Daniel Cooke

I can see the logic of that if `stdout` has already been written to, but here it is just opened and closed again. I think this is pretty reasonable usage;...

I think the best case that I can make is that it provides a neater definition that is more in line with the rest of the specification. The working definition...

@jmarshall A record with smaller or equal `POS` (so yes, an earlier record in the same VCF if it's co-ordinate sorted). Problematic how, for reconstructing haplotypes? How is this different...

> It looks like the --refcall option has no effect with polyclone. Right, the `--refcall` functionality is currently only implemented in the `individual` calling model, and even here I wouldn't...

Thanks for the bug report. Probably the quickest way to get this resolved is if you provide me with the BAM and FASTA files. Either Google Drive or DropBox works.

Thanks for the bug report. Though there is no official FASTA/Q specification, I don't believe a `.` would be considered a valid base by any well-established tool. However, I agree...

What version are you using? Are you able to provide a minimal dataset that triggers the error?

Thanks for the test data but I cannot reproduce with your command line, please can you confirm that you can reproduce on the data you provided? If so, please could...

Hi, thanks for the bug report. Please can you provide the output of `stdlog`?

Thanks - you're hitting an error/bug: ```shell [2021-08-31 19:14:40] Encountered a problem whilst calling 19:23213199-23954187(HaplotypeTree::prune_unique called with matching Haplotype not in tree) ``` There's also a lot of haplotype skipping...