{
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  "Package": "Rminibwa",
  "Title": "Native R Bindings and SIMD Dispatch for 'minibwa'",
  "Version": "0.7.0-0.0.1.9000",
  "Authors@R": "c(\nperson(given = \"Sounkou Mahamane\", family = \"Toure\",\nemail = \"sounkoutoure@gmail.com\", role = c(\"aut\", \"cre\")),\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, selects\nportable scalar, SSE4, or AVX2 code at runtime without global\ninstruction-set compiler flags, and on native platforms links\nto the exact 'htslib' build supplied by 'Rduckhts' as its\nalignment-format dependency.",
  "License": "GPL (>= 2)",
  "SystemRequirements": "GNU make, zlib",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "Additional_repositories": "https://rgenomicsetl.r-universe.dev,\nhttps://sounkou-bioinfo.r-universe.dev",
  "URL": "https://github.com/RGenomicsETL/Rminibwa,\nhttps://rgenomicsetl.github.io/Rminibwa/",
  "BugReports": "https://github.com/RGenomicsETL/Rminibwa/issues",
  "Config/roxygen2/version": "8.0.0",
  "Repository": "https://rgenomicsetl.r-universe.dev",
  "Date/Publication": "2026-10-05 13:56:13 UTC",
  "RemoteUrl": "https://github.com/RGenomicsETL/Rminibwa",
  "RemoteRef": "HEAD",
  "RemoteSha": "0e7d6072711847e4f1b281eda09cb2675ac16f03",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-12 23:38:54 UTC",
    "User": "root"
  },
  "Author": "Sounkou Mahamane Toure [aut, cre],\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>",
  "_user": "rgenomicsetl",
  "_type": "src",
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  "_expires": "2027-01-21T00:12:51.000Z",
  "_created": "2026-10-12T23:38:54.000Z",
  "_published": "2026-10-13T00:12:53.547Z",
  "_buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/38322856482",
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    "author": "sounkou-bioinfo <sounkoutoure@gmail.com>",
    "committer": "sounkou-bioinfo <sounkoutoure@gmail.com>",
    "message": "Keep developer benchmark Python-only\n",
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    "email": "sounkoutoure@gmail.com",
    "login": "sounkou-bioinfo",
    "mastodon": "@bioinfhotep@genomic.social",
    "description": "Sequences and Consequences.",
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  "_owner": "rgenomicsetl",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
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      "week": "2026-25",
      "n": 3
    },
    {
      "week": "2026-26",
      "n": 6
    },
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  ],
  "_tags": [
    {
      "name": "v0.7.0-0.0.1",
      "date": "2026-10-05"
    }
  ],
  "_topics": [
    "alignment",
    "altrep",
    "bioinformatics",
    "c-api",
    "genomics",
    "minibwa",
    "simd",
    "zlib"
  ],
  "_stars": 0,
  "_contributors": [
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    "type": "organization",
    "name": "GenomicsETL",
    "followers": 10,
    "description": "Composable genomics in DuckDB, with R, the browser and agents as front ends"
  },
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/Rminibwa"
  },
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    "extra/citation.json",
    "extra/citation.txt",
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    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
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  "_exports": [
    "mb_align_cigar_words",
    "mb_align_col",
    "mb_align_n",
    "mb_align_read_col",
    "mb_align_read_n",
    "mb_fastx_iter",
    "mb_fastx_n",
    "mb_fastx_next",
    "mb_index_build",
    "mb_index_contigs",
    "mb_index_load",
    "mb_map",
    "mb_map_batch",
    "mb_map_fastx_batch",
    "mb_map_pair_batch",
    "mb_opts",
    "mb_query_group_input_order",
    "mb_query_group_n_reads",
    "mb_query_group_n_records",
    "mb_query_group_name",
    "mb_query_stream",
    "mb_query_stream_cancel",
    "mb_query_stream_error",
    "mb_query_stream_next",
    "minibwa_available",
    "minibwa_cli",
    "minibwa_index",
    "minibwa_map",
    "minibwa_path",
    "minibwa_upstream_info",
    "minibwa_version",
    "rminibwa_htslib_info",
    "simd_backend",
    "simd_info",
    "simd_set_backend"
  ],
  "_help": [
    {
      "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",
      "title": "Map a batch of query sequences with native minibwa",
      "topics": [
        "mb_map_batch"
      ]
    },
    {
      "page": "mb_map_pair_batch",
      "title": "Map paired query sequence batches with native minibwa",
      "topics": [
        "mb_map_pair_batch"
      ]
    },
    {
      "page": "mb_opts",
      "title": "Native minibwa options",
      "topics": [
        "mb_opts"
      ]
    },
    {
      "page": "mb_query_stream",
      "title": "Open a lossless native FASTQ query-group stream",
      "topics": [
        "mb_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"
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    {
      "page": "minibwa_available",
      "title": "Test whether the minibwa CLI is available",
      "topics": [
        "minibwa_available"
      ]
    },
    {
      "page": "minibwa_cli",
      "title": "Run the minibwa CLI",
      "topics": [
        "minibwa_cli"
      ]
    },
    {
      "page": "minibwa_index",
      "title": "Build a minibwa index through the CLI",
      "topics": [
        "minibwa_index"
      ]
    },
    {
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      "title": "Map reads through the minibwa CLI",
      "topics": [
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    },
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    },
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