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 #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)
[X] 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:
[X] My code follows the style guidelines of this project
[X] I have performed a self-review of my own code
[X] I have commented my code, particularly in hard-to-understand areas
[X] I have made corresponding changes to the documentation
[X] My changes generate no new warnings
[X] I have added tests that prove my fix is effective or that my feature works
[X] New and existing unit tests pass locally with my changes
Description
Type of change
Please delete options that are not relevant.
How Has This Been Tested?
the unit test is created and updated, regression test in our TC box was created.
Checklist: