a9245 Optional copy of GATB-CORE as third party
new 9750e14 Correct path
new e5a337e prototype of sorted and compressed partition file
new 71f10ba printf compressed ratio
new 740171a cosmit
new f9fdc17 First draft
new 31ed01a Move "versions" directory
new e33f94a Hack checking that the library is also reachable (check only on headers file so far)
new 2800b44 Compiler version management => tells whether C++ extensions (including lambda expressions) should be used.
new 9a22f14 1) avoid systematic headers copy (no need to cmake .. each time a header file is changed) 2) Default 4 kmer sizes are defined => possibility to define a 'kmax' value during cmake, for instance "cmake -Dkmax=256 .."
new d76f80c remove rvalues table (redundant with DebloomAlgorithm.pri)
new 70a6f70 1) Kmer size constants management 2) Lambda expressions management
new 9ec27ec Kmer size constants management
new 71331b6 Add another way to iterate the result of the ThreadObject (not only through a functor)
new 41ae777 Avoid unknown constant on Linux (not perfect, to be improved)
new 2a151b8 Kmer size constants management
new 0177ec1 Improve output
new d810413 Lambda expressions management
new 5a9efba API changes, including 1) Kmer size constants management 2) Lambda expressions management
new 5881e30 cosmit
new 0b77454 Move warnings management at upper level
new 10a81dc cosmit
new 48645e5 Modify the way we add URL in the album bank
new f539d72 Use copy instead of reference
new d46e835 Use 'abundance' instead of 'nks'
new 9d59c2e Use 'abundance' instead of 'nks'
new 0d9bd76 1) cosmit (better documentation) 2) avoid lambda exp in some cases
new 13fea5f Add operator== for Abundance (needed after Guillaume's work on GZ storage)
new 4a20f41 change in var name for lamda expressions
new cac5be5 Add missing attribute init in a constructor
new 2901a03 cosmit
new 8b3930a cosmit
new 2263aa1 cleaning to prepare the separation of PartitionsCommand from SortingCount
new b6d40b3 put a part of SortingCountAlgorithms into PartitionsCommand.cpp to speed up compilation time, also removed some interdependencies
new 5ea7c55 dsk compiles without these headers soo.. let's remove them
new 936e7f7 separated template instantiations in SortingCountAlgorithm to speed up compilation
new d5c3b94 forgot some files + removed a comment in the code about PLAST
new e6846bc fix gzread() bug in IteratorGzFile
new a86745c added a question to Erwan as a comment in thecode
new 8ffb442 Add missing include (not compiling on Linux with gcc 4.4.7)
new b163b36 Customization of data line size
new 6b46296 Add complete value semantics.
new 3b4a2fa Add ProgressNone class (that doesn't give progress feedback)
new cd88e01 Add Terminator and Traversal includes.
new 33eaf47 1) successors/predecessors from a couple of nodes 2) mutations of a node
new 7e4f617 Add tests for mutations
new 522b65f first version
new e99b7b9 cosmit
new df8f0c2 cosmit
new 859a07a Add missing namespaces (compilation error with some compilers)
new ded9ba8 Avoid toupper
new 7e5ce95 Add missing include
new e2e4cbc Variant configuration has to be updated after branching node algorithm execution
new a134f51 cosmit
new 8c452f5 first version
new 8daa5ac Add search engine for doxygen
new 86fb9e9 first version
new 880738c Add BankDownload
new 025a505 cosmit
new 6bd1cd1 first version
new e71d2a6 Add get/setAttribute (aka file metadata)
new 77c742d Add get/setAttribute (aka file metadata)
new c141ec8 Use u_in64_t instead of Type
new fdca3e8 Add 'exists' method
new 76d1ef1 Add strings constants
new 86d81c5 Correct include for MacOs
new b35ef2b get/setAttribute for Linux
new c203dd7 get/setAttribute for Linux
new d3f7c6b get/setAttribute for MacOs
new 476304c Correct bad include for Linux (compil error on genocluster3)
new 162159d first version
new 0986f6d Use copy of boost as embedded thirdparty
new 02e3748 Add all dependencies needed for variant usage
new 5c9680c Remove -Wno-ambiguous-member-template => compilation on genocluster with GCC 4.1.2
new 90f3ef2 Avoid warnings with GCC 4.1.2
new e8ee5ca Move BankDownload to gatb-tools
new 8520bf1 Management of data line size for FASTA bank
new 44eb18e cosmit
new 10c0d6e Correct management of exceptions thrown in working threads.
new 3a87828 option parser 'remove'
new d0f382b compute auto cutoff for kmer abundance
new a05b77a changed cmake/CppUnit.cmake to enable it to find CppUnit in my custom location
new b1fe06a cosmit
new 160611f Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new 0b3720f -help in composite tool
new 500a1bf Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new 08deea0 max auto cutoff at 0.4 total kmers eliminated
new 8301922 Add missing reinit ('first' didn't work twice)
new 203c542 Add ContainerNodeNoCFP => Titus mode
new ca53f09 Correcting memory leak
new 5df279a Add a check before write
new e8aa4a4 Improvement for BankAlbum and BankRegistery; now using an album file works
new f291a60 Preliminary work for -save-only option
new 6830e2e Add a string
new 457cf10 Add a clear interface definition for Bloom filters (Container + Bag)
new 523b256 Add an assert
new 59d3fc4 cosmit
new 7dbb5bd Add a constructor with Storage (used by Graph)
new b1725bf cosmit
new fd78e08 first version
new 3e78360 first version
new 88041d7 New strings
new 272f56b cosmit
new 93fe67e Force exception on non empty warnings list
new b118f04 FilterIterator is a now a ISmartIterator
new cf19fb5 first version
new d829d41 Enum management (now in Enums.hpp)
new 32d73c2 addProperty and getProperty in Group interface
new 266bf1b Enum management (now in Enums.hpp)
new 3510365 Introducing graph state machine
new 2142fed Add displayWarnings for options parser
new 8b6044c New test for different way of building a graph
new 6be6167 Change storage management
new ca04075 Change storage management
new 1f1d769 Bank interface modif
new ef2f7a0 Rollback modif on warnings (issue with ToolComposite in Bloocoo)
new b13465b template for value in Hash16
new 8e0328b Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new f0592bb minor
new 19c092a ignore
new 021a9c3 Add -bank-convert option ('none', 'tmp', 'keep')
new 03385c0 cosmit
new 7f3cbb1 Customization of k1,k2,k3,k4 through cmake
new d1ed887 WARNING: comment test because of k1,k2,k3,k4 customization through cmake (compilation error to be investigated)
new 269fa9e Customization of k1,k2,k3,k4 through cmake
new 1c37556 ignore
new 512bdf1 cosmit
new 0a079a8 Temporary disable bank convert option
new 8f9301a Correct handle leak.
new 5ef63e1 optimism 0 dsk
new 7ce8a07 first version
new dde1bfa first version
new 432ddfb 1) correct bad fastq detection 2) add fastq unit tests
new e56555f cosmit
new 2b5b132 Correct potential flaw in case of multithreaded iteration
new daa17b5 Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new 44aabca dsk bug (MBYTE enum int) et malloc bug in Hash 16
new 22f10a0 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new 24335f4 Initial commit of the MPHF code! Introducing a perfect hash function (from the emphf package) to keep track of abundance of each kmer, and can be extended to store arbitrary information per kmer
new 78fc310 merged MPHF (from 11 July commit) to master today
new dd478b8 added most covered bubble path selection in Minia, added cmdline parameter to disable mphf
new c0346c8 dsk deadlock bug
new ef0f63a simpler Hash16 creator
new 654c05f dsk deadlock bug
new 841473a simpler Hash16 creator
new 13805df 64 bit malloc
new 43811db added support detecting g++ version for old cmakes
new 728440e added #ifdef's around MPHF for old gcc compilers
new 8973c76 Correct potential flaws for big kmer sizes
new d8faa2c Correct data format for random banks
new 5389f9b Add catch for const char* messages
new b5923ea New implementation of Model classes for kmer management, including the introduction of minimizers
new d4c43d0 Correct bad typedef
new 322431f Add 'position' and 'hasChanged' methods for KmerMinimizer
new fe9c57e API change
new 9e1232a cosmit
new ee598d3 Explicit usage of ModelCanonical (instead of Model)
new 01ee836 WARNING !!! skip some tests parts because of issue with boost variant for big kmers (KSIZE_2 and more).
new 43eab83 1) adaptation to new Kmer::Model implementation 2) tests on minimizers
new 182b8dc adaptation to new Kmer::Model implementation
new f2113ec cosmit
new 10ec460 Add a setter for ModelCanonical::Kmer type
new 4757e8d Add a setter for ModelCanonical::Kmer type
new fe5848e Version number
new b454631 Correct compilation issue on MacOs
new 661d156 Better MPHF compilation flag management (according to GCC version)
new bad24cd Better MPHF compilation flag management
new ec9124f Correct bad variable name in CMakeLists.txt
new f4ee6f7 MPHF compilation on MacOs
new c7971f9 Correct bad variable name in CMakeLists.txt
new 062a623 First version
new 9185ff8 First version
new 8f1ac59 kmer5 needs lambda expressions
new 9669b7c kmer5 needs lambda expressions
new 32aab74 first version
new 056776b first version
new 1e0abfd Merge branch 'refs/heads/master' into minim
new 64d3066 temp
new 2c5703d first version in this directory
new 0cd3797 first version
new dfe952e minor
new 90a6df7 minim freq based m 7
new c570174 init
new 9d92345 Add another 'getItems' method (used for ostream wrapper for HDF5)
new 1aebbee Add another 'getItems' method (used for ostream wrapper for HDF5)
new add901a Add IterableAdaptor
new c88da8e Add a IteratorListener::reset method (introduced for emphf notifications)
new 8318ae3 Add IteratorAdaptor
new 85e2589 Add a IteratorListener::reset method (introduced for emphf notifications)
new 55df1f8 Add missing #include for some GCC versions
new 16cf0c2 MPHF and map based on MPHF
new e49e874 Now, provides two ways for getting kmers 1) Count (kmer+abundance) 2) Type (kmer only)
new 2e73979 Uses MPHF and map based on MPHF
new 794e294 Add #include
new 6a0ccde first version (ostream and istream wrappers for HDF5)
new c2a30f8 ostream and istream wrappers for HDF5
new c7334ef Move some code (non template) from .tpp to .cpp
new 993d32b Add new getItems method
new d6207ac ostream and istream wrappers for HDF5 now exist, so previous hack no longer needed
new 6598d06 Need to keep a reference on the storage.
