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::AlignerClientprivate
AlignerClient(double gc_content_estimate=vg::default_gc_content)vg::AlignerClientprivate
compute_path_interval(const PathPositionHandleGraph *graph, const Alignment &source, path_handle_t path_handle, const vector< path_chunk_t > &path_chunks) 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
gc_content_estimatevg::AlignerClientprivate
get_aligner(bool have_qualities=true) constvg::AlignerClientprivate
get_qual_adj_aligner() constvg::AlignerClientprivate
get_regular_aligner() constvg::AlignerClientprivate
graphvg::Surjectorprivate
load_scoring_matrix(std::ifstream &matrix_stream)vg::AlignerClientprivate
make_null_alignment(const Alignment &source)vg::Surjectorprivatestatic
path_chunk_t typedefvg::Surjector
qual_adj_alignervg::AlignerClientprivate
regular_alignervg::AlignerClientprivate
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::AlignerClientprivate
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
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) constvg::Surjector
surject(const Alignment &source, const set< string > &path_names, bool allow_negative_scores=false) constvg::Surjector
Surjector(const PathPositionHandleGraph *graph)vg::Surjector