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

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

alignervg::GaplessExtender
cluster_type typedefvg::GaplessExtender
extend(cluster_type &cluster, const std::string &sequence, const gbwtgraph::CachedGBWTGraph *cache=nullptr, size_t max_mismatches=MAX_MISMATCHES, double overlap_threshold=OVERLAP_THRESHOLD) constvg::GaplessExtender
full_length_extensions(const std::vector< GaplessExtension > &result, size_t max_mismatches=MAX_MISMATCHES)vg::GaplessExtenderstatic
GaplessExtender()vg::GaplessExtender
GaplessExtender(const gbwtgraph::GBWTGraph &graph, const Aligner &aligner)vg::GaplessExtenderexplicit
get_handle(seed_type seed)vg::GaplessExtenderinlinestatic
get_node_offset(seed_type seed)vg::GaplessExtenderinlinestatic
get_pos(seed_type seed)vg::GaplessExtenderinlinestatic
get_read_offset(seed_type seed)vg::GaplessExtenderinlinestatic
graphvg::GaplessExtender
MAX_MISMATCHESvg::GaplessExtenderstatic
OVERLAP_THRESHOLDvg::GaplessExtenderstatic
seed_type typedefvg::GaplessExtender
to_seed(pos_t pos, size_t read_offset)vg::GaplessExtenderinlinestatic
transform_alignment(Alignment &aln, const std::vector< std::vector< handle_t >> &haplotype_paths) constvg::GaplessExtender
unfold_haplotypes(const std::unordered_set< nid_t > &subgraph, std::vector< std::vector< handle_t >> &haplotype_paths, bdsg::HashGraph &unfolded, const gbwtgraph::CachedGBWTGraph *cache=nullptr) constvg::GaplessExtender