Merge pull request #134 from epifluidlab/remove-sam

Remove sam
epifluidlab · Dec 22, 2024 · b99b38e · b99b38e
2 parents a2af496 + 6a4a330
commit b99b38e
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Showing 7 changed files with 1 addition and 26 deletions.
diff --git a/docs/_build/doctrees/documentation/user_guide/inputdata.doctree b/docs/_build/doctrees/documentation/user_guide/inputdata.doctree
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/html/_sources/documentation/user_guide/inputdata.rst.txt b/docs/_build/html/_sources/documentation/user_guide/inputdata.rst.txt
@@ -4,14 +4,6 @@ Input Data
 
 **FinaleToolkit** is compatible with almost any paired-end sequence data.
 
-SAM
-^^^^^^^^^^^
-
-A sequence alignment map (SAM) file is a human-readable file format that stores
-the results of sequence alignment. It contains information about the alignment
-of each read to the reference genome, as well as information about the read
-itself. 
-
 BAM
 ^^^^^^^^^^^
 

diff --git a/docs/_build/html/documentation/user_guide/index.html b/docs/_build/html/documentation/user_guide/index.html
@@ -357,7 +357,6 @@ <h1>User Guide<a class="headerlink" href="#user-guide" title="Link to this headi
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="what.html">Introduction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="inputdata.html">Input Data</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="inputdata.html#sam">SAM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="inputdata.html#bam">BAM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="inputdata.html#cram">CRAM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="inputdata.html#fragment-file">Fragment File</a></li>

diff --git a/docs/_build/html/documentation/user_guide/inputdata.html b/docs/_build/html/documentation/user_guide/inputdata.html
@@ -357,13 +357,6 @@
   <section id="input-data">
 <h1>Input Data<a class="headerlink" href="#input-data" title="Link to this heading">#</a></h1>
 <p><strong>FinaleToolkit</strong> is compatible with almost any paired-end sequence data.</p>
-<section id="sam">
-<h2>SAM<a class="headerlink" href="#sam" title="Link to this heading">#</a></h2>
-<p>A sequence alignment map (SAM) file is a human-readable file format that stores
-the results of sequence alignment. It contains information about the alignment
-of each read to the reference genome, as well as information about the read
-itself.</p>
-</section>
 <section id="bam">
 <h2>BAM<a class="headerlink" href="#bam" title="Link to this heading">#</a></h2>
 <p>A binary alignment file (BAM) that stores the results of sequence alignment.
@@ -462,7 +455,6 @@ <h2>Fragment File<a class="headerlink" href="#fragment-file" title="Link to this
   </div>
   <nav class="bd-toc-nav page-toc" aria-labelledby="pst-page-navigation-heading-2">
     <ul class="visible nav section-nav flex-column">
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#sam">SAM</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#bam">BAM</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#cram">CRAM</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#fragment-file">Fragment File</a></li>

diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js
diff --git a/docs/documentation/user_guide/inputdata.rst b/docs/documentation/user_guide/inputdata.rst
@@ -4,14 +4,6 @@ Input Data
 
 **FinaleToolkit** is compatible with almost any paired-end sequence data.
 
-SAM
-^^^^^^^^^^^
-
-A sequence alignment map (SAM) file is a human-readable file format that stores
-the results of sequence alignment. It contains information about the alignment
-of each read to the reference genome, as well as information about the read
-itself. 
-
 BAM
 ^^^^^^^^^^^