Merge pull request #16 from sc13-bioinf/master

Support EAGER version and DeDup all reads as merged

src/main/DeDupDialog.form

@@ -0,0 +1,107 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<form xmlns="http://www.intellij.com/uidesigner/form/" version="1" bind-to-class="main.DeDupDialog">
+  <grid id="27dc6" binding="contentPane" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
+    <margin top="10" left="10" bottom="10" right="10"/>
+    <constraints>
+      <xy x="20" y="20" width="1742" height="3285"/>
+    </constraints>
+    <properties/>
+    <border type="none"/>
+    <children>
+      <grid id="bb831" layout-manager="GridLayoutManager" row-count="2" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
+        <margin top="0" left="0" bottom="0" right="0"/>
+        <constraints>
+          <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
+        </constraints>
+        <properties/>
+        <border type="none"/>
+        <children>
+          <grid id="3dd8e" layout-manager="GridLayoutManager" row-count="1" column-count="2" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
+            <margin top="0" left="0" bottom="0" right="0"/>
+            <constraints>
+              <grid row="1" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="2" fill="1" indent="0" use-parent-layout="false"/>
+            </constraints>
+            <properties/>
+            <border type="none"/>
+            <children>
+              <grid id="8bab4" layout-manager="GridLayoutManager" row-count="2" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
+                <margin top="0" left="0" bottom="0" right="0"/>
+                <constraints>
+                  <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
+                </constraints>
+                <properties/>
+                <border type="none"/>
+                <children>
+                  <component id="1befd" class="javax.swing.JButton" binding="buttonOk">
+                    <constraints>
+                      <grid row="1" column="0" row-span="1" col-span="1" vsize-policy="0" hsize-policy="3" anchor="0" fill="1" indent="0" use-parent-layout="false"/>
+                    </constraints>
+                    <properties>
+                      <text value="Ok"/>
+                    </properties>
+                  </component>
+                  <vspacer id="50942">
+                    <constraints>
+                      <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="6" hsize-policy="1" anchor="0" fill="2" indent="0" use-parent-layout="false"/>
+                    </constraints>
+                  </vspacer>
+                </children>
+              </grid>
+              <grid id="9eaec" layout-manager="GridLayoutManager" row-count="1" column-count="1" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
+                <margin top="0" left="0" bottom="0" right="0"/>
+                <constraints>
+                  <grid row="0" column="1" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
+                </constraints>
+                <properties/>
+                <border type="none"/>
+                <children>
+                  <component id="9101f" class="javax.swing.JButton" binding="buttonCancel">
+                    <constraints>
+                      <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="0" hsize-policy="3" anchor="0" fill="1" indent="0" use-parent-layout="false"/>
+                    </constraints>
+                    <properties>
+                      <text value="Cancel"/>
+                    </properties>
+                  </component>
+                </children>
+              </grid>
+            </children>
+          </grid>
+          <grid id="5cf0e" layout-manager="GridLayoutManager" row-count="1" column-count="2" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
+            <margin top="0" left="0" bottom="0" right="0"/>
+            <constraints>
+              <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="3" hsize-policy="3" anchor="0" fill="3" indent="0" use-parent-layout="false"/>
+            </constraints>
+            <properties/>
+            <border type="none"/>
+            <children>
+              <component id="2de1" class="javax.swing.JCheckBox" binding="checkBox_allReadsAsMerged">
+                <constraints>
+                  <grid row="0" column="1" row-span="1" col-span="1" vsize-policy="0" hsize-policy="3" anchor="8" fill="0" indent="0" use-parent-layout="false"/>
+                </constraints>
+                <properties>
+                  <text value="Treat all reads as merged"/>
+                </properties>
+              </component>
+              <component id="c8733" class="javax.swing.JTextArea" binding="textArea_allReadsAsDescription">
+                <constraints>
+                  <grid row="0" column="0" row-span="1" col-span="1" vsize-policy="6" hsize-policy="6" anchor="0" fill="3" indent="0" use-parent-layout="false">
+                    <preferred-size width="150" height="50"/>
+                  </grid>
+                </constraints>
+                <properties>
+                  <editable value="false"/>
+                  <enabled value="true"/>
+                  <lineWrap value="true"/>
+                  <rows value="6"/>
+                  <text value="This option applies if you are using the DeDup tool:&#10;&#10;Check this box unless your read names have prefixes indicating merged, forward or reverse (M_,F_,R_).&#10;&#10;If your reads are NOT from ClipAndMerge then you will probably want to check this box."/>
+                  <wrapStyleWord value="true"/>
+                </properties>
+              </component>
+            </children>
+          </grid>
+        </children>
+      </grid>
+    </children>
+  </grid>
+</form>

