[16-Sep-03] ASPEX version 2.5

-- Updates to COPYING license, and additional documentation.

[16-Nov-00] ASPEX version 2.4

-- Changed sib_phase, sib_ibd to report more digits in verbose output.
-- Added separate p-value calculations for transmissions through each
   parent to sib_tdt when "sex_split" is true.
-- Changed sib_clean to produce more conventional sex-linked output.
-- Fixed sib_map bug that could sometimes cause premature termination
   of the likelihood maximization algorithm on weakly linked markers.
-- Fixed bug in sib_kin four_way evaluation.
-- Fixed bug in sib_clean output when used with a mix of files with
   and without disease status information.
-- Fixed another bug in header parsing of raw linkage-format files.
-- Fixed bug in handling of allele frequency definitions, which caused
   core dumps if the 'freq' command was called with an odd number of
   arguments.

[13-Sep-99] ASPEX version 2.3

-- Added sib_clean program for removing data inconsistencies.
-- Fixed sib_phase to calculate IBS statistics after removing all data
   inconsistencies.
-- Fixed bug in 'fix_step' handling in sib_ibd and sib_phase.
-- Added 'example' directory with sample parameter and data files.
-- Changed all programs to also handle linkage files with just
   affected-status data, and no genotype data.
-- Changed sib_tdt to force discard_partial.
-- Improved ligate filter, so it can recode allele identifiers, or
   fill in information for missing people.

[03-May-99] ASPEX version 2.2

-- Added 'show_pairs' option to sib_phase and sib_ibd to report IBD
   estimates for each sib pair.
-- Replaced old '-vv' flag to report allele frequencies in sib_phase
   and sib_map with the 'show_freqs' option.
-- Fixed data file parsing to recognize more whitespace characters.
-- Fixed sib_tdt to respect the 'omit' parameter.
-- More output format tweaks and cleanups across all programs.  Got
   rid of ()'s in tables, since they make parsing more complicated.
-- Changed default support level for sib_map support intervals to 0.6
   LOD units: the old 1.0 LOD unit level is very strict, and 0.6 seems
   to be roughly comparable to a 90% confidence interval.
-- Added min_reps and max_reps parameters for controlling the sampling
   algorithm for p-values in sib_tdt.
-- Fixed sib_ibd '-vv' output to show results after error detection.
-- Fixed bug in header parsing of raw linkage-format files.
-- Fixed pair counting bug in sib_kin.

[07-Jan-99] ASPEX version 2.1

-- Increased maximum length of family ID's, person ID's, and allele
   names to 15 characters.
-- Changed sib_kin to respect error_freq parameter, and removed cousin
   test since it had little power.  Also, non-verbose output now
   excludes families where all relationships are consistent.
-- fixed ligate and restrict scripts to catch more data file format
   problems.
-- Fixed apparently rare memory corruption bug in sib_phase and
   sib_map that could cause the error detection code to loop forever.
-- Fixed bug in no_Dv maximum likelihood calculation, in normally
   unlikely case where the input data has no evidence favoring IBD=0
   or IBD=2.
-- Increased minimum number of iterations in sib_tdt permutation test
   to 1000, and changed the output format for p-values.

[18-Nov-99] ASPEX version 2.0

-- Major speedup in sib_phase and sib_map for larger families, and
   various other smaller performance improvements.
-- Changed how 'ligate' labels columns, to handle more input files.
-- Added more and less verbose output formats to sib_tdt.
-- Added p-value estimation to sib_tdt.
-- Added 'one_sib' option to sib_tdt.
-- Added keep/remove options to 'restrict' to filter by family ID's.
-- Renamed 'kinship' to 'sib_kin', and improved output format.
-- Minor cleanups, convergence improvements for sib_map.
-- Made marker name lookups case-insensitive.
-- Added check for missing allele frequencies with 'fixed_freq'.
-- Fixed some corner cases in sib_ibd and sib_phase, so that for
   verbose output, results are generated at each 'telomere' unless
   the distance to the nearest marker in the map is 0.
-- Fixed bug in sib_phase handling of sex-linked data, mostly
   affecting lod score calculations beyond the ends of the data.

[16-Jun-98] ASPEX version 1.18

-- Added 'osf' makefile target for DEC Unix.
-- Added 'count_unaffected' option to sib_tdt.
-- Fixed bug in handling of likely typing errors, affecting sib_ibd,
   where they were reported but not omitted from analysis.
-- Fixed bug in 'fix_step' handling in sib_phase introduced in 1.15.
-- Fixed possible memory corruption bug in handling of families with
   no sibs.

