{"id":32563025,"url":"https://github.com/smithlabcode/-deprecated-amrfinder","last_synced_at":"2025-10-29T02:56:22.776Z","repository":{"id":16379643,"uuid":"19130134","full_name":"smithlabcode/-DEPRECATED-amrfinder","owner":"smithlabcode","description":"DEPRECATED: ACTIVELY MANAGED SOFTWARE IN METHPIPE REPOSITORY.","archived":false,"fork":false,"pushed_at":"2016-04-12T22:26:37.000Z","size":5105,"stargazers_count":0,"open_issues_count":1,"forks_count":1,"subscribers_count":14,"default_branch":"master","last_synced_at":"2025-04-01T00:29:57.084Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://github.com/smithlabcode/methpipe","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/smithlabcode.png","metadata":{"files":{"readme":"README.txt","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2014-04-25T01:33:53.000Z","updated_at":"2016-04-12T22:24:40.000Z","dependencies_parsed_at":"2022-09-22T13:03:39.271Z","dependency_job_id":null,"html_url":"https://github.com/smithlabcode/-DEPRECATED-amrfinder","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"purl":"pkg:github/smithlabcode/-DEPRECATED-amrfinder","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2F-DEPRECATED-amrfinder","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2F-DEPRECATED-amrfinder/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2F-DEPRECATED-amrfinder/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2F-DEPRECATED-amrfinder/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/smithlabcode","download_url":"https://codeload.github.com/smithlabcode/-DEPRECATED-amrfinder/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2F-DEPRECATED-amrfinder/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":281549786,"owners_count":26520515,"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","status":"online","status_checked_at":"2025-10-29T02:00:06.901Z","response_time":59,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":[],"created_at":"2025-10-29T02:56:08.527Z","updated_at":"2025-10-29T02:56:22.770Z","avatar_url":"https://github.com/smithlabcode.png","language":"C++","readme":"\nThis respository has been marked as DEPRECATED as of 2014, after the\nactively maintained code of `amrfinder`, `amrtester`, and `allelicmeth`\nwas merged into [Methpipe](https://github.com/smithlabcode/methpipe).\n\nPlease see the methpipe repository for updated and actively maintained\nversion of these programs.\n\n========================================================================\n\nThis is the README file for the first release of amrfinder version 1.02.\namrfinder is a program for identifying allele-specific DNA methylation\nfrom bisulfite short-read sequencing technology\n(such as Solexa/Illumina).\n\n\nCONTACT INFORMATION:\n========================================================================\nFang Fang: ffang@usc.edu\nAndrew D Smith: andrewds@usc.edu\n\nSYSTEM REQUIREMENTS:\n========================================================================\nThe amrfinder software will only run on UNIX-type system with GNU Scientific\nLibrary (GSL, http://www/gmi/prg/software/gsl) and GNU Compiler Collection \n(GCC, http://gcc.gnu.org/). Also, amrfinder will only run on 64-bit machines.\n\n\nINSTALLATION:\n========================================================================\nUnpack the archive and change into the archive\ndirectory. Then type 'make install'. A 'bin' directory will be created\nin the current directory, and it will contain the program\nbinaries. These can be moved around, and also do not depend on any\ndynamic libraries, so they should simply work when executed.\n\n\nUSAGE EXAMPLES:\n========================================================================\nEach program included in this software package will print a list of\noptions if executed without any command line arguments. Many of the\nprograms use similar options (for example, output files are specified\nwith '-o'). For the most basic usage of scanning allelically methylted \nregions (AMRs), use the command:\n\n     amrfinder -o output.bed -c chroms_dir input_reads.mr\n\nThe output will appear in output.bed, and the output is in BED format\n(see the UCSC Genome Browser Help documentation for details of this\nformat). Each line of the file indicates the location of an AMR in the \nCpG numbering format. The directory including corresponding chromosomes (e.g. hg18) \nshould be indicated. The input read file in a format called 'MappedRead',\nwhich consists of 8 columns with the first 6 the same as in BED format and\nthe last two columns being the sequence and quality score of the read.\n\nLICENSE\n========================================================================\nThis program is free software: you can redistribute it and/or modify\nit under the terms of the GNU General Public License as published by\nthe Free Software Foundation, either version 3 of the License, or (at\nyour option) any later version.\n\nThis program is distributed in the hope that it will be useful,\nbut WITHOUT ANY WARRANTY; without even the implied warranty of\nMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\nGNU General Public License for more details.\n\nYou should have received a copy of the GNU General Public License\nalong with this program.  If not, see \u003chttp://www.gnu.org/licenses/\u003e.\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsmithlabcode%2F-deprecated-amrfinder","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsmithlabcode%2F-deprecated-amrfinder","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsmithlabcode%2F-deprecated-amrfinder/lists"}