[Next-Generation Sequencing Book]

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[ Ticket #563 ] Reading multiple wig files (chr1-3), one bed file (chr1)
Date:
12/10/08 07:05
Submitted by:
glyn_dk 		Assigned to:
glyn_dk
Category:
conversion wig -> pwig 		Priority:
5
Ticket group:
reproducible 		Resolution:
Resolved
Summary:
Reading multiple wig files (chr1-3), one bed file (chr1)
Original submission:
(running: CATCH3 svn revision 205 on catch1-desktop)
Thes files listed below are the ones that I sent to Richard in a previous mail.

peaktrack_example_chr1.bed *
peaktrack_example_chr2.bed
peaktrack_example_chr3.bed

ERDD_T7_BR1_chr1.wig *
ERDD_T7_BR1_chr2.wig *
ERDD_T7_BR1_chr3.wig *
ERDD_T7_BR2_chr1.wig *
ERDD_T7_BR2_chr2.wig *
ERDD_T7_BR2_chr3.wig *
ERDD_T7_BR3_chr1.wig *
ERDD_T7_BR3_chr2.wig *
ERDD_T7_BR3_chr3.wig *

When adding all the wig files and only one bed file (indicated by star *), I get an exception:
Exception in thread "AWT-EventQueue-0"
java.lang.ArrayIndexOutOfBoundsException: -1
at java.util.ArrayList.remove(ArrayList.java:390)
at data.DataSet.readSequences(DataSet.java:416)
at data.DataSet.addTrack(DataSet.java:292)
at fileControllers.FileHandlers.importDataSet(FileHandlers.java:45)
at fileControllers.ExtractWiggleLines.conversionPartTwo(ExtractWiggleLines.java:68)
at fileControllers.ExtractWiggleLines.conversionsteptwo(ExtractWiggleLines.java:57)
at fileManager.FileInterfaceGui.convert(FileInterfaceGui.java:395)
at fileManager.FileInterfaceGui.gatherData(FileInterfaceGui.java:429)
at fileManager.FileInterfaceGui.convertAndAddInCatchButtonActionPerformed(FileInterfaceGui.java:449)
at fileManager.FileInterfaceGui.access$1(FileInterfaceGui.java:447)
at fileManager.FileInterfaceGui$2.actionPerformed(FileInterfaceGui.java:154)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
at java.awt.Component.processMouseEvent(Component.java:6041)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3265)
at java.awt.Component.processEvent(Component.java:5806)
at java.awt.Container.processEvent(Container.java:2058)
at java.awt.Component.dispatchEventImpl(Component.java:4413)
at java.awt.Container.dispatchEventImpl(Container.java:2116)
at java.awt.Component.dispatchEvent(Component.java:4243)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4322)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3986)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3916)
at java.awt.Container.dispatchEventImpl(Container.java:2102)
at java.awt.Window.dispatchEventImpl(Window.java:2440)
at java.awt.Component.dispatchEvent(Component.java:4243)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:273)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:183)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:173)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:168)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:160)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:121)
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Followups
Comment Date By
Fixed by returning from readSequences when there are no profiles defined in the file. 01/11/09 08:54 glyn_dk
Berry:
Unfortunately I don't know how to deal with this one. The bug is caused by the ERDD_T7_BR1_chr2.wig * file, after I/O is done and this is run:

if (seqpositions.size() < 2) {
// the sequence must have at least two measuring points
// remove the sequence from the sequencenames, reference positions
seqnames.remove(seqnames.size() - 1);
refposList.remove(refposList.size() - 1);

What the meaning of the code around here is and what might cause this issue, I unfortunately do not know.


Fiona:
I think this will have to be rewritten to fix the bug...
(and I am probably the one who has to rewrite it)
I guess that the bug is caused by some window for which the wig file
has less than two measuring points, but why it is not handled right. I don't know.

QuickFIX: catch any exception, and notify the user which file CATCH
had problems reading.
(then the user has the possibility to deselect the problematic file
and continue with other files)

Berry:
QuickFix implemented.

String errorMessage = "The following file has encountered a known bug:nn" + files[filei] + "nn" +
"This bug will be fixed as soon as possible. For now, please deselect this file and try again.";
JOptionPane.showMessageDialog(null, errorMessage, "Error", JOptionPane.ERROR_MESSAGE);
return; 		01/05/09 09:34 glyn_dk
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Ticket change history
Field Old value Date By
status_id Pending 01/11/09 08:54 glyn_dk
assigned_to unset 01/11/09 08:54 glyn_dk
resolution_id Not Resolved 01/11/09 08:54 glyn_dk
close_date 12/31/69 19:00 01/11/09 08:54 glyn_dk
status_id Unset 01/05/09 09:34 glyn_dk
resolution_id Unset 01/05/09 09:34 glyn_dk

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