SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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This is the complete list of members for seqan3::format_bam, including all inherited members.
arithmetic_buffer | seqan3::detail::format_sam_base | private |
char_to_sam_rank | seqan3::format_bam | privatestatic |
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 | inlineprivate |
file_extensions | seqan3::format_bam | inlinestatic |
format_bam()=default | seqan3::format_bam | |
format_bam(format_bam const &)=default | seqan3::format_bam | |
format_bam(format_bam &&)=default | seqan3::format_bam | |
format_sam_base()=default | seqan3::detail::format_sam_base | private |
format_sam_base(format_sam_base const &)=default | seqan3::detail::format_sam_base | private |
format_sam_base(format_sam_base &&)=default | seqan3::detail::format_sam_base | private |
format_version | seqan3::detail::format_sam_base | privatestatic |
get_tag_dict_str(sam_tag_dictionary const &tag_dict) | seqan3::format_bam | inlineprivatestatic |
header_was_read | seqan3::format_bam | private |
header_was_written | seqan3::detail::format_sam_base | private |
operator=(format_bam const &)=default | seqan3::format_bam | |
operator=(format_bam &&)=default | seqan3::format_bam | |
seqan3::detail::format_sam_base::operator=(format_sam_base const &)=default | seqan3::detail::format_sam_base | private |
seqan3::detail::format_sam_base::operator=(format_sam_base &&)=default | seqan3::detail::format_sam_base | private |
parse_binary_cigar(std::string_view const cigar_str) const | seqan3::format_bam | inlineprivate |
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_bam | inlineprotected |
read_arithmetic_field(std::string_view const &str, arithmetic_target_type &arithmetic_target) | seqan3::detail::format_sam_base | inlineprivate |
read_float_byte_field(stream_view_type &&stream_view, float &target) | seqan3::format_bam | inlineprivate |
read_forward_range_field(stream_view_type &&stream_view, target_range_type &target) | seqan3::detail::format_sam_base | inlineprivate |
read_forward_range_field(std::string_view const str, target_range_type &target) | seqan3::detail::format_sam_base | inlineprivate |
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 | inlineprivate |
read_integral_byte_field(stream_view_type &&stream_view, number_type &target) | seqan3::format_bam | inlineprivate |
read_integral_byte_field(std::string_view const str, number_type &target) | seqan3::format_bam | inlineprivate |
read_sam_dict(std::string_view const tag_str, sam_tag_dictionary &target) | seqan3::format_bam | inlineprivate |
read_sam_dict_vector(seqan3::detail::sam_tag_variant &variant, std::string_view const str, value_type const &value) | seqan3::format_bam | inlineprivate |
ref_info_present_in_header | seqan3::detail::format_sam_base | private |
reg2bin(int32_t beg, int32_t end) noexcept | seqan3::format_bam | inlineprivatestatic |
soft_clipping_at_front(std::vector< cigar > const &cigar_vector) const | seqan3::detail::format_sam_base | inlineprivate |
string_buffer | seqan3::format_bam | 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, cigar_type &&cigar_vector, sam_flag const flag, uint8_t const mapq, mate_type &&mate, tag_dict_type &&tag_dict, double e_value, double bit_score) | seqan3::format_bam | inlineprotected |
write_header(stream_t &stream, sam_file_output_options const &options, header_type &header) | seqan3::format_bam | inlineprivate |
~format_bam()=default | seqan3::format_bam | |
~format_sam_base()=default | seqan3::detail::format_sam_base | private |