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| 1 | Package:·seqan3-doc | 1 | Package:·seqan3-doc |
| 2 | Source:·seqan3 | 2 | Source:·seqan3 |
| 3 | Version:·3.4.0~rc.1+ds-1~0exp0 | 3 | Version:·3.4.0~rc.1+ds-1~0exp0 |
| 4 | Architecture:·all | 4 | Architecture:·all |
| 5 | Maintainer:·Debian·Med·Packaging·Team·<debian-med-packaging@lists.alioth.debian.org> | 5 | Maintainer:·Debian·Med·Packaging·Team·<debian-med-packaging@lists.alioth.debian.org> |
| 6 | Installed-Size:·501 | 6 | Installed-Size:·50170 |
| 7 | Depends:·doxygen-awesome-css | 7 | Depends:·doxygen-awesome-css |
| 8 | Suggests:·libseqan3-dev | 8 | Suggests:·libseqan3-dev |
| 9 | Section:·doc | 9 | Section:·doc |
| 10 | Priority:·optional | 10 | Priority:·optional |
| 11 | Multi-Arch:·foreign | 11 | Multi-Arch:·foreign |
| 12 | Homepage:·https://www.seqan.de/ | 12 | Homepage:·https://www.seqan.de/ |
| 13 | Description:·C++·library·for·the·analysis·of·biological·sequences·v3·(documentation) | 13 | Description:·C++·library·for·the·analysis·of·biological·sequences·v3·(documentation) |
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| 6 | ········['../group__alignment.html#autotoc_md3',·1,·'Alignments·represented·as·CIGAR·String·used·in·SAM/BAM·Files'] | 6 | ········['../group__alignment.html#autotoc_md3',·1,·'Alignments·represented·as·CIGAR·String·used·in·SAM/BAM·Files'] |
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| 8 | ····['sam_20file_4',·['sam·file',·['../cookbook.html#autotoc_md65',·1,·'Map·reads·and·write·output·to·SAM·file'], | 8 | ····['sam_20file_4',·['sam·file',·['../cookbook.html#autotoc_md65',·1,·'Map·reads·and·write·output·to·SAM·file'], |
| 9 | ········['../group__io__sam__file.html',·1,·'SAM·File'] | 9 | ········['../group__io__sam__file.html',·1,·'SAM·File'] |
| 10 | ····]], | 10 | ····]], |
| 11 | ····['sam_20file_20and_20constructing_20an_20alignment_5',·['Reading·the·CIGAR·information·from·a·SAM·file·and·constructing·an·alignment',·['../cookbook.html#autotoc_md64',·1,·'']]], | 11 | ····['sam_20file_20and_20constructing_20an_20alignment_5',·['Reading·the·CIGAR·information·from·a·SAM·file·and·constructing·an·alignment',·['../cookbook.html#autotoc_md64',·1,·'']]], |
| 12 | ····['sam_20file_20fields_6',·['SAM·file·fields',·['../tutorial_sam_file.html#autotoc_md201',·1,·'']]], | 12 | ····['sam_20file_20fields_6',·['SAM·file·fields',·['../tutorial_sam_file.html#autotoc_md201',·1,·'']]], |
| 13 | ····['sam_20files_7',·['sam·files',·['../tutorial_sam_file.html#autotoc_md203',·1,·'Reading·SAM·files'], | ||
| 14 | ······ | 13 | ····['sam_20files_7',·['sam·files',·['../md__2build_2reproducible-path_2seqan3-3_84_80_0irc_81_09ds_2doc_2fragments_2io__sam__file__input.html',·1,·'Reading·SAM·files'], |
| 14 | ········['../tutorial_sam_file.html#autotoc_md203',·1,·'Reading·SAM·files'], | ||
| 15 | ········['../md__2build_2reproducible-path_2seqan3-3_84_80_0irc_81_09ds_2doc_2fragments_2io__sam__file__output.html',·1,·'Writing·SAM·files'] | 15 | ········['../md__2build_2reproducible-path_2seqan3-3_84_80_0irc_81_09ds_2doc_2fragments_2io__sam__file__output.html',·1,·'Writing·SAM·files'] |
| 16 | ····]], | 16 | ····]], |
| 17 | ····['sam_20format_8',·['SAM·format',·['../tutorial_sam_file.html#autotoc_md199',·1,·'']]], | 17 | ····['sam_20format_8',·['SAM·format',·['../tutorial_sam_file.html#autotoc_md199',·1,·'']]], |
| 18 | ····['sam_20input_20and_20output_20in_20seqan_9',·['SAM·Input·and·Output·in·SeqAn',·['../tutorial_sam_file.html',·1,·'']]], | 18 | ····['sam_20input_20and_20output_20in_20seqan_9',·['SAM·Input·and·Output·in·SeqAn',·['../tutorial_sam_file.html',·1,·'']]], |
| 19 | ····['sam_5ffile_2finput_2ehpp_10',·['input.hpp',·['../sam__file_2input_8hpp.html',·1,·'']]], | 19 | ····['sam_5ffile_2finput_2ehpp_10',·['input.hpp',·['../sam__file_2input_8hpp.html',·1,·'']]], |
| 20 | ····['sam_5ffile_2finput_5fformat_5fconcept_2ehpp_11',·['input_format_concept.hpp',·['../sam__file_2input__format__concept_8hpp.html',·1,·'']]], | 20 | ····['sam_5ffile_2finput_5fformat_5fconcept_2ehpp_11',·['input_format_concept.hpp',·['../sam__file_2input__format__concept_8hpp.html',·1,·'']]], |
| 21 | ····['sam_5ffile_2finput_5foptions_2ehpp_12',·['input_options.hpp',·['../sam__file_2input__options_8hpp.html',·1,·'']]], | 21 | ····['sam_5ffile_2finput_5foptions_2ehpp_12',·['input_options.hpp',·['../sam__file_2input__options_8hpp.html',·1,·'']]], |
| 22 | ····['sam_5ffile_2foutput_5fformat_5fconcept_2ehpp_13',·['output_format_concept.hpp',·['../sam__file_2output__format__concept_8hpp.html',·1,·'']]], | 22 | ····['sam_5ffile_2foutput_5fformat_5fconcept_2ehpp_13',·['output_format_concept.hpp',·['../sam__file_2output__format__concept_8hpp.html',·1,·'']]], |
