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  "Package": "Rminibwa",
  "Title": "Native R Bindings and SIMD Dispatch for 'minibwa'",
  "Version": "0.4.0-0.0.1.9000",
  "Authors@R": "c(\nperson(given = \"Sounkou Mahamane\", family = \"Toure\",\nemail = \"sounkoutoure@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(given = \"Abiomix FZ LLC\", role = c(\"cph\", \"fnd\"),\ncomment = \"Copyright holder and funder of Abiomix contributions\"),\nperson(given = \"Dana-Farber Cancer Institute\", role = \"cph\",\ncomment = \"Copyright holder of upstream minibwa\"),\nperson(given = \"Ilya\", family = \"Grebnov\", role = \"cph\",\ncomment = \"libsais copyright holder\"),\nperson(given = \"N. Jesper\", family = \"Larsson\", role = \"cph\",\ncomment = \"QSufSort copyright holder\"),\nperson(given = \"Wong\", family = \"Chi Kwong\", role = \"cph\",\ncomment = \"BWT-SW/bwtgen copyright holder\")\n)",
  "Description": "Provides native R bindings to the 'minibwa' genomic read\naligner with raw-vector query input, external-pointer alignment\nbatches, ALTREP column views, and an installed C API for\ndownstream packages. The package builds staged Single\nInstruction Multiple Data ('SIMD') KSW backends and selects\nportable scalar, SSE4, or AVX2 code at runtime without global\ninstruction-set compiler flags.",
  "License": "GPL (>= 2)",
  "SystemRequirements": "GNU make, zlib",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
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  "Additional_repositories": "https://abiomix.r-universe.dev",
  "URL": "https://github.com/abiomix/abiomix-r-open,\nhttps://github.com/sounkou-bioinfo/Rminibwa,\nhttps://sounkou-bioinfo.github.io/Rminibwa/",
  "BugReports": "https://github.com/abiomix/abiomix-r-open/issues",
  "Config/abiomix/public-license": "GPL-2.0-or-later",
  "Config/abiomix/commercial-license": "Separate written agreement for\nAbiomix-owned contributions",
  "Config/abiomix/license-policy": "https://github.com/abiomix/abiomix-r-open/blob/main/LICENSES.md",
  "Config/pak/sysreqs": "make zlib1g-dev",
  "Repository": "https://abiomix.r-universe.dev",
  "Date/Publication": "2026-07-13 08:37:42 UTC",
  "RemoteUrl": "https://github.com/abiomix/abiomix-r-open",
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  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-07-13 12:23:27 UTC",
    "User": "root"
  },
  "Author": "Sounkou Mahamane Toure [aut, cre],\nAbiomix FZ LLC [cph, fnd] (Copyright holder and funder of Abiomix\ncontributions),\nDana-Farber Cancer Institute [cph] (Copyright holder of upstream\nminibwa),\nIlya Grebnov [cph] (libsais copyright holder),\nN. Jesper Larsson [cph] (QSufSort copyright holder),\nWong Chi Kwong [cph] (BWT-SW/bwtgen copyright holder)",
  "Maintainer": "Sounkou Mahamane Toure <sounkoutoure@gmail.com>",
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    "author": "sounkou-bioinfo <sounkoutoure@gmail.com>",
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    "message": "Update bundled minibwa to upstream 0.4\n\nRefresh the pinned native sources to minibwa 0.4-r400 while retaining the reviewed portability and SIMD patch queue. Update the package version, installed provenance, CLI version assertion, and release documentation.\n",
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    "email": "sounkoutoure@gmail.com",
    "login": "sounkou-bioinfo",
    "mastodon": "@bioinfhotep@genomic.social",
    "description": "Sequences and Consequences.",
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  "_selfowned": true,
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    "description": "Litpeaks Github Organization"
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/Rminibwa"
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  "_topics": [
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    "extra/citation.json",
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    "mb_align_col",
    "mb_align_n",
    "mb_align_read_col",
    "mb_align_read_n",
    "mb_fastx_iter",
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    "mb_fastx_next",
    "mb_index_build",
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    "mb_index_load",
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    "mb_map_batch",
    "mb_map_fastx_batch",
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    "minibwa_cli",
    "minibwa_index",
    "minibwa_map",
    "minibwa_path",
    "minibwa_upstream_info",
    "minibwa_version",
    "simd_backend",
    "simd_info",
    "simd_set_backend"
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    {
      "page": "mb_align_n",
      "title": "Inspect native minibwa alignment batches",
      "topics": [
        "mb_align_cigar_words",
        "mb_align_col",
        "mb_align_n",
        "mb_align_read_col",
        "mb_align_read_n"
      ]
    },
    {
      "page": "mb_fastx_iter",
      "title": "Iterate FASTA/FASTQ batches without R sequence materialization",
      "topics": [
        "mb_fastx_iter",
        "mb_fastx_n",
        "mb_fastx_next",
        "mb_map_fastx_batch"
      ]
    },
    {
      "page": "mb_index_build",
      "title": "Build a minibwa index with the native library",
      "topics": [
        "mb_index_build"
      ]
    },
    {
      "page": "mb_index_contigs",
      "title": "Return minibwa index contigs",
      "topics": [
        "mb_index_contigs"
      ]
    },
    {
      "page": "mb_index_load",
      "title": "Load a native minibwa index",
      "topics": [
        "mb_index_load"
      ]
    },
    {
      "page": "mb_map",
      "title": "Map raw sequence bytes with native minibwa",
      "topics": [
        "mb_map"
      ]
    },
    {
      "page": "mb_map_batch",
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      "topics": [
        "mb_map_batch"
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    },
    {
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      "topics": [
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      ]
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      "title": "Run the minibwa CLI",
      "topics": [
        "minibwa_cli"
      ]
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