Details
-
Type:
Bug
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: 9.0.1 Minor Release
-
Labels:None
-
Sprint:Fall 2017
Description
This issue is related to HELP-275 from the User Support Project.
The user gets errors when viewing Oxford Nanopore Long or Pacbio reads.
From user:
I was wondering if you had any experience trying to view long read RNA alignments from Oxford Nanopore or Pacbio in IGB. I have some ON DRS data that I've aligned with gmap. The bam alignments looks good from the aligner. When I load it in IGB everything slows to a crawl. Ona really small window with only one-or-two genes in it its 10s seconds to load and seconds to do anything else. With a large region it becomes unusable.
I think the issue is related to parsing and understanding the long complex cigar strings for the long reads (they are error prone and indel heavy). If I have the console open when I load them I get lots of instances of 'String index out of range' like this:
java.lang.StringIndexOutOfBoundsException: String index out of range: 143
at java.lang.String.substring(String.java:1963)
at com.affymetrix.genometry.symmetry.impl.BAMSym.interpretCigar(BAMSym.java:489)
at com.affymetrix.genometry.symmetry.impl.BAMSym.getBaseQuality(BAMSym.java:440)
at com.affymetrix.genometry.symmetry.impl.BAMSym.access$100(BAMSym.java:27)
at com.affymetrix.genometry.symmetry.impl.BAMSym$BamChildSingletonSeqSym.getBaseQuality(BAMSym.java:166)
at com.affymetrix.genometry.symmetry.impl.BAMSym$BamChildSingletonSeqSym.getAverageQuality(BAMSym.java:177)
at com.affymetrix.genometry.symmetry.impl.BAMSym$BamChildSingletonSeqSym.cloneProperties(BAMSym.java:222)
at com.affymetrix.igb.tiers.TierLabelManager.determineProps(TierLabelManager.java:738)
at com.affymetrix.igb.view.SeqMapView.determineProps(SeqMapView.java:2236)
at com.affymetrix.igb.property.PropertyView.getPropertiesRow(PropertyView.java:234)
at com.affymetrix.igb.view.SeqMapView.setToolTip(SeqMapView.java:2087)
at com.affymetrix.igb.view.SeqMapView.setToolTip(SeqMapView.java:2045)
at com.affymetrix.igb.view.SeqMapViewMouseListener.oldToolTip(SeqMapViewMouseListener.java:210)
at com.affymetrix.igb.view.SeqMapViewMouseListener.mouseMoved(SeqMapViewMouseListener.java:192)
at com.affymetrix.genoviz.widget.NeoWidget.heardMouseEvent(NeoWidget.java:1339)
at com.affymetrix.genoviz.widget.NeoMap.heardMouseEvent(NeoMap.java:1589)
at com.affymetrix.genoviz.widget.NeoAbstractWidget.mouseMoved(NeoAbstractWidget.java:827)
at com.affymetrix.genoviz.bioviews.View.heardMouseEvent(View.java:978)
at com.affymetrix.genoviz.bioviews.View.mouseMoved(View.java:887)
at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329)
at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329)
at java.awt.Component.processMouseMotionEvent(Component.java:6580)
at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342)
at java.awt.Component.processEvent(Component.java:6304)
at java.awt.Container.processEvent(Container.java:2236)
at java.awt.Component.dispatchEventImpl(Component.java:4891)
at java.awt.Container.dispatchEventImpl(Container.java:2294)
at java.awt.Component.dispatchEvent(Component.java:4713)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
at java.awt.Container.dispatchEventImpl(Container.java:2280)
at java.awt.Window.dispatchEventImpl(Window.java:2750)
at java.awt.Component.dispatchEvent(Component.java:4713)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.awt.EventQueue$4.run(EventQueue.java:729)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Any ideas what the problem is? I can probably send you the bam file to take a look at tomorrow if that'd help....
Attachments
Issue Links
- relates to
-
HELP-275
IGB and Oxford Nanopore Long reads....
-
- To-Do
-
Activity
| Field | Original Value | New Value |
|---|---|---|
| Description |
This issue is related to HELP-275 from the User Support Project.
The user gets this error when viewing Oxford Nanopore Long or Pacbio reads: |
This issue is related to HELP-275 from the User Support Project.
