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rhshah · Jun 6, 2016 · ced4fd7 · ced4fd7
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Showing 11 changed files with 60 additions and 24 deletions.
diff --git a/README.rst b/README.rst
@@ -39,7 +39,10 @@ Required Data Files
 This files are given in the ``data`` folder inside iCallSV.
 
 
-:BlackListFile:: (blacklist.txt) Tab-delimited file wihout header having black listed regions in order chromosome 1, breakpoint 1, chromosome 2, breakpoint 2 
+:BlackListFile: (blacklist.txt) Tab-delimited file wihout header having black listed regions in order:
+
+				**chromosome 1, breakpoint 1, chromosome 2, breakpoint 2**
+
 
 	:Example:
 
@@ -54,7 +57,9 @@ This files are given in the ``data`` folder inside iCallSV.
 
 		CNOT4
 
-:HotspotFile: (hotspotgenes.txt) Tab-delimited file wihout header having hotspot regions in order chromosome, start, end, name 
+:HotspotFile: (hotspotgenes.txt) Tab-delimited file wihout header having hotspot regions in order:
+
+			  **chromosome, start, end, name**
 
 	:Example:
 

diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/iCallSV.doctree b/docs/_build/doctrees/iCallSV.doctree
diff --git a/docs/_build/html/_sources/iCallSV.txt b/docs/_build/html/_sources/iCallSV.txt
@@ -18,7 +18,11 @@ Required Data Files
 
 This files are given in the ``data`` folder inside iCallSV.
 
-:BlackListFile:: (blacklist.txt) Tab-delimited file wihout header having black listed regions in order chromosome 1, breakpoint 1, chromosome 2, breakpoint 2 
+
+:BlackListFile: (blacklist.txt) Tab-delimited file wihout header having black listed regions in order:
+
+				**chromosome 1, breakpoint 1, chromosome 2, breakpoint 2**
+
 
 	:Example:
 
@@ -33,7 +37,9 @@ This files are given in the ``data`` folder inside iCallSV.
 
 		CNOT4
 
-:HotspotFile: (hotspotgenes.txt) Tab-delimited file wihout header having hotspot regions in order chromosome, start, end, name 
+:HotspotFile: (hotspotgenes.txt) Tab-delimited file wihout header having hotspot regions in order:
+
+			  **chromosome, start, end, name**
 
 	:Example:
 

diff --git a/docs/_build/html/iCallSV.html b/docs/_build/html/iCallSV.html
@@ -78,22 +78,25 @@ <h1>Required Packages<a class="headerlink" href="#required-packages" title="Perm
 <div class="section" id="required-data-files">
 <h1>Required Data Files<a class="headerlink" href="#required-data-files" title="Permalink to this headline">¶</a></h1>
 <p>This files are given in the <code class="docutils literal"><span class="pre">data</span></code> folder inside iCallSV.</p>
-<p>:BlackListFile:: (blacklist.txt) Tab-delimited file wihout header having black listed regions in order chromosome 1, breakpoint 1, chromosome 2, breakpoint 2</p>
-<blockquote>
-<div><table class="docutils field-list" frame="void" rules="none">
+<table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Example:</th><td class="field-body">7       140498077       5       175998094</td>
-</tr>
-</tbody>
-</table>
+<tr class="field-odd field"><th class="field-name">BlackListFile:</th><td class="field-body"><p class="first">(blacklist.txt) Tab-delimited file wihout header having black listed regions in order:</p>
+<blockquote>
+<div><p><strong>chromosome 1, breakpoint 1, chromosome 2, breakpoint 2</strong></p>
 </div></blockquote>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">BlackListGenes:</th><td class="field-body"><p class="first">(blacklistgenes.txt) Gene listed one per line wihout header that are to be removed</p>
+<tr class="field-odd field"><th class="field-name">Example:</th><td class="field-body">7       140498077       5       175998094</td>
+</tr>
+</tbody>
+</table>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">BlackListGenes:</th><td class="field-body"><p class="first">(blacklistgenes.txt) Gene listed one per line wihout header that are to be removed</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -106,7 +109,10 @@ <h1>Required Data Files<a class="headerlink" href="#required-data-files" title="
 </table>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">HotspotFile:</th><td class="field-body"><p class="first">(hotspotgenes.txt) Tab-delimited file wihout header having hotspot regions in order chromosome, start, end, name</p>
+<tr class="field-even field"><th class="field-name">HotspotFile:</th><td class="field-body"><p class="first">(hotspotgenes.txt) Tab-delimited file wihout header having hotspot regions in order:</p>
+<blockquote>
+<div><p><strong>chromosome, start, end, name</strong></p>
+</div></blockquote>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />

diff --git a/docs/_build/json/_sources/iCallSV.txt b/docs/_build/json/_sources/iCallSV.txt
@@ -18,7 +18,11 @@ Required Data Files
 
 This files are given in the ``data`` folder inside iCallSV.
 
