Sourced from com.github.samtools:htsjdk's releases.

4.1.0

What's Changed

• Updated the way that tribble creates SeekableStreams. It will now prefer available http / ftp FileSystemProvider plugins if they are available instead of using the legacy http / ftp support. This is intended to support downstream use of plugins such as org.broadinstitute:http-nio which may provide more robust handling of various URIs.

Compatibility note

• Tribble now requires all fully specified absolute paths to be already encoded. Specifically, this means that ftp / http URIs which used to be written with spaces or special characters must now be already percent encoded before handing them to tribble.
  For example, the previous ftp path style:

• ftp://example.org/ftp/my file with spaces.txt should now be entered as

• ftp://example.org/ftp/my%20file%20with%20spaces.txt This is more awkward in some cases but it aligns the legacy ftp/http access with the IOPath standard of always requiring a fully encoded URI if a scheme is specified. File paths that don't include a file:// scheme are still handled unencoded so this should have limited impact. See the documentation for HtsPath for more details information.

• Deprecated SeekableStreamFactory.isFilePath() and replaced it with the clearer but more verbose isBeingHandledByLegacyUrlSupport

• Some changes to error handling in HtsPath now reject certain paths which previously would be treated as local file paths.

  • Paths with only a scheme, or a missing scheme are invalid now:
    • file://, ://mypath, ://
  • Paths which contain a scheme but are not parseable as a uri are now rejected instead of being treated as a local file path
    • http://example.org/filename I forgot to encode
    • These are much more likely to be an attempt to access an unencoded URI instead of an attempt to create a local file path named file:///<workingdir>/http:/example.org/filename I forgot to encode

Full Changelog: samtools/htsjdk@4.0.2...4.1.0

• b23c36a Improving the last changes to HtsPath (#1694)
• 40e3a8b Pefer FileSystemProvider plugins for http/ftp over legacy handlers(#1693)
• See full diff in compare view

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