feat(preprocessor): an option to not perform a gVCF check

Bypass the issue when INFO/END is used in cases other than a gVCF or structural variations.

Fix-for: #174

preprocessor/pharmcat_vcf_preprocessor.py

@@ -59,6 +59,8 @@
                                 help="(Optional) a path to the bcftools program.  Defaults to bcftools in PATH.")
     advanced_group.add_argument("-bgzip", "--path-to-bgzip", type=str, metavar='</path/to/bgzip>',
                                 help="(Optional) a path to the bgzip program.  Defaults to bgzip in PATH.")
+    advanced_group.add_argument("-G", "--no-gvcf-check", action="store_true",
+                                help="(Optional) do not check whether input is a gVCF, false by default.")
 
     parser.add_argument("-v", "--verbose", action="count", default=0,
                         help="(Optional) print more verbose messages")
@@ -146,11 +148,15 @@
             print("Error: no VCF input")
             sys.exit(1)
 
-        for file in m_vcf_files:
-            if preprocessor.is_gvcf_file(file):
-                print('%s is a gVCF file, which is not currently supported.\n'
-                      'The PharmCAT VCF Preprocessor will support block gVCF in the future.' % str(file))
-                sys.exit(1)
+        # check whether input is a gVCF, which currently does not support yet
+        if args.no_gvcf_check:
+            print('\nBypass the gVCF check.\n')
+        else:
+            for file in m_vcf_files:
+                if preprocessor.is_gvcf_file(file):
+                    print('%s is a gVCF file, which is not currently supported.\n'
+                          'The PharmCAT VCF Preprocessor will support block gVCF in the future.' % str(file))
+                    sys.exit(1)
 
         m_samples: List[str] = []
         if args.sample_file:

preprocessor/preprocessor/utilities.py

@@ -860,11 +860,6 @@ def extract_pgx_variants(pharmcat_positions: Path, reference_fasta: Path, vcf_fi
                         fields = line.split('\t')
                         input_chr_pos = (fields[0], fields[1])
 
-                        # check whether input is a block gVCF
-                        # this is a backup check - it should already have been checked earlier
-                        if re.search('END', fields[7]):
-                            raise ReportableException('gVCF is not supported')
-
                         # match chromosome positions
                         if input_chr_pos in ref_pos_static:
                             '''