Jim Robinson

@jmarshall Maybe its a "foible", but IGV supports ~ 45 file formats plus a few web services, and in most cases it would not be possible to detect file format...

@jmarshall The "class-header" option works great for reads, thanks for that, but how does it work for variants? AFAIK the only required line in a VCF header is the format...

@jmarshall Thanks, that would work for me (##contig). I just need the names, so even the short form would work. I will build in workarounds if they are missing, which...

@jmarshall BTW servers must already be "divining" the reference names in a dataset since they are supposed to return an error if a request is made for a reference name...

@jmarshall It's been more than 2 years since I last worked on this until recently, so I'm getting back up to speed. Yes there is a way for BAM files,...

@jmarshall Nothing, that's it, the optional ##contig header. I'm sure you're right, they are unusual, unusual files are way over represented in my world because they generally end up as...

Totally confused about what issue I'm responding to via email, sorry for confusion. All is good for now, if htsget is extended to other formats this might need revisited.

I was just searching for a definition of "top strand" myself, to interpret the samtags spec. I have no idea what it means. I also am slightly confused by the...

Thanks for the explanation @jkbonfield . I'm trying to insure IGV correctly handles the "-" fields correctly, as in "G-m", and ham hampered due to lack of real data that...

@jkbonfield Thanks for responding, really helpful, I had a feeling I was "missing something" but I don't think I was. BTW the unit test data, which I think you created...