SamReaderFactory should use current defaults when makeDefault() is called #1666
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lbergelson
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May 24, 2023
* 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
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Jun 2, 2023
* 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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Currently
SamReaderFactorystores a DEFAULT factory as a static variable. Certain operations update this default so whenSamReaderFactory.makeDefault()is called it returns different values. However, some default values are set through other mechanisms likeBlockGunzipper.setDefaultInflaterFactorywhich can lead to unexpected results when they are not propagated through calls to make default.The text was updated successfully, but these errors were encountered: