{"id":25437974,"url":"https://github.com/alexcoppe/genomicpp","last_synced_at":"2025-05-15T07:12:09.177Z","repository":{"id":225697131,"uuid":"733574592","full_name":"alexcoppe/genomicpp","owner":"alexcoppe","description":"A bunch of C++ programs for working with bioinformatics files","archived":false,"fork":false,"pushed_at":"2024-03-23T21:20:53.000Z","size":33,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2024-03-23T22:26:01.877Z","etag":null,"topics":["bioinformatics","biology","cpp","vcf"],"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/alexcoppe.png","metadata":{"files":{"readme":"README.md","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,"governance":null,"roadmap":null,"authors":null,"dei":null}},"created_at":"2023-12-19T16:26:59.000Z","updated_at":"2024-03-03T17:47:54.000Z","dependencies_parsed_at":"2024-03-23T22:25:44.062Z","dependency_job_id":"0d7e0d9e-4c86-45b8-b32f-63ea9feee26f","html_url":"https://github.com/alexcoppe/genomicpp","commit_stats":null,"previous_names":["alexcoppe/genomicpp"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alexcoppe%2Fgenomicpp","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alexcoppe%2Fgenomicpp/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alexcoppe%2Fgenomicpp/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alexcoppe%2Fgenomicpp/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/alexcoppe","download_url":"https://codeload.github.com/alexcoppe/genomicpp/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239264768,"owners_count":19610060,"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","biology","cpp","vcf"],"created_at":"2025-02-17T09:28:22.406Z","updated_at":"2025-02-17T09:28:23.075Z","avatar_url":"https://github.com/alexcoppe.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# genomiC++ :dna:\nA bunch of C++ programs for working with bioinformatics files. It uses only the standard libraries of C++ and it's in continuos alpha version as I create and iprove the difereent programs when needed.\n\nIts compilation and functionality have been verified on the following operating system:\n\n- macOS :green_apple:\n- Linux :penguin:\n\n\n# Download and Compilation :floppy_disk:\n\n```console\n\u003e\u003e\u003e git clone https://github.com/alexcoppe/genomicpp.git\n\u003e\u003e\u003e cd genomicpp\n\u003e\u003e\u003e make\n```\n\nAfter compilation, move the generated executables to a directory listed in the $PATH variable. You can identify these directories by using the ```echo $PATH``` command.\n\n# Programs available :man_technologist:\n\n## vcf_to_table\n\nThis software transforms an uncompressed VCF file to a tab-separated values (tsv) file. It also operates with VCFs generated by [SnpEff](https://pcingola.github.io/SnpEff/) and [ANNOVAR](https://annovar.openbioinformatics.org/en/latest/). To run it, you need two arguments: the VCF file and a text file specifying the desired fields. Refer to the table below for guidance on creating this file.\n\nWhen utilizing a [SnpEff](https://pcingola.github.io/SnpEff/) annotated VCF, the tool currently displays each transcript indicated by SnpEff in separate rows.\n\nStarting character | What you get\n------------ | -------------\nNone | get the fields from the VCF\n : | get a subfield from the INFO field added by SnpEff\n ; | get a specific subfiled from the IMFO field \n \\| | get a specific subfield from the Genotype fields \n\nExample of a text file specifying the desired fields and subfields:\n\n```console\n:hgvs_c\nposition\n;gnomAD_genome_AMR\n|AD\n```\n\nLaunching the program with the above text file\n\n```console\nvcf_to_table a_vcf_file_path.vcf wanted_fields.txt\n```\n\nOutput:\n\n```console\nn.-3702C\u003eT      157370625       0.0020  14,1    31,5\nn.*1931C\u003eT      157370625       0.0020  14,1    31,5\nn.-3707C\u003eT      157370630       0       15,1    33,4\n...\n```\n\nCurrently, the software operates exclusively on 1 or 2 genotype fields.\n\nThe table below displays all the sub-fields added by [SnpEff](https://pcingola.github.io/SnpEff/) along with the corresponding sub-field names used in vcf_to_table (listed in the first column). \n\nSubfield by vcf_to_table | Subfield by SnpEff | Explanation\n------------ | ------------- | -------------\n:allele | Allele (or ALT) | The alternative allele\n:annotation | Annotation (a.k.a. effect) | Annotated using Sequence Ontology terms\n:putative_impact | Putative_impact | A simple estimation of putative impact / deleteriousness : {HIGH, MODERATE, LOW, MODIFIER}\n:gene_name | Gene Name | Common gene name (HGNC)\n:gene_id | Gene ID | Gene ID\n:feature_type | Feature type | Which type of feature is in the next field\n:feature_id | Feature ID | Depends on the annotation\n:transcript_biotype | Transcript biotype | The bare minimum is at least a description on whether the transcript is {\"Coding\", \"Noncoding\"}. Whenever possible, use ENSEMBL biotypes\n:rank | Rank / total | Exon or Intron rank / total number of exons or introns\n:hgvs_c | HGVS.c | Variant using HGVS notation (DNA level)\n:hgvs_p | HGVS.p | If variant is coding, this field describes the variant using HGVS notation (Protein level)\n:cdna_position | cDNA_position / cDNA_len | Position in cDNA and trancript's cDNA length (one based)\n:cds_position | CDS_position / CDS_len | Position and number of coding bases (one based includes START and STOP codons)\n:protein_position | Protein_position / Protein_len | Position and number of AA (one based, including START, but not STOP)\n:distance_to_feature | Distance to feature | All items in this field are options see SnpEff page for details\n:errors | Errors, Warnings or Information messages | Errors, warnings or informative message that can affect annotation accuracy\n\n\n## get_pass_variants\n\nThis program filters a VCF file annotated by [SnpEff](https://pcingola.github.io/SnpEff/), retaining only the variants marked as 'PASS' in the FILTER field.\n\nOption | What does it do\n------------ | -------------\n-h | Show help\n\n##### Example\n\n```console\n\u003e\u003e\u003e get_pass_variants /path_to_vcf_file/variants.vcf\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falexcoppe%2Fgenomicpp","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Falexcoppe%2Fgenomicpp","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falexcoppe%2Fgenomicpp/lists"}