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LAST BUILD ON BRANCH intel_var_header_merger

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• intel_var_header_merger
• ak_fix_samples_to_include_in_variant_reader
• ak_hadle_samples_in_variant_reader
• ak_ignore_emacs_temporaries
• ak_n_samples_error
• bh_IndividualFieldValueIterator_minus
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• dr_copy_foghorn_submodule_update_script
• dr_fix_IndividualFieldValue_missing
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• dr_fix_float_missing_check
• dr_fix_genotype_encoding_of_vector_ends
• dr_fix_genotype_handling_of_vector_end
• dr_fix_includes_in_merged_lut
• dr_improve_variant_builder_doxygen
• dr_monolithic_gamgee_header
• dr_prevent_gt_field_set_using_integer_setters
• dr_remove_header_deep_copying
• dr_remove_obsolete_call_in_merge_variant_headers
• dr_rename_samtag_is_missing
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• dr_rev_htslib_nov6
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• dr_variant_builder
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• intel_boost-build
• intel_clang_fix
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• intel_int_cast_missing_end_fix
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• jt_VariantHeaderBuilder_212
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• ks_genotype_field_value_jul_17
• ks_genotype_field_value_jul_22
• ks_genotype_field_value_jul_23
• ks_genotype_field_value_jul_24
• ks_genotype_field_value_jul_25
• ks_index_based_access_for_shared_and_individual_fields_aug_12
• ks_interval_sam_iteration_using_indexed_files_aug_14
• ks_interval_sam_iteration_using_indexed_files_issue_7
• ks_non_ref_het_211
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• ldg_updateReadme
• master
• mc_add_field_conversion_api_175
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• mc_build_release_by_default
• mc_centralize_exceptions_170
• mc_cmake_clion
• mc_contig_renaming
• mc_contigs_highlander
• mc_coveralls
• mc_eliminate_gq_and_pl
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• mc_fix_filter_unpacking
• mc_fix_n_samples
• mc_fix_variant_field_iterators
• mc_generic_test_utils_206
• mc_include_guards
• mc_index_based_api_162
• mc_individual_operator_equals_187
• mc_insert_size
• mc_interval_support_163
• mc_mate_alignment_stop
• mc_missing_string_value
• mc_missing_vector_105
• mc_more_tests
• mc_operator_equals_shared_186
• mc_random_cleanups
• mc_readme_updates_for_blog
• mc_refactor_fetch_next_record_192
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• mc_relase_mode_testing
• mc_remove_ycm_files
• mc_rename_format_field_type_171
• mc_rename_info_and_format
• mc_sam_header_fixes
• mc_snps_and_indels
• mc_travis_experiments
• mc_travis_update_cmake
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• mc_website_dox_update
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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, =