James Bonfield

I like this change. Although I expect it was accidental, being forced down hopen vs open in order to get kgetline functionality, it's worth noting in the commit message that...

That's one possible solution. I am a bit uneasy given I could imagine us getting bug reports for files not round-tripping correctly. Given as I understand it the intention is...

I've been experimenting with adding explicit flush calls, as the simplest option (to-do: headers). It's trivial and seems minimal of CPU cost. ``` diff --git a/sam.c b/sam.c index 393a3b2..23da760 100644...

Looking at this again, I see one minor glitch due to the option rename: ``` diff --git a/bgzip.c b/bgzip.c index c7d61b5..0d51c4a 100644 --- a/bgzip.c +++ b/bgzip.c @@ -173,7 +173,7 @@...

I've squashed and rebased it off current develop (including the one char fix for -a vs -n), added a minimal test (just duplicated the round-trip but with -a) and updated...

Good point on automatic detection. As for strrchr, that itself is a bad function as it needs a null terminated string and it scans forward first before scanning backwards, as...

I may be in the minority, but I couldn't actually work out what bioconda is from their fluffy (but trendy style) home page. It claims to be cloud package management,...

Ah ok, it's the "does not require root privs" bit which makes it popular then. I understood it was a package manager, but not really what distinguished it from all...

What's the conda philosophy when it comes to supporting different OSes? Is it to go with lowest common denominator, or to build whatever each system supports? Eg the curses part...

I'll need to investigate properly, but if you're getting sequence out of it then it's likely it's reporting a failure to obtain the sequence via one method and then falling...