Fix stack overflow in IndelRealigner serialization #1190

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fnothaft opened this Issue Oct 1, 2016 · 0 comments

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fnothaft commented Oct 1, 2016

95f3528 fixed the ZippedTargetSetSerializer, but not the TargetSetSerializer. For some reason, this fix worked OK on many files but not all. Not sure what the underlying change was... Something in Kryo/Spark?

@fnothaft fnothaft added the bug label Oct 1, 2016

@fnothaft fnothaft self-assigned this Oct 1, 2016

fnothaft added a commit to fnothaft/adam that referenced this issue Oct 1, 2016

[ADAM-1190] Manually (un)pack IndelRealignmentTarget set.
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.

@heuermh heuermh closed this in #1191 Oct 3, 2016

heuermh added a commit that referenced this issue Oct 3, 2016

[ADAM-1190] Manually (un)pack IndelRealignmentTarget set.
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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