[ADAM-1190] Manually (un)pack IndelRealignmentTarget set. #1191

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fnothaft commented 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 #1190.

I have tested this on the cluster.

[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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Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1512/
Test PASSed.

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1512/
Test PASSed.

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heuermh approved these changes Oct 3, 2016

@heuermh heuermh merged commit b903cfd into bigdatagenomics:master Oct 3, 2016

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heuermh Oct 3, 2016

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Thank you, @fnothaft!

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heuermh commented Oct 3, 2016

Thank you, @fnothaft!

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