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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
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