initial commit with gradle
added gradle wrapper to make things easier to build without installing gradle
1 - Added default Jnomics parameter "verbose", passes appropriate flag to job.waitForCompletion().
    Updated standard tools appropriately.
2 - Deprecated NLineInputFormat.java (Jnomics no longer uses it; exists in newer Hadoop versions)
3 - Examples: A little formatting.
1 - Moving scripts in core/scripts to bin (since most are project-wide anyway).
    Some of the Hydra scripts are still in there, but I think that's okay for now.
2 - Minor tweaks in tests; removed blank format type from standard tool help.
Moving standard Jnomics Hadoop configuration xml from bin/ to conf/
Added comments, so folks know why these are set the way they are.
moved examples from tools into their own top level project

added gradle task to download example data from the web
merged
tools jar now has main class specified in the manifest
gradle will now download and extract example data on its own
use task downloadExampleData to download example data
Updated the jnomics command script. Should work much better now.
Fixing default command filtering.
+README.txt and INSTALL.txt
Added a Fasta FileFormat So that fasta files can be read- testing still incomplete
Fixed a parameter parsing bug.
Merge branch 'master' of ssh://git.code.sf.net/p/jnomics/code
updated examples
Merge branch 'master' of ssh://git.code.sf.net/p/jnomics/code
Fixed ArrayIndexOutOfBoundsException thrown on 1-char long sequence ID's.