MACARON 1.0 (Big Release)

This is a big MACARON Release, greatly worked with the newest version of GATK (4.1.7).

Update to MACARON, now version 1.0

Some news:

Now compatible with latest version of GATK4 (4.1.7) - GATK3 is no longer supported (the previous version of MACARON will still work great with GATK3).
GATK4 is now used as default, and MACARON relies on gatk wrapper instead of the .jar file.
For version of GATK4 before 4.1.4.1, the option of IndexFeatureFile is different. The option --gatk4_previous must be added when using these older versions of GATK4.
MACARON can also handle the snpEff wrapper (available via bioconda). The extension of the file (either '.jar' or no extension) will allow MACARON to determine if the wrapper is used or the .jar file.
If gatk and snpEff are accessible via $PATH, there is no need for the user to provide the path of these programs to MACARON.
Animation is now an option, use -c option to visualize the wheel turning (great to pass the time!).
A bug with grep has been fixed to allow the use of MACARON with MacOS !
Global refactoring (classes dropped, and some more).
Option --keep_temp was added to not delete temporary files (useful for debugging)

To do:

GATK4 is not completely silent despite setting QUIET and verbosity parameters. Need to find a way to hide it in the next version...

MACARON (updated)

0.7

Merge branch 'master' of https://github.com/waqasuddinkhan/MACARON-Ge…

MACARON - First Release

MACARON Direct-Usage Version