-:BlackListFile:: (blacklist.txt) Tab-delimited file wihout header having black listed regions in order chromosome 1, breakpoint 1, chromosome 2, breakpoint 2 
+
+:BlackListFile: (blacklist.txt) Tab-delimited file wihout header having black listed regions in order:
+
+				**chromosome 1, breakpoint 1, chromosome 2, breakpoint 2**
+
 
 	:Example:
 
@@ -33,7 +37,9 @@ This files are given in the ``data`` folder inside iCallSV.
 
 		CNOT4
 
-:HotspotFile: (hotspotgenes.txt) Tab-delimited file wihout header having hotspot regions in order chromosome, start, end, name 
+:HotspotFile: (hotspotgenes.txt) Tab-delimited file wihout header having hotspot regions in order:
+
+			  **chromosome, start, end, name**
 
 	:Example:
 

diff --git a/docs/_build/json/environment.pickle b/docs/_build/json/environment.pickle
diff --git a/docs/_build/json/iCallSV.fjson b/docs/_build/json/iCallSV.fjson
diff --git a/docs/_build/json/searchindex.json b/docs/_build/json/searchindex.json
diff --git a/docs/_build/latex/iCallSV.tex b/docs/_build/latex/iCallSV.tex
@@ -197,16 +197,19 @@ \section{Required Packages}
 \section{Required Data Files}
 \label{iCallSV:required-data-files}
 This files are given in the \code{data} folder inside iCallSV.
-
-:BlackListFile:: (blacklist.txt) Tab-delimited file wihout header having black listed regions in order chromosome 1, breakpoint 1, chromosome 2, breakpoint 2
+\begin{quote}\begin{description}
+\item[{BlackListFile}] \leavevmode
+(blacklist.txt) Tab-delimited file wihout header having black listed regions in order:
 \begin{quote}
+
+\textbf{chromosome 1, breakpoint 1, chromosome 2, breakpoint 2}
+\end{quote}
 \begin{quote}\begin{description}
 \item[{Example}] \leavevmode
 7       140498077       5       175998094
 
 \end{description}\end{quote}
-\end{quote}
-\begin{quote}\begin{description}
+
 \item[{BlackListGenes}] \leavevmode
 (blacklistgenes.txt) Gene listed one per line wihout header that are to be removed
 \begin{quote}\begin{description}
@@ -218,7 +221,11 @@ \section{Required Data Files}
 \end{description}\end{quote}
 
 \item[{HotspotFile}] \leavevmode
-(hotspotgenes.txt) Tab-delimited file wihout header having hotspot regions in order chromosome, start, end, name
+(hotspotgenes.txt) Tab-delimited file wihout header having hotspot regions in order:
+\begin{quote}
+
+\textbf{chromosome, start, end, name}
+\end{quote}
 \begin{quote}\begin{description}
 \item[{Example}] \leavevmode
 2       29416089        30143525        ALK

diff --git a/docs/iCallSV.rst b/docs/iCallSV.rst
@@ -18,7 +18,11 @@ Required Data Files
 
 This files are given in the ``data`` folder inside iCallSV.
 
-:BlackListFile:: (blacklist.txt) Tab-delimited file wihout header having black listed regions in order chromosome 1, breakpoint 1, chromosome 2, breakpoint 2 
+
+:BlackListFile: (blacklist.txt) Tab-delimited file wihout header having black listed regions in order:
+
+				**chromosome 1, breakpoint 1, chromosome 2, breakpoint 2**
+
 
 	:Example:
 
@@ -33,7 +37,9 @@ This files are given in the ``data`` folder inside iCallSV.
 
 		CNOT4
 
-:HotspotFile: (hotspotgenes.txt) Tab-delimited file wihout header having hotspot regions in order chromosome, start, end, name 
+:HotspotFile: (hotspotgenes.txt) Tab-delimited file wihout header having hotspot regions in order:
+
+			  **chromosome, start, end, name**
 
 	:Example: