{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T01:29:00Z","timestamp":1772155740476,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2017,11,24]],"date-time":"2017-11-24T00:00:00Z","timestamp":1511481600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Reformatting and filtering bioinformatics files are common tasks for bioinformaticians. Standard Linux tools and specific programs are usually used to perform such tasks but there is still a gap between using these tools and the programming interface of some existing libraries.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this study, we developed a set of tools namely bioalcidae, samjs and vcffilterjs that reformat or filter files using a JavaScript engine or a pure java expression and taking advantage of the java API for high-throughput sequencing data (htsjdk).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/lindenb\/jvarkit.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx734","type":"journal-article","created":{"date-parts":[[2017,11,23]],"date-time":"2017-11-23T20:16:26Z","timestamp":1511468186000},"page":"1224-1225","source":"Crossref","is-referenced-by-count":39,"title":["bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0148-9787","authenticated-orcid":false,"given":"Pierre","family":"Lindenbaum","sequence":"first","affiliation":[{"name":"Cardiovascular Genetics, L\u2019Institut du Thorax, INSERM, CNRS, UNIV Nantes, Nantes, France"}]},{"given":"Richard","family":"Redon","sequence":"additional","affiliation":[{"name":"Cardiovascular Genetics, L\u2019Institut du Thorax, INSERM, CNRS, UNIV Nantes, Nantes, France"}]}],"member":"286","published-online":{"date-parts":[[2017,11,24]]},"reference":[{"key":"2023012712570460500_btx734-B1","volume-title":"The AWK Programming Language","author":"Aho","year":"1987"},{"key":"2023012712570460500_btx734-B2","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly (Austin)"},{"key":"2023012712570460500_btx734-B3","doi-asserted-by":"crossref","first-page":"2037","DOI":"10.1093\/bioinformatics\/btx100","article-title":"BCFtools\/csq: haplotype-aware variant consequences","volume":"33","author":"Danecek","year":"2017","journal-title":"Bioinformatics"},{"key":"2023012712570460500_btx734-B4","doi-asserted-by":"crossref","first-page":"R44","DOI":"10.1186\/gb-2005-6-5-r44","article-title":"The Sequence Ontology: a tool for the unification of genome annotations","volume":"6","author":"Eilbeck","year":"2005","journal-title":"Genome Biol"},{"key":"2023012712570460500_btx734-B5","author":"Lindenbaum","year":"2015"},{"key":"2023012712570460500_btx734-B6","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res"},{"key":"2023012712570460500_btx734-B7","doi-asserted-by":"crossref","first-page":"2069","DOI":"10.1093\/bioinformatics\/btq330","article-title":"Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor","volume":"26","author":"McLaren","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012712570460500_btx734-B8","doi-asserted-by":"crossref","first-page":"e1002216","DOI":"10.1371\/journal.pcbi.1002216","article-title":"BioStar: an online question & answer resource for the bioinformatics community","volume":"7","author":"Parnell","year":"2011","journal-title":"PLoS Comput. Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/7\/1224\/48914516\/bioinformatics_34_7_1224.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/7\/1224\/48914516\/bioinformatics_34_7_1224.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T12:57:12Z","timestamp":1674824232000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/7\/1224\/4657066"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,11,24]]},"references-count":8,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2018,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx734","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,4,1]]},"published":{"date-parts":[[2017,11,24]]}}}