| 23 | ····['sam_5ffile_2foutput_5foptions_2ehpp_14',·['output_options.hpp',·['../sam__file_2output__options_8hpp.html',·1,·'']]], | 23 | ····['sam_5ffile_2foutput_5foptions_2ehpp_14',·['output_options.hpp',·['../sam__file_2output__options_8hpp.html',·1,·'']]], |
| 24 | ····['sam_5ffile_2frecord_2ehpp_15',·['record.hpp',·['../sam__file_2record_8hpp.html',·1,·'']]], | 24 | ····['sam_5ffile_2frecord_2ehpp_15',·['record.hpp',·['../sam__file_2record_8hpp.html',·1,·'']]], |
| 25 | ····['sam_5ffile_5fheader_16',·['sam_file_header',·['../classseqan3_1_1sam__file__header.html#a95ab27758113162816cf23dad1b6472f',·1,·'seqan3::sam_file_header::sam_file_header()'], | ||
| 25 | ···· | 26 | ········['../classseqan3_1_1sam__file__header.html',·1,·'seqan3::sam_file_header<·ref_ids_type·>'], |
| 27 | ········['../classseqan3_1_1sam__file__header.html#ac9432473c5730672f9291b8fcc1247cf',·1,·'seqan3::sam_file_header::sam_file_header()=default'], | ||
| 26 | ········['../classseqan3_1_1sam__file__header.html#af3a0cd3e24612f97071c002eb1f571f9',·1,·'seqan3::sam_file_header::sam_file_header(ref_ids_type·&&ref_ids)'], | 28 | ········['../classseqan3_1_1sam__file__header.html#af3a0cd3e24612f97071c002eb1f571f9',·1,·'seqan3::sam_file_header::sam_file_header(ref_ids_type·&&ref_ids)'], |
| 27 | ········['../classseqan3_1_1sam__file__header.html#a48504cfc1e94046226931ef746c6523b',·1,·'seqan3::sam_file_header::sam_file_header(ref_ids_type·&ref_ids)'], | 29 | ········['../classseqan3_1_1sam__file__header.html#a48504cfc1e94046226931ef746c6523b',·1,·'seqan3::sam_file_header::sam_file_header(ref_ids_type·&ref_ids)'], |
| 28 | ········['../classseqan3_1_1sam__file__header.html#a73c8624122e34608794e122035978891',·1,·'seqan3::sam_file_header::sam_file_header(sam_file_header·&&)=default'] | 30 | ········['../classseqan3_1_1sam__file__header.html#a73c8624122e34608794e122035978891',·1,·'seqan3::sam_file_header::sam_file_header(sam_file_header·&&)=default'] |
| 29 | ········['../classseqan3_1_1sam__file__header.html#a95ab27758113162816cf23dad1b6472f',·1,·'seqan3::sam_file_header::sam_file_header(sam_file_header·const·&)=delete'], | ||
| 30 | ········['../classseqan3_1_1sam__file__header.html#ac9432473c5730672f9291b8fcc1247cf',·1,·'seqan3::sam_file_header::sam_file_header()=default'] | ||
| 31 | ····]], | 31 | ····]], |
| 32 | ····['sam_5ffile_5finput_17',·['sam_file_input',·['../classseqan3_1_1sam__file__input.html#a66020c4402b4f74f2b82472920baf105',·1,·'seqan3::sam_file_input::sam_file_input(stream_type·&&stream,·file_format·const·&)·->·sam_file_input<·typename·sam_file_input<>::traits_type,·typename·sam_file_input<>::selected_field_ids,·type_list<·file_format·>·>'], | ||
| 33 | ········['../classseqan3_1_1sam__file__input.html#afa266630de6a69ef1a72ee39e352a44a',·1,·'seqan3::sam_file_input::sam_file_input(stream_type·&stream,·file_format·const·&,·selected_field_ids·const·&)·->·sam_file_input<·typename·sam_file_input<>::traits_type,·selected_field_ids,·type_list<·file_format·>·>'], | ||
| 32 | ····['sam_5ffile_5finput_17',·['sam_file_input',·['../classseqan3_1_1sam__file__input.html#a258f44d17d3744e224d791c972d0cfa6',·1,·'seqan3::sam_file_input::sam_file_input(stream_type·&&stream,·ref_ids_t·&,·ref_sequences_t·&,·file_format·const·&)·->·sam_file_input<·sam_file_input_default_traits<·std::remove_reference_t<·ref_sequences_t·>,·std::remove_reference_t<·ref_ids_t·>·>,·typename·sam_file_input<>::selected_field_ids,·type_list<·file_format·>·>'], | ||
| 33 | ········['../classseqan3_1_1sam__file__input.html#a921e12f2336bc1ffd11a66a97c97f2d7',·1,·'seqan3::sam_file_input::sam_file_input(stream_type·&stream,·ref_ids_t·&,·ref_sequences_t·&,·file_format·const·&,·selected_field_ids·const·&)·->·sam_file_input<·sam_file_input_default_traits<·std::remove_reference_t<·ref_sequences_t·>,·std::remove_reference_t<·ref_ids_t·>·>,·selected_field_ids,·type_list<·file_format·>·>'], | ||
| 34 | ········['../classseqan3_1_1sam__file__input.html#add3ca53ee442fbb178b423c9207fc16c',·1,·'seqan3::sam_file_input::sam_file_input(stream_type·&&stream,·ref_ids_t·&,·ref_sequences_t·&,·file_format·const·&,·selected_field_ids·const·&)·->·sam_file_input<·sam_file_input_default_traits<·std::remove_reference_t<·ref_sequences_t·>,·std::remove_reference_t<·ref_ids_t·>·>,·selected_field_ids,·type_list<·file_format·>·>'], | ||
