Closed hassanfa closed 2 years ago
Looking in the code, it seems pos
is assigned but chrom
is not:
https://github.com/rust-bio/rust-bio-tools/blob/d1a60cc8876eb8ea2b6cffb21bdcee44a00d2dc4/src/bcf/report/table_report/create_report_table.rs#L85-L110
I'll look into the contribution guide and give this is a go.
Hello @hassanfa,
thanks again for reporting this issue. Are you sure you are using the latest version? I recently updated the error messages to have the variants reported as <CHROM>:<POS>
. Your error seems to be from a previous version since the :
would be missing, even if chrom
was empty (which i don't think it should be).
Regarding the 0-based position i absolutely agree. The reported position should be 1-based to make it much more convenient for the user to search for the problematic record. I'll tackle this in an incoming PR shortly.
@fxwiegand thanks for the quick fix. Yes, you are absolutely right that I was not using the latest version.
@fxwiegand thanks for the quick fix. Yes, you are absolutely right that I was not using the latest version.
Ok great! Thank you though for pointing out the wrongly payed position! 😊
In my VCF file, I have a variant at the following specific position:
Above variant is missing HGVSg and
vcf-report
clearly reports it. But it reports a 0-based position. It is a minor issue, but it'd be useful to either properly have it 1-based or clearly specify what convention vcf-report is using for reporting. I prefer the former, it just makes the debugging easier.Also, it does not report chromosome either.
Here is the
vcf-report
output:Ideally the output could be something like: