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Read coverage refactor2

Ghost User requested to merge read_coverage_refactor2 into local_py2_test
  • Refactored the _modules.functions_Phageterm.readsCoverage() function into the _modules.functions_Phageterm.ReadsCoverage class, and associated methods.
  • Passes existing tests.
  • Involves altering APIs and calls in PhageTerm.py and the test suite.
  • Ran all the other "tests" (e.g. python PhageTerm.py -t V) and found that results are essentially the same qualitatively, but there are small quantitative differences. I am attaching 2 reports with the source and destination branch results. I am not sure what to make of this, in light of @julian.garneau 's discussion with @vlegrand. It sounds like in some cases small quantitative differences can be ok due to some stochastic behavior of the mapper. I don't know whether these are small enough (see especially Headful in the reports).

py2_test_Test-Virome_PhageTerm_report.pdf ReadsCoverageRefactor_Test-Virome_PhageTerm_report.pdf

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