tidy up qbasepileup

[ChristinaXu2017]

Description

restructure options and document:

• fix error options in qbasepileup:

  -o parsed twice, has to delete one --mincov never be called inside, has to delete. parser.accepts("maxcov", Messages.getMessage("OPTION_MIN_COV")) seems wired, it should be mincov

• merge redundant options into one: --pindel, --strelka, --gatk to --indel-format [gatk,strelka, pindle]
• to correct misleading messages, such as input SNP file format message error:

• -f Format of SNPs file [ddc1,maf,db,dccq,vcf,torrent,RNA,DNA], Def=dcc1. should be

• follow our option name conversion, change the short option to long option. These new options looks like: ...

Fixes # (issue)

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?

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration

• [ ] Test A
• [ ] Test B

Are WDL Updates Required?

Please detail what changes are required to any wdl files to support this change. For example:

qmotif.wdl will need to be updated to reflect new option names

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