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uclahs-cds · Apr 1, 2024 · 1652114 · 1652114
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diff --git a/development/contributors/index.html b/development/contributors/index.html
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     <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">Contributors</li>
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-          <a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/628b9e15016a7b29f7d7d097298f4fc920361bb6/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/015011a0968378d5a2ed3ff4d0fbbe9124bad8c1/README.md" class="icon icon-github"> Edit on GitHub</a>
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diff --git a/development/discussions/index.html b/development/discussions/index.html
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+          <a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/015011a0968378d5a2ed3ff4d0fbbe9124bad8c1/README.md" class="icon icon-github"> Edit on GitHub</a>
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diff --git a/development/flow-diagram/index.html b/development/flow-diagram/index.html
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       <li class="breadcrumb-item active">Flow Diagram</li>
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+          <a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/015011a0968378d5a2ed3ff4d0fbbe9124bad8c1/README.md" class="icon icon-github"> Edit on GitHub</a>
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diff --git a/development/how-to-run/index.html b/development/how-to-run/index.html
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       <li class="breadcrumb-item active">How To Run</li>
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+          <a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/015011a0968378d5a2ed3ff4d0fbbe9124bad8c1/README.md" class="icon icon-github"> Edit on GitHub</a>
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diff --git a/development/index.html b/development/index.html
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     <li><a href="." class="icon icon-home" aria-label="Docs"></a></li>
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+          <a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/015011a0968378d5a2ed3ff4d0fbbe9124bad8c1/README.md" class="icon icon-github"> Edit on GitHub</a>
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@@ -191,5 +191,5 @@ <h1 id="calculate-targeted-coverage">Calculate Targeted Coverage</h1>
 
 <!--
 MkDocs version : 1.5.3
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+Build Date UTC : 2024-04-01 20:00:35.603341+00:00
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diff --git a/development/inputs-and-configuration/index.html b/development/inputs-and-configuration/index.html
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-          <a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/628b9e15016a7b29f7d7d097298f4fc920361bb6/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/015011a0968378d5a2ed3ff4d0fbbe9124bad8c1/README.md" class="icon icon-github"> Edit on GitHub</a>
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diff --git a/development/license/index.html b/development/license/index.html
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+          <a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/015011a0968378d5a2ed3ff4d0fbbe9124bad8c1/README.md" class="icon icon-github"> Edit on GitHub</a>
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diff --git a/development/outputs/index.html b/development/outputs/index.html
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     <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">Outputs</li>
     <li class="wy-breadcrumbs-aside">
-          <a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/628b9e15016a7b29f7d7d097298f4fc920361bb6/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/015011a0968378d5a2ed3ff4d0fbbe9124bad8c1/README.md" class="icon icon-github"> Edit on GitHub</a>
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@@ -128,6 +128,10 @@ <h2 id="outputs">Outputs</h2>
 <td>New target file including original target intervals and intervals encompassing coverage-enriched off-target dbSNP sites.</td>
 </tr>
 <tr>
+<td><code>*target-with-enriched-off-target-intervals.bed.gz</code></td>
+<td>New compressed target file including original target intervals and intervals encompassing coverage-enriched off-target dbSNP sites.</td>
+</tr>
+<tr>
 <td><code>*off-target-dbSNP-depth-per-base.bed</code></td>
 <td>Per-base read depth at dbSNP loci outside of targeted regions.</td>
 </tr>

diff --git a/development/overview/index.html b/development/overview/index.html
@@ -102,7 +102,7 @@
     <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">Overview</li>
     <li class="wy-breadcrumbs-aside">
-          <a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/628b9e15016a7b29f7d7d097298f4fc920361bb6/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/015011a0968378d5a2ed3ff4d0fbbe9124bad8c1/README.md" class="icon icon-github"> Edit on GitHub</a>
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diff --git a/development/pipeline-steps/index.html b/development/pipeline-steps/index.html
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       <li class="breadcrumb-item active">Pipeline Steps</li>
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-          <a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/628b9e15016a7b29f7d7d097298f4fc920361bb6/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/015011a0968378d5a2ed3ff4d0fbbe9124bad8c1/README.md" class="icon icon-github"> Edit on GitHub</a>
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diff --git a/development/references/index.html b/development/references/index.html
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     <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
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+          <a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/015011a0968378d5a2ed3ff4d0fbbe9124bad8c1/README.md" class="icon icon-github"> Edit on GitHub</a>
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@@ -112,9 +112,9 @@
 
                 <h2 id="references">References</h2>
 <ol>
-<li><a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/628b9e15016a7b29f7d7d097298f4fc920361bb6/links-to-papers/external-code/documentation/metadata/other-repos/or-anything-else">Reference 1</a></li>
-<li><a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/628b9e15016a7b29f7d7d097298f4fc920361bb6/links-to-papers/external-code/documentation/metadata/other-repos/or-anything-else">Reference 2</a></li>
-<li><a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/628b9e15016a7b29f7d7d097298f4fc920361bb6/links-to-papers/external-code/documentation/metadata/other-repos/or-anything-else">Reference n</a></li>
+<li><a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/015011a0968378d5a2ed3ff4d0fbbe9124bad8c1/links-to-papers/external-code/documentation/metadata/other-repos/or-anything-else">Reference 1</a></li>
+<li><a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/015011a0968378d5a2ed3ff4d0fbbe9124bad8c1/links-to-papers/external-code/documentation/metadata/other-repos/or-anything-else">Reference 2</a></li>
+<li><a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/015011a0968378d5a2ed3ff4d0fbbe9124bad8c1/links-to-papers/external-code/documentation/metadata/other-repos/or-anything-else">Reference n</a></li>
 </ol>
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diff --git a/development/sitemap.xml.gz b/development/sitemap.xml.gz
diff --git a/development/testing-and-validation/index.html b/development/testing-and-validation/index.html
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       <li class="breadcrumb-item active">Testing and Validation</li>
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-          <a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/628b9e15016a7b29f7d7d097298f4fc920361bb6/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/015011a0968378d5a2ed3ff4d0fbbe9124bad8c1/README.md" class="icon icon-github"> Edit on GitHub</a>
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@@ -157,9 +157,9 @@ <h3 id="validation">Validation \<version number></h3>
 </tbody>
 </table>
 <ul>
-<li><a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/628b9e15016a7b29f7d7d097298f4fc920361bb6/link">Reference/External Link/Path 1 to any files/plots or other validation results</a></li>
-<li><a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/628b9e15016a7b29f7d7d097298f4fc920361bb6/link">Reference/External Link/Path 2 to any files/plots or other validation results</a></li>
-<li><a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/628b9e15016a7b29f7d7d097298f4fc920361bb6/link">Reference/External Link/Path n to any files/plots or other validation results</a></li>
+<li><a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/015011a0968378d5a2ed3ff4d0fbbe9124bad8c1/link">Reference/External Link/Path 1 to any files/plots or other validation results</a></li>
+<li><a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/015011a0968378d5a2ed3ff4d0fbbe9124bad8c1/link">Reference/External Link/Path 2 to any files/plots or other validation results</a></li>
+<li><a href="https://github.com/uclahs-cds/pipeline-calculate-targeted-coverage/blob/015011a0968378d5a2ed3ff4d0fbbe9124bad8c1/link">Reference/External Link/Path n to any files/plots or other validation results</a></li>
 </ul>
 <h3 id="validation-tool">Validation Tool</h3>
 <p>Included is a template for validating your input files. For more information on the tool check out: https://github.com/uclahs-cds/tool-validate-nf</p>

diff --git a/versions.json b/versions.json
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