ValueError: cannot set null allele

[wwood]

Hi,

Been running strangr on some genomes, feeding in bam files from bwa, and getting stuff like this - any ideas?

$ straingr  view --vcf /tmp/a.vcf data/straingr-out/per-sample/mock1/GCA_000156375.1.fna.output
2023-04-24 16:08:12,971 - INFO:root:Loading data from HDF5 file data/straingr-out/per-sample/mock1/GCA_000156375.1.fna.output
ref     name    length  coverage        uReads  abundance       median  callable        callablePct     confirmed       confirmedPct    snps    snpPct  multi   multiPct        lowmq   lowmqPct        high    highPct  gapCount        gapLength
na      GCA_000156375.1.fna$DS996351.1  382994  5.100   13950   0.034   5       354594  92.585  347205  97.916  7389    2.084   5       0.001   0       0.000   0       0.000   0       0
na      GCA_000156375.1.fna$DS996352.1  6862    0.204   13      0.000   0       379     5.523   374     98.681  5       1.319   0       0.000   0       0.000   0       0.000   0       0
na      GCA_000156375.1.fna$DS996353.1  121189  4.785   4162    0.010   5       111067  91.648  108736  97.901  2331    2.099   2       0.002   0       0.000   0       0.000   0       0
na      GCA_000156375.1.fna$DS996354.1  239511  4.598   7836    0.019   4       220277  91.969  215703  97.924  4574    2.077   11      0.005   0       0.000   0       0.000   0       0
na      GCA_000156375.1.fna$DS996355.1  491996  4.419   15446   0.037   4       448637  91.187  439306  97.920  9326    2.079   20      0.004   0       0.000   0       0.000   0       0

... (snip)

2023-04-24 16:08:15,381 - INFO:root:Generating VCF file...
Traceback (most recent call last):
  File ".snakemake/conda/16aa680dd00c9d5a6169055bdad760d4_/bin/straingr", line 11, in <module>
    sys.exit(straingr_cli())
  File ".snakemake/conda/16aa680dd00c9d5a6169055bdad760d4_/lib/python3.10/site-packages/strainge/cli/main.py", line 110, in __call__
    self.run(args)
  File ".snakemake/conda/16aa680dd00c9d5a6169055bdad760d4_/lib/python3.10/site-packages/strainge/cli/registry.py", line 83, in run
    rc = subcommand_func(**args_dict)
  File ".snakemake/conda/16aa680dd00c9d5a6169055bdad760d4_/lib/python3.10/site-packages/strainge/cli/straingr.py", line 582, in __call__
    write_vcf(call_data, vcf, verbose_vcf)
  File ".snakemake/conda/16aa680dd00c9d5a6169055bdad760d4_/lib/python3.10/site-packages/strainge/io/variants.py", line 478, in write_vcf
    for record in record_iter:
  File ".snakemake/conda/16aa680dd00c9d5a6169055bdad760d4_/lib/python3.10/site-packages/strainge/io/variants.py", line 422, in vcf_records_for_scaffold
    record = writer.new_record(
  File "pysam/libcbcf.pyx", line 4480, in pysam.libcbcf.VariantFile.new_record
  File "pysam/libcbcf.pyx", line 2101, in pysam.libcbcf.VariantHeader.new_record
  File "pysam/libcbcf.pyx", line 3250, in pysam.libcbcf.VariantRecord.alleles.__set__
ValueError: cannot set null allele

I've attached the file, using conda version:

$ straingr --version
1.3.7

Thanks in advance.