Filter BAM by BED

[owlang]

Since bedtools intersect doesn't appear to support filtering by specific parts of the BAM read overlap, this tool should be implemented for the BAM Manipulation tool group. Using the TagPileup encodings, keep/remove BAM read(s/ pairs) whose encoding overlaps a user-provided BED file.

Checklist

New tools should be written on branches. A pull request to the main branch can then be submitted and a reviewer will review the code and accept the merge.

• Write tests
• Write tool (list minimum changed files)
  • objects.ToolDescriptions.java
  • scripts.BAM_Manipulation.FilterBAMByBED.java
  • cli.BAM_Manipulation.FilterBAMByBEDCLI.java
  • window_interface.BAM_Manipulation.FilterBAMByBEDWindow.java
  • window_interface.BAM_Manipulation.FilterBAMByBEDOutput.java
  • main.ScriptManagerGUI.java
  • main.ScriptManager.java
• Include logging support
• Update documentation
• Write Galaxy wrapper /galaxy/wrapper/scriptmanager_XXXX.xml

Then you can pull your changes into main! 🎉