new 1026e10 Adapt implementation due to MPHF changes
new 93247d3 1) add progress notification mechanism 2) null output stream
new 952e213 Test for IteratorAdaptor
new 7f3e29b Rename getSolidKmers into getSolidCounts
new 9d030b2 Adapt implementation due to MPHF changes
new 8cc032d new test
new 6e3f7bc first version
new 48e3523 cosmit
new cb81ac3 Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new fb359b5 deleted files
new 0ac4a88 first version
new 514c53e Correct bad minimizer computation when data is encoding in binary
new d9750d2 Merge branch 'refs/heads/master' into minim
new 6b07dbb test minimizer
new 3b18fce new minim test
new 3a59dda comment
new 9e87976 coorec
new 28c3d45 some cleanup
new 2b6e2ea correc
new b51795d testing minim filtr
new 1a8d2fd better NewDelivery process
new 101259f better NewDelivery process
new 46460d4 Better NewScript process
new 94d79f5 with parall radix sort
new a7433fa Add the possibility to use external libraries
new d4ed326 Cleanup
new 714149b Use bit hacks for computing revcomp64
new eab4cb5 first version
new 510b950 Correct hard coded filename
new c97bc7a proto k1 mer
new ac9fae7 using k4-mers
new 804f6b9 Improve minimizer implementation (thanx to G.Rizk)
new 5fc3f1e compil error
new 4567909 compil error
new 998d537 Merge branch 'minim' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core into minim
new 6c28494 Correction for new HDF5 organization
new 062c462 cosmit
new f56844c Now, the Model class handles bad nucleotides characters (like 'N') when reading ASCII data source.
new ad5a2c3 kmer8 uses lambda expression
new 0fbbdd6 Merge branch 'minim' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core into minim
new 97aac83 Merge branch 'minim' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core into minim
new 3c28e2c Merge branch 'refs/heads/master' into minim
new f7b11db Add operator<<= and operator>>=
new 1cbc710 merge model no N, minim m8, reglages
new 15c0f3d minor
new bc990c9 avoid infinite loop when nbtask==0
new ba30daa small optimizations
new 393b135 ram correc
new 5f20841 ram correc
new a002030 Merge branch 'minim' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core into minim
new d4962d4 debug info
new 0460f35 correc
new 8950dfa updated distrib func
new 29afae2 with precomputed forbidden minims
new 4f78df4 minor
new 1a030d4 ram update
new ede63cf mem pool
new 5c8e63b large k bug
new 6c9b3c6 snippet debruijn24
new 927f7ce some cleanup
new 8e575e6 minor
new 5a2fa07 Merge branch 'refs/heads/minim'
new 79c00a2 Add 'remove' method
new 4e774c9 Add 'getComposition' method
new b14eaf5 Use of IBank::remove instead of directly remove the bank file (which doesn't work any more in case the bank is a composite)
new 632adb3 Snippets improvements
new 62f8baf Conversion in an album of binary banks when the input bank is itself a composite bank
new 86257e0 Add missing using namespace
new 7e5e594 Add missing namespaces
new 7117d72 temp bloom test
new ff08816 temp test
new 435f06d implementation of a linear counter to estimate number of distinct kmers before counting (slow, disabled by default)
new 4a5aae2 pretty messy merge
new 0dc7753 fixing things due to merge, hopefully ok?
new 5130314 minor
new e2867f9 default: no mphf construction
new c7af351 Merge branch 'refs/heads/master' into minim
new d48fa10 Correction due to API change in Graph
new e95b34e Correction due to API change in Graph
new 3ba544a test bloom
new 2ff50cb Merge branch 'refs/heads/master' into minim
new f5a47df threadgroup mutex bug : init was missing
new 0737a98 threadgroup mutex bug : init was missing
new 4e5c6f1 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new 66b90aa warning
new c201148 Merge branch 'refs/heads/master' into minim
new f5d9f27 debug
new c9f8337 Add test for bad operator>> with 0 shift
new d31a06b Correct bad LargeInt::operator>> for 0 shift
new bd26b2c missed a spot in setting MPHF construction to none by default; but still, dbgh5 did not construct mphf by default; so for some reason, the default command-line option is not what decides if an option is set during Graph() constructor?
new 78e593b added iterateOutgoingNeighbors and iterateIncomingNeighbors to the API
new 6fcc144 convenient const hack for iterateIncomingNeighbors api given usage in tigops
new c4cc462 renamed BankRegistery to Bank as Erwan said that BankRegistery is supposed to be the main bank-opener
new 7d070a5 Correct bad behavior on composite banks (thanx to Rayan & Pierre)
new 1be2d45 1) add a mask to iterateNeighbors function 2) add ModelMinimizer::getMinimizerValue method
new 0fbce70 Add the possibility to iterate the items after having sorted them (may be used with debloom+minimizer)
new 22679c9 Add DebloomImpl stuff
new 842cdad storage::Partition implements now Iterable => used by SortingCount, ie solid kmers can be retrieved by partition
new 0bad1ac Correct bad qualified name for Collection
new 589e917 1) add contains8 2) take care of kmerSize in BloomFactory
new e3863e9 Force kmerSize parameter to 31 (because remove default value for kmersize parameter in BloomFactory)
new 3b4d54e No longer lazy accessor (for performance) => one has to be sure that the distribution is computed before using it...
new a1253ac Take care of kmer size
new cae4f82 Add the possibility to iterate the items after having sorted them (may be used with debloom+minimizer)
new ae284dc Output of SortingCount is now a Partition, ie we keep (previously temporary) partition information => can be used for instance in debloom for speeding up
new d308070 1) can use different version of debloom (the default one is based on minimizer usage) 2) remove autodelete mode for solid kmers output 3) use (by default) the BloomNeighbor implemention
new 77a7439 New implemention of debloom, based on solid kmers partition (done by using minimizers)
new 5cd8ee1 New SortingCount output as Partition
new d1db144 API changes
new 4c1136d Bug correction
new 0a0c9be Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new 8262c39 cosmit
new 783cf37 1) use bitset in Model 2) cache for Count chunks
new 538d670 Add -mphf option
new 3662596 Verbosity with env var CPPUNIT_VERBOSE
new 6df6549 -mphf command line option is now deactivated if emphf is not compiled
new e78e61a output stream management for visitor of IProperty object
new f70b06e Throw an exception in case of an unrognized option
new 660c194 cosmit
new beaa69f cosmit
new 9264dfb New gatb-core version is now 1.0.6
new 602fa11 Add output statistics
new 2b2341c Add MemoryPeak and Cpu usage
new d38d345 1) dump system information for Algorithm objects 2) set explicit number of cores for BranchingAlgorithm (previously used all cores)
new 2fc46ae CPU usage
new c4cf800 cosmit
new cc38417 Add possibility to send email with stats
new 5f6d609 1) get memory usage by current process 2) get CPU usage by current process
new 77bf7c1 Add ProgressTimerAndSystem class (system monitoring)
new f2ef05a Add getMemorySelfMaxUsed
new 4a01ee6 Add constants for HDF5 management (including workaround)
new 871e0df Improvements
new f55c2c6 Add 'hide' method
new 5c9a322 add -integer-precision
new c402657 Add missing flush implementation
new 6697890 cosmit
new 0ed740f Change parallelization scheme in finalize_debloom_file
new 9dd7ffb Uses Storage::ostream and Storage::istream => less HDF5 cache memory usage
new d9255bf Correct bad precision for HDF5 output of LargeInt
new b8a4715 Add constants for HDF5 management (including workaround)
new a71d0d1 integer precision management
new 0f7fe3f First version of the new implementation
new 1d3058d Use CollectionHDF5Patch (less HDF5 resources leaks)
new 7ee7f83 New BranchingAlgorithm (merge/sort) using less memory
new 5dadf4a Add startIndex for some methods
new f90991e new test file
new 27f0a27 Add a unit test that compares Minia SVN results (branching nodes checksum) to GATB-CORE results (with many different parameters)
new ed4ea13 Add binary to ascii conversion
new 6ff8717 first version
new 8401443 doxygen
new 476d5b4 Avoid warnings
new c3252b0 Use correct comparison while sorting branching nodes.
