{"id":13751625,"url":"https://github.com/lh3/bioawk","last_synced_at":"2025-04-12T23:42:41.286Z","repository":{"id":2168908,"uuid":"3115288","full_name":"lh3/bioawk","owner":"lh3","description":"BWK awk modified for biological data","archived":false,"fork":false,"pushed_at":"2022-08-11T01:06:45.000Z","size":130,"stargazers_count":611,"open_issues_count":25,"forks_count":118,"subscribers_count":35,"default_branch":"master","last_synced_at":"2025-04-12T23:42:37.979Z","etag":null,"topics":["bioinformatics","sequence-analysis"],"latest_commit_sha":null,"homepage":"","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/lh3.png","metadata":{"files":{"readme":"README.awk","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":"2012-01-06T03:05:25.000Z","updated_at":"2025-04-10T22:51:43.000Z","dependencies_parsed_at":"2022-08-08T08:30:19.243Z","dependency_job_id":null,"html_url":"https://github.com/lh3/bioawk","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lh3%2Fbioawk","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lh3%2Fbioawk/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lh3%2Fbioawk/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lh3%2Fbioawk/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lh3","download_url":"https://codeload.github.com/lh3/bioawk/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248647255,"owners_count":21139081,"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":["bioinformatics","sequence-analysis"],"created_at":"2024-08-03T09:00:50.229Z","updated_at":"2025-04-12T23:42:41.266Z","avatar_url":"https://github.com/lh3.png","language":"C","funding_links":[],"categories":["Ranked by starred repositories","Books"],"sub_categories":[],"readme":"/****************************************************************\nCopyright (C) Lucent Technologies 1997\nAll Rights Reserved\n\nPermission to use, copy, modify, and distribute this software and\nits documentation for any purpose and without fee is hereby\ngranted, provided that the above copyright notice appear in all\ncopies and that both that the copyright notice and this\npermission notice and warranty disclaimer appear in supporting\ndocumentation, and that the name Lucent Technologies or any of\nits entities not be used in advertising or publicity pertaining\nto distribution of the software without specific, written prior\npermission.\n\nLUCENT DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,\nINCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS.\nIN NO EVENT SHALL LUCENT OR ANY OF ITS ENTITIES BE LIABLE FOR ANY\nSPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES\nWHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER\nIN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION,\nARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF\nTHIS SOFTWARE.\n****************************************************************/\n\nThis is the version of awk described in \"The AWK Programming Language\",\nby Al Aho, Brian Kernighan, and Peter Weinberger\n(Addison-Wesley, 1988, ISBN 0-201-07981-X).\n\nChanges, mostly bug fixes and occasional enhancements, are listed\nin FIXES.  If you distribute this code further, please please please\ndistribute FIXES with it.  If you find errors, please report them\nto bwk@cs.princeton.edu.  Thanks.\n\nThe program itself is created by\n\tmake\nwhich should produce a sequence of messages roughly like this:\n\n\tyacc -d awkgram.y\n\nconflicts: 43 shift/reduce, 85 reduce/reduce\n\tmv y.tab.c ytab.c\n\tmv y.tab.h ytab.h\n\tcc -c ytab.c\n\tcc -c b.c\n\tcc -c main.c\n\tcc -c parse.c\n\tcc maketab.c -o maketab\n\t./maketab \u003eproctab.c\n\tcc -c proctab.c\n\tcc -c tran.c\n\tcc -c lib.c\n\tcc -c run.c\n\tcc -c lex.c\n\tcc ytab.o b.o main.o parse.o proctab.o tran.o lib.o run.o lex.o -lm\n\nThis produces an executable a.out; you will eventually want to\nmove this to some place like /usr/bin/awk.\n\nIf your system does not have yacc or bison (the GNU\nequivalent), you must compile the pieces manually.  We have\nincluded yacc output in ytab.c and ytab.h, and backup copies in\ncase you overwrite them.  We have also included a copy of\nproctab.c so you do not need to run maketab.\n\nNOTE: This version uses ANSI C, as you should also.  We have\ncompiled this without any changes using gcc -Wall and/or local C\ncompilers on a variety of systems, but new systems or compilers\nmay raise some new complaint; reports of difficulties are\nwelcome.\n\nThis also compiles with Visual C++ on all flavors of Windows,\n*if* you provide versions of popen and pclose.  The file\nmissing95.c contains versions that can be used to get started\nwith, though the underlying support has mysterious properties,\nthe symptom of which can be truncated pipe output.  Beware.  The\nfile makefile.win gives hints on how to proceed; if you run\nvcvars32.bat, it will set up necessary paths and parameters so\nyou can subsequently run nmake -f makefile.win.  Beware also that\nwhen running on Windows under command.com, various quoting\nconventions are different from Unix systems: single quotes won't\nwork around arguments, and various characters like % are\ninterpreted within double quotes.\n\nThis compiles without change on Macintosh OS X using gcc and\nthe standard developer tools.\n\nThis is also said to compile on Macintosh OS 9 systems, using the\nfile \"buildmac\" provided by Dan Allen (danallen@microsoft.com),\nto whom many thanks.\n\nThe version of malloc that comes with some systems is sometimes\nastonishly slow.  If awk seems slow, you might try fixing that.\nMore generally, turning on optimization can significantly improve\nawk's speed, perhaps by 1/3 for highest levels.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flh3%2Fbioawk","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flh3%2Fbioawk","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flh3%2Fbioawk/lists"}