The user gets errors when viewing Oxford Nanopore Long or Pacbio reads. From user: I was wondering if you had any experience trying to view long read RNA alignments from Oxford Nanopore or Pacbio in IGB. I have some ON DRS data that I've aligned with gmap. The bam alignments looks good from the aligner. When I load it in IGB everything slows to a crawl. Ona really small window with only one-or-two genes in it its 10s seconds to load and seconds to do anything else. With a large region it becomes unusable. I think the issue is related to parsing and understanding the long complex cigar strings for the long reads (they are error prone and indel heavy). If I have the console open when I load them I get lots of instances of 'String index out of range' like this: java.lang.StringIndexOutOfBoundsException: String index out of range: 143 at java.lang.String.substring(String.java:1963) at com.affymetrix.genometry.symmetry.impl.BAMSym.interpretCigar(BAMSym.java:489) at com.affymetrix.genometry.symmetry.impl.BAMSym.getBaseQuality(BAMSym.java:440) at com.affymetrix.genometry.symmetry.impl.BAMSym.access$100(BAMSym.java:27) at com.affymetrix.genometry.symmetry.impl.BAMSym$BamChildSingletonSeqSym.getBaseQuality(BAMSym.java:166) at com.affymetrix.genometry.symmetry.impl.BAMSym$BamChildSingletonSeqSym.getAverageQuality(BAMSym.java:177) at com.affymetrix.genometry.symmetry.impl.BAMSym$BamChildSingletonSeqSym.cloneProperties(BAMSym.java:222) at com.affymetrix.igb.tiers.TierLabelManager.determineProps(TierLabelManager.java:738) at com.affymetrix.igb.view.SeqMapView.determineProps(SeqMapView.java:2236) at com.affymetrix.igb.property.PropertyView.getPropertiesRow(PropertyView.java:234) at com.affymetrix.igb.view.SeqMapView.setToolTip(SeqMapView.java:2087) at com.affymetrix.igb.view.SeqMapView.setToolTip(SeqMapView.java:2045) at com.affymetrix.igb.view.SeqMapViewMouseListener.oldToolTip(SeqMapViewMouseListener.java:210) at com.affymetrix.igb.view.SeqMapViewMouseListener.mouseMoved(SeqMapViewMouseListener.java:192) at com.affymetrix.genoviz.widget.NeoWidget.heardMouseEvent(NeoWidget.java:1339) at com.affymetrix.genoviz.widget.NeoMap.heardMouseEvent(NeoMap.java:1589) at com.affymetrix.genoviz.widget.NeoAbstractWidget.mouseMoved(NeoAbstractWidget.java:827) at com.affymetrix.genoviz.bioviews.View.heardMouseEvent(View.java:978) at com.affymetrix.genoviz.bioviews.View.mouseMoved(View.java:887) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329) at java.awt.Component.processMouseMotionEvent(Component.java:6580) at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342) at java.awt.Component.processEvent(Component.java:6304) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4891) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4713) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2750) at java.awt.Component.dispatchEvent(Component.java:4713) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Any ideas what the problem is? I can probably send you the bam file to take a look at tomorrow if that'd help.... |
| Rank | Ranked higher |
| Attachment | GoToIgb.html [ 14007 ] |
| Attachment | GoToIgb.html [ 14007 ] |
| Attachment | GoToIgb.html [ 14008 ] |
| Assignee | Sanket Patil [ spatil26 ] |
| Assignee | Sanket Patil [ spatil26 ] | Ashwini Kadam [ akadam3 ] |
| Sprint | Spring 2017 [ 47 ] |
| Rank | Ranked lower |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Ashwini Kadam [ akadam3 ] | Sanket Patil [ spatil26 ] |
| Status | Needs 1st Level Review [ 10005 ] | Reviewing [ 10301 ] |
First level review:
=====================
Functional Review:
IGB is able to load the given bam file which was causing the problem earlier. Other Bam files are also getting loaded successfully. No error on console as well.
Code Review:
- Changes looks appropriate.
- New check for start is appropriately placed after a null check. This will avoid null pointer.
- Changes are well documented.
Overall changes looks good.
Moving back to "Needs first level review" for 2nd level review.
| Status | Reviewing [ 10301 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Sanket Patil [ spatil26 ] | Ann Loraine [ aloraine ] |
Second level review:
See comment added to the commit on AK's branch.
Addressed all comments given in second level review. File has been updated and committed to fork.
Updated fix can be found at :
https://bitbucket.org/ashwiniK27/integrated-genome-browser/commits/12c61e9086d06b0081cbde5025441019de4555c8?at=IGBF-1173
| Status | Needs 1st Level Review [ 10005 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Ready for Pull Request [ 10304 ] |
Submit pull request.
| Assignee | Ann Loraine [ aloraine ] | Ashwini Kadam [ akadam3 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Ashwini Kadam [ akadam3 ] |
| Status | Pull Request Submitted [ 10101 ] | Ready for Pull Request [ 10304 ] |
I'm not seeing the pull request - please check:
https://bitbucket.org/lorainelab/integrated-genome-browser
| Assignee | Ashwini Kadam [ akadam3 ] |
| Status | Ready for Pull Request [ 10304 ] | Needs Testing [ 10002 ] |
| Assignee | Ashwini Kadam [ akadam3 ] | Mason Meyer [ mason ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
After a round of testing, it appears that this issue is now resolved. The test BAM file as well as all other BAM files are opening properly and being visualized as expected. There are also no exceptions in the console. I have contacted the user who originally reported this issue so they can test this on our development branch and help verify that the fix is working properly. I will wait for their feedback before closing this issue.
The user has responded and verified that IGB is functioning properly for his test files. Since this has been verified by the user who originally reported this issue as well as my testing, I am marking this story as resolved.
| Resolution | Done [ 10000 ] | |
| Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Fix Version/s | 9.0.1 Minor Release [ 10500 ] |
| Workflow | Loraine Lab Workflow [ 17834 ] | Fall 2019 Workflow Update [ 19807 ] |
| Workflow | Fall 2019 Workflow Update [ 19807 ] | Revised Fall 2019 Workflow Update [ 21926 ] |
Ann made a small test file you can use to reproduce the bug. To see the bug in action, download the attached HTML (Web) file and follow the instructions.