freecontact (1.0.21) unstable; urgency=low

  * lib/freecontact.h no longer includes boost/format.hpp.

 -- Laszlo Kajan <lkajan@rostlab.org>  Sat, 28 Sep 2013 09:43:07 +0200

freecontact (1.0.20) unstable; urgency=low

  * Fixed runtime issues with timer_create(CLOCK_PROCESS_CPUTIME_ID,...) on
    kfreebsd.

 -- Laszlo Kajan <lkajan@rostlab.org>  Thu, 19 Sep 2013 18:26:56 +0200

freecontact (1.0.19) unstable; urgency=low

  * Changed the condition on which x86intrin.h is included.
  * Updated lib/Doxyfile.in.

 -- Laszlo Kajan <lkajan@rostlab.org>  Wed, 18 Sep 2013 17:55:09 +0200

freecontact (1.0.18) unstable; urgency=low

  * Fixed compiler SSE2 support detection problem (Debian bug #721380).
  * Fixed perlpod =item <number> issue (Debian bug #721381).
  * Fixed issue with including x86intrin.h on non-x86 (Debian bug #721379).

 -- Laszlo Kajan <lkajan@rostlab.org>  Tue, 17 Sep 2013 17:10:34 +0200

freecontact (1.0.17) unstable; urgency=low

  * Edited _print_help() message.

 -- Laszlo Kajan <lkajan@rostlab.org>  Mon, 15 Jul 2013 15:14:48 +0200

freecontact (1.0.16) unstable; urgency=low

  * Extended command line help.
  * Edited man page.
  * Renamed parameter 'gap-incovm' to 'apply-gapth'.

 -- Laszlo Kajan <lkajan@rostlab.org>  Tue, 02 Jul 2013 17:05:47 +0200

freecontact (1.0.15) unstable; urgency=low

  * Added lib/config.h to distributable tar.xz (and as SOURCE where it is).
  * Added mincontsep-dependent alignment length (minimum) checks.
  * Explained the meaning of mincontsep (j-i) better in docs.
  * Decresed memory usage through clearing copies of the covariance matrix as
    soon as they are not needed.
  * Smaller memory usage: precision of pairfreq matrix is now float (changed
    from double).

 -- Laszlo Kajan <lkajan@rostlab.org>  Mon, 17 Jun 2013 15:43:02 +0200

freecontact (1.0.14) unstable; urgency=low

  * Sequence weighting is now done in a separate method, and can be used on its
    own.
  * Fixed very long loop on 1-sequence "alignment" bug.

 -- Laszlo Kajan <lkajan@rostlab.org>  Thu, 13 Jun 2013 20:03:11 +0200

freecontact (1.0.13) unstable; urgency=low

  * Added --icme-timeout to fail program if the inverse covariance matrix
    estimation runs too long.
  * Added -pthread and -lrt to lib/Makefile.am for timer_create et al.

 -- Laszlo Kajan <lkajan@rostlab.org>  Fri, 07 Jun 2013 20:40:13 +0200

freecontact (1.0.12) unstable; urgency=low

  * Added parameter set 'ps_psicov_sd' for PSICOV sensible default
   (as defined in PSICOV README).
  * 'sparsity' is renamed to 'density'.

 -- Laszlo Kajan <lkajan@rostlab.org>  Thu, 06 Jun 2013 13:07:24 +0200

freecontact (1.0.11) unstable; urgency=low

  * Out-of-bounds vector index bug in fc.h, resulting in malloc() and double
    free errors is fixed.

