ReferenceBlockSplittingVariantIterator
- uses htslib hack to modify Variant (TODO: use VariantBuilder)
- TODO: test ref bases
MultipleVariantReader changes causes the test case for Issue #209 to pass
- but the issue still exists, so add a new test case
1. Modified ReferenceBlockSplittingVariantIterator to insert 'N' as the
reference allele for a split <NON_REF> GVCF interval. This is done by
introducing a function set_reference_allele() in Variant.
2. Uncommented the test cases for
ReferenceBlockSplittingVariantIteratorr reference allele
3. The problem*.vcf files failed because their headers did not declare
an END field. htslib assumes that fields which are not declared are of
type String. Declaring END as an integer field in these files solves the
problem.
Make temporary mutators private
Merge pull request #354 from broadinstitute/jt_kg_rbs

ReferenceBlockSplittingVariantIterator