cc610239716fe32f9c774d98a71f75e8c6b5fba3
braney
  Tue Apr 21 17:23:50 2026 -0700
mafToBigMafSummary: new utility that emits bed3+4 input ready for bedToBigBed -as=mafSummary.as, replacing the hgLoadMafSummary -test / cut -f2- / sort hack documented in bigMaf.html. Companion to mafToBigMaf. The summary scoring/merging logic is intentionally duplicated from hgLoadMafSummary.c (see header comment) — that code is stable and refactoring would force retesting all the makedocs that call hgLoadMafSummary. Also fixes a bug in the duplicated copy of mafSplitSrcGetChrom: the original errAborts on plain 'hg38.chrY' style master src because of an inverted differentString check; rewritten with cleaner correct logic. Updates bigMaf.html and trackDb/trackDbLibrary.shtml to reference the new tool. refs #37404

diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
index ee95faa7e84..caaa4a44e5a 100644
--- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
+++ src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
@@ -4063,31 +4063,32 @@
     <P><I>Deprecated</I></P>
     <P>Much more rarely used, this setting can
     replace <code>speciesOrder</code> and <code>speciesGroups</code>.
     Set the <code>speciesUseFile</code> to a path relative to the apache cgi-bin.
     The file should contain a single species name as the first word of each line.</P>
     <P><B>Example:</B></P>
     <pre>    speciesUseFile speciesLists/conserved8Way.txt</pre>
 </DIV>
 
 <DIV class="summary"><span class="types wigMaf bigMaf"></span>
 <div class="format"><code>summary &lt;tableName/url&gt;</code></div>
     <P>This setting contains a table name containing a  MAF summary table, or a url that points to a 
     bigBed containing that information. The summary
     view is used when the browser display is zoomed out to contain a million
     or more basepairs.  A summary table is created from a multiple alignment MAF
-    file using the utility <code>hgLoadMafSummary</code>.  For bigMaf, the value is assumed to be bigBed,
+    file using the utility <code>hgLoadMafSummary</code> (SQL track) or
+    <code>mafToBigMafSummary</code> (bigMaf).  For bigMaf, the value is assumed to be bigBed,
     Read about <a href="../bigMaf.html#frames_summary">bigMaf supporting files</a> on the help page.</p>
     <P><B>Example:</B></P>
     <pre>   summary hg17Maf8waySummary</pre>
 </DIV>
 
 <DIV class="treeImage"><span class="types wigMaf"></span>
 <div class="format"><code>treeImage &lt;imageFile&gt;</code></div>
     <P>The phylogenetic tree
     can used to show the relations of the species in the multiple
     alignment should be included as an image file.  This path is
     relative to the htdocs images directory (usually /images).</P>
     <P><B>Example:</B></P>
     <pre>   treeImage phylo/hg17Maf8way.jpg</pre>
 </DIV>