Don't break with strange INFO or FILTER (or other) headers

At the end of the snpEffBuildAndRun process we check that there are not too many warnings in the VCF output. This uses PyVCF. Unfortunately PyVCF isn't able to parse some headers, in this case some INFO and FILTER headers. These aren't what we're looking to check so I've updated the script to ignore them entirely.

A future version of PyVCF might be able to parse these headers better, in which case these commits could be reverted, but this seems like a pragmatic solution for now.

Specify java memory for -version

Specifies how much memory to allocate to the JVM when running java -version. This helps on our farm which doesn't seem to like allocating the default memory without the job being bsub'd

Add more java sources

snpEff needs a copy of Java 1.7 to be happy, this now looks in more places to find a copy.

Fixes NFS bug by closing a file

Merge pull request #4 from bewt85/bt5_fix_nfs_dir_delete

Close annotated VCF

Renamed project to SnpEffWrapper

Merge pull request #3 from bewt85/bt5_rename_everything

Rename project to snpEffWrapper