| 35 | ········['../classseqan3_1_1sam__file__input.html#a01739c6518938fa18b3c23509aac6005',·1,·'seqan3::sam_file_input::sam_file_input(std::filesystem::path·path,·ref_ids_t·&,·ref_sequences_t·&)·->·sam_file_input<·sam_file_input_default_traits<·std::remove_reference_t<·ref_sequences_t·>,·std::remove_reference_t<·ref_ids_t·>·>,·typename·sam_file_input<>::selected_field_ids,·typename·sam_file_input<>::valid_formats·>'], | ||
| 36 | ········['../classseqan3_1_1sam__file__input.html',·1,·'seqan3::sam_file_input<·traits_type_,·selected_field_ids_,·valid_formats_·>'], | ||
| 37 | ········['../classseqan3_1_1sam__file__input.html#a0ceba2a2fb2c1995c82ae303fa269a1a',·1,·'seqan3::sam_file_input::sam_file_input(std::filesystem::path·path,·ref_ids_t·&,·ref_sequences_t·&,·selected_field_ids·const·&)·->·sam_file_input<·sam_file_input_default_traits<·std::remove_reference_t<·ref_sequences_t·>,·std::remove_reference_t<·ref_ids_t·>·>,·selected_field_ids,·typename·sam_file_input<>::valid_formats·>'], | ||
| 38 | ········['../classseqan3_1_1sam__file__input.html#a3834b2194234b5cd25bdb2916023beeb',·1,·'seqan3::sam_file_input::sam_file_input(stream_type·&stream,·file_format·const·&)·->·sam_file_input<·typename·sam_file_input<>::traits_type,·typename·sam_file_input<>::selected_field_ids,·type_list<·file_format·>·>'], | 34 | ········['../classseqan3_1_1sam__file__input.html#a3834b2194234b5cd25bdb2916023beeb',·1,·'seqan3::sam_file_input::sam_file_input(stream_type·&stream,·file_format·const·&)·->·sam_file_input<·typename·sam_file_input<>::traits_type,·typename·sam_file_input<>::selected_field_ids,·type_list<·file_format·>·>'], |
| 35 | ········['../classseqan3_1_1sam__file__input.html#a0ceba2a2fb2c1995c82ae303fa269a1a',·1,·'seqan3::sam_file_input::sam_file_input(std::filesystem::path·path,·ref_ids_t·&,·ref_sequences_t·&,·selected_field_ids·const·&)·->·sam_file_input<·sam_file_input_default_traits<·std::remove_reference_t<·ref_sequences_t·>,·std::remove_reference_t<·ref_ids_t·>·>,·selected_field_ids,·typename·sam_file_input<>::valid_formats·>'], | ||
| 36 | ········['../classseqan3_1_1sam__file__input.html#a01739c6518938fa18b3c23509aac6005',·1,·'seqan3::sam_file_input::sam_file_input(std::filesystem::path·path,·ref_ids_t·&,·ref_sequences_t·&)·->·sam_file_input<·sam_file_input_default_traits<·std::remove_reference_t<·ref_sequences_t·>,·std::remove_reference_t<·ref_ids_t·>·>,·typename·sam_file_input<>::selected_field_ids,·typename·sam_file_input<>::valid_formats·>'], | ||
| 37 | ········['../classseqan3_1_1sam__file__input.html#add3ca53ee442fbb178b423c9207fc16c',·1,·'seqan3::sam_file_input::sam_file_input(stream_type·&&stream,·ref_ids_t·&,·ref_sequences_t·&,·file_format·const·&,·selected_field_ids·const·&)·->·sam_file_input<·sam_file_input_default_traits<·std::remove_reference_t<·ref_sequences_t·>,·std::remove_reference_t<·ref_ids_t·>·>,·selected_field_ids,·type_list<·file_format·>·>'], | ||
| 38 | ········['../classseqan3_1_1sam__file__input.html#a921e12f2336bc1ffd11a66a97c97f2d7',·1,·'seqan3::sam_file_input::sam_file_input(stream_type·&stream,·ref_ids_t·&,·ref_sequences_t·&,·file_format·const·&,·selected_field_ids·const·&)·->·sam_file_input<·sam_file_input_default_traits<·std::remove_reference_t<·ref_sequences_t·>,·std::remove_reference_t<·ref_ids_t·>·>,·selected_field_ids,·type_list<·file_format·>·>'], | ||
| 39 | ········['../classseqan3_1_1sam__file__input.html#a258f44d17d3744e224d791c972d0cfa6',·1,·'seqan3::sam_file_input::sam_file_input(stream_type·&&stream,·ref_ids_t·&,·ref_sequences_t·&,·file_format·const·&)·->·sam_file_input<·sam_file_input_default_traits<·std::remove_reference_t<·ref_sequences_t·>,·std::remove_reference_t<·ref_ids_t·>·>,·typename·sam_file_input<>::selected_field_ids,·type_list<·file_format·>·>'], | ||
| 39 | ········['../classseqan3_1_1sam__file__input.html#a5c6e6f5ce32db427de2c88b2a1ef8967',·1,·'seqan3::sam_file_input::sam_file_input(stream_type·&stream,·ref_ids_t·&,·ref_sequences_t·&,·file_format·const·&)·->·sam_file_input<·sam_file_input_default_traits<·std::remove_reference_t<·ref_sequences_t·>,·std::remove_reference_t<·ref_ids_t·>·>,·typename·sam_file_input<>::selected_field_ids,·type_list<·file_format·>·>'], | 40 | ········['../classseqan3_1_1sam__file__input.html#a5c6e6f5ce32db427de2c88b2a1ef8967',·1,·'seqan3::sam_file_input::sam_file_input(stream_type·&stream,·ref_ids_t·&,·ref_sequences_t·&,·file_format·const·&)·->·sam_file_input<·sam_file_input_default_traits<·std::remove_reference_t<·ref_sequences_t·>,·std::remove_reference_t<·ref_ids_t·>·>,·typename·sam_file_input<>::selected_field_ids,·type_list<·file_format·>·>'], |
