2013-11-29  mancheron

	* [r2735] configure.ac, src/Makefile.am, src/gkArrays.cpp,
	  src/gkCFPSBuilder.cpp, src/gkIFABuilder.cpp, src/gkSABuilder.cpp,
	  src/libProgressBar-1.1.2, src/libProgressBar-1.2.0,
	  src/libProgressBar-1.2.0/ChangeLog,
	  src/libProgressBar-1.2.0/Makefile.am,
	  src/libProgressBar-1.2.0/Makefile.in,
	  src/libProgressBar-1.2.0/configure,
	  src/libProgressBar-1.2.0/configure.in,
	  src/libProgressBar-1.2.0/doc/Makefile.in,
	  src/libProgressBar-1.2.0/doc/libProgressBar.3,
	  src/libProgressBar-1.2.0/libProgressBar/Makefile.in,
	  src/libProgressBar-1.2.0/libProgressBar/progressBar.cpp,
	  src/libProgressBar-1.2.0/libProgressBar/progressBar.h,
	  src/libProgressBar-1.2.0/libProgressBar/testPB.cpp: Updating
	  libProgressBar library. Enhance display. Remove pkg-config usage
	  to detect library since some people dislike it.

2013-11-28  mancheron

	* [r2730] ChangeLog:
	* [r2729] src/gkSABuilder.cpp,
	  src/libProgressBar-1.1.2/doc/libProgressBar.3: Bug Fix:
	  Multithreading displayed the progress bar twice for SA
	  construction.
	* [r2728] ., configure.ac, src/Makefile.am, src/gkArrays.cpp,
	  src/gkArrays.h, src/gkCFPSBuilder.cpp, src/gkIFABuilder.cpp,
	  src/gkSABuilder.cpp, src/libProgressBar-1.1.2: New release

2013-09-30  salson

	* [r2564] GkSABuilder: Prevent loop variables to go out the
	  boundaries

2013-09-28  salson

	* [r2559] Release 2.0.6: - Correction in quicksort algorithm: pivot
	  choice changed to avoid long computations in very specific cases
	* [r2558] GkSABuilder: Remove med function not needed anymore
	  (pivot choice method changed)
	* [r2557] gkSABuilder: Change the way pivot is chosen: pick one
	  randomly.
	  
	  Choosing the median could generate some highly inefficient
	  processing in specific conditions (array sorted in reverse order)
	* [r2555] Release 2.0.5: - Fixed a bug when processing (very) large
	  files. A uint value should have been a uintSA - Fixed some
	  autotools issues

2013-09-27  salson

	* [r2554] GkIFABuilder: uintSA instead of uint
	  
	  Using a uint provoked an overflow on very large files, when
	  computing i+j (which was therefore done as a uint).

2013-05-21  salson

	* [r2446] GkArrays: Check for libpthread in GkArrays
	* [r2445] GkArrays: Remove config.h.in file

2013-05-07  nphilippe

	* [r2424] -fixed typo error in configure.ac -remove AC_PROG_RANLIB
	  obsolete

2013-04-29  salson

	* [r2395] GkArrays: remove Makefile.in, configure scripts and so
	  on. Generate them usign aclocal && autoconf && autoheader &&
	  automake --add-missing

2013-04-19  nphilippe

	* [r2352]

2013-04-19  salson

	* [r2349] GkArrays: Typo in configure.ac (space missing) and check
	  that kpsewhich exists

2013-04-17  salson

	* [r2288] Release 2.0.3: - Bug correction on the number of bits
	  used with the bitvector version - Bug correction on the size of
	  an array, that could cause segfault in very specific cases - Some
	  compilation warnings removed
	* [r2287] GkArrays: Array values'' must be of size nb_kmers+1 just
	  in case all the kmers are distinct

2013-04-16  salson

	* [r2274] GkArrays: gkSABuilder uses the new SolArray constructor
	  since gkSA is not really a permutation (GkSA length is not the
	  maximal value that can be stored in the array
	* [r2273] GkArrays: solArrays have another constructor that take as
	  a parameter the maximal value that can be stored in the array
	* [r2272] GkArrays: computation of number of bits needed for an
	  array did not work depending on the endianness
	* [r2271] GkArrays: Use bitvectors in consistency tests.

