bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files.

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. Contact: pierre.lindenbaum@univ-nantes.fr.