| 41 | ········['../classseqan3_1_1sam__file__input.html',·1,·'seqan3::sam_file_input<·traits_type_,·selected_field_ids_,·valid_formats_·>'], | ||
| 40 | ········['../classseqan3_1_1sam__file__input.html#a66020c4402b4f74f2b82472920baf105',·1,·'seqan3::sam_file_input::sam_file_input(stream_type·&&stream,·file_format·const·&)·->·sam_file_input<·typename·sam_file_input<>::traits_type,·typename·sam_file_input<>::selected_field_ids,·type_list<·file_format·>·>'], | ||
| 41 | ········['../classseqan3_1_1sam__file__input.html#afa266630de6a69ef1a72ee39e352a44a',·1,·'seqan3::sam_file_input::sam_file_input(stream_type·&stream,·file_format·const·&,·selected_field_ids·const·&)·->·sam_file_input<·typename·sam_file_input<>::traits_type,·selected_field_ids,·type_list<·file_format·>·>'], | ||
| 42 | ········['../classseqan3_1_1sam__file__input.html#ada95b46c63da232c3fdbba740a8c166f',·1,·'seqan3::sam_file_input::sam_file_input(stream_type·&&stream,·file_format·const·&,·selected_field_ids·const·&)·->·sam_file_input<·typename·sam_file_input<>::traits_type,·selected_field_ids,·type_list<·file_format·>·>'], | 42 | ········['../classseqan3_1_1sam__file__input.html#ada95b46c63da232c3fdbba740a8c166f',·1,·'seqan3::sam_file_input::sam_file_input(stream_type·&&stream,·file_format·const·&,·selected_field_ids·const·&)·->·sam_file_input<·typename·sam_file_input<>::traits_type,·selected_field_ids,·type_list<·file_format·>·>'], |
| 43 | ········['../classseqan3_1_1sam__file__input.html#a835762bf9ac079e9ac22a4c74e35b3bd',·1,·'seqan3::sam_file_input::sam_file_input(stream_t·&&stream,·typename·traits_type::ref_ids·&ref_ids,·typename·traits_type::ref_sequences·&ref_sequences,·file_format·const·&format_tag,·selected_field_ids·const·&fields_tag=selected_field_ids{})'], | 43 | ········['../classseqan3_1_1sam__file__input.html#a835762bf9ac079e9ac22a4c74e35b3bd',·1,·'seqan3::sam_file_input::sam_file_input(stream_t·&&stream,·typename·traits_type::ref_ids·&ref_ids,·typename·traits_type::ref_sequences·&ref_sequences,·file_format·const·&format_tag,·selected_field_ids·const·&fields_tag=selected_field_ids{})'], |
| 44 | ········['../classseqan3_1_1sam__file__input.html#a452be6fb64e2b02b33fa60765c7beb6a',·1,·'seqan3::sam_file_input::sam_file_input(stream_t·&stream,·typename·traits_type::ref_ids·&ref_ids,·typename·traits_type::ref_sequences·&ref_sequences,·file_format·const·&format_tag,·selected_field_ids·const·&fields_tag=selected_field_ids{})'], | 44 | ········['../classseqan3_1_1sam__file__input.html#a452be6fb64e2b02b33fa60765c7beb6a',·1,·'seqan3::sam_file_input::sam_file_input(stream_t·&stream,·typename·traits_type::ref_ids·&ref_ids,·typename·traits_type::ref_sequences·&ref_sequences,·file_format·const·&format_tag,·selected_field_ids·const·&fields_tag=selected_field_ids{})'], |
| 45 | ········['../classseqan3_1_1sam__file__input.html#aa2f7b26a662b6425ba78baaff5d37dc6',·1,·'seqan3::sam_file_input::sam_file_input(std::filesystem::path·filename,·typename·traits_type::ref_ids·&ref_ids,·typename·traits_type::ref_sequences·&ref_sequences,·selected_field_ids·const·&fields_tag=selected_field_ids{})'], | 45 | ········['../classseqan3_1_1sam__file__input.html#aa2f7b26a662b6425ba78baaff5d37dc6',·1,·'seqan3::sam_file_input::sam_file_input(std::filesystem::path·filename,·typename·traits_type::ref_ids·&ref_ids,·typename·traits_type::ref_sequences·&ref_sequences,·selected_field_ids·const·&fields_tag=selected_field_ids{})'], |
| 46 | ········['../classseqan3_1_1sam__file__input.html#adbfad94af9d36a694d85a8c378a47077',·1,·'seqan3::sam_file_input::sam_file_input(stream_t·&&stream,·file_format·const·&format_tag,·selected_field_ids·const·&fields_tag=selected_field_ids{})'], | 46 | ········['../classseqan3_1_1sam__file__input.html#adbfad94af9d36a694d85a8c378a47077',·1,·'seqan3::sam_file_input::sam_file_input(stream_t·&&stream,·file_format·const·&format_tag,·selected_field_ids·const·&fields_tag=selected_field_ids{})'], |
| 47 | ········['../classseqan3_1_1sam__file__input.html#a6728de987ff2748d70da58e8c1ea3a23',·1,·'seqan3::sam_file_input::sam_file_input(stream_t·&stream,·file_format·const·&format_tag,·selected_field_ids·const·&fields_tag=selected_field_ids{})'], | 47 | ········['../classseqan3_1_1sam__file__input.html#a6728de987ff2748d70da58e8c1ea3a23',·1,·'seqan3::sam_file_input::sam_file_input(stream_t·&stream,·file_format·const·&format_tag,·selected_field_ids·const·&fields_tag=selected_field_ids{})'], |