new 1017be5 Add unit test that checks that the branching nodes are sorted
new 5082794 1) add correct sort functor 2) add a check in case some vectors are empty
new 4027629 First version
new 169721d Comments
new 5dd12df cosmit
new badc68b first version
new 224ec97 1) API change (Bank::open) 2) doxygen
new c984aa3 doxygen
new 87b12c6 cosmit
new 73efe69 cosmit
new 641e8d7 first version
new 3926286 API change
new 67960f8 API change
new 1f016ec Add histogram stats
new ead4b16 Add a constructor
new 4667698 Constructor changed (use pointers instead of references)
new d5202c0 Add a const
new 5715c25 Add -topology-stats feature
new 953c0fd Add BankStats structure
new 3e4584b Little reorganization of statistics (using BankStats)
new 1a55934 Add methods for mean and deviation
new 7c11e03 1) Add get_first_peak 2) documentation
new fd55baa Compute genome size estimation
new 4f6a455 no option failure for toolcomposite
new 98c7f9f buffer size can be set (static method)
new 99ba484 use ofstream
new 1c8b563 cosmit
new 4e2aaf8 first version
new ff7617b Add an exception when a 'pool_malloc' call fails (ie no more memory in the pool)
new df25c82 new strings
new c6411f9 Add KmerSolidityKind
new fe8900c Improve TruncateIterator (copy semantics instead of reference)
new c9d4aca 'addBank' is now public
new 26225aa copy semantic
new 69b11d3 'Count' uses now u_int32_t instead of u_int16_t
new 54574d8 Kmers counting per bank : introduction of option -solidity-kind
new ed68596 Add options (-solidity-kind, -abundance-min, -abundance-max)
new 54f0295 Change -abundance in -abundance-min
new b617fbd API change
new ec8d679 API change
new c02f76e New tests for kmer counting per bank
new 162aae6 Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new 14eb468 first version
new 379f74e Correct bad file names for Collection in case of STORAGE_FILE
new 2d1a1e6 Add new 'add' method
new e43ec5f Add IterableHelpers class (with getItems method)
new 85ff042 fixed segfault when incorrect parameters are given to Graph::create(). Now returns a meaningful exception
new ea35788 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new 0857155 fixed a cmake error (GatbCore not found) when gatb-core does not reside in a thirdparty/ folder
new e7092b3 Create README.md
new f30cd72 Merge branch 'master' of https://github.com/GATB/gatb-core
new 9dea830 updated readme
new 3b69a48 comment
new a19d912 comment
new 138c81f Modifications for mapsembler_extend
new f4e530b cosmit
new 13de72f TR1 management
new 12f77dd Add GATB_USE_CUSTOM_ALLOCATOR management
new 1a703ae Add GATB_USE_CUSTOM_ALLOCATOR management
new a805663 Use macros for memory management (ex: malloc => MALLOC)
new 215d949 Use macros for memory management (ex: malloc => MALLOC)
new c83e8fd Use macros for memory management (ex: malloc => MALLOC)
new 46a8c4f Add getOptionsParser methods
new 6a5fe07 New version of OptionsParser => now, it's a Composite dp
new 9022592 Use of new OptionsParser impl
new 3855faa Little API change
new 452fc1b Add test for OptionsParser
new 0242a9e Use of new OptionsParser impl
new 3af2b4d Use of new OptionsParser impl
new dd1c488 SORRY GATB CORE I REALLY NEED THOSE CHANGES FOR THE NEXT 3 DAYS AND I HOPE THEY WONT BREAK ANYTHING BUT MAYBE THEY WILL BREAK DSK A LITTLE just don't blame me too much it's for the greater good of bcalm
new 936a70b Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core into HEAD
new f5e9c59 implemented frequency-based minimizers, for Bcalm. some of the code is ugly
new 3794c43 minor
new 88fb621 minor
new c896def repartition of partitions that respect the order of frequency-based minimizers, first draft
new cdac3b0 cosmit
new 6d64ac9 Correction crash on big datasets with multibanks
new 12b8a36 Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new 3fa33c9 cosmit
new ee86cbf correct compil issue on macos with old clang (and likely optimize the loop as well)
new eb2ca30 Back compatibility
new 0c07104 2 things: added minimizer size as a parameter to graph creation / kmer counting; also improved repartition of buckets with freq-based minimizers
new 67e4edb merge
new 7bf36e7 removed debug printf(
new 57f36e8 a repartition of lexicographical minimizers that respects minimizer order (added it by default, might wat to remove that behavior, but i need it for bcalm
new 95286bf First version
new e7cd8a7 cosmit
new 215dc50 Add missing include
new 10bdddb Add 'displayVersion' method
new 2a9bb69 New strings
new 3c06f32 New options parser implementation
new 57fe9de First version
new eb2be23 New options parser implementation
new 8d72bc1 New options parser implementation
new c328463 Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new 433c228 cosmit
new 49460ce Improvements for gatb-tools
new 0731836 reverted gatb-core's kmer counting back to normal, sorry for the turbulences and thanks for your cooperation gatb core
new b04b5b3 oops, previous commit was fail
new 303d00a Update after OptionsParser modification
new 64f4b29 Move ConvertXXX stuff from Model to Data
new 8a658c9 Add magic number for BankBinary => skip issue when providing an input being no album, no fasta/q and no binary
new 1c9b2d7 First version
new 4fdf992 First version
new 2ea9cae Correct bad parsing for OptionNoParam
new 41ef1cc slightly changed CppUnit detection method, let me know if it fails to detect cppunit on your system
new 115fe3c Little optimization
new 0c816d6 Correct bad Data copy in case of BINARY encoding
new c6c5823 Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new 7c2b03b Update
new 804ed05 Update
new fa9d0d5 Update
new c002912 Update
new 222debc added emphf option trigger for Graph
new f784b19 merged
new 646892d Add magic number for BankBinary
new 7812bf9 Add dummy include_frequency for default impl (otherwise some snippets won't compile)
new 233ed0d Update of examples
new d1b67f1 Go back to previous version
new e538a01 Remove constructors that manage several files => this is done by the BankRegistery
new 4e536a9 getMaxNbFiles is now private (could be removed eventually)
new 321d980 Remove constructors that manage several files => this is done by the BankRegistery
new fed2cfa cosmit
new 194ae25 Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new 2f31d48 Documentation update
new 6522e41 minor
new d37e1d7 Correct doxygen warnings
new a2cb8f6 1) Documentation update 2) put traversal kind in Enums.hpp
new a16ca25 Correct bad management of OptionNoParam
new 0d71779 Correct potential display bug.
new bd43ccd Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new d3814ee Add a constructor for BankAlbum with a vector of filenames (replace the previous BankFasta constructor).
new 101b733 Use enum constants instead of duplicated strings
new 59b02d4 Move max memory and max disk options from graph options parser to sorting count options parser
new 994a857 Correct bad exception type
new ed4e31f Improvements
new d9e419b Allows to get an existing Partition without knowing the number of Collection objects inside.
new f40dae8 Allows to get an existing Partition without knowing the number of Collection objects inside.
new 3c68417 Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new e60f919 Forget to remove (now useless) reference to "nb_partitions" property
new 25c1e11 API change for setMessage (use string, no more ellipsis)
new 0e19b2d API change for setMessage (use string, no more ellipsis)
new bee5e8b Correction (hope so) of the display bug on progress bar
new 02de6e4 Use string instead of ... for IteratorListener::setMessage
new e170dff Correct potential bug (crash on unit test but not on big sets)
new 138ae60 Correct bad progress bar display (mainly on macos)
new b337fc4 Add missing catch
new ebaec93 Backward compatibility with old hdf5 files.
new 4a2bb87 cosmit
new ea21bba Cleanup and add -max-memory management => continuous integration servers have not a lot of memory, so we must use a low value here.
new a5a3dfa Correct bad bank creation
new 2c2b807 cosmit
new 0bd7058 Use smart pointer semantics
new a038e1a Use smart pointer semantics
new 65fe2b6 1) doc update 2) snippet update
new 93a5066 doxygen update
new 2a13a1c doxygen update
new f49a86a cosmit
new 970f1dd Add kmer11 snippet : statistics about solid partitions
new b7ea98a updated README regarding generating doc for core developers
new 23f6633 CompressionUtils, RangeCoder from Leon to utils/compression
new bb2f963 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core into HEAD
new 16a66cd Compression headers in gatb_core.hpp
new 5e8083c compilation fix
new c981d68 static linking of dbgh5, dbginfo, h5dump for minia/dsk binary distribution compatibility
new f50f37d automatically set memory to less than system memory when -max-memory not specified
new 0df2ddd removed static compilation flag on macs
new 73b86f0 minor
new 531f9e7 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new 99310e4 method displayVersion in Tool to be able to customize the version message in each class inheriting from Tool
new 41e226b added the -repartition-type kmer counting parameter, to switch dsk between bcalm compatibility mode or not (whether partitions keep minimizer order or not)
new 4b53ce4 removing debug info
new 25361e0 Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new b122255 fix getBaseName() when multi extension path
new 8427ae4 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core into HEAD
new e1ef5f4 fixed repartition for bcalm
new fb74080 static build only if gcc >= 4.5
new dcc8112 made static compilation optional, -Dstatic=1
new af69373 cosmit Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new 41d3434 first version
new f73f9cd cosmit
new 6cd0176 cosmit
new 1ae56a4 Add include
new c4c01c4 Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new ae7be98 Improvement on IProperty
new 090fd78 Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new 9eed3bc cosmit
new f6e7b5f fixed DSK counts overflow above 65535, reported by Marek Kokot (KMC2), fix suggested by Erwan
new bb98a99 switch to 0.25 threshold max kmer elim for auto cutoff
new 69d4d40 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new 0c00280 seuil automatique verifie toujours >=3
new 51fa574 compressed stderr output to avoid linefeeds in console
new 0572b52 Print important stats (# solid kmers, # branching nodes) every time a Graph is created
new 142d668 new attribute min_auto_cutoff for SortingCountAlgorithm to prevent the auto_cutoff from being below this value
new 8187be2 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new d6d8019 Correct bad thread group deletion => use ThreadGroup::destroy
new c011b2a Scripts correction
new 37ba33e New version number
new b01d5d8 disallowed k<=4 for kmer counting as it's buggy with superkmers
new b5f4f9d make DSK not crash with memory issue in case of larger than expected partition; instead it just prints a warning and allocate memory anyway, as long as it's below system mem
new 9367976 Add getSizeItems method to get the total size of items in the partition
new b1758c7 Add a Iterator::finalize method that may be called when an iteration is finished (used for instance in CompositeIterator)
new 309b8f9 remove trace
new 58cdc75 Define BankIdType for multibanks dsk
new b5f4788 cosmit
new 970e991 Release file handle when iteration is done
new 33f1f5e nbPasses management
new e455ab9 Use BankIdType (ie u_int16_t) instead of u_int8_t
new 597df79 nbPasses management
new f88a447 Correct bad max value in case of composite banks
new 766ccc4 Add a second "concat" method that deals with kmers stats only (and not sequences stats)
new 5205bd7 Add DSK_multibank (crash with uint128 on macos with multibanks input)
new c82c035 Add missing implementation of BankSplitter::estimate. This is now important for SortingCountAlgorithm::configure
new 4daca3a Add getProcess and getTemporaryFilename methods
new fcfe41c Temporary files have now unique names (holding process id)
new e2fa6a2 cosmit
new 6916413 1) re-introduce multi-passes when needed 2) put Repartitor before mainloop 3) Correct bad nbPass number in some cases
new dc1632c New version number
new a3c7fc0 Add "align" and "getSynchro" methods
new 4bfd53d Force synchronization and pool alignment (16 bytes alignment constraint)
new 3e3b7d3 update with corrections
new e5ac234 cosmit
new fcd1ee8 cosmit
new 74e0ad3 Add "-check" option
new fbbb214 Correct bad kmers statistics in case of several passes
new 2bea46f Possibility to set a special separator for file dump
new 614c0d0 cosmit with progress bar
new 2753b30 Add -check-dump option
new 48a426b cosmit
new 1b7bc1f Use another constructor for ofstream (otherwise may not compile with old compilers versions)
new 627c9d7 Use another constructor for ofstream (otherwise may not compile with old compilers versions)
new 41f1c28 first version
new 7df528c cosmit
new 8c4dd1f Avoid two small memory leaks during unit tests
new bc6915e Display (part of) bank name in first progress bar
new 0223afa Dump in GBytes
new 01d35e0 cosmit
new 013eebc Better management of HDF5 errors
new 824adac Improve "bank split" snippet
new ea19600 cosmit
new 030a298 Add a 'finalize' method in IBank => used by BankFasta to close the file handle (see bank10 snippet)
new 1577655 Add a hack to avoid an invalid write (seen by valgring) when a seuqnece has a header holding a space at index being a power of 2.
