{
  "_id": "6a15e21aacfb0bcc41d6b70a",
  "Package": "BamScale",
  "Type": "Package",
  "Title": "Bioconductor-Friendly Multithreaded BAM Processing",
  "Version": "0.99.10",
  "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)",
  "RoxygenNote": "7.3.3",
  "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/pak/sysreqs": "libbz2-dev liblzma-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-26 05:52:36 UTC",
  "RemoteUrl": "https://github.com/bioc/BamScale",
  "RemoteRef": "HEAD",
  "RemoteSha": "026ff90e052d4769cd73251ec81124cc2fb3bfd1",
  "Packaged": {
    "Date": "2026-05-26 18:04:56 UTC",
    "User": "root"
  },
  "Author": "Chirag Parsania [aut, cre]",
  "Maintainer": "Chirag Parsania <chirag.parsania@gmail.com>",
  "MD5sum": "535d9bfbd3ec8ff8f9caddaa9b254541",
  "_user": "bioc",
  "_type": "src",
  "_file": "BamScale_0.99.10.tar.gz",
  "_fileid": "a03c45cf91cd8d0c3c77c3a2a865e9e320642790f003b8fef6490d98eab3112a",
  "_filesize": 2553440,
  "_sha256": "a03c45cf91cd8d0c3c77c3a2a865e9e320642790f003b8fef6490d98eab3112a",
  "_created": "2026-05-26T18:04:56.000Z",
  "_published": "2026-05-26T18:10:34.774Z",
  "_jobs": [
    {
      "job": 77926703649,
      "time": 219,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7222439029"
    },
    {
      "job": 77926703728,
      "time": 229,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7222442839"
    },
    {
      "job": 77926703662,
      "time": 246,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7222448395"
    },
    {
      "job": 77926703738,
      "time": 237,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7222445695"
    },
    {
      "job": 77926703720,
      "time": 262,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7222454207"
    },
    {
      "job": 77926703775,
      "time": 127,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7222408620"
    },
    {
      "job": 77926703706,
      "time": 292,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7222463627"
    },
    {
      "job": 77926703670,
      "time": 149,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7222415775"
    },
    {
      "job": 77926703671,
      "time": 226,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7222442016"
    },
    {
      "job": 77925852098,
      "time": 280,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7222363968"
    },
    {
      "job": 77926703645,
      "time": 164,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7222420615"
    },
    {
      "job": 77926703668,
      "time": 186,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7222428656"
    },
    {
      "job": 77926703851,
      "time": 144,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7222414325"
    },
    {
      "job": 77926703660,
      "time": 195,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7222432011"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 7
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26465852482",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/BamScale",
  "_commit": {
    "id": "026ff90e052d4769cd73251ec81124cc2fb3bfd1",
    "author": "Chirag Parsania <chirag.parsania@gmail.com>",
    "committer": "Chirag Parsania <chirag.parsania@gmail.com>",
    "message": "Increment version number to 0.99.10\n",
    "time": 1779774756
  },
  "_maintainer": {
    "name": "Chirag Parsania",
    "email": "chirag.parsania@gmail.com",
    "login": "cparsania",
    "twitter": "@ChiragParsania",
    "description": "Bioinformatics. Postdoc at @centenary institute. ",
    "uuid": 10338600
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "ompBAM",
      "role": "LinkingTo"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "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": "GenomeInfoDb",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "readr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "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
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "0.99.9",
      "bioc": "3.24"
    }
  ],
  "_topics": [
    "software",
    "dataimport",
    "sequencing",
    "coverage",
    "alignment",
    "qualitycontrol",
    "cpp"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "cparsania",
      "count": 47,
      "uuid": 10338600
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_devurl": "https://github.com/cparsania/bamscale",
  "_pkgdown": "https://cparsania.github.io/BamScale/",
  "_searchresults": 0,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/BamScale.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/cparsania/bamscale",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "bam_count",
    "bam_read",
    "decode_compact_qual",
    "decode_compact_seq",
    "decode_seqqual_compact"
  ],
  "_help": [
    {
      "page": "bam_count",
      "title": "Count BAM records with Bioconductor-compatible filtering",
      "topics": [
        "bam_count"
      ]
    },
    {
      "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"
      ]
    }
  ],
  "_pkglogo": "https://github.com/bioc/BamScale/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/bioc/BamScale/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "cigarillo",
    "codetools",
    "cpp11",
    "crayon",
    "DelayedArray",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicRanges",
    "IRanges",
    "lambda.r",