| 48 | ········['../classseqan3_1_1sam__file__input.html#a2cc3ca29cfd45dc351b27d2482b26cac',·1,·'seqan3::sam_file_input::sam_file_input(std::filesystem::path·filename,·selected_field_ids·const·&fields_tag=selected_field_ids{})'], | 48 | ········['../classseqan3_1_1sam__file__input.html#a2cc3ca29cfd45dc351b27d2482b26cac',·1,·'seqan3::sam_file_input::sam_file_input(std::filesystem::path·filename,·selected_field_ids·const·&fields_tag=selected_field_ids{})'], |
| Offset 51, 43 lines modified | Offset 51, 43 lines modified | ||
| 51 | ········['../classseqan3_1_1sam__file__input.html#a8df4871eefacb6b7cd5eed41fd509858',·1,·'seqan3::sam_file_input::sam_file_input()=delete'] | 51 | ········['../classseqan3_1_1sam__file__input.html#a8df4871eefacb6b7cd5eed41fd509858',·1,·'seqan3::sam_file_input::sam_file_input()=delete'] |
| 52 | ····]], | 52 | ····]], |
| 53 | ····['sam_5ffile_5finput_5fdefault_5ftraits_18',·['sam_file_input_default_traits',·['../structseqan3_1_1sam__file__input__default__traits.html',·1,·'seqan3']]], | 53 | ····['sam_5ffile_5finput_5fdefault_5ftraits_18',·['sam_file_input_default_traits',·['../structseqan3_1_1sam__file__input__default__traits.html',·1,·'seqan3']]], |
| 54 | ····['sam_5ffile_5finput_5fformat_19',·['sam_file_input_format',·['../classseqan3_1_1sam__file__input__format.html',·1,·'seqan3']]], | 54 | ····['sam_5ffile_5finput_5fformat_19',·['sam_file_input_format',·['../classseqan3_1_1sam__file__input__format.html',·1,·'seqan3']]], |
| 55 | ····['sam_5ffile_5finput_5foptions_20',·['sam_file_input_options',·['../structseqan3_1_1sam__file__input__options.html',·1,·'seqan3']]], | 55 | ····['sam_5ffile_5finput_5foptions_20',·['sam_file_input_options',·['../structseqan3_1_1sam__file__input__options.html',·1,·'seqan3']]], |
| 56 | ····['sam_5ffile_5finput_5foptions_3c_20typename_20traits_5ftype_3a_3asequence_5flegal_5falphabet_20_3e_21',·['sam_file_input_options<·typename·traits_type::sequence_legal_alphabet·>',·['../structseqan3_1_1sam__file__input__options.html',·1,·'seqan3']]], | 56 | ····['sam_5ffile_5finput_5foptions_3c_20typename_20traits_5ftype_3a_3asequence_5flegal_5falphabet_20_3e_21',·['sam_file_input_options<·typename·traits_type::sequence_legal_alphabet·>',·['../structseqan3_1_1sam__file__input__options.html',·1,·'seqan3']]], |
| 57 | ····['sam_5ffile_5finput_5ftraits_22',·['sam_file_input_traits',·['../interfaceseqan3_1_1sam__file__input__traits.html',·1,·'']]], | 57 | ····['sam_5ffile_5finput_5ftraits_22',·['sam_file_input_traits',·['../interfaceseqan3_1_1sam__file__input__traits.html',·1,·'']]], |
| 58 | ····['sam_5ffile_5foutput_23',·['sam_file_output',·['../classseqan3_1_1sam__file__output.html#aced58fe82b4335f06de9064bc71f2f45',·1,·'seqan3::sam_file_output::sam_file_output(stream_type·&&stream,·file_format·const·&format_tag,·selected_field_ids·const·&fields_tag=selected_field_ids{})'], | ||
| 59 | ········['../classseqan3_1_1sam__file__output.html#af11b62d2791f8da52f44cf686e6579c0',·1,·'seqan3::sam_file_output::sam_file_output(std::filesystem::path·const·&,·ref_ids_type·&&,·ref_lengths_type·&&,·selected_field_ids·const·&)·->·sam_file_output<·selected_field_ids,·typename·sam_file_output<>::valid_formats,·std::remove_reference_t<·ref_ids_type·>·>'], | ||
| 58 | ···· | 60 | ········['../classseqan3_1_1sam__file__output.html#afc79827be66dc11fe25f5e7a67f92c99',·1,·'seqan3::sam_file_output::sam_file_output(stream_type·&,·file_format·const·&)·->·sam_file_output<·typename·sam_file_output<>::selected_field_ids,·type_list<·file_format·>,·ref_info_not_given·>'], |
| 59 | ········['../classseqan3_1_1sam__file__output.html#a6e6b84c86826f69b6e8d5d6ac8af5541',·1,·'seqan3::sam_file_output::sam_file_output(std::filesystem::path,·selected_field_ids·const·&)·->·sam_file_output<·selected_field_ids,·typename·sam_file_output<>::valid_formats,·ref_info_not_given·>'], | ||
| 60 | ········['../classseqan3_1_1sam__file__output.html#aa69f7d96189a3a3ac6cc0b233ec82a86',·1,·'seqan3::sam_file_output::sam_file_output(stream_type·&&,·file_format·const·&)·->·sam_file_output<·typename·sam_file_output<>::selected_field_ids,·type_list<·file_format·>,·ref_info_not_given·>'], | 61 | ········['../classseqan3_1_1sam__file__output.html#aa69f7d96189a3a3ac6cc0b233ec82a86',·1,·'seqan3::sam_file_output::sam_file_output(stream_type·&&,·file_format·const·&)·->·sam_file_output<·typename·sam_file_output<>::selected_field_ids,·type_list<·file_format·>,·ref_info_not_given·>'], |
| 61 | ········['../classseqan3_1_1sam__file__output.html#ad88a4de1ce5c46aae81ac07ad1e8c6c0',·1,·'seqan3::sam_file_output::sam_file_output(stream_type·&,·file_format·const·&,·selected_field_ids·const·&)·->·sam_file_output<·selected_field_ids,·type_list<·file_format·>,·ref_info_not_given·>'], | 62 | ········['../classseqan3_1_1sam__file__output.html#ad88a4de1ce5c46aae81ac07ad1e8c6c0',·1,·'seqan3::sam_file_output::sam_file_output(stream_type·&,·file_format·const·&,·selected_field_ids·const·&)·->·sam_file_output<·selected_field_ids,·type_list<·file_format·>,·ref_info_not_given·>'], |
