final development push before v0.14#100
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WilliamKMLai merged 18 commits intomasterfrom Oct 25, 2022
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This is the first of the quick Perl scripts collection to integrate into scriptmanager (#92) and can serve as a model for the other tools going forward. * Includes Gzipped BED support (#91) both in extension-based file selection and extension-independent gzip format detection (#88) * supports selection of either BED or GFF file formats (#47) * includes JavaDoc-formatted comments script* * single class with two static methods, each specific to either BED or GFF formats window_interface* * based on ExpandBED window design, toggle between loading BED formats or loading GFF formats main * update ScriptManagerGUI with button to instantiate a ShiftIntervalWindow objects.ToolDescriptions: * add description for new tool
This utility class should support the implementation of changes for #88 Boolean-returning methods or checking either an newly initialized InputStream or a File for the GZip MAGIC bytes to confirm gzip file-format.
Use the new GZipUtilities class to check for GZip file format in both ShiftInterval/Shift coord tool and the Two-color heatmap tool (#88). Remove unnecessary imports along the way.
Leftover and inaccurate comment was corrected to describe behavior of file parsing in ShiftCoord and TwoColorHeatmap
Layout of UI was reorganized for clarity in describing *Directional* shift and renaming tool in main GUI window to use generalized "Coordinate" over BED since this tool is generalized. #92
fix errors in window_interface:
- "Execute" ran only for BED files before. Now GFF is supported.
- Remove GFF button now properly removes files
- "Gzip output" checkbox renamed to match TagPileup ("Output GZIP")
fix errors in script:
- the wrong token index was used in the GFF shift script for "-" strands
- add error statements to unexpected input formats
CLI for ShiftCoord script for #92
Add support for gzipped input BED files for the ExpandBED script. #91 - Decorated classes with JavaDocs tags - Reorganized argument validation in ExpandBEDCLI to both support -z flag and clarify output filename logic - Update BufferedReader and output stream objects to detect and support Gzipped files - add input validation logic to script - Update ExpandBED window with an "Output GZIP" checkbox that is added to the script call - update file selector to include gzipped file extensions - change "Convert" to "Execute" buttons - Reorganize default output filepath determination logic
Add Gzip support for the UI file selection classes. #91 - FileSelection: Specifically, the extension-based single file selection was adjusted to add support for ignoring or including files with a ".gz" extension. - ExtensionFileFilter: add a stripExtension method that works on String-type filenames - decorate both classes with JavaDocs
Add Gzip support for the Sort BED tool. #91 CDTUtilities - updated to support gzipped input CDT files - decorate with Javadocs SortBEDWindow - update file selection (both BED & CDT) to include gzipped extensions of *.bed and *.cdt - update to support gzipping output files with "output GZIP" checkbox - update default filename to use input BED filename and update with ".gz" according to the gzip checkbox - adjust margins so components aren't up agains the edge oft the window frame - switch "Convert" to "Execute" in component naming and display text - decorate with JavaDocs SortBED - add support for gzipped inputs and efficient file parsing with BufferedReader for both .bed and .cdt inputs - add support for gzipping outputs with gzOutput boolean to method signature - decorate with JavaDocs SortBEDCLI - add gzip flag and update script method call - remove input extension restrictions on CLI
For compatibility with Galaxy, extension requirements are removed from TagPileupCLI in this commit
Address issue ticket #80 by adding `hg38` and `hg38_contigs` genome options to TileGenome and RandomCoordinate tools util.GenomeSizeReference - update initialize options to include both versions of hg38 - add JavaDocs comments scripts.RandomCoordinate - turn script into a public static void method - add JavaDocs comments scripts.TileGenome - turn script into a public static void method - add JavaDocs comments window_interface.RandomCoordinateWindow - add hg38 as selection options - adjust script call to use public static method - add JavaDocs comments window_interface.TileGenomeWindow - add hg38 as selection options - adjust script call to use public static method - add JavaDocs comments cli.RandomCoordinateCLI - add hg38 as selection options in help message of Parameter - adjust script call to use public static method - add JavaDocs comments cli.TileGenomeCLI - add hg38 as selection options in help message of Parameter - adjust script call to use public static method - add JavaDocs comments
Address ticket #97 to swap height and width to appropriate arguments of the command line version of the composite plot figure generating tool.
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-Singularity def and docs added
-Add hg38/GrCh38 support to TileGenome and RandCoord (#80)
-Add ShiftCoord tool (part of #92)
-Add Gzip support to Expand and Sort BED (#88)