ALT/HLA support for differential calling scripts

- Skipping the addition of 'chr' prefix for the ALT and HLA contigs in hg38
- Update tabix command for ALT and HLA contigs in hg38

Version 1.4.1

• Added file readability checks to analyzeBamHeader.sh
• Added online IO checks to some Perl scripts (not all)

Version 1.4.0

• Update to Roddy 3.5
• Default to "version_1" sample name extraction
• API extensions on WorkflowUsingMergedBams (getTumorBamFiles etc.)

Version 1.3.0

- Change tests to extend the RoddyTestSpec class in Roddy 3.4.0
- Changed tests in WorkflowUsingMergedBamsSpec to use flags instead of getContext() method.
  * The ContextResource @Rule did not work anymore for the tests.
  * Makes it easier to read, flags are boolean values now.
  * Context and file objects are now created in the test methods.
- Updated copyright notes.
- Added compareTo(), equals() and hashCode() to Sample class.
- In COMetadataAccessor class:
  * Added the 'extractSampleNameOnlyFromBamFiles' flag which tells extractSamplesFromOutputFiles() to ignore non BAM files.
    * Added variable and description to the xml.
  * Minimized the code in extractSamplesFromFilenames() by reusing existing code. 
- Add another sample from filename extraction method and move code from the COMetadataAccessor
  to custom strategy classes (SampleFromFilenameExtractionVersionOne/Two)  
    * Add variable and descriptions for the new (and old) method to the xml.
    * Add a lot of tests for the new method.
- Add the COConfigSpec test class.
- Rename the SampleTest class to SampleSpec and make it extend RoddyTestSpec.

Prerelease of 1.3.0 (distributed as 1.2.1) - Use 1.3.0 instead!

The code and jar were already shipped to @GWarsow and it is necessary
to freeze the code. Unfortunately, it diverges a bit from master and cannot be commit
to master (and tagged on master). Keep it in a separate branch!

Distribution was done as COWorkflowsBasePlugin:1.2.1 with a
dependency to Roddy API 3.3