Check sequence dictionary compatibility at startup

[droazen]

We need to port the GATK code that checks sequence dictionary compatibility of reads vs reference, and have this check run at startup, since the engine assumes compatibility. This will require a few modifications, since the legacy code is hardcoded to look for certain references/contigs in a few places, such as where it checks for non-canonical human ordering.

[akiezun]

is this happening for AyeAye?

[droazen]

Note that a compatibility check was added to CachingIndexedFastaSequenceFile as part of #357. We might be able to remove this check once we have comprehensive up-front compatibility checks in place.

[droazen]

This will require porting SequenceDictionaryUtils.validateDictionaries() from the old GATK.

[droazen]

Step #1: Port as much of SequenceDictionaryUtils as needed from the old GATK (remove garbage like validation exclusions, fix terrible things like non-canonical human order check if possible, if not create tickets). Port unit tests as well.

Step #2: Hook up sequence dictionary validation to hellbender engine, and add integration tests to prove that dictionary incompatibilities are detected. Best place to hook this up is probably GATKTool.onStartup(), since it manages all the engine-level inputs for tools.