update readme

R/RcppExports.R

@@ -60,7 +60,14 @@
 #' @field setInfoInt Modify the given tag of INT type in the INFO of current variant
 #' @field setInfoFloat Modify the given tag of FLOAT type in the INFO of current variant
 #' @field setInfoStr Modify the given tag of STRING type in the INFO of current variant
+#' @field setGenotypes Modify the genotypes of current variant
+#' @field setFormatInt Modify the given tag of INT type in the FORMAT of current variant
+#' @field setFormatFloat Modify the given tag of FLOAT type in the FORMAT of current variant
+#' @field setFormatStr Modify the given tag of STRING type in the FORMAT of current variant
 #' @field rmInfoTag Remove the given tag from the INFO of current variant
+#' @field setVariant Modify current variant by adding a vcf line
+#' @field addINFO Add a INFO in the header of the vcf
+#' @field addFORMAT Add a FORMAT in the header of the vcf
 NULL
 
 #' @name vcfwriter

README.Rmd

@@ -13,26 +13,35 @@ knitr::opts_chunk$set(
 )
 ```
 
-# vcfppR: rapid manipulation of the VCF/BCF files
+# vcfppR: rapid manipulation of the VCF/BCF file
 
 <!-- badges: start -->
 ![R-CMD-check](https://github.com/Zilong-Li/vcfppR/actions/workflows/check-release.yaml/badge.svg)
 <a href="https://github.com/Zilong-Li/random/blob/main/vcfppR.png"><img src="https://raw.githubusercontent.com/Zilong-Li/random/main/vcfppR.png" height="200" align="right" /></a> 
 <!-- badges: end -->
 
-The vcfppR package implements various useful functions for manipulating the VCF/BCF files in R using the C++ API of [vcfpp.h](https://github.com/Zilong-Li/vcfpp).
+The vcfppR package implements various useful functions for manipulating the VCF/BCF file in R using the C++ API of [vcfpp.h](https://github.com/Zilong-Li/vcfpp).
 
 ## Installation
 
 You can install the development version of vcfppR with the system dependencies of `libcurl`.
 
 ``` r
+## install.package("vcfppR")
 devtools::install_github("Zilong-Li/vcfppR")
 ```
 
-## Examples
+## API
 
-In the examples, we use the URL link as filename, which can be directly fed to vcfppR, and the performance will depend on your connection to the servers.
+There are two classes i.e. ***vcfreader*** and ***vcfwriter*** offering the full R-bindings of vcfpp.h. Check out the examples in the [tests](tests/testthat) folder or refer to the manual.
+
+```r
+?vcfppR::vcfreader
+```
+
+In addtion to two classes for R-bindings of vcfpp.h, there are some useful functions in the package, e.g. ***vcftable***, ***vcfsummary*** and ***vcfpopgen***. In the following examples, we use the URL link as filename, which can be directly fed to vcfppR, and the performance will depend on your connection to the servers.
+
+## Read VCF as tabular data in R
 
 This example shows how to read only SNP variants with FILTER="PASS" and GT format in the VCF/BCF into R tables:
 ```r

README.md

@@ -1,7 +1,7 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# vcfppR: rapid manipulation of the VCF/BCF files
+# vcfppR: rapid manipulation of the VCF/BCF file
 
 <!-- badges: start -->
 
@@ -10,7 +10,7 @@
 <!-- badges: end -->
 
 The vcfppR package implements various useful functions for manipulating
-the VCF/BCF files in R using the C++ API of
+the VCF/BCF file in R using the C++ API of
 [vcfpp.h](https://github.com/Zilong-Li/vcfpp).
 
