Here is a list of all class members with links to the classes they belong to:

- s -

• s : __kstring_t , __linkbuf_t , cram_decode_job
• S : cram_feature
• s : cram_record , hts_opt
• Sam() : gamgee::Sam
• SamBuilder : gamgee::BaseQuals , gamgee::Cigar , gamgee::ReadBases , gamgee::Sam , gamgee::SamBuilder , gamgee::SamHeader
• SamBuilderDataField() : gamgee::SamBuilderDataField
• SamHeader() : gamgee::SamHeader
• SamIterator() : gamgee::SamIterator
• SamPairIterator() : gamgee::SamPairIterator
• sample : gamgee::ReadGroup
• sample_index() : gamgee::VariantHeader
• samples : bcf_hdr_t , bcf_sr_t , bcf_srs_t , gamgee::VariantHeader
• SamReader() : gamgee::SamReader< ITERATOR >
• SamTag() : gamgee::SamTag< TAG_TYPE >
• SamWriter : gamgee::Sam , gamgee::SamHeader , gamgee::SamWriter
• save_bin : __hts_idx_t
• save_off : __hts_idx_t
• save_tid : __hts_idx_t
• sc : tbx_conf_t
• sdict : bam_hdr_t
• se : tbx_intv_t
• secondary() : gamgee::Sam
• seek : hFILE_backend
• seek_offset : knetFile_s
• select_if() : gamgee::Variant
• sep : ks_tokaux_t
• seq : _regidx_t , cram_record , ref_entry
• seq2regs : _regidx_t
• seq_hash : _bcf_sr_regions_t
• seq_idx : cram_feature
• seq_names : _bcf_sr_regions_t , _regidx_t
• seqs_blk : cram_slice
• seqs_per_slice : cram_fd
• sequence() : gamgee::Fastq
• sequence_length() : gamgee::SamHeader
• sequence_name() : gamgee::SamHeader
• serial : t_pool_job , t_res
• set() : gamgee::utils::ShortValueOptimizedStorage< ELEMENT_TYPE > , gamgee::VariantBuilderCoreField< FIELD_TYPE >
• set_alignment_start() : gamgee::Sam , gamgee::SamBuilder , gamgee::VariantBuilder
• set_alignment_stop() : gamgee::VariantBuilder
• set_alt_allele() : gamgee::VariantBuilder , gamgee::VariantBuilderSharedRegion
• set_alt_alleles() : gamgee::VariantBuilder , gamgee::VariantBuilderSharedRegion
• set_base() : gamgee::ReadBases
• set_base_quals() : gamgee::SamBuilder
• set_bases() : gamgee::SamBuilder
• set_boolean_shared_field() : gamgee::VariantBuilder
• set_chr() : gamgee::Interval
• set_chromosome() : gamgee::Sam , gamgee::SamBuilder , gamgee::VariantBuilder
• set_cigar() : gamgee::SamBuilder
• set_comment() : gamgee::Fastq
• set_duplicate() : gamgee::Sam , gamgee::SamBuilder
• set_enable_validation() : gamgee::VariantBuilder , gamgee::VariantBuilderIndividualRegion , gamgee::VariantBuilderSharedRegion
• set_entire_field() : gamgee::VariantBuilderIndividualField< ENCODED_TYPE, BULK_CHANGE_TYPE >
• set_fail() : gamgee::Sam , gamgee::SamBuilder
• set_filters() : gamgee::VariantBuilder , gamgee::VariantBuilderSharedRegion
• set_first() : gamgee::Sam , gamgee::SamBuilder
• set_float_field_by_sample() : gamgee::VariantBuilderIndividualRegion
• set_float_individual_field() : gamgee::VariantBuilder
• set_float_shared_field() : gamgee::VariantBuilder
• set_genotype() : gamgee::VariantBuilder
• set_genotype_field_by_sample() : gamgee::VariantBuilderIndividualRegion
• set_genotypes() : gamgee::VariantBuilder
• set_id() : gamgee::VariantBuilder , gamgee::VariantBuilderSharedRegion
• set_info_field() : gamgee::VariantBuilderSharedRegion
• set_insert_size() : gamgee::Sam
• set_integer_field_by_sample() : gamgee::VariantBuilderIndividualRegion
• set_integer_individual_field() : gamgee::VariantBuilder
• set_integer_shared_field() : gamgee::VariantBuilder
• set_last() : gamgee::Sam , gamgee::SamBuilder
• set_mapping_qual() : gamgee::Sam
• set_mate_alignment_start() : gamgee::Sam , gamgee::SamBuilder
• set_mate_chromosome() : gamgee::Sam , gamgee::SamBuilder
• set_mate_reverse() : gamgee::Sam , gamgee::SamBuilder
• set_mate_unmapped() : gamgee::Sam , gamgee::SamBuilder
• set_name() : gamgee::Fastq , gamgee::SamBuilder
• set_not_duplicate() : gamgee::Sam , gamgee::SamBuilder
• set_not_fail() : gamgee::Sam , gamgee::SamBuilder
