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.

COPYRIGHT

@@ -1 +1 @@
-Copyright 2016, 2017 Lingfei Wang
+Copyright 2016-2018 Lingfei Wang

Makefile

@@ -15,11 +15,10 @@ URL_BIN_REL="$(URL_BIN)/releases"
 URL_R_REL="$(URL_R)/releases"
 VERSION1=1
 VERSION2=0
-VERSION3=5
+VERSION3=6
 LICENSE=AGPL-3
 LICENSE_FULL="GNU Affero General Public License, Version 3"
 LICENSE_URL="https://www.gnu.org/licenses/agpl-3.0"
-#UNAME=$$(uname)
 ifdef INCLUDE_MAKEFILE_BEFORE
 #Input package info here
 include $(INCLUDE_MAKEFILE_BEFORE)
@@ -39,7 +38,8 @@ DIR_SRC=.
 endif
 DIR_INSTALL_PREFIX=$(PREFIX)
 DIR_INSTALL_LIB=$(DIR_INSTALL_PREFIX)/lib
-DIR_INSTALL_INC=$(DIR_INSTALL_PREFIX)/include/$(LIB_NAME)
+DIR_INSTALL_INC0=$(DIR_INSTALL_PREFIX)/include
+DIR_INSTALL_INC=$(DIR_INSTALL_INC0)/$(LIB_NAME)
 
 CC=gcc
 CFLAGSI=$(addprefix -I ,. $(R_INCLUDE_DIR) $(PREFIX)/include /usr/local/include)
@@ -66,10 +66,24 @@ INC_INSTALL_FILES=$(LIB_H)
 INC_INSTALL_DIRS=$(dir $(LIB_H))
 LIB_UNINSTALL=$(addprefix $(DIR_INSTALL_LIB)/,$(notdir $(LIB_DPRODUCT)))
 INC_UNINSTALL=$(DIR_INSTALL_INC)
+PKGCONFIG=$(LIB_NAME).pc
+PKGCONFIG_UNINSTALL=$(DIR_INSTALL_LIB)/pkgconfig/$(LIB_NAME).pc
 
 .PHONY: all clean distclean install-lib install-inc install uninstall
 
-all: $(LIB_DPRODUCT)
+all: $(LIB_DPRODUCT) $(PKGCONFIG)
+
+$(PKGCONFIG):
+	@echo "prefix=$(DIR_INSTALL_PREFIX)" > $@
+	@echo "exec_prefix=$(DIR_INSTALL_PREFIX)" >> $@
+	@echo "libdir=$(DIR_INSTALL_LIB)" >> $@
+	@echo "includedir=$(DIR_INSTALL_INC0)" >> $@
+	@echo >> $@
+	@echo "Name: $(LIB_NAME)" >> $@
+	@echo "Description: Fast Inference of Networks from Directed Regulations" >> $@
+	@echo "Version: $(VERSION1).$(VERSION2).$(VERSION3)" >> $@
+	@echo "Libs: -L$(DIR_INSTALL_LIB) -l$(LIB_NAME) -lgsl" >> $@
+	@echo "Cflags: -I$(DIR_INSTALL_INC0)" >> $@
 
 $(LIB_CONFIG):
 	@echo "#ifndef _HEADER_LIB_CONFIG_AUTO_H_" > $@
@@ -100,23 +114,14 @@ clean:
 	$(RM) $(LIB_PRODUCT)
 
 distclean: clean
-	$(RM) $(LIB_DPRODUCT)
-	$(RM) $(LIB_CONFIG)
-	$(RM) Makefile.flags $(TMP_FILE)
+	$(RM) $(LIB_DPRODUCT) $(PKGCONFIG) $(LIB_CONFIG) Makefile.flags $(TMP_FILE)
 
 install-lib: SHELL:=/bin/bash
 install-lib: all
 	umask 0022 && mkdir -p $(DIR_INSTALL_LIB) && \
 	cp $(LIB_DPRODUCT) $(DIR_INSTALL_LIB)/ && \
 	chmod 0755 $(DIR_INSTALL_LIB)/$(notdir $(LIB_DPRODUCT)) && \
-	if [ "$$(uname)" == "Linux" ]; then \
-		ldconfig $(DIR_INSTALL_LIB) || true; \
-	fi; \
-	tcyg=$$(uname | grep -io "cygwin"); \
-	if [ -n "$$tcyg" ]; then \
-		ln -s $(DIR_INSTALL_LIB)/$(notdir $(LIB_DPRODUCT)) $(basename $(DIR_INSTALL_LIB)/$(notdir $(LIB_DPRODUCT))).dll; \
-	fi
-
+	ldconfig $(DIR_INSTALL_LIB) || true
 
 install-inc: SHELL:=/bin/bash
 install-inc: $(LIB_CONFIG)
@@ -130,10 +135,15 @@ install-inc: $(LIB_CONFIG)
 		chmod 0644 $(DIR_INSTALL_INC)/$$fname || exit 1; \
 	done
 