| 62 | ········['../classseqan3_1_1sam__file__output.html#adad77cb637aa9a1e888a5eec9ab3322d',·1,·'seqan3::sam_file_output::sam_file_output(stream_type·&&,·file_format·const·&,·selected_field_ids·const·&)·->·sam_file_output<·selected_field_ids,·type_list<·file_format·>,·ref_info_not_given·>'], | 63 | ········['../classseqan3_1_1sam__file__output.html#adad77cb637aa9a1e888a5eec9ab3322d',·1,·'seqan3::sam_file_output::sam_file_output(stream_type·&&,·file_format·const·&,·selected_field_ids·const·&)·->·sam_file_output<·selected_field_ids,·type_list<·file_format·>,·ref_info_not_given·>'], |
| 64 | ········['../classseqan3_1_1sam__file__output.html#a6e6b84c86826f69b6e8d5d6ac8af5541',·1,·'seqan3::sam_file_output::sam_file_output(std::filesystem::path,·selected_field_ids·const·&)·->·sam_file_output<·selected_field_ids,·typename·sam_file_output<>::valid_formats,·ref_info_not_given·>'], | ||
| 63 | ········['../classseqan3_1_1sam__file__output.html#ab6e19fdf51322d9ac5824bb9f5b70bbc',·1,·'seqan3::sam_file_output::sam_file_output(stream_type·&&stream,·ref_ids_type_·&&ref_ids,·ref_lengths_type·&&ref_lengths,·file_format·const·&format_tag,·selected_field_ids·const·&fields_tag=selected_field_ids{})'], | 65 | ········['../classseqan3_1_1sam__file__output.html#ab6e19fdf51322d9ac5824bb9f5b70bbc',·1,·'seqan3::sam_file_output::sam_file_output(stream_type·&&stream,·ref_ids_type_·&&ref_ids,·ref_lengths_type·&&ref_lengths,·file_format·const·&format_tag,·selected_field_ids·const·&fields_tag=selected_field_ids{})'], |
| 64 | ········['../classseqan3_1_1sam__file__output.html#a65b9841105266a2dfef9daafd1b109f4',·1,·'seqan3::sam_file_output::sam_file_output(std::filesystem::path·const·&filename,·ref_ids_type_·&&ref_ids,·ref_lengths_type·&&ref_lengths,·selected_field_ids·const·&fields_tag=selected_field_ids{})'], | 66 | ········['../classseqan3_1_1sam__file__output.html#a65b9841105266a2dfef9daafd1b109f4',·1,·'seqan3::sam_file_output::sam_file_output(std::filesystem::path·const·&filename,·ref_ids_type_·&&ref_ids,·ref_lengths_type·&&ref_lengths,·selected_field_ids·const·&fields_tag=selected_field_ids{})'], |
| 65 | ········['../classseqan3_1_1sam__file__output.html#a | 67 | ········['../classseqan3_1_1sam__file__output.html#a113b0735dfce27d6ac095f4bdf046148',·1,·'seqan3::sam_file_output::sam_file_output(stream_type·&,·ref_ids_type·&&,·ref_lengths_type·&&,·file_format·const·&,·selected_field_ids·const·&)·->·sam_file_output<·selected_field_ids,·[·...·truncated·by·diffoscope;·len:·82,·SHA:·96d8722ab461ba8b788e1da437938e7f314bfcf07e2f30c6d8e96d8135ac1fda·...·]'], |
| 66 | ········['../classseqan3_1_1sam__file__output.html#a9acf2655ed86ce8f52577d2891f19d0c',·1,·'seqan3::sam_file_output::sam_file_output(stream_type·&stream,·file_format·const·&format_tag,·selected_field_ids·const·&fields_tag=selected_field_ids{})'], | 68 | ········['../classseqan3_1_1sam__file__output.html#a9acf2655ed86ce8f52577d2891f19d0c',·1,·'seqan3::sam_file_output::sam_file_output(stream_type·&stream,·file_format·const·&format_tag,·selected_field_ids·const·&fields_tag=selected_field_ids{})'], |
| 67 | ········['../classseqan3_1_1sam__file__output.html#aab04103f3a2eae510f6500bd7823fc47',·1,·'seqan3::sam_file_output::sam_file_output(std::filesystem::path·filename,·selected_field_ids·const·&fields_tag=selected_field_ids{})'], | 69 | ········['../classseqan3_1_1sam__file__output.html#aab04103f3a2eae510f6500bd7823fc47',·1,·'seqan3::sam_file_output::sam_file_output(std::filesystem::path·filename,·selected_field_ids·const·&fields_tag=selected_field_ids{})'], |
| 68 | ········['../classseqan3_1_1sam__file__output.html#ac74960d2135550f9f9337bae1f782cc1',·1,·'seqan3::sam_file_output::sam_file_output(sam_file_output·&&)=default'], | 70 | ········['../classseqan3_1_1sam__file__output.html#ac74960d2135550f9f9337bae1f782cc1',·1,·'seqan3::sam_file_output::sam_file_output(sam_file_output·&&)=default'], |
| 69 | ········['../classseqan3_1_1sam__file__output.html#a23c49af0c3ea9326354b01d830fb6d1f',·1,·'seqan3::sam_file_output::sam_file_output(sam_file_output·const·&)=delete'], | ||
| 70 | ········['../classseqan3_1_1sam__file__output.html#a24f28077041840769a5d287581d49e94',·1,·'seqan3::sam_file_output::sam_file_output()=delete'], | ||
