Add options for outputting gzipped/bzip2ed sequence

[ctb]

It'd be nice if normalize-by-median etc could compress files on output.

[mr-c]

Do you see this being a screed feature or a khmer/oxli feature?

[ctb]

On Fri, Jun 20, 2014 at 11:52:27AM -0700, Michael R. Crusoe wrote:

Do you see this being a screed feature or a khmer/oxli feature?

Both, I think.

[mr-c]

Huh, I can't unassign myself. @b-wyss has claimed this

[mr-c]

Must be done with a switch to not change existing behavior

[bocajnotnef]

re lessened animosity towards breaking API: Do we still need a switch?

[mr-c]

We need sane defaults and override switches.

If we generate the filename then use the same compression as the
corresponding input, naming the output accordingly.

If the user specifies the filename then infer the compression type that
way.

Support --no-compression and --bzip2, --gzip to override the above.

On Sat, May 16, 2015 at 11:20 AM Jake Fenton notifications@github.com
wrote:

re lessened animosity towards breaking API: Do we still need a switch?

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Reply to this email directly or view it on GitHub
#505 (comment).

[ctb]

+1 let's avoid too much cleverness, too, at least for now - I'd be fine with simply appending .gz or .bz2 if appropriate switch is used, turning on gz or bz2 if filename ends with .gz or .bz2, etc. I would change default to use bz2 first, gz next, uncompressed if neither works (I think bz2 is not on all platforms, but gz should be on almost all). this logic should be encapsulated in a khmer module, of course :)

[bocajnotnef]

Added in #747, closing #505