Bugfix for #79 #85 #83#94
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WilliamKMLai merged 7 commits intomasterfrom Sep 13, 2022
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owlang
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Aug 22, 2022
owlang
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- add gzip support for cli 2-color heatmap
- add alerts for odd-sized sliding window requirements on TagPileup
- update PE Stat Output GUI so that user is alerted when BAI is missing
Bugfix for #85 to support gzipped input CDT/TAB files in the CLI for two-color heatmap. * Add utility method to extension file filter for an ignoreGZ version of stripExtension (in building default filenames) * remove extension enforcement on two-color-heatmap CLI tool * Use ZipException to detect gzipped files and create the appropriate BufferedReader object according to format. Merge parsing of Gzipped and non-gzipped files to use the same Reader object (just different instantiated types depending on file format)
Regarding #79, both GUI and CLI now have restrictions to window size selection to only allow for odd sized windows (ensures smoothing is symmetric)
Relating to issue #83, user interface does not notify user when stats can not be generated due to a missing BAI index. This commit pastes the BAI check code and if-statement from TagPileupOutput.
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Throw a customized IllegalArgumentException when a genome name not included in the reference `util.GenomeSizeReference` class is given. Add Exception handling to GUI repective tool scripts and GUI window_interface classes
The Eclipse `.metadata` directory that stores workspace configuration information should not be tracked in the git repo.
For the purpose of building out a GUI for the composite plot image generating tool (#96), the CLI class is broken up in this commit to separate out the input data parsing and chart building from command line parsing and input validation components in the CLI class. The new class organization further added minor adjustments to script behavior: - the default filepath suffix is now "_plot.png" - color defaults are determined by a null input and n>2 condition uses YEP color palette instead of Kelly colors - data parsing issues throw Exceptions rather than print statements - input/output extensions no longer restricted The new ColorSeries class saves color palettes and can be reused and expanded upon for future tools.
Build the actual GUI for the composite plot image generating tool (#96). Include JavaDocs linking to other classes. GUI, unlike CLI, does not yet offer color customization options or title customization.
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Along with bugfixes this branch now also includes the addition of the composite tool (#96). |
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