Shaun Jackman

I just noticed that `bgzip` has a `-@, --threads` option! I'll use that.

:+1: Yes, please!

:+1: In particular, the GFF version 3 header `##gff-version 3` must be maintained.

`bedtools sort -header` works perfect! Thanks, Aaron. I was reading [this documentation](http://bedtools.readthedocs.org/en/latest/content/tools/sort.html) which doesn't show the `-header` option. I expected `-header` to be the default behaviour. Perhaps instead a `-noheader`...

_From @jkbonfield on July 8, 2015 16:19_ It took some head scratching to understand how j and is_flip work there. Confusing but probably less so that `1+(j!=is_flip)` :-) From my...

Which is the canonical version of wgsim, `samtools/samtools` or `lh3/wgsim`?

_From @jkbonfield on July 9, 2015 8:25_ I assume lh3/wgsim as it's newer and his README seems to imply this too. However I don't know for sure.

The default shell used by GNU Make is `$SHELL $.SHELLFLAGS` where `SHELL=/bin/sh` and `.SHELLFLAGS=-c` or `.SHELLFLAGS=-ec` in POSIX compatibility mode. I prefer `-ec` myself. See https://www.gnu.org/software/make/manual/html_node/Choosing-the-Shell.html

I didn't know this: > Unlike most variables, the variable SHELL is never set from the environment. This is because the SHELL environment variable is used to specify your personal...

Cool idea! `.SHELLFLAGS` is useful for other interpreters that use e.g. `-e` rather than `-c`. https://www.gnu.org/software/make/manual/html_node/Choosing-the-Shell.html