[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