v1.05 Initial version (not recommended use 1.06 instead)
v1.06 Few optimizations brought, mainly all modifications made to ease installation
v1.07 Easier to provide other blas/lapack libraries, warn about not handling missing phenotype values and check ordering between input data files.
v2.01 Linear fit algorithm has changed to avoid the use of external BLAS/LAPACK libraries. In addition, weights are now used to limit the matrix size, thus providing a significant performance boost.
Data storage has been shrunk to its minimum to reduce IO bottleneck. Moreover the new format is independant of the x86 or x86_64 architecture.
Big endian architecture can now compile, the code ran on IBM BlueGene/P performing hundreds of millions interactions per seconds!
Additional features were added to the pre- stage to account for missing phenotypes, these people should now be removed from the population. However some issue remains on how to deal with multiple phenotypes, choice was made to stop with warning in the case the individual presents partial miss.
SMP version bears additional features not yet implemented on the MPI version. Indeed, the QR algorithm has been implemented in several ways using SSE intrinsics. Choice is performed by the --method option. We measured best performance using --method 4. Note that this version is superseded by 2.02 due to a bug encountered in single phenotype data reading which caused every 2 values to be zero!
v2.03 Corrected version of 2.01 and 2.02
SMP version has an added feature to run epistatic tests on binary trait data. So far this feature is triggered when no phenotype file is provided and requires the phenotype data within the standard plink files to be in the format 1 is unaffected and 2 is affected. We would like to emphasize that this is still under heavy implementation and should be considered BETA software.
MPI version nows allow command line option to alter thresholds hence no need to rerun preFastEpistasis anymore for such purpose. Furthermore SSE intrinsics functions are now provided as in SMP and can be adjusted throught the use of --method option.
Do not attempt to run MPI version on multiple phenotypes. This is not yet ready.
v2.05 Corrected version of 2.03
PreFastEpistasis correctly handles SNP names therefore you should no longer have errors rising when checking the phenotypes ordering file.
In the special case of pure disjoint sets i.e. set A inter set B is empty not, all epistatic tests are now performed.
Added feature to avoid giving a set file when all to all interaction snps are concerned, simply do not provide a set file to preFastEpistasis.
Added compile time feature to enable genetic data in 2 bit format rather than 1 byte. This considerably reduces preFastEpistasis output size. Nevertheless, it is recommended not to use old preFastEpistasis output format (prior to 2.05) with this and the future versions.
Added software QRTest to test QR speed.
Added software SNPxSNPTest to compute snp A - snp B epistatic interaction.
Still do not attempt to run MPI version on multiple phenotypes. This is not yet ready.
