To test in IGB:

Add this link as a new Quickload under the Data Access tab in Available Data - Configure:
https://bitbucket.org/nfreese/quickload-genome-in-a-bottle/raw/release-v1.0.1/quickload/

Open the H_sapiens_Dec_2013 human genome.
Navigate to chr1:80,644,218-80,644,359
Select one of the Quickload files and click Load Data.
Look to see that the data load and no errors are thrown.
Repeat for every Quickload file.

Open the H_sapiens_Feb_2009 human genome.
Navigate to chr1:77,876,660-77,876,761
Select one of the Quickload files and click Load Data.
Look to see that the data load and no errors are thrown.
Repeat for every Quickload file.

I have tested each quickload file in the 2 scenarios.

When I tested in the first scenario using H_sapiens_Dec_2013 human genome, part of the data was not loaded and mostly they are Soft-clips.
I have added 5 images for that scenario and log for the error is:

15:31:13.752 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: https://bitbucket.org/nfreese/quickload-genome-in-a-bottle/raw/release-v1.0.1/quickload/species.txt
15:31:13.826 INFO o.l.i.appstore.IgbAppServerLauncher - Started REST endpoint.

When I tested in the first scenario using H_sapiens_Dec_2009 human genome, this issue is not there but in AshkenazimTrio --> Son --> Illumina_6kb_matepair was not loaded and log for the error is:

17:31:38.694 INFO c.a.igb.view.load.GeneralLoadUtils - Loaded RefGene in 2.188 s
org.lorainelab.igb.bam.BAM$BamIndexNotFoundException: Could not find Bam Index File.
at org.lorainelab.igb.bam.BAM.findIndexFile(BAM.java:433)
at org.lorainelab.igb.bam.BAM.getBamIndexUriStr(BAM.java:139)
at org.lorainelab.igb.bam.BAM.getSAMFileReader(BAM.java:98)
at org.lorainelab.igb.bam.BAM.init(BAM.java:157)
at org.lorainelab.igb.bam.XAM.getChromosomeList(XAM.java:100)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:153)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:139)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:119)
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:751)
at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:693)
at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:688)
at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73)
at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at javax.swing.SwingWorker.run(SwingWorker.java:334)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

cc: Dr.Nowlan Freese

I'm not seeing any issues with the 2013 Human genome from the log or images 1-5.

The AshkenazimTrio --> Son --> Illumina_6kb_matepair was pointing at the wrong bam file. I have updated the annots.xml and it is now working correctly.

Next step: I need to update igbDefaultPrefs.json

A number of comments are included in this declined pull request.

I think the least amount of work for us would be to leave igbDefaultPrefs.json pointed at the 1.0.0 branch. If we need to update a link in the annots.xml, the change will be made to the 1.0.0 branch, but no new branch will be created. This way all versions of IGB will have the most up to date Quickload info and there will still be a record of the changes (commit history for that branch). If at some point in the future we create a new Quickload format then we could create a new branch and subsequent versions of IGB would point at the new branch.

All of the changes have been merged into the release-v1.0.0 branch. No changes need to be made to IGB. I have tested that AshkenazimTrio --> Son --> Illumina_6kb_matepair works in IGB 9.1.8.

Closing issue.