From a5d0cb204ef34176dc23f1a2610a3df9f2c29e54 Mon Sep 17 00:00:00 2001
From: Aron Skaftason <arontommi@gmail.com>
Date: Fri, 12 Jan 2018 07:51:46 +0100
Subject: [PATCH] some documentation added

---
 .idea/workspace.xml | 34 +++++++++++++++++-----------------
 Readme.md           |  8 ++++++--
 2 files changed, 23 insertions(+), 19 deletions(-)

diff --git a/.idea/workspace.xml b/.idea/workspace.xml
index d08c0d4..6f42f80 100644
--- a/.idea/workspace.xml
+++ b/.idea/workspace.xml
@@ -30,7 +30,7 @@
           </provider>
         </entry>
       </file>
-      <file leaf-file-name="smallerbam.py" pinned="false" current-in-tab="true">
+      <file leaf-file-name="smallerbam.py" pinned="false" current-in-tab="false">
         <entry file="file://$PROJECT_DIR$/smallerbam.py">
           <provider selected="true" editor-type-id="text-editor">
             <state relative-caret-position="541">
@@ -42,12 +42,12 @@
           </provider>
         </entry>
       </file>
-      <file leaf-file-name="Readme.md" pinned="false" current-in-tab="false">
+      <file leaf-file-name="Readme.md" pinned="false" current-in-tab="true">
         <entry file="file://$PROJECT_DIR$/Readme.md">
           <provider selected="true" editor-type-id="split-provider[text-editor;MarkdownPreviewEditor]">
             <state split_layout="SPLIT">
               <first_editor relative-caret-position="45">
-                <caret line="3" column="160" selection-start-line="3" selection-start-column="160" selection-end-line="3" selection-end-column="160" />
+                <caret line="3" column="4" selection-start-line="3" selection-start-column="4" selection-end-line="3" selection-end-column="4" />
                 <folding />
               </first_editor>
               <second_editor>
@@ -70,8 +70,8 @@
     <option name="CHANGED_PATHS">
       <list>
         <option value="$PROJECT_DIR$/samtools_view.sh" />
-        <option value="$PROJECT_DIR$/Readme.md" />
         <option value="$PROJECT_DIR$/smallerbam.py" />
+        <option value="$PROJECT_DIR$/Readme.md" />
       </list>
     </option>
   </component>
@@ -334,19 +334,6 @@
     <watches-manager />
   </component>
   <component name="editorHistoryManager">
-    <entry file="file://$PROJECT_DIR$/Readme.md">
-      <provider selected="true" editor-type-id="split-provider[text-editor;MarkdownPreviewEditor]">
-        <state split_layout="SPLIT">
-          <first_editor relative-caret-position="45">
-            <caret line="3" column="160" selection-start-line="3" selection-start-column="160" selection-end-line="3" selection-end-column="160" />
-            <folding />
-          </first_editor>
-          <second_editor>
-            <js_state />
-          </second_editor>
-        </state>
-      </provider>
-    </entry>
     <entry file="file://$PROJECT_DIR$/samtools_view.sh">
       <provider selected="true" editor-type-id="text-editor">
         <state relative-caret-position="90">
@@ -365,5 +352,18 @@
         </state>
       </provider>
     </entry>
+    <entry file="file://$PROJECT_DIR$/Readme.md">
+      <provider selected="true" editor-type-id="split-provider[text-editor;MarkdownPreviewEditor]">
+        <state split_layout="SPLIT">
+          <first_editor relative-caret-position="45">
+            <caret line="3" column="4" selection-start-line="3" selection-start-column="4" selection-end-line="3" selection-end-column="4" />
+            <folding />
+          </first_editor>
+          <second_editor>
+            <js_state />
+          </second_editor>
+        </state>
+      </provider>
+    </entry>
   </component>
 </project>
\ No newline at end of file
diff --git a/Readme.md b/Readme.md
index 7e40b7b..fb21a7d 100644
--- a/Readme.md
+++ b/Readme.md
@@ -1,8 +1,12 @@
 
 
 
-##### this is a simple wrapper around samtools to subset bam files to later view in Igv for less command line literate people for visual validation of variants.
+#### this is a simple wrapper around samtools to subset bam files to later view in Igv for less command line literate people for visual validation of variants.
 
 additional objects are for the writer to improve software documentasion as well as use click to manage inputs
 
-The idea is to continue to add functionality, ideally being able
\ No newline at end of file
+it is possible to run multiple files by using a simple headerless csv
+
+##### example of csv :
+
+        inputfile,region,outputfile
\ No newline at end of file