merging works now for a single file

svrunner_utils.py

@@ -106,20 +106,6 @@ def get_contigs(reference):
     return contigs
 
 
-# def chromNum(chrom):
-#     m = re.search(r"[cC]hr(?P<num>[\dXY]+)", chrom)
-#     if m is not None:
-#         if m.group('num') == 'X':
-#             num = 100
-#         elif m.group('num') == 'Y':
-#             num = 101
-#         else:
-#             num = int(m.group('num'))
-#         return num
-#     else:
-#         return chrom
-
-
 def addContigInfosTovcf(vcffile, outvcffile, reference):
     """
     Add contig infos to vcf
@@ -150,8 +136,6 @@ def addContigInfosTovcf(vcffile, outvcffile, reference):
                     for ctg in contigs:
                         fout.write('##contig=<ID=%s,length=%d>\n'
                                    % (ctg.name, ctg.length))
-                    #  for ctg in sorted(contigs,
-                    #                    key=lambda x: chromNum(x.name)):
 
                 fout.write(line)
     # bgzip file

svtyper_utils.py

@@ -62,22 +62,25 @@ def genotype_multiple_samples(bamlist, vcf_in, vcf_out, cores=1):
     pool = multiprocessing.Pool(processes=cores)
     launch_ind = partial(genotype_single_sample,
                          vcf_in=vcf_in, out_dir=tmp_dir)
-
     vcf_files = pool.map(launch_ind, bamfiles)
 
-    merge_cmd = "bcftools merge -m id "
-
-    if vcf_out != sys.stdout:
-        merge_cmd += "-O z " + " -o " + vcf_out + " "
-
-    merge_cmd += " ".join(vcf_files)
+    # Now merge result files
+    if len(bamfiles) == 1:
+        if vcf_out != sys.stdout:
+            cmd = "cp %s %s" % (vcf_files[0], vcf_out)
+        else:
+            cmd = "bcftools view %s" % vcf_files[0]
+    else:
+        cmd = "bcftools merge -m id "
+        if vcf_out != sys.stdout:
+            cmd += "-O z " + " -o " + vcf_out + " "
+        cmd += " ".join(vcf_files)
 
-    exit_code = call(merge_cmd, shell=True)
+    exit_code = call(cmd, shell=True)
 
     if exit_code == 0:
         if vcf_out != sys.stdout:
             tabix_index(vcf_out, force=True, preset="vcf")
-
         shutil.rmtree(tmp_dir)
     else:
         print("Failed: bcftools merge exits with status %d" % exit_code)