{"id":18373540,"url":"https://github.com/shujiahuang/refhap","last_synced_at":"2026-03-07T16:03:28.040Z","repository":{"id":72302116,"uuid":"90510132","full_name":"ShujiaHuang/RefHap","owner":"ShujiaHuang","description":"A Reliable and Fast Algorithm for Single Individual Haplotyping","archived":false,"fork":false,"pushed_at":"2017-05-07T05:57:57.000Z","size":361,"stargazers_count":5,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-04-14T00:15:04.254Z","etag":null,"topics":["algorithm","dna","haplotypes","ngs"],"latest_commit_sha":null,"homepage":"https://dl.acm.org/doi/10.1145/1854776.1854802","language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ShujiaHuang.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"COPYING","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2017-05-07T05:04:53.000Z","updated_at":"2024-11-01T06:03:47.000Z","dependencies_parsed_at":"2023-09-17T04:16:31.954Z","dependency_job_id":null,"html_url":"https://github.com/ShujiaHuang/RefHap","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/ShujiaHuang%2FRefHap","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ShujiaHuang%2FRefHap/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ShujiaHuang%2FRefHap/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ShujiaHuang%2FRefHap/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ShujiaHuang","download_url":"https://codeload.github.com/ShujiaHuang/RefHap/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248799953,"owners_count":21163404,"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":["algorithm","dna","haplotypes","ngs"],"created_at":"2024-11-06T00:10:45.454Z","updated_at":"2026-03-07T16:03:22.999Z","avatar_url":"https://github.com/ShujiaHuang.png","language":"Java","readme":"SingleIndividualHaplotyper(SIH) - Efficient heuristic algorithms for the SIH problem\nVersion 1.0.0 (15/06/11)\n===============================================================================\nThis package contains implementations of eight different algorithms for to solve \nthe Single Individual Haplotyping (SIH) problem. By default it runs **ReFHap**, which is\na very efficient and accurate algorithm to assemble haplotypes from different kinds of\nfragment data.\n\nBuilding SingleIndividualHaplotyper\n-----------------------------------\n\nSingleIndividualHaplotyper has been compiled and run successfully\non the standard jdk version 1.6.0. To build the distribution\nlibrary sih.jar on a command line environment \nrun the following commands in the directory\nwhere RefHap is located:\n\n```\ncd SingleIndividualHaplotyper\nmake all\n```\n\nRunning SingleIndividualHaplotyper\n----------------------------------\n\nThe front class of SingleIndividualHaplotyper is mpg.molgen.sih.main.SIH and\non default settings calls the ReFHap algorithm for haplotyping. Basic usage just requires \na file with the description of the fragments (the format is explained below) and the path for\nthe output file. The full usage is as follows: \n```\nUsage: \n\njava -cp SIH.jar mpg.molgen.sih.main.SIH \u003cOPTIONS\u003e \u003cINPUT_FILE\u003e \u003cOUTPUT_FILE\u003e\n\nOPTIONS:\n\t\t-v FILE\t\t\t: Text file with genomic coordinates of variants. By default it assumes that \n\t\t\t\t\t\t\tcoordinates are located in the first column\n\t\t-c INT\t\t\t: Column in the variants file where coordinates are located. Fields in this \n\t\t\t\t\t\t\tcolumn must be integers. \n\t\t-a STRING\t\t: Name of the algorithm to run. Options are Refhap, DGS, and FastHare. SHRThree, \n\t\t\t\t\t\t\tSpeedhap, TwoDMEC, and WMLF are also supported although they are in general less accurate\n```\n\nThe input file is a text file with one line per fragment. Since fragments are allowed to have gaps, each fragment\nmust be divided in segments of continuous calls. The first field is the number of such segments. The second field is\nthe id of the fragment. Two fields are then added for each subfragment, the first is the one based relative start\nof the subfragment and the second is a binary string with the calls. For HapCUT users, the format is the same \nas HapCUT. A sample file is provided with this distribution.\n\nThe output is a tab delimited text file with the list of blocks. Each block has a header with the \none based relative position of the first variant, the size of the block and the number of variants phased.\nThen, there is one line per variant with the following fields:\n- Relative position of the variant\n- Allele in the first haplotype\n- Allele in the second haplotype\n\nIf a file is provided with genomic locations of variants through the -v option, then the relative positions are replaced \nwith the positions contained in this file.\n\nExample 1. Simple usage:\n```\njava -cp SIH.jar mpg.molgen.sih.main.SIH example.frags example1.phase\n```\n\nExample 2. Including genomic coordinates\n```\njava -cp SIH.jar mpg.molgen.sih.main.SIH -v example.allvars -c 2 example.frags example2.phase\n```\n\nExample 3. Running an algorithm different than ReFHap\n```\njava -cp SIH.jar mpg.molgen.sih.main.SIH -a DGS -v example.allvars -c 2 example.frags example3.phase\n```\n\nLicense\n-------\n\nSingleIndividualHaplotyper 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\n(at your option) any later version.\n \nSingleIndividualHaplotyper 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 SingleIndividualHaplotyper.  If not, see \u003chttp://www.gnu.org/licenses/\u003e.\n\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fshujiahuang%2Frefhap","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fshujiahuang%2Frefhap","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fshujiahuang%2Frefhap/lists"}