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.
Then you can pull your changes into main! 🎉
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
mainbranch can then be submitted and a reviewer will review the code and accept the merge.objects.ToolDescriptions.javascripts.BAM_Manipulation.FilterBAMByBED.javacli.BAM_Manipulation.FilterBAMByBEDCLI.javawindow_interface.BAM_Manipulation.FilterBAMByBEDWindow.javawindow_interface.BAM_Manipulation.FilterBAMByBEDOutput.javamain.ScriptManagerGUI.javamain.ScriptManager.java/galaxy/wrapper/scriptmanager_XXXX.xmlThen you can pull your changes into main! 🎉