[ADAM-439] Fix ADAM to account for BDG-FORMATS-35
Fixed flipped index in indel realigner.
Merge branch '440-fix-indelrealigner' of https://github.com/fnothaft/adam into fnothaft-440-fix-indelrealigner

* '440-fix-indelrealigner' of https://github.com/fnothaft/adam:
  Fixed flipped index in indel realigner.
  [ADAM-439] Fix ADAM to account for BDG-FORMATS-35

Conflicts:
	adam-core/src/main/scala/org/bdgenomics/adam/converters/VCFLineConverter.scala
	adam-core/src/main/scala/org/bdgenomics/adam/models/SequenceDictionary.scala
Merge branch 'fnothaft-440-fix-indelrealigner' into ADAM-439

* fnothaft-440-fix-indelrealigner:
  Fixed flipped index in indel realigner.
  [ADAM-439] Fix ADAM to account for BDG-FORMATS-35