[bug report] "cnvkit.py call" can not accept "purity" and "-m clonal" at the same time

[b-niu]

Hi etal,
In current call.py (2019/03/11), the 27-45th lines are:

I found if one has proivde a parameter of purity in a range of (0, 1.0) will make the parameter method == "clonal" disabled.

I have test this in cnvkit version 0.9.6.dev0 (from conda), with the command:

cnvkit.py call 2018030901_T1.call.cns -y -v 2018030901_T1.vardict.snp.filtered.vcf -m clonal --purity 0.7 -o test.call.cns

The logging info reports:

WARNING: VCF file contains multiple samples; returning the first sample '2018030901_T1'
Selected test sample 2018030901_T1
Loaded 28088 records; skipped: 0 somatic, 0 depth
Kept 17053 heterozygous of 28088 VCF records
Treating sample 2018030901_T1.call as male
Rescaling sample with purity 0.7, ploidy 2
Wrote test.call.cns with 274621 regions

We can see that the logging info "logging.info("Calling copy number with clonal ploidy %d", ploidy)" did not appear.

It may be a bug.

[etal]

I'll see about fixing the error messages. The call command should work the way you expect if you use --purity without -m clonal.

[b-niu]

Thanks! @etal

If I am not making a misunderstanding, when we use the command in the document of CNVKIT:

# https://cnvkit.readthedocs.io/en/stable/pipeline.html#call
cnvkit.py call Sample.cns -y -v Sample.vcf -m clonal --purity 0.7 -o Sample.call.cns

The script in call.py should be as shown in the figure below, but not

### elif method == "clonal":

Could you think about fixing it?

[etal]

To clarify one point from the report: -m clonal and --purity do work together, and the copy-number output is correct — when --purity is given, CNVkit uses the purity-aware clonal calculation, which already incorporates the clonal/ploidy model, so -m clonal is honored. The only real issue is cosmetic: the log line confirming clonal mode isn't printed in that combination, which makes it look like -m clonal was ignored. (Swapping the branch as suggested would drop the purity adjustment, so that isn't the fix.) Keeping this open to add the missing confirmation message.