src/main/DeDupDialog.java

@@ -0,0 +1,50 @@
+package main;
+
+import javax.swing.*;
+import IO.Communicator;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+/**
+ * Created by clayton on 25/07/16.
+ */
+public class DeDupDialog extends JDialog {
+
+    private JPanel contentPane;
+    private JButton buttonOk;
+    private JButton buttonCancel;
+    private JCheckBox checkBox_allReadsAsMerged;
+    private JTextArea textArea_allReadsAsDescription;
+
+    public DeDupDialog (final Communicator c) {
+        setValues(c);
+        setContentPane(contentPane);
+        setModal(true);
+
+        buttonOk.addActionListener(new ActionListener() {
+            public void actionPerformed(ActionEvent e) {
+                onOk(c);
+            }
+        });
+
+        buttonCancel.addActionListener(new ActionListener() {
+            public void actionPerformed(ActionEvent e) {
+                onCancel();
+            }
+        });
+    }
+
+    private void setValues(Communicator c) {
+        checkBox_allReadsAsMerged.setSelected(c.isRmdup_allReadsAsMerged());
+    }
+
+    private void onOk (Communicator c) {
+        c.setRmdup_allReadsAsMerged(checkBox_allReadsAsMerged.isSelected());
+        dispose();
+    }
+
+    private void onCancel () {
+        dispose();
+    }
+}

src/main/EAGER.form

@@ -321,6 +321,14 @@
               <text value="Use system tmp dir"/>
             </properties>
           </component>
+          <component id="7fe59" class="javax.swing.JButton" binding="dedup_advanced_button">
+            <constraints>
+              <grid row="10" column="3" row-span="1" col-span="1" vsize-policy="0" hsize-policy="3" anchor="0" fill="1" indent="0" use-parent-layout="false"/>
+            </constraints>
+            <properties>
+              <text value="Advanced"/>
+            </properties>
+          </component>
         </children>
       </grid>
       <component id="b04e5" class="javax.swing.JButton" binding="selectInputFqFilesButton" default-binding="true">

src/main/EAGER.java

@@ -38,6 +38,8 @@
  * To change this template use File | Settings | File Templates.
  */
 public class EAGER {
+    private final String EAGER_VERSION = "1.92.12";
+
     private String filepath;
     private JCheckBox fastQCAnalysisCheckBox;
     private JCheckBox qualityFilteringCheckBox;
@@ -81,6 +83,7 @@ public class EAGER {
     private JCheckBox schmutzi_checkbox;
     private JButton schmutzi_advanced_button;
     private JCheckBox useSystemTmpDirCheckBox;
+    private JButton dedup_advanced_button;
     private JMenuBar jmenubar;
     private JMenu jmenu;
     public Image icon;
@@ -628,6 +631,17 @@ public void actionPerformed(ActionEvent e) {
 
             }
         });
+
+        dedup_advanced_button.addActionListener(new ActionListener() {
+            @Override
+            public void actionPerformed(ActionEvent e) {
+                DeDupDialog deDupDialog = new DeDupDialog(communicator);
+                setWindowPosition(deDupDialog);
+                deDupDialog.setSize(650, 650);
+                deDupDialog.setVisible(true);
+            }
+        });
+
         schmutzi_advanced_button.addActionListener(new ActionListener() {
             @Override
             public void actionPerformed(ActionEvent e) {
@@ -724,6 +738,7 @@ private void generateConfiguration(Communicator c) throws IOException {
      * tasks of the pipeline, to generate the appropriate configuration files
      */
     private void generateConfiguration(Communicator c, String resultspath) throws IOException {
+        generateEagerVersionConfiguration(communicator);
         generateRGConfiguration(communicator);
 
         ConfigGenerator cg = new ConfigGenerator(communicator, resultspath, this, this.runReportGenerator.isSelected());
@@ -742,6 +757,10 @@ public static void setWindowPosition(java.awt.Window window) {
 
     }
 
+    private void generateEagerVersionConfiguration(Communicator communicator) {
+        this.communicator.setEager_verison(EAGER_VERSION);
+    }
+
     private void generateRGConfiguration(Communicator communicator) {
         String filenames = Files.getNameWithoutExtension(this.communicator.getGUI_inputfiles().get(0));
         String readgroup = "@RG" + "\\t" + "ID:ILLUMINA-" + filenames + "\\t" + "SM:" + filenames + "\\t" + "PL:illumina";