{"id":19434640,"url":"https://github.com/ekg/hapviz","last_synced_at":"2025-04-24T20:32:13.497Z","repository":{"id":1349744,"uuid":"1297038","full_name":"ekg/hapviz","owner":"ekg","description":"indel haplotype visualization on the command line from BAM files","archived":false,"fork":false,"pushed_at":"2014-03-12T15:40:43.000Z","size":208,"stargazers_count":11,"open_issues_count":0,"forks_count":2,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-04-03T10:38:03.424Z","etag":null,"topics":[],"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/ekg.png","metadata":{"files":{"readme":"README","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":"2011-01-26T22:32:58.000Z","updated_at":"2021-11-26T07:57:04.000Z","dependencies_parsed_at":"2022-07-29T08:48:58.376Z","dependency_job_id":null,"html_url":"https://github.com/ekg/hapviz","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/ekg%2Fhapviz","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ekg%2Fhapviz/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ekg%2Fhapviz/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ekg%2Fhapviz/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ekg","download_url":"https://codeload.github.com/ekg/hapviz/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":250704863,"owners_count":21473775,"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":[],"created_at":"2024-11-10T14:47:04.496Z","updated_at":"2025-04-24T20:32:13.222Z","avatar_url":"https://github.com/ekg.png","language":"C++","funding_links":[],"categories":["based"],"sub_categories":[],"readme":"hapviz: region-bounded haplotype pileup visualization for BAM files\n\nit all happens in the terminal!\n\n    % hapviz --help\n    usage: hapviz [options] bam file [... bam file]\n\n    options:\n        -b, --bam           bam file to from which to extract reads\n                            (may also be specified as positional arguments)\n        -r, --region        region from which to extract grouped reads\n        -a, --show-all      When visualizing, show all alignments, not just variant ones.\n        -f, --reference     FASTA reference against which alignments have been aligned\n        -q, --min-base-quality\n                            minimum base quality required for all bases in a read\n\n    Displays haplotype groups from the specified region across the BAM files provided as input.\n\n\nNote: If you list 'stdin' as one of the BAM files, you can pipe BAM directly into hapviz.\n\nThis (slightly modified) example output shows how each indel haplotype is\ngrouped, and the reads from it are aligned to a reference sequence.  Relative\ndeletions between the reference and reads are replaced by '-'.\n\n\n17 i:16817:GGCAC\n                      16788   CCCAGCACTTCAGGGCTTTAGCTGGGAGGGA-----GGCAGTCCACAGGAATGAATTCATCACT   16862\nsample08 31M5I34M              CCAGCACTTCAGGGCTTTAGCTGGGAGGGAGGCACGGCAGTCCACAGGAAT\nsample03 30M5I35M               CAGCACTTCAGGGCTTTAGCTGGGAGGGAGGCACGGCAGTCCACAGGAATG\nsample02 27M5I38M                 GCACTTCAGGGCTTTAGCTGGGAGGGAGGCACGGCAGTCCACAGGAATGAAT\nsample05 26M5I39M                  CACTTCAGGGCTTTAGCTGGGAGGGAGGCACGGCAGTCCACAGGAATGAATT\nsample05 24M5I41M                    CTTCAGGGCTTTAGCTGGGAGGGAGGCACGGCAGTCCACAGGAATGAATTCA\nsample07 21M5I44M                       CAGGGCTTTAGCTGGGAGGGAGGCACGGCAGTCCACAGGAATGAATTCATCA\nsample07 21M5I44M                       CAGGGCTTTAGCTGGGAGGGAGGCACGGCAGTCCACAGGAATGAATTCATCA\nsample03 19M5I46M                         GGGCTTTAGCTGGGAGGGAGGCACGGCAGTCCACAGGAATGAATTCATCACT\nsample08 14M5I51M                              TTAGCTGGGAGGGAGGCACGGCAGTCCACAGGAATGAATTCATCACT\n--------------------------------------------------------------\n1 i:16817:GGCAG\n                      16765   GTGCTGCCCTCTCCCCAGCACTTCAGGGCTTTAGCTGGGAGGGA-----GGCAGTCCACAGG   16829\nsample03 52M5I13M             GTGCTGCCCTCTCCCCAGCACTTCAGGGCTTTAGCTGGGAGGGAGGCAGGGCAGTCCACAGG\n--------------------------------------------------------------\n1 i:16821:T\n                      16758   ATACAGGGTGCTGCCCTCTCCCCAGCACTTCAGGGCTTTAGCTGGGAGGGAGGCA-GTC   16823\nsample03 63M1I3M3S            ATACAGGGTGCTGCCCTCTCCCCAGCACTTCAGGGCTTTAGCTGGGAGGGAGGCATGTC\n--------------------------------------------------------------\n\n\nEnjoy!\n\n\nauthor: erik garrison \u003cerik.garrison@bc.edu\u003e\nlicense: free\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fekg%2Fhapviz","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fekg%2Fhapviz","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fekg%2Fhapviz/lists"}