| 71 | ········['../classseqan3_1_1sam__file__output.html',·1,·'seqan3::sam_file_output<·selected_field_ids_,·valid_formats_,·ref_ids_type·>'], | ||
| 72 | ········['../classseqan3_1_1sam__file__output.html#a11bf92fd2ae7fdd7ee91186b5cc9169c',·1,·'seqan3::sam_file_output::sam_file_output(std::filesystem::path·const·&,·ref_ids_type·&&,·ref_lengths_type·&&)·->·sam_file_output<·typename·sam_file_output<>::selected_field_ids,·typename·sam_file_output<>::valid_formats,·std::remove_reference_t<·ref_ids_type·>·>'], | 71 | ········['../classseqan3_1_1sam__file__output.html#a11bf92fd2ae7fdd7ee91186b5cc9169c',·1,·'seqan3::sam_file_output::sam_file_output(std::filesystem::path·const·&,·ref_ids_type·&&,·ref_lengths_type·&&)·->·sam_file_output<·typename·sam_file_output<>::selected_field_ids,·typename·sam_file_output<>::valid_formats,·std::remove_reference_t<·ref_ids_type·>·>'], |
| 73 | ········['../classseqan3_1_1sam__file__output.html#a944fd9481b8297e63f8bfca4adf8b938',·1,·'seqan3::sam_file_output::sam_file_output(stream_type·&&,·ref_ids_type·&&,·ref_lengths_type·&&,·file_format·const·&,·selected_field_ids·const·&)·->·sam_file_output<·selected_field_ids,·type_list<·file_format·>,·std::remove_reference_t<·ref_ids_type·>·>'], | 72 | ········['../classseqan3_1_1sam__file__output.html#a944fd9481b8297e63f8bfca4adf8b938',·1,·'seqan3::sam_file_output::sam_file_output(stream_type·&&,·ref_ids_type·&&,·ref_lengths_type·&&,·file_format·const·&,·selected_field_ids·const·&)·->·sam_file_output<·selected_field_ids,·type_list<·file_format·>,·std::remove_reference_t<·ref_ids_type·>·>'], |
| 74 | ········['../classseqan3_1_1sam__file__output.html#a113b0735dfce27d6ac095f4bdf046148',·1,·'seqan3::sam_file_output::sam_file_output(stream_type·&,·ref_ids_type·&&,·ref_lengths_type·&&,·file_format·const·&,·selected_field_ids·const·&)·->·sam_file_output<·selected_field_ids,·type_list<·file_format·>,·std::remove_reference_t<·ref_ids_type·>·>'], | ||
| 75 | ········['../classseqan3_1_1sam__file__output.html#a76c052aec39abaff3af022a1bb8f039d',·1,·'seqan3::sam_file_output::sam_file_output(stream_type·&&,·ref_ids_type·&&,·ref_lengths_type·&&,·file_format·const·&)·->·sam_file_output<·typename·sam_file_output<>::selected_field_ids,·type_list<·file_format·>,·std::remove_reference_t<·ref_ids_type·>·>'], | 73 | ········['../classseqan3_1_1sam__file__output.html#a76c052aec39abaff3af022a1bb8f039d',·1,·'seqan3::sam_file_output::sam_file_output(stream_type·&&,·ref_ids_type·&&,·ref_lengths_type·&&,·file_format·const·&)·->·sam_file_output<·typename·sam_file_output<>::selected_field_ids,·type_list<·file_format·>,·std::remove_reference_t<·ref_ids_type·>·>'], |
| 76 | ········['../classseqan3_1_1sam__file__output.html#a01e86819d4ebd7a35149d541f0d77dcd',·1,·'seqan3::sam_file_output::sam_file_output(stream_type·&,·ref_ids_type·&&,·ref_lengths_type·&&,·file_format·const·&)·->·sam_file_output<·typename·sam_file_output<>::selected_field_ids,·type_list<·file_format·>,·std::remove_reference_t<·ref_ids_type·>·>'], | 74 | ········['../classseqan3_1_1sam__file__output.html#a01e86819d4ebd7a35149d541f0d77dcd',·1,·'seqan3::sam_file_output::sam_file_output(stream_type·&,·ref_ids_type·&&,·ref_lengths_type·&&,·file_format·const·&)·->·sam_file_output<·typename·sam_file_output<>::selected_field_ids,·type_list<·file_format·>,·std::remove_reference_t<·ref_ids_type·>·>'], |
| 77 | ········['../classseqan3_1_1sam__file__output.html#a | 75 | ········['../classseqan3_1_1sam__file__output.html#a23c49af0c3ea9326354b01d830fb6d1f',·1,·'seqan3::sam_file_output::sam_file_output(sam_file_output·const·&)=delete'], |
| 76 | ········['../classseqan3_1_1sam__file__output.html#a24f28077041840769a5d287581d49e94',·1,·'seqan3::sam_file_output::sam_file_output()=delete'], | ||
| 77 | ········['../classseqan3_1_1sam__file__output.html',·1,·'seqan3::sam_file_output<·selected_field_ids_,·valid_formats_,·ref_ids_type·>'] | ||
| 78 | ····]], | 78 | ····]], |
| 79 | ····['sam_5ffile_5foutput_5fformat_24',·['sam_file_output_format',·['../classseqan3_1_1sam__file__output__format.html',·1,·'seqan3']]], | 79 | ····['sam_5ffile_5foutput_5fformat_24',·['sam_file_output_format',·['../classseqan3_1_1sam__file__output__format.html',·1,·'seqan3']]], |
| 80 | ····['sam_5ffile_5foutput_5foptions_25',·['sam_file_output_options',·['../structseqan3_1_1sam__file__output__options.html',·1,·'seqan3']]], | 80 | ····['sam_5ffile_5foutput_5foptions_25',·['sam_file_output_options',·['../structseqan3_1_1sam__file__output__options.html',·1,·'seqan3']]], |
