{
  "_id": "6aa9327d089bafb098cfd934",
  "Package": "BamScale",
  "Type": "Package",
  "Title": "Bioconductor-Friendly Multithreaded BAM Processing",
  "Version": "0.99.14",
  "Authors@R": "c(\nperson(\"Chirag\", \"Parsania\", email = \"chirag.parsania@gmail.com\", role = c(\"aut\", \"cre\"))\n)",
  "Description": "Multithreaded sequential BAM processing built on top of\nthe ompBAM C++ engine. BamScale provides user-friendly BAM read\nand scan interfaces designed for compatibility with existing\nBioconductor workflows.",
  "License": "MIT + file LICENSE",
  "biocViews": "Software, DataImport, Sequencing, Coverage, Alignment,\nQualityControl",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "SystemRequirements": "C++17, OpenMP",
  "NeedsCompilation": "yes",
  "URL": "https://cparsania.github.io/BamScale/",
  "BugReports": "https://github.com/cparsania/BamScale/issues",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "libbz2-dev liblzma-dev libssl-dev xz-utils\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-08-13 04:50:17 UTC",
  "RemoteUrl": "https://github.com/bioc/BamScale",
  "RemoteRef": "HEAD",
  "RemoteSha": "39795de37096adadd8a8b44773b097576aef2df6",
  "Packaged": {
    "Date": "2026-09-15 11:37:31 UTC",
    "User": "root"
  },
  "Author": "Chirag Parsania [aut, cre]",
  "Maintainer": "Chirag Parsania <chirag.parsania@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "BamScale_0.99.14.tar.gz",
  "_fileid": "https://r2.ropensci.org/6a50ca45797a025a8ff7e22f870f540e7899d16cd897fc92074ec6f3a7f6ecd2",
  "_filesize": 1984256,
  "_sha256": "6a50ca45797a025a8ff7e22f870f540e7899d16cd897fc92074ec6f3a7f6ecd2",
  "_expires": "2026-12-24T11:56:43.000Z",
  "_created": "2026-09-15T11:37:31.000Z",
  "_published": "2026-09-15T11:56:45.476Z",
  "_bioccheck": {
    "error": 1,
    "warning": 0,
    "note": 6
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/34963903056",
  "_status": "success",
  "_upstream": "https://github.com/bioc/BamScale",
  "_commit": {
    "id": "39795de37096adadd8a8b44773b097576aef2df6",
    "author": "Chirag Parsania <chirag.parsania@gmail.com>",
    "committer": "Chirag Parsania <chirag.parsania@gmail.com>",
    "message": "CI: trim check matrix to R-release on the three OSes\n\nBamScale's dependencies resolve from the Bioconductor repo paired with R\nrelease, so the CRAN-style oldrel-1/devel legs cannot install binary\ndependencies and stall in hour-long source builds (the recurring 'cancelled'\njobs). The Bioc-devel combination is covered by Bioconductor's own build\nmachines once the package syncs to git.bioconductor.org.\n\nCo-Authored-By: Claude Fable 5 <noreply@anthropic.com>\n",
    "time": 1786596617
  },
  "_maintainer": {
    "name": "Chirag Parsania",
    "email": "chirag.parsania@gmail.com",
    "login": "cparsania",
    "twitter": "@ChiragParsania",
    "description": "Bioinformatics. Postdoc at @centenary institute. ",
    "uuid": 10338600
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 104365148515,
      "time": 185,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "10394567402"
    },
    {
      "job": 104365148850,
      "time": 373,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "10394576682"
    },
    {
      "job": 104365148709,
      "time": 349,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10394456974"
    },
    {
      "job": 104365148663,
      "time": 435,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "10395116733"
    },
    {
      "job": 104365148670,
      "time": 1097,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "10394854125"
    },
    {
      "job": 104365148701,
      "time": 556,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10395002282"
    },
    {
      "job": 104365148596,
      "time": 769,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10395352100"
    },
    {
      "job": 104363829118,
      "time": 268,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10394377635"
    },
    {
      "job": 104365148645,
      "time": 165,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "10394636233"
    },
    {
      "job": 104365148678,
