diff --git a/ontology/vg.html b/ontology/vg.html index 982fc7a668a..586ed09aaa5 100644 --- a/ontology/vg.html +++ b/ontology/vg.html @@ -688,7 +688,7 @@

rdfs:comment - "A step along a path in the variant graph. A series of steps along a path represent an assembled sequence that was originally inserted into the the variant graph. A step points to a :Node or the reverse complement of a node and has a rank (step number)." + "A step along a path in the variant graph. A series of steps along a path represent an assembled sequence that was originally inserted into the variant graph. A step points to a :Node or the reverse complement of a node and has a rank (step number)." xsd:string diff --git a/ontology/vg.ttl b/ontology/vg.ttl index 056e421fa01..39ef0fc795b 100644 --- a/ontology/vg.ttl +++ b/ontology/vg.ttl @@ -31,7 +31,7 @@ . :Step rdf:type owl:Class ; - rdfs:comment "A step along a path in the variant graph. A series of steps along a path represent an assembled sequence that was originally inserted into the the variant graph. A step points to a :Node or the reverse complement of a node and has a rank (step number)."^^xsd:string ; + rdfs:comment "A step along a path in the variant graph. A series of steps along a path represent an assembled sequence that was originally inserted into the variant graph. A step points to a :Node or the reverse complement of a node and has a rank (step number)."^^xsd:string ; rdfs:label "Step"^^xsd:string ; rdfs:subClassOf owl:Thing ; . diff --git a/src/algorithms/k_widest_paths.cpp b/src/algorithms/k_widest_paths.cpp index 3576b71ae02..5bcfd0267b8 100644 --- a/src/algorithms/k_widest_paths.cpp +++ b/src/algorithms/k_widest_paths.cpp @@ -246,7 +246,7 @@ vector>> yens_k_widest_paths(const HandleGraph* g, forgotten_nodes.insert(g->flip(prev_path[j])); } - // find our path from the the spur_node to the sink + // find our path from the spur_node to the sink pair> spur_path_v = widest_dijkstra(g, spur_node, sink, node_weight_callback, edge_weight_callback, [&](handle_t h) {return forgotten_nodes.count(h);}, [&](edge_t e) {return forgotten_edges.count(e);}, diff --git a/src/cactus.cpp b/src/cactus.cpp index 7d5a6bc8ac3..a66c8e90e22 100644 --- a/src/cactus.cpp +++ b/src/cactus.cpp @@ -148,7 +148,7 @@ void getReachableBridges(stCactusEdgeEnd *edgeEnd1, stList *bridgeEnds) { } /** - * Finds an arbitrary pair of telomeres in a Cactus graph, which are are either + * Finds an arbitrary pair of telomeres in a Cactus graph, which are either * a pair of bridge edge ends or a pair of chain edge ends, oriented such that * they form a pair of boundaries. * diff --git a/src/cluster.cpp b/src/cluster.cpp index 8c3a9b60419..ec60a525357 100644 --- a/src/cluster.cpp +++ b/src/cluster.cpp @@ -735,7 +735,7 @@ void MEMClusterer::HitGraph::prune_low_scoring_edges(vector>& com } cerr << strm.str(); #endif - // the the original component + // the original component components[component_idx] = move(new_components[0]); // add the remaining to the end for (size_t i = 1; i < new_components.size(); i++) { diff --git a/src/graph_caller.cpp b/src/graph_caller.cpp index 5dd250282c5..921c941f02e 100644 --- a/src/graph_caller.cpp +++ b/src/graph_caller.cpp @@ -2302,7 +2302,7 @@ string NestedFlowCaller::flatten_alt_allele(const string& nested_allele, int all // todo: passing in a single ploidy simplisitic, would need to derive from the calls when // reucrising // in practice, the results will nearly the same but still needs fixing - // we try to get the the allele from the genotype if possible, but fallback on the fallback_allele + // we try to get the allele from the genotype if possible, but fallback on the fallback_allele int trav_allele = fallback_allele >= 0 ? fallback_allele : record.genotype_by_ploidy[ploidy-1].first[allele]; const SnarlTraversal& traversal = record.travs[trav_allele]; string nested_snarl_allele = trav_string(graph, traversal); diff --git a/src/index_registry.cpp b/src/index_registry.cpp index 83a9c1b4a58..8f48b15ddc6 100644 --- a/src/index_registry.cpp +++ b/src/index_registry.cpp @@ -780,7 +780,7 @@ IndexRegistry VGIndexes::get_vg_index_registry() { } } - // we'll partition sequences that have the same samples (chunking the the VCFs + // we'll partition sequences that have the same samples (chunking the VCFs // ultimately requires that we do this) map, vector> sample_set_contigs; for (int i = 0; i < vcf_samples.size(); ++i) { diff --git a/src/splicing.cpp b/src/splicing.cpp index 2cb7f94ffd6..c4e1727ccfe 100644 --- a/src/splicing.cpp +++ b/src/splicing.cpp @@ -1633,7 +1633,7 @@ multipath_alignment_t&& fuse_spliced_alignments(const Alignment& alignment, } } else if (!have_right_linker) { - // the splice segment on the right side is empty, make connection the the left side + // the splice segment on the right side is empty, make connection the left side auto connection = left_mp_aln.mutable_subpath(right_subpaths_begin - 1)->add_connection(); connection->set_next(left_mp_aln.subpath_size()); connection->set_score(splice_score); diff --git a/src/transcriptome.hpp b/src/transcriptome.hpp index 90d3ba13bad..42214df12cb 100644 --- a/src/transcriptome.hpp +++ b/src/transcriptome.hpp @@ -281,7 +281,7 @@ class Transcriptome { /// Parse gtf/gff3 attribute value. string parse_attribute_value(const string & attribute, const string & name) const; - /// Returns the the mean node length of the graph + /// Returns the mean node length of the graph float mean_node_length() const; /// Adds the exon coordinates to a transcript.