-install: install-lib install-inc
+install-pkgconfig: $(PKGCONFIG)
+	umask 0022 && mkdir -p $(DIR_INSTALL_LIB)/pkgconfig && \
+	cp $< $(DIR_INSTALL_LIB)/pkgconfig/
+	chmod 0644 $(DIR_INSTALL_LIB)/pkgconfig/$(notdir $<)
+
+install: install-lib install-inc install-pkgconfig
 
 uninstall:
-	$(RM) -R $(LIB_UNINSTALL) $(INC_UNINSTALL)
+	$(RM) -R $(LIB_UNINSTALL) $(INC_UNINSTALL) $(PKGCONFIG_UNINSTALL)
 
 TMP_FILE=.tmp
 Makefile.flags:

UPDATES

@@ -1,8 +1,15 @@
+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:
-	Updated Makefiles to account for different make environments.
+	Updated Makefiles to account for different make environments (reported by sritchie73@github).
 1.0.1:
 	Bug correction:
-		Updated LDFLAGS for R interface.
+		Updated LDFLAGS for R interface (reported by audreyqyfu@github).
 1.0.0:
 	New functions:
 		Included P-value computation for 4 tests in pijs_gassist_pv and correlation test in pij_rank_pv.

base/config.h

@@ -1,4 +1,4 @@
-/* Copyright 2016, 2017 Lingfei Wang
+/* Copyright 2016-2018 Lingfei Wang
  * 
  * This file is part of Findr.
  * 

base/const.h

@@ -1,4 +1,4 @@
-/* Copyright 2016, 2017 Lingfei Wang
+/* Copyright 2016-2018 Lingfei Wang
  * 
  * This file is part of Findr.
  * 

base/data_process.c

@@ -1,4 +1,4 @@
-/* Copyright 2016, 2017 Lingfei Wang
+/* Copyright 2016-2018 Lingfei Wang
  * 
  * This file is part of Findr.
  * 
@@ -18,6 +18,7 @@
 #include "config.h"
 #include <stdlib.h>
 #include <stdio.h>
+#include <stdint.h>
 #include <math.h>
 #include <tgmath.h>
 #include "types.h"
@@ -435,7 +436,72 @@ void MATRIXFF(minmax_nodiag)(const MATRIXF* d,FTYPE* restrict dmin,FTYPE* restri
 	}
 }
 
+/* Quick hash of VECTORF using bitwise operation
+ * Return: hash of VECTORF as FTYPE
+ */
+static inline FTYPE VECTORFF(hash)(const VECTORF* v)
+{
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wstrict-aliasing"
+#define	TFUTYPE CONCATENATE3(uint,FTYPEBITS,_t)
+	TFUTYPE	h;
+	size_t	i;
+
+	h=*(const TFUTYPE*)VECTORFF(const_ptr)(v,0);
+	for(i=1;i<v->size;i++)
+	{
+		h=(h<<1)|(h>>(FTYPEBITS-1));
+		h^=*(const TFUTYPE*)VECTORFF(const_ptr)(v,i);
+	}
+	return *(FTYPE*)(&h);
+}
+
+int MATRIXFF(cmprow)(const MATRIXF* m1,const MATRIXF* m2,VECTORF* buff1,VECTORF* buff2,char nodiag,char warn)
+{
+	size_t	i,j;
+	size_t	ng,nt;
+	union	u
+	{
+		FTYPE	f;
+		TFUTYPE	u;
+	} t;
+	FTYPE	fmin,fmax;
+	int	test;
 
+	ng=m1->size1;
+	nt=m2->size1;
+	assert((m2->size2==m1->size2)&&(buff->size1==ng)&&(buff1->size==ng)&&(buff2->size==m1->size2));
+
+	for(i=0;i<ng;i++)
+	{
+		VECTORFF(const_view) vv=MATRIXFF(const_row)(m1,i);
+		VECTORFF(set)(buff1,i,VECTORFF(hash)(&vv.vector));
+	}
+
+	for(i=0;i<nt;i++)
+	{
+		VECTORFF(const_view) vv=MATRIXFF(const_row)(m2,i);
+		t.f=VECTORFF(hash)(&vv.vector);
+		for(j=0;j<ng;j++)
+		{
+			test=nodiag&&(i==j);
+			if(test^(t.u!=*((const TFUTYPE*)VECTORFF(const_ptr)(buff1,j))))
+				continue;
+			VECTORFF(memcpy)(buff2,&vv.vector);
+			VECTORFF(const_view) vv2=MATRIXFF(const_row)(m1,j);
+			VECTORFF(sub)(buff2,&vv2.vector);
+			VECTORFF(minmax)(buff2,&fmin,&fmax);
+			if(test^((fmin!=0)||(fmax!=0)))
+				continue;
+			if(warn)
+				LOG(5,"Detected identical rows in dt and dt2 (at the same or different row numbers), or different rows at the same row number when nodiag is true. Make sure your input data and the nodiag flag are correct.")
+			return 1;
+		}
+	}
+	return 0;
+#undef TFUTYPE
+#pragma GCC diagnostic pop
+}
 
