Qsignature qio

[ChristinaXu2017]

Description

1. The org.qcmg.illumina package is deleted from qio, the alternative new pacake is org.qcmg.qio.illumina based on org.qcmg.qio.record.RecordReader (refer to pull request create universal reader and writer #209).
2. update qmule::SnpPicker which uses org.qcmg.qio.illumina
3. update qSignature which uses org.qcmg.qio.illumina
4. use org.junit.Assert to replace the deprecated junit.framework.Assert inside unit tests
5. delete deprecated qSignature classes, it seems they are no longer used.

• SignatureCompareRelated,
• SignatureCompareRelatedSimple,
• SignatureCompareRelatedSimpleGenotype.java
• SignatureFindRelated.java
• SignatureFindRelatedMulti.java
• SignatureWTFExomes.java

here we should also consider issue #233. We may add or remove the "Deprecated" annotation on some qsignature executable classes.

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 updated, there is also a regression test on our TC box

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]

thanks for deleting the deprecated files