Fixed check_file_status error

[TheOneHyer]

check_file_status requires two arguments: file_path and force. find-knots.py only gave the first argument, this update adds in the force argument.

[ged-jenkins]

Can one of the admins verify this patch?

[ged-jenkins]

Can one of the admins verify this patch?

[mr-c]

Jenkins, okay to test

[mr-c]

Jenkins, test this please

[mr-c]

Thanks @TheOneHyer! Can you fill out this checklist? http://khmer.readthedocs.org/en/latest/dev/coding-guidelines-and-review.html#checklist

[ged-jenkins]

Can one of the admins verify this patch?

[ged-jenkins]

Can one of the admins verify this patch?

[mr-c]

This was missed due to #358

[TheOneHyer]

• [Yes ] Is it mergeable?
• [*See note below ] Did it pass the tests?
• [ No new functionality] If it introduces new functionality in scripts/ is it tested?
  Check for code coverage with make clean diff-cover
• [ No changes made that would change formatting] Is it well formatted? Look at make pep8, make diff_pylint_report,
  make cppcheck, and make doc output. Use make format and manual
  fixing as needed.
• [ No change to command -line interface] Did it change the command-line interface? Only additions are allowed
  without a major version increment. Changing file formats also requires a
  major version number increment.
• [See Added change log entry for #860 #891] Is it documented in the ChangeLog?
  http://en.wikipedia.org/wiki/Changelog#Format
• [ Yes] Was a spellchecker run on the source code and documentation after
  changes were made?

*Note: The proposed change was made on the lab server at the lab where I work, I do not have write permission to program files on the server yet (I am undergoing sys admin training and will have permissions soon). My personal machine is not powerful enough to run khmer on metagenomic data in a time effective manner. Thus I have not personally tested the change on any real data (I did email the current sys admin the fix but he did not want to implement because mr-c gave ged-jenkins permission to test and he figured you guys would do a better job testing the script).

[mr-c]

@TheOneHyer Thanks for completing the checklist. To add the ChangeLog you can make additional commits to the branch this pull request is from: the 'master' branch of your fork of the repository.

[mr-c]

Jenkins, ok to test

[TheOneHyer]

I've moved my ChangeLog to this pull and closed (#891). I apologize about my sloppiness, I'm quite new to GitHub.

[mr-c]

@TheOneHyer It is no problem! Have you seen http://khmer.readthedocs.org/en/latest/dev/getting-started.html ?

[mr-c]

Can you make your branch mergable? We've updated the master branch since you started.

If you've been following http://khmer.readthedocs.org/en/latest/dev/getting-started.html then the following commands should work:

git fetch --all
git merge ged/master

You may need to manually fix a few conflicts using git mergetool

[TheOneHyer]

ready for review!

[mr-c]

Jenkins, test this please

[mr-c]

I tested this by executing the doc/run-corn-50m.sh script which includes a call to find-knots.py. Despite not being tested automatically by Jenkins this script successfully completed.

[mr-c]

Since your pull request will be the latest addition to the project when we merge it should be at the top of the file with a date newer than the preceding entry.

[mr-c]

@TheOneHyer Once you get your ChangeLog entry moved to the top of the file I'll merge this. Thank you for catching and fixing this bug!

[TheOneHyer]

ready for review!

[mr-c]

@TheOneHyer, Congratulations on your first commit to the khmer project! Your name will be included in the release notes for the next version and you'll be listed amongst our other contributors in the next software release paper.