seqan3::format_sam Member List

This is the complete list of members for seqan3::format_sam, including all inherited members.

arithmetic_buffer	seqan3::detail::format_sam_base	protected
check_and_assign_ref_id(ref_id_type &ref_id, ref_id_tmp_type &ref_id_tmp, header_type &header, ref_seqs_type &)	seqan3::detail::format_sam_base	inlineprotected
default_header	seqan3::format_sam	private
default_or(detail::ignore_t) const noexcept	seqan3::format_sam	inlineprivate
default_or(t &&v) const noexcept	seqan3::format_sam	inlineprivate
dummy	seqan3::format_sam	privatestatic
file_extensions	seqan3::format_sam	inlinestatic
format_sam()=default	seqan3::format_sam
format_sam(format_sam const &)=delete	seqan3::format_sam
format_sam(format_sam &&)=default	seqan3::format_sam
format_sam_base()=default	seqan3::detail::format_sam_base	protected
format_sam_base(format_sam_base const &)=default	seqan3::detail::format_sam_base	protected
format_sam_base(format_sam_base &&)=default	seqan3::detail::format_sam_base	protected
format_version	seqan3::detail::format_sam_base	protectedstatic
header_was_written	seqan3::detail::format_sam_base	protected
operator=(format_sam const &)=delete	seqan3::format_sam
operator=(format_sam &&)=default	seqan3::format_sam
seqan3::detail::format_sam_base::operator=(format_sam_base const &)=default	seqan3::detail::format_sam_base	protected
seqan3::detail::format_sam_base::operator=(format_sam_base &&)=default	seqan3::detail::format_sam_base	protected
raw_record	seqan3::format_sam	private
read_alignment_record(stream_type &stream, sam_file_input_options< seq_legal_alph_type > const &options, ref_seqs_type &ref_seqs, sam_file_header< ref_ids_type > &header, stream_pos_type &position_buffer, seq_type &seq, qual_type &qual, id_type &id, ref_seq_type &ref_seq, ref_id_type &ref_id, ref_offset_type &ref_offset, cigar_type &cigar_vector, flag_type &flag, mapq_type &mapq, mate_type &mate, tag_dict_type &tag_dict, e_value_type &e_value, bit_score_type &bit_score)	seqan3::format_sam	inlineprotected
read_arithmetic_field(std::string_view const &str, arithmetic_target_type &arithmetic_target)	seqan3::detail::format_sam_base	inlineprotected
read_forward_range_field(stream_view_type &&stream_view, target_range_type &target)	seqan3::detail::format_sam_base	inlineprotected
read_forward_range_field(std::string_view const str, target_range_type &target)	seqan3::detail::format_sam_base	inlineprotected
read_header(stream_view_type &&stream_view, sam_file_header< ref_ids_type > &hdr, ref_seqs_type &, sam_file_input_options< seq_legal_alph_type > const &options)	seqan3::detail::format_sam_base	inlineprotected
read_sam_byte_vector(seqan3::detail::sam_tag_variant &variant, std::string_view const str)	seqan3::format_sam	inlineprivate
read_sam_dict(std::string_view const tag_str, sam_tag_dictionary &target)	seqan3::format_sam	inlineprivate
read_sam_dict_vector(seqan3::detail::sam_tag_variant &variant, std::string_view const str, value_type value)	seqan3::format_sam	inlineprivate
read_sequence_record(stream_type &stream, sequence_file_input_options< seq_legal_alph_type > const &options, stream_pos_type &position_buffer, seq_type &sequence, id_type &id, qual_type &qualities)	seqan3::format_sam	inlineprotected
ref_info_present_in_header	seqan3::detail::format_sam_base	protected
soft_clipping_at_front(std::vector< cigar > const &cigar_vector) const	seqan3::detail::format_sam_base	inlineprotected
tmp_qual	seqan3::format_sam	private
write_alignment_record(stream_type &stream, sam_file_output_options const &options, header_type &&header, seq_type &&seq, qual_type &&qual, id_type &&id, ref_seq_type &&ref_seq, ref_id_type &&ref_id, std::optional< int32_t > ref_offset, std::vector< cigar > const &cigar_vector, sam_flag const flag, uint8_t const mapq, mate_type &&mate, tag_dict_type &&tag_dict, e_value_type &&e_value, bit_score_type &&bit_score)	seqan3::format_sam	inlineprotected
write_header(stream_t &stream, sam_file_output_options const &options, header_type &header)	seqan3::detail::format_sam_base	inlineprotected
write_range_or_asterisk(stream_it_t &stream_it, field_type &&field_value)	seqan3::format_sam	inlineprivate
write_range_or_asterisk(stream_it_t &stream_it, char const *const field_value)	seqan3::format_sam	inlineprivate
write_sequence_record(stream_type &stream, sequence_file_output_options const &options, seq_type &&sequence, id_type &&id, qual_type &&qualities)	seqan3::format_sam	inlineprotected
write_tag_fields(stream_it_t &stream, sam_tag_dictionary const &tag_dict, char const separator)	seqan3::format_sam	inlineprivate
~format_sam()=default	seqan3::format_sam
~format_sam_base()=default	seqan3::detail::format_sam_base	protected