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Fix/787 #830

Merged
merged 6 commits into from
Feb 25, 2015
Merged

Fix/787 #830

merged 6 commits into from
Feb 25, 2015

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aditi9783
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Replaced 'accuracy' with 'quality' in sandbox/ files. Fixes #787.

@ged-jenkins
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Can one of the admins verify this patch?

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@ged-jenkins
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Can one of the admins verify this patch?

@aditi9783
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  • Is it mergeable?
  • Did it pass the tests?
  • If it introduces new functionality in scripts/ is it tested?
    Check for code coverage with make clean diff-cover
  • 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.
  • 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.
  • Is it documented in the ChangeLog?
    http://en.wikipedia.org/wiki/Changelog#Format
  • Was a spellchecker run on the source code and documentation after
    changes were made?

ctb
ctb reviewed Feb 23, 2015
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ChangeLog
@@ -1,3 +1,7 @@
2015-02-23 Aditi Gupta <agupta@msu.edu>

* sandbox/collect-reads.py, correct-errors.py, normalize-by-median-pct.py, slice-reads-by-coverage.py, sweep-files.py, sweep-reads3.py, to-casava-1.8-fastq.py: Replaced 'accuracy' with 'quality'. Fixes #787.
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Please shorten line to < 80 char

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also use notation: sandbox/{collect-reads.py,correct-errors.py,...}

@ctb
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ctb commented Feb 23, 2015

add to test list

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ctb commented Feb 23, 2015

add to testlist

@aditi9783
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Ready to review.

mr-c
mr-c reviewed Feb 23, 2015
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ChangeLog
@@ -1,3 +1,10 @@
2015-02-23 Aditi Gupta <agupta@msu.edu>
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Just two spaces between the date and your name and just two spaces between your name and your email address.

@mr-c
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mr-c commented Feb 23, 2015

Otherwise it looks good!

@aditi9783
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Ready to review.

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mr-c commented Feb 24, 2015

LGTM. As soon as this is mergeable I shall do so.

mr-c added a commit that referenced this pull request Feb 25, 2015
@mr-c
Merge pull request #830 from aditi9783/fix/787
a3bcc9d 
Fix/787
@mr-c mr-c merged commit a3bcc9d into dib-lab:master Feb 25, 2015
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mr-c commented Feb 25, 2015

Thanks!

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ctb commented Feb 25, 2015

Just in case you're wondering, khmer-recipes works with this.

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Fix all sandbox/ files to use 'quality' instead of 'accuracy' for FASTQ.
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@aditi9783 @ged-jenkins @ctb @mr-c