Arrow warning: Some reference contigs aligned against are not found in the reference FASTA. about pbbioconda

[pb-dseifert]

@peterjc @bruc provide a PR and I will merge it and cut a new release

[bruc]

In my use case, this issue is not a problem.

I have a large (>10 gbp) genome I want to polish, and in order to parallelize the variant calls, I need to split the merged, sorted BAM file and the genome assembly. The merged, sorted BAM file has a header covering all the contigs in the assembly, but in the split jobs, I only reference a small number of contigs per job. I use the header lines from the big merged, sorted BAM file, and I do get the warning message, and that's fine.

Please do not change the code to make this error. Instead, please provide an option to allow the user to make this an error if they choose to do so. Then, 'pb-dseifert' can achieve the program behavior he or she needs, and my use case still works.

Thanks.

[peterjc]

It is good to have an explicit use-case for why the FASTA file might not match the BAM alignment, but rather a subset of the alignment. [In this case you could likely subset the BAM file, but I can can see it is convenient not to have to]. Here those names in common would have matching lengths in the reference FASTA and the alignment header (and indeed their sequence MD5 would match if that were checked)

i.e. I don't think checking names and lengths for consistency would block @bruc's use case - I think you would still get the same warning as now:

[WARNING] Some reference contigs aligned against are not found in the reference FASTA.  Will process only those contigs supported by the reference FASTA.

[armintoepfer]

Closing due to lack of activity.