 ## Installation
@@ -19,14 +19,27 @@ You can install the development version of vcfppR with the system
 dependencies of `libcurl`.
 
 ``` r
+## install.package("vcfppR")
 devtools::install_github("Zilong-Li/vcfppR")
 ```
 
-## Examples
+## API
 
-In the examples, we use the URL link as filename, which can be directly
-fed to vcfppR, and the performance will depend on your connection to the
-servers.
+There are two classes i.e. ***vcfreader*** and ***vcfwriter*** offering
+the full R-bindings of vcfpp.h. Check out the examples in the
+[tests](tests/testthat) folder or refer to the manual.
+
+``` r
+?vcfppR::vcfreader
+```
+
+In addtion to two classes for R-bindings of vcfpp.h, there are some
+useful functions in the package, e.g. ***vcftable***, ***vcfsummary***
+and ***vcfpopgen***. In the following examples, we use the URL link as
+filename, which can be directly fed to vcfppR, and the performance will
+depend on your connection to the servers.
+
+## Read VCF as tabular data in R
 
 This example shows how to read only SNP variants with FILTER=“PASS” and
 GT format in the VCF/BCF into R tables:

src/vcf-reader.cpp

@@ -62,7 +62,14 @@ using namespace std;
 //' @field setInfoInt Modify the given tag of INT type in the INFO of current variant
 //' @field setInfoFloat Modify the given tag of FLOAT type in the INFO of current variant
 //' @field setInfoStr Modify the given tag of STRING type in the INFO of current variant
+//' @field setGenotypes Modify the genotypes of current variant
+//' @field setFormatInt Modify the given tag of INT type in the FORMAT of current variant
+//' @field setFormatFloat Modify the given tag of FLOAT type in the FORMAT of current variant
+//' @field setFormatStr Modify the given tag of STRING type in the FORMAT of current variant
 //' @field rmInfoTag Remove the given tag from the INFO of current variant
+//' @field setVariant Modify current variant by adding a vcf line
+//' @field addINFO Add a INFO in the header of the vcf
+//' @field addFORMAT Add a FORMAT in the header of the vcf
 class vcfreader {
    public:
     vcfreader(const std::string& vcffile) {
@@ -204,9 +211,25 @@ class vcfreader {
     inline void setRefAlt(const std::string& s) { var.setRefAlt(s.c_str()); }
     inline void setInfoInt(std::string tag, int v) { var.setINFO(tag, v); }
     inline void setInfoFloat(std::string tag, double v) { var.setINFO(tag, v); }
-    inline void setInfoStr(std::string tag, const std::string& v) { var.setINFO(tag, v); }
+    inline void setInfoStr(std::string tag, const std::string& s) { var.setINFO(tag, s); }
+    inline void setGenotypes(std::string tag, const vector<int>& v) { var.setGenotypes(v); }
+    inline void setFormatInt(std::string tag, const vector<int>& v) { var.setFORMAT(tag, v); }
+    inline void setFormatFloat(std::string tag, const vector<double>& v) {
+        vector<float> f(v.begin(), v.end());
+        var.setFORMAT(tag, f);
+    }
+    inline void setFormatStr(std::string tag, const std::string& s) { var.setINFO(tag, s); }
     inline void rmInfoTag(std::string s) { var.removeINFO(s); }
-
+    inline void setVariant(const std::string& s) { var.addLineFromString(s); }
+    inline void addINFO(const std::string& id, const std::string& number, const std::string& type,
+                        const std::string& desc) {
+        bw.header.addINFO(id, number, type, desc);
+    }
+    inline void addFORMAT(const std::string& id, const std::string& number, const std::string& type,
+                          const std::string& desc) {
+        bw.header.addFORMAT(id, number, type, desc);
+    }
+
    private:
     vcfpp::BcfReader br;
     vcfpp::BcfRecord var;
@@ -270,5 +293,12 @@ RCPP_MODULE(vcfreader) {
         .method("setInfoInt", &vcfreader::setInfoInt)
         .method("setInfoFloat", &vcfreader::setInfoFloat)
         .method("setInfoStr", &vcfreader::setInfoStr)
+        .method("setGenotypes", &vcfreader::setGenotypes)
+        .method("setFormatInt", &vcfreader::setFormatInt)
+        .method("setFormatFloat", &vcfreader::setFormatFloat)
+        .method("setFormatStr", &vcfreader::setFormatStr)
+        .method("setVariant", &vcfreader::setVariant)
+        .method("addINFO", &vcfreader::addINFO)
+        .method("addFORMAT", &vcfreader::addFORMAT)
         .method("rmInfoTag", &vcfreader::rmInfoTag);
 }