{ "_id": "6a1ac10b1d7bb097a09d763b", "Package": "ompBAM", "Title": "C++ Library for OpenMP-based multi-threaded sequential profiling\nof Binary Alignment Map (BAM) files", "Version": "1.17.0", "Date": "2024-09-14", "Authors@R": "c(person(\"Alex Chit Hei\", \"Wong\", email=\"alexchwong.github@gmail.com\", \nrole=c(\"aut\", \"cre\", \"cph\")))", "Description": "This packages provides C++ header files for developers\nwishing to create R packages that processes BAM files. ompBAM\nautomates file access, memory management, and handling of\nmultiple threads 'behind the scenes', so developers can focus\non creating domain-specific functionality. The included\nvignette contains detailed documentation of this API, including\nquick-start instructions to create a new ompBAM-based package,\nand step-by-step explanation of the functionality behind the\nexample packaged included within ompBAM.", "License": "MIT + file LICENSE", "VignetteBuilder": "knitr", "biocViews": "Alignment, DataImport, RNASeq, Software, Sequencing,\nTranscriptomics, SingleCell", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "URL": "https://github.com/alexchwong/ompBAM", "BugReports": "https://support.bioconductor.org/", "Config/testthat/edition": "3", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:58:18 UTC", "RemoteUrl": "https://github.com/bioc/ompBAM", "RemoteRef": "HEAD", "RemoteSha": "bd0dbacf43cf8270252d6b0bb96b54fbd271320c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 07:20:26 UTC", "User": "root" }, "Author": "Alex Chit Hei Wong [aut, cre, cph]", "Maintainer": "Alex Chit Hei Wong ", "MD5sum": "66c6ea565e15b85e0b114263d8b346a5", "_user": "bioc", "_type": "src", "_file": "ompBAM_1.17.0.tar.gz", "_fileid": "795fa46446a7f7223f912913a9bde0e98405e7283a96e6c0ab91d8d9045b784c", "_filesize": 3135739, "_sha256": "795fa46446a7f7223f912913a9bde0e98405e7283a96e6c0ab91d8d9045b784c", "_created": "2026-05-30T07:20:26.000Z", "_published": "2026-05-30T10:50:51.338Z", "_jobs": [ { "job": 78633091090, "time": 466, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7306468236" }, { "job": 78633091080, "time": 221, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306439904" }, { "job": 78633091086, "time": 156, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306433199" }, { "job": 78633091076, "time": 129, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7307548361" }, { "job": 78633091083, "time": 117, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307548302" }, { "job": 78632920012, "time": 192, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306416393" }, { "job": 78633091071, "time": 118, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306429148" }, { "job": 78633091092, "time": 138, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306431680" }, { "job": 78633091087, "time": 107, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306428079" }, { "job": 78633091088, "time": 107, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306428145" } ], "_bioccheck": { "error": 0, "warning": 2, "note": 5 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677852283", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/ompBAM", "_commit": { "id": "bd0dbacf43cf8270252d6b0bb96b54fbd271320c", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381098 }, "_maintainer": { "name": "Alex Chit Hei Wong", "email": "alexchwong.github@gmail.com" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "utils", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "RcppProgress", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "roxygen2", "role": "Suggests" }, { "package": "devtools", "role": "Suggests" }, { "package": "usethis", "role": "Suggests" }, { "package": "desc", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 2, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.17.0", "bioc": "3.24" }, { "branch": "release", "version": "1.16.0", "bioc": "3.23" } ], "_topics": [ "alignment", "dataimport", "rnaseq", "software", "sequencing", "transcriptomics", "singlecell" ], "_stars": 4, "_contributors": [ { "user": "alexchwong", "count": 132, "uuid": 80015046 }, { "user": "jwokaty", "count": 14, "uuid": 1744257 }, { "user": "nturaga", "count": 2, "uuid": 2746443 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 344, "source": "https://www.bioconductor.org/packages/stats/bioc/ompBAM" }, "_devurl": "https://github.com/alexchwong/ompbam", "_searchresults": 8, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/ompBAM.