Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:5
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Epic Link:
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Sprint:Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar
Description
Situation: Because the bai file does not include the chromosome information, we have been assuming that the order of the bai file chromosomes are the same as that in IGB. However, many bai files are not ordered exactly the same as IGB. The only way to know for sure the order of the bai file is to look at the header of the bam file. However, because we allow the user to load a bai file directly, there may not be a readable bam file.
Task: If a bam header was retrieved successfully, use the chromosome order from the bam header instead of the genome.txt order to assign chromosome values to the bai data. For example, if the order in the bam header is chr3, chr1, chr2, then this is the order that the data will be retrieved from the bai file. You do not need to sort the data.
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
|
| Description |
Situation: Because the bai file does not include the chromosome information, we have been assuming that the order of the bai file chromosomes are the same as that in IGB. However, many bai files are not ordered exactly the same as IGB. The only way to know for sure the order of the bai file is to look at the header of the bam file. However, because we allow the user to load a bai file directly, there may not be a readable bam file.
Task: Within the BAI index visualization handler plugin, write code to identify if there is a readable bam file. The bam file should be located in the same directory as the bai file and should have the same name as the bai file, but with a .bam extension. Note that the bai itself may have .bam in front of the .bai extension (EXAMPLE.bam.bai). If a bam file is present, use the appropriate Samtools method to retrieve the bam header. |
Situation: Because the bai file does not include the chromosome information, we have been assuming that the order of the bai file chromosomes are the same as that in IGB. However, many bai files are not ordered exactly the same as IGB. The only way to know for sure the order of the bai file is to look at the header of the bam file. However, because we allow the user to load a bai file directly, there may not be a readable bam file.
Task: If a bam header was retrieved successfully, use the chromosome order from the bam header instead of the genome.txt order to assign chromosome values to the bai data. For example, if the order in the bam header is chr3, chr1, chr2, then this is the order that the data will be retrieved from the bai file. You do not need to sort the data. |
| Sprint | Spring 3 : 3 Feb to 14 Feb [ 86 ] | Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 21 Feb [ 86, 87 ] |
| Rank | Ranked higher |
| Attachment | galaxy_outOfOrder.bam [ 14656 ] | |
| Attachment | galaxy_outOfOrder.bam.bai [ 14657 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb [ 86, 87 ] | Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar [ 86, 87, 89 ] |
| Rank | Ranked higher |
| Attachment | sorted.bam [ 14664 ] | |
| Attachment | sorted.bam.bai [ 14665 ] | |
| Attachment | sorted.sam [ 14666 ] | |
| Attachment | unsorted.bam [ 14667 ] | |
| Attachment | unsorted.bam.bai [ 14668 ] | |
| Attachment | unsorted.sam [ 14669 ] |
Pushed the changes to my branch
https://bitbucket.org/pawanbole/integrated-genome-browser-pawan/src/IGBF-2269/
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Pawan Bole [ pbole ] | Nowlan Freese [ nfreese ] |
| Story Points | 3 | 5 |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Attachment | sorted.bam [ 14664 ] |
| Attachment | sorted.bam.bai [ 14665 ] |
| Attachment | sorted.sam [ 14666 ] |
| Attachment | unsorted.bam [ 14667 ] |
| Attachment | unsorted.bam.bai [ 14668 ] |
| Attachment | unsorted.sam [ 14669 ] |
| Attachment | galaxy_outOfOrder.bam [ 14656 ] |
| Attachment | galaxy_outOfOrder.bam.bai [ 14657 ] |
Example files found in google drive: https://drive.google.com/open?id=1Y9krI6VX3vBzTKEcneGy1McnMJEK739m
Note that chr1_3_2.bam.bai has data for the first three chromosomes in the order of 1,3,2. Chromosome 3 has no data for the majority of the chromosome.
Loading the out of order bai file (chr1_3_2.bai) locally while the bam file is in the same directory works correctly, the data is loaded for the correct chromosomes.
Loading the bai file via url does not work, with or without the bam file in the same directory.
Moving the bam file out of the same directory locally causes the bai file to fail to load (null pointer exception).
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at org.lorainelab.igb.bai.BaiToBedgraphConverter.initializeChromosomes(BaiToBedgraphConverter.java:178)
at org.lorainelab.igb.bai.BaiToBedgraphConverter.<init>(BaiToBedgraphConverter.java:57)
at org.lorainelab.igb.bai.BaiFileHandler.createSymLoader(BaiFileHandler.java:38)
at com.affymetrix.genometry.util.ServerUtils.determineLoader(ServerUtils.java:31)
at com.affymetrix.igb.view.load.GeneralLoadUtils.getDataSet(GeneralLoadUtils.java:1128)
at com.affymetrix.igb.view.load.GeneralLoadUtils.openURI(GeneralLoadUtils.java:972)
at com.affymetrix.igb.IgbServiceImpl.openURI(IgbServiceImpl.java:347)
at com.affymetrix.igb.shared.OpenURIAction.openURI(OpenURIAction.java:89)
at com.affymetrix.igb.action.LoadFileAction.actionPerformed(LoadFileAction.java:192)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
at com.apple.laf.ScreenMenuItem.actionPerformed(ScreenMenuItem.java:125)
at java.awt.MenuItem.processActionEvent(MenuItem.java:669)
at java.awt.MenuItem.processEvent(MenuItem.java:628)
at java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:357)
at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:345)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:763)
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:74)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
at java.awt.EventQueue$4.run(EventQueue.java:733)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
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)
Check if span is null on line 178 and 199
Test URL:
https://data.cyverse.org/dav-anon/iplant/home/nowlanf/SmokeTesting/H_sapiens_Dec_2013/chr1_3_2.bam.bai
https://data.cyverse.org/dav-anon/iplant/home/nowlanf/SmokeTesting/H_sapiens_Dec_2013/chr1_3_2.bam
http://igbquickload.org/smokeTestingQuickload/H_sapiens_Dec_2013/Bam/Bam_HomoSapien.bai
http://igbquickload.org/smokeTestingQuickload/H_sapiens_Dec_2013/Bam/Bam_HomoSapien.bam
ONLY the bai file (no bam file in same location)
https://data.cyverse.org/dav-anon/iplant/home/nowlanf/testThree/chr1_3_2.bam.bai
Checking span for null allows the bai file to load via URL and if the bam file is not located within the same directory locally.
When the bai file is located in the same directory as the bam file and loaded via URL, it is not loaded correctly, most likely due to the bam file not being found. Pawan is aware of this issue and is working on it.
Recommend checking span is null and fixing issue with bam not found in URL.
| Assignee | Nowlan Freese [ nfreese ] | Pawan Bole [ pbole ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar [ 86, 87, 89 ] | Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar [ 86, 87, 89, 90 ] |
| Rank | Ranked higher |
Pushed the changes related for the files present on the internet and also handled the missing null checks.
| Assignee | Pawan Bole [ pbole ] | Nowlan Freese [ nfreese ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Loading the bai file via url works correctly with or without the bam file in the same directory.
Loading the bai file locally works correctly with or without the bam file in the same directory.
Recommend pull request.
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Nowlan Freese [ nfreese ] | Pawan Bole [ pbole ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Pawan Bole [ pbole ] | Nowlan Freese [ nfreese ] |
| Assignee | Nowlan Freese [ nfreese ] | Ann Loraine [ aloraine ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
sorted and unsorted files are from 2009 human version