Improve coverage in Feature unit tests #1106

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fnothaft opened this Issue Aug 9, 2016 · 0 comments

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fnothaft commented Aug 9, 2016

After #1104, the ignored round trip interval list test will fail right now because the interval list parsing code itself doesn't work. We should add better tests for the parsing code.

I'll tack this on to #1104.

@fnothaft fnothaft added the bug label Aug 9, 2016

@fnothaft fnothaft self-assigned this Aug 9, 2016

fnothaft added a commit to fnothaft/adam that referenced this issue Aug 10, 2016

[ADAM-1106] Improve feature unit test coverage.
Resolves #1106. Improves round trip coverage by checking feature counts after
writing out, and spot checking converted feature lines.

* Split out all string encoding functions for features to make them easier to
  test, and wrote tests to spot check the correctness of these features.
* Made end-to-end feature tests pass.
* Eliminated some redundant tests.
* Added assertions to check that the same number of features were present in the
  input and output files when writing between different formats.
* Rewrote interval list parser and encoder.
* Fixed various bugs:
  * GFF2/GTF/GFF3 parser would discard lines that lacked an attribute column.
  * NarrowPeak parser would discard INDEPENDENT strand.
  * NarrowPeak signal intensities should be written as Ints, not Floats.

fnothaft added a commit to fnothaft/adam that referenced this issue Aug 30, 2016

[ADAM-1106] Improve feature unit test coverage.
Resolves #1106. Improves round trip coverage by checking feature counts after
writing out, and spot checking converted feature lines.

* Split out all string encoding functions for features to make them easier to
  test, and wrote tests to spot check the correctness of these features.
* Made end-to-end feature tests pass.
* Eliminated some redundant tests.
* Added assertions to check that the same number of features were present in the
  input and output files when writing between different formats.
* Rewrote interval list parser and encoder.
* Fixed various bugs:
  * GFF2/GTF/GFF3 parser would discard lines that lacked an attribute column.
  * NarrowPeak parser would discard INDEPENDENT strand.
  * NarrowPeak signal intensities should be written as Ints, not Floats.

fnothaft added a commit to fnothaft/adam that referenced this issue Sep 6, 2016

[ADAM-1106] Improve feature unit test coverage.
Resolves #1106. Improves round trip coverage by checking feature counts after
writing out, and spot checking converted feature lines.

* Split out all string encoding functions for features to make them easier to
  test, and wrote tests to spot check the correctness of these features.
* Made end-to-end feature tests pass.
* Eliminated some redundant tests.
* Added assertions to check that the same number of features were present in the
  input and output files when writing between different formats.
* Rewrote interval list parser and encoder.
* Fixed various bugs:
  * GFF2/GTF/GFF3 parser would discard lines that lacked an attribute column.
  * NarrowPeak parser would discard INDEPENDENT strand.
  * NarrowPeak signal intensities should be written as Ints, not Floats.

@heuermh heuermh closed this in c66da78 Sep 7, 2016

@heuermh heuermh modified the milestone: 0.20.0 Sep 7, 2016

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