upgrading qio

[ChristinaXu2017]

Description

In this pull request, we update qio project and fixe #196, #197, #198, #213, #217, #218, #219.

1. Created new packages, based on the new "org.qcmg.qio.record" package; These new packages named with "qio" string, it will be easy for the user to identify the package belongs.

• org.qcmg.qio.record replace org.qcmg.string, org.qcmg.tab, org.qcmg.pileup.pileup*, org.qcmg.record
• org.qcmg.qio.gff replace org.qcmg.gff
• org.qcmg.qio.fasta replace org.qcmg.fasta
• org.qcmg.qio.gff3 replace org.qcmg.gff3
• org.qcmg.qio.illumina replace org.qcmg.illumina
• org.qcmg.qio.ma replace org.qcmg.ma

2. Deprecated unused packages:

• org.qcmg.reader
• org.qcmg.primerdesignsummary
• org.qcmg.maf
• org.qcmg.consensuscalls,
• org.qcmg.bed,
• org.qcmg.genesymbol,
• org.qcmg.primeroutput,
• org.qcmg.simple,
• org.qcmg.primerinput,
• org.qcmg.Utils

3. Rename packages by adding "qmule" string ,which are only used by qmule project. Here qmule is a collection of temporary tools, they are not well maintained:

• org.qcmg.qmule.pileup;
• org.qcmg.qmule.chrconv;
• org.qcmg.qmule.record;
• org.qcmg.qmule.tab;
• org.qcmg.qmule.germlinedb;
• org.qcmg.qmule.gff3;
• org.qcmg.qmule.dbsnp;
• org.qcmg.qmule.exception;

4. qio is widely applied in our most adamajava project, the above updates are also applied to the below projects:

• qsv
• qsv
• q3tiledaligner
• qsignature
• qsnp
• qprofiler
• qcoverage
• q3panel
• qmaftools
• qbamannotate
• qpileup
• qmule

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; whole adamajava gradle build is run; TC regression tests are created which test the output from qsv, q3tiledaligner, qsignature, qsnp, q3indel , q3vcftools, qannotate, qprofiler2, qprofiler, qvisualise, qbammerge, qcoverage. However, TC regression tests don't cover q3panel, qmaftools, qbamannotate, qpileup, qmule; these project maybe dated and plan to deprecate.

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]

This PR is referencing 7 issues.
Could you please raise seperate PR's for each issue to make it easier to review - thanks!

[ChristinaXu2017]

Let me try to split them into multi pull requests.