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Ran 18 Nov 2014 05:19PM UTC

Files 192

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Committed 18 Nov 2014 04:59PM UTC coverage: 91.402% (+2.7%) from 88.657%

Job # 1447.2

Build Type

push

travis-ci

Committed by Karthik Gururaj

Commit Message

1. Added VariantHeaderMerger and MergedVCFLUT for fast field look up
between input VCFs and merged VCF.
2. VariantHeaderMerger accepts both shared_ptr<bcf_hdr_t> and
VariantHeader& as inputs. To do this, VariantHeaderMerger
is now a friend of VariantHeader so that m_header can be directly
accessed.
3. Created two VariantHeaderMerger variants optimized for two different
purposes
  a. InputOrderedVariantHeaderMerger - fast traversal of all fields for
a single input VCF
  a. FieldOrderedVariantHeaderMerger - fast traversal of all input VCFs
for a single field
4. Created more rigorous tests for LUT.

5. Store shared_ptr<bcf_hdr_t> within VariantHeaderMerger. Use raw
pointers only when needed
6. Added a get_input_vcf_headers() function for MultipleVariantReader
7. Missing values in VariantHeaderMerger are represented by
bcf_int32_missing

8. Added get_field_name(), get_sample_name() in VariantHeader

9. VariantHeaderMerger can store merged field idx for a user defined
enum. Updated comments with information about how to use this feature

10. Move constructor, = for VariantHeaderMerger - disable deep copy
constructor, =

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