    "lattice",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "ompBAM",
    "Rcpp",
    "Rhtslib",
    "Rsamtools",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "SparseArray",
    "SummarizedExperiment",
    "XVector"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "benchmark-results.Rmd",
      "filename": "benchmark-results.html",
      "title": "Benchmarking BamScale Across Step1, GAlignments, and SeqQual Workloads",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Data Loading",
        "Benchmark Provenance",
        "Methods Rationale",
        "Input Files",
        "Reference Counts",
        "Best-Observed Summary",
        "BamScale-versus-Comparator Fold Change",
        "Single-File step1",
        "Single-File galignments",
        "Multi-File step1",
        "Multi-File galignments",
        "Single-File seqqual",
        "Multi-File seqqual",
        "Compact-versus-Compatible seqqual",
        "Interpretation",
        "Session Information"
      ],
      "created": "2026-04-20 06:18:30",
      "modified": "2026-04-20 06:18:30",
      "commits": 1
    },
    {
      "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": 4.903089986991944,
  "_indexed": true,
  "_nocasepkg": "bamscale",
  "_universes": [
    "bioc",
    "cparsania"
  ],
  "_previous": "0.99.9",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.99.10",
      "date": "2026-05-26T18:08:36.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "026ff90e052d4769cd73251ec81124cc2fb3bfd1",
      "fileid": "53599fabfb93eac1c1e41952f892ffd9e9961a871f64e153a73faa37aa1316b6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26465852482"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.99.10",
      "date": "2026-05-26T18:08:45.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "026ff90e052d4769cd73251ec81124cc2fb3bfd1",
      "fileid": "5ca188e24505b3a73acf3075973fd08500c57011e5157d257b18a4d51fb84936",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26465852482"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.99.10",
      "date": "2026-05-26T18:08:43.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "026ff90e052d4769cd73251ec81124cc2fb3bfd1",
      "fileid": "9c1b2d05a9ec627b2e65ef9271de1d14a553b137fbec5d14efb3ba309c2ad951",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26465852482"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.99.10",
      "date": "2026-05-26T18:09:00.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "026ff90e052d4769cd73251ec81124cc2fb3bfd1",
      "fileid": "6ed9bfe03e4cbc413e60def1af49b37c9e408df6b1d9782bc6d2096042024b0b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26465852482"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.99.10",
      "date": "2026-05-26T18:06:57.000Z",
      "arch": "aarch64",
      "commit": "026ff90e052d4769cd73251ec81124cc2fb3bfd1",
      "fileid": "4bbffc26bff1ee095c5a3002a1420511c6d9509b42d66650f9b935325d7ae401",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26465852482"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.99.10",
      "date": "2026-05-26T18:09:01.000Z",
      "arch": "x86_64",
      "commit": "026ff90e052d4769cd73251ec81124cc2fb3bfd1",
      "fileid": "e22dd3da11d643f085fe19410ac4dd01515cf710cd00c8918ccdfcedb67b3103",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26465852482"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.99.10",
      "date": "2026-05-26T18:07:13.000Z",
      "arch": "aarch64",
      "commit": "026ff90e052d4769cd73251ec81124cc2fb3bfd1",
      "fileid": "4009a64aa1fd93000e7738158f5ae3e2e58fc51339df147b1b7db88d65b0eafc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26465852482"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.99.10",
      "date": "2026-05-26T18:08:09.000Z",
      "arch": "x86_64",
      "commit": "026ff90e052d4769cd73251ec81124cc2fb3bfd1",
      "fileid": "ec91731cda5b6aabc9f025b2483eb97587e77f78347ba56f1f1d7ad876e924d8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26465852482"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.99.10",
      "date": "2026-05-26T18:07:58.000Z",
      "arch": "emscripten",
      "commit": "026ff90e052d4769cd73251ec81124cc2fb3bfd1",
      "fileid": "01f3fb6bc89a4fef9f05495bfed3418647e062020700bcc1e4e9ccc23ae97af8",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26465852482"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.99.10",
      "date": "2026-05-26T18:07:07.000Z",
      "arch": "x86_64",
      "commit": "026ff90e052d4769cd73251ec81124cc2fb3bfd1",
      "fileid": "89649d7153aec4c58d63327e2afa198d39874ba1ee439abd66e7d5084cf4ee68",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26465852482"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.99.10",
      "date": "2026-05-26T18:06:41.000Z",
      "arch": "x86_64",
      "commit": "026ff90e052d4769cd73251ec81124cc2fb3bfd1",
      "fileid": "9be7cc7770f3ae16485a55c001705510f0fe38ad6dd117817d09ef6605730cb8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26465852482"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.99.10",
      "date": "2026-05-26T18:07:25.000Z",
      "arch": "x86_64",
      "commit": "026ff90e052d4769cd73251ec81124cc2fb3bfd1",
      "fileid": "b339714e2a572c7f6d369a95ca8d3f94542627c258c81d47251bcacc8a32cff2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26465852482"
    }
  ]
}