Current behaviour is this output if clustering results in bu

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Handle no variants after clustering about gramtools HOT 8 CLOSED

martinghunt commented on June 23, 2024

Handle no variants after clustering

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Comments (8)

martinghunt commented on June 23, 2024 1

Looks good to me. Thanks for testing :)

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martinghunt commented on June 23, 2024

Actually, looks like it's the clustering that is failing, resulting in a VCF with no records.

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bricoletc commented on June 23, 2024

@martinghunt I think this is fixed through cluster_vcf_records module?

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martinghunt commented on June 23, 2024

Yes I fixed cluster_vcf_records, so that example works now. But I'm wondering if it's still possible to end up with no records in the VCF. What will gramtools do in that case?

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bricoletc commented on June 23, 2024

I see.

Here is the behaviour if you gramtools build using a VCF with no records:

$ gramtools build --reference toy_datasets/noRecords/H37Rv.fasta --vcf toy_datasets/noRecords/mutant.vcf --gram-dir test
2020-01-07 10:02:48,084 gramtools    INFO     Start process: build
2020-01-07 10:02:48,085 gramtools    INFO     Running vcf_record_clustering on ['toy_datasets/noRecords/mutant.vcf'].
2020-01-07 10:02:48,085 gramtools    INFO     Running vcf_to_PRG_string_conversion on /home/brice/Desktop/work_PhD/git_repos/gramtools/tmp_work/test/build.vcf
2020-01-07 10:02:48,097 gramtools    INFO     stdout:

maximum thread count: 1
Executing build command
Generating integer encoded PRG
Number of characters in integer encoded linear PRG: 2660
Generate coverage graph
Number of variant sites: 0
No variant sites found.
Exiting 1

2020-01-07 10:02:48,099 gramtools    ERROR    Error code != 0
2020-01-07 10:02:48,100 gramtools    ERROR    Unsuccessful build. Process reported to /home/brice/Desktop/work_PhD/git_repos/gramtools/tmp_work/test/build_report.json

I figure that's good behaviour: clustering and prg string production happen, and then we exit stating no variants found.

What do you think?

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