Merge branch 'master' of github.com:DEploid-dev/DEploid-Utilities

.Rbuildignore

@@ -4,13 +4,33 @@
 LICENSE
 .github
 \*\.o
-src/vcf/vcfReader.o
-src/vcf/gzstream/gzstream.o
-src/vcf/txtReader.o
-src/vcf/variantIndex.o
-src/vcf/vcfReaderDebug.o
-DEploid.utils/libs/DEploid.utils.so
 \*\.png
 \*\.pdf
 DEploid-vcf-lib
 codecov.yml
+
+
+# submodule
+vcf/src/gzstream/version
+src/vcf/.git
+src/vcf/.ci/
+src/vcf/.circleci/
+src/vcf/.github/
+src/vcf/.gitignore
+src/vcf/Brewfile
+src/vcf/COPYING
+src/vcf/CPPLINT.cfg
+src/vcf/Makefile.am
+src/vcf/README.md
+src/vcf/bootstrap
+src/vcf/configure.ac
+src/vcf/coverage/
+src/vcf/data/
+src/vcf/main.cpp
+src/vcf/tests/
+src/vcf/version
+src/vcf/src/gzstream/gzstream.o
+src/vcf/src/txtReader.o
+src/vcf/src/variantIndex.o
+src/vcf/src/vcfReader.o
+src/vcf/src/vcfReaderDebug.o

.github/workflows/R-CMD-check.yaml

@@ -32,6 +32,8 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
+        with:
+          submodules: recursive
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/pr-commands.yaml

@@ -19,6 +19,8 @@ jobs:
       contents: write
     steps:
       - uses: actions/checkout@v4
+        with:
+          submodules: recursive
 
       - uses: r-lib/actions/pr-fetch@v2
         with:

.github/workflows/test-coverage.yaml

@@ -18,6 +18,8 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
+        with:
+          submodules: recursive
 
       - uses: r-lib/actions/setup-r@v2
         with:

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "DEploid-vcf-lib"]
-	path = DEploid-vcf-lib
+	path = src/vcf
 	url = https://github.com/DEploid-dev/DEploid-vcf-lib

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: DEploid.utils
 Title: 'DEploid' Data Analysis and Results Interpretation  
-Version: 0.0.1
+Version: 0.0.2
 Authors@R: c(
     person("Joe", "Zhu", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-7566-2787")),

src/Makevars.win

@@ -1,11 +1,11 @@
 OBJECTS.vcfr = rvcf.o \
   RcppExports.o \
-  vcf/txtReader.o \
-  vcf/variantIndex.o \
-  vcf/vcfReader.o \
-  vcf/gzstream/gzstream.o \
-  vcf/vcfReaderDebug.o
+  vcf/src/txtReader.o \
+  vcf/src/variantIndex.o \
+  vcf/src/vcfReader.o \
+  vcf/src/gzstream/gzstream.o \
+  vcf/src/vcfReaderDebug.o
 
 OBJECTS = $(OBJECTS.vcfr)
-PKG_CXXFLAGS = -I/usr/share/R/include/ -Ivcf/ -Ivcf/gzstream/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS
+PKG_CXXFLAGS = -I/usr/share/R/include/ -Ivcf/src/ -Ivcf/src/gzstream/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS
 PKG_LIBS = -lz

src/rvcf.cpp

@@ -1,5 +1,5 @@
 #include <Rcpp.h>
-#include "vcf/vcfReader.hpp"
+#include "vcf/src/vcfReader.hpp"
 
 using namespace Rcpp;