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Commit a0b64dd5 authored by tjc's avatar tjc
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add options to command line

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15859 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent 2ff13cd7
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...@@ -3159,6 +3159,12 @@ public class BamView extends JPanel ...@@ -3159,6 +3159,12 @@ public class BamView extends JPanel
bam.add(args[i]); bam.add(args[i]);
} }
int nbasesInView = 1000; int nbasesInView = 1000;
String chr = null;
String vw = null;
boolean orientation = false;
boolean covPlot = false;
boolean snpPlot = false;
int base = 0;
for(int i=0;i<args.length; i++) for(int i=0;i<args.length; i++)
{ {
...@@ -3176,18 +3182,35 @@ public class BamView extends JPanel ...@@ -3176,18 +3182,35 @@ public class BamView extends JPanel
} }
else if(args[i].equals("-r")) else if(args[i].equals("-r"))
reference = args[++i]; reference = args[++i];
else if(args[i].equals("-v")) else if(args[i].equals("-n"))
nbasesInView = Integer.parseInt(args[++i]); nbasesInView = Integer.parseInt(args[++i]);
else if(args[i].equals("-s")) else if(args[i].equals("-s"))
System.setProperty("samtoolDir", args[++i]); System.setProperty("samtoolDir", args[++i]);
else if(args[i].equals("-c"))
chr = args[++i].trim();
else if(args[i].equals("-b"))
base = Integer.parseInt(args[++i].trim());
else if(args[i].equals("-v"))
vw = args[++i].trim();
else if(args[i].equals("-o"))
orientation = true;
else if(args[i].equals("-pc"))
covPlot = true;
else if(args[i].equals("-ps"))
snpPlot = true;
else if(args[i].startsWith("-h")) else if(args[i].startsWith("-h"))
{ {
System.out.println("-h\t show help"); System.out.println("-h\t show help");
System.out.println("-a\t BAM/SAM file to display"); System.out.println("-a\t BAM/SAM file to display");
System.out.println("-r\t reference file (optional)"); System.out.println("-r\t reference file (optional)");
System.out.println("-v\t number of bases to display in the view (optional)"); System.out.println("-n\t number of bases to display in the view (optional)");
/*System.out.println("-s\t samtool directory");*/ System.out.println("-c\t chromosome name (optional)");
System.out.println("-v\t view (optional - IS (inferred size), S (stack, default), PS (paired stack), ST (strand), C (coverage))");
System.out.println("-b\t base position (optional)");
System.out.println("-o\t show orientation (optional)");
System.out.println("-pc\t plot coverage (optional)");
System.out.println("-ps\t plot SNP (optional and only with -r)");
System.exit(0); System.exit(0);
} }
} }
...@@ -3196,6 +3219,34 @@ public class BamView extends JPanel ...@@ -3196,6 +3219,34 @@ public class BamView extends JPanel
(JPanel)frame.getContentPane(), frame); (JPanel)frame.getContentPane(), frame);
frame.setTitle("BamView v"+view.getVersion()); frame.setTitle("BamView v"+view.getVersion());
if(chr != null)
view.combo.setSelectedItem(chr);
if(vw != null)
{
if(vw.equalsIgnoreCase("IS"))
view.cbIsizeStackView.setSelected(true);
if(vw.equalsIgnoreCase("PS"))
view.cbPairedStackView.setSelected(true);
if(vw.equalsIgnoreCase("ST"))
view.cbStrandStackView.setSelected(true);
if(vw.equalsIgnoreCase("C"))
view.cbCoverageView.setSelected(true);
}
if(base > 0)
view.scrollBar.setValue(base);
if(orientation)
view.isOrientation = true;
if(covPlot)
{
view.isCoverage = true;
view.coveragePanel.setVisible(true);
}
if(snpPlot)
{
view.isSNPplot = true;
view.snpPanel.setVisible(true);
}
// translucent // translucent
//frame.getRootPane().putClientProperty("Window.alpha", new Float(0.9f)); //frame.getRootPane().putClientProperty("Window.alpha", new Float(0.9f));
frame.addWindowFocusListener(new WindowFocusListener() frame.addWindowFocusListener(new WindowFocusListener()
......
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