| 81 | ····['sam_5ffile_5fprogram_5finfo_5ft_26',·['sam_file_program_info_t',·['../structseqan3_1_1sam__file__program__info__t.html',·1,·'seqan3']]], | 81 | ····['sam_5ffile_5fprogram_5finfo_5ft_26',·['sam_file_program_info_t',·['../structseqan3_1_1sam__file__program__info__t.html',·1,·'seqan3']]], |
| 82 | ····['sam_5fflag_27',·['sam_flag',·['../group__io__sam__file.html#ga12cf4f15e81e65c02a1a5899b75ca962',·1,·'seqan3']]], | 82 | ····['sam_5fflag_27',·['sam_flag',·['../group__io__sam__file.html#ga12cf4f15e81e65c02a1a5899b75ca962',·1,·'seqan3']]], |
| 83 | ····['sam_5fflag_2ehpp_28',·['sam_flag.hpp',·['../sam__flag_8hpp.html',·1,·'']]], | 83 | ····['sam_5fflag_2ehpp_28',·['sam_flag.hpp',·['../sam__flag_8hpp.html',·1,·'']]], |
| 84 | ····['sam_5frecord_29',·['sam_record',·['../classseqan3_1_1sam__record.html#a | 84 | ····['sam_5frecord_29',·['sam_record',·['../classseqan3_1_1sam__record.html#a8d32a79396e78c3e0622bd865fc7bad1',·1,·'seqan3::sam_record::sam_record()=default'], |
| 85 | ········['../classseqan3_1_1sam__record.html#a64bf707b5d361dabd06ed5b8b8530978',·1,·'seqan3::sam_record::sam_record(sam_record·const·&)=default'], | 85 | ········['../classseqan3_1_1sam__record.html#a64bf707b5d361dabd06ed5b8b8530978',·1,·'seqan3::sam_record::sam_record(sam_record·const·&)=default'], |
| 86 | ········['../classseqan3_1_1sam__record.html#a | 86 | ········['../classseqan3_1_1sam__record.html#a90bbca3b71fa4dfe14a2af8912e59f12',·1,·'seqan3::sam_record::sam_record(sam_record·&&)=default'], |
| 87 | ········['../classseqan3_1_1sam__record.html',·1,·'seqan3::sam_record<·field_types,·field_ids·>'] | 87 | ········['../classseqan3_1_1sam__record.html',·1,·'seqan3::sam_record<·field_types,·field_ids·>'] |
| 88 | ····]], | 88 | ····]], |
| 89 | ····['sam_5frecord_3c_20detail_3a_3aselect_5ftypes_5fwith_5fids_5ft_3c_20field_5ftypes_2c_20field_5fids_2c_20selected_5ffield_5fids_20_3e_2c_20selected_5ffield_5fids_20_3e_30',·['sam_record<·detail::select_types_with_ids_t<·field_types,·field_ids,·selected_field_ids·>,·selected_field_ids·>',·['../classseqan3_1_1sam__record.html',·1,·'seqan3']]], | 89 | ····['sam_5frecord_3c_20detail_3a_3aselect_5ftypes_5fwith_5fids_5ft_3c_20field_5ftypes_2c_20field_5fids_2c_20selected_5ffield_5fids_20_3e_2c_20selected_5ffield_5fids_20_3e_30',·['sam_record<·detail::select_types_with_ids_t<·field_types,·field_ids,·selected_field_ids·>,·selected_field_ids·>',·['../classseqan3_1_1sam__record.html',·1,·'seqan3']]], |
| 90 | ····['sam_5frequire_5fheader_31',·['sam_require_header',·['../structseqan3_1_1sam__file__output__options.html#a6fe52f5b4619b9c225d974200cd939ce',·1,·'seqan3::sam_file_output_options']]], | 90 | ····['sam_5frequire_5fheader_31',·['sam_require_header',·['../structseqan3_1_1sam__file__output__options.html#a6fe52f5b4619b9c225d974200cd939ce',·1,·'seqan3::sam_file_output_options']]], |
| 91 | ····['sam_5ftag_5fdictionary_32',·['sam_tag_dictionary',·['../classseqan3_1_1sam__tag__dictionary.html',·1,·'seqan3']]], | 91 | ····['sam_5ftag_5fdictionary_32',·['sam_tag_dictionary',·['../classseqan3_1_1sam__tag__dictionary.html',·1,·'seqan3']]], |
| 92 | ····['sam_5ftag_5fdictionary_2ehpp_33',·['sam_tag_dictionary.hpp',·['../sam__tag__dictionary_8hpp.html',·1,·'']]], | 92 | ····['sam_5ftag_5fdictionary_2ehpp_33',·['sam_tag_dictionary.hpp',·['../sam__tag__dictionary_8hpp.html',·1,·'']]], |
| 93 | ····['sam_5ftag_5ftype_34',·['sam_tag_type',·['../structseqan3_1_1sam__tag__type.html',·1,·'seqan3']]], | 93 | ····['sam_5ftag_5ftype_34',·['sam_tag_type',·['../structseqan3_1_1sam__tag__type.html',·1,·'seqan3']]], |
| Offset 143, 39 lines modified | Offset 143, 39 lines modified | ||
| 143 | ····]], | 143 | ····]], |
| 144 | ····['scoring_56',·['Scoring',·['../group__alignment__scoring.html',·1,·'']]], | 144 | ····['scoring_56',·['Scoring',·['../group__alignment__scoring.html',·1,·'']]], |
| 145 | ····['scoring_20and_20gap_20schemes_57',·['Using·scoring·and·gap·schemes',·['../group__alignment__pairwise.html#autotoc_md15',·1,·'']]], | 145 | ····['scoring_20and_20gap_20schemes_57',·['Using·scoring·and·gap·schemes',·['../group__alignment__pairwise.html#autotoc_md15',·1,·'']]], |
| 146 | ····['scoring_20gaps_58',·['Scoring·gaps',·['../group__alignment__pairwise.html#autotoc_md17',·1,·'']]], | 146 | ····['scoring_20gaps_58',·['Scoring·gaps',·['../group__alignment__pairwise.html#autotoc_md17',·1,·'']]], |
| 147 | ····['scoring_20scheme_59',·['Define·a·custom·scoring·scheme',·['../cookbook.html#autotoc_md61',·1,·'']]], | 147 | ····['scoring_20scheme_59',·['Define·a·custom·scoring·scheme',·['../cookbook.html#autotoc_md61',·1,·'']]], |
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