AdamaJava / adamajava

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delete and deprecate string and tab package in qio #249

Closed ChristinaXu2017 closed 3 years ago

ChristinaXu2017 commented 3 years ago

Description

deleted org.qcmg.string from qio, which is replaced by org.qcmg.qio.record created on #209.
deprecate org.qcmg.tab in qio, which is replaced by org.qcmg.qio.record.
deprecated some qmule classes which using old org.qcmg.tab. Here qmule contains a list of dated classes and may delete on the next pull requests.
updated q3tiledaligner due to the above two issues.
updated qmaftools due to the above two issues.
updated qsv due to the above two issues.

Type of change

[X] New feature (non-breaking change which adds functionality)

How Has This Been Tested?

[X] Test A: existing unit tests already covered these IO issues
[X] Test B: run q3tiledalginer on reference file and then compare to adama nightly

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