James Bonfield

I wasn't talking about *our* tests (actually mine - that one came from io_lib), but other peoples. It certainly broke some of the internal pipeline tests for example. It's not...

We'll just have to agree to disagree on what's irrelevant. Also: > When your file already contains several @PG chains, it's lots of extra lines of spurious verbiage Wrong. If...

Note you can get the unadulterated data in pure "view" form using `htsfile -c`. This is generally more useful for debugging purposes than the kitchen sink view sub-command as it...

Could you please provide some short examples of PG being added incorrectly? I just tested `samtools collate` and it worked fine for me.

Sadly it's not uncommon to find files with a myriad of unconnected PG lines which then causes an explosion. The format itself also frankly sucks as there is no way...

The vcfutils.pl command is still part of the latest distribution, although it's more on "life support" than supported. I haven't tried to see if it still works, but it may...

> Specifically, the ones that write to a file non specified by an option argument, because these are the ones that can cause data loss. Now, `merge` can be used...

So being more practical about what can be done to improve uniformity while maintaining backwards compatibility. > Tools that do not currently support `-o`: > > * tview Could add,...

Thanks for bumping this again John. It'd slipped off my radar, but there are a few low hanging fruits that definitely need fixing (eg calmd and fixmate).

Thank you