Formatting chromosomes properly.
Updated Maven Shade plug-in

There seems to be an issue with Maven 3.1+ and `maven-shade-plugin:2.0`.
When running `mvn install`, the following error is encountered:

    [ERROR] Failed to execute goal org.apache.maven.plugins:maven-shade-plugin:2.0:shade (default)
    Execution default of goal org.apache.maven.plugins:maven-shade-plugin:2.0:shade failed:
    A required class was missing while executing org.apache.maven.plugins:maven-shade-plugin:2.0:shade: org/sonatype/aether/version/VersionConstraint

Updating `maven-shade-plugin` to 2.1 fixes the build.
Logging to log, not stderr. Removed System.exit()

Made jannovar messages go to log instead of stdout/stderr, and removed
all System.exit() calls. Now if Jannovar errors out, it won't bring
down the parent application (however, it will abort/cancel a variant
import job).