2008-07-27  Alex Lancaster <alexl AT users sourceforge net>
	
	* emhaplofreq.h (NAME_LEN): Increase maximum size of allele name to 20.

2008-06-08  Richard M. Single <rsingle@uvm.edu>

	* emhaplofreq.h: Changed MAX_ROWS from 1023 to a conservative
	value of 5000.  Changed MAX_GENOS from 20000 to 40000.  Tests
	based on NMDP data with 10000 individuals required ~30000 for
	MAX_GENOS.

	* emhaplofreq.c: Array genopheno[] was removed throughout. Space
	was allocated for this array, but it was not used. genopheno[] was
	used (at one point in time) to keep track of the geno-pheno
	relationships for each permutation, thus it had been incremented
	as "genopheno[i][0]=permu+1;" to avoid having to be initialized
	with each permu. But, it is no longer used. The array gp[] stores
	the genotype- phenotype relationships. The 1st dimension of the
	gp[] array was changed from MAX_GENOS to MAX_GENOS_PER_PHENO
	since, for a given phenotype, space only needs to be allocated for
	each of the possible genotypes for that phenotype
	[not all possible genotypes across all phenotypes].

	(emalc): Some of the initialization loops (for ambig[] and
	addto_ambig[]) were rearranged to avoid looping through these
	arrays more than necessary.  This speeds up computations
	especially for large files with a lot of phenotpyes.

	Also in the emcalc() routine, the criterion for setting
	error_flag=2 was changed from "if (expected_freq_sum < .00000001)"
	to "if (expected_freq_sum < 1.e-16)". This is only an issue for
	very large datasets. The check based on error_flag=3 is still a
	safety measure for the condition that error_flag=2 is checking. It
	may be possible to remove error_flag=2 altogether (setting
	expected_freq_sum=1.e-16 if it is less than this value), but
	additional testing with very large datasets is needed to determine
	if that is ok.

2007-09-21  Alex Lancaster  <alexl AT users.sourceforge.net>

	* emhaplofreq.h (xmlfprintf): Define new macro to be used for
	printing out XML (or other) statements that should be returned
	back to the external SWIG wrapper, expands to pyfprintf in SWIG
	context, otherwise it defaults back to fprintf to maintain
	compatibility with command-line version.  This was done because
	the "-Dfprintf=pyfprintf" compiler directive no longer appears to
	work with GCC 4.1.2 and because overwriting standard library
	functions via preprocessor directives is deprecated.

	* emhaplofreq.c (main_proc, linkage_diseq): Use it throughout.

2005-06-15  Alex Lancaster  <alexl AT users.sourceforge.net>

	* emhaplofreq.c: Change prototypes to match function calls
	exactly, e.g. replace (*)[] invalid ANSI constructs with (*)[VAR]
	constructs which is valid ANSI C and also to placate GCC 4.0.

2004-12-23  Alex Lancaster  <alexl AT users.sourceforge.net>

	* emhaplofreq_wrap.i: %module _Emhaplofreq -> Emhaplofreq for
	compatibility with most recent SWIG.

2004-07-20  Owen Solberg  <solberg@mws11.biol.berkeley.edu>

	* emhaplofreq.c (linkage_diseq): Add new alloc memory structure
	called summary_d to store the 'unprimed' LD measure.  This is
	calculated by multiplying summary_dprime by dmax, which appears to
	yield the expected behavior.  Also prints this value to the XML
	stream next to where summary_dprime is printed.

2004-02-09  Alex Lancaster  <alexl AT socrates.berkeley.edu>

	* emhaplofreq_wrap.i (main_proc): Accept new integer
	max_init_cond, in function prototype.

	* emhaplofreq.c: Add extra int to prototype of main_proc.
	(main): Hardcode MAX_INIT only when invoked from command-line (to
	preserve existing behavior).
	(main_proc): Accept new function parameter: max_init_cond, so that
	wrappers can use alternative number of initial conditions.  Don't
	assign this value from the hardcoded value in the header file.

2003-12-17  Alex Lancaster  <alexl AT socrates.berkeley.edu>

	* emhaplofreq_wrap.i (main_proc): Add matching parameter in
	prototype for SWIG wrapper.

	* emhaplofreq.c (main_proc): Add a new parameter 'permu_print', if
	set to 1 the likelihood statistic will printed to the
	output (either the permu file or the XML output depending on
	compile-time option).  Used to suppress lengthy permutation
	information when not required.
	(main): When calling from command-line, enable permu_print.
	(emcalc): Initialize 'prev_loglike' to 0.0, to
	quit compiler warning.

2003-12-12  Alex Lancaster  <alexl AT socrates.berkeley.edu>

	* emhaplofreq_wrap.i (main_proc): Update wrapper to reflect new
	function syntax.

	* emhaplofreq.c (main_proc): Add new parameters: max_permu and
	max_init_for_permu which are no longer hard-coded and can be
	passed in from an outside invocation of this function.  Use them
	in calloc()ing the 'like_ratio' and 'error_flag_permu' arrays.
	MAX_PERMU -> max_permu and MAX_INIT_FOR_PERMU ->
	max_init_for_permu throughout.
	(main): Pass the hard-coded MAX_PERMU and MAX_INIT_FOR_PERMU from
	emhaplofreq, when invoked in command-line mode, until we add
	getopt-parsed options for them.

	* Start ChangeLog.

