v0.15

What's Changed

✨ New Tools

• Peak_Analysis > FRiX Calculator by @owlang in #6, #155
• Peak_Analysis > Sort By Distance by @benjaminbeer256 in #35, #145
• Read_Analysis > Transpose Matrix by @benjaminbeer256 in #14, #140
• BAM_Statistics > Cross Correlation (ported over from Archtex) by @WilliamKMLai #120

🚀 New Features

• Gzip support 🤐 for input/output of plain text formats (e.g. BED, GFF, CDT) by @benjaminbeer256 in #91, #143
• Picard-based tools (BAMIndexer, BAMFileSort, and MergeSamFiles) updated to run Picard directly @Erikpav in #123
• New TagPileup graphics and GUI option organization to improve clarity by @owlang in #115, #119
• Most extension requirement restrictions in the CLI have been removed
• BAM to scIDX new option to shift tags #172
• Reorganize DNAShape tools option selection by @benjaminbeer256 in #126, #142
• Peak-Align new option for strand-matching #168
• BAM Genome Correlation now supports the 🌈 Jet color scheme #102
• Paired-end statistics updated to include more info (mimic Galaxy version for core pipeline) #146
• Single-end BAM statistics default output file behavior changed #148

🐛 Bugfixes

• BAM Genome Correlation now maps read encodings in PileupParameters correctly #101 and progress bar fixed #118
• TagPileup's single-end read error #153, the TagExtend 0 or 1 index bug #133, and the "separate" typo #150
• Four color plot now supports multi-line FASTA input #149

🌌 Galaxy support

Draft wrappers for Galaxy users to use scriptmanager for their workflows #171, #137, #151
@cleson28, @DeanZ3

📝 Logging (Beta)

You can now track the exact commands executed during a GUI session by saving a log file of the CLI execution for everything you did with the GUI interface. This new feature is still undergoing testing so proceed with caution and please let us know if you encounter any errors. #127, #132, #147
@cleson28, @DeanZ3, @benjaminbeer256, @owlang

👩‍💻 For Developers

• Restructure main GUI window to generalize addition of new tools #138
• source directory reorganization from src/... to src/main/java/scriptmanager/... #110
• JavaDocs drafting finished by @benjaminbeer256 in #136
• rename master --> main
• no more separation of dev branch for staging changes to the default branch
• upgrade Gradle to 7.5 for Java 17 by @owlang in #112, #113

Full Changelog: v0.14...v0.15

If you want to see what's up next, you can check out our release notes for an idea of priorities and issue tickets that are on deck.