2013-04-13  salson

	* [r2270] GkArrays: filename parameters to the constructors are now
	  const char*

2013-04-12  salson

	* [r2261] GkArrays: Remove compilation warnings

2013-04-12  nphilippe

	* [r2258] new release 2.0.2

2013-04-10  jaudoux

	* [r2245] [BUG] Correction of bug #15561 paired-end iterators were
	  having a trouble in numbering.

2013-04-05  salson

	* [r2223] GkArrays: Bug #15583 corrected (concerning problems in
	  tests/Makefile.am). Version 2.0.1 issued

2013-04-05  nphilippe

	* [r2222] configure.ac

2013-04-03  jaudoux

	* [r2192] Correct the read numeration of readsIterator. The first
	  tag has now the id 0.

2013-03-21  salson

	* [r2127] GkArrays: Changelog of version 2.0.0
	* [r2126] GkArrays: testGkArrays.cpp: Added some comments to
	  explain the possibilities with the constructor
	* [r2125] GkArrays: src/Makefiles: Many headers must be installed
	* [r2124] GkArrays: Code cleanup
	* [r2123] GkArrays: Example for new users
	* [r2122] GkArrays: Tests: Add tests for bit vectors. Add
	  information in case of failed tests
	* [r2121] GkArrays: Bit vector implementation by Alban Mancheron
	  included, replaced former one. Beware: we only use bit vectors on
	  a multiple of 8bits to avoid race conditions with multi-threading
	* [r2118] GkArrays: Add a --coverage option in configure script to
	  compute the code coverage

2013-03-20  nphilippe

	* [r2117] put Solarray type for values table and modify code in
	  function

2013-03-20  jaudoux

	* [r2115] Add a method in readsReader to get the read number

2013-03-20  salson

	* [r2113] GkArrays: Javadoc: specify that arrays on the output are
	  sorted

2013-03-18  salson

	* [r2104] GkArrays: Unit tests: Produce a .tap file when tests are
	  launched [file testing.h forgotten]
	* [r2103] GkArrays: Unit tests: Produce a .tap file when tests are
	  launched

2013-03-12  salson

	* [r2100] GkArrays: Keep a N in dataset files.

2013-03-11  salson

	* [r2099] GkArrays: Makefile.in file deleted during a previous
	  commit, put back on the SVN

2013-03-10  nphilippe

	* [r2095] last cleanup for gk-arrays 2.0.0

2013-03-08  salson

	* [r2094] GkArrays: Fixed some Javadoc problems (typos in the
	  command name, parameter not documented, unknown parameter
	  documented, ...)

2013-03-08  jaudoux

	* [r2089] * New headers for each soure file * Change copyright year
	  * Add IRB/INSERM in copyright * Add a name of developpers in a
	  specific part * Tests added for pairedEnd classes * Builtables
	  can now be run using pairedEnd reads * New methods in readsReader
	  for switching between paired-end reads

2013-03-07  salson

	* [r2083] GkArrays: Changed the delay for waiting the children. It
	  is now small (for the start) and increases until it reaches an
	  upper bound Moved the place sem_post is put. sem_post must be
	  executed each time we leave a thread. Since we may launch the
	  insertion sort in a thread, sem_post had to be executed after
	  that too.

2013-03-06  salson

	* [r2082] GkArrays: - Removed two unnecessary variables (not used
	  anymore) - Removed a comparison between signed and unsigned
	  interger

2013-03-03  salson

	* [r2048] GkArrays: GkSABuilder: quicksort has now a better
	  parallel implementation and uses all the available resources (but
	  not more)
	* [r2047] Bug #15429 corrected: use of uintSA rather than uint for
	  the end position of a read in C_R.

2013-03-01  jaudoux

	* [r2037] Add an ifndef declaration in readsReader class.

2013-03-01  nphilippe

	* [r2035] -oops

2013-03-01  jaudoux

	* [r2034] Add missing comments and JavaDoc in readsReader class and
	  gkarrays class.

2013-03-01  nphilippe

	* [r2033] Version 1.3.1 with the following modifs: - integration of
	  paired reads - threading of gkIFA and gkSA - modification of
	  architecture

2013-02-28  salson

	* [r2032] GkArrays: Benchmarks: Evaluate performance depending on
	  the constant values
	* [r2022] Gkarrays tests: Also perform tests on multi-threaded
	  implementation. On the variable and fixed consistency, check also
	  with changing values of k and with the stranded or non-stranded
	  implementation
	* [r2021] GkArrays: Constant changed for the minimal size to call a
	  thread. This size has been changed according to the benchmarks
	  performed.

