Promote error correction scripts from sandbox

[wltrimbl]

This is an attempt to bring two (of only three) CLI scripts that use ReadAligner up to date with the khmer codebase, error_correct_pass2 and correct-reads. Tests were added, and the scripts were moved from sandbox to scripts.

• Is it mergeable?
• make test Did it pass the tests?
• make clean diff-cover If it introduces new functionality in
  scripts/ is it tested?
• make format diff_pylint_report cppcheck doc pydocstyle Is it well
  formatted?
• Did it change the command-line interface? Only backwards-compatible
  additions are allowed without a major version increment. Changing file
  formats also requires a major version number increment.
• For substantial changes or changes to the command-line interface, is it
  documented in CHANGELOG.md? See keepachangelog
  for more details.
• Was a spellchecker run on the source code and documentation after
  changes were made?
• Do the changes respect streaming IO? (Are they
  tested for streaming IO?)

Checklist for moving scripts from sandbox to scripts:

• most or all lines of code are covered by automated tests (see output of make diff-cover)
• make diff_pylint is clean
• the script has been updated with a get_parser() and added to doc/user/scripts.txt
• argparse help text exists, with an epilog docstring, with examples and options
• standard command line options are implemented
• version and citation information is output to STDERR (khmer_args.info(...))
• support '-' (STDIN) as an input file, if appropriate
• support designation of an output file (including STDOUT), if appropriate
• script reads and writes sequences in compressed format
• runtime diagnostic information (progress, etc.) is output to STDERR
• script has been removed from sandbox/README.rst

[ctb]

thanks, Will, this is excellent! If you separate the move to scripts/ from the edits in sandbox/, this will likely get merged much faster.

[standage]

Awesome!

In addition to @ctb's comment, see http://khmer.readthedocs.io/en/latest/dev/scripts-and-sandbox.html#upgrading-a-script-from-sandbox-to-scripts.

[codecov-io]

Codecov Report

Merging #1743 into master will decrease coverage by <.01%.
The diff coverage is n/a.

@@            Coverage Diff            @@
##           master   #1743      +/-   ##
=========================================
- Coverage    0.05%   0.05%   -0.01%     
=========================================
  Files          90      92       +2     
  Lines       11336   11572     +236     
  Branches     2992    3032      +40     
=========================================
  Hits            6       6              
- Misses      11330   11566     +236

Impacted Files	Coverage Δ
scripts/correct-reads.py	0% <ø> (ø)
scripts/error-correct-pass2.py	0% <ø> (ø)

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[wltrimbl]

FailToUnderstandError: Do you want another issue, to separate move vs. patch, or do you want me to clean up the commits here?

[standage]

FailToUnderstandError

Lol

Do you want another issue, to separate move vs. patch, or do you want me to clean up the commits here?

It doesn't matter much whether you adjust this PR or make a new one: whichever is least inconvenient to you. But it would help the review process to separate 1) the changes you've been making to the scripts from 2) the changes that will be required to upgrade a script from sandbox/ to scripts/.

Let me know if that computes. ;-)

[wltrimbl]

The automatic build/testing doesn't find scripts that are in sandbox, so the tests I added failed; i thought I had to move the scripts (or the testing would fail horribly)

Is force pushing to a PR branch acceptable after rebasing, or is this impolite to git and travis?

Any idea why codecov doesn't seem to be reporting accurately?

[ctb]

force pushing is fine.

@betatim any thoughts re codecov?

[betatim]

force pushing

I do it all the time coughcough when I rebase my PR/amend commits. The only downside might be that inline comments sometimes get collapsed but other than that ... no one ever notices it seems :p