 
 

base/data_process.h

@@ -1,4 +1,4 @@
-/* Copyright 2016, 2017 Lingfei Wang
+/* Copyright 2016-2018 Lingfei Wang
  * 
  * This file is part of Findr.
  * 
@@ -193,6 +193,7 @@ static inline void MATRIXDF(set_nan)(MATRIXD* m,double val);
 
 // Sets all old value to new value
 static inline void MATRIXFF(set_value)(MATRIXF* m,FTYPE vold,FTYPE vnew);
+static inline void VECTORFF(set_value)(VECTORF* v,FTYPE vold,FTYPE vnew);
 
 /* Locates the first not number in a vector/matrix, and return its location.
  * If not found, return -1.
@@ -351,8 +352,19 @@ static inline void VECTORFF(fluc)(VECTORF* v,FTYPE fluc);
 
 void MATRIXFF(minmax_nodiag)(const MATRIXF* d,FTYPE* restrict dmin,FTYPE* restrict dmax,long nodiagshift);
 
-
-
+/* Look for any (non)identical rows of two matrices efficiently.
+ * m1:		(ng,ns) Matrix 1
+ * m2:		(nt,ns) Matrix 2
+ * buff1:	(ng) Buffer vector 1
+ * buff2:	(ns) Buffer vector 2
+ * nodiag:	Whether to the same rows should be the same in both matrices
+ * warn:	Whether to show warning in log before returning 1
+ * Return:	1 if any of the following 3 conditions are satisfied, and 0 otherwise.
+ * 	1. row i in m1 = row j in m2 and i!=j
+ *	2. row i in m1 = row i in m2 and !nodiag
+ * 	3. row i in m1 != row i in m2 and nodiag
+ */
+int MATRIXFF(cmprow)(const MATRIXF* m1,const MATRIXF* m2,VECTORF* buff1,VECTORF* buff2,char nodiag,char warn);
 
 
 
@@ -655,7 +667,6 @@ static inline void MATRIXDF(set_nan)(MATRIXD* m,double val)
 	MATRIXDF(set_cond)(m,gsl_isnan,val);
 }
 
-
 static inline void MATRIXFF(set_value)(MATRIXF* m,FTYPE vold,FTYPE vnew)
 {
 	size_t	i,j;
@@ -665,7 +676,13 @@ static inline void MATRIXFF(set_value)(MATRIXF* m,FTYPE vold,FTYPE vnew)
 				MATRIXFF(set)(m,i,j,vnew);
 }
 
-
+static inline void VECTORFF(set_value)(VECTORF* v,FTYPE vold,FTYPE vnew)
+{
+	size_t	i;
+	for(i=0;i<v->size;i++)
+		if(VECTORFF(get)(v,i)==vold)
+			VECTORFF(set)(v,i,vnew);
+}
 
 static inline void MATRIXFF(cov1)(const MATRIXF* m,MATRIXF* cov)
 {

base/data_struct.h

@@ -1,4 +1,4 @@
-/* Copyright 2016, 2017 Lingfei Wang
+/* Copyright 2016-2018 Lingfei Wang
  * 
  * This file is part of Findr.
  * 

base/data_struct_heap.c

@@ -1,4 +1,4 @@
-/* Copyright 2016, 2017 Lingfei Wang
+/* Copyright 2016-2018 Lingfei Wang
  * 
  * This file is part of Findr.
  * 

base/data_struct_heap.h

@@ -1,4 +1,4 @@
-/* Copyright 2016, 2017 Lingfei Wang
+/* Copyright 2016-2018 Lingfei Wang
  * 
  * This file is part of Findr.
  * 

base/data_struct_ll.c

@@ -1,4 +1,4 @@
-/* Copyright 2016, 2017 Lingfei Wang
+/* Copyright 2016-2018 Lingfei Wang
  * 
  * This file is part of Findr.
  * 

base/data_struct_ll.h

@@ -1,4 +1,4 @@
-/* Copyright 2016, 2017 Lingfei Wang
+/* Copyright 2016-2018 Lingfei Wang
  * 
  * This file is part of Findr.
  *