new 098b4d3 When iterating multi banks, the 'finalize' call was not done (which releases the file handle)
new d5633bc Add the choice to delete functors at the end of a dispatcher iterate: synchronously or asynchronously
new e9d69b4 correct bad constructor call for old compiler version
new df3128e Correct bad computation of max seq length in BankFasta => made some problems with new way to estimate kmers number in SortingCountAlgorithm::configure
new af21e95 cosmit
new 2e86063 Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new 2606292 Use -Wall (minus a few warning options) and correct many (minor) warnings
new de507e9 Correct bad "finalize" call on first iterator in case of multi banks
new 20eb7fe update -W options (remove some because of continuous integration servers)
new c1636d9 minor modif to error message
new 79a7612 Retrieve git sha1 and use it in config.h file; dump the sha1 as output of dbgh5
new 1eb05a7 Merge branch 'master' of ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new 52420e6 cosmit
new 22b4611 Reintroduce a prototype for 'iterate'
new bbbb937 SHA1 management
new 358262b SHA1 management
new 6114e6b sha1
new fb7fb20 sha1
new 2477a8d first version
new 78aec4f sha1 management
new 7f98049 more explicit error message in params
new 9e5777c iterator on Hash16
new 487a107 Correct bad minimize size usage by Debloom classes
new 8d1f1bb Adjustement for small kmer sizes (for instance in unit tests)
new 17d5198 First version
new f573de3 Correct bad path
new 4ddbf8c cosmit
new c5afd44 cosmit
new 1c24131 minor exception message improv
new d2622f0 Add a warning message about old gcc versions
new 42ccae9 Merge branch 'master' of ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new a159257 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new 9887c83 big changes: adding support for deleting nodes in Graph, to switch minia to graph simplifications
new 7dcb13d frontline changes for minia's assembly algo
new fde94a4 minor bugfix, and tightened progress format to fit on my 14' laptop
new 887ae2a new traversal stats on simplepathtraversal
new 16c33ed traversal now reports if it stopped at a deadend (helpful for minia)
new bcc9f26 default abundance-min is 2 now. Is there a good reason why it should be 3 now? before, it was because minia choked on too complex graphs, not anymore now.
new 2334ca7 some mphf-related refactoring
new 2dbc7ee minor mphf fix
new b7f18f3 minor debug info for most_abundance_consensus
new ffb198b minor bugfix
new 48b4089 Add setDefaultValue
new 61e6a20 minor
new f683a54 first version
new b70235f New design for SortingCountAlgorithm
new 8072d6c Can be used with a specific dbgh5 binary; otherwise a git clone is done and a brand new dbgh5 binary is compiled and used
new 5a27cdb Change consensuses_identity accordingly to the value in master branch
new a356749 Go back to -abundance-min 3 by default
new a5c809d add STR_KMER_ABUNDANCE_MIN_THRESHOLD
new fe3c253 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new 0ba7cd0 cosmit
new 7db1848 cosmit
new 3630321 first version
new bde3616 Add StringLine class that allows to split a string to a given size or fill with spaces to a given size
new a600879 cosmit
new fb9db31 Small redesign + documentation
new 2b04ada Version number
new 81e3fbf cosmit
new 0d74e7f cosmit
new 43b81ba Correct warnings on MacOs
new cd470c1 Uncomment unit tests (was commented by mistake)
new 4db44cf cosmit
new b71c372 first version
new 0910605 doxygen
new fe23fb2 Correct potential memory pool allocation issue due to alignment and bad 'capacity' attribute initialization
new d8e3aab Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new 3addf2b added Edge comparator, and Traversal stats
new c4370a8 removed kmer buffer in Sequence2superkmer
new 433ebc1 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new e5115a7 Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new 58036ac extended Graph.cpp slightly with more templating
new 4c001fe minor linker fix
new 7a6ed6b improved, in some sense, FrontlineReachable, to make it less strict. for some reason minia hanged after bubble popping more or less at the same time. so, consider this patch not completely tested, but anyhow, i'm moving to bulge removing
new c43ec92 Correct script
new 44de690 Merge branch 'master' of git+ssh://edrezen@scm.gforge.inria.fr//gitroot/gatb-core/gatb-core.git
new e56c1fc Improve test
new 1befe45 supported 4 more k-mer sizes
new 61468f5 minor
new 9ddaca7 temporary fix for loading huge mphfs
new 2ac69b8 this fucking static_visitor type bug.. prevented me from creating CAMI_high assemblies
new ff83c5d New version (sub part of) boost needed by gatb-core
new 6702199 First version of "template specialization" files
new 6082c83 Make management of supported kmer size completly generic
new 10fc924 Make management of supported kmer size completly generic
new f5e2604 Generic management of supported kmer sizes.
new 5090560 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new addf673 minor
new 6096984 adjusted usedSeqLen in the case of mean seq len lower than kmer size
new d549a6c re-alloc memory pool if needed
new 4a2ee6b Management of several ICountProcessor associated to SortingCountAlgorithm => allows to manage automatic cutoff
new c443e92 Management of several ICountProcessor associated to SortingCountAlgorithm => allows to manage automatic cutoff
new fb317e6 use addProcessor
new 8c0a0fa cosmit
new bd448c2 first version
new dd0a2a6 Add getter on Repartitor instance
new 2a8a261 Add a snippet kmer15 using custom ICountProcessor
new 7d88769 minor
new b3eb7a3 cosmit
new 50508d7 save configuration information in the storage (ie hdf5) object
new 4fe596c cosmit
new e610d49 For solidity kind in [sum,min,max], the auto cutoff is computed on the concatenation of all the banks (and not a cutoff per bank).
new a318aea avoid to use 'std::accumulate'
new 690130a Correct bad load of Configuration information
new 9b5ed88 Change semantics of BankFiltered => if the reference is a composite, the result is still a composite, each sub bank being encapsulated by the filter.
new cba59e8 One filter per bank
new 1905f5f fixed bug, input bank was not closed
new c6f5565 BankFiltered: remove filter copy (redundant code)
new 9d1cc7d Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core into HEAD
new 4804919 Add BloomMinimizerCoherent algo
new 5f438ac New version of BloomMinimizerCoherent algo
new fecfad0 Remove BloomMinimizerCoherent algo
new 5ef6242 Add ExtendedNeighborCoherent algo
new 06467f0 Bloom: ExtendedNeighborCoherent algo optimization
new 169fa6b Bloom: Update ExtendedNeighborCoherent algo (hpart + facto + precompute)
new e99b117 We can obtain sequence's comment until first space.
new a72b208 Bloom: Add contains4 and clean code
new b6d293d added a remark in FileSystemCommon for Erwan
new c2e2d0b DSK: out-tmp option for temporary files
new 4866248 added missing func in SubjectIterator
new 7270718 Bloom: new version of ExtendedNeighborCoherent algo
new 23a62eb Bloom: ExtendedNeighborCoherent algo: new version
new 56d65c7 Bloom: ExtendedNeighborCoherent::contains4
new b3c2e7f Bloom: NeighborCoherentAlgo adjustments
new 6a929d8 param problem
new 72e114e estimateNbItem per sub bank
new 1896a85 Configuration.hpp: add save() and load() hdf5 methods
new 50d17a4 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core into HEAD
new ef13e3a Modif of BranchingTerminator for sharing keys (ie branching kmers) by several instances
new a0df8e5 split build_visitor of Graph.cpp into two components. passes all tests. also added setProperty in StorageHDF5
new 00bb069 now, if you give a h5 file (instead of reads) as input for a tool which is going to create a Graph, assuming this h5 file contains at the least solid kmers (it may also contain the whole graph), then GATB will finish constructing the graph (according to default/passed parameters). E.g. Minia can take as input a DSK output.
