Added Landau / exact HMP implementation; updated licenses; added deta…

…iled references

LICENCES

@@ -0,0 +1,21 @@
+
+Subdirectories within src/ include code and source files from several other open-source projects. I am grateful to the individuals who developed these resources and made them available to the open source software community. 
+
+Code and source files within these subdirectories are subject to the licenses issued by the original authors rather than the license for GAMBIT primary source files. These licenses are included separately within each subdirectory. 
+
+Distribution functions (cdflib/, eigenmvn/, ROOT_Math/, libMvtnorm/): 
+* cdflib is from https://people.sc.fsu.edu/~jburkardt/cpp_src/cdflib/cdflib.html
+* eigenmvn.hpp is used from https://github.com/beniz/eigenmvn
+* libMvtnorm is used from https://github.com/zhanxw/libMvtnorm
+* ROOT_Math/ code is adapted from CERN ROOT library https://root.cern.ch/
+
+Hopscotch hashing (tsl/):
+* tsl is from https://github.com/Tessil/hopscotch-map
+
+Eigen matrix library (Eigen/):
+* Source files are from http://eigen.tuxfamily.org
+
+Tabix and HTSLIB (htslib/ and tabixpp/):
+* tabixpp/ source files are adapted from https://github.com/ekg/tabixpp
+* htslib/ source files are from HTSLIB: https://github.com/samtools/htslib 
+

Makefile

@@ -1,16 +1,17 @@
-VERSION=0.2
+VERSION=0.3
 
-CPPFLAGS= -Ofast -flto -pipe 
+CPPFLAGS= -Ofast -flto -pipe -I$(cdir)/src/htslib -I$(cdir)/src/cdflib -I$(cdir)/src/tabixpp -L$(cdir)/src/htslib -L$(cdir)/src/cdflib -L$(cdir)/src/tabixpp 
 CXXFLAGS= -std=c++11 -DNDEBUG 
 FFLAGS=
-
 LDFLAGS= -lz -lm
 
-cppsrc = $(wildcard src/*.cpp) src/tabix_util/tabix.cpp
-csrc = $(wildcard src/*.c) src/tabix_util/index.c src/tabix_util/bgzf.c
+cppsrc = $(wildcard src/*.cpp) $(wildcard src/ROOT_Math/*.cpp) $(wildcard src/cdflib/*.cpp)  $(wildcard src/tabixpp/*.cpp)
+csrc = $(wildcard src/*.c) src/htslib/bgzf.c src/htslib/kstring.c src/htslib/knetfile.c src/htslib/index.c
 
 objs = $(cppsrc:.cpp=.o) $(csrc:.c=.o) 
 
+cdir = ${CURDIR}
+
 bin/GAMBIT: $(objs) src/libMvtnorm/libMvtnorm.a
 	$(CXX) $(CPPFLAGS) -o $@ $^ $(LDFLAGS)
 

README.md

@@ -89,7 +89,32 @@ UTR       UTR5              Utr5
 ```
 
 - **Window size.** The window size for dTSS-weighted gene-based tests can be modified by specifying `--tss-window BASEPAIRS` (500 Kbp by default).
-- **dTSS decay function.** The relative weight assigned to variants nearer/farther from the TSS can be modified by specifying `--tss-alpha ALPHA`, where alpha=0 implies all variants receive equal weight, and larger values confer more weight to variants nearer the TSS. `--tss-alpha` also accepts comma-separated lists of alpha values, in which case GAMBIT computes ombinbus test p-values across all specified values (individual p-values are reported in `INFO` output field). By default, GAMBIT uses dTSS alpha values `1e-4,5e-5,1e-5,5e-6`. 
+- **dTSS decay function.** The relative weight assigned to variants nearer/farther from the TSS can be modified by specifying `--tss-alpha ALPHA`, where alpha=0 implies all variants receive equal weight, and larger values confer more weight to variants nearer the TSS. `--tss-alpha` also accepts comma-separated lists of alpha values, in which case GAMBIT computes global test p-values across all specified values (individual p-values are reported in `INFO` output field). By default, GAMBIT uses dTSS alpha values `1e-4,5e-5,1e-5,5e-6`. 
+
+## Methods References
+
+Statistical methods implemented in GAMBIT:
+- Sequence Kernel Association Test (SKAT): [Wu et al. (2011), *AJHG*](https://doi.org/10.1016/j.ajhg.2011.05.029)
+- TWAS: [Gusev et al. (2016), *Nat Genet*](https://www.nature.com/articles/ng.3506)
+- PrediXcan: [Gamazon et al. (2015), *Nat Genet*](https://www.nature.com/articles/ng.3367) and [Barbeira et al. (2018), *Nat Comm*](https://www.nature.com/articles/s41467-018-03621-1)
+- Aggregated Cauchy Association Test (ACAT): [Liu et al. (2019), *AJHG*](https://doi.org/10.1016/j.ajhg.2019.01.002) and [Liu and Xie (2018), *arXiv*](https://arxiv.org/abs/1808.09011)
+- Asymptotically exact Harmonic Mean P-value (HMP): [Wilson (2019), *PNAS*](https://doi.org/10.1073/pnas.1814092116)
+
+## Software References
+
+Libraries and resources used or adapted in GAMBIT:
+**PDF, CDF, and quantile functions**
+- [CDFLIB, Brown et al.](https://people.sc.fsu.edu/~jburkardt/cpp_src/cdflib/cdflib.html)
+- [eigenmvn, Benazera et al.](https://github.com/beniz/eigenmvn)
+- [libMvtnorm, Zhan et al.](https://github.com/zhanxw/libMvtnorm)
+- [CERN's ROOT system library](https://root.cern.ch/)
+**Hopscotch hashing**
+- [tsl library, Tessil et al.](https://github.com/Tessil/hopscotch-map)
+**Tabix and HTSLIB** 
+- [tabixpp, ekg et al.](https://github.com/ekg/tabixpp)
+- [htslib, samtools team](https://github.com/samtools/htslib)
+**Matrix libraries** 
+- [Eigen matrix library](http://eigen.tuxfamily.org)
 
 ## Feedback and bug reports
 

src/Main.cpp

@@ -41,7 +41,7 @@ int main (int argc, char *argv[]) {
 	string dfile = "";
 	string afile = "";
 	string sfile = "";
-	string ldfile = "/net/snowwhite/home/corbinq/panels/G1K_EUR_3V5/chr$.vcf.gz";
+	string ldfile = "G1K_EUR_3V5/chr$.vcf.gz";
 	string outfile = "";
 	string tfile = "";
 	string tssfile = "";