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• jt_rbs_checkpoint_1
• 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
• bh_select_if_doc
• bh_vimbup_gitignore
• boost-build
• db_iterator_patch
• db_read_groups
• dr_VariantBuilderMultiSampleVector_bounds_checking
• dr_copy_foghorn_submodule_update_script
• dr_fix_IndividualFieldValue_missing
• dr_fix_additional_reader_segfaults_on_nonexistent_files
• 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
• dr_rev_htslib_and_remove_synced_reader_hack
• dr_rev_htslib_nov6
• dr_test_multi_sample_vector_with_max_size_zero
• dr_variant_builder
• dr_variant_header_builder_case_sensitivity_bug
• dr_variant_missing_function
• dr_variantreader_fix_segfault_on_nonexistent_file
• dr_vb_auto_encode_genotypes
• dr_vb_flattened_vector_helper_functions
• htslib_revup
• intel_boost-build
• intel_clang_fix
• intel_header_field_length
• intel_individual_field_value_iterator_increment
• intel_int_cast_missing_end_fix
• intel_iterator_inc_dec
• intel_multi_iterator_fix
• intel_resize_lut
• intel_signed_comparison
• intel_signed_comparison_fixes
• intel_test_branch
• intel_var_header_merger
• intel_vector_end
• intel_whitespace_fix
• jt_VariantHeaderBuilder_212
• jt_alignment_stop
• jt_allele_strings
• jt_api_226
• jt_bcf_close
• jt_comments
• jt_compression_161
• jt_directories
• jt_field_type
• jt_file_index
• jt_front_back
• jt_gamgee_h
• jt_gitignore
• jt_individual_field_value_missing
• jt_kg_rbs
• jt_max_field
• jt_misc
• jt_misc_fixes
• jt_move_field_type
• jt_mvr_126
• jt_mvr_fixes
• jt_mvr_nondeterminism
• jt_mvr_optimization
• jt_parse_rlen
• jt_pending_vector
• jt_pqueue
• jt_raw_pointer_removal
• jt_rbs
• jt_rbs_updates
• jt_rbs_v10
• jt_rbs_v6
• jt_rbs_v7
• jt_rbs_v8
• jt_rbs_v9
• jt_rbs_vb
• jt_rbs_vb2
• jt_readme
• jt_ref_api
• jt_ref_block
• jt_ref_block_mc
• jt_ref_block_traversal
• jt_single_reader_vectors
• jt_sparse_SVI
• jt_sync_cache_headers
• jt_sync_no_intervals
• jt_synced
• jt_tmp_pq
• jt_travis
• jt_tsca_tiling_const
• jt_unsigned
• jt_variant_header_merge
• jt_variant_intervals
• jt_vh_sample_index
• jt_vr_test_cleanup
• ks_genotype_field_value
• 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
• lb_276_add_interval_accessor
• lb_277_move_interval_changes_to_gamgee
• lb_rename_alleles_keys
• ldg_updateReadme
• master
• mc_add_field_conversion_api_175
• mc_add_sam_tests
• mc_api_docs_158
• mc_banish_all_const_member_variables
• 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
• mc_eliminate_is
• mc_expunge_copy_then_move
• 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
• mc_reimplement_shared_fields
• 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
• mc_update_boundary_checks
• mc_variant_id_field
• mc_variant_string_format_field_fix
• mc_website_dox_update
• mc_zip_iterator

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.