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SamReaderFactory should use current defaults when makeDefault() is called #1666

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lbergelson opened this issue May 24, 2023 · 0 comments
Open

SamReaderFactory should use current defaults when makeDefault() is called #1666

lbergelson opened this issue May 24, 2023 · 0 comments

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@lbergelson
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Currently SamReaderFactory stores a DEFAULT factory as a static variable. Certain operations update this default so when SamReaderFactory.makeDefault() is called it returns different values. However, some default values are set through other mechanisms like BlockGunzipper.setDefaultInflaterFactory which can lead to unexpected results when they are not propagated through calls to make default.
lbergelson added a commit to broadinstitute/picard that referenced this issue May 24, 2023
@lbergelson
Fix longstanding bug so we use the Intel Inflater when it is requested
2baa273 
*  We have been using the Java Inflater even when the Intel one was available and requested
   due to a bug in the configuration of the default inflater.
   The fix is fairly brittle because it depends on the order of initialization of various things.
*  This will be fixed more generally by samtools/htsjdk#1666
lbergelson added a commit to broadinstitute/picard that referenced this issue Jun 2, 2023
@lbergelson
Enable IntelInflater (#1885)
983e073 
* Fix longstanding bug so we use the Intel Inflater when it is requested

*  We have been using the Java Inflater even when the Intel one was available and requested
   due to a bug in the configuration of the default inflater.
   The fix is fairly brittle because it depends on the order of initialization of various things.
*  This will be fixed more generally by samtools/htsjdk#1666
* Add a test
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