|
vg
tools for working with variation graphs
|
This is the complete list of members for vg::SplicedHTSAlignmentEmitter, including all inherited members.
| atomic_header | vg::HTSWriter | protected |
| backing_files | vg::HTSWriter | protected |
| BGZF_FOOTER_LENGTH | vg::HTSWriter | protectedstatic |
| convert_alignment(const Alignment &aln, vector< pair< int, char >> &cigar, bool &pos_rev, int64_t &pos, string &path_name) const | vg::SplicedHTSAlignmentEmitter | privatevirtual |
| convert_paired(Alignment &aln1, Alignment &aln2, bam_hdr_t *header, int64_t tlen_limit, vector< bam1_t * > &dest) | vg::HTSAlignmentEmitter | private |
| convert_unpaired(Alignment &aln, bam_hdr_t *header, vector< bam1_t * > &dest) | vg::HTSAlignmentEmitter | private |
| emit_extra_message(const std::string &tag, std::string &&data) | vg::io::AlignmentEmitter | virtual |
| emit_mapped_pair(vector< Alignment > &&alns1, vector< Alignment > &&alns2, int64_t tlen_limit=0) | vg::io::AlignmentEmitter | virtual |
| emit_mapped_pairs(vector< vector< Alignment >> &&alns1_batch, vector< vector< Alignment >> &&alns2_batch, vector< int64_t > &&tlen_limit_batch) | vg::HTSAlignmentEmitter | virtual |
| emit_mapped_single(vector< Alignment > &&alns) | vg::io::AlignmentEmitter | virtual |
| emit_mapped_singles(vector< vector< Alignment >> &&alns_batch) | vg::HTSAlignmentEmitter | virtual |
| emit_pair(Alignment &&aln1, Alignment &&aln2, int64_t tlen_limit=0) | vg::io::AlignmentEmitter | virtual |
| emit_pairs(vector< Alignment > &&aln1_batch, vector< Alignment > &&aln2_batch, vector< int64_t > &&tlen_limit_batch) | vg::HTSAlignmentEmitter | virtual |
| emit_single(Alignment &&aln) | vg::io::AlignmentEmitter | virtual |
| emit_singles(vector< Alignment > &&aln_batch) | vg::HTSAlignmentEmitter | virtual |
| ensure_header(const string &read_group, const string &sample_name, size_t thread_number) | vg::HTSWriter | protected |
| format | vg::HTSWriter | protected |
| graph | vg::SplicedHTSAlignmentEmitter | private |
| header_mutex | vg::HTSWriter | protected |
| hts_mode | vg::HTSWriter | protected |
| HTSAlignmentEmitter(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::HTSAlignmentEmitter | |
| HTSAlignmentEmitter(const HTSAlignmentEmitter &other)=delete | vg::HTSAlignmentEmitter | |
| HTSAlignmentEmitter(HTSAlignmentEmitter &&other)=delete | vg::HTSAlignmentEmitter | |
| 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::SplicedHTSAlignmentEmitter | |
| multiplexer | vg::HTSWriter | protected |
| operator=(const HTSAlignmentEmitter &other)=delete | vg::HTSAlignmentEmitter | |
| operator=(HTSAlignmentEmitter &&other)=delete | vg::HTSAlignmentEmitter | |
| vg::HTSWriter::operator=(const HTSWriter &other)=delete | vg::HTSWriter | |
| vg::HTSWriter::operator=(HTSWriter &&other)=delete | vg::HTSWriter | |
| out_file | vg::HTSWriter | protected |
| output_is_bgzf | vg::HTSWriter | protected |
| path_order_and_length | vg::HTSWriter | protected |
| sam_files | vg::HTSWriter | protected |
| sam_header | vg::HTSWriter | protected |
| save_records(bam_hdr_t *header, vector< bam1_t * > &records, size_t thread_number) | vg::HTSWriter | protected |
| spliced_cigar_against_path(const Alignment &aln, const string &path_name, int64_t pos, bool rev) const | vg::SplicedHTSAlignmentEmitter | private |
| SplicedHTSAlignmentEmitter(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, const PathPositionHandleGraph &graph, size_t max_threads) | vg::SplicedHTSAlignmentEmitter | |
| subpath_to_length | vg::HTSWriter | protected |
| ~AlignmentEmitter()=default | vg::io::AlignmentEmitter | virtual |
| ~HTSAlignmentEmitter()=default | vg::HTSAlignmentEmitter | |
| ~HTSWriter() | vg::HTSWriter | |
| ~SplicedHTSAlignmentEmitter()=default | vg::SplicedHTSAlignmentEmitter |
1.8.17