 -- Laszlo Kajan <lkajan@rostlab.org>  Tue, 04 Jun 2013 13:47:34 +0200

freecontact (1.0.10) unstable; urgency=low

  * Moved fc::parset_t << operator out of lib, into src/freecontact.cpp.
  * Fixed printing of --clustpc argument value.
  * Corrected spelling errors.
  * First line of .aln input is not required to be the query - updated
    documentation to reflect this.
  * More aggressive (0.5 : 2) rho control in glasso iterations.
  * Initialize fp_t sparsity = -1, prev_spar = -1;

 -- Laszlo Kajan <lkajan@rostlab.org>  Mon, 27 May 2013 18:52:11 +0200

freecontact (1.0.9) unstable; urgency=low

  * Added overloaded ali_t::push(const char *__al, uint16_t __alilen).
  * Number of threads is now controlled in predictor::run().
  * freecontact executable parameter profile no longer contains number
    of threads and output format.
  * fc::predictor::run() parameter profile is moved into library.
  * Library exports constant parameter profiles corresponding to as-published
    parameter sets of methods.
  * Based on BioXSD-1.1.2, no XSD restrictions.
  * Fixed XSD import in freecontact.wsdl <types><schema><import>.

 -- Laszlo Kajan <lkajan@rostlab.org>  Mon, 29 Apr 2013 18:04:08 +0200

freecontact (1.0.8) unstable; urgency=low

  * Added bash completion for freecontact.
  * Renamed library header to 'freecontact.h'.
  * Renamed freecontact class to predictor.

 -- Laszlo Kajan <lkajan@rostlab.org>  Wed, 24 Apr 2013 19:03:09 +0200

freecontact (1.0.7) unstable; urgency=low

  * Added --pep (print effective parameters) cmd line option.
  * Added timing results as parameter to run() method.
  * Fixed unnecessary libxerces-c dependency when xsdcxx is /not/ found.

 -- Laszlo Kajan <lkajan@rostlab.org>  Sat, 20 Apr 2013 14:50:27 +0200

freecontact (1.0.6) unstable; urgency=low

  * Fixed parallel build issue once more with more make rules (no sync).

 -- Laszlo Kajan <lkajan@rostlab.org>  Sat, 20 Apr 2013 14:08:55 +0200

freecontact (1.0.5) unstable; urgency=low

  * Optimized loops and OMP parallelization to allow more CPU cache hits.
  * Added autoconf macros for CPU feature detection.

 -- Laszlo Kajan <lkajan@rostlab.org>  Fri, 12 Apr 2013 12:54:50 +0200

freecontact (1.0.4) unstable; urgency=low

  * No longer needs OMP atomic updates.
  * Set OMP schedule to dynamic everywhere, with a low number.
  * Added xsdcxx autodetection. Compilation can handle missing Xerces or
    xsdcxx, with the consequence of no XML support.
  * Renamed multifasta2aln to a2m2aln, as the input format is 'A2M',
    a known extension of FASTA.
  * Fixed parallel build issue with xsdcxx-generated code.

 -- Laszlo Kajan <lkajan@rostlab.org>  Fri, 05 Apr 2013 18:47:39 +0200

freecontact (1.0.3) unstable; urgency=low

  * BioXSD XML output format.
  * Added WSDL 2.0 file for web service.
  * Renamed mfDCA -> EVfold-mfDCA (mfdca -> evfold-mfdca) (D. S. Marks'
    suggestion)
  * Software title is 'FreeContact' whenever mentioned, the command line
    interface 'freecontact', package name is 'freecontact'.

 -- Laszlo Kajan <lkajan@rostlab.org>  Fri, 29 Mar 2013 10:14:27 +0100

freecontact (1.0.2) unstable; urgency=low

  * DCA->mfDCA rename (mean-field direct-coupling analysis).

 -- Laszlo Kajan <lkajan@rostlab.org>  Fri, 15 Mar 2013 11:43:37 +0100

freecontact (1.0.1) unstable; urgency=low

  * Fixed Doxygen issues with files not cleaned up after build.
  * Wrote man page for freecontact.

 -- Laszlo Kajan <lkajan@rostlab.org>  Wed, 13 Mar 2013 16:42:07 +0100

freecontact (1.0.0) unstable; urgency=low

  * Initial release.

 -- Laszlo Kajan <lkajan@rostlab.org>  Fri, 09 Nov 2012 18:15:28 +0100