2013-02-27  jaudoux

	* [r2015] Integration of stranded for paired-end reads in values
	  array. Reverse complement the first read of each pair and keep
	  the second read of the pair as forward
	* [r2013] Bug correction on paired-end iterator.

2013-02-26  jaudoux

	* [r2010] Function getPair now return -1 if data are not paired-end
	* [r2009] - Add header to files : readsReader.h readsReader.cpp -
	  Correcting the function to reverse complement reads when using
	  paired-end - Add the function getPair(uint i), to get the read
	  associated to an other when using paired-end data
	* [r2008] Correcting warnings display in case of paired-end. Only
	  show them the first time we run trough the reads files

2013-02-25  salson

	* [r2007] Bug correction: read_lengths is of type uint64_t and not
	  size_t, therefore we must specify the type uint64_t to Calloc
	* [r2006] Tests: NDEBUG must not be set so that tests work

2013-02-25  jaudoux

	* [r2002] Correct the way to discard reads when using paired-end
	  files : - if one of the read has its length < k or <
	  expectedLength, both reads are discarded - Display the number of
	  tags discarded with informations about wich tag was in cause

2013-02-25  nphilippe

	* [r2000] change version with an integreted paired reads management

2013-02-25  jaudoux

	* [r1999] Add paired-end files management : - files management is
	  no longer in gkarrays.h class but in the new class readsReader.h
	  - for reading FASTA and FASTQ files, create an readReader object
	  using the simple file constructor for singleRead or double file
	  constructor for pairedEnd. - Use method begin() of readsReader in
	  order to get an generic iterator for getting reads - Don't forget
	  to delete the iterator.

2013-02-24  salson

	* [r1993] Tests: constant DATADIR was removed during a merge,
	  recovered
	* [r1992] Added benchmarks to test the best values for the
	  constants
	* [r1991] * Replaced the hard-coded value for the minimal size of
	  the array to call a thread, by a constant * Added ifndef in
	  const.h to allow defining the constant at compilation time

2013-02-23  salson

	* [r1990] GkArrays: getGkCFALength() now really returns GkCFA
	  length, ie. the number of distinct factors
	* [r1989] Building GkSA: quicksort must not be launched on an empty
	  range
	* [r1988] Tests: getGkCFALength() now really returns GkCFA length,
	  ie. the number of distinct factors
	* [r1987] * Updated call to GkArrays constructor: we do consider
	  the dataset is stranded (otherwise the tests would fail) * Solved
	  memory leaks

2013-02-18  nphilippe

	* [r1973] add isLarge() and isStranded() in gkArrays.h
	* [r1972] test for MAC configuration

2013-02-17  nphilippe

	* [r1970] add isLarge() and isStranded() in gkArrays.h
	* [r1969] add isLarge() and isStranded() in gkArrays.h
	* [r1968] add missing file
	* [r1967] add missing file
	* [r1966] add missing file
	* [r1963] - cleanup libdivsufsort
	* [r1962] - integration of gk-arrays stranded with a direct
	  construction of gkIFA and gkCFPS from values array - optimization
	  of the parallelization of gkSA
	* [r1961] code cleanup and mv int64 -> uint64

2013-02-15  salson

	* [r1927] configure.ac: Added -g flag at compilation
	* [r1926] Unit test: check consistency → corrected a memory leak
	* [r1921] GkArrays: Actually, getGkCFALength() had no good reason
	  to return the size of nb_commons. Given its name, the function
	  must return the number of element in GkCFA
	* [r1920] GkArrays: size_t was used for storing bits, which was a
	  pretty bad idea for 32-bit architecture
	* [r1919] testConsistency: Changed the order of the tests. Start by
	  the query of the table, and finish by more complex queries

