Fail clearly when a CRAM query needs to seek but cannot - #1791
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CRAMFileReader can be constructed from an InputStream together with an index. If that stream is not a SeekableStream, getSeekableStreamOrFailWithRTE -- despite its name -- returned null instead of failing, and the null surfaced later as a bare NullPointerException from whichever query call the user made. Throw an IllegalStateException naming the actual constraint: query and index operations need a File, a Path, or a SeekableStream. Sequential iteration does not seek and is unaffected, which the test pins down.
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Three test classes added in #1789, #1791 and #1792 used snake_case method names without the conventional test prefix, which is neither idiomatic Java nor what this repo does: of 2417 test methods, 2020 start with "test" and only 199 contain an underscore at all. Rename the nine offending methods in these three classes to testXxx camelCase. Test bodies are untouched; this is naming only.
Three test classes added in #1789, #1791 and #1792 used snake_case method names without the conventional test prefix, which is neither idiomatic Java nor what this repo does: of 2417 test methods, 2020 start with "test" and only 199 contain an underscore at all. Rename the nine offending methods in these three classes to testXxx camelCase. Test bodies are untouched; this is naming only.
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Closes #426.
CRAMFileReadercan be constructed from anInputStreamtogether with an index. If that stream is not aSeekableStream,getSeekableStreamOrFailWithRTE— despite its name — returnednullrather than failing, and thenullsurfaced later as a bareNullPointerExceptionfrom whichever query call the user made.It now throws an
IllegalStateExceptionnaming the actual constraint: query and index operations need aFile, aPath, or aSeekableStream.Sequential iteration does not seek and is unaffected, which one of the tests pins down. I also confirmed the test genuinely covers the bug by reverting the fix and watching it fail with the original
NullPointerException.