svimmer --join-mode crashes with TypeError

[RegnDai]

Hi,

I ran into a crash when using svimmer --join-mode on three per-sample SV VCFs (Manta first, then Delly and Smoove), using bgzip-compressed and tabix-indexed VCF inputs.

Environment

• svimmer checked out from source
• pixi environment:

[workspace]
channels = ["conda-forge", "bioconda"]
name = "svimmer"
platforms = ["linux-64"]
version = "0.1.0"

[tasks]

[dependencies]
python = ">=3.13.12,<3.14"
pysam = ">=0.23.3,<0.24"
samtools = ">=1.23.1,<2"
bcftools = ">=1.23.1,<2"

• run as python src/svimmer
• input files are bgzip-compressed and tabix-indexed VCFs

Command

pixi run python src/svimmer.patch \
  --threads "${SLURM_CPUS_PER_TASK}" \
  --join-mode \
  --ignore-bnd \
  --output "${RAW_OUT}" \
  "${JOIN_LIST}" \
  "${AUTOSOMES[@]}"

ERR

Traceback (most recent call last):
  File "/env/svimmer/src/svimmer", line 232, in <module>
    all_svs = append_svs_from_vcf(line_in, chrom)
  File "/env/svimmer/src/svimmer", line 97, in append_svs_from_vcf
    if new_sv.is_sv and new_sv.begin >= start:
TypeError: '>=' not supported between instances of 'int' and 'NoneType'

What I observed

The crash happens in --join-mode.
It looks like start becomes None for at least some calls to append_svs_from_vcf().

I changed the --join-mode loop so that region_start / region_end are also passed for the later input VCFs, not only the first one.

Before:

for line_in in lines[1:]:
    all_svs = append_svs_from_vcf(line_in, chrom)

After:

for line_in in lines[1:]:
    all_svs = append_svs_from_vcf(line_in, chrom, args.region_start, args.region_end)

After this change, the script no longer throws the TypeError.

This makes me suspect that in --join-mode, the first VCF is read with explicit region bounds, but subsequent VCFs are not, which leaves start=None and eventually causes the comparison new_sv.begin >= start to fail.

Please let me know if this matches the intended behavior.

Thanks!