add vcfwriter

NAMESPACE

@@ -5,5 +5,6 @@ export(vcfpopgen)
 export(vcfreader)
 export(vcfsummary)
 export(vcftable)
+export(vcfwriter)
 importFrom(Rcpp,loadModule)
 useDynLib(vcfppR, .registration = TRUE)

R/RcppExports.R

@@ -2,7 +2,7 @@
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
 #' @name vcfreader
-#' @title API for reading read the VCF/BCF.
+#' @title API for reading the VCF/BCF.
 #' @description Type the name of the class to see its methods
 #' @field new Constructor given a vcf file \itemize{
 #' \item Parameter: vcffile - The path of a vcf file
@@ -50,6 +50,15 @@
 #' @field hasOVERLAP Test if current variant has a OVERLAP or not
 NULL
 
+#' @name vcfwriter
+#' @title API for writing the VCF/BCF.
+#' @description Type the name of the class to see its methods
+#' @field new Constructor given a vcf file \itemize{
+#' \item Parameter: vcffile - The path of a vcf file. don't start with "~"
+#' \item Parameter: version - The version of VCF specification
+#' }
+NULL
+
 #' calculate the number of heterozygous SNPs for each sample
 #' @param vcffile path to the VCF file with index
 #' @param region  region to extract, default "" for all

R/zzz.R

@@ -1,4 +1,6 @@
 # Export the "vcfreader" C++ class by explicitly requesting vcfreader be
 # exported via roxygen2's export tag.
 #' @export vcfreader
+#' @export vcfwriter
 loadModule("vcfreader", TRUE)
+loadModule("vcfwriter", TRUE)

src/RcppExports.cpp

@@ -101,6 +101,7 @@ END_RCPP
 }
 
 RcppExport SEXP _rcpp_module_boot_vcfreader();
+RcppExport SEXP _rcpp_module_boot_vcfwriter();
 
 static const R_CallMethodDef CallEntries[] = {
     {"_vcfppR_heterozygosity", (DL_FUNC) &_vcfppR_heterozygosity, 5},
@@ -109,6 +110,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"_vcfppR_summaryVariants", (DL_FUNC) &_vcfppR_summaryVariants, 5},
     {"_vcfppR_summarySVs", (DL_FUNC) &_vcfppR_summarySVs, 5},
     {"_rcpp_module_boot_vcfreader", (DL_FUNC) &_rcpp_module_boot_vcfreader, 0},
+    {"_rcpp_module_boot_vcfwriter", (DL_FUNC) &_rcpp_module_boot_vcfwriter, 0},
     {NULL, NULL, 0}
 };
 

src/vcf-reader.cpp

@@ -4,7 +4,7 @@
 using namespace std;
 
 //' @name vcfreader
-//' @title API for reading read the VCF/BCF.
+//' @title API for reading the VCF/BCF.
 //' @description Type the name of the class to see its methods
 //' @field new Constructor given a vcf file \itemize{
 //' \item Parameter: vcffile - The path of a vcf file
@@ -175,9 +175,23 @@ class vcfreader {
     inline bool hasOTHER() const { return var.hasOTHER(); }
     inline bool hasOVERLAP() const { return var.hasOVERLAP(); }
 
+    // WRITE
+    inline void output(std::string vcffile) {
+        bw.open(vcffile);
+        bw.initalHeader(br.header);
+    }
+    inline void write() { bw.writeRecord(var); }
+    inline void close() { bw.close(); }
+
+    inline void setCHR(std::string s) { var.setCHR(s.c_str()); }
+    inline void setID(std::string s) { var.setID(s.c_str()); }
+    inline void setPOS(int pos) { var.setPOS(pos); }
+    inline void setRefAlt(std::string s) { var.setRefAlt(s.c_str()); }
+
    private:
     vcfpp::BcfReader br;
     vcfpp::BcfRecord var;
+    vcfpp::BcfWriter bw;
     vector<int> v_int;
     vector<float> v_float;
     vector<std::string> v_str;
@@ -224,6 +238,5 @@ RCPP_MODULE(vcfreader) {
         .method("hasMNP", &vcfreader::hasMNP)
         .method("hasBND", &vcfreader::hasBND)
         .method("hasOTHER", &vcfreader::hasOTHER)
-        .method("hasOVERLAP", &vcfreader::hasOVERLAP)
-        ;
+        .method("hasOVERLAP", &vcfreader::hasOVERLAP);
 }

src/vcf-writer.cpp

@@ -0,0 +1,51 @@
+#include <Rcpp.h>
+#include "vcfpp.h"
+
+using namespace std;
+
+//' @name vcfwriter
+//' @title API for writing the VCF/BCF.
+//' @description Type the name of the class to see its methods
+//' @field new Constructor given a vcf file \itemize{
+//' \item Parameter: vcffile - The path of a vcf file. don't start with "~"
+//' \item Parameter: version - The version of VCF specification
+//' }
+class vcfwriter {
+   public:
+    vcfwriter(std::string vcffile, std::string version) : bw(vcffile, version) {}
+    ~vcfwriter() {}
+
+    inline void close() { bw.close(); }
+
+    // WRITE ONLY
+    inline void writeline(std::string line) { bw.writeLine(line); }
+    inline void addLine(std::string str) { bw.header.addLine(str); }
+    inline void addSample(std::string str) { bw.header.addSample(str); }
+    inline void addContig(std::string str) { bw.header.addContig(str); }
+    inline void addFILTER(std::string id, std::string desc) { bw.header.addFILTER(id, desc); }
+    inline void addINFO(std::string id, std::string number, std::string type, std::string desc) {
+        bw.header.addINFO(id, number, type, desc);
+    }
+    inline void addFORMAT(std::string id, std::string number, std::string type, std::string desc) {
+        bw.header.addFORMAT(id, number, type, desc);
+    }
+
+   private:
+    vcfpp::BcfWriter bw;
+};
+
+RCPP_EXPOSED_CLASS(vcfwriter)
+RCPP_MODULE(vcfwriter) {
+    using namespace Rcpp;
+    class_<vcfwriter>("vcfwriter")
+        .constructor<std::string, std::string>("construct vcfwriter given vcf file and the version")
+        .method("close", &vcfwriter::close)
+        .method("writeline", &vcfwriter::writeline)
+        .method("addLine", &vcfwriter::addLine)
+        .method("addSample", &vcfwriter::addSample)
+        .method("addContig", &vcfwriter::addContig)
+        .method("addFILTER", &vcfwriter::addFILTER)
+        .method("addINFO", &vcfwriter::addINFO)
+        .method("addFORMAT", &vcfwriter::addFORMAT)
+        ;
+}

src/vcfpp.h

@@ -1042,12 +1042,6 @@ type as noted in the other overloading function.
         return line->pos + 1;
     }
 
-    /** @brief modify position given 1-based value */
-    inline void setAlleleStr(const char * alleles_string)
-    {
-        bcf_update_alleles_str(header.hdr, line, alleles_string);
-    }
-
     /** @brief modify CHROM value */
     inline void setCHR(const char * chr)
     {
@@ -1060,6 +1054,18 @@ type as noted in the other overloading function.
         line->pos = p - 1;
     }
 
+    /** @brief update ID */
+    inline void setID(const char * s)
+    {
+        bcf_update_id(header.hdr, line, s);
+    }
+
+    /** @brief set REF and ALT alleles given a string seperated by comma */
+    inline void setRefAlt(const char * alleles_string)
+    {
+        bcf_update_alleles_str(header.hdr, line, alleles_string);
+    }
+
     /** @brief return 0-base start of the variant (can be any type) */
     inline int64_t Start() const
     {