From f35afa2adfa8437d67f650546b197a1dd9e0a5f4 Mon Sep 17 00:00:00 2001 From: Ozonov Date: Tue, 3 Oct 2023 11:43:41 +0200 Subject: [PATCH] edit NAMESPACE, rename hpp --- DESCRIPTION | 10 +++------- NAMESPACE | 2 +- src/Makevars | 6 +++--- src/Makevars.in | 6 +++--- src/coocCntTable-class.cpp | 2 +- src/{coocCntTable-class.hpp => coocCntTable-class.h} | 0 src/fetch_data_from_bam.cpp | 2 +- src/{fetch_data_from_bam.hpp => fetch_data_from_bam.h} | 5 ++--- src/fragData-class.cpp | 2 +- src/{fragData-class.hpp => fragData-class.h} | 8 ++++---- src/functions_export_rcpp.cpp | 2 +- ...nctions_export_rcpp.hpp => functions_export_rcpp.h} | 6 +++--- src/protectStats-class.cpp | 2 +- src/{protectStats-class.hpp => protectStats-class.h} | 0 src/refSeqInfo-class.cpp | 2 +- src/{refSeqInfo-class.hpp => refSeqInfo-class.h} | 2 +- src/regionData-class.cpp | 2 +- src/{regionData-class.hpp => regionData-class.h} | 6 +++--- src/utils_globvars.cpp | 2 +- src/{utils_globvars.hpp => utils_globvars.h} | 0 20 files changed, 31 insertions(+), 36 deletions(-) rename src/{coocCntTable-class.hpp => coocCntTable-class.h} (100%) rename src/{fetch_data_from_bam.hpp => fetch_data_from_bam.h} (93%) rename src/{fragData-class.hpp => fragData-class.h} (96%) rename src/{functions_export_rcpp.hpp => functions_export_rcpp.h} (94%) rename src/{protectStats-class.hpp => protectStats-class.h} (100%) rename src/{refSeqInfo-class.hpp => refSeqInfo-class.h} (98%) rename src/{regionData-class.hpp => regionData-class.h} (95%) rename src/{utils_globvars.hpp => utils_globvars.h} (100%) diff --git a/DESCRIPTION b/DESCRIPTION index 62ea491..5770b44 100644 --- a/DESCRIPTION +++ b/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 = "evgeniy.ozonov@fmi.ch", 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), diff --git a/NAMESPACE b/NAMESPACE index 3dfee54..6de0244 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,3 +1,3 @@ useDynLib(fetchNOMe, .registration=TRUE) importFrom(Rcpp, evalCpp) -exportPattern("^[[:alpha:]]+") +export(get_data_matrix_from_bams) diff --git a/src/Makevars b/src/Makevars index 71a32c8..4358887 100644 --- a/src/Makevars +++ b/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()") $(RHTSLIB_LIBS) -fopenmp diff --git a/src/Makevars.in b/src/Makevars.in index f7f9e96..203a76f 100644 --- a/src/Makevars.in +++ b/src/Makevars.in @@ -9,8 +9,8 @@ RHTSLIB_CPPFLAGS=$(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@ diff --git a/src/coocCntTable-class.cpp b/src/coocCntTable-class.cpp index a32b2ef..6b2b16a 100644 --- a/src/coocCntTable-class.cpp +++ b/src/coocCntTable-class.cpp @@ -1,4 +1,4 @@ -#include "coocCntTable-class.hpp" +#include "coocCntTable-class.h" // constructors diff --git a/src/coocCntTable-class.hpp b/src/coocCntTable-class.h similarity index 100% rename from src/coocCntTable-class.hpp rename to src/coocCntTable-class.h diff --git a/src/fetch_data_from_bam.cpp b/src/fetch_data_from_bam.cpp index 7eefea5..796468f 100644 --- a/src/fetch_data_from_bam.cpp +++ b/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, diff --git a/src/fetch_data_from_bam.hpp b/src/fetch_data_from_bam.h similarity index 93% rename from src/fetch_data_from_bam.hpp rename to src/fetch_data_from_bam.h index ee464c5..c8e1f3a 100644 --- a/src/fetch_data_from_bam.hpp +++ b/src/fetch_data_from_bam.h @@ -12,9 +12,8 @@ #include #include #include -#include "refSeqInfo-class.hpp" -//#include "coocCntTable-class.hpp" -#include "regionData-class.hpp" +#include "refSeqInfo-class.h" +#include "regionData-class.h" #ifdef __cplusplus extern "C" { diff --git a/src/fragData-class.cpp b/src/fragData-class.cpp index 54687b5..6cbf2ea 100644 --- a/src/fragData-class.cpp +++ b/src/fragData-class.cpp @@ -1,4 +1,4 @@ -#include "fragData-class.hpp" +#include "fragData-class.h" fragData::fragData(){ diff --git a/src/fragData-class.hpp b/src/fragData-class.h similarity index 96% rename from src/fragData-class.hpp rename to src/fragData-class.h index 5805fc4..eb7e839 100644 --- a/src/fragData-class.hpp +++ b/src/fragData-class.h @@ -10,10 +10,10 @@ #include #include #include -#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; diff --git a/src/functions_export_rcpp.cpp b/src/functions_export_rcpp.cpp index 2ed99a4..8f6c5c5 100644 --- a/src/functions_export_rcpp.cpp +++ b/src/functions_export_rcpp.cpp @@ -1,4 +1,4 @@ -#include "functions_export_rcpp.hpp" +#include "functions_export_rcpp.h" diff --git a/src/functions_export_rcpp.hpp b/src/functions_export_rcpp.h similarity index 94% rename from src/functions_export_rcpp.hpp rename to src/functions_export_rcpp.h index 3301b65..33de338 100644 --- a/src/functions_export_rcpp.hpp +++ b/src/functions_export_rcpp.h @@ -13,9 +13,9 @@ #include #include #include -#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; diff --git a/src/protectStats-class.cpp b/src/protectStats-class.cpp index 7b82bc2..704de0f 100644 --- a/src/protectStats-class.cpp +++ b/src/protectStats-class.cpp @@ -1,4 +1,4 @@ -#include "protectStats-class.hpp" +#include "protectStats-class.h" // constructors/destructors protectStatsTable::protectStatsTable(){}; diff --git a/src/protectStats-class.hpp b/src/protectStats-class.h similarity index 100% rename from src/protectStats-class.hpp rename to src/protectStats-class.h diff --git a/src/refSeqInfo-class.cpp b/src/refSeqInfo-class.cpp index 1b782a7..661dd3b 100644 --- a/src/refSeqInfo-class.cpp +++ b/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 diff --git a/src/refSeqInfo-class.hpp b/src/refSeqInfo-class.h similarity index 98% rename from src/refSeqInfo-class.hpp rename to src/refSeqInfo-class.h index de5c389..7d2c803 100644 --- a/src/refSeqInfo-class.hpp +++ b/src/refSeqInfo-class.h @@ -6,7 +6,7 @@ #include #include #include -#include "utils_globvars.hpp" +#include "utils_globvars.h" using namespace std; diff --git a/src/regionData-class.cpp b/src/regionData-class.cpp index 2b61678..a282bae 100644 --- a/src/regionData-class.cpp +++ b/src/regionData-class.cpp @@ -1,4 +1,4 @@ -#include "regionData-class.hpp" +#include "regionData-class.h" regionData::regionData(){}; regionData::regionData(const string& regchr, diff --git a/src/regionData-class.hpp b/src/regionData-class.h similarity index 95% rename from src/regionData-class.hpp rename to src/regionData-class.h index e64f7ef..4d1e944 100644 --- a/src/regionData-class.hpp +++ b/src/regionData-class.h @@ -7,9 +7,9 @@ #include #include -#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; diff --git a/src/utils_globvars.cpp b/src/utils_globvars.cpp index 9c8ea5b..afa0fc8 100644 --- a/src/utils_globvars.cpp +++ b/src/utils_globvars.cpp @@ -1,4 +1,4 @@ -#include "utils_globvars.hpp" +#include "utils_globvars.h" diff --git a/src/utils_globvars.hpp b/src/utils_globvars.h similarity index 100% rename from src/utils_globvars.hpp rename to src/utils_globvars.h