Can load bai file from File > Open URL..., File > Open File..., and dragging and dropping the bai file.
Note: Both files are from Illumina short read sequencing of the whole genome.
Tested using file (attached) - HG002.GRCh38.2x250.bam.bai
Tested URL - ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG004_NA24143_mother/NIST_Illumina_2x250bps/novoalign_bams/HG004.GRCh38.2x250.bam.bai
Testing on PacBio URL data results in a null pointer exception some of the time. First time I tried to load it threw a null pointer exception (below), second time it loaded it fine.
Tested URL - ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/PacBio_SequelII_CCS_11kb/HG002_GRCh38/HG002_GRCh38.haplotag.10x.bam.bai
As the Illumina short read files are working consistently, and the pacbio somewhat consistently, I think this issue should be closed. However, it may be worth looking into the null pointer exception being thrown on the pacbio url. Note that when I downloaded the pacbio file itself and loaded it locally, it worked correctly consistently, so this may be an issue with loading the pacbio URL.
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at org.lorainelab.igb.bai.BaiToBedgraphConverter.initializeChromosomes(BaiToBedgraphConverter.java:127)
at org.lorainelab.igb.bai.BaiToBedgraphConverter.<init>(BaiToBedgraphConverter.java:48)
at org.lorainelab.igb.bai.BaiFileHandler.createSymLoader(BaiFileHandler.java:41)
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.shared.LoadURLAction.loadURL(LoadURLAction.java:127)
at com.affymetrix.igb.shared.LoadURLAction.actionPerformed(LoadURLAction.java:60)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:842)
at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:886)
at java.awt.Component.processMouseEvent(Component.java:6539)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
at java.awt.Component.processEvent(Component.java:6304)
at java.awt.Container.processEvent(Container.java:2239)
at java.awt.Component.dispatchEventImpl(Component.java:4889)
at java.awt.Container.dispatchEventImpl(Container.java:2297)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)
at java.awt.Container.dispatchEventImpl(Container.java:2283)
at java.awt.Window.dispatchEventImpl(Window.java:2746)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
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)
Note: I'm not exactly sure how partial loading of the bai file will work.