From bb5c4c09970b799e32538f803b752eddb790c079 Mon Sep 17 00:00:00 2001
From: Ben Langmead <ben.langmead@gmail.com>
Date: Fri, 4 Jun 2021 09:56:47 -0400
Subject: [PATCH 1/3] levioSAM website additions

---
 doc/website/recent_news.ssi |  9 ++++++++
 doc/website/rhsidebar.ssi   | 46 +++++++++++++++++++++++++++++++++++--
 2 files changed, 53 insertions(+), 2 deletions(-)

diff --git a/doc/website/recent_news.ssi b/doc/website/recent_news.ssi
index e4fce9fa..9fb665db 100644
--- a/doc/website/recent_news.ssi
+++ b/doc/website/recent_news.ssi
@@ -1,3 +1,12 @@
+<h2>LevioSAM paper and indel-aware major allele references - June 4, 2021</h2>
+<ul>
+    <li>The <a href="https://doi.org/10.1093/bioinformatics/btab396">levioSAM paper</a> is out in the journal <em>Bioinformatics</em>
+    <li>LevioSAM is a tool that rapidly "lifts" alignments between reference genomes related through a VCF file or chain file
+    <li>LevioSAM makes it easy to align to one reference with Bowtie 2 (or other aligner), then immediately translate the alignments to a different coordinate system
+    <li>As a demonstration, we are adding new major-allele versions of human references (GRCh38 and h19) that contain both major-allele SNVs and major-allele (small) indels.  Because they include indels, these are more comprehensive than the SNV-only major-allele reference we released previously.  LevioSAM provides the ability to translate the alignments back to the original (indel-less) references immediately after.
+    <li>Detailed instructions on using levioSAM+Bowtie2 in this context are available in the <a href="https://github.com/alshai/levioSAM">levioSAM repo</a> <a href="https://github.com/alshai/levioSAM/blob/master/README.md">README.md</a>
+</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 70c7e9b4..cd4299ce 100644
--- a/doc/website/rhsidebar.ssi
+++ b/doc/website/rhsidebar.ssi
@@ -64,14 +64,28 @@
 
       <tr>
         <td>
-            <a href="https://genome-idx.s3.amazonaws.com/bt/grch38_1kgmaj.zip"><i>H. sapiens</i>, GRCh38 + major SNVs</a>
+            <a href="https://genome-idx.s3.amazonaws.com/bt/grch38_1kgmaj_snvs_bt2.zip"><i>H. sapiens</i>, GRCh38 + major SNVs</a>
         </td>
         <td align="right">
             NCBI+1KG
         </td>
       </tr>
       <tr>
-        <td colspan="2" style="font-size: x-small">&nbsp;&nbsp;<a href="https://github.com/BenLangmead/bowtie-majref">How we built this</a>, <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/grch38_1kgmaj.fa.gz">FASTA</a>
+        <td colspan="2" style="font-size: x-small">&nbsp;&nbsp;<a href="https://github.com/BenLangmead/bowtie-majref">How we built this</a>, <a href="https://genome-idx.s3.amazonaws.com/bt/grch38_1kgmaj_snvs.fa.gz">FASTA</a>
+        </td>
+      </tr>
+
+      <!-- New as of 6/3/2021 -->
+      <tr>
+        <td>
+            <a href="https://genome-idx.s3.amazonaws.com/bt/grch38_1kgmaj_snvindels_bt2.zip"><i>H. sapiens</i>, GRCh38 + major SNVs &amp; indels</a>
+        </td>
+        <td align="right">
+            NCBI+1KG
+        </td>
+      </tr>
+      <tr>
+        <td colspan="2" style="font-size: x-small">&nbsp;&nbsp;<a href="https://github.com/BenLangmead/bowtie-majref">How we built this</a>, <a href="https://github.com/alshai/levioSAM/blob/master/README.md">Use with levioSAM</a>, <a href="https://genome-idx.s3.amazonaws.com/bt/grch38_1kgmaj_snvindels.fa.gz">FASTA</a>
         </td>
       </tr>
 
