rhilker/readxplorer

ReadXplorer - Visualization and Analysis of Mapped Sequences

readxplorer's Issues

Project status and Java version

First of all - impressive and cool project looking at it from a non-researcher/layman perspective. Thank you Dr. Hilker and everyone involved for this software as a free option. I have a few general questions I hope you could answer:

1. Project Status
   1. is it alive and planned to be developed further?
   2. Are forks/pull requests welcome or encouraged?
   3. Is there some sort of (maybe unofficial?) roadmap of some sort regarding planned or desirable features?
2. A short while ago I helped a friend of mine setting up ReadXplorer when the .exe installers with the included java version weren't available because some of the download links were dead (pointed to an old, decommissioned FTP server at uni Giessen). The links have since been fixed.
   1. Because of Oracle's policies and Java no longer being free of charge, some institutions do no longer allow installing Java. When my friend tried to set up ReadXplorer with a lab colleague using OpenJDK, they couldn't get it to run due to an error saying cannot find java 1.7 or higher. I tried different versions and had the same result. It only works when using OpenJDK 8. All newer versions lead to this error, regardless of PATH or JAVA_HOME variable content. Is this deemed fine or are there any necessary or planned changes?

Make code of these modules accessible for Github RX project

Some dependencies are only hosted in the Gießen Artifactory -> no external programmer can actually build the RX project without these dependencies.
This needs to be fixed!

de.cebitec.common:geneticcodes:jar:1.0.1,
de.cebitec.common:parser.fasta:jar:0.4.0

Will add the source code including license we added back then with conscent of author

Read Pair Viewer: Add calculation of read pair fragment length

Additional to the total length of a read pair mapping in reference coordinates (may be > 100,000 bp, depending on mapping location), add calculation of read pair fragment length to the tooltip in the read pair viewer.

Read Count & Coverage Analyses: Make sure only mapped portions of reads are counted

Read Count & Coverage Analyses: Make sure only mapped portions of reads are counted for spliced read mappings.
It is not the case for:

• the Read Count & Normalization analysis
• others?