Commit new auto-generated docs

classvg_1_1Surjector.html

@@ -162,7 +162,9 @@
 <tr class="separator:a59034e11562bb0969c25defd215f166b"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a1df336db06fea7951c960f71265d513d"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1Surjector.html#a1df336db06fea7951c960f71265d513d">low_complexity_p_value</a> = .001</td></tr>
 <tr class="separator:a1df336db06fea7951c960f71265d513d"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="memitem:a5a735901a421d305e6cbf13a016fdc9d"><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1Surjector.html#a5a735901a421d305e6cbf13a016fdc9d">max_anchors</a> = 200</td></tr>
+<tr class="memitem:a0f304005022b214c309ff60a1f186b1f"><td class="memItemLeft" align="right" valign="top">int64_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1Surjector.html#a0f304005022b214c309ff60a1f186b1f">max_low_complexity_anchor_prune</a> = 32</td></tr>
+<tr class="separator:a0f304005022b214c309ff60a1f186b1f"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a5a735901a421d305e6cbf13a016fdc9d"><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1Surjector.html#a5a735901a421d305e6cbf13a016fdc9d">max_anchors</a> = numeric_limits&lt;size_t&gt;::max()</td></tr>
 <tr class="separator:a5a735901a421d305e6cbf13a016fdc9d"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a99dc61c54ce73a8db8526b0f935a14c9"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1Surjector.html#a99dc61c54ce73a8db8526b0f935a14c9">annotate_with_all_path_scores</a> = false</td></tr>
 <tr class="separator:a99dc61c54ce73a8db8526b0f935a14c9"><td class="memSeparator" colspan="2">&#160;</td></tr>
@@ -1781,12 +1783,26 @@ <h2 class="memtitle"><span class="permalink"><a href="#a5a735901a421d305e6cbf13a
 <div class="memproto">
       <table class="memname">
         <tr>
-          <td class="memname">size_t vg::Surjector::max_anchors = 200</td>
+          <td class="memname">size_t vg::Surjector::max_anchors = numeric_limits&lt;size_t&gt;::max()</td>
         </tr>
       </table>
 </div><div class="memdoc">
 <p>How many anchors (per path) will we use when surjecting using anchors? Excessive anchors will be pruned away. </p>
 
+</div>
+</div>
+<a id="a0f304005022b214c309ff60a1f186b1f"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a0f304005022b214c309ff60a1f186b1f">&#9670;&nbsp;</a></span>max_low_complexity_anchor_prune</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int64_t vg::Surjector::max_low_complexity_anchor_prune = 32</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
 </div>
 </div>
 <a id="a77d7a865fffb0ebbc979ba8139f026c5"></a>

functions_func_r.html

@@ -83,7 +83,7 @@ <h3><a id="index_r"></a>- r -</h3><ul>
 , <a class="el" href="classvg_1_1io_1_1ProtobufIterator.html#acf75c4c7a16e406f9bb860e3f0c7dae9">vg::io::ProtobufIterator&lt; T &gt;</a>
 </li>
 <li>Range()
-: <a class="el" href="structvg_1_1Range.html#a08e1ef06cddbc0efcb0660d34cf3bc5d">vg::Range&lt; Number &gt;</a>
+: <a class="el" href="structvg_1_1Range.html#a10c624eaeb6a83b450c9d24fdbaa8555">vg::Range&lt; Number &gt;</a>
 </li>
 <li>rank_by_support()
 : <a class="el" href="classvg_1_1PoissonSupportSnarlCaller.html#a300ca3bbff527fb43fbc12e65177d053">vg::PoissonSupportSnarlCaller</a>

