[IGBF-1471] Fix bigwig parsing code in 9.0.2 - JIRA UNCC

Details

Type: Bug
Status: Closed (View Workflow)
Priority: Blocker
Resolution: Done
Affects Version/s: None
Fix Version/s: 9.0.2 Minor Release
Labels:
- Advanced

Story Points:
1
Sprint:
Winter 2018 Sprint 1

Description

User writes:

"I have just upgraded IGB to version 9.0.2 (windows 10).
I cannot upload bigWig files which did load in the previous version.
The message is "Unable to load data set for this file. Would you like to remve this file...".
Have tested several bigWig files, all with the same response.
I was able to load BED file.
Restarted the PC and restarted the application a couple of times."

Note: IGB 9.0.2 is using code from this library to open and read bigwig files:
https://bitbucket.org/lorainelab/bigwig

Attachments

Issue Links

relates to

HELP-316 Unable to load bigWig files

Closed

HELP-324 file opening

Closed

HELP-327 Failure to load files with 'Provider "XXX" not found' error

Closed

HELP-328 Cannot load bigWig files IGB 9.1.0

Closed

IGBF-2217 Release 9.1.2

Closed

IGBF-3670 Fix IGB unable to load files/folders with spaces

Closed

Show 1 more links (1 relates to)

Activity

Ascending order - Click to sort in descending order

Hide

Permalink

Nowlan Freese added a comment - 29/Nov/18 9:36 AM

The bigWig test file test.bigWig loads correctly in IGB 9.0.2 on macOS 0.13.6.

Show

Nowlan Freese added a comment - 29/Nov/18 9:36 AM The bigWig test file test.bigWig loads correctly in IGB 9.0.2 on macOS 0.13.6.

Hide

Permalink

Nowlan Freese added a comment - 29/Nov/18 9:48 AM - edited

Windows 8.1
IGB 9.0.2 release
Java 1.8.0_191
Exception when loading test.bigWig:

Nov 29, 2018 9:47:28 AM com.affymetrix.genometry.quickload.QuickLoadSymLoader logException
WARNING: Provider "C" not found
java.nio.file.ProviderNotFoundException: Provider "C" not found
at java.nio.file.FileSystems.newFileSystem(Unknown Source)
at htsjdk.samtools.util.IOUtil.getPath(IOUtil.java:1126)
at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:101)
at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:77)
at com.gene.bigwighandler.BigWigSymLoader.initbbReader(BigWigSymLoader.java:89)
at com.gene.bigwighandler.BigWigSymLoader.init(BigWigSymLoader.java:62)
at com.gene.bigwighandler.BigWigSymLoader.getChromosomeList(BigWigSymLoader.java:106)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.getChromosomeList(QuickLoadSymLoader.java:254)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:1002)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:996)
at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73)
at javax.swing.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at javax.swing.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)

Show

Nowlan Freese added a comment - 29/Nov/18 9:48 AM - edited Windows 8.1 IGB 9.0.2 release Java 1.8.0_191 Exception when loading test.bigWig: Nov 29, 2018 9:47:28 AM com.affymetrix.genometry.quickload.QuickLoadSymLoader logException WARNING: Provider "C" not found java.nio.file.ProviderNotFoundException: Provider "C" not found at java.nio.file.FileSystems.newFileSystem(Unknown Source) at htsjdk.samtools.util.IOUtil.getPath(IOUtil.java:1126) at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:101) at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:77) at com.gene.bigwighandler.BigWigSymLoader.initbbReader(BigWigSymLoader.java:89) at com.gene.bigwighandler.BigWigSymLoader.init(BigWigSymLoader.java:62) at com.gene.bigwighandler.BigWigSymLoader.getChromosomeList(BigWigSymLoader.java:106) at com.affymetrix.genometry.quickload.QuickLoadSymLoader.getChromosomeList(QuickLoadSymLoader.java:254) at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:1002) at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:996) at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source)

Hide

Permalink

Srishti Tiwari (Inactive) added a comment - 29/Nov/18 9:55 AM - edited

on IGB release 9.0.2 when loading test.bigWig (Windows 10, Java 1.8.0_181), I am getting this exception:

