hall-lab / svtools

Tools for processing and analyzing structural variants.
MIT License
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svtools lsort KeyError: 'CIPOS' #328

Open hcsun1 opened 7 months ago

hcsun1 commented 7 months ago

Hello,

I have encountered an issue. Could you please help me check it and suggest how to solve it? I really appreciate your assistance.

command:

svtools lsort F_hapAB.RefF.variants.sort.vcf.gz Ga.RefF.variants.sort.vcf.gz G.RefF.variants.sort.vcf.gz | bgzip -c > sort.vcf.gz

erro

Traceback (most recent call last): File "/data/lilab/hcsun1/miniconda3/envs/py27/bin/svtools", line 8, in sys.exit(main()) File "/data/lilab/hcsun1/miniconda3/envs/py27/lib/python2.7/site-packages/svtools/cli.py", line 79, in main sys.exit(args.entry_point(args)) File "/data/lilab/hcsun1/miniconda3/envs/py27/lib/python2.7/site-packages/svtools/lsort.py", line 123, in run_from_args sorter.execute() File "/data/lilab/hcsun1/miniconda3/envs/py27/lib/python2.7/site-packages/svtools/lsort.py", line 58, in execute self.vcf_lines.sort(key=l_bp.vcf_line_key) File "/data/lilab/hcsun1/miniconda3/envs/py27/lib/python2.7/site-packages/svtools/l_bp.py", line 158, in vcf_line_key v1 = split_v(l1)[:8] File "/data/lilab/hcsun1/miniconda3/envs/py27/lib/python2.7/site-packages/svtools/l_bp.py", line 133, in split_v start_l = pos_l + int(m['CIPOS'].split(',')[0]) KeyError: 'CIPOS'