      "time": 394,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "10394478208"
    },
    {
      "job": 104365148795,
      "time": 444,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "10394722811"
    },
    {
      "job": 104365148730,
      "time": 343,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "10394777289"
    },
    {
      "job": 104365148680,
      "time": 356,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10394651393"
    },
    {
      "job": 104365148717,
      "time": 332,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10395265466"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "ompBAM",
      "role": "LinkingTo"
    },
    {
      "package": "S4Vectors",
      "role": "LinkingTo"
    },
    {
      "package": "IRanges",
      "role": "LinkingTo"
    },
    {
      "package": "XVector",
      "role": "LinkingTo"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "GenomeInfoDb",
      "role": "Imports"
    },
    {
      "package": "GenomicAlignments",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "ompBAM",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "Rsamtools",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "chipseqDBData",
      "role": "Suggests"
    },
    {
      "package": "dplyr",
      "role": "Suggests"
    },
    {
      "package": "ExperimentHub",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "readr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "rtracklayer",
      "role": "Suggests"
    },
    {
      "package": "scales",
      "role": "Suggests"
    },
    {
      "package": "tibble",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "tidyr",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-08",
      "n": 15
    },
    {
      "week": "2026-09",
      "n": 2
    },
    {
      "week": "2026-11",
      "n": 5
    },
    {
      "week": "2026-12",
      "n": 7
    },
    {
      "week": "2026-13",
      "n": 6
    },
    {
      "week": "2026-17",
      "n": 3
    },
    {
      "week": "2026-19",
      "n": 3
    },
    {
      "week": "2026-22",
      "n": 3
    },
    {
      "week": "2026-31",
      "n": 3
    },
    {
      "week": "2026-33",
      "n": 10
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "0.99.14",
      "bioc": "3.24"
    }
  ],
  "_topics": [
    "software",
    "dataimport",
    "sequencing",
    "coverage",
    "alignment",
    "qualitycontrol",
    "zlib",
    "cpp",
    "openmp"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "cparsania",
      "count": 68,
      "uuid": 10338600
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 468,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 450,
    "source": "https://www.bioconductor.org/packages/stats/bioc/BamScale"
  },
  "_devurl": "https://github.com/cparsania/bamscale",
  "_pkgdown": "https://cparsania.github.io/BamScale/",
  "_searchresults": 0,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/BamScale.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/cparsania/bamscale",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "bam_count",
    "bam_coverage",
    "bam_coverage_bigwig",
    "bam_read",
    "decode_compact_qual",
    "decode_compact_seq",
    "decode_seqqual_compact",
    "fragment_sizes",
    "mapq_dist"
  ],
  "_help": [
    {
      "page": "bam_count",
      "title": "Count BAM records with Bioconductor-compatible filtering",
      "topics": [
        "bam_count"
      ]
    },
    {
      "page": "bam_coverage",
      "title": "Per-base coverage, aggregated in C++",
      "topics": [
        "bam_coverage"
      ]
    },
    {
      "page": "bam_coverage_bigwig",
      "title": "Write per-base coverage to a bigWig, computed in C++",
      "topics": [
        "bam_coverage_bigwig"
      ]
    },
    {
      "page": "bam_read",
      "title": "Fast BAM reading with Bioconductor-compatible arguments",
      "topics": [
        "bam_read"
      ]
    },
    {
      "page": "decode_compact_qual",
      "title": "Decode compact BamScale quality output",
      "topics": [
        "decode_compact_qual"
      ]
    },
    {
      "page": "decode_compact_seq",
