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abaumann avatar abaumann commented on June 9, 2024

Currently there is not a plan to provide either copy constructors or copy factory methods, and clone is utilized in many places throughout that ideally would be changed as well if we went the copy constructor/factory route. The clone method there is also shallow, so a full copy method may be a nice (or needed depending on how you are planning to use it) addition.

If these copy methods are needed for SAMRecord and SAMFileHeader they could be added and a pull request made. Looking in existing code, I see clone() and copy() (for deep copy) used all over the place, and the only occurrence I can find of a copy constructor or static factory method is the copy constructor in VariantContextBuilder, so for consistency perhaps implement as a copy constructor rather than static factory method? VariantContextBuilder provides a copy() method that calls the copy constructor FWIW...

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akiezun avatar akiezun commented on June 9, 2024

Can you at least modify the signature so that clone() returns a SAMRecord? (long time ago, return types in java were invariant (had to match superclass) but they can be covariant now (can be subtypes of what the superclass says))

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akiezun avatar akiezun commented on June 9, 2024

also the signature says throws CloneNotSupportedException which I think can never happen so put undue burden on the caller. I have to both type cast and handle the exception (that is never thrown so the current code in htsjdk makes me write dead code)

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