- s -

• Sam() : gamgee::Sam
• SamBuilder() : gamgee::SamBuilder
• SamBuilderDataField() : gamgee::SamBuilderDataField
• SamHeader() : gamgee::SamHeader
• SamIterator() : gamgee::SamIterator
• SamPairIterator() : gamgee::SamPairIterator
• sample_index() : gamgee::VariantHeader
• samples() : gamgee::VariantHeader
• SamReader() : gamgee::SamReader< ITERATOR >
• SamTag() : gamgee::SamTag< TAG_TYPE >
• SamWriter() : gamgee::SamWriter
• secondary() : gamgee::Sam
• select_if() : gamgee::Variant
• sequence() : gamgee::Fastq
• sequence_length() : gamgee::SamHeader
• sequence_name() : gamgee::SamHeader
• 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_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
• SharedField() : gamgee::SharedField< TYPE >
• SharedFieldIterator() : gamgee::SharedFieldIterator< VALUE_TYPE >
• ShortValueOptimizedStorage() : gamgee::utils::ShortValueOptimizedStorage< ELEMENT_TYPE >
• SingleInputException() : gamgee::SingleInputException
• size() : gamgee::BaseQuals , gamgee::Cigar , gamgee::Genotype , gamgee::IndividualField< TYPE > , gamgee::IndividualFieldValue< VALUE_TYPE > , gamgee::Interval , gamgee::ReadBases , gamgee::SharedField< TYPE > , gamgee::VariantFilters , gamgee::VariantFiltersIterator
• snp() : gamgee::Genotype
• start() : gamgee::Interval
• stop() : gamgee::Interval
• 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() : gamgee::Interval
• string_individual_field() : gamgee::Variant
• string_shared_field() : gamgee::Variant
• string_tag() : gamgee::Sam
• supplementary() : gamgee::Sam
• SyncedVariantIterator() : gamgee::SyncedVariantIterator
• SyncedVariantReader() : gamgee::SyncedVariantReader< ITERATOR >