Fix bug which causes insert fail of VariantCalls read failures which are also not imputed

[aneilbaboo]

• Partially addresses #354 (VariantCall validation on end fails)
  • we either need some changes to bioinformatics or need to do some more work on this branch.
• Fixes #341 (Genotype likelihood validation needs to support alt bases)
• Fixes #343 (Allow empty alt bases)
• May address part of the problem mentioned in #353 (Handle gene import errors)
• Adds readFail boolean to VariantCall