copyHeader with specific samples

tools/Makefile

@@ -21,4 +21,6 @@ clean:
 
 test:
 	./vcf_addDS -i test.vcf.gz -o out.vcf.gz
+	./vcf_addDS -i test.vcf.gz -s Ind3,Ind1 -o out.vcf.gz
 	./vcf_addINFO -i test.vcf.gz -o out.vcf.gz
+	./vcf_addINFO -i test.vcf.gz -s Ind0,Ind2 -o out.vcf.gz

tools/vcf_addDS.cpp

@@ -35,8 +35,8 @@ int main(int argc, char * argv[])
     }
     // ========= core calculation part ===========================================
     BcfReader vcf(invcf, region, samples);
-    BcfWriter bw(outvcf, vcf.header);
-    bw.copyHeader(invcf);
+    BcfWriter bw(outvcf);
+    bw.copyHeader(invcf, samples);
     bw.header.addFORMAT("DS", "1", "Float", "Diploid Genotype Dosage"); // add DS tag into the header
     int nsamples = vcf.nsamples;
     vector<float> gps, ds(nsamples);

tools/vcf_addINFO.cpp

@@ -37,7 +37,7 @@ int main(int argc, char * argv[])
     // ========= core calculation part ===========================================
     BcfReader vcf(invcf, region, samples);
     BcfWriter bw(outvcf);
-    bw.copyHeader(invcf);
+    bw.copyHeader(invcf, samples);
     bw.header.addINFO("INFO", "1", "Float", "INFO score given genotype probability");
     bw.header.addINFO("EAF", "1", "Float", "Estimated Allele Frequency");
     int N = vcf.nsamples, i{0};

vcfpp.h

@@ -1750,12 +1750,13 @@ class BcfWriter
         hp = &h;
     }
 
-    /// copy header of given VCF
-    void copyHeader(const std::string & vcffile)
+    /// copy header of given VCF and restrict on samples
+  void copyHeader(const std::string & vcffile, std::string samples = "-")
     {
         htsFile * fp2 = hts_open(vcffile.c_str(), "r");
         if(!fp2) throw std::invalid_argument("I/O error: input file is invalid");
         header.hdr = bcf_hdr_read(fp2);
+        header.setSamples(samples);
         hts_close(fp2);
         initalHeader(header);
     }