restructure MarkDup - adjust TagPileupWindow - remove CLI ext validation #134
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owlang
commented
Jun 29, 2023
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owlang
commented
- restructure MarkDuplicates to be called as a static void method from the script class
- fix TagPileup GUI default - tag extend should default to 0 TagPileup GUI tag extend - 2bp by default - should be 1bp #133
- fix TagPileup GUI display - pulldown spacing for read encoding selection
- remove file extension validation (too stringent and interferes with Galaxy wrapper writing)
Picard tools will be run using system calls that can be wrapped in a static method of a script class. For MarkDuplicates, the unnecessary constructor and class attributes were removed so that a static call could be made and the window_interface was modified accordingly.
This commit changes the pulldown selection strings to use less space and allow the full Read Output pulldown options to be displayed. The "Require PE" for Midpoint and Full Fragment selection strings of Read Aspect were too long and took space away from Read Output.
- change default Tag Extend value to 0 in TagPileupWindow - add validate option to pop-up dialog if Tag Extend value is negative - add error-style formatting to JOptionPane dialogs that notify user of input errors #133
This commit removes unnecessary extension filename validation from the CLI tools. This validation is too restrictive and interferes with development of Galaxy wrappers by forcing workarounds (Galaxy uses `.dat` extensions).
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