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vg
tools for working with variation graphs
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This is the complete list of members for vg::MultipathAlignmentEmitter, including all inherited members.
| add_annotations(const multipath_alignment_t &mp_aln, bam1_t *bam) const | vg::MultipathAlignmentEmitter | private |
| aln_emitters | vg::MultipathAlignmentEmitter | private |
| atomic_header | vg::HTSWriter | protected |
| backing_files | vg::HTSWriter | protected |
| BAM enum value | vg::MultipathAlignmentEmitter | private |
| BGZF_FOOTER_LENGTH | vg::HTSWriter | protectedstatic |
| convert_to_alignment(const multipath_alignment_t &mp_aln, Alignment &aln, const string *prev_name=nullptr, const string *next_name=nullptr) const | vg::MultipathAlignmentEmitter | private |
| convert_to_hts_paired(const string &name_1, const string &name_2, const multipath_alignment_t &mp_aln_1, const multipath_alignment_t &mp_aln_2, const string &ref_name_1, bool ref_rev_1, int64_t ref_pos_1, const string &ref_name_2, bool ref_rev_2, int64_t ref_pos_2, int64_t tlen_limit, bam_hdr_t *header, vector< bam1_t * > &dest) const | vg::MultipathAlignmentEmitter | private |
| convert_to_hts_unpaired(const string &name, const multipath_alignment_t &mp_aln, const string &ref_name, bool ref_rev, int64_t ref_pos, bam_hdr_t *header, vector< bam1_t * > &dest) const | vg::MultipathAlignmentEmitter | private |
| CRAM enum value | vg::MultipathAlignmentEmitter | private |
| create_alignment_shim(const string &name, const multipath_alignment_t &mp_aln, Alignment &shim, const string *prev_name=nullptr, const string *next_name=nullptr) const | vg::MultipathAlignmentEmitter | private |
| emit_pairs(const string &name_1, const string &name_2, vector< pair< multipath_alignment_t, multipath_alignment_t >> &&mp_aln_pairs, vector< pair< tuple< string, bool, int64_t >, tuple< string, bool, int64_t >>> *path_positions=nullptr, vector< int64_t > *tlen_limits=nullptr) | vg::MultipathAlignmentEmitter | |
| emit_singles(const string &name, vector< multipath_alignment_t > &&mp_alns, vector< tuple< string, bool, int64_t >> *path_positions=nullptr) | vg::MultipathAlignmentEmitter | |
| ensure_header(const string &read_group, const string &sample_name, size_t thread_number) | vg::HTSWriter | protected |
| format | vg::MultipathAlignmentEmitter | private |
| GAF enum value | vg::MultipathAlignmentEmitter | private |
| GAM enum value | vg::MultipathAlignmentEmitter | private |
| GAMP enum value | vg::MultipathAlignmentEmitter | private |
| graph | vg::MultipathAlignmentEmitter | private |
| header_mutex | vg::HTSWriter | protected |
| hts_mode | vg::HTSWriter | protected |
| HTSWriter(const string &filename, const string &format, const vector< pair< string, int64_t >> &path_order_and_length, const unordered_map< string, int64_t > &subpath_to_length, size_t max_threads) | vg::HTSWriter | |
| HTSWriter(const HTSWriter &other)=delete | vg::HTSWriter | |
| HTSWriter(HTSWriter &&other)=delete | vg::HTSWriter | |
| initialize_sam_file(bam_hdr_t *header, size_t thread_number, bool keep_header=false) | vg::HTSWriter | protected |
| min_splice_length | vg::MultipathAlignmentEmitter | private |
| mp_aln_emitters | vg::MultipathAlignmentEmitter | private |
| MultipathAlignmentEmitter(const string &filename, size_t num_threads, const string out_format="GAMP", const PathPositionHandleGraph *graph=nullptr, const vector< pair< string, int64_t >> *path_order_and_length=nullptr) | vg::MultipathAlignmentEmitter | |
| multiplexer | vg::HTSWriter | protected |
| operator=(const HTSWriter &other)=delete | vg::HTSWriter | |
| operator=(HTSWriter &&other)=delete | vg::HTSWriter | |
| out_file | vg::HTSWriter | protected |
| output_format_t enum name | vg::MultipathAlignmentEmitter | private |
| output_is_bgzf | vg::HTSWriter | protected |
| path_order_and_length | vg::HTSWriter | protected |
| read_group | vg::MultipathAlignmentEmitter | private |
| SAM enum value | vg::MultipathAlignmentEmitter | private |
| sam_files | vg::HTSWriter | protected |
| sam_header | vg::HTSWriter | protected |
| sample_name | vg::MultipathAlignmentEmitter | private |
| save_records(bam_hdr_t *header, vector< bam1_t * > &records, size_t thread_number) | vg::HTSWriter | protected |
| set_min_splice_length(int64_t min_splice_length) | vg::MultipathAlignmentEmitter | |
| set_read_group(const string &read_group) | vg::MultipathAlignmentEmitter | |
| set_sample_name(const string &sample_name) | vg::MultipathAlignmentEmitter | |
| subpath_to_length | vg::HTSWriter | protected |
| ~HTSWriter() | vg::HTSWriter | |
| ~MultipathAlignmentEmitter() | vg::MultipathAlignmentEmitter |
1.8.17