functions_m.html

@@ -530,6 +530,9 @@ <h3><a id="index_m"></a>- m -</h3><ul>
 <li>max_lookback_bases
 : <a class="el" href="classvg_1_1MinimizerMapper.html#ae94869146878dba80c980d4e35830abe">vg::MinimizerMapper</a>
 </li>
+<li>max_low_complexity_anchor_prune
+: <a class="el" href="classvg_1_1Surjector.html#a0f304005022b214c309ff60a1f186b1f">vg::Surjector</a>
+</li>
 <li>max_ma_bias
 : <a class="el" href="classvg_1_1RatioSupportSnarlCaller.html#ac6d48f0372786d80db440fa67523af9e">vg::RatioSupportSnarlCaller</a>
 </li>
@@ -830,7 +833,7 @@ <h3><a id="index_m"></a>- m -</h3><ul>
 : <a class="el" href="classvg_1_1MEMAccelerator.html#a89dfd34874f065088799dfce96c11649">vg::MEMAccelerator</a>
 </li>
 <li>MemoizingGraph()
-: <a class="el" href="classvg_1_1MemoizingGraph.html#aef84e6abc0084e0f910bc99edc760345">vg::MemoizingGraph</a>
+: <a class="el" href="classvg_1_1MemoizingGraph.html#aa6030fdc5e73a8d88059bc31f1886746">vg::MemoizingGraph</a>
 </li>
 <li>memory_high_water_kb
 : <a class="el" href="classvg_1_1Watchdog.html#aa759f3d73ebe15aeb95a13a8c86a0b59">vg::Watchdog</a>
@@ -1300,7 +1303,7 @@ <h3><a id="index_m"></a>- m -</h3><ul>
 : <a class="el" href="classvg_1_1AbstractReadSampler.html#a679c8195e5411d7460725453298b50f2">vg::AbstractReadSampler</a>
 </li>
 <li>multi_surject()
-: <a class="el" href="classvg_1_1Surjector.html#ab8b34cbb819829cd493bdc901a6e3060">vg::Surjector</a>
+: <a class="el" href="classvg_1_1Surjector.html#a0ed6215f3860203803deb2f3078d93b4">vg::Surjector</a>
 </li>
 <li>multiallelic_sv_warned
 : <a class="el" href="classvg_1_1Constructor.html#ad4a4e56154c62990a784f7e51e7368cd">vg::Constructor</a>
@@ -1309,7 +1312,7 @@ <h3><a id="index_m"></a>- m -</h3><ul>
 : <a class="el" href="classvg_1_1MultipathMapper.html#a7af0cb7af3f7a3e3ab60627f3793aa0a">vg::MultipathMapper</a>
 </li>
 <li>multipath_alignment_t()
-: <a class="el" href="classvg_1_1multipath__alignment__t.html#ae7f715f63023d3043c01ed29193ea6a1">vg::multipath_alignment_t</a>
+: <a class="el" href="classvg_1_1multipath__alignment__t.html#a55b4c1fee893c4b596f0a654a624bccc">vg::multipath_alignment_t</a>
 </li>
 <li>multipath_map()
 : <a class="el" href="classvg_1_1MultipathMapper.html#a9ea318c04336aa79020b7c012e468ef8">vg::MultipathMapper</a>
@@ -1321,7 +1324,7 @@ <h3><a id="index_m"></a>- m -</h3><ul>
 : <a class="el" href="classvg_1_1MultipathAlignmentEmitter.html#a022247fcbd889aeb51b35b0cae1c3622">vg::MultipathAlignmentEmitter</a>
 </li>
 <li>MultipathAlignmentGraph()
-: <a class="el" href="classvg_1_1MultipathAlignmentGraph.html#afd75ac7afd23901c4b8f38eb126bdba0">vg::MultipathAlignmentGraph</a>
+: <a class="el" href="classvg_1_1MultipathAlignmentGraph.html#a89b441f028fd26c177a9ce8d8188b7c1">vg::MultipathAlignmentGraph</a>
 </li>
 <li>MultipathMapper()
 : <a class="el" href="classvg_1_1MultipathMapper.html#a4d3a7e85dfc2d7cda41912a4f87fd5ac">vg::MultipathMapper</a>
@@ -1345,10 +1348,10 @@ <h3><a id="index_m"></a>- m -</h3><ul>
 : <a class="el" href="classvg_1_1subpath__t.html#aa967fceb620f92e73e965345d4cd0b67">vg::subpath_t</a>
 </li>
 <li>mutable_edit()
-: <a class="el" href="classvg_1_1path__mapping__t.html#aeb9d50accda37c8829c49cd8567f72bc">vg::path_mapping_t</a>
+: <a class="el" href="classvg_1_1path__mapping__t.html#a56c059138a051e7889f4083a74c5401f">vg::path_mapping_t</a>
 </li>
 <li>mutable_mapping()
-: <a class="el" href="classvg_1_1path__t.html#aac0ad10ace8970358d471d779061b22d">vg::path_t</a>
+: <a class="el" href="classvg_1_1path__t.html#ab3f1eeeefe1c604dacdeff019488ff07">vg::path_t</a>
 </li>
 <li>mutable_next()
 : <a class="el" href="classvg_1_1subpath__t.html#ae1331c79838d972ccb8be4e98ac87954">vg::subpath_t</a>

