ScanMST v0.1.9

Release v0.1.9

✨ Features

• Added --refine-threshold option to control the node merging threshold during graph refinement (default: 3).

🐛 Bug Fixes

• Fixed a bin boundary issue in the graph refinement step.

📝 Documentation

• Documented --refine-threshold in the CLI reference.
• Updated README, citation, license, and index pages.

Full Changelog: v0.1.8...v0.1.9

ScanMST v0.1.8

Release v0.1.8

📝 Documentation

• Generate documentation using MkDocs.
• Update and clarify parameter descriptions.

🐛 Bug Fixes

• Refined output file header formatting to improve readability and clarity.

Full Changelog: v0.1.7...v0.1.8

ScanMST v0.1.7

Release v0.1.7

🔄 Project Renaming: ScanNLS is now ScanMST

This release marks the official rebranding of the project from ScanNLS to ScanMST.

• The source code package has been renamed to scanmst.
• CLI entry points, internal logic, and documentation have been updated to reflect the new name.

✨ New Features

Automatic BLAT Dependency Management:

• Auto-Download: When running with --aligner blat, the appropriate BLAT binaries are securely downloaded from UCSC servers to the local installation directory if they are missing.
• Cross-Platform Support: ScanMST now automatically detects the host operating system (Linux vs. macOS) and CPU architecture (Intel x86_64 vs. Apple Silicon arm64).

🐛 Bug Fixes

• Resolved various issues to improve stability and performance.

📝 Documentation

• Updated README.md to include specific licensing information regarding the use of BLAT.

Full Changelog: v0.1.6...v0.1.7

v0.1.6

Release v0.1.6

We're excited to announce the sixth release of ScanNLS with several key enhancements and improvements:

What's New

• TSG Format Output: Added support for a new TSG output format to enhance data interoperability
• Updated Naming Convention: Implemented a revised naming scheme for improved consistency and clarity
• Graph Refinement: Enhanced traversal algorithms with a new post-processing refinement function for better accuracy

Bug Fixes

• Resolved various issues to improve stability and performance

For a complete list of changes, see the full changelog.

ScanNLS v0.1.5

Fifth release

• Used edge info. signature to sorting paths
• Fixed bugs affecting polyA tail determination, and merging two tail nodes.
• Fixed bugs affecting self-loop forming paths.

ScanNLS v0.1.4

Fourth release

• Enhanced distance calculation for head-to-head and tail-to-tail nodes, making gene_id more inclusive.
• Refined node merging rules for both 5' and 3' ends (internal polyA only).
• Added microhomology inference for long soft-clipped segments in non-chimeric reads and soft-clipped ends in chimeric reads when using BLAT.
• Exported aurora_id in GTF output for visualization purposes.
• Ensured output files are generated with the specified output prefix, unaffected by BLAT's folder change behavior.
• Fixed bugs affecting type compatibility and new node inference from soft-clipped ends in chimeric reads.

ScanNLS v0.1.3

Third release

• Improved 5' end merging to account for degraded ends, as the official library preparation lacks a 5' cap selection step.
• BLAT alignment is now triggered only for insertions exceeding the specified threshold (100bp by default).
• Enhanced error handling for BAM files generated without the --cs and -Y parameters.

ScanNLS v0.1.2

Second release

• In addition to handling long insertions, long soft-clipping segments, and the head or tail soft-clipping ends of reads when forming ordered chains, BLAT is also utilized to correct misaligned chimeric reads.
• The most likely alignment produced by BLAT will be utilized.
• cs tag of BAM is required to determine variants with ease.

ScanNLS v0.1.0

First release

• Powerful and accurate non-colinear transcript detection using long-read data.
• Support PacBio Iso-Seq, ONT direct RNA, and ONT direct cDNA.