POS =0

[xuefzhao]

I got this error when there are SVs with POS=0:

 (pysam_XZ) svtk standardize           --prefix delly_Penn-DNA-PFC-058-reprep           --contigs /data/talkowski/tools/ref/human_g1k_v37/human_g1k_v37.fasta.fai           --min-size 50           data/raw_vcfs/delly/delly.Penn-DNA-PFC-058-reprep.vcf.gz std_vcfs/delly.Penn-DNA-PFC-058-reprep.vcf delly




Traceback (most recent call last):
  File "/apps/lab/miket/anaconda/4.3.30/envs/pysam_XZ/bin/svtk", line 6, in <module>
    exec(compile(open(__file__).read(), __file__, 'exec'))
  File "/data/talkowski/xuefang/local/src/svtk/scripts/svtk", line 67, in <module>
    main()
  File "/data/talkowski/xuefang/local/src/svtk/scripts/svtk", line 64, in main
    getattr(cli, command)(sys.argv[2:])
  File "/data/talkowski/xuefang/local/src/svtk/svtk/cli/standardize_vcf.py", line 99, in main
    for record in standardizer.standardize_vcf():
  File "/data/talkowski/xuefang/local/src/svtk/svtk/standardize/standardize.py", line 130, in standardize_vcf
    for std_rec in self.standardize_records():
  File "/data/talkowski/xuefang/local/src/svtk/svtk/standardize/standardize.py", line 116, in standardize_records
    yield self.standardize_record(std_rec, record)
  File "/data/talkowski/xuefang/local/src/svtk/svtk/standardize/standardize.py", line 170, in standardize_record
    std_rec.pos = raw_rec.pos
  File "pysam/libcbcf.pyx", line 3056, in pysam.libcbcf.VariantRecord.pos.__set__
ValueError: Position must be positive