Package: Rminibwa 0.4.0-0.0.1.9000

Sounkou Mahamane Toure

Rminibwa: Native R Bindings and SIMD Dispatch for 'minibwa'

Provides native R bindings to the 'minibwa' genomic read aligner with raw-vector query input, external-pointer alignment batches, ALTREP column views, and an installed C API for downstream packages. The package builds staged Single Instruction Multiple Data ('SIMD') KSW backends and selects portable scalar, SSE4, or AVX2 code at runtime without global instruction-set compiler flags.

Authors:Sounkou Mahamane Toure [aut, cre], Dana-Farber Cancer Institute [cph], Ilya Grebnov [cph], N. Jesper Larsson [cph], Wong Chi Kwong [cph]

Rminibwa_0.4.0-0.0.1.9000.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Rminibwa/json (API)

# Install 'Rminibwa' in R:
install.packages('Rminibwa', repos = c('https://rgenomicsetl.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sounkou-bioinfo/rminibwa/issues

Uses libs:
  • zlib– Compression library

On CRAN:

Conda:

alignmentaltrepbioinformaticsc-apigenomicsminibwasimdzlib

3.90 score 34 exports 1 dependencies

Last updated from:a752739320. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK174
linux-devel-x86_64OK163
source / vignettesOK227
linux-release-arm64OK169
linux-release-x86_64OK167
macos-release-arm64OK93
macos-release-x86_64OK196
macos-oldrel-arm64OK126
macos-oldrel-x86_64OK247
windows-devel-x86_64OK147
windows-release-x86_64OK132
windows-oldrel-x86_64OK119
wasm-releaseOK128

Exports:mb_align_cigar_wordsmb_align_colmb_align_nmb_align_read_colmb_align_read_nmb_fastx_itermb_fastx_nmb_fastx_nextmb_index_buildmb_index_contigsmb_index_loadmb_mapmb_map_batchmb_map_fastx_batchmb_map_pair_batchmb_optsmb_query_group_input_ordermb_query_group_n_readsmb_query_group_n_recordsmb_query_group_namemb_query_streammb_query_stream_cancelmb_query_stream_errormb_query_stream_nextminibwa_availableminibwa_climinibwa_indexminibwa_mapminibwa_pathminibwa_upstream_infominibwa_versionsimd_backendsimd_infosimd_set_backend

Dependencies:RsimdDispatch

Downstream C API
Build a tiny alignment batch | The downstream C consumer | Compile and call it with Rtinycc | Lossless query-group stream
Rendered fromdownstream-c-api.Rmdusingknitr::rmarkdown

Last update: 2026-07-22
Started: 2026-06-23

Getting Started
Rendered fromgetting-started.Rmdusingknitr::rmarkdown

Last update: 2026-06-23
Started: 2026-06-18

Vendoring minibwa
Pin file | Patch queue | Developer checkout | Vendored source
Rendered fromvendoring-minibwa.Rmdusingknitr::rmarkdown

Last update: 2026-06-23
Started: 2026-06-18

SIMDe Dispatch Design
Boundary | Backends | R surface | Validation
Rendered fromsimde-dispatch.Rmdusingknitr::rmarkdown

Last update: 2026-06-23
Started: 2026-06-18

Readme and manuals

Help Manual

Help pageTopics
Inspect native minibwa alignment batchesmb_align_cigar_words mb_align_col mb_align_n mb_align_read_col mb_align_read_n
Iterate FASTA/FASTQ batches without R sequence materializationmb_fastx_iter mb_fastx_n mb_fastx_next mb_map_fastx_batch
Build a minibwa index with the native librarymb_index_build
Return minibwa index contigsmb_index_contigs
Load a native minibwa indexmb_index_load
Map raw sequence bytes with native minibwamb_map
Map a batch of query sequences with native minibwamb_map_batch
Map paired query sequence batches with native minibwamb_map_pair_batch
Native minibwa optionsmb_opts
Open a lossless native FASTQ query-group streammb_query_group_input_order mb_query_group_name mb_query_group_n_reads mb_query_group_n_records mb_query_stream mb_query_stream_cancel mb_query_stream_error mb_query_stream_next
Test whether the minibwa CLI is availableminibwa_available
Run the minibwa CLIminibwa_cli
Build a minibwa index through the CLIminibwa_index
Map reads through the minibwa CLIminibwa_map
Locate the packaged minibwa executableminibwa_path
Report the pinned upstream minibwa sourceminibwa_upstream_info
Report the minibwa CLI versionminibwa_version
Report the selected SIMD backendsimd_backend
Report SIMD dispatch diagnosticssimd_info
Select the runtime SIMD backendsimd_set_backend