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.

v0.14

What's Changed

The major update of this release is the addition of new encoding options to TagPileup including full fragment which mimics other standard bioinformatic tools & 3 prime ends for datasets from assays such as PRO-seq (#70). To support this more complicated encoding structure, a new live-update cartoon was added to the TagPileup GUI too show where markings are being encoded on a sequenced read (#71).

Some other TagPileup related issues were addressed in this release including an update to the insert size calculation (#76) and the addition of a TagExtend option (#73).

New Tools:

• Heatmap Labeler (#54)
• Three Color Heatmap (#48)
• GUI for Composite plot tool & bugfix to CLI (#96,#97)
• Shift Coordinate (#92)

Other updates:

• Gzip support added for several tools (#88,#91)
• Two color heatmap now supports transparent trace heatmaps (#66)
• Add seed option to Randomize FASTA (#45)
• Alert users to odd-sized TP sliding window requirement (#79)
• Support for newer hg38 human genome build (#80)
• Converter between chromosome numeral systems for yeast genome builds (#49)
• Bugfix: PE-Stats bulk GUI only processing single file (#83)
• Bugfix: Two Color Heatmap Gzip incompatibility (#85)
• Bugfix: TagPileup off by 1bp error (#11,#75)
• Add Singularity definition file
• Update JFree dependencies (#82)
• Deprecate JTV file format (#64)
• New documentation website(Docusaurus) with homepage designed (@ashhh97,#89,#90)

Full Changelog: v0.13...v0.14

v0.13

The major feature of this release is the addition of a Command Line Interface (CLI) for the tools. Each tool in ScriptManager not modeled after an existing command line tool has been written to have command line capability. For help and usage, execute the jar file with the -h flag.

This will allow for Galaxy integration and the creation of Conda packages and Docker images to wrap ScriptManager.

v0.12

Release v0.12

Official v0.12 release

v0.11

Rearrange button position