- GERMLINE turns 10!
- New website.
- Updated default flags.
- Can now be run from command line with -input and -output.
- Removed deprecated flags (only plink format now supported).
- Fixed minor formatting bug with runs of homozygosity
- 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.
- Fixed bug with -to_snp/-from_snp commands
- Added -homoz-only flag for simple homozygosity analysis
- Fixed bug in PHASE format input
- Fixed bug in files with multiple chromosomes
- Fixed bug with overlapping segments from -h_extend feature
- Allows self-matches between individuals (include -homoz flat)
- Added columns to indicate weather match is homozygous or heterozygous
- 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.
- 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
- 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.
- Updated the HapMap format input - auto-detection of trio or unrelated input.
- 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).