Code For this is in the branch :
https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1098-sam-so

And also you can find the installers at :
https://bitbucket.org/kkorey/kkorey-igb/downloads/

I completed a General Smoke Testing Checklist by loading all the file types mentioned here (https://wiki.transvar.org/display/ITD/General+Smoke+Testing) + Sam file.
Things look good for now but need in-depth testing I'm expecting a lot of issues (But wish for none).

I created a Google doc to organize the testing process for this.
https://docs.google.com/document/d/19_EYNgiJr-GJT5zSQ99ogrLw8_aO5rl2ejXiNUYwq9M/edit?usp=sharing

Is there a test file that we know contains the SO flag?
How are the errors observed? Are they simply printed to the console?

I am re-assigning to Kiran to add testing instructions.
(Or tell me I need to find/make a test file)

I don't have the test file.
Yes if there are any errors they are simply printed in the console.

**NOTE: No changes are made specific to SO flag, just the library is updated.

Just some notes to be tidy...

This branch has two commits. For one the message is just "Initial commit". If there is a reason for splitting the work into multiple commits, that reason needs to be clear. If there is no reason, then the commits should be merged.

Avoid introducing * in import statements. That should be changed in these files:
(note, this is a TINY proportion of the files that had to be changed in this endeavor)
plugins/bam/src/main/java/org/lorainelab/igb/bam/SAM.java
plugins/bam/src/main/java/org/lorainelab/igb/bam/BAM.java
core/genometry/src/main/java/com/affymetrix/genometry/symloader/BaiZoomSymLoader.java
I think this rule applies to the pom files as well (not sure), see
core/shared-lib-wrapper/pom.xml
core/genometry/pom.xml

It looks like a method called getBinIter (in BaiZoomSymLoader.java) is commented out.
Please include explanation for commenting out this method.

A method called readIndex is commented out in genometry/symloader/SymLoaderTabix.java.
Please include explanation for commenting out this method.

It looks like some method names changed for something called tabixReader in genometry/symloader/SymLoaderTabix.java.
If these were changes to the code to reflect changes in the library, I think these changes warrant their own commit with a message (and perhaps comments as well) to explain the library update version (from what version to what version) so the reasoning behind this change is clear for future developers.

It looks like a similar case for plugins/bam/src/main/java/org/lorainelab/igb/bam/BAM.java
where SamFileReader became SamReader.

Splitting up work that is already grouped into a single commit is difficult (maybe there is some git magic I am not familiar with that does this).
I don't see any reason to separate out the change about passing an index. I think the best thing is to:
-rebase the branch from master
-add comments where there are changes to the code (beyond import statements)
-squash the commits
-give the one commit a helpful message that indicates what library(ies) was updated, from what version and to what version.

None of that requires any change to the code, the just comments and commits. The only thing that I think will require review before merging is the methods that were commented out. Should they really be commented out (with explanation) or simply removed? and is the explanation clear enough?

The functional review is covered as issue IGBF-1321, the previous comment covers the code review and git review.

I am reassigning to Kiran to make the modifications to comments and commits.

The few things that need to be reviewed after that are best reviewed by Dr. Loraine.
So, make the changes, submit a pull request, and emphasize in the pull request that she should review these comments and the new changes as part of the pull request review.

Merged pull request as-is. Recommend leaving comments as-is to aid with testing & removing commented code later once we are sure there are no problems.

I tested this story by ensuring all files from the Smoke Testing Quickload site could be loaded and visualized properly without console error. All files loaded, as expected, and there seem to be no side effects related to this change, so I will now mark this issue as resolved.

Re-assigning to original developer for record-keeping purposes.

Possible error with bigbed format file.
To repeat, try to load a bb (bigbed) file.
Can use one from Galaxy History as follows:

• Open Galaxy history https://usegalaxy.org/u/aloraine/h/cold-stress-fastq
• Select Data Set 56 PollenJuncs.noScore.bb
• Clicked display in IGB View link
• Open IGB Console & observe exception:

java.lang.NoClassDefFoundError: net/sf/samtools/seekablestream/SeekableStreamFactory

Please add link to new branch.

Link to a new branch:

https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1371-library

Unpack bigBedHandler-9.0.2.jar from IGB-IGBF-1371-library.jar and review its META-INF/MANIFEST.MF and OSGI-INF/BigBedHandler.xml files.
net.sf.samtools and related packages are being included in the bundle and are accessible on its classpath
Why are they being exported?