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/alexchwong/ompbam", "_realowner": "bioc", "_cranurl": false, "_exports": [ "example_BAM", "install_ompBAM_example", "use_ompBAM" ], "_help": [ { "page": "ompBAM-package", "title": "ompBAM: C++ header library for parallel sequential reading of BAM files", "topics": [ "ompBAM-package", "ompBAM" ] }, { "page": "example_BAM", "title": "Returns the path of a test BAM file", "topics": [ "example_BAM" ] }, { "page": "install_ompBAM_example", "title": "ompBAM Example", "topics": [ "install_ompBAM_example" ] }, { "page": "use_ompBAM", "title": "Sets up the package in the given directory to use ompBAM", "topics": [ "use_ompBAM" ] } ], "_readme": "https://github.com/bioc/ompBAM/raw/HEAD/README.md", "_rundeps": [ "Rcpp" ], "_vignettes": [ { "source": "ompBAM-API-Docs.Rmd", "filename": "ompBAM-API-Docs.html", "title": "ompBAM API Documentation", "author": "Alex C H Wong", "engine": "knitr::rmarkdown", "headings": [ "(0) Installation and Quick-Start", "Installation", "Creating and testing an example ompBAM-based package", "To create an ompBAM-based package from within RStudio:", "(1) Requirements to setting up a new R package to include ompBAM", "(1a) Making a new package that compiles with ompBAM", "(1b) Dependencies required to compile with ompBAM", "(1c) Make Files", "(1d) OpenMP compatibility", "(2) Step-by-step guide to creating your first ompBAM-powered package", "(2a) Headers and Includes", "(2b) Sanity check for number of threads", "(2c) Opening BAM files with ompBAM", "Note 3 things:", "(2d) Obtaining chromosome names and lengths", "(2e) Constructing a loop to read the BAM file using ompBAM", "(2f) Processing BAM reads using an OpenMP parallel FOR loop", "(2g) Getting thread-specific reads from ompBAM", "(2g:i) Checking \"validity\" of reads and \"realizing\" reads", "(2h) Counting chromosome-specific reads", "(2h:i) Obtaining the chromosome ID of each aligned read", "(2h:ii) Tallying reads to a variable external to the parallel FOR loop", "(2i) Closing the BAM file", "(2j) Summarizing the tallied reads", "(2k) Adding a progress bar", "(3) pbam_in function documentation", "(3a) Constructor", "Usage", "Parameters", "Details", "Examples", "(3b) openFile()", "(3c) SetInputHandle()", "(3d) closeFile()", "(3e) obtainChrs()", "Return value", "(3f) fillReads()", "(3g) supplyRead()", "(3h) remainingThreadReadsBuffer();", "(3i) Progress and File Size Functions", "(4) pbam1_t function documentation", "(4a) Constructor", "(4b) validate()", "(4c) realize()", "(4d) isReal()", "(4e) Getters of Read Core Data", "(4f) Getters of Cigar Data", "(4g) Getters of Alignment Sequence and Quality score", "(4h) Tag Getters", "(5) SessionInfo" ], "created": "2021-09-06 22:06:45", "modified": "2024-07-27 01:39:36", "commits": 25 } ], "_score": 5.681241237375588, "_indexed": true, "_nocasepkg": "ompbam", "_universes": [ "bioc", "alexchwong" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.17.0", "date": "2026-05-30T07:23:56.000Z", "distro": "noble", "commit": "bd0dbacf43cf8270252d6b0bb96b54fbd271320c", "fileid": "217577d61f92f262745ef8a82ea764e9518f52c3b1cc737514aa40d351164a4f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677852283" }, { "r": "4.6.0", "os": "linux", "version": "1.17.0", "date": "2026-05-30T07:22:56.000Z", "distro": "noble", "commit": "bd0dbacf43cf8270252d6b0bb96b54fbd271320c", "fileid": "1d49d6cfca68f53460689fd2c8cff782c299dc23ab752e259d865450d9c08718", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677852283" }, { "r": "4.5.3", "os": "mac", "version": "1.17.0", "date": "2026-05-30T10:34:17.000Z", "commit": "bd0dbacf43cf8270252d6b0bb96b54fbd271320c", "fileid": "66fdd16bfcd428f1403e835c0cf9e36c60be443b5b2a969017f80b88d2235cba", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677852283" }, { "r": "4.6.0", "os": "mac", "version": "1.17.0", "date": "2026-05-30T10:34:20.000Z", "commit": "bd0dbacf43cf8270252d6b0bb96b54fbd271320c", "fileid": "e2f513739151c6ce6b989f7c20addfefaf4aea47217f2827fcc56030ed36cebc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677852283" }, { "r": "4.6.0", "os": "wasm", "version": "1.17.0", "date": "2026-05-30T07:22:38.000Z", "commit": "bd0dbacf43cf8270252d6b0bb96b54fbd271320c", "fileid": "18ab33d44bc7bd6fea8bf6995df8a84ebc7756606844de1173f881d908d8b140", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677852283" }, { "r": "4.7.0", "os": "win", "version": "1.17.0", "date": "2026-05-30T07:22:08.000Z", "commit": "bd0dbacf43cf8270252d6b0bb96b54fbd271320c", "fileid": "f591ea8a3b6ff42c8ab2b4a41f2daa38a43ecacb5e5073c131d1dd0d749193f8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677852283" }, { "r": "4.5.3", "os": "win", "version": "1.17.0", "date": "2026-05-30T07:21:39.000Z", "commit": "bd0dbacf43cf8270252d6b0bb96b54fbd271320c", "fileid": "3653ced69c1359c6dfc99ebb62a077114a982a460c9504e318815a3d8f13315b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677852283" }, { "r": "4.6.0", "os": "win", "version": "1.17.0", "date": "2026-05-30T07:21:37.000Z", "commit": "bd0dbacf43cf8270252d6b0bb96b54fbd271320c", "fileid": "01eb26e0a46c98a7c48765b6001a642a36fb2d4391fc771a2b8ed08469f62d32", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677852283" } ] }