1.0.6

1.0.6:
Corrected a bug that may produce biased output in pij_gassist, pij_gassist_trad, and pijs_gassist when nodiag is set or when memlimit is small so computation is split into chunks.
Now setting histogram bounds based on the maximum of all LLRs (as opposed to the maximum of the chunk when memlimit is small) in pij_gassist, pij_gassist_trad, and pijs_gassist. This ensures the output is independent of memlimit (related to question from sritchie73@github).
Added sanity checks for agreement between input data and nodiag flag for pij functions excluding _pv (suggested by sritchie73@github).
Lots of internal function renaming and code restructuring.
Removed some unneeded files and functions.
Now support pkg-config setup.

1.0.5

1.0.5:
Updated Makefiles to account for different make environments.
1.0.1:
Bug correction:
Updated LDFLAGS for R interface.

1.0.0

1.0.0:
New functions:
Included P-value computation for 4 tests in pijs_gassist_pv and correlation test in pij_rank_pv.
Included using continuous anchors (instead of discrete genotypes) for causal inference in pij(s)_cassist*.
Revisions:
Minor adjustments on adding fluctuations for supernormalized data when the number of samples is small (<30).
Updated logging.
Minor adjustments in conversion from LLR to local FDR.
Minor bug corrections on defensive programming.

0.5.0

0.5.0:
New function: reconstruction of directed acyclic graph from prior information of edge significance. For details, see library function netr_one_greedy, doc.pdf, or UPDATES in any interface.
0.4.1:
Extreme situation behavior:
Added error checking for few samples (<4).
Added special consideration for extremely skewed LLR during local FDR estimation.
Updated copyright notice.

v0.4.0

Changes from 0.3.0:

Interface changes:
    Removed trailing _a's for all interface function names.
    Removed _tot functions. (See Obsoletes.)
    Binary interface has an extra parameter specifying memory usage limit.
    Python interface has an optional parameter specifying memory usage limit.

Improvements:
    We have introduced the function pij_gassist_trad for traditional inference test.
    We have parallelized the remaining part of major computation and obtained even faster speed.
    We have modified functions to perform inplace operations as much as possible to save memory.
    We have introduced memory usage limit as a parameter (except R interface). Large datasets will be automatically split before calculation to keep memory usage under limit.
    We have included p1 calculation for nodiag=1 case.
    Better input validity checks for interfaces.
    Bug corrections.

Obsoletes:
    In order to reduce effort in improving and maintaining the package, we decided to obsolete several non-essential functions. They include:
    pij(s)_*_tot functions: they will be hardly needed as more genes can be measured by advancing technologies.
    Windows native support: The latest version of Windows has provided support for Ubuntu Bash. All interfaces should integrate better with Bash on Windows. (https://msdn.microsoft.com/commandline/wsl)

v0.2.0

This release includes previous patches and supports Windows with MinGW64 from MSYS2. On Mac and Linux, installing from the source would be more convenient, while on Windows, we recommend using the pre-built binary release. The binary release can be installed by right clicking on install.cmd and choosing run as administrator.

v0.1.0

This is the initial release of Findr library. The source code is available for download, and binary build available for Windows. It can be installed by right clicking on install.cmd and choosing run as administrator. The binary build is based on Cygwin, so there are potential incompatibility issues with programs outside Cygwin.