BLAST Ring Image Generator Files

Highlights

• Multithreaded BLAST (#42) — adds -num_threads to all BLAST calls; defaults to all available CPUs; configurable via --threads <n> CLI option or blastThreads XML profile attribute
• Fix same-filename collision (#53) — BLAST output .tab files are now prefixed with ring/sequence indices (r{ring}s{seq}_) so files with the same name in different directories never overwrite each other
• Configurable GC skew/content window (#56) — new --gc-window <n> CLI option and gcWindow XML attribute let users set the window size for GC calculations; falls back to auto-scaling when not set
• Auto-release workflow — merging a PR labelled release into master automatically bumps the patch version, creates a tag, and triggers the existing release pipeline to build DMG/MSI/JAR packages

Other changes

• Bump actions/upload-artifact to v7, actions/download-artifact to v8
• Bump maven-shade-plugin from 3.6.1 to 3.6.2
• CI now installs BLAST+ via pixi and runs E2E tests
• Added pixi.toml for reproducible BLAST+ dependency management

Minor version changes

• Bump org.apache.maven.plugins:maven-surefire-plugin from 3.2.5 to 3.5.5 by @dependabot[bot] in https://github.com/happykhan/BRIG/pull/41
• Bump actions/setup-java from 4 to 5 by @dependabot[bot] in https://github.com/happykhan/BRIG/pull/40
• Bump actions/upload-artifact from 4 to 6 by @dependabot[bot] in https://github.com/happykhan/BRIG/pull/38
• Bump org.apache.maven.plugins:maven-install-plugin from 3.1.1 to 3.1.4 by @dependabot[bot] in https://github.com/happykhan/BRIG/pull/37
• Bump org.apache.maven.plugins:maven-jar-plugin from 3.3.0 to 3.5.0 by @dependabot[bot] in https://github.com/happykhan/BRIG/pull/39
• Bump org.apache.maven.plugins:maven-compiler-plugin from 3.11.0 to 3.15.0 by @dependabot[bot] in https://github.com/happykhan/BRIG/pull/35
• Bump actions/download-artifact from 4 to 7 by @dependabot[bot] in https://github.com/happykhan/BRIG/pull/34
• Bump actions/setup-python from 5 to 6 by @dependabot[bot] in https://github.com/happykhan/BRIG/pull/36
• Bump org.jdom:jdom from 1.1.3 to 2.0.2 by @dependabot[bot] in https://github.com/happykhan/BRIG/pull/43
• Bump com.github.samtools:htsjdk from 1.128 to 4.3.0 by @dependabot[bot] in https://github.com/happykhan/BRIG/pull/44
• Bump org.slf4j:slf4j-api from 2.0.9 to 2.0.17 by @dependabot[bot] in https://github.com/happykhan/BRIG/pull/45
• Bump ch.qos.logback:logback-classic from 1.4.14 to 1.5.32 by @dependabot[bot] in https://github.com/happykhan/BRIG/pull/47
• Bump org.apache.maven.plugins:maven-shade-plugin from 3.5.1 to 3.6.1 by @dependabot[bot] in https://github.com/happykhan/BRIG/pull/48
• Bump com.github.samtools:htsjdk from 1.128 to 1.143 by @dependabot[bot] in https://github.com/happykhan/BRIG/pull/50
• Bump org.junit.jupiter:junit-jupiter from 5.10.2 to 6.0.3 by @dependabot[bot] in https://github.com/happykhan/BRIG/pull/49
• Add multithreaded BLAST, fix same-filename collision, configurable GC window, auto-release by @happykhan in https://github.com/happykhan/BRIG/pull/52
• Fix auto-release: tag-only to avoid branch protection block by @happykhan in https://github.com/happykhan/BRIG/pull/58
• Fix auto-release: explicitly trigger release workflow by @happykhan in https://github.com/happykhan/BRIG/pull/59
• Fix auto-release: pass version to trigger step by @happykhan in https://github.com/happykhan/BRIG/pull/60

New Contributors

• @dependabot[bot] made their first contribution in https://github.com/happykhan/BRIG/pull/41
• @happykhan made their first contribution in https://github.com/happykhan/BRIG/pull/52

Downloads

What is BRIG?

BRIG generates circular comparison images of multiple genomes using BLAST. It visualises sequence similarity, GC content, read coverage, and custom annotations as concentric rings around a reference genome.

Full Changelog: https://github.com/happykhan/BRIG/compare/v1.0.0...v1.1.1