Dave Lawrence

@andreasprlic I've been playing a bit and I can see this being really useful! A few nit-picks: **Suggest changing ```PrettyPrint.__init__``` to be initialised with AssemblyMapper** Advantages are to support any...

Hi, sorry for slow reply it's summer here and I was at the beach I haven't been able to recreate it using: ``` print(Reader(filename).raw_header) ``` Though I am pretty sure...

I like the [robustness principle](https://en.m.wikipedia.org/wiki/Robustness_principle) > be conservative in what you do, be liberal in what you accept from others And def agree that if I was writing a VCF...

Dupe of #85 (Mar 23, 2018) I know because I asked this [Jun 16, 2021](https://github.com/atks/vt/issues/116) - looks like this project has been abandoned :(

@pettyalex - ```strace``` may help here, can give you visiblity into system calls Network related ones something like: ```strace -ff -e trace=file,open,read,write,connect,sendto,recvfrom,sendmsg,recvmsg,poll -s 200 -o strace.log bcftools ...``` And ```tcpdump```...

Thanks for feedback. I think 20kb explicit works but if you think it is purely a length problem not symbolic/explicit maybe write a warning out once if detected like symbolic...

FYI I'm going to use 1kb as a maximum cutoff, let me know if that's wildly wrong. I know it's somewhat arbitrary Is the problem not so much the length...

I am using 1kb as a max cutoff for length attempting lift over, it seems you recommended against long variants, not just symbolic > You can rewrite the variant as...

Hi, thanks for the feedback. Could you please clarify exactly what you mean? > the BCFtools/liftover model would not work that well and is not appropriate for this Could you...

Sorry I re read the paper and couldn't find the info. Could you please link to the examples that demonstrate why "model would not work that well and is not...