Phasing mode not working

[yekaizhou]

The usual mode works well for me (w/o phasing).

Apart from the usual inputs and settings. I set phasing_on = True in my config file, and add -f snp.vcf in my command.

And the error looks like this:

Process Process-28:
Traceback (most recent call last):
  File "/home/ykzhou/anaconda3/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/home/ykzhou/anaconda3/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/home/ykzhou/anaconda3/lib/python3.8/site-packages/nanosv/utils/../utils/parse_bam.py", line 150, in parse_chr_bam
    read_snp_vcf(contig)
  File "/home/ykzhou/anaconda3/lib/python3.8/site-packages/nanosv/utils/../utils/parse_bam.py", line 328, in read_snp_vcf
    find_SNPs(columns[0], int(columns[1]))
  File "/home/ykzhou/anaconda3/lib/python3.8/site-packages/nanosv/utils/../utils/parse_bam.py", line 362, in find_SNPs
    variants[chromosome][bin][int(snp_position)] = variant
KeyError: 0
Process Process-25:
Traceback (most recent call last):
  File "/home/ykzhou/anaconda3/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/home/ykzhou/anaconda3/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/home/ykzhou/anaconda3/lib/python3.8/site-packages/nanosv/utils/../utils/parse_bam.py", line 150, in parse_chr_bam
    read_snp_vcf(contig)
  File "/home/ykzhou/anaconda3/lib/python3.8/site-packages/nanosv/utils/../utils/parse_bam.py", line 328, in read_snp_vcf
    find_SNPs(columns[0], int(columns[1]))
  File "/home/ykzhou/anaconda3/lib/python3.8/site-packages/nanosv/utils/../utils/parse_bam.py", line 362, in find_SNPs
    variants[chromosome][bin][int(snp_position)] = variant
KeyError: 50

It repeats ~20 times, with KeyError mostly different.