Link to test bigbed:http://localhost:7085/IGBControl?version=H_sapiens_Dec_2013&seqid=chr1&start=0&end=248956422&loadresidues=false&create=2018%2F09%2F04+17%3A47%3A28&modified=2018%2F09%2F04+17%3A47%3A28&feature_url_0=http%3A%2F%2Figbquickload.org%2Fquickload%2FH_sapiens_Dec_2013%2FcytoBand.cyt&sym_method_0=__cytobands&sym_ypos_0=0&sym_yheight_0=50&sym_col_0=0x0247FE&sym_bg_0=0xFFFFFF&sym_name_0=__cytobands&feature_url_1=http%3A%2F%2Figbquickload.org%2Fquickload%2FH_sapiens_Dec_2013%2FH_sapiens_Dec_2013_refGene.bed.gz&sym_method_1=http%3A%2F%2Figbquickload.org%2Fquickload%2FH_sapiens_Dec_2013%2FH_sapiens_Dec_2013_refGene.bed.gz&sym_ypos_1=0&sym_yheight_1=50&sym_col_1=0x000000&sym_bg_1=0xFFFFFF&sym_name_1=RefGene&feature_url_2=http%3A%2F%2Figbquickload.org%2FsmokeTestingQuickload%2FH_sapiens_Dec_2013%2FBigBed%2FBigBed_HomoSapien.bigbed&sym_method_2=BigBed_HomoSapien&sym_ypos_2=0&sym_yheight_2=50&sym_col_2=0x0247FE&sym_bg_2=0xFFFFFF&sym_name_2=BigBed_HomoSapien&query_url=http%3A%2F%2Figbquickload.org%2Fquickload%2FH_sapiens_Dec_2013%2FcytoBand.cyt&query_url=http%3A%2F%2Figbquickload.org%2Fquickload%2FH_sapiens_Dec_2013%2FH_sapiens_Dec_2013_refGene.bed.gz&query_url=http%3A%2F%2Figbquickload.org%2FsmokeTestingQuickload%2FH_sapiens_Dec_2013%2FBigBed%2FBigBed_HomoSapien.bigbed&server_url=http%3A%2F%2Figbquickload.org%2Fquickload%2F&server_url=http%3A%2F%2Figbquickload.org%2Fquickload%2F&server_url=http%3A%2F%2Figbquickload.org%2FsmokeTestingQuickload%2F

BigBedSymLoader class in BigBedHandler module uses org.broad.tribble.util.SeekableStreamFactory from tribble-ext artifact, which in turn uses net.sf.samtools.seekablestream.SeekableStreamFactory from sam-ext artifact.

Even though tribble-ext is dependent on sam-ext it is not mentioned as a dependency (This can be verified by investigating the manifest of tribble-ext).

So in order to make net.sf.samtools available when tribble-ext expects it we need to export it and make it accessible in the classpath.

Find source code git repository for:

• tribble-ext

• sam-ext

Also, see: https://www.biostars.org/p/6129/

Please note: bigbed and bigwig are not readable in IGB 9.0.2. They are fine in IGB 9.0.1.
We discovered this during the Galaxy testing. https://wiki.transvar.org/display/ITD/Galaxy

Using the installer from this branch:
https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1371-library

git note: The commit message says 1317, please change to 1371.

functional test:
I can open the bigwig and bigbed files from galaxy, and load data. : ) Good!
I can open the bigwig and bigbed files from the smoke testing quickload: http://igbquickload.org/smokeTestingQuickload/, and load data. Good!

You can find the tribble jar at the path : https://github.com/nh13/IGV/tree/master/lib
Steps followed:
Renamed the downloaded jar to tribble-ext-1.111 and replaced the existing jar in the local maven repository.
Now IGB is new the new jar as tribble-ext and this is not dependent on net.sf.samtools, but it is dependent on the org.apache.log4j so we will need to add it as the library.

Also if you want to look at the source code of this new jar please use Intellij.
Look for Maven:org.broad:tribble-ext:1.111 and expand the arrow next to it.

Using the new jar IGB loads the BigBed and BigWig without any error.

Please locate version control repository for tribble-ext artifacts so that we can fork the repository and build it as bundle natively.

This link has similar code to what tribble-ext has https://github.com/samtools/htsjdk/tree/master/src/main/java/htsjdk/tribble

We will create an htsjdk bundle and distribute to the project via https://nexus.bioviz.org. This issue is now replaced with https://jira.transvar.org/browse/IGBF-1418

Closing this issue because strategy for reaching a solution has changed.