Description of the issue:

This issue is related to:

• input streams opened from Paths fail when the underlying file is a pipe #1084
• Fix regression regarding pipeing #1124
• Add HtsgetBAMFileReader #1494

Describe your issue here.
When creating instances of SamInputResource, there are two overloads that take a java.nio.Path:

1. public static SamInputResource of(final Path path)
2. public static SamInputResource of(final Path path, Function<SeekableByteChannel, SeekableByteChannel> wrapper)

As of #1124, these two methods have very different behaviors on non-regular files. Overload 1 partially handles the issues described in #1084, while overload 2 does not.

To choose between the overloads, code such as in #1494 checks if the caller has passed in a null wrapper to call overload 1 or 2. Direct link: https://github.com/samtools/htsjdk/pull/1494/files#diff-1001d1e3b784b6fa1bab848edafb7430f4f031dd17fa0bee7a5482880d2a1a7aR159-R161

However, as of HTSJDK 4.1.1, this same conditional logic is missing from the SamReaderFactory method public SamReader open(final Path path, Function<SeekableByteChannel, SeekableByteChannel> dataWrapper, Function<SeekableByteChannel, SeekableByteChannel> indexWrapper).

Unlike the code linked above in #1494, the SamReaderFactory.open method does not check for null wrappers. This ultimately means that non-regular files passed as java.io.File end up being treated differently than the exact same file passed as java.nio.file.Path.

Your environment:

• version of htsjdk: 4.1.1
• version of java: 21-tem
• which OS: macOS 14.6.1

Steps to reproduce

Call:

File irregularFile = new File("/dev/stdin");
SamReader fileReader = SamReaderFactory.makeDefault().open(irregularFile);
SamReader pathReader = SamReaderFactory.makeDefault().open(irregularFile.toPath());
System.out.println(fileReader.getResourceDescription())
System.out.println(pathReader.getResourceDescription())

Expected behaviour

data=FILE:/dev/null;index=null
data=FILE:/dev/null;index=null

Actual behaviour

data=FILE:/dev/null;index=null
data=PATH:/dev/null;index=null

Workaround

While this is being fixed, you are able to write your own open method that works correctly. Something like:

public static SamReader open(final Path path, final SamReaderFactory factory) {
    final SamInputResource r = SamInputResource.of(path);
    final Path indexMaybe = SamFiles.findIndex(path);
    if (indexMaybe != null) r.index(indexMaybe);
    return factory.open(r);
}