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.
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.