edit NAMESPACE, rename hpp

DESCRIPTION

@@ -4,20 +4,16 @@ Title: Package for fast and convenient retrieval of NOMe-seq data from BAM files
 Version: 0.1
 Date: 2023-10-02
 Authors@R: person(given = "Evgeniy A.", family="Ozonov", email = "[email protected]", role = c("aut", "cre"))
-Description: This R package is tailored for fast and convenient retrieval of NOMe-seq data from BAM files aligned with QuasR, Bismark and biscuit. 
+Description: This R package is tailored for fast and convenient retrieval of NOMe-seq data from BAM files aligned with QuasR, Bismark and BISCUIT. 
 License: MIT + file LICENSE
 Imports: 
-    checkmate,
     parallel,
     Rcpp (>= 0.12.17),
     Rsamtools (>= 2.13.1),
-    stats,
-    stringr,
     tibble,
-    truncdist,
     GenomicRanges,
-    GenomeInfoDb,
-    methods
+    IRanges,
+    GenomeInfoDb
 LinkingTo: 
     Rcpp (>= 0.12.0),
     RcppEigen (>= 0.3.3.3.0),

NAMESPACE

@@ -1,3 +1,3 @@
 useDynLib(fetchNOMe, .registration=TRUE)
 importFrom(Rcpp, evalCpp)
-exportPattern("^[[:alpha:]]+")
+export(get_data_matrix_from_bams)

src/Makevars

@@ -9,8 +9,8 @@ RHTSLIB_CPPFLAGS=$(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e \
     'Rhtslib::pkgconfig("PKG_CPPFLAGS")')
 
 
-PKG_CPPFLAGS = -I"../inst/include" -I"$(STANHEADERS_SRC)" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error $(RHTSLIB_CPPFLAGS)
-PKG_CXXFLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::CxxFlags()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::CxxFlags()") -fopenmp
-PKG_LIBS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::RcppParallelLibs()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::LdFlags()") $(RHTSLIB_LIBS) -fopenmp
+PKG_CPPFLAGS = -I"../inst/include" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error $(RHTSLIB_CPPFLAGS)
+PKG_CXXFLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::CxxFlags()") -fopenmp
+PKG_LIBS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::RcppParallelLibs()") $(RHTSLIB_LIBS) -fopenmp
 
 

src/Makevars.in

@@ -9,8 +9,8 @@ RHTSLIB_CPPFLAGS=$(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e \
     'Rhtslib::pkgconfig("PKG_CPPFLAGS")')
 
 
-PKG_CPPFLAGS = -I"../inst/include" -I"$(STANHEADERS_SRC)" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error $(RHTSLIB_CPPFLAGS)
-PKG_CXXFLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::CxxFlags()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::CxxFlags()") @OPENMP_CXXFLAGS@
-PKG_LIBS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::RcppParallelLibs()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::LdFlags()") $(RHTSLIB_LIBS) @OPENMP_CXXFLAGS@
+PKG_CPPFLAGS = -I"../inst/include" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error $(RHTSLIB_CPPFLAGS)
+PKG_CXXFLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::CxxFlags()") @OPENMP_CXXFLAGS@
+PKG_LIBS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::RcppParallelLibs()") $(RHTSLIB_LIBS) @OPENMP_CXXFLAGS@
 
 

src/coocCntTable-class.cpp

@@ -1,4 +1,4 @@
-#include "coocCntTable-class.hpp"
+#include "coocCntTable-class.h"
 
 
 // constructors

src/fetch_data_from_bam.cpp

@@ -1,4 +1,4 @@
-#include "fetch_data_from_bam.hpp"
+#include "fetch_data_from_bam.h"
 
 // fetch data from bam file
 bool fetch_data_from_bam(const string& bamfile,

src/fetch_data_from_bam.hpp → src/fetch_data_from_bam.h

@@ -12,9 +12,8 @@
 #include <algorithm>
 #include <cstdint>
 #include <stdbool.h>
-#include "refSeqInfo-class.hpp"
-//#include "coocCntTable-class.hpp"
-#include "regionData-class.hpp"
+#include "refSeqInfo-class.h"
+#include "regionData-class.h"
 
 #ifdef __cplusplus
 extern "C" {

src/fragData-class.cpp

@@ -1,4 +1,4 @@
-#include "fragData-class.hpp"
+#include "fragData-class.h"
 
 
 fragData::fragData(){

src/fragData-class.hpp → src/fragData-class.h

@@ -10,10 +10,10 @@
 #include <cstdint>
 #include <stdbool.h>
 #include <stdlib.h>
-#include "refSeqInfo-class.hpp"
-#include "utils_globvars.hpp"
-#include "protectStats-class.hpp"
-#include "coocCntTable-class.hpp""
+#include "refSeqInfo-class.h"
+#include "utils_globvars.h"
+#include "protectStats-class.h"
+#include "coocCntTable-class.h""
 
 
 using namespace std;

src/functions_export_rcpp.cpp

@@ -1,4 +1,4 @@
-#include "functions_export_rcpp.hpp"
+#include "functions_export_rcpp.h"
 
 
 

src/functions_export_rcpp.hpp → src/functions_export_rcpp.h

@@ -13,9 +13,9 @@
 #include <algorithm>
 #include <cstdint>
 #include <stdbool.h>
-#include "refSeqInfo-class.hpp"
-#include "regionData-class.hpp"
-#include "fetch_data_from_bam.hpp"
+#include "refSeqInfo-class.h"
+#include "regionData-class.h"
+#include "fetch_data_from_bam.h"
 
 
 using namespace std;

src/protectStats-class.cpp

@@ -1,4 +1,4 @@
-#include "protectStats-class.hpp"
+#include "protectStats-class.h"
 
 // constructors/destructors
 protectStatsTable::protectStatsTable(){};

src/refSeqInfo-class.cpp

@@ -1,4 +1,4 @@
-#include "refSeqInfo-class.hpp"
+#include "refSeqInfo-class.h"
 
 // constructors/destructors
 refSeqInfo::refSeqInfo(const string& seqstring, //sequence of a region

src/refSeqInfo-class.hpp → src/refSeqInfo-class.h

@@ -6,7 +6,7 @@
 #include <map>
 #include <string>
 #include <algorithm>
-#include "utils_globvars.hpp"
+#include "utils_globvars.h"
 
 using namespace std;
 

src/regionData-class.cpp

@@ -1,4 +1,4 @@
-#include "regionData-class.hpp"
+#include "regionData-class.h"
 
 regionData::regionData(){};
 regionData::regionData(const string& regchr,

src/regionData-class.hpp → src/regionData-class.h

@@ -7,9 +7,9 @@
 #include <string>
 #include <algorithm>
 
-#include "fragData-class.hpp"
-#include "utils_globvars.hpp"
-#include "protectStats-class.hpp"
+#include "fragData-class.h"
+#include "utils_globvars.h"
+#include "protectStats-class.h"
 
 using namespace std;
 

src/utils_globvars.cpp

@@ -1,4 +1,4 @@
-#include "utils_globvars.hpp"
+#include "utils_globvars.h"