Version 3.0.5 is built on grade 7.6. The only change we have to make is in the build.gradle, which is the upload archives function. I am currently reading the Gradle documentation to learn how to publish a repository after version 7.0.0. I have reviewed everything and it all appears to be satisfactory, with the exception of this one change.

• The build process for htsjdk-3.0.5 was successful, and no issues were encountered.
• After configuring the same version, the IGB was run, and no compile or runtime errors were found.
  Test Instructions:
• Create a build of this branch
• run: ./gradlew clean build -x test
• delete htsjdk-igb artifact in local repository (.m2)
• run: ./gradlew install (a new version of htsjdk-igb will be installed)
• clone the Bigwig project from Loraine lab workspace
• change the htsjdk-igb version to 3.0.5
• run: ./gradlew clean build
• delete org/broad/igv/bigwig located in .m2
• run: ./gradlew install (an artifact of bigwig will be downloaded in local)
• open IGB and change the version of htsjdk-igb to 3.0.5
• run: mvn clean install
• Input basic file tracks such as bai, bam to IGB and test basic functionalities

Tested following above instructions on Mac:

• Fetched the igb-3.0.5 branch from Kaushik's branch.
• Ran ./gradlew clean build -x test. The jar, sources, and javadoc files all appeared in the build > libs folder.
• In the MANIFEST.MF file the Bundle-SymbolicName was listed as htsjdk-igb
• Ran gradle install. The htsjdk-igb 3.0.5 files were installed into my local .m2 repository.
• Updated and ran igb to specify htsjdk-igb version 3.0.5.
• Able to add and load data from a bam file from IGB Quickload.
• Able to add and load data (visualize) a bai file.
• Able to create a depth graph from a bam file.
• Able to add and load data from a local bam file.
• Able to add and load data from a local bed file.
• Able to add and load data from a local sam file.

Ready for pull request.

• PR cannot be submitted since there is no target branch in lorainelab/htsjdk-igb
• [~aloraine], fetch this branch into your local, and kindly follow the test instructions mentioned above.

For future reference: if code is ready to be merged, even if the original developer was not able to submit the PR, as was the case here, kindly move the ticket to "PR submitted" just so that we can see what the status of the ticket is on the board. Speaking for myself, as a maintainer I tend to ignore things that are not in a "ready for review" or "PR submitted column"

attn: Kaushik Gopu

Working on this now

New branch igb-3.0.5 is now available on lorainelab fork of htsjdk.

See: https://github.com/lorainelab/htsjdk-igb/

Also, I have changed the above repository's to use the new branch "igb-3.0.5" as the default branch for our repository.

Moving to ready for testing.

Testing on Mac

• Cloned the htsjdk-igb repo
• Default branch shows as igb-3.0.5
• Built artifact using ./gradlew clean build -x test
• Build created jar/sources/javadoc
• In the manifest I see Bundle-SymbolicName: htsjdk-igb
• Installed artifact locally with ./gradlew install. The artifact 3.0.5 was installed in my local .m2 folder.
• Updated and ran igb to specify htsjdk-igb version 3.0.5.
• Able to add and load data from a bam file from IGB Quickload.
• Able to add and load data (visualize) a bai file.
• Able to create a depth graph from a bam file.
• Able to add and load data from a local bam file.
• Able to add and load data from a local bed file.
• Able to add and load data from a local sam file.

Closing ticket.

Kaushik Gopu - Need to update htsjdk-igb to 3.0.5 in project pom and fix the test issue in GenotypingResults pom. Would be similar to this commit: https://bitbucket.org/kaushik-gopu/kgopu_integrated-genome-browser/commits/543ea431d2dc86f0c2a0bb9b72e350cccf388e0a