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VG Doc Bot committed Jul 18, 2024
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6 changes: 3 additions & 3 deletions classvg_1_1MultipathAlignmentGraph-members.html
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<table class="directory">
<tr class="even"><td class="entry"><a class="el" href="classvg_1_1MultipathAlignmentGraph.html#a99e7522a1341bc3d5e7d0876156d0e24">add_decomposed_tail_alignments</a>(const Alignment &amp;alignment, const HandleGraph &amp;align_graph, multipath_alignment_t &amp;multipath_aln_out, unordered_set&lt; size_t &gt; &amp;prohibited_merges, vector&lt; pair&lt; path_t, int32_t &gt;&gt; &amp;shared_tail_alns, vector&lt; vector&lt; pair&lt; path_t, int32_t &gt;&gt;&gt; &amp;unshared_tail_alns, size_t attachment_idx, bool to_left, size_t unmergeable_len, const GSSWAligner *aligner, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function&lt; pair&lt; id_t, bool &gt;(id_t)&gt; *project=nullptr)</td><td class="entry"><a class="el" href="classvg_1_1MultipathAlignmentGraph.html">vg::MultipathAlignmentGraph</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
<tr><td class="entry"><a class="el" href="classvg_1_1MultipathAlignmentGraph.html#a2bf6b811ae4c3f0c993d3ac4a11359f0">add_reachability_edges</a>(const HandleGraph &amp;vg, const function&lt; pair&lt; id_t, bool &gt;(id_t)&gt; &amp;project, const unordered_multimap&lt; id_t, pair&lt; id_t, bool &gt;&gt; &amp;injection_trans, vector&lt; size_t &gt; *path_node_provenance=nullptr)</td><td class="entry"><a class="el" href="classvg_1_1MultipathAlignmentGraph.html">vg::MultipathAlignmentGraph</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classvg_1_1MultipathAlignmentGraph.html#a0441b6564d570a37a778d9966e180e43">align</a>(const Alignment &amp;alignment, const HandleGraph &amp;align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, bool simplify_topologies, size_t unmergeable_len, size_t band_padding, multipath_alignment_t &amp;multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function&lt; pair&lt; id_t, bool &gt;(id_t)&gt; *project=nullptr, bool allow_negative_scores=false, unordered_map&lt; handle_t, bool &gt; *left_align_strand=nullptr)</td><td class="entry"><a class="el" href="classvg_1_1MultipathAlignmentGraph.html">vg::MultipathAlignmentGraph</a></td><td class="entry"></td></tr>
<tr><td class="entry"><a class="el" href="classvg_1_1MultipathAlignmentGraph.html#a8afc1b58038770a8376fe27ca6d6ce3c">align</a>(const Alignment &amp;alignment, const HandleGraph &amp;align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, bool simplify_topologies, size_t unmergeable_len, function&lt; size_t(const Alignment &amp;, const HandleGraph &amp;)&gt; band_padding_function, multipath_alignment_t &amp;multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function&lt; pair&lt; id_t, bool &gt;(id_t)&gt; *project=nullptr, bool allow_negative_scores=false, unordered_map&lt; handle_t, bool &gt; *left_align_strand=nullptr)</td><td class="entry"><a class="el" href="classvg_1_1MultipathAlignmentGraph.html">vg::MultipathAlignmentGraph</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classvg_1_1MultipathAlignmentGraph.html#aba2fbcf9b7fb1368cdb033d3ecc69bf0">align_tails</a>(const Alignment &amp;alignment, const HandleGraph &amp;align_graph, const GSSWAligner *aligner, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, size_t min_paths, unordered_set&lt; size_t &gt; *sources=nullptr)</td><td class="entry"><a class="el" href="classvg_1_1MultipathAlignmentGraph.html">vg::MultipathAlignmentGraph</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classvg_1_1MultipathAlignmentGraph.html#abde01b7f7289e1041f962e88f215d22e">align</a>(const Alignment &amp;alignment, const HandleGraph &amp;align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, size_t max_tail_length, bool simplify_topologies, size_t unmergeable_len, size_t band_padding, multipath_alignment_t &amp;multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function&lt; pair&lt; id_t, bool &gt;(id_t)&gt; *project=nullptr, bool allow_negative_scores=false, unordered_map&lt; handle_t, bool &gt; *left_align_strand=nullptr)</td><td class="entry"><a class="el" href="classvg_1_1MultipathAlignmentGraph.html">vg::MultipathAlignmentGraph</a></td><td class="entry"></td></tr>
<tr><td class="entry"><a class="el" href="classvg_1_1MultipathAlignmentGraph.html#a27a7ca4063b3ca96c0c296d9894e8852">align</a>(const Alignment &amp;alignment, const HandleGraph &amp;align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, size_t max_tail_length, bool simplify_topologies, size_t unmergeable_len, function&lt; size_t(const Alignment &amp;, const HandleGraph &amp;)&gt; band_padding_function, multipath_alignment_t &amp;multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function&lt; pair&lt; id_t, bool &gt;(id_t)&gt; *project=nullptr, bool allow_negative_scores=false, unordered_map&lt; handle_t, bool &gt; *left_align_strand=nullptr)</td><td class="entry"><a class="el" href="classvg_1_1MultipathAlignmentGraph.html">vg::MultipathAlignmentGraph</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classvg_1_1MultipathAlignmentGraph.html#ab340ca598eea6944dc841a9b76b73d48">align_tails</a>(const Alignment &amp;alignment, const HandleGraph &amp;align_graph, const GSSWAligner *aligner, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, size_t min_paths, size_t max_tail_length, unordered_set&lt; size_t &gt; *sources=nullptr)</td><td class="entry"><a class="el" href="classvg_1_1MultipathAlignmentGraph.html">vg::MultipathAlignmentGraph</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
<tr><td class="entry"><a class="el" href="classvg_1_1MultipathAlignmentGraph.html#af112f1a5af47cf079a163eec1c2e31f4">clear_reachability_edges</a>()</td><td class="entry"><a class="el" href="classvg_1_1MultipathAlignmentGraph.html">vg::MultipathAlignmentGraph</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classvg_1_1MultipathAlignmentGraph.html#a8f309bbf60941b009379bd9661cb9060">collapse_order_length_runs</a>(const HandleGraph &amp;graph, gcsa::GCSA *gcsa, vector&lt; size_t &gt; &amp;path_node_provenance)</td><td class="entry"><a class="el" href="classvg_1_1MultipathAlignmentGraph.html">vg::MultipathAlignmentGraph</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
<tr><td class="entry"><a class="el" href="classvg_1_1MultipathAlignmentGraph.html#ae053f01b2505d284a43a5d0c2046c82b">count_reachability_edges</a>() const</td><td class="entry"><a class="el" href="classvg_1_1MultipathAlignmentGraph.html">vg::MultipathAlignmentGraph</a></td><td class="entry"></td></tr>
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