Can not handle missing genotype in VCF file

[whtop]

When there is missing genotype ("./.") in SNV VCF:

TypeError                                 Traceback (most recent call last)
<ipython-input-136-616bc7531471> in <module>
----> 1 app.vcf(["chr17.ALL.vcf.gz], use_index=True, chroms=['chr17'], sample="sample")

~/anaconda3/lib/python3.9/site-packages/CNVpytor-1.2.1-py3.9.egg/cnvpytor/root.py in vcf(self, vcf_files, chroms, sample, no_counts, ad_tag, gt_tag, filter, callset, use_index)
    347         """
    348         for vcf_file in vcf_files:
--> 349             self._read_vcf(vcf_file, chroms, sample, no_counts=no_counts, ad_tag=ad_tag, gt_tag=gt_tag, filter=filter,
    350                            callset=callset, use_index=use_index)
    351             self.io.add_meta_attribute("VCF", vcf_file)

~/anaconda3/lib/python3.9/site-packages/CNVpytor-1.2.1-py3.9.egg/cnvpytor/root.py in _read_vcf(self, vcf_file, chroms, sample, use_index, no_counts, ad_tag, gt_tag, filter, callset)
    272                     nref, nalt = np.zeros_like(pos), np.zeros_like(pos)
    273                 else:
--> 274                     pos, ref, alt, nref, nalt, gt, flag, qual = vcff.read_chromosome_snp(c, sample, ad_tag=ad_tag,
    275                                                                                          gt_tag=gt_tag, filter=filter)
    276

~/anaconda3/lib/python3.9/site-packages/CNVpytor-1.2.1-py3.9.egg/cnvpytor/vcf.py in read_chromosome_snp(self, chr_name, sample, ad_tag, gt_tag, filter)
    159                             gt.append(gt_from_str(rec.samples[sample][gt_tag]))
    160                         else:
--> 161                             gt.append(gt_from_list(rec.samples[sample][gt_tag], rec.samples[sample].phased))
    162         except ValueError:
    163             _logger.error("Variant file reading problem. Probably index file is missing or corrupted.")

~/anaconda3/lib/python3.9/site-packages/CNVpytor-1.2.1-py3.9.egg/cnvpytor/utils.py in gt_from_list(l, phased)
   1049
   1050 def gt_from_list(l, phased):
-> 1051     haps = list(map(int1, l))
   1052     ones, n = sum(haps), len(haps)
   1053     x = int(phased) * 4

~/anaconda3/lib/python3.9/site-packages/CNVpytor-1.2.1-py3.9.egg/cnvpytor/utils.py in int1(x)
   1032
   1033     """
-> 1034     return int(int(x) == 1)
   1035
   1036

TypeError: int() argument must be a string, a bytes-like object or a number, not 'NoneType' 

[arpanda]

Could you please share the command you used.

-Arijit