new 21a614f more explicit memory realloc message for dsk
new 43324dc small refactor of dsk parameters
new 74542db avoid warning
new 141bc41 Activate zlib compression inside HDF5 files. The default compression level is 0 (means no compression), and the compression level can be set (from 0 to 9) with the '-out-compress N' option
new c80be47 minor version override option in delivery.sh
new faf4553 minor changes to delivery.sh to allow overwriting
new 779714f Add "-config-only" option => compute configuration and stop
new ade0c42 Fixed getBaseName. Before, getBaseName('a.b.c.ext') = 'a', now it is 'a.b.c'
new 08f6ca6 extended getBaseName so that it takes an optional argument to revert to previous behavior
new 7510d95 Add findThreadInfo function that allows to get the current thread index inside a thread group
new 7d7fe55 Optimization of PartitionCache usage
new 0bc9dac minor fix to display whenever gatbcore isn't found
new 70e6847 updated Gatb-core cmake for kissplice
new f2d3568 a change to forceVector (might need to update Simka)
new 90bb066 refinement of dsk forcevector modification
new 8998d6d segfault fix
new ea05570 default max memory for dsk is now 5 GB instead of 2 GB
new 25ae97e reduce DSK memory usage in high number of partitions/cores scenarios: optimize the number of cached items per partition per core
new 4c347b0 minor warning removal
new ce7136f getting rid of old unreachable code related to forceHashing
new 422a36a fixed a misnomer. by the way, i noticed the two existing benchmarks don't compile
new 201d2e3 Config: add _nb_cache_item in config serialization
new c91b925 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core into HEAD
new 1500f0c added bench_mphf; to use, type 'make bench_mphf' in gatb-core build directory
new 542712b additional gatbcore location in cmake for bcalm
new e241cbe comment
new 10f456b new code for 2x faster minimizer computation (not yet doug's algorithm)
new 18129fd activated new minimizer code by default
new 12e7f6a big change: 3-10x faster minimizers
new 76cc4a1 minor
new ff541d3 fixed a series of bugs related to minimizers computation, to make unit test pass also, quite intriguing, if it put a if to check whether (mainbuffer == NULL), this prevents a segfault whenever more memory was allocated in the pool than was avaialble on the system. there might be a memory issue somewhere
new d220a08 minor
new 5f4a037 oops, two commits below, i introduced a bug by thinking i solved one
new e0ea654 fixed bench_minim
new f301de0 avoid to_string compilation error on clang
new d6baaf4 updated boost to 1.59
new 223f974 this is THE big commit for GATB-core of november 2015. changelog is:
new b905313 Instantiations2.cpp was not compiling on old compilers
new 82e818e so I removed Instantiations2.cpp
new 4137d52 got rid of old template specializations for Graph -- API changed a bit.
new e8c2f6e got rid of old template specializations for Graph -- API changed a bit. getting rid of Instantiations.hpp/cpp
new c9b5e62 minor
new 898c1dd minor
new ccf5e78 minor
new 6bb7f46 found a bug in largeint (going to fix soon); also, attempt to fix compilation on gcc 4.7
new 85b9380 more fixed for gcc 4.7
new d2c367e fixed the largeint bug, added a unit test
new c281fa8 had to suspiciously change a unit test so that it works. hope i didn't mess up. it has to do with getNodes() and how it is implemented with respect to DIR_INCOMING.
new e9136b1 minor
new d89794f added a NO_SSE flag for centos5 releases
new c1fb7f6 towards compatibility with c++98 (and clang) again
new abda14b towards compatibility with c++98 (and clang) again
new 95e2ea4 erwan's snippet for pierre / multiple files of files
new 2a075ea towards compatibility with c++98 (and clang) again
new 4768f6a towards compatibility with c++98 (and clang) again
new 4c308a5 towards compatibility with c++98 (and clang) again
new 7a8eaac towards compatibility with c++98 (and clang) again
new a84c416 towards compatibility with c++98 (and clang) again
new ca8556c towards compatibility with c++98 (and clang) again
new 0ae47a3 minor
new bc835cc minor
new c3ca879 minor
new 89d9201 minor
new a82fe16 minor
new 8558fa1 minor
new c7bf533 minor
new 6371925 parallel (with locks) nodes deletion
new 43588ec minor
new 92b4fc3 slight modification to Progress code in EMPHF
new 5b64938 added missing boost file
new 9905a3f fixes for clang; graph_mutate crashes clang (!!), so i disabled it
new 59d06ee more c++98 fixes
new b30ab6d attempt to fix an apple clang issue
new 2b36850 minor
new 6ec5a7b added an investiation note on tips removal related to why we can't just ignore non-branching nodes forever during simplifications (they may become dead-ends after tip removal); this removes the possibility of a faster nodes iteration (that wouldn't compute a mphf index for each node)
new 0c9a323 switching to HEM mode of mphf for faster construction; still takes quite a bit of construction memory though; also, slightly longer query times. could be solved by switching to compute_mphf_seq but i wanted to try with superspeedy construction.
new d840193 bugfix
new 3f2a6d3 minor
new 4e22ed7 fix for gcc 4.7
new f0cf4b1 testing this fix for clang and emphf
new f15bb18 bug fix for clang and emphf
new 8c720d2 minor fixes cmakelists/bench_graph
new a4aa365 incorporated boophf into gatb (initial attempt)
new 7c53a5b boophf now using same number of threads as other graph construction steps
new e184643 switched emphf back to scan_mmap because HEM is buggy with k=21. have not investigated why
new d069238 updated README regarding KSIZE_LIST
new 952c9e1 added CancellableIterator and applied it to RepartitionAlgorithm, a more robust estimation of minimizers repartition. before, short reads could lead to incorrect estimation as we only read a fixed number for reads; but now, we require to read a certain number of superkmers. will see if that fixes the OAHash max rehashes bug.
new 3fedf5a updated boophf to fix collision bug with spruce
new 48cfa6d fixed bug when out-dir doesn't exist
new 1b2786f minor, removing unused variable
new e5af15c Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new cac6c74 RepartitionAlgorithm was missing a custom number of cores. not anymore
new c84e718 added exception when no solid kmers found
new ea99ed2 fixed improper init of boomphf hasher
new 306b606 minimizers repartition was estimated in parallel by a dispatcher? it makes no sense that all threads were not gathered together. was bad for performance (obserevd 1 hour to compute that estimation on human genome) i mean human-sized genome (genoscope) reveted to single-threaad repartition estimation
new 2ad9bab Configuration.cpp: temp fix bad serialization
new d9fa091 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core into HEAD
new cdbebc3 Config
new e7ef9cb aconfig
new a4323c8 implemented much faster node deletion for small number of nodes to delete (<10M), which should be most of the cases
new 6a2e5a3 fixed bad nodes deletion when multithreads
new 85e6481 minor doc
new 090f8fd small optimization of tip removal, also more verbose timings
new 25c66a6 more useful verbose info
new a166037 update auto-update method description
new 8779601 add scripts for automatic handling of gatb-core releases on Inria Forge and Github
new bcf5383 minor
new ede7e98 RepartitionAlgo: get sample from each bank when multi bank counting
new c517188 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core into HEAD
new 45474a3 nasty bug TestDSK failed with just 'error' without throwing an exception but it should have because I called getInt() with a parameter that doesnt exist
new 6e46317 oops, previous commit didnt compile
new 69e40ee fixed a nasty bug in bcalm - fast minimizer computation shouldn't be done at all in freq order
new e9243c8 minor
new bf8f78b it seems that assert()'s didnt really work. this is because gatb-core was never compiled in true debug mode. CMake thought it was release so it inserted DNDEBUG this commit fixes that
new f00cfad added DNDEBUG in non-debug mode
new c56289e strange change that was needed on a machine
new 36e6b84 more verbose and non-blocking error message for adjacency
new 0c9c623 Repart multi bank
new 0a2cde9 Fix bug graph endl; missing
new 6ca123d Repart multibank
new 8b3ecb0 add new delivery system including Inria Forge tagging and Github mirroring
new 59b9e27 remove delivery.sh, not used anymore
new 123b460 minor
new 6a73d42 repart
new 3f2a100 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new 6802d25 Temporarily desactivate TestMap
new e6a786b [ci] script for jenkins
new 66d2511 update delivery process to use both Inria Forge and Github
new dfbd277 Merge branch 'master' of git+ssh://scm.gforge.inria.fr/gitroot/gatb-core/gatb-core
new 215d366 repart multi bank
new 9279366 [ci] update Jenkins script
new 6f289d5 update links to target official GATB web site at http://project.inria.fr/gatb
new 0ee77b2 automate publication of doc on Inria Forge garb-core public directory
new 950fa24 [ci] update Jenkins script
new 6ba13ed [ci] update Jenkins script
new a175f13 [ci] update Jenkins script
new 324021c deactivating minimizer fastmode, bug lead to kmer duplication
new 35622d4 [ci] update Jenkins script
new 92595cc for compatibility with autonomous gatb-tools
new 081d401 deploy garb-core doc into doc/api sub-folder on Inria Forge htdocs
new 4d50615 reorganisation of NewProject script : clean gatb-tool skeleton ; documentation updated accordingly
new 52a2ec2 [ci] for compatibility with Jenkins tasks
new 4d76136 [ci] cosmit
new 612596d fix typos in documentation
new fe2e472 Merge branch 'master' of git+ssh://scm.gforge.inria.fr/gitroot/gatb-core/gatb-core
new 1e5bb96 add link to on-line GATB-Core doc
new ed1a24b [ci] minor changes
new ce734dd now use Hash16 as a fallback plan for dsk fillsolid
new 208fb39 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new 56fb07c [ci] new tasks: macos build, and linux/macos release delivery
new 814f1db getting snippets to compile with new Graph API
new 4ff3dcc Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new 3d8d874 added Erwan's snippet do to multibank kmer counting and report list of kmers also a small fix he suggested
new 1af00b8 minor fix for example for clang
new 912b3fa enabled mphf compilation with linux/clang-3.7
new 3b13f0f updated boophf to bbhash!
