Deal appropriately with --unique-kmers argument

[ctb]

The addition of -U/--unique-kmers should not have applied to all scripts (see https://github.com/dib-lab/khmer/pull/1126/files#diff-2ebccdb74ba5df72b22cff1bd70d9696R63) if it was going to be ignored by all of them! We should either make it work for all scripts (which should be easy after #1050, no?) or move the parameter addition into the one bit of code that uses it on oxli/functions.py.

[ctb]

If we make it work for all scripts, this will fix #347.

[ctb]

Oh, and I found a reference to args.unique_kmers in scripts/normalize-by-median.py - this should be moved into khmer_args.py, and the warning message starting with WARNING: You are loading a saved k-mer table from... should be updated.

[ctb]

Note the argument optimization language should change to counting table size will NOT be set automatically. as per https://github.com/dib-lab/khmer/pull/1126/files#r34570761.

[SensibleSalmon]

I'll get this sorted once #1170 lands.

[ctb]

#1170 has landed. ;)

[SensibleSalmon]

Hooplah!

On Tue, Jul 21, 2015 at 6:59 PM C. Titus Brown notifications@github.com
wrote:

#1170 #1170 has landed. ;)

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#1179 (comment).

[ctb]

ping @bocajnotnef

[SensibleSalmon]

Yup, this is up next after I finish current stuff.

On Wed, Jul 29, 2015 at 4:15 PM C. Titus Brown notifications@github.com
wrote:

ping @bocajnotnef https://github.com/bocajnotnef

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#1179 (comment).

[ctb]

Ping wrt #1117.