Be explicit about setting the snpEff -onlyCoding option in the pipeline

When run without an explicit -onlyCoding option, as we've been doing up to
now, snpEff automatically sets -onlyCoding to "true" provided that there is
at least one transcript marked as "protein_coding", which will always be the
case for us in practice (and indeed, all pipeline runs so far with snpEff
2.0.5 have run with -onlyCoding auto-set to "true").

However, given the disastrous effect on annotation quality setting
"-onlyCoding false" has, we wish to be explicit with this option
rather than relying on snpEff's auto-detection logic.

public/scala/src/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala

@@ -47,12 +47,16 @@ class SnpEff extends JavaCommandLineFunction {
   @Argument(doc="verbose", required=false)
   var verbose = true
 
+  @Argument(doc="onlyCoding", required=false)
+  var onlyCoding = true
+
   @Output(doc="snp eff output")
   var outVcf: File = _
 
   override def commandLine = super.commandLine +
                              required("eff") +
                              conditional(verbose, "-v") +
+                             required("-onlyCoding", onlyCoding.toString) +
                              optional("-c", config) +
                              required("-i", "vcf") +
                              required("-o", "vcf") +