d139f387c9952df1f43550ae1a418b843dd5ecb3
brianlee
  Sun Jun 26 07:52:53 2022 -0700
Adding doc of -maxWordLength=N option for ixIxx to trix.html

diff --git src/hg/htdocs/goldenPath/help/trix.html src/hg/htdocs/goldenPath/help/trix.html
index 08d18ec..e4c1096 100755
--- src/hg/htdocs/goldenPath/help/trix.html
+++ src/hg/htdocs/goldenPath/help/trix.html
@@ -32,32 +32,37 @@
 </ol>
 <h3 id="ex2">Example 2</h3>
 <ol>
   <li>
   If you have a bigBed track with unique gene names such as
   <code>SIRT1, BRCA1, TP53</code> in the fourth name
   column, and you built the bigBed using the option of
   <code>-extraIndex=name</code> to index the name field you can create an
   input.txt such as the following that associates the bigBed name with other
   identifiers people might search for or with shorter spellings of the names:
   <pre>
     SIRT1 sirt1 sir sirt SIR SIRT Sirtuin SIR2-Like ENSG00000096717 NM_012238
     BRCA1 brca1 brca brc BRC BRCA breast cancer 1 ENSG00000012048 NM_007300
     TP53 tp53 tp5 TP5 Tumor Protein P53 ENSG00000141510 NM_001126112</pre></li>
   <li>
-  You would then run the <code>ixIxx</code> program on your text file.<br>
+  You would then run the <code>ixIxx</code> program on your text file,
+  taking into account the length of your longest word.<br>
   <pre><code>    ixIxx input.txt myTrix.ix myTrix.ixx</code></pre></li>
 </ol>
+<p>
+The <code>ixIxx</code> utility has a default of 31 characters for words. If you build an input.txt
+with longer words, such as very long accessions, you neeed to add the option <code>-maxWordLength=N</code>
+to override the default and expand it to the size you are using for the longest words in your index.</p>
 
 <h3 id="resources">Resources and examples</h3>
 <p>
 If you want to use your Trix index in a track hub, see the <code>searchTrix</code> setting in the 
 <a href="trackDb/trackDbHub.html#searchTrix">Track Database Definition Document</a>.</p>
 <p>
 Review our <a href="hubQuickStartSearch.html" target="_blank">Quick Start Guide to Searchable track hubs</a>
 for illustrated steps building a track hub.</p>
 <p>
 There are also tools available for taking genePred format to trix format, such as
 this <a href="https://genome-source.gi.ucsc.edu/gitlist/kent.git/blob/master/src/hg/utils/automation/gpToIx.pl"
 target="_blank">gpToIx.pl</a> perl script.</p>
 
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