{"id":18583310,"url":"https://github.com/alexpreynolds/convert2bed","last_synced_at":"2025-05-16T05:08:19.024Z","repository":{"id":22989852,"uuid":"26340263","full_name":"alexpreynolds/convert2bed","owner":"alexpreynolds","description":"Convert common binary and text genomic formats to BED","archived":false,"fork":false,"pushed_at":"2020-08-25T01:17:38.000Z","size":197,"stargazers_count":2,"open_issues_count":0,"forks_count":2,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-02-17T16:38:49.706Z","etag":null,"topics":["bam","bed","c","conversion"],"latest_commit_sha":null,"homepage":"http://alexpreynolds.github.io/convert2bed/","language":"C","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/alexpreynolds.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2014-11-07T22:11:09.000Z","updated_at":"2020-08-25T01:17:40.000Z","dependencies_parsed_at":"2022-08-21T08:11:03.802Z","dependency_job_id":null,"html_url":"https://github.com/alexpreynolds/convert2bed","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alexpreynolds%2Fconvert2bed","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alexpreynolds%2Fconvert2bed/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alexpreynolds%2Fconvert2bed/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alexpreynolds%2Fconvert2bed/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/alexpreynolds","download_url":"https://codeload.github.com/alexpreynolds/convert2bed/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254471057,"owners_count":22076585,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bam","bed","c","conversion"],"created_at":"2024-11-07T00:21:50.938Z","updated_at":"2025-05-16T05:08:17.825Z","avatar_url":"https://github.com/alexpreynolds.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"convert2bed\n===========\n\nNote! Hey! Read this! This is really important!\n-----------------------------------------------\n\nHi! At this time, all active development on `convert2bed` is being done within [BEDOPS](https://github.com/bedops/bedops). If you want the latest features and bug fixes in `convert2bed` (and there have been many since 2015!), I very strongly suggest you fork or review the code in BEDOPS.\n\n[![Build Status](https://travis-ci.org/alexpreynolds/convert2bed.svg?branch=master)](https://travis-ci.org/alexpreynolds/convert2bed)\n\nStop reading and go download BEDOPS! This code is dead!\n-------------------------------------------------------\n\nThe `convert2bed` tool converts common binary and text genomic formats ([BAM](http://samtools.github.io/hts-specs/SAMv1.pdf), [GFF](http://www.sequenceontology.org/gff3.shtml), [GTF](http://mblab.wustl.edu/GTF22.html), [GVF](http://www.sequenceontology.org/resources/gvf.html#summary), [PSL](http://genome.ucsc.edu/FAQ/FAQformat.html#format2), [RepeatMasker annotation output](http://www.repeatmasker.org/webrepeatmaskerhelp.html), [SAM](http://samtools.github.io/hts-specs/SAMv1.pdf), [VCF](http://samtools.github.io/hts-specs/VCFv4.2.pdf) and [WIG](http://genome.ucsc.edu/goldenpath/help/wiggle.html)) to unsorted or [sorted, extended BED](http://bedops.readthedocs.org/en/latest/content/reference/file-management/sorting/sort-bed.html) or [BEDOPS Starch](http://bedops.readthedocs.org/en/latest/content/reference/file-management/compression/starch.html) (compressed BED) with additional per-format options. \n\nConvenience wrapper `bash` scripts are provided for each format that convert standard input to unsorted or sorted BED, or to BEDOPS Starch (compressed BED). Scripts expose format-specific ``convert2bed`` options. \n\nWhy are you still reading this?! Please use BEDOPS!\n---------------------------------------------------\n\nWe also provide ``bam2bed_sge``, ``bam2bed_gnuParallel``, ``bam2starch_sge`` and ``bam2starch_gnuParallel`` convenience scripts, which parallelize the conversion of indexed BAM to BED or to BEDOPS Starch via a [Sun Grid Engine](http://en.wikipedia.org/wiki/Oracle_Grid_Engine)-based computational cluster or local [GNU Parallel](http://en.wikipedia.org/wiki/GNU_parallel) installation.\n\nInstallation\n------------\n\nThe following compiles `convert2bed` and copies the binary and wrappers to `/usr/local/bin`:\n\n    $ make \u0026\u0026 make install\n\nUsage\n-----\n\nGenerally, to convert data in format `xyz` to sorted BED:\n\n    $ convert2bed -i xyz \u003c input.xyz \u003e output.bed\n\nAdd the `-o starch` option to write a BEDOPS Starch file, which stores compressed BED data and feature metadata:\n\n    $ convert2bed -i xyz -o starch \u003c input.xyz \u003e output.starch\n\nWrappers are available for each of the supported formats to convert to BED or Starch, *e.g.*:\n\n    $ bam2bed \u003c reads.bam \u003e reads.bed\n    $ bam2starch \u003c reads.bam \u003e reads.starch\n\nFormat-specific options are available for each wrapper; use `--help` with a wrapper script or `--help-bam`, `--help-gff` etc. with `convert2bed` to get a format-specific description of the conversion procedure and options.\n\nDependencies\n------------\n\nThis tool is dependent upon [`samtools`](https://github.com/samtools/samtools) to handle BAM conversion, and BEDOPS [`sort-bed`](http://bedops.readthedocs.org/en/latest/content/reference/file-management/sorting/sort-bed.html) and [`starch`](http://bedops.readthedocs.org/en/latest/content/reference/file-management/compression/starch.html) to generate sorted BED and Starch (compressed BED) output. The directory containing these binaries should be present in the end user's `PATH` environment variable. \n\nIf the `samtools` binary is not present, BAM conversion will fail. If the `sort-bed` binary is not installed, all format conversions will fail with default sort rules applied. If the `starch` binary is not installed, the `starch` output format option will be unavailable.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falexpreynolds%2Fconvert2bed","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Falexpreynolds%2Fconvert2bed","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falexpreynolds%2Fconvert2bed/lists"}