ZeroDivisionError in whatshap stats when heterozygous variants are absent on one of the contigs

[mhulsman]

Whatshap stats (using version 2.0) generates an ZeroDivisionError exception if there is no heterozygous variant on one of the contigs.

Command line: whatshap stats whatshap_phased.vcf > phase.stats
Results in:

Traceback (most recent call last):
File "/home/hulsmanm/.snakemake/3846fa4274a6ef7f4cc91bf7fe3c9b94_/bin/whatshap", line 10, in
sys.exit(main())
File "/home/hulsmanm/.snakemake/3846fa4274a6ef7f4cc91bf7fe3c9b94_/lib/python3.10/site-packages/whatshap/main.py", line 64, in main
module.main(args)
File "/home/hulsmanm/.snakemake/3846fa4274a6ef7f4cc91bf7fe3c9b94_/lib/python3.10/site-packages/whatshap/cli/stats.py", line 565, in main
run_stats(**vars(args))
File "/home/hulsmanm/.snakemake/3846fa4274a6ef7f4cc91bf7fe3c9b94_/lib/python3.10/site-packages/whatshap/cli/stats.py", line 544, in run_stats
detailed_stats = stats.get_detailed_stats(chr_lengths)
File "/home/hulsmanm/.snakemake/3846fa4274a6ef7f4cc91bf7fe3c9b94_/lib/python3.10/site-packages/whatshap/cli/stats.py", line 316, in get_detailed_stats
phased_snvs_fraction=phased_snvs / self.heterozygous_snvs,
ZeroDivisionError: division by zero

Information:

• WhatsHap version 2.0, Python version 3.10
• Installed with conda

[pontushojer]

Yes, getting the ZeroDivisionError is not very useful here. I implemented a fix in PR #471. Now stats should be generated regardless if you don't have any heterozygous or phased variants in your VCF