Nov 29, 2018 9:51:11 AM com.affymetrix.genometry.quickload.QuickLoadSymLoader logException
WARNING: Provider "E" not found
java.nio.file.ProviderNotFoundException: Provider "E" not found
at java.nio.file.FileSystems.newFileSystem(Unknown Source)
at htsjdk.samtools.util.IOUtil.getPath(IOUtil.java:1126)
at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:101)
at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:77)
at com.gene.bigwighandler.BigWigSymLoader.initbbReader(BigWigSymLoader.java:89)
at com.gene.bigwighandler.BigWigSymLoader.init(BigWigSymLoader.java:62)
at com.gene.bigwighandler.BigWigSymLoader.getChromosomeList(BigWigSymLoader.java:106)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.getChromosomeList(QuickLoadSymLoader.java:254)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:1002)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:996)
at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73)
at javax.swing.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at javax.swing.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)

Show

Srishti Tiwari (Inactive) added a comment - 29/Nov/18 9:55 AM - edited on IGB release 9.0.2 when loading test.bigWig (Windows 10, Java 1.8.0_181), I am getting this exception: Nov 29, 2018 9:51:11 AM com.affymetrix.genometry.quickload.QuickLoadSymLoader logException WARNING: Provider "E" not found java.nio.file.ProviderNotFoundException: Provider "E" not found at java.nio.file.FileSystems.newFileSystem(Unknown Source) at htsjdk.samtools.util.IOUtil.getPath(IOUtil.java:1126) at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:101) at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:77) at com.gene.bigwighandler.BigWigSymLoader.initbbReader(BigWigSymLoader.java:89) at com.gene.bigwighandler.BigWigSymLoader.init(BigWigSymLoader.java:62) at com.gene.bigwighandler.BigWigSymLoader.getChromosomeList(BigWigSymLoader.java:106) at com.affymetrix.genometry.quickload.QuickLoadSymLoader.getChromosomeList(QuickLoadSymLoader.java:254) at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:1002) at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:996) at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source)

Hide

Permalink

Srishti Tiwari (Inactive) added a comment - 29/Nov/18 3:46 PM - edited

Fixed the issue and tested on windows 10, ubuntu and mac.
Please review the changes:
https://bitbucket.org/srishtitiwari/integrated-genome-browser/commits/67a5b9879c243289f1fcd9e81041a4701ae79069?at=release-9.0.2

Show

Srishti Tiwari (Inactive) added a comment - 29/Nov/18 3:46 PM - edited Fixed the issue and tested on windows 10, ubuntu and mac. Please review the changes: https://bitbucket.org/srishtitiwari/integrated-genome-browser/commits/67a5b9879c243289f1fcd9e81041a4701ae79069?at=release-9.0.2

Hide

Permalink

Srishti Tiwari (Inactive) added a comment - 29/Nov/18 5:29 PM

Pull request submitted:

https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/651/igbf-1471-fix-for-bigwig-file-parsing/diff

Show

Srishti Tiwari (Inactive) added a comment - 29/Nov/18 5:29 PM Pull request submitted: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/651/igbf-1471-fix-for-bigwig-file-parsing/diff

Hide

Permalink

Ann Loraine added a comment - 29/Nov/18 5:33 PM

merged into release-9.0.2

Show

Ann Loraine added a comment - 29/Nov/18 5:33 PM merged into release-9.0.2

Hide

Permalink

Ann Loraine added a comment - 30/Nov/18 3:56 AM - edited

tested on Windows, Mac, Linux: bigwig, bigbed files loaded locally, from Quickload
deployed to Bioviz.org

Show

Ann Loraine added a comment - 30/Nov/18 3:56 AM - edited tested on Windows, Mac, Linux: bigwig, bigbed files loaded locally, from Quickload deployed to Bioviz.org

People

Assignee:

Srishti Tiwari (Inactive)

Reporter:

Ann Loraine

Votes:

0 Vote for this issue

Watchers:

3 Start watching this issue

Dates

Created:

29/Nov/18 8:17 AM

Updated:

24/Apr/24 2:21 PM

Resolved:

30/Nov/18 3:55 AM