ChangeLog
1.5.0 (09.17.10)
Major computational overhaul - algorithm should run 2-3 times faster with 4-fold memory reduction on large datasets.
Added a binary output option (flag -bin_out) to reduce output size, see documentation.
Added a stand-alone C++ script to convert from binary file to standard readable match file.
Added -haploid flag to treat each input individual as two distinct haplotypes, output IDs will have .0/.1 suffix indicating which respective haplotype the match is on. This is effective for short windows with very well phased data.
1.4.2 (07.22.10)
Fixed bug with -to_snp/-from_snp commands
Added -homoz-only flag for simple homozygosity analysis
1.4.1 (03.22.10)
Fixed bug in PHASE format input
Fixed bug in files with multiple chromosomes
Fixed bug with overlapping segments from -h_extend feature
1.4.0 (08.14.09)
Allows self-matches between individuals (include -homoz flat)
Added columns to indicate weather match is homozygous or heterozygous
1.3.0 (12.22.08)
Now handles unphased data (omit -h_extend flag).
Added options for homozygous / heterozygous in-exact matching.
Output now specifies if match is in cM or MB.
1.2.1 (09.17.08)
Now using the boost dynamic_bitset libraries. These are packaged with the source and do not effect installation/dependency.
Added -bits flag to explicitly define word-length.
Included sample input data & test-case called upon compilation by 'make test_case'.
1.2.0 (09.03.08)
Output format has changed to provide more detailed SNP information (see above).
Can now iteratively process multi-chromosomal data (for PLINK / PED format only).
Genotype calling has been removed for the time being.
Genetic map restructured (see above) and processed as a parameter.
1.0.2 (08.12.08)
Updated the HapMap format input - auto-detection of trio or unrelated input.
1.0.1 (06.09.08)
Added options to perform analysis on specific region (see -from_snp, -to_snp flags).
Added option to print haplotypes and matches (see: -haps, -print flags).
