Multi-allelic split code may fail when accessing PL

[fnothaft]

When splitting a multi-allelic variant from a VCF, the VCF record may be tagged with the PLs, but not have all of the PLs attached. E.g.:

fnothaft$ ./bin/adam-submit vcf2adam ALL.chrY.phase3_integrated.20130502.genotypes.vcf chrY.adam
Spark assembly has been built with Hive, including Datanucleus jars on classpath
2014-11-14 17:07:48.306 java[50061:1903] Unable to load realm info from SCDynamicStore
2014-11-14 17:07:53 WARN  NativeCodeLoader:52 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[HG00096 T* GQ 99 PL 0,1238,68 {CN=1, CNL=-123.78,-0,-6.77, CNP=-125.44,-0,-9.85, CNQ=98.5, GP=-0,-125.44,-9.85}] / 2
true
[0, 1238, 68]
[0, 3, 5]
2014-11-14 17:08:25 ERROR Executor:96 - Exception in task 0.0 in stage 1.0 (TID 6)
java.lang.ArrayIndexOutOfBoundsException: 3
    at org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$convert$3$$anonfun$1.apply$mcII$sp(VariantContextConverter.scala:141)
    at org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$convert$3$$anonfun$1.apply(VariantContextConverter.scala:141)
    at org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$convert$3$$anonfun$1.apply(VariantContextConverter.scala:141)
    at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
    at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
    at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
    at scala.collection.mutable.ArrayOps$ofInt.foreach(ArrayOps.scala:156)
    at scala.collection.TraversableLike$class.map(TraversableLike.scala:244)
    at scala.collection.mutable.ArrayOps$ofInt.map(ArrayOps.scala:156)