new 6a69a25 fixed load/save features of boophf. also made mphf (using boophf) default graph behavior we should think about phasing out no-mphf support. gcc < 4.7 is becoming obsolete. let's make mphf mandatory
new df5023d small mphf bugfixes
new cd73a32 reverted some unwanted changes in simplifications (not fully finished) also, added memory limit for unit tests
new 887b036 fixes found by Karel Brinda
new 5bddd2e update doc to prepare new release
new 047d70a [ci] bug fix: copy test db to scratchdir (for cppunit)
new ea884ea restored TestMap
new 95a3fb8 [ci] bug fix, continuation
new 9039088 [ci] scriptes for delivery tasks
new 967c758 [ci] update ci osx script
new ad88740 fixed Graph::load() problem
new 0d48420 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new 3834ac3 minor
new a4bcca4 more aggressive simplification stopping heuristic, to avoid too many reps on spruce
new 78d288a minor update boophf
new e180aeb fixed graph simplification rounds
new 0dec221 minor
new 0346f9e fix boophf from Guillaume, precision bug
new c49f10b recent boophf fixes from guillaume
new 5f81989 display downloads field for flist command
new 0e5acf6 Merge branch 'master' of git+ssh://scm.gforge.inria.fr/gitroot/gatb-core/gatb-core
new fda6c23 leak boophf
new 06e923a compil prob mphf
new 0b65486 fix load boophf
new 9b8955a boophf progress bar back
new e7afb1c corrections mineures (petits mem leaks) et désactivation d'un test U non utile.
new e1be628 boophf bugfix
new fc02702 warning
new 9381816 FileSystem: add listdir method
new 591a6b0 SortCount Config: remove forcing the minimum of 31 partitions
new e831248 added non-canonical kmer counting mode, enable with: cmake .. -DNONCANONICAL=1
new baa242c disabled k<=2 as it seems buggy
new e4598e0 fixing some oopsies
new 2c33975 minor fix for gcc4.4
new e5d2b5f -mphf option present even when mphf cannot compile, for command line compatibility
new 62441de make SortingCount remember its configuration
new e19ea52 minor
new 4d56866 improved timing of simplifications
new 9d1cab5 minor
new 4e8dc68 update doc and add Jenkins CI build status
new 86eef3c Add missing "contains" method in Bloom interface
new 3f0fcd5 boophf progress bar removed when in verbose 0
new 93245ea suppressed progress message for adjacency precomputation during tests
new 906a24f [ci] put valgrind checks in a separate jenkins item
new 2e29200 [ci] new jenkins item for compiling snippets
new 2929360 fix for multi-threaded kmer16 example
new ba68c63 cosmit
new 70097f9 [ci] bug fix
new 4ef2f3a [ci] bug fix
new ce54f87 toggle verbose for simplifications in tests
new b0b089d [ci] new jenkins item for compiling snippets
new 9facedc fix for multi-threaded kmer16 example
new 7a55b96 cosmit
new 0784667 [ci] bug fix
new dab7a64 [ci] bug fix
new cd545dc toggle verbose for simplifications in tests
new c4a998b clarified option
new c1e84c0 Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core into HEAD
new 3cead49 update formatting of document
new 4051d21 updated release notes
new a4438e3 differences between linux/osx clang versions taken into account in CMakeFile.txt
new 3b38738 switch to release 1.2.0
new 7f0b9a4 add tests directory and update README.md
new 1e3a834 fix Jenkins tasks to create Inria Forge archives
new 9b0e40e ignore QtCreator generated file
new 5e964c1 take into Jenkins Tag name to create package archives
new 24a7e58 fix Jenkins OSX script
new 32ec829 deprecating dont_use_tr1 variable in favor of use_new_cxx
new 0f13920 -Duse new cxx tr1 compil
new bd6d0e0 latest boophf fixes a .h5 reload segfault; + cosmetic changes
new 6d9525e a dynamic caching mechanism for non-simple nodes. helps speed up graph simplifications
new 9d954fd added timings
new 561bc10 refactoring hmcp + raised threshold of node deletion cache
new 8c3721a fixed debruijn27. now, Graph.load() by default loads a MPHF. hopefully won't break other parts?
new 0776db2 minor
new cb338a2 [ci] add badge icon for linux/gcc4.8
new 7b0fd7c [ci] bug fix in markdown array
new b7edb0d fixed bug when graph contains on FP external node
new 25035e9 fixes when MPHF is queries for a false positive node
new dcfe57f fixing some graph functions definitions, passing args by ref instead of value
new eafa78a test commit, please disregard
new 4cbc626 another test commit, attempting to fix a bug
new 45d47b7 so if i don't put this-> before graph objects in dipatcher, there is a crash?
new 5b680c9 apparently yes. that previous commit was even crashing the compiler on the gcc4.7 CI slave!
new 603b4f7 minor
new d9a4039 [ci] new script for koriscale slave
new eb49b43 fixed bug, sometimes didnt use count by hash when needed
new 85b71c0 add missing boost includes in binary package
new 4aa18b1 fix compiling command
new 7533f0e release notes 1.2.1 draft
new 326fc5d Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/gatb-core/gatb-core
new e1efddb add release number in API doc
new 49fc307 Merge branch 'master' of git+ssh://scm.gforge.inria.fr/gitroot/gatb-core/gatb-core
new 6ae8074 add Jenkins task to prepare and publish API doc
new 1627a9a add Jenkins task to prepare and publish API doc
new cf500e7 update version number
new 43c24d1 tr1 macro switch for unordered map
new f6cc1bd 1) added graph.contains(kmer) and modified a nullptr to NULL
new 9a9747e bugfix for previous commit
new 1f26900 attempt to fix old clang compilation
new 6ffe77e more old clang compat fix
new 86a11c3 HMCP under refactoring for unitigs; not working yet; old HMCP activated by default
new 0d2dcf0 merge
new c811f71 fix from previous commit which fixed a bug, but then backtracking limit needed to be higher
new 40bd3ee graph simplifications: fixed unitigs version of HMCP
new f990a57 restored const Functor in iterate(), addresses issue #9
new 2ceca9d big commit of July :) incorporated GraphUnitigs what seems to be working, but not unit-tested: graph traversal what's yet to implement: - incorporation of bcalm in gatb-core - computation of unitigs abundance
new 35d4177 increased gamma in boophf wrapper
new 0c8260f second big commit of july :D - incorporated bcalm in gatb-core - bcalm now supports arbitrary k - bcalm now includes mean abundance per unitig what's left to do: - bugfixes, assembly still isn't the same as regular graph
new 0dba589 bugfixing and unit testing, one bug at a time, now it was getEdges
new 241adb5 :fire: another important bugfix in Simplification (some bubbles were not popped); also fixed compilation with multiple-k
new aa44700 more bugs fixed, some unit test added, maybe some bugs introduced. i'm close
new 7c1bee7 this was the last bugfix :D minia with graphunitigs looks ready!
new 9a721ea getting rid of debugs. BTW: still some misassemblies, check parameters
new 0de9c3c oops, simplifications were deleting on the fly, again. delayed them
new e2699b6 small tweaks
new 8044a03 tuning
new 6a25ef0 minor fixes
new c67d592 more bugfixing related to nodes deleter
new 32f2a59 many fixes. especially, fixes bcalm large k; also observed some problems with operator= and () initialization of LargeInt's, so got rid of those
new fe5ecd8 fixed unit test
new c12f918 fixed memory leak due to, apparently, missing move operator
new 7b4c5af some tweaks: - tests can now be compiled with k=32 only - fixed simplifications unit test for EC - ExtremityInfo (12 bytes) isn't stored in memory in GraphUnitigs, just a uint32 (4 bytes)
new ecfd009 major bugfix in GraphUnitigs, because i forgot that unitigs could be deleted, so need to traverse many of them to have simple paths. still doesn't fix all bugs yet
new d0b134e prepared gatb-core for stand-alone bcalm
new 8b69f05 another bugfix, now assemblies of bacteria look good
new b9c2165 more debugging of graphunitigs. found a compaction bug in latest bcalm and coded a dirty workaround in graphunitigs around it, until antoine has a look
new 25d2405 fixed an endless loop during bubble popping, and some minor optimizations
new f09c035 raised GraphUnitigs utig hashmap values from 32 bits to 64 bits, because unitigs were stored in 2^27 bits, really not enough
new 9f13c59 oops, forgot to remove a debug
new 695c06f changed bcalm2 FASTA header output to '>id LN:i:<length> KC:i:<total_kmer_abundances> KM:f:<mean_kmer_abundance>'
new b8ce2bc oops forgot a few things
new c0690d1 committing intermediate work, because i mistakenly edited gatb-core in two different folders. this will break gatb-core, but i'm fixing it over the weekend, promise!
new 891f360 part 2 of committing intermediate work, because i mistakenly edited gatb-core in two different folders. this will break gatb-core, but i'm fixing it over the weekend, for sure
new 5d07202 merging conflicts. code is still untested
new 4619a8d at least now gatb-core compiled. will need to bugfix
new 62f44e7 so many fixes! now unit test for DebruinUnitigs passes!
new a4a3d02 bugs cancelling themselves..
new 6fe9d2f continuing bugfixes, now both unit tests pass
new 86c8e36 fixed more bugs. finally assembles genome10k correctly
new 1ce1a82 small but important fix
new 4449070 minor
new 52f7c03 more bugfixing, related to edge cases
new 5c446a8 setting a larger minimizer size, seems to help bcalm
new 4407b31 switched unitigs packed representation from 32 bits to 64 bits to support more than 1B unitigs
new 1152f20 renamed h5dump to gatb-h5dump following https://github.com/GATB/minia/issues/5
new 13a67de removed debug
new 7575428 Merge branch 'master' of https://github.com/GATB/gatb-core
new 61073cd minor to debug compilation issues
new 5e0a1a2 testing
new 08ee9c2 testing
new 8db02d0 testing 2
new 8701de9 fixes for travis
new cd5a669 more testing for travis-ci
new f553249 fixing a unit test bug
new 4ea5875 minor text fixes
new bc291fb fixed examples
new cdb79b8 gcc 4.7 build passing :D
new 90df359 merge
new 5018715 minor text fix
new 011debd implemented STORAGE_FILE, now by default in GraphUnitigs; this fixes the memroy leaks by getting rid of HDF5
new 0bfb1a0 forgot json lib
new 127d025 RepartitionAlgorithm.cpp: close bank files when grab stats on bank subsamples
new 2e9c4ad clang tr1 fix
new 1db889a fixes for 'make package'
new 3180a20 BooPHF update
new b9b0556 swapped json library for better compiler compatibility
new 600834b major compilation fixes
new 0aad108 removed debug messages
new 091f265 still shipping emphf, until we properly get rid of it
new 10577b4 fixed storage6 example
new c098147 minor update example microsnp
new 9bceadb add link to the new online GATB-Core Tutorial
new e0fa420 minor doc update
new 8bc0ab0 minor doc update
new 3324918 minor explicit error messages
new da555b4 muted a debug message that appeared in unit tests
new f516ec5 attempt at fixing a clang unit test segfault
new e019188 attempt at fixing a clang unit test segfault
new 4862dfd merge
new 535b2cc Storage fix for OSX
new c54a873 fix of the fix
new a929012 put storage_file files in [prefix]_gatb/ directory instead of current directory
new 475dc5c introduced doesExistDirectory
new ecb49bd lowered the number of partitions by 4x in STORAGE_FILE mode
new 8e272de dsk now has an option to output raw files instead of hdf5
new 4d5a3ce minor
new eae708b fixes
new b637090 fix
new 9e2d289 fix minor
new 79e5ff5 bbhash minor
new a135b10 minor test
new 5ecff3c bbhash removed warnings
new 9b7d6c7 update link to doc
new bdd9909 debug dsk for k > 255
new 90722fe modified partitions computation for storage-file
new d56b198 debug message
new 5669762 more doc
new bf1a309 added a test for file storage
new 0971bdf minor
new efb6b4b storage_file isn't ready
new 136763c made graph simplifications optional
new 0dc5728 micro bug dans NewProject avec option -t
new 09eaf14 added some memory info
new 5c01cb8 minor fix
new 2e7eb78 tentative fix
new 184e503 custom solidity kind
new 1f73dab custom solidity info moved to config class
new 1df4e09 empty param fix
new 1027740 correct sum when solidity custom
new def82f1 doc
new 11a2aa1 fix for bcalm when -out points to another directory. Also did a minor change in Bank, hopefully inconsequential
new 56a6e0e removing the trashme_ folders
new 05aa37c doc of kmer16
new e0c9525 -version and -help now embedded in the tool class
new ee142c9 removed debug info
new 0d43ab9 fixed for mapsembler2/clang
new 7c2247b further clang/osx fixes attempts, json compilation warning too
new 0efe38c added a nodemphfindex unit test
new f8b812d temporarily comment dbcheck tests
new d0bd13b temporarily comment dbcheck tests
new 9204948 add Valgrind badge
new e2687c9 updated help/version system for tools
new 76009da include Licence and Thirdparties.md in bin distrib
new 1070763 update documentation
new d61a149 add Jenkins Task to check bin package on Linux
new 0d1ce6c add Jenkins task to test bin package on OSX
new acbbdfa fix unit testing procedure
new 29c568a Avoid full recompilations caused by build timestamp updates.
new f503857 Switch to HDF5 1.8.13
new 3f906b1 apply patch as described in commit bf8f78b made by Rayan Chikhi on Dec 28, 2015
new 9960332 cleanup old hdf5 files
new 1381751 switch to HDF5 1.8.18 source code
new 2032c3b update Cmake files of HDF5
new 20e9f5e fasta one line output
new 9a8451a added a small example to compile any user program using gatb release
new 2ad53b2 add Docker support
new 92d019d some superkmer stuff, in progress
new ac6fda5 add Docker file to compile GATB-Core using clang as the c++ compiler
new 158c19b remove echo line
new f990e4c in progress
new c57ced7 superkwriter in progress
new a68dcd8 compil
new 16b5bae fix compiling of hdf5_tools
new 60aafee gatb-core now requires CMake 3.1.0
new 03a692e fix path to db files
new b67b702 added multithreading7 test case
new dcc3e97 efficient superK storage working for sum mode
new a087000 fix multithreading examples (ty grizk)
new 5c7dc5e updated doc
new 86c5a28 Fix a warnings about ignoring vasprintf return code. Factor uses of vasprintf with Stringify::format.
new c025cb2 Add parentheses on ambiguous statements (-Wparentheses)
new e4dfb46 Remove unused variables (-Wunused-variable)
new 6232139 Removing CFLAGS -Wno-unused-variable -Wno-parentheses -Wno-strict-aliasing -Wno-array-bounds
new 6787c5d fix unused variables
new 052f374 Merge branch 'mk_merge'
new 0bd9770 add vim
new ac65fb4 buffer update
new ce11fcb fix for use within Inria/Jenkins slave
new 800140d update doc w/regards to Jenkins use
new 0b98be3 removed bank_datalinesize unit test
new f521f5f fix target name due to cmake generation error
new e2eb044 added doc for Terminator and Traversal
new e37ae74 add jenkins task to compile using clang on OSX slave
new 088fefc Merge branch 'master' of git+ssh://scm.gforge.inria.fr/gitroot/gatb-core/gatb-core
new 4130d8f update docker build instructions to reduce image size
new 24c5b84 add jenkins task for OSX/clang 6
new 86b93cd Merge branch 'hdf5_1-8-18' of git+ssh://scm.gforge.inria.fr/gitroot/gatb-core/gatb-core into hdf5_1-8-18
new 22bb120 code snippet for parallel minimizerization
new 1682fed getting rid of emphf; enabling BooPHF by default for Graph, in prevision of dropping support for non-c++11 compilers
new 84d32ef minor compilation fix
new aed27de another minor compilation fix
new 2aa4891 added some debug info
new ba4e631 fixed nocircular test
new 0565902 UKL in progress
new 46bcd7e ukl data file
new 97bd52c minor
new 4b16d8b debug ukl
new 09a7ac7 some stats
new d683fa8 update doc for 1.3.0 release
new a7b7bd3 Merge branch 'hdf5_1-8-18' GATB-Core now uses HDF5 release 1.8.18
new ad7d15d switch to release 1.3.0
new c9113c0 update snippets doc
new ca8010d dump cmake version
new bdf5779 fixed bank12
new 5aa0ec9 explain how to use snippets
new e29a64f explain how to use snippets
new e8497ee Remove conditional compilation on WITH_LAMBDA_EXPRESSION
new c29d96c Remove conditional compilation on USE_NEW_CXX
new 5859d43 CMake fails with compiler without c++11 support
new 36cdaa9 fix use of c++11 on OSX
new 37bce90 restore cmake std way of setting up DEBUG mode
new fbf4eb8 explain how to use snippets
new 4958e3f explain how to use snippets
new b2d94f7 testing MmersFrequency with modelCanonical/ModelDirect
new 99864d8 fixed minimizer-type 1 repartition, thanks guillaume!
new 4e17d74 add MicroSNP test data set
new f91433f Merge branch 'master' of git+ssh://scm.gforge.inria.fr/gitroot/gatb-core/gatb-core
new cc859af explain how to use snippets
new 0058b34 add Jenkins script to test all snippets
new 62caaa7 update links to online tuto
new 35cc3e7 Fix a rounding error in Data assignment when size() is a multiple of 4
new ddfe74a fixing bubble unit test
new 51695c6 fix Debug instruction for cmake
new 8ef22c8 add CLOC support
new da83a82 update CLOC support
new bcd902c fix debug mode and add link to Ecplise manual
new c3b53c4 update 1.3.0 doc
new e81c8d0 fix typo
new 7c9f494 that last unit test fix was messed up, here is a real fix
new ae3c995 add badges
new b4ddcdd add build status badges for all platforms
new eda2a92 fix table for Github
new d28d742 fix table for Github
new a30d893 fix link to c++11 ISO page
new 1118980 Fixes memory leaks in bglue_algo.cpp
new 7fa0fee Fixes iterator leaks in DSK
new b5a704d max memory is now strict, will dump into subparts and merge-sort partitions that are too big
new c3cc1c3 update script variable names and path to gatb-core bin bundles
new 5c79504 rename script
new 72c79ee add Jenkins Docker sample task
new 62b39db use cmake 3.7
new 765e1ce remove -j8
new be2d883 add Fedora 20 - gcc 4.8 build status
new 35057fe set default stack size to 8MB for new pthreads
new 10bb00f remove useless GetDate; not anymore required with cmake 3.1+
new 931e523 Bank::getType() will now return fastq or fasta correctly
new 9a63a46 fixing quite significant memory leak in bcalm (thank Mael for the sanitize technique)
new 6634d0a more debugging
new 7efe46f fix test bank
new 2f99b40 Merge branch 'master' of https://scm.gforge.inria.fr/authscm/grizk/git/gatb-core/gatb-core
new d531f82 part 2 of the commit i meant to commit yesterday
new d3a544e preparing the ground for 2bit compaction of unitigs in GraphUnitig
new 9e43aba implemented 2bit storage of unitigs, not as great results as expected
new e0df217 compressed vectors for unitigs representation
new c331313 rangecoder type
new 4dc2ef0 leon ibank working
new 354d30a some leon cleaning, and added leon tool inside gatb-core
new 7691f5f some cleaning, removed universal kmer set
new 2614240 removed ukl files
new 904a23d Merge branch 'dsk3'
new 10bcb77 guillaume pointed out that IterableFile opened the file twice, indeed, once for iterator() and once for getItems(). Fixed as follows: the file for getItems() is opened only at the first call of getItems()
new f4059a1 major changes to UnitigsConstructionAlgorithm and bglue to scrap some memory: made several passes in link_unitigs modified many parts in bglue to save some memory here and there, might have fixed minor bugs along the way, also made the code more readable link_unitigs is still not multithreaded some changes in bcalm but haven't fixed the 'soft' memory leak there
new 7faace7 minor
new 96c082c short tip prefilter in graphunitigs
new 884ff81 woops, short tips filter isnt ready
new a1ffeb5 removing debug stuff
new 13a9b46 mandatory bugfixing'
new 45c8f38 fixed a DSK valgrind problem + fixed all the small bugs in recent major bcalm modification
new db4e353 minor
new 2f36b13 all unit tests pass now 🙌
new b5ca5cc old compilers fix
new 2b07c65 multi-pass'd bglue first step for reduced mem usage, using a simple disk idea, yay
new 0969c30 optimization coded in 15 minutes at 2am that reduced by 40% the mem usage during gluing of partition..🔥
new bdecbdf bankleon getsize() getnbitems()
new b28b91b cleaner bcalm logging system
new 91f010a forgot some files
new dfc9f30 oops didnt mean to commit that much
new 33369b2 free storage
new da6cdfe Merge branch 'master' of https://scm.gforge.inria.fr/authscm/grizk/git/gatb-core/gatb-core
new 587e988 close storage
new 31ab195 Modif for MindTheGap when gap-filling contigs, able to stop the extensions of branches containing exactly one of the targets (in a concatenated string), should not impact other tools, modifies the behavior of construct_linear_seqs only when parameter swf=true
new c032566 massive changes in bcalm_algo: got rid of the memory-fragmenting queue of kmers per minimizer, replaced with flat vectors, one per thread. this seems to have solved the memory leak problem (fragmentation-type, not a real leak) also did multithreaded optimizations related to traveller kmers loading now bcalm_algo should be much faster and it seems that, at least on chr14, its memory leak is no longer a problem. finally. took me two weeks.
new 95b2d59 minor bglue tweaks
new 85a598e extra stats
new 0edafbf small but major bugfix for counting kmers in large genomes: estimation of minimizers now looks at 50M reads at most. see if it's a problem
new 47c24c7 minor better printing in bglue
new 8e931db auto number of glue partitions
new c8ba5a6 leon fix delete
new 2c3802b fixing yet another leak
new 5fd9870 add sample file to test Leon compressor
new db38546 made Leon::READ_PER_BLOCK updatable through command-line
new 03c4e19 add sample data files for Leon cppunit
new 6bef574 add FastQ/Leon comparator snippet code
new 9c55db0 add a code snippet to cut a FastQ file given nb sequences
new b9c2ec5 made prepare_uf in bglue faster. it used to be using locks to populate 1000 vectors, now i'm doing 1vector=1thread, no locks, and a priority queue to merge should be just fine. maybe some memory fragmentation
new 1a7c937 added -skip-bcalm, -skip-bglue, -skip-links
new 3fbc928 lol, this one simple trick will fix a bug in the bulge removal that was here since 2015; i mis-copied spades' criteria
new 0ee64c9 fixing small bug and also improving unit test, i'm being good
new a70d4ed add test for Leon parallel compression
new 7aec12f fix visibility of -reads and -verbose
new 582a5c2 bulge bugfix; and debug info
new bf5f9d4 cleaner tuning of bulge removal
new b5aee39 isolated LinkTigs code
new 8ebf6e4 minor compilation fix
new 81b89ab better kmer volume estimation
new 1a55f70 an attempt at reducing bglue memory even more
new e0c921d fix
new 5e0758e leon: print some metadata with -print-metadata
new b7270af gcc4.7 didnt like lambda inside lambdaception
new e4a91c4 minor changes for merci
new 118d1bd following some debugging of merci
new 11bc911 minor
new 067947c Revert "leon: print some metadata with -print-metadata" these changes broken Leon This reverts commit 5e0758e60837ef66b373369d8336ea642bc4d2b5.
new 5d3c2a6 restore the execution of all Leon unit tests
new fb8ca36 replace std::cout by getInfo()->add()
new a12421e restore loop execution
new 2e62ace add curl sample use
new f080d21 copy of bank15 but using a ProgressIterator
new 7b1a7bc remove .DS_Store files (OSX stuff)
new ca7a7c5 explain how to compile and run code snippets
new 083623f fixed -out parameter for bcalm
new a37119f secure use of assert if not in Debug mode
new b0cfb69 secure use of assert in snippets
new 7dedf78 add link to doc on how to use Xcode
new 7372b6d add bank24 snippet
new ca490d5 Merge branch 'master' of git+ssh://scm.gforge.inria.fr/gitroot/gatb-core/gatb-core
new a6b3886 force use of assert() even in Release mode
new 9afd71a add dedicated snippet to lest Leon compress
new e82f9da add dedicated snippet to lest Leon compress
new 253d99f removed fseeko for cygwin compatibility
new 6593046 attempts at cygwin compatibility
new 0d8a920 replace bank14 by bank27 to test Leon on Jenkins
new e91c7e2 add code snippet to control Leon
new 6c83cfe fix format
new 9f6a94a add Leon large scale test framework
new 3d8270e fix typo
new f69d987 minor comment
new 67d2b1d add other data structures available in GATB-Core
new 88c5eb0 mael's strerror GNU compat patch from https://github.com/Piezoid/gatb-core/commit/93c6eaab4196d7b51a1d9aea387eb73b974ba9cc
new cd761fd https://s-media-cache-ak0.pinimg.com/originals/b3/75/99/b37599bc588eeec1d2e7bc0f5e465fb8.gif
new bccb417 fixes #1
new 0d5ffe3 commented out cout calls
new feea2df secure code if using file that does not exist
new f902ef3 fix doc typos
new 67a3740 Merge branch 'master' of git+ssh://scm.gforge.inria.fr/gitroot/gatb-core/gatb-core
new ce58279 fixes https://github.com/GATB/dsk#1
new 748b0ef removed scary zlib warning
new 1229448 removed error when zlib is not present on the system - gatb-core will just compile without zlib support in hdf5
new 9add7e9 replaced KM to km as per GFA1 spec
new b1a6f6a oops commited some debug stuff
new e6c8d45 specialized template of compositeiterator for sequences so that seq index is correctly computed for multi-banks
new 612bfe7 Merge branch 'master' of https://scm.gforge.inria.fr/authscm/grizk/git/gatb-core/gatb-core
new 2c214f0 preventing double-counting in simplification removal stats
new f4e4f47 starting to expose some simplifications
new 9b71d84 starting to implement GFA loading. code doesn't work yet; also, changed KM field in fasta output to km, for GFA compatibility
new fac2dbc minor syntax compilation fix
new 9de069b Change way code snippets are compiled to enable smooth Xcode integration. Now, to compile code snippets, use cmake as follows: cmake -DGATB_CORE_INCLUDE_EXAMPLES=True ..
new dbe66bb add link to Xcode doc and examples README.md
new cc4cbf0 finally! a GFA input support that doesn't crash
new d5521d3 graph simplifications, exposed
new 8806c21 minor
new f5c402f minor
new 2c87657 parameterized covmult in bulges (the 1.1)
new 6696b66 leon: fixed bug quality compression when read size < kmer size
new 5bb2ad9 fix compiler warnings on signed/unsigned comparisons
new 6a9754c fix compiler warnings on sign/unsigned int comparissons
new 246771c fix compiler warnings on sign/unsigned int comparissons
new c8a1347 add help message
new c0264f6 slightly change gatb-core-cppunit exec cmd-line
new d8e3832 slightly change gatb-core-cppunit exec cmd-line
new e9c8b8d discrete abundance in mapmphf from 1 to 50k with max 10% error, on 8 bits
new acd9152 correction discrete abundance
new 0a3a287 include example snippets in binary archive
new e300839 start preparing GATB-Core 1.4.0
new 13367ae add Jenkins badge
new cb9cbf7 add Jenkins badge
new 1342d1d init discret scheme when loading
new 2ace8fe minor, comment
new aa54568 minor
new 3fd0ea9 corrected a bcalm2 bug where unitig abundances were not correctly estimated (also inconsistent in multithreaded executions)
new 207009f Merge branch 'master' of https://scm.gforge.inria.fr/authscm/grizk/git/gatb-core/gatb-core and change return type of Mapmphf
new 296a7b1 fix making examples bin
new 3823647 use make -j2
new 3f018b1 remove useless vtimes.h include
new c0281b4 restoring support for multi-bank counting. Done with the old less efficient superkmer storage system, and leads to some ugly code duplication. Will be improved later.
new 43a123a bringing back online unit test for multi-bank counting
new 28bdc1d existing HDF5 files are now opened as read-only instead of read-write. to do this, I added a 'append' parameter for Storage.create() that is enabled only when Graph.create() has a .h5 file as input instead of reads
new 21bf261 update doc generation script for dual use on koriscale or gatb-core-ubuntu16-docker
new ead0e9e travis file
new 5751e56 fix CC and CXX declaration
new f3e3862 provisioning an ubuntu 16.04 LTS slave (for ci use with jenkins)
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