first commit

Makefile

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+VERSION=0.2
+
+CPPFLAGS= -Ofast -flto -pipe
+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
+
+objs = $(cppsrc:.cpp=.o) $(csrc:.c=.o) 
+
+bin/GaMBIT: $(objs) src/libMvtnorm/libMvtnorm.a
+	$(CXX) $(CPPFLAGS) -o $@ $^ $(LDFLAGS)
+
+src/libMvtnorm/libMvtnorm.a:
+	cd src/libMvtnorm && $(MAKE)
+
+.PHONY: clean
+
+clean: 
+	rm -f src/*.o src/*/*.o bin/*
+	cd src/libMvtnorm && $(MAKE) clean
+

README.md

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+# GAMBIT
+
+A C++ tool for Gene-based Analysis with oMniBus, Integrative Tests
+
+- Implements SKAT, burden, and ACAT gene-based test methods using variant- or region-based functional annotations
+- Calculates annotation-stratified gene-based tests (e.g., TWAS/PrediXcan tests using eSNPs, gene-based tests using only coding variants, and gene-based tests using enhancer-to-target-gene maps)
+- Calculates omnibus gene-based tests by aggregating across annotation classes
+- Inputs: GWAS association summary statistics file (chromosome, position, ref/alt allele, and z-score or beta-hat + se), annotation files, and LD reference panel
+
+#### Feedback and bug reports
+- Feel free to contact Corbin Quick (corbinq@gmail.com) with bug reports or feedback
+

copyrights/LICENSE.txt

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+/*
+ * Copyright (c) 2009 Regents of the University of Michigan
+ * 
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ * 
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * 
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+

defs.txt

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+Coding	Protein_Altering	Nonsynonymous,Start_Loss,Stop_Gain,Stop_Loss,CodonGain,CodonLoss,Frameshift
+Coding	Splice_Site	Essential_Splice_Site,Normal_Splice_Site
+UTR3	UTR3	Utr3
+UTR5	UTR5	Utr5
+Exon	Exon	Exon,Synonymous,Insertion,Deletion
+Promoter	Promoter	promoter
+Proximal	Proximal	Upstream,Downstream

format_gwas_summary_stats.sh

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+#!/bin/sh
+
+infile=$1
+prefix=$2
+
+echo "input format:"
+echo "     CHR POS REF ALT RSID N Z"
+echo ""
+echo "annotating $infile..."
+
+path_epacts=/net/snowwhite/home/corbinq/statgen/EPACTS
+
+anno_bin=$path_epacts/src/anno
+gfile=$path_epacts/data/hg19_refFlat.txt.gz
+cfile=$path_epacts/data/codon.txt
+pfile=$path_epacts/data/priority.txt
+rfile=$path_funcwas/data/human_g1k_v37.fasta
+
+$anno_bin -i $infile -o $prefix.tmp -g $gfile --inputFormat plain -c $cfile -p $pfile -r $rfile
+
+cut -f1-8 $prefix.tmp | bgzip -c > $prefix.az.gz
+
+echo "annotated gwas output written to $prefix.az.gz"
+
+rm -f $prefix.tmp*
+
+tabix -p vcf $prefix.az.gz

src/Eigen/Array

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+#ifndef EIGEN_ARRAY_MODULE_H
+#define EIGEN_ARRAY_MODULE_H
+
+// include Core first to handle Eigen2 support macros
+#include "Core"
+
+#ifndef EIGEN2_SUPPORT
+  #error The Eigen/Array header does no longer exist in Eigen3. All that functionality has moved to Eigen/Core.
+#endif
+
+#endif // EIGEN_ARRAY_MODULE_H

src/Eigen/CMakeLists.txt

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+include(RegexUtils)
+test_escape_string_as_regex()
+
+file(GLOB Eigen_directory_files "*")
+
+escape_string_as_regex(ESCAPED_CMAKE_CURRENT_SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}")
+
+foreach(f ${Eigen_directory_files})
+  if(NOT f MATCHES "\\.txt" AND NOT f MATCHES "${ESCAPED_CMAKE_CURRENT_SOURCE_DIR}/[.].+" AND NOT f MATCHES "${ESCAPED_CMAKE_CURRENT_SOURCE_DIR}/src")
+    list(APPEND Eigen_directory_files_to_install ${f})
+  endif()
+endforeach(f ${Eigen_directory_files})
+
+install(FILES
+  ${Eigen_directory_files_to_install}
+  DESTINATION ${INCLUDE_INSTALL_DIR}/Eigen COMPONENT Devel
+  )
+
+add_subdirectory(src)

src/Eigen/Cholesky

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+#ifndef EIGEN_CHOLESKY_MODULE_H
+#define EIGEN_CHOLESKY_MODULE_H
+
+#include "Core"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+/** \defgroup Cholesky_Module Cholesky module
+  *
+  *
+  *
+  * This module provides two variants of the Cholesky decomposition for selfadjoint (hermitian) matrices.
+  * Those decompositions are accessible via the following MatrixBase methods:
+  *  - MatrixBase::llt(),
+  *  - MatrixBase::ldlt()
+  *
+  * \code
+  * #include <Eigen/Cholesky>
+  * \endcode
+  */
+
+#include "src/misc/Solve.h"
+#include "src/Cholesky/LLT.h"
+#include "src/Cholesky/LDLT.h"
+#ifdef EIGEN_USE_LAPACKE
+#include "src/Cholesky/LLT_MKL.h"
+#endif
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN_CHOLESKY_MODULE_H
+/* vim: set filetype=cpp et sw=2 ts=2 ai: */

src/Eigen/CholmodSupport

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+#ifndef EIGEN_CHOLMODSUPPORT_MODULE_H
+#define EIGEN_CHOLMODSUPPORT_MODULE_H
+
+#include "SparseCore"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+extern "C" {
+  #include <cholmod.h>
+}
+
+/** \ingroup Support_modules
+  * \defgroup CholmodSupport_Module CholmodSupport module
+  *
+  * This module provides an interface to the Cholmod library which is part of the <a href="http://www.suitesparse.com">suitesparse</a> package.
+  * It provides the two following main factorization classes:
+  * - class CholmodSupernodalLLT: a supernodal LLT Cholesky factorization.
+  * - class CholmodDecomposiiton: a general L(D)LT Cholesky factorization with automatic or explicit runtime selection of the underlying factorization method (supernodal or simplicial).
+  *
+  * For the sake of completeness, this module also propose the two following classes:
+  * - class CholmodSimplicialLLT
+  * - class CholmodSimplicialLDLT
+  * Note that these classes does not bring any particular advantage compared to the built-in
+  * SimplicialLLT and SimplicialLDLT factorization classes.
+  *
+  * \code
+  * #include <Eigen/CholmodSupport>
+  * \endcode
+  *
+  * In order to use this module, the cholmod headers must be accessible from the include paths, and your binary must be linked to the cholmod library and its dependencies.
+  * The dependencies depend on how cholmod has been compiled.
+  * For a cmake based project, you can use our FindCholmod.cmake module to help you in this task.
+  *
+  */
+
+#include "src/misc/Solve.h"
+#include "src/misc/SparseSolve.h"
+
+#include "src/CholmodSupport/CholmodSupport.h"
+
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN_CHOLMODSUPPORT_MODULE_H
+