Re-Ordering priority in SeekableStreamFactory

samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

http://samtools.github.io/htsjdk/

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Closed lbergelson closed 9 months ago

lbergelson commented 10 months ago

Now when constructing streams it will prefer NIO plugins.
If no http / ftp plugin exists it will fall back to the htsjdk bulit in
No longer special casing local files, these will now be handled through NIO as well.
Deprecating SeekableStreamFactory.isFilePath() since it is no longer used and interacts poorly with nio filesystem providers

droazen commented 10 months ago

Can you also fix the order in ParsingUtils.openInputStream() (used by TribbleIndexedFeatureReader.readHeader())?