Bgzip+tabix genotypes simulated vcf file

build_pop.py

@@ -112,7 +112,8 @@ with open(os.path.join(prg_path, "template.vcf"), "r") as template:
 
 with open(os.path.join(tmp_dir, "reference-sv.bed"), "r") as bed:
     vcf_reader = vcf.Reader(filename=os.path.join(tmp_dir, 'template.vcf'))
-    vcf_writer = vcf.Writer(open(os.path.join(output_dir, "genotypes.vcf"), "w"), vcf_reader)
+    output_vcf = os.path.join(output_dir, "genotypes.vcf")
+    vcf_writer = vcf.Writer(open(output_vcf, "w"), vcf_reader)
     for line in bed:
         parts = line.replace("\n", "").split("\t")
         freq = float(parts[4])
@@ -136,6 +137,13 @@ with open(os.path.join(tmp_dir, "reference-sv.bed"), "r") as bed:
         vcf_writer.write_record(vcf_record)
     vcf_writer.close()
 
+    # Bgzip + tabix:
+    os.system("bgzip -c " + output_vcf + " > " + output_vcf + ".gz")
+    os.unlink(output_vcf)
+    output_vcf += ".gz"
+    os.system("tabix -p vcf " + output_vcf)
+
+
 
 ###############################################
 # Build fasta chromosomes for each individual #