vg
tools for working with variation graphs
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This is the complete list of members for vg::Surjector, including all inherited members.
adjust_alignments_for_base_quality | vg::AlignerClient | private |
AlignerClient(double gc_content_estimate=vg::default_gc_content) | vg::AlignerClient | private |
compute_path_interval(const PathPositionHandleGraph *graph, const Alignment &source, path_handle_t path_handle, const vector< path_chunk_t > &path_chunks) const | vg::Surjector | private |
extract_linearized_path_graph(const PathPositionHandleGraph *graph, MutableHandleGraph *into, path_handle_t path_handle, size_t first, size_t last) const | vg::Surjector | private |
extract_overlapping_paths(const PathPositionHandleGraph *graph, const Alignment &source, const unordered_set< path_handle_t > &surjection_paths) const | vg::Surjector | private |
gc_content_estimate | vg::AlignerClient | private |
get_aligner(bool have_qualities=true) const | vg::AlignerClient | private |
get_qual_adj_aligner() const | vg::AlignerClient | private |
get_regular_aligner() const | vg::AlignerClient | private |
graph | vg::Surjector | private |
load_scoring_matrix(std::ifstream &matrix_stream) | vg::AlignerClient | private |
make_null_alignment(const Alignment &source) | vg::Surjector | privatestatic |
path_chunk_t typedef | vg::Surjector | |
qual_adj_aligner | vg::AlignerClient | private |
regular_aligner | vg::AlignerClient | private |
set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus, uint32_t xdrop_max_gap_length=default_xdrop_max_gap_length) | vg::AlignerClient | private |
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) const | vg::Surjector | private |
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) const | vg::Surjector | |
surject(const Alignment &source, const set< string > &path_names, bool allow_negative_scores=false) const | vg::Surjector | |
Surjector(const PathPositionHandleGraph *graph) | vg::Surjector |