[29-May-98] ASPEX version 1.17

-- Added support for default parameter files ('aspexrc1', 'aspexrc2')
   that are processed before and after other command-line options are
   evaluated.
-- Added 'exclusion_level' parameter for getting constant-LOD-score
   exclusion maps.
-- Added options for controlling how affected-status field in input
   data is interpreted.
-- Added 'omit' parameter to exclude specific families or individuals
   from analysis.
-- Added 'loc_width' parameter for setting marker name widths, and
   cleaned up some minor table format issues.
-- Updated Makefile to automate compiling for various platforms.
-- Cleaned up various things that could generate compiler warnings.
-- Changed sib_tdt to score transmissions when one parent is typed and
   the parent and child are both heterozygous, but for different
   alleles (i.e., parent AB, child AC).

[17-Mar-98] ASPEX version 1.16

-- Fixed bug in sib_phase handling of sex-specific maps.
-- Fixed inconsistency in ordering of male and female results for
   non-maximum-likelihood output of sib_ibd and sib_phase, and
   clarified this in the documentation.

[12-Mar-98] ASPEX version 1.15

-- Updated sib_ibd, sib_map, and sib_phase to support sex-specific
   recombination maps, and optionally report separate maternal and
   paternal LOD scores.
-- Minor updates to the documentation.
-- Fixed core dump in sib_ibd with sex linked data.
-- Fixed rec_dist to work with current sib_ibd output format.
-- Fixed all programs to not croak on families with no sibs.

[29-Jan-98] ASPEX version 1.14

-- Added 'error_freq' parameter to sib_ibd, sib_phase, and sib_map,
   used for automatic likelihood-based error detection.
-- Added code to automatically prune completely untyped siblings.
-- Added 'limit_build' parameter to sib_ibd, for more predictable
   reconstruction of missing parent genotypes.
-- Minor layout fixes in sib_tdt.
-- Fixed bug in chi-squared calculations for observed IBS values in
   sib_phase table output.  The reported values were always low.
-- Fixed allele frequency code to not complain if the parameter file
   includes frequencies for markers not in the current map.
-- Fixed ligate script to also translate affected status if '-a' or
   '-n' is requested.
-- Fixed convergence criteria in maximum likelihood calculation for
   the two-degree-of-freedom maximization: the old way incorrectly
   assumed convergence if just z1 converged.

[03-Dec-97] ASPEX version 1.13

-- Improved the 'shuffle' output of sib_map a bit.
-- Changed sib_ibd very-verbose output to be haplotype-oriented for
   easier interpretation.
-- Fixed file handling bug that limited the number of marker data
   files that could be processed in one run.
-- Some speedups in marker data file processing, also some algorithmic
   improvements in the multipoint code.
-- Better complexity-estimating in sib_phase, also fixed a bug in
   handling of several loci at the same map position.

[05-Sep-97] ASPEX version 1.12

-- Added 'kinship' program for checking relationships.
-- Fixed some (apparently) minor memory allocation errors.
-- Fixed several typos in the 'ligate' filter.
-- Fixed bug in sex-linked data handling introduced in version 1.11.
-- Fixed bug in calculation of expected IBS for sex-linked data when
   discordant pairs are counted.
-- Changed LOD score 'truncation' in maximum likelihood calculations
   so that for discordant pair calculations, sharing above 50% will be
   truncated to 50% (as opposed to concordant pairs, where sharing
   below 50% is truncated to 50%).

ASPEX version 1.11

-- Changed sib_tdt to reject families with only one typed parent.
-- Changed sib_ibd and sib_phase to print z0/z1/z2 values whenever
   a maximum likelihood calculation is done, not just for the two
   degree of freedom model.
-- Changed all programs to autodetect all input file formats, so
   'linkage_format' and 'has_disease_data' flags are unnecessary.
-- Added '-q' (quiet) flag, for suppressing warnings about Mendelian
   incompatibilities in sib_ibd and sib_phase.
-- Added the 'ligate' filter for cutting and pasting linkage data
   files, and the 'restrict' filter, to replace the *_sick, *_kids,
   and *_parent filters.

ASPEX version 1.10

-- Added 'fix_step' parameter for maps with fixed step size between
   points.
-- Added two-parameter fitting algorithm to the maximum likelihood
   calculations.
-- More consistency checks for marker input files.
-- Minor improvements in output formatting.
-- Fixed a couple of special cases for processing of sex linked data
   in linkage format.

