Version 0.4.1

• Bug fix: consistent ordering between gene ids and gene names when dealing with ambiguity.
• Bug fix: rely on breakpoint ordering in visualization script.
• Improvement: gene names are assigned automatically in visualization script.
• Improvement: visualization script can now take SAM files as input.
• Improvement: visualization script can now take a breakpoint number (these aren't always unique, so it's best to still give a single entry).

Version 0.4.0

• Improvement: Improved ambiguous gene resolution.
• Improvement: read lzma-compressed annotations in text and binary format.
• Improvement: Support multiple bam/fofn (File-Of-FileNames) inputs.
• Improvement: reduced false-positive fusions.
• Improvement: Additional metadata for putative fusion candidates.
• Improvement: Updated cached binary format. WARNING: this is a breaking change. Old binary annotation files will need to be re-generated.
• Alteration: reduced chaining distance for clustering breakpoints.
• Alteration: emit sense-antisense events by default.
• Improvement: Maintain read ordering in reporting fusions.
• Bug fix: Update reported breakpoints so that the interval described is the last-in-read and the second is first-soft-clipped.
• Improvement: Add gene names to annotation in order they occur in reads.
• Improvement: Report all breakpoint coordinates for reads in a breakpoint cluster, add as a new tag.
• Improvement: Update read-through annotation such that we define it based on the breakpoint distance instead of the distance between genes.

Version 0.3.1

Bug fix: resolving query position sorting.

Version 0.3.0

• Bug fix: resolving strandness breakpoint errors.
• Bug fix: GTF parsing of overlapping annotations.
• Bug fix: annoting gtf records without parent gene entries.

Version 0.2.2

• Update CLI for single binary
• Add more filtering options

pbfusion v0.1.0

First release of pbfusion 🥇