convert Runtime exceptions in the CRAM code into CRAMExceptions (also… #1526
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cmnbroad
reviewed
Jan 11, 2021
| @@ -73,7 +74,7 @@ public CRAMReferenceRegion(final CRAMReferenceSource cramReferenceSource, final | |||
| final SAMSequenceRecord sequence = samFileHeader.getSequence(referenceIndex); | |||
| referenceBases = referenceSource.getReferenceBases(sequence, true); | |||
| if (referenceBases == null) { | |||
| throw new IllegalArgumentException( | |||
| throw new CRAMException( | |||
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I'm not sure what the original intent of CRAMException was, but starting with the CRAM rewrite I restricted it's use to internal error conditions, such as malformed input as reported in broadinstitute/picard#1624. Not all of the CRAM codebase is conforming yet, but I don't think this is a case where CRAMException makes sense, since this is a user error.
| @@ -422,7 +423,7 @@ private EncodingDetails buildEncodingForTag(final List<CRAMCompressionRecord> re | |||
| new ExternalByteArrayEncoding(tagID)).toEncodingDescriptor(); | |||
| return details; | |||
| default: | |||
| throw new IllegalArgumentException("Unknown tag type: " + (char) type); | |||
| throw new CRAMException("Unknown tag type: " + (char) type); | |||
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This one does seem like an appropriate case for CRAMException.
| @@ -88,7 +90,7 @@ public static long writeCramEOF(final CRAMVersion cramVersion, final OutputStrea | |||
| throw new RuntimeIOException(e); | |||
| } | |||
|
|
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| throw new IllegalArgumentException(String.format("Unrecognized CRAM version %s", cramVersion)); | |||
| throw new CRAMException(String.format("Unrecognized CRAM version %s", cramVersion)); | |||
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This one is borderline, but I'd err on leaving it as IllegalArgumentException, or else RuntimeException.
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… runtime)
(sorry again about the push to master)
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