@@ -120,6 +134,34 @@
         </td>
       </tr>
 
+      <!-- New as of 6/3/2021 -->
+      <tr>
+        <td>
+            <a href="https://genome-idx.s3.amazonaws.com/bt/hg19_1kgmaj_snvs_bt2.zip"><i>H. sapiens</i>, hg19 + major SNVs</a>
+        </td>
+        <td align="right">
+            UCSC+1KG
+        </td>
+      </tr>
+      <tr>
+        <td colspan="2" style="font-size: x-small">&nbsp;&nbsp;<a href="https://github.com/BenLangmead/bowtie-majref">How we built this</a>, <a href="https://genome-idx.s3.amazonaws.com/bt/hg19_1kgmaj_snvs.fa.gz">FASTA</a>
+        </td>
+      </tr>
+
+      <!-- New as of 6/3/2021 -->
+      <tr>
+        <td>
+            <a href="https://genome-idx.s3.amazonaws.com/bt/hg19_1kgmaj_snvindels_bt2.zip"><i>H. sapiens</i>, hg19 + major SNVs &amp; indels</a>
+        </td>
+        <td align="right">
+            UCSC+1KG
+        </td>
+      </tr>
+      <tr>
+        <td colspan="2" style="font-size: x-small">&nbsp;&nbsp;<a href="https://github.com/BenLangmead/bowtie-majref">How we built this</a>, <a href="https://github.com/alshai/levioSAM/blob/master/README.md">Use with levioSAM</a>, <a href="https://genome-idx.s3.amazonaws.com/bt/hg19_1kgmaj_snvindels.fa.gz">FASTA</a>
+        </td>
+      </tr>
+
       <tr>
         <td>
             <a href="https://genome-idx.s3.amazonaws.com/bt/hg18.zip"><i>H. sapiens</i>, hg18</a>

From 0edb9d7295ab9e6fd7544527249ac8c9c5ee641d Mon Sep 17 00:00:00 2001
From: Ben Langmead <ben.langmead@gmail.com>
Date: Fri, 4 Jun 2021 10:01:04 -0400
Subject: [PATCH 2/3] updating with clearer pointer to sidebar

---
 doc/website/recent_news.ssi | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/website/recent_news.ssi b/doc/website/recent_news.ssi
index 9fb665db..6f39c689 100644
--- a/doc/website/recent_news.ssi
+++ b/doc/website/recent_news.ssi
@@ -3,7 +3,7 @@
     <li>The <a href="https://doi.org/10.1093/bioinformatics/btab396">levioSAM paper</a> is out in the journal <em>Bioinformatics</em>
     <li>LevioSAM is a tool that rapidly "lifts" alignments between reference genomes related through a VCF file or chain file
     <li>LevioSAM makes it easy to align to one reference with Bowtie 2 (or other aligner), then immediately translate the alignments to a different coordinate system
-    <li>As a demonstration, we are adding new major-allele versions of human references (GRCh38 and h19) that contain both major-allele SNVs and major-allele (small) indels.  Because they include indels, these are more comprehensive than the SNV-only major-allele reference we released previously.  LevioSAM provides the ability to translate the alignments back to the original (indel-less) references immediately after.
+    <li>As a demonstration, we are adding new major-allele versions of human references (GRCh38 and h19) that contain both major-allele SNVs and major-allele (small) indels.  Because they include indels, these are more comprehensive than the SNV-only major-allele reference we released previously.  LevioSAM provides the ability to translate the alignments back to the original (indel-less) references immediately after.  These are in the "Indexes" sidebar on the right.
     <li>Detailed instructions on using levioSAM+Bowtie2 in this context are available in the <a href="https://github.com/alshai/levioSAM">levioSAM repo</a> <a href="https://github.com/alshai/levioSAM/blob/master/README.md">README.md</a>
 </ul>
 

From e93634f6657ef938a827b5182a83474b06da4fa4 Mon Sep 17 00:00:00 2001
From: Ben Langmead <ben.langmead@gmail.com>
Date: Sat, 5 Jun 2021 10:10:54 -0400
Subject: [PATCH 3/3] remove statement about chain files

---
 doc/website/recent_news.ssi | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/website/recent_news.ssi b/doc/website/recent_news.ssi
index 6f39c689..609b0b0b 100644
--- a/doc/website/recent_news.ssi
+++ b/doc/website/recent_news.ssi
@@ -1,7 +1,7 @@
 <h2>LevioSAM paper and indel-aware major allele references - June 4, 2021</h2>
 <ul>
     <li>The <a href="https://doi.org/10.1093/bioinformatics/btab396">levioSAM paper</a> is out in the journal <em>Bioinformatics</em>
-    <li>LevioSAM is a tool that rapidly "lifts" alignments between reference genomes related through a VCF file or chain file
+    <li>LevioSAM is a tool that rapidly "lifts" alignments between reference genomes related through a VCF file.
     <li>LevioSAM makes it easy to align to one reference with Bowtie 2 (or other aligner), then immediately translate the alignments to a different coordinate system
     <li>As a demonstration, we are adding new major-allele versions of human references (GRCh38 and h19) that contain both major-allele SNVs and major-allele (small) indels.  Because they include indels, these are more comprehensive than the SNV-only major-allele reference we released previously.  LevioSAM provides the ability to translate the alignments back to the original (indel-less) references immediately after.  These are in the "Indexes" sidebar on the right.
     <li>Detailed instructions on using levioSAM+Bowtie2 in this context are available in the <a href="https://github.com/alshai/levioSAM">levioSAM repo</a> <a href="https://github.com/alshai/levioSAM/blob/master/README.md">README.md</a>