ASPEX version 1.9

-- Better error handling for various marker data format errors.
-- Fixed all the filters (only_sick, two_kids, more_kids, no_parent,
   one_parent, two_parent) to not drop the last family in a file.
-- Fixed linkage format to handle sex linked data where males are
   coded as homozygotes.

ASPEX version 1.8

-- Added '-V' flag to report program version number, for all programs.
-- Added family size checks and a few extra sanity checks to sib_ibd,
   sib_map, and sib_phase.
-- Fixed a bug in LINKAGE input file processing.

ASPEX version 1.7

-- Changed LINKAGE format to allow using '1' and '2' for 'm' and 'f'
   in the gender field, and fixed bug if the mother is listed before
   the father in a pedigree.
-- Deleted the sib_only program, since sib_phase is always better and
   usually faster, and sib_only has a bias problem.
-- Incorporated the IBS calculations from sib_only into sib_phase.

ASPEX version 1.6

-- Speed improvements in sib_map.
-- Changed default blank allele from '00' to '0'.
-- Added ability to read LINKAGE format marker data.
-- Added 'do_shuffle' option to sib_map to verify map order and/or add
   new markers to a map.
-- Fixed problem in the maximum likelihood routines for exclusion maps
   that sometimes resulted in extremely slow convergence.
-- Fixed floating point overflow bug in sib_map.
-- Fixed sib_tdt to handle sex-linked data.
-- Fixed sib_phase and sib_map to skip families with less than two
   kids.
-- Fixed bug in allele counting when some alleles have non-numeric
   names.

ASPEX version 1.5

-- Added new 'sib_map' program for multipoint marker mapping from
   sibship data.
-- Fixed off-by-one error in the default sib_ibd output, where the
   quoted LOD score and % sharing for each marker is actually the
   value for the preceding marker.
-- Fixed sib_tdt to ignore 'freq' commands in parameter files.

ASPEX version 1.4

-- Changed sib_only to only discard data for markers that are actually
   inconsistent, rather than discarding all sib pairs with any
   inconsistent data.  Now sib_only should be consistent with sib_ibd
   and sib_phase in this respect.
-- Changed sib pair programs to all recognize three disease states
   (affected, unaffected, unknown).  Unknown sibs will not be used to
   construct pairs, but will be used for parent reconstruction.
-- Added 'truncate_sharing' parameter for determining if maximum
   likelihood calculations should only report sharing of at least 50%.

ASPEX version 1.3

-- Even more speed-ups in sib_phase.
-- Added new parameters 'count_unaffected' and 'count_discordant' to
   sib_ibd, sib_only, and sib_phase, to allow control over what types
   of sib pairs are counted.
-- Changed xmgr_map to avoid overlapping tick labels along X-axis, and
   a few more cosmetic tweaks.
-- Minor improvements in rec_dist.
-- Fixed input routines to handle case where a family has data for
   different people in different marker data files.

ASPEX version 1.2

-- More speed-ups in sib_phase.
-- Fixed problems with sex-linked data in sib_phase.
-- Fixed xmgr_map to handle parameter files with allele frequency
   information.

ASPEX version 1.1

-- Sped up sib_phase a lot, using sparse array methods and a few other
   tricks.  Most big families should now run in reasonable time.
-- Fixed sib_ibd to ignore 'freq' commands, so the same parameter file
   can be used with sib_only/sib_phase.
-- Fixed a bug in sib_ibd: one part of the calculation disregarded the
   mapping function setting and assumed Kosambi.
-- Fixed bug in sib_ibd where turning off no_Dv also turned off
   most_likely.
-- Fixed bug in 'cost of...' messages in sib_phase.  Also fixed an
   uninitialized variable error in sib_phase.

ASPEX version 1.0

-- New package name.
-- Reorganized the documentation.
-- Renamed sib_state to sib_phase, and merged sib_map into sib_ibd.
-- Updated sib_ibd, sib_map, and sib_state to handle sex-linked data.
-- Updated the marker data input routines to include line numbers in
   error messages.  Also improved some other error messages.
-- Changed sib_ibd to count sharing when the parent of the shared
   allele can't be determined (AB x AB -> AA & AB).  Also fixed the
   counting of sibs in families with one typed parent, to remove a
   bias problem.
-- Fixed sib pair counting in sib_phase.  Also improved estimation of
   cost of calculation for large families