Filter BAM by BED
Opened this issue · 0 comments
owlang commented
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)
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objects.ToolDescriptions.java
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scripts.BAM_Manipulation.FilterBAMByBED.java
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cli.BAM_Manipulation.FilterBAMByBEDCLI.java
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window_interface.BAM_Manipulation.FilterBAMByBEDWindow.java
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window_interface.BAM_Manipulation.FilterBAMByBEDOutput.java
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main.ScriptManagerGUI.java
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main.ScriptManager.java
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- Include logging support
- Update documentation
- Write Galaxy wrapper
/galaxy/wrapper/scriptmanager_XXXX.xml
Then you can pull your changes into main! 🎉