SamReaderFactory opens non-regular File and Path the same way

[kshakir]

Description

To close #1716, copies the logic from here:

htsjdk/src/main/java/htsjdk/samtools/SamInputResource.java

Lines 159 to 161 in 127f3de

	return wrapper == null
	? of(path)
	: of(path, wrapper);

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• Make sure your changes compile and new tests pass locally.
• Add new tests or update existing ones:
  • A bug fix should include a test that previously would have failed and passes now.
  • New features should come with new tests that exercise and validate the new functionality.
• Extended the README / documentation, if necessary
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  • Breaking changes should be mentioned in the commit message.