functions_r.html

@@ -101,7 +101,7 @@ <h3><a id="index_r"></a>- r -</h3><ul>
 , <a class="el" href="classvg_1_1MaximalExactMatch.html#a8652369dde83e159dd8c5638745a749c">vg::MaximalExactMatch</a>
 </li>
 <li>Range()
-: <a class="el" href="structvg_1_1Range.html#a08e1ef06cddbc0efcb0660d34cf3bc5d">vg::Range&lt; Number &gt;</a>
+: <a class="el" href="structvg_1_1Range.html#a7bf784228c365aa72150fec926de77ae">vg::Range&lt; Number &gt;</a>
 </li>
 <li>RANGE_END_MATCH
 : <a class="el" href="classhandlegraph_1_1PathMetadata.html#a938d44c0ba47de41907a6987c6487878">handlegraph::PathMetadata</a>

functions_s.html

@@ -1178,7 +1178,7 @@ <h3><a id="index_s"></a>- s -</h3><ul>
 , <a class="el" href="classvg_1_1GraphSynchronizer_1_1Lock.html#af564269e9eaf8eb68f4c4c3ce1ba3932">vg::GraphSynchronizer::Lock</a>
 , <a class="el" href="structvg_1_1HaplotypePartitioner_1_1Subchain.html#a16932e227f0ac0972fb63bc300a5374d">vg::HaplotypePartitioner::Subchain</a>
 , <a class="el" href="structvg_1_1Haplotypes_1_1Subchain.html#af3baaf52c08ac684ac2571a9f4f56ec0">vg::Haplotypes::Subchain</a>
-, <a class="el" href="classvg_1_1multipath__alignment__t.html#ae79344b60aed1577a39391b4b42574f3">vg::multipath_alignment_t</a>
+, <a class="el" href="classvg_1_1multipath__alignment__t.html#a4cd9b91704e89c799019d9c8962b16bb">vg::multipath_alignment_t</a>
 , <a class="el" href="structvg_1_1MultipathAlignment.html#a8003b8991108e99465d8fd80fc74cc03">vg::MultipathAlignment</a>
 , <a class="el" href="classvg_1_1NetGraph.html#a2d7b0b659aae1f47312bb76aae43dda0">vg::NetGraph</a>
 , <a class="el" href="structvg_1_1Range.html#a372fbc9ba00e9eb4785fcd049b2451cf">vg::Range&lt; Number &gt;</a>
@@ -1549,10 +1549,10 @@ <h3><a id="index_s"></a>- s -</h3><ul>
 : <a class="el" href="classvg_1_1PhasedGenome.html#a181b4e71f8debc78ceccf476ce36abcd">vg::PhasedGenome</a>
 </li>
 <li>swap_node_id()
-: <a class="el" href="classvg_1_1VG.html#a63f2ffa39d84f80e5ab8068a25a03ee9">vg::VG</a>
+: <a class="el" href="classvg_1_1VG.html#afee31880eaf65a1a6d1a250663271b54">vg::VG</a>
 </li>
 <li>swap_node_ids()
-: <a class="el" href="classvg_1_1Paths.html#aba01c4d1b1d415622634db97f62b1188">vg::Paths</a>
+: <a class="el" href="classvg_1_1Paths.html#a3190f22ab39a9039ec9288e1c065ca9c">vg::Paths</a>
 </li>
 <li>swap_nodes()
 : <a class="el" href="classvg_1_1VG.html#aa402d1cf817f83ca44f72f6112b6a2e3">vg::VG</a>

functions_t.html

@@ -641,7 +641,7 @@ <h3><a id="index_t"></a>- t -</h3><ul>
 : <a class="el" href="classvg_1_1io_1_1VPKG.html#a695e5a53bfbc9a5b36c5ea2306f253db">vg::io::VPKG</a>
 </li>
 <li>try_load_first()
-: <a class="el" href="classvg_1_1io_1_1VPKG.html#a58ed1c37748fed4b15d4e611659ce4c3">vg::io::VPKG</a>
+: <a class="el" href="classvg_1_1io_1_1VPKG.html#a504e965a2a019ce27267ea85c106a91b">vg::io::VPKG</a>
 </li>
 <li>try_load_first_bare()
 : <a class="el" href="classvg_1_1io_1_1VPKG.html#a2707edbb6b28a6623ea8ae11e607c861">vg::io::VPKG</a>

