search

magicDGS / ReadTools

A Universal Toolkit for Handling Sequence Data from Different Sequencing Platforms
https://magicdgs.github.io/ReadTools/
MIT License
6 stars 3 forks source link

Non-file FASTQ inputs does fail as inputs #472

Closed magicDGS closed 6 years ago

magicDGS commented 6 years ago

The current implementation in our reader factory uses File.toPath for opening FASTQ files, but this will fail with non-local java.nio.Path (e.g., HDFS). This should be fixed to open the Path as a stream instead of using the default FastqReader constructor.

magicDGS commented 6 years ago

Actually this is a bug that should be fixed.