ChangeLog ============================================================= CHANGES AFTER PUBLIC RELEASE OF MERLIN ============================================================= MERLIN 0.9.9 ============ * Improved Portability. Removed all (void *) to (int) conversions to allow compilation on some 64-bit architectures. In addition, provided replacement snprintf for architectures with a buggy version in the system library. * Improved PDF Graph Layout. Graphs in PedStats now provide better handling of missing data. * Fixed Problems With Internal Allele Recoding. The new allele recoding engine, introduced in version 0.9.8, did not track allele frequencies of the alleles not present in the pedigree file. This could cause Merlin to crash when the --simulate option was used. MERLIN 0.9.8 ============ * Basic PDF output. Merlin and Merlin-Regress now produce a simple PDF file with one LOD score plot per page when the --pdf option is used. Each trait, chromosome and analysis option is plotted on a separate page. * Pedigree Trimming. Merlin and Merlin-Regress can now remove uninformative individuals from pedigrees to speed up analysis. To use this functionality, use the --trim command line option. * Microsatellite Allele Sizes. Allele numbers are now recoded internally, allowing microsatellite allele sizes to be used in the pedigree file. * Extended IBD state information. Extended allele IBD state probabilities, which distinguish maternal and paternal allele sharing and provide additional information on inbreeding can now be calculated. * Multiple Trait Models for Regression Analyses. MERLIN-REGRESS now accepts an optional table describing mean, variance and heritability for each trait. This facilitates analyses of pedigree files with multiple traits. * Founder couple symmetries can be optionally disabled with the --noCoupleBits option. * For variance components analysis, fixed bug that led to non-invertible matrices when the parameter estimated variance components are close to zero. This condition could produce a crash in earlier versions. * Fixed bug in Merlin-Regress that caused crashes in families with more than 4 pairs of grand-parents with no phenotype or genotype data. This condition would produce a crash in earlier versions. * Fixed aggressive optimization that could cause the --all option (which lists all non-recombinant haplotypes) to miss some haplotype states. Formerly, markers were labelled uninformative whenever they implied identical likelihoods for all inheritance vectors. This version implements a stricter definition that also requires that the same allelic state is implied for each vector. MERLIN 0.9.3 ============ * Minor source code changes for compatibility with GCC version 3. * Horizontal haplotypes are no longer output by default, but require --horizontal flag. MERLIN 0.9.2 ============ * Public release incorporating changes in versions 0.9.0 and 0.9.1. MERLIN 0.9.1 ============ * Added general pedigree regression analysis. This is an early implementation of the approach proposed by Sham et al (2002) in the AJHG. It is still somewhat slow, but functional. Run as a separate program, MERLIN-REGRESS. * Added --horizontal option which selects horizontal haplotype layout in [merlin.chr] output file. * Stopped Merlin from automatically loading [merlin.freq] allele frequency file. To load allele frequencies, the -f filename option must be specified explicitly. * Added --useCovariates options to support covariates in variance components linkage analyses. * Fixed bug that led to crashes when the number of alleles in the pedigree exceeded those in the allele frequency file by exactly one. * Renamed the option --marker-names as --markerNames, for consistency with other two word options, such as --minStep and --maxStep. MERLIN 0.9.0 ============ * Support for X chromosome incorporated. Runs as a separate program, Merlin In X (MINX). * New --frequencies output option saves allele frequencies as estimated by merlin in merlin.freq file. * New --perFamily output option saves information and NPL scores for individual families in separate files. * Quiet output no longer includes warning when markers with very low information are skipped. * Input pedigree files now checked for the presence of parents with identical sexes. If a pedigree file has more than one formatting problem, Merlin tries to report as many problems as possible before stopping. * Linkage datafiles where lines end precisely with "<<" or ">>" now handled correctly. In previous versions, these lines would be rejected by Merlin with an error message. * Changed scaling of non-parametric linkage statistics in Simwalk2 interface file. * Minor changes in source code to improve portability. Specifically, there are no longer any return statements with void arguments or new style type casts. This should allow compilation with Sun Workshop C++ compiler. * Minor changes in Makefile to improve portability. Specifically, ar and ranlib are now invoked separately to allow compilation in Mac OS X systems. MERLIN 0.8.8 ============ * Fixed problem reading linkage files with liability class information. Previous versions printed a spurious warning about trailing columns in input pedigree and ignored the last column in input. MERLIN 0.8.7a ============= * Families with impossible recombination patterns excluded from NPL analyses (previously scored as zero) and variance components analyses. MERLIN 0.8.7 ============ * Merlin now estimates kinship between inbred parents and their offspring (previously assumed to be 0.25). MERLIN 0.8.6 ============ * Fixed singlepoint so correct marker names are displayed. (Problem occurred when --steps, --minStep, --maxStep, and --grid, --start and --stop options were introduced) * Change optimization default from -O3 to -O2 to avoid crashing gcc-2.95.3. ============================================================= CHANGES BEFORE PUBLIC RELEASE OF MERLIN ============================================================= MERLIN 0.8.5 ============ * Added --steps, --minStep, --maxStep as well as --grid, --start and --stop for fine control of analysis locations. * The --steps option now replaces the old -i (steps per interval) option. * Now includes intermediate output at all markers, even those that map at the same location, for --simwalk2 analyses. * Fixed in variance components that resulted in non- positive definite matrices in some pedigrees with uninformative grand-parents. * Added pedwipe to MERLIN distribution. MERLIN 0.8.3 ============ * Check whether recombination fractions or centiMorgan distances are provided in linkage datafiles. MERLIN 0.8.2 ============ * Maintain ordering for markers separate by the recombination fractions of zero. Previously, the output order for these markers was random. The new version keeps the same order as in the linkage datafile (linkage format) or mapfile (qtdt format) * Output IBD probabilities with 5 digit precision. MERLIN-0.8.1 ============ * Major editing of tree traversal and construction code to account for changes in operator precedence between gcc version 3.0 and versions 2.95.*. (and you thought C++ was pretty well established, eh?) * Minor fix to code which optimizes ordering of individuals within pedigrees. No effect on results, but may sometimes speed things up. MERLIN-0.7.3 ============ * Catch out of memory errors during haplotyping and gracefully skip to next pedigree. MERLIN-0.7.1 ============ * Attempt to recover from memory allocation failures. In 32-bit systems some failures are unrecoverable (e.g., trying to allocate memory blocks > 2GB), so the --megabytes option is necessary so Merlin doesn't try to allocate these huge blocks. * The --bits option now replaces the old -b option. MERLIN-0.6.1 ============ * Very unlikely genotypes now have scores in scientific notation, e.g., 1e-10 instead of 0.00000. * Added support for variance components analysis. MERLIN-0.5.1 ============ * First version distributed outside Oxford. ============================================================= OLDER VERSIONS OF MERLIN ONLY USED INTERNALLY =============================================================