functions_v.html

@@ -90,7 +90,7 @@ <h3><a id="index_v"></a>- v -</h3><ul>
 : <a class="el" href="classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a74a157bf3bce2696b04754f1c6dd72b9">vg::Option&lt; vector&lt; Item &gt;, Parser &gt;</a>
 </li>
 <li>value()
-: <a class="el" href="classvg_1_1ProblemDumpExplainer.html#a97c2e3c2f810e01cf79d3e4c0cf4ae47">vg::ProblemDumpExplainer</a>
+: <a class="el" href="classvg_1_1ProblemDumpExplainer.html#a9847ed10905a3633101e1c71f36abc7a">vg::ProblemDumpExplainer</a>
 , <a class="el" href="classvg_1_1SmallBitset.html#a486a8a8a5a30fab268ae96a9cf464fdd">vg::SmallBitset</a>
 , <a class="el" href="structvg_1_1subcommand_1_1Valuation.html#a88e369b92873968c8d7b68cc78ce1b1d">vg::subcommand::Valuation&lt; T &gt;</a>
 , <a class="el" href="structvg_1_1subcommand_1_1ValueArgSpec.html#a518e378dc3759f070912c8cf42ae83cd">vg::subcommand::ValueArgSpec&lt; T, Receiver, Holder &gt;</a>
@@ -241,17 +241,19 @@ <h3><a id="index_v"></a>- v -</h3><ul>
 </li>
 <li>VERSION
 : <a class="el" href="structvg_1_1Haplotypes_1_1Header.html#a68bfc0fe68e8fc1b42ad078eaa234777">vg::Haplotypes::Header</a>
-, <a class="el" href="classvg_1_1Version.html#a06ae288f165de69ddbfdec65c217d222">vg::Version</a>
 </li>
 <li>Version()
 : <a class="el" href="classvg_1_1Version.html#a05bb9f14c7597bf90a2981db7e59b058">vg::Version</a>
 </li>
+<li>VERSION
+: <a class="el" href="classvg_1_1Version.html#a06ae288f165de69ddbfdec65c217d222">vg::Version</a>
+</li>
 <li>vg
 : <a class="el" href="classvg_1_1FlowSort.html#abd481c5b9e6c9c5aeaf846652dd3c76f">vg::FlowSort</a>
 </li>
 <li>VG
 : <a class="el" href="structvg_1_1IndexingParameters.html#af607873fad40d1de55b8f4f6e04fdf10a5e978449ccc729202c33e2dc543b8327">vg::IndexingParameters</a>
-, <a class="el" href="classvg_1_1VG.html#a0fbb777fd8ab6050124a6eaf9eca9133">vg::VG</a>
+, <a class="el" href="classvg_1_1VG.html#af4d321b31b873153431c261090d052af">vg::VG</a>
 </li>
 <li>vg_filename
 : <a class="el" href="classvg_1_1IndexedVG.html#a0399d7902920da48ad515ef358aa65e0">vg::IndexedVG</a>
@@ -260,7 +262,7 @@ <h3><a id="index_v"></a>- v -</h3><ul>
 : <a class="el" href="classvg_1_1io_1_1VGAlignmentEmitter.html#af278878b244808a182eae17640f23a45">vg::io::VGAlignmentEmitter</a>
 </li>
 <li>VGset()
-: <a class="el" href="classvg_1_1VGset.html#a5ff9a6c4fa0223bcee7072f86a657751">vg::VGset</a>
+: <a class="el" href="classvg_1_1VGset.html#a6adbb25be82de20911fd901da4e9fe41">vg::VGset</a>
 </li>
 <li>visit
 : <a class="el" href="structvg_1_1SnarlTraversal.html#aff14559c1e4fb55bdf87320f3a4ee636">vg::SnarlTraversal</a>

functions_vars_m.html

@@ -353,6 +353,9 @@ <h3><a id="index_m"></a>- m -</h3><ul>
 <li>max_lookback_bases
 : <a class="el" href="classvg_1_1MinimizerMapper.html#ae94869146878dba80c980d4e35830abe">vg::MinimizerMapper</a>
 </li>
+<li>max_low_complexity_anchor_prune
+: <a class="el" href="classvg_1_1Surjector.html#a0f304005022b214c309ff60a1f186b1f">vg::Surjector</a>
+</li>
 <li>max_ma_bias
 : <a class="el" href="classvg_1_1RatioSupportSnarlCaller.html#ac6d48f0372786d80db440fa67523af9e">vg::RatioSupportSnarlCaller</a>
 </li>