vg
tools for working with variation graphs
vg::Surjector Member List

This is the complete list of members for vg::Surjector, including all inherited members.

adjust_alignments_for_base_qualityvg::AlignerClient
AlignerClient(double gc_content_estimate=vg::default_gc_content)vg::AlignerClientprotected
compute_path_interval(const PathPositionHandleGraph *graph, const Alignment &source, path_handle_t path_handle, const vector< path_chunk_t > &path_chunks) constvg::Surjectorprivate
connected_components(const vector< vector< size_t >> &adj, const vector< vector< size_t >> &rev_adj, size_t *num_comps_out) constvg::Surjectorprivate
extract_linearized_path_graph(const PathPositionHandleGraph *graph, MutableHandleGraph *into, path_handle_t path_handle, size_t first, size_t last) constvg::Surjectorprivate
extract_overlapping_paths(const PathPositionHandleGraph *graph, const Alignment &source, const unordered_set< path_handle_t > &surjection_paths) constvg::Surjectorprivate
find_constriction_edges(const vector< vector< size_t >> &adj) constvg::Surjectorprivate
gc_content_estimatevg::AlignerClientprivate
get_aligner(bool have_qualities=true) constvg::AlignerClientprotected
get_qual_adj_aligner() constvg::AlignerClientprotected
get_regular_aligner() constvg::AlignerClientprotected
graphvg::Surjectorprivate
make_null_alignment(const Alignment &source)vg::Surjectorprivatestatic
min_splice_lengthvg::Surjectorprivate
parse_matrix(std::istream &matrix_stream)vg::AlignerClientstatic
path_chunk_t typedefvg::Surjector
qual_adj_alignervg::AlignerClientprivate
realigning_surject(const PathPositionHandleGraph *graph, const Alignment &source, const path_handle_t &path_handle, const vector< path_chunk_t > &path_chunks, bool allow_negative_scores, bool preserve_N_alignments=false, bool preserve_tail_indel_anchors=false) constvg::Surjectorprivate
regular_alignervg::AlignerClientprivate
reverse_adjacencies(const vector< vector< size_t >> &adj) constvg::Surjectorprivate
set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)vg::AlignerClient
set_alignment_scores(std::istream &matrix_stream, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)vg::AlignerClient
set_alignment_scores(const int8_t *score_matrix, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)vg::AlignerClient
set_path_position(const PathPositionHandleGraph *graph, const Alignment &surjected, path_handle_t best_path_handle, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out) constvg::Surjectorprivate
set_path_position_inexact(const PathPositionHandleGraph *graph, const Alignment &surjected, path_handle_t best_path_handle, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out) constvg::Surjectorprivate
spliced_surject(const PathPositionHandleGraph *path_position_graph, const Alignment &source, const path_handle_t &path_handle, const vector< path_chunk_t > &path_chunks, const vector< pair< step_handle_t, step_handle_t >> &ref_chunks, bool allow_negative_scores) constvg::Surjectorprivate
surject(const Alignment &source, const set< string > &path_names, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out, bool allow_negative_scores=false, bool preserve_deletions=false) constvg::Surjector
surject(const Alignment &source, const set< string > &path_names, bool allow_negative_scores=false, bool preserve_deletions=false) constvg::Surjector
Surjector(const PathPositionHandleGraph *graph)vg::Surjector
transitive_reduction(const vector< vector< size_t >> &adj) constvg::Surjectorprivate