From 09841c61c520b7144485131c1020ae5a4fd0f352 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 7 Dec 2010 16:04:08 +0000
Subject: [PATCH] VCF record filtering
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15197 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/variant/VCFFilter.java | 154 ++++++++++++++++++
1 file changed, 154 insertions(+)
create mode 100644 uk/ac/sanger/artemis/components/variant/VCFFilter.java
diff --git a/uk/ac/sanger/artemis/components/variant/VCFFilter.java b/uk/ac/sanger/artemis/components/variant/VCFFilter.java
new file mode 100644
index 000000000..3333c5c4d
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/variant/VCFFilter.java
@@ -0,0 +1,154 @@
+package uk.ac.sanger.artemis.components.variant;
+
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JButton;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+
+import uk.ac.sanger.artemis.components.Utilities;
+
+public class VCFFilter extends JFrame
+{
+ private static final long serialVersionUID = 1L;
+ private static float MIN_QUALITY = 0;
+ private static int MIN_DP = 0;
+ private static float MIN_MQ = 0;
+ private static float MIN_AF1 = 0;
+
+ /**
+ * Filter VCF records by different values in the record, QUAL, DP, MQ and AF1.
+ * @param vcfView
+ */
+ public VCFFilter(final VCFview vcfView)
+ {
+ super("Filter");
+ GridBagConstraints c = new GridBagConstraints();
+
+ JPanel panel = (JPanel)getContentPane();
+ panel.setLayout(new GridBagLayout());
+
+ // min quality
+ c.gridy = 0;
+ c.gridx = 0;
+ c.anchor = GridBagConstraints.WEST;
+ panel.add(new JLabel("Minimum quality score (QUAL):"), c);
+ final JTextField minQuality = new JTextField(Float.toString(MIN_QUALITY), 15);
+ c.gridx = 1;
+ panel.add(minQuality, c);
+
+ // min DP
+ c.gridy = c.gridy+1;
+ c.gridx = 0;
+ panel.add(new JLabel("Minimum combined depth across samples (DP):"), c);
+ final JTextField minDP = new JTextField(Integer.toString(MIN_DP), 15);
+ c.gridx = 1;
+ panel.add(minDP, c);
+
+ // min MQ
+ c.gridy = c.gridy+1;
+ c.gridx = 0;
+ panel.add(new JLabel("Minimum RMS mapping quality (MQ):"), c);
+ final JTextField minMQ = new JTextField(Float.toString(MIN_MQ),15);
+ c.gridx = 1;
+ panel.add(minMQ, c);
+
+ // min AF1
+ c.gridy = c.gridy+1;
+ c.gridx = 0;
+ panel.add(new JLabel("Minimum site frequency of strongest non-reference allele (AF1):"), c);
+ final JTextField minAF1 = new JTextField(Float.toString(MIN_AF1),15);
+ c.gridx = 1;
+ panel.add(minAF1, c);
+
+ //
+ c.gridy = c.gridy+1;
+ c.gridx = 0;
+ c.anchor = GridBagConstraints.EAST;
+ JButton apply = new JButton("Apply");
+ apply.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ MIN_QUALITY = Float.parseFloat(minQuality.getText());
+ MIN_DP = Integer.parseInt(minDP.getText());
+ MIN_MQ = Float.parseFloat(minMQ.getText());
+ MIN_AF1 = Float.parseFloat(minAF1.getText());
+ vcfView.repaint();
+ }
+ catch(NumberFormatException ex)
+ {
+ JOptionPane.showMessageDialog(null,
+ ex.getMessage(),
+ "Format Error", JOptionPane.ERROR_MESSAGE);
+ }
+ }
+ });
+ panel.add(apply, c);
+
+ c.gridx = 1;
+ c.anchor = GridBagConstraints.WEST;
+ JButton close = new JButton("Close");
+ close.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ dispose();
+ }
+ });
+ panel.add(close, c);
+
+ pack();
+ Utilities.centreFrame(this);
+ setVisible(true);
+ }
+
+ /**
+ * Test for a given VCF record to see if it passes the filters.
+ * @param record
+ * @return
+ */
+ protected static boolean passFilter(VCFRecord record)
+ {
+ try
+ {
+ if(record.getQuality() < VCFFilter.MIN_QUALITY)
+ return false;
+
+ try
+ {
+ if(VCFFilter.MIN_DP > 0 && Integer.parseInt(record.getInfoValue("DP")) < VCFFilter.MIN_DP)
+ return false;
+ }
+ catch(NullPointerException npe){}
+
+ try
+ {
+ if(VCFFilter.MIN_MQ > 0 && Float.parseFloat(record.getInfoValue("MQ")) < VCFFilter.MIN_MQ)
+ return false;
+ }
+ catch(NullPointerException npe){}
+
+ try
+ {
+ if(VCFFilter.MIN_AF1 > 0 && Float.parseFloat(record.getInfoValue("AF1")) < VCFFilter.MIN_AF1)
+ return false;
+ }
+ catch(NullPointerException npe){}
+ }
+ catch(NumberFormatException e)
+ {
+ System.err.println(e.getMessage());
+ }
+
+ return true;
+ }
+}
\ No newline at end of file
--
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