Qprofiler qio

[ChristinaXu2017]

Description

• The org.qcmg.ma, org.qcmg.fast and org.qcmg.gff are deleted from qio, the alternative new pacake is org.qcmg.qio.ma, org.qcmg.qio.fasta and org.qcmg.qio.gff. these new package is based on org.qcmg.qio.record.RecordReader (refer to pull request create universal reader and writer #209).
• update qprofiler by using new qio packages.
• update qbamannotate by using new qio::ma package
• use org.junit.Assert to replace the deprecated junit.framework.Assert inside unit tests
• add unit test method to delete output qprofiler.xml after each test run.
• tidy up code.

Type of change

Please delete options that are not relevant.

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

How Has This Been Tested?

the unit test is created and updated, regression test in our TC box was created.

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes

[holmeso]

delete

[ChristinaXu2017]

done

[holmeso]

It's generally safer to use the TemporaryFolder class to setup files in each test method, as that way, junit takes care of removing the files once they have been used. I know that in this case the original code is not yours - do you know which test method is producing the qprofiler.xml file? If so, perhaps that method(s) can be updated to take a temp file as the output?

[ChristinaXu2017]

qprofiler.xml is a default output if the "--output" option is not called.
I think it is a good idea, but I agree it should not be always tested. The unit test is updated, hence we test the qprofiler with "--output" option, unless the unit testing the default output.

This problem should be solved

[holmeso]

thanks for the changes