• set_not_first() : gamgee::Sam , gamgee::SamBuilder
• set_not_last() : gamgee::Sam , gamgee::SamBuilder
• set_not_mate_reverse() : gamgee::Sam , gamgee::SamBuilder
• set_not_mate_unmapped() : gamgee::Sam , gamgee::SamBuilder
• set_not_paired() : gamgee::Sam , gamgee::SamBuilder
• set_not_reverse() : gamgee::Sam , gamgee::SamBuilder
• set_not_secondary() : gamgee::Sam , gamgee::SamBuilder
• set_not_supplementary() : gamgee::Sam , gamgee::SamBuilder
• set_not_unmapped() : gamgee::Sam , gamgee::SamBuilder
• set_output_type() : gamgee::Interval
• set_paired() : gamgee::Sam , gamgee::SamBuilder
• set_qual() : gamgee::VariantBuilder
• set_quals() : gamgee::Fastq
• set_ref_allele() : gamgee::VariantBuilder , gamgee::VariantBuilderSharedRegion
• set_reverse() : gamgee::Sam , gamgee::SamBuilder
• set_sample_field_value() : gamgee::VariantBuilderIndividualField< ENCODED_TYPE, BULK_CHANGE_TYPE >
• set_sample_value() : gamgee::VariantBuilderMultiSampleVector< ELEMENT_TYPE >
• set_sample_values() : gamgee::VariantBuilderMultiSampleVector< ELEMENT_TYPE >
• set_secondary() : gamgee::Sam , gamgee::SamBuilder
• set_sequence() : gamgee::Fastq
• set_start() : gamgee::Interval
• set_stop() : gamgee::Interval
• set_string_field_by_sample() : gamgee::VariantBuilderIndividualRegion
• set_string_individual_field() : gamgee::VariantBuilder
• set_string_shared_field() : gamgee::VariantBuilder
• set_supplementary() : gamgee::Sam , gamgee::SamBuilder
• set_unmapped() : gamgee::Sam , gamgee::SamBuilder
• shared : bcf1_t
• shared_dirty : bcf_dec_t
• shared_field_as_float() : gamgee::Variant
• shared_field_as_integer() : gamgee::Variant
• shared_field_as_string() : gamgee::Variant
• shared_field_type() : gamgee::VariantHeader
• shared_fields() : gamgee::VariantHeader
• shared_ref : cram_fd
• SharedField() : gamgee::SharedField< TYPE >
• SharedFieldIterator() : gamgee::SharedFieldIterator< VALUE_TYPE >
• ShortValueOptimizedStorage() : gamgee::utils::ShortValueOptimizedStorage< ELEMENT_TYPE >
• shutdown : t_pool
• SingleInputException() : gamgee::SingleInputException
• size : bcf_fmt_t , cache_t , cram_map , fmt_aux_t , gamgee::BaseQuals , gamgee::Cigar , gamgee::Genotype , gamgee::IndividualField< TYPE > , gamgee::IndividualFieldValue< VALUE_TYPE > , gamgee::Interval , gamgee::ReadBases , gamgee::SharedField< TYPE > , gamgee::VariantFilters , gamgee::VariantFiltersIterator , mFILE
• size_cmd : knetFile_s
• slice : cram_container , cram_index
• slice_num : cram_fd
• slice_rec : cram_container
• slices : cram_container
• slices_per_container : cram_fd
• snp() : gamgee::Genotype
• soft_blk : cram_slice
• ss : tbx_intv_t
• start : _bcf_sr_regions_t , cram_index , cram_range , gamgee::Interval , RansDecSymbol , reg_t , region1_t
• start_offset : gamgee::SharedBufferSpan
• start_prev : _regidx_t
• stats : cram_container
• stop : cram_byte_array_stop_decoder , gamgee::Interval
• store : cram_codec
• store_merged_field_idx_for_enum() : gamgee::VariantHeaderMerger< fields_forward_LUT_ordering, fields_reverse_LUT_ordering, samples_forward_LUT_ordering, samples_reverse_LUT_ordering >
• str : _regidx_t , gamgee::Interval , SAM_hdr_tag_s , string_t
• str_pool : SAM_hdr
• strat : cram_metrics
• streaming : bcf_srs_t
• string_individual_field() : gamgee::Variant
• string_shared_field() : gamgee::Variant
• string_tag() : gamgee::Sam
• strings : string_alloc_t
• subexp : cram_codec
• substitution_matrix : cram_block_compression_hdr
• supplementary() : gamgee::Sam
• symbol : cram_huffman_code
• SyncedVariantIterator() : gamgee::SyncedVariantIterator
• SyncedVariantReader() : gamgee::SyncedVariantReader< ITERATOR >
• sz_bzip2 : cram_metrics
• sz_gz_def : cram_metrics
• sz_gz_rle : cram_metrics
• sz_lzma : cram_metrics
• sz_rans0 : cram_metrics
• sz_rans1 : cram_metrics