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dib-lab / kProcessor

kProcessor: kmers processing framework.
https://kprocessor.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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kmerDecoder migration #82

Closed mr-eyes closed 3 years ago

mr-eyes commented 3 years ago

This PR updates the kmerDecoder submodule with some modifications on kProcessor for compatibility.

@shokrof please review and check if the tests are running as expected. I now have only 5 failing tests in this branch.

[  PASSED  ] 138 tests.
[  FAILED  ] 5 tests, listed below:
[  FAILED  ] testFrames/kDataFrameTest.saveAndLoadChangeDefaultColumn/2, where GetParam() = ("MAP", 21)
[  FAILED  ] testFrames/kDataFrameTest.saveAndLoadChangeDefaultColumn/4, where GetParam() = ("PHMAP", 21)
[  FAILED  ] testFrames/kDataFrameTest.saveAndIterateOverAllKmers/4, where GetParam() = ("PHMAP", 21)
[  FAILED  ] testFrames/kDataFrameTest.saveAndIterateOverAllKmers/5, where GetParam() = ("PHMAP", 31)
[  FAILED  ] testFrames/kDataFrameTest.transformPlus10/0, where GetParam() = ("MQF", 21)

This is a checkpoint. I will continue working on this migration one step at a time to make sure nothing will fail.

mr-eyes commented 3 years ago

I pulled the latest changes from v2 and ran the tests.

[  PASSED  ] 136 tests.
[  FAILED  ] 7 tests, listed below:
[  FAILED  ] testFrames/kDataFrameTest.saveAndLoadChangeDefaultColumn/4, where GetParam() = ("PHMAP", 21)
[  FAILED  ] testFrames/kDataFrameTest.saveAndIterateOverAllKmers/2, where GetParam() = ("MAP", 21)
[  FAILED  ] testFrames/kDataFrameTest.saveAndIterateOverAllKmers/3, where GetParam() = ("MAP", 31)
[  FAILED  ] testFrames/kDataFrameTest.saveAndIterateOverAllKmers/4, where GetParam() = ("PHMAP", 21)
[  FAILED  ] testFrames/kDataFrameTest.saveAndIterateOverAllKmers/5, where GetParam() = ("PHMAP", 31)
[  FAILED  ] testFrames/kDataFrameTest.transformFilterLessThan5MultipleColumns/4, where GetParam() = ("PHMAP", 21)
[  FAILED  ] testFrames/kDataFrameTest.transformFilterLessThan5MultipleColumns/5, where GetParam() = ("PHMAP", 31)