      "title": "Decode compact BamScale sequence output",
      "topics": [
        "decode_compact_seq"
      ]
    },
    {
      "page": "decode_seqqual_compact",
      "title": "Decode compact 'seq' and 'qual' columns in BamScale output",
      "topics": [
        "decode_seqqual_compact"
      ]
    },
    {
      "page": "fragment_sizes",
      "title": "Fragment-size distribution, aggregated in C++",
      "topics": [
        "fragment_sizes"
      ]
    },
    {
      "page": "mapq_dist",
      "title": "Mapping-quality (MAPQ) distribution, aggregated in C++",
      "topics": [
        "mapq_dist"
      ]
    }
  ],
  "_pkglogo": "https://github.com/bioc/BamScale/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/bioc/BamScale/raw/HEAD/README.md",
  "_rundeps": [
    "askpass",
    "BH",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "cigarillo",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicRanges",
    "httr",
    "IRanges",
    "jsonlite",
    "lambda.r",
    "mime",
    "ompBAM",
    "openssl",
    "R6",
    "Rcpp",
    "Rhtslib",
    "Rsamtools",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "sys",
    "UCSC.utils",
    "XVector"
  ],
  "_sysdeps": [
    {
      "shlib": "libz",
      "package": "zlib1g",
      "headers": "zlib1g-dev",
      "source": "zlib",
      "version": "1:1.3.dfsg+really1.3.1-1ubuntu3.1",
      "name": "zlib",
      "homepage": "http://zlib.net/",
      "description": "compression library - runtime"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    },
    {
      "shlib": "libgomp",
      "package": "libgomp1",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "openmp",
      "homepage": "http://gcc.gnu.org/",
      "description": "GCC OpenMP (GOMP) support library"
    }
  ],
  "_vignettes": [
    {
      "source": "benchmark-results.Rmd",
      "filename": "benchmark-results.html",
      "title": "Benchmarking BamScale: reader throughput and end-to-end workflow impact",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Read throughput on a single large BAM",
        "End-to-end impact tracks the read fraction",
        "A note on cores and fairness",
        "Beyond reading: in-reader aggregation (new in 0.99.14)",
        "Output is identical to the standard tools",
        "Try it",
        "Reproducing the full benchmarks",
        "Session information"
      ],
      "created": "2026-04-20 06:18:30",
      "modified": "2026-08-12 04:52:09",
      "commits": 3
    },
    {
      "source": "BamScale-intro.Rmd",
      "filename": "BamScale-intro.html",
      "title": "Getting started with BamScale",
      "author": "Chirag Parsania",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Basic usage",
        "Metadata-oriented BAM access",
        "Filtering with ScanBamParam",
        "Alignment-object output",
        "Sequence and quality extraction",
        "Fast count summaries",
        "Relationship to existing Bioconductor tools",
        "Session information"
      ],
      "created": "2026-04-20 06:18:30",
      "modified": "2026-05-04 05:29:45",
      "commits": 2
    }
  ],
  "_score": 5,
  "_indexed": true,
  "_nocasepkg": "bamscale",
  "_universes": [
    "bioc",
    "cparsania"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.99.14",
      "date": "2026-08-13T09:05:10.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "39795de37096adadd8a8b44773b097576aef2df6",
      "fileid": "https://r2.ropensci.org/342872c333deb13a366b784e217374ae46c972dad2fdccf35b67a9ca0904386e",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/31684320016"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.99.14",
      "date": "2026-09-15T11:40:37.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "39795de37096adadd8a8b44773b097576aef2df6",
      "fileid": "https://r2.ropensci.org/d4b5d58f524cd60da202c7356fb5625177ea60de0d50efed07bd4aa0e4a9a82b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/34963903056"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.99.14",
      "date": "2026-09-15T11:40:26.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "39795de37096adadd8a8b44773b097576aef2df6",
