Bioalcidae, samjs and vcffilterjs: Object-oriented formatters and filters for bioinformatics files

Abstract

Motivation 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. Results 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). Availability and implementation https://github.com/lindenb/jvarkit.