New upstream version 2.4.5

4 files changed, 40 insertions, 2 deletions

diff --git a/doc/manual.html b/doc/manual.html
index b5c6c06..f313cb6 100644
--- a/doc/manual.html
+++ b/doc/manual.html
@@ -1555,6 +1555,14 @@ Sequence-N  &lt;name&gt;  &lt;len&gt;</code></pre>
 </td>
 </tr>
 <tr>
+<td id="bowtie2-inspect-options-o">
+<pre><code>-o/--output &lt;filename&gt;</code></pre>
+</td>
+<td>
+<p>Save output to user-specified filename (default: stdout)</p>
+</td>
+</tr>
+<tr>
 <td>
 <pre><code>-v/--verbose</code></pre>
 </td>
diff --git a/doc/website/manual.ssi b/doc/website/manual.ssi
index 03b1da3..1a578a9 100644
--- a/doc/website/manual.ssi
+++ b/doc/website/manual.ssi
@@ -1529,6 +1529,14 @@ Sequence-N  &lt;name&gt;  &lt;len&gt;</code></pre>
 </td>
 </tr>
 <tr>
+<td id="bowtie2-inspect-options-o">
+<pre><code>-o/--output &lt;filename&gt;</code></pre>
+</td>
+<td>
+<p>Save output to user-specified filename (default: stdout)</p>
+</td>
+</tr>
+<tr>
 <td>
 <pre><code>-v/--verbose</code></pre>
 </td>
diff --git a/doc/website/recent_news.ssi b/doc/website/recent_news.ssi
index e4fce9f..ae3f1ce 100644
--- a/doc/website/recent_news.ssi
+++ b/doc/website/recent_news.ssi
@@ -1,3 +1,25 @@
+<h2>Version 2.4.5 - Jan 16, 2022</h2>
+<h3 id="bowtie2">bowtie2</h3>
+<ul>
+    <li>Fixed issues with <code>bowtie2</code> BAM parser that would cause <code>bowtie2</code> to crash when processing input that was encoded with tools other than samtools e.g. Picard.</li>
+    <li>Fixed an issue causing <code>bowtie2</code> to drop certain optional fields when when aligning BAM reads with the <code><a href="manual.shtml#bowtie2-options-preserve-tags">--preserve-tags</a></code> option.</li>
+    <li>Fixed an issue causing <code>bowtie2</code> to produce mangled SAM output when specifying <code><a href="manual.shtml#bowtie2-options-sam-append-comment">--sam-append-comment</a></code> together with the <code>--passthrough</code> option.</li>
+    <li>Appended <code>GO:query</code> to SAM <code>@HD</code> entry to indicate that reads are grouped by query name, bump SAM version to 1.5 to indicate support for this change.</li>
+</ul>
+
+<h3 id="bowtie2-build">bowtie2-build</h3>
+<ul>
+    <li>Implemented thread pool to address performance regressions introduced during the switch to C++11 threads.</li>
+    <li>Fixed an issue causing masked-sequence metadata to be omitted from index. This issue would subsequently result in sequence data, <code>@SQ</code>, being left out from alignment SAM header.</li>
+    <li>Included <code>.tmp</code> extension to index files currenlty being built. The extension is removed only upon successful build. This change seeks to address the assumption that <code>bowtie2-build</code> ran successfully without building the reverse indexes.</li>
+    <li>Fixed an issue causing <code>bowtie2-build</code> to sometimes incorrectly calculate input size. This issue would result in the wrong index type being chosen and only happened with GZip compressed files.</li>
+</ul>
+
+<h3 id="bowtie2-inspect">bowtie2-inspect</h3>
+<ul>
+    <li>Added a new <code><a href="manual.shtml#bowtie2-inspect-options-o">-o/--output</a></code> option to save the output of <code>bowtie2-inspect</code> to a file instead of being dumped to standard output.</li>
+</ul>
+
 <h2>Version 2.4.4 - May 23, 2021</h2>
 <ul>
     <li>Fixed an issue that would sometimes cause deadlocks in <code>bowtie2</code> when running multithreaded</li>
diff --git a/doc/website/rhsidebar.ssi b/doc/website/rhsidebar.ssi
index 70c7e9b..d3525ec 100644
--- a/doc/website/rhsidebar.ssi
+++ b/doc/website/rhsidebar.ssi
@@ -18,10 +18,10 @@
         </tr>
       <tr>
       <td>
-        <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.4.4">Bowtie2 v2.4.4</a>
+        <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.4.5">Bowtie2 v2.4.5</a>
       </td>
       <td align="right">
-        23/05/21&nbsp;
+        16/01/22&nbsp;
       </td>
       </tr>
       <tr>