      "fileid": "https://r2.ropensci.org/5fb4757963dafe5a5b10be8df1db153f67a2469f9c3ec5e2f23171912c6f2e34",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/34963903056"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.99.14",
      "date": "2026-09-15T11:37:32.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "39795de37096adadd8a8b44773b097576aef2df6",
      "fileid": "https://r2.ropensci.org/a015e44b11618cbc094b848779f83d75f16260c83cdf86d3007df29a2a29fec3",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/34963903056"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.99.14",
      "date": "2026-09-15T11:39:40.000Z",
      "arch": "aarch64",
      "commit": "39795de37096adadd8a8b44773b097576aef2df6",
      "fileid": "https://r2.ropensci.org/763f024aaadee4fcb5e82c2aff435a7c87ca90ed4d3a5b5b78951e342ec3ddb3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/34963903056"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.99.14",
      "date": "2026-09-15T11:43:24.000Z",
      "arch": "x86_64",
      "commit": "39795de37096adadd8a8b44773b097576aef2df6",
      "fileid": "https://r2.ropensci.org/243943578bc6bcba82c913d7e508c08da44aa690ebfd5b39767a45cc66bd00c6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/34963903056"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.99.14",
      "date": "2026-09-15T11:40:01.000Z",
      "arch": "aarch64",
      "commit": "39795de37096adadd8a8b44773b097576aef2df6",
      "fileid": "https://r2.ropensci.org/2e85e13b6448bd3288ef848442d5677aee437c649cf0d35ccd1e042a87b0e40b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/34963903056"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.99.14",
      "date": "2026-09-15T11:40:52.000Z",
      "arch": "x86_64",
      "commit": "39795de37096adadd8a8b44773b097576aef2df6",
      "fileid": "https://r2.ropensci.org/4d29360742e088991ed35048ccd41a99205180a2eaf7ee6ecdf89300c3d349fe",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/34963903056"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.99.14",
      "date": "2026-09-15T11:40:45.000Z",
      "arch": "emscripten",
      "commit": "39795de37096adadd8a8b44773b097576aef2df6",
      "fileid": "https://r2.ropensci.org/bb9acbb22c7e3b4a0048241c8adcd5c25eb77d17bcf920921485f41f18967131",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/34963903056"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.99.14",
      "date": "2026-09-15T11:41:10.000Z",
      "arch": "aarch64",
      "commit": "39795de37096adadd8a8b44773b097576aef2df6",
      "fileid": "https://r2.ropensci.org/7b68d8ad4455e6d00bf38e2b46f6cf32d456774eb5cda2b5b7ca8fc8b8180a01",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/34963903056"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.99.14",
      "date": "2026-09-15T11:39:38.000Z",
      "arch": "x86_64",
      "commit": "39795de37096adadd8a8b44773b097576aef2df6",
      "fileid": "https://r2.ropensci.org/99ae371f0cd218b72cf73dfafc24f97f5bebbe906cfd52b6b1efbdf653a0dfbe",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/34963903056"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.99.14",
      "date": "2026-09-15T11:39:34.000Z",
      "arch": "x86_64",
      "commit": "39795de37096adadd8a8b44773b097576aef2df6",
      "fileid": "https://r2.ropensci.org/7ff8e97e9e8bbc976fd05638517d21dd8333bc59b4707ebb6e94e0c25768fbd5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/34963903056"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.99.14",
      "date": "2026-09-15T11:41:04.000Z",
      "arch": "aarch64",
      "commit": "39795de37096adadd8a8b44773b097576aef2df6",
      "fileid": "https://r2.ropensci.org/78a28e8e7ebcb3671576eb4e4f88bc381aaab4c8c21173603a9bbf70506fc99d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/34963903056"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.99.14",
      "date": "2026-09-15T11:39:23.000Z",
      "arch": "x86_64",
      "commit": "39795de37096adadd8a8b44773b097576aef2df6",
      "fileid": "https://r2.ropensci.org/4f05931a42bf46f924c40bc41d13f7562dce150dc5f501f20f5f760804e02503",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/34963903056"
    }
  ]
}