NEWS
metabinR 2.0.0
Breaking changes
- The three binning entry points —
abundance_based_binning(),
composition_based_binning(), hierarchical_binning() — now return a
MetabinResult S4 object instead of a plain data.frame. The v1.x
tabular layout is available via as.data.frame(result).
- The Java backend no longer exposes a command-line interface; the shaded
JAR dropped the
commons-cli dependency. R is the only supported entry
point.
- Minimum Java runtime is now 17 (previously 8).
New features
- New
MetabinResult class with accessors assignments(), nClusters(),
parameters(), algorithm(), plus show() and as.data.frame()
methods.
- Binning functions accept, in addition to file paths,
Biostrings::DNAStringSet, Biostrings::QualityScaledDNAStringSet, and
ShortRead::ShortReadQ objects. Non-file inputs are staged to a
tempfile before the Java backend runs.
numOfThreads defaults to BiocParallel::bpworkers().metabinR_jvm_options() and the metabinR.jvm.flags option let users
customise JVM flags at load time without losing the default G1GC +
string-deduplication tuning.- Parameter validation is centralised via
checkmate; errors surface
through cli::cli_abort() with classed conditions
(metabinR_error_*).
Internal
- Java sources build via Maven (
java/metabinR/pom.xml,
tools/build-jar.sh); the shaded JAR is reproducible
(project.build.outputTimestamp pinned).
- Typed JNI entry points on
MTxAB, MTxCB, MTxABxCB return
tab-separated assignments directly to R, removing the previous
round-trip through on-disk CLI output.
metabinR 1.5.1 (2024-04-07)
- Preparing for next Bioconductor Release.
metabinR 1.5.0 (2023-10-29)
- Bump x.y.z version to odd y following creation of RELEASE_3_18 branch.
metabinR 1.2.0 (2023-04-21)
- Bump x.y.z version to even y prior to creation of RELEASE_3_17 branch.
metabinR 1.1.0 (2022-11-01)
- Bump x.y.z version to odd y following creation of RELEASE_3_16 branch.
metabinR 1.0.0 (2022-11-01)
- Bioconductor 3.16 Release. New package metabinR, Abundance and
Compositional Based Binning of Metagenomes.
metabinR 0.99.3 (2022-10-30)
metabinR 0.99.2 (2022-10-26)
- Remove citation message on package attach.
metabinR 0.99.1 (2022-10-11)
- Precheck changes on vignette.
metabinR 0.99.0 (2022-10-05)
- Submitted to Bioconductor.