Update documentation in preparation for release 1.3.1

NEWS

@@ -5,7 +5,7 @@ Bowtie NEWS
 
    Bowtie is now available for download.  0.9.0 is the first version to
 be released under the OSI Artistic License (see `LICENSE') and freely
-available to the public for download.  The current version is 1.3.0.
+available to the public for download.  The current version is 1.3.1.
 
 Reporting Issues
 ================
@@ -23,6 +23,18 @@ Keep up with our releases on the GitHub releases page:
 
 Version Release History
 =======================
+Version 1.3.1 - Sep 13, 2021
+
+    * Fixed an overflow issue in `bowtie-build` that would sometimes
+      yield corrupt "large" (64-bit) indexes; the resulting index
+      would sometimes cause `bowtie` to hang. Note: `bowtie2-build`
+      does not have this issue.
+    * Fixed an issue in `bowtie` causing XM:i SAM optional field to
+      sometimes be off by 1 when using the `-m/-M` flags.
+    * Fixed an issue that would sometimes cause deadlocks in `bowtie`
+      when running multithreaded.
+    * Fixed an issue causing build errors when compiling against
+      a pre-C++11 standard.
 
 Version 1.3.0 - Jul 22, 2020
 

VERSION

@@ -1 +1 @@
-1.3.0
+1.3.1

doc/website/manual.ssi

@@ -1,5 +1,5 @@
 <h1>Table of Contents</h1>
-<p>Bowtie 1.3.0</p>
+<p>Bowtie 1.3.1</p>
 
 <nav id="TOC" role="doc-toc">
 <ul>

doc/website/recent_news.ssi

@@ -1,3 +1,11 @@
+<h2>1.3.1 - 09/13/2021</h2>
+<ul>
+    <li>Fixed an overflow issue in <code>bowtie-build</code> that would sometimes yield corrupt "large" (64-bit) indexes; the resulting index would sometimes cause <code>bowtie</code> to hang. Note: <code>bowtie2-build</code> does not have this issue.</li>
+    <li>Fixed an issue in <code>bowtie</code> causing XM:i SAM optional field to sometimes be off by 1 when using the <code><a href="manual.shtml#bowtie-options-m">-m</a>/<a href="manual.shtml#bowtie-options-M">-M</a></code> flags.</li>
+    <li>Fixed an issue that would sometimes cause deadlocks in <code>bowtie</code> when running multithreaded.</li>
+    <li>Fixed an issue causing build errors when compiling against a pre-C++11 standard.</li>
+</ul>
+
 <h2>1.3.0 - 07/22/2020</h2>
 <ul>
     <li>Fixed an issue causing <code>bowtie</code> to report incorrect results when using a Bowtie 2 index.</li>

doc/website/rhsidebar.ssi

@@ -18,10 +18,10 @@
 	</tr>
         <tr>
           <td>
-            <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.3.0">Bowtie 1.3.0</a>
+            <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.3.1">Bowtie 1.3.1</a>
           </td>
           <td align="right">
-            07/22/20
+            09/13/21
           </td>
         </tr>
         <tr>