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ompBAM

C++ Library for Parallel BAM processing

https://github.com/alexchwong/ompbam

Science Score: 13.0%

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    Low similarity (11.0%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

C++ Library for Parallel BAM processing

Basic Info
  • Host: GitHub
  • Owner: alexchwong
  • License: mit
  • Language: C++
  • Default Branch: main
  • Homepage:
  • Size: 2.95 MB
Statistics
  • Stars: 4
  • Watchers: 1
  • Forks: 0
  • Open Issues: 2
  • Releases: 0
Created about 5 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.md

ompBAM

C++ Library for OpenMP-based multi-threaded sequential profiling of Binary Alignment Map (BAM) files

Description

Although various tools for multi-threaded BAM processing (samtools, sambamba) are available, currently there are none available to the R/Bioconductor environment. Parallelism in R is achieved using BiocParallel or related packages. Typical alternatives include processing multiple BAM files, each using a single core. Although easy to set up, memory-intensive applications limit such approaches. ompBAM is a header-only C++ library based on OpenMP, allowing developers to implement OpenMP-based parallelism for the sequential reading of BAM files. ompBAM makes it easy by handling all the parallel file-access and bgzf decompression, allowing developers to focus on multi-threaded handling of individual reads.

Installation

On current R (>= 4.0.0)

  • Development version from Github: library("devtools") install_github("alexchwong/ompBAM", dependencies=TRUE, build_vignettes = TRUE)

Documentation

Access the ompBAM-API-Docs via its included vignette. This includes: * How to set up a new package R-project, ready-to-compile with ompBAM, as well as a 'Hello World' equivalent example function of the 'idxstats' function to demonstrate ompBAM * A step-by-step guide of how the idxstats function implemented in the example code is constructed * Detailed documentation of the pbam_in and pbam1_t objects that comprise ompBAM.

browseVignettes("ompBAM")

Owner

  • Name: Alex CH Wong
  • Login: alexchwong
  • Kind: user
  • Location: Centenary Institute
  • Company: Gene and Stem Cell Therapy Program

Research Officer

GitHub Events

Total
  • Push event: 1
  • Pull request event: 1
Last Year
  • Push event: 1
  • Pull request event: 1

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 125
  • Total Committers: 2
  • Avg Commits per committer: 62.5
  • Development Distribution Score (DDS): 0.016
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
alexchwong 8****g 123
Nitesh Turaga n****a@g****m 2

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 2
  • Total pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: about 1 month
  • Total issue authors: 1
  • Total pull request authors: 2
  • Average comments per issue: 6.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 2 months
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • barracuda156 (2)
Pull Request Authors
  • jeroen (2)
  • alexchwong (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 7,797 total
  • Total dependent packages: 1
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: ompBAM

C++ Library for OpenMP-based multi-threaded sequential profiling of Binary Alignment Map (BAM) files

  • Versions: 5
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 7,797 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 29.6%
Downloads: 88.8%
Maintainers (1)
alexchwong.github@gmail.com
Last synced: 12 months ago

Dependencies

DESCRIPTION cran
  • Rcpp * imports
  • utils * imports
  • zlibbioc * imports
  • RcppProgress * suggests
  • desc * suggests
  • devtools * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • roxygen2 * suggests
  • testthat >= 3.0.0 suggests
  • usethis * suggests
inst/examples/ompBAMExample/DESCRIPTION cran
  • Rcpp * imports
  • zlibbioc * imports