2013-02-14  salson

	* [r1918] Tests: Now compile with distcheck.
	* [r1913] readIterator: add a isFinished() method to know when the
	  file has been completely read
	* [r1912] GkArrays: unit tests. Added unit tests for the GkArrays,
	  to check that variable and fixed-length implementation give the
	  same result and to test that all the results in the GkArrays are
	  consistent. Some little datasets have been added. They should be
	  completed in the future.
	* [r1911] GkArrays: the comment of getGkCFALength() was not
	  accurate enough: the number returned is not exactly the number of
	  distinct k-mers. There is one more cell, to deal with the sum
	  properly.
	* [r1910] GkArrays: in getGkSA(), no reason for transforming the
	  P-position in Q-position: the comment said the opposite. I
	  checked that no other function would be impacted
	* [r1908] Autotools file updates for creating version 1.1.0
	* [r1907] GkArrays: Removed code duplication by using another class
	  that makes the choice between a large and a small array

2013-02-11  nphilippe

	* [r1885] bug fixed between configure.ac and doc
	* [r1884] bug fixed between configure.ac and doc

2013-02-11  salson

	* [r1881] Gk-Arrays: Add solArray type to deal with arrays
	  containing 32-bit or 64-bit integers

2013-02-10  salson

	* [r1873] variableAndFixedLength: Int overflow when computing
	  position queried in getTagNum. Replaced int type for uintSA
	* [r1872] variableAndFixedLength: Test getTagNum function on each
	  position of the read concatenation, check that the results are
	  correct; test read length for each read and check the result is
	  correct
	* [r1871] Delete PRINT_VAR that were in the middle of the code!
	  Sorry for the disturbance...

2013-02-09  salson

	* [r1870] GkArrays test case: add output information on assert
	  failure
	* [r1869] Disable NDEBUG macro so that asserts are evaluated

2013-02-04  salson

	* [r1841] Added a tests directory with a test to check that
	  variable and fixed length implementations give the same results
	* [r1840] New assert macro for displaying a message (with variable
	  values for instance)
	* [r1839] Code of getGkCFALength()
	* [r1838] Added a getGkCFALength() method that returns the number
	  of elements in GkCFA

2013-01-30  salson

	* [r1824] Cancel previous commit and modified getTagFactor code so
	  that we can retrieve substrings of length < 4
	* [r1823] Add a pre-condition to getTagFactor() and getTextFactor()
	  to tell that the shortest factor must be of length 4 at least

2012-07-02  salson

	* [r1708] Changing minor version to 1.0.1

2012-06-29  salson

	* [r1707] * Added comments to detail class and function roles *
	  Added static method isDiscarded in gkArrays to know if a read is
	  discarded * Bug corrected in readIterator: now we do not take
	  into account reads that should be discarded -> parameters have
	  been added to the constructors so that we can determine if a read
	  must be discarded

2012-05-18  salson

	* [r1631] Updated documentation: remove reference to four library
	  versions and added procedure for installing
	* [r1630] Adding Doxygen configuration file
	* [r1629] Do not display anymore the bit version. That is
	  meaningless now.
	* [r1628] Bug: kseq/kseq.h was not included with 'make install'.
	  Solved.

2012-04-26  nphilippe

	* [r1613] bug fixed about the limit between large et small SA

2012-04-25  nphilippe

	* [r1612] bug fixed about the limit between large et small SA

2012-04-05  salson

	* [r1591] Solved memory leaks

2012-04-04  salson

	* [r1581] * Bug correction: in readIterator finished was not
	  modified properly * Bug correction: in readIterator seq was not
	  initialised properly (first item was missed)

2012-04-03  nphilippe

	* [r1578]
	* [r1577] add iterators in input file

2012-04-02  nphilippe

	* [r1566] one lib for all version (fixed,variable,32bits,64 bits)
	* [r1565] one lib for all version (fixed,variable,32bits,64 bits)
	* [r1564] one lib for all version (fixed,variable,32bits,64 bits)
	* [r1563] one lib for all version (fixed,variable,32bits,64 bits)
	* [r1562] one lib for all version (fixed,variable,32bits,64 bits)
	* [r1561] one lib for all version (fixed,variable,32bits,64 bits)
	* [r1560] one lib for all version (fixed,variable,32bits,64 bits)
	* [r1558] pour le developpement
	* [r1550] update svn struct

2011-07-11  salson

	* [r781] Release 0.2.0
	* [r780] Not the newest

2011-07-10  salson

	* [r775] Right version of the release (hopefully)
	* [r768] Release 0.2.0 of GkArrays
	* [r767] Gk arrays tag directory