Fix stack overflow in IndelRealigner serialization #1190
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fnothaft
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Oct 1, 2016
Updates `org.bdgenomics.adam.rdd.read.realignment.TargetSetSerializer` to manually (de)serialize each set element, instead of delegating to Kryo. This eliminates a stack overflow from inside of Kryo. Resolves bigdatagenomics#1190.
heuermh
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Oct 3, 2016
Updates `org.bdgenomics.adam.rdd.read.realignment.TargetSetSerializer` to manually (de)serialize each set element, instead of delegating to Kryo. This eliminates a stack overflow from inside of Kryo. Resolves #1190.
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95f3528 fixed the
ZippedTargetSetSerializer, but not theTargetSetSerializer. For some reason, this fix worked OK on many files but not all. Not sure what the underlying change